From 530ed34f0050275e486299a8f9a89a479ace4c19 Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 20:23:27 +0200 Subject: [PATCH 01/11] removed bsd --- msmtools/analysis/__init__.py | 25 ----------------- msmtools/analysis/dense/assessment_test.py | 25 ----------------- msmtools/analysis/dense/birth_death_chain.py | 25 ----------------- msmtools/analysis/dense/committor.py | 25 ----------------- msmtools/analysis/dense/committor_test.py | 25 ----------------- msmtools/analysis/dense/correlations.py | 25 ----------------- msmtools/analysis/dense/correlations_test.py | 25 ----------------- msmtools/analysis/dense/expectations.py | 25 ----------------- msmtools/analysis/dense/expectations_test.py | 25 ----------------- msmtools/analysis/dense/fingerprints.py | 25 ----------------- msmtools/analysis/dense/fingerprints_test.py | 25 ----------------- .../analysis/dense/hitting_probability.py | 25 ----------------- .../dense/hitting_probability_test.py | 25 ----------------- .../analysis/dense/mean_first_passage_time.py | 25 ----------------- .../dense/mean_first_passage_time_test.py | 25 ----------------- msmtools/analysis/dense/pcca.py | 25 ----------------- msmtools/analysis/dense/pcca_test.py | 25 ----------------- msmtools/analysis/dense/sensitivity.py | 25 ----------------- msmtools/analysis/dense/sensitivity_test.py | 25 ----------------- msmtools/analysis/sparse/assessment_test.py | 25 ----------------- msmtools/analysis/sparse/birth_death_chain.py | 25 ----------------- msmtools/analysis/sparse/committor.py | 25 ----------------- msmtools/analysis/sparse/committor_test.py | 25 ----------------- msmtools/analysis/sparse/fingerprints.py | 25 ----------------- msmtools/analysis/sparse/fingerprints_test.py | 25 ----------------- .../sparse/mean_first_passage_time.py | 25 ----------------- .../sparse/mean_first_passage_time_test.py | 25 ----------------- msmtools/analysis/tests/birth_death_chain.py | 25 ----------------- msmtools/analysis/tests/test_assessment.py | 25 ----------------- msmtools/analysis/tests/test_committor.py | 25 ----------------- msmtools/analysis/tests/test_decomposition.py | 25 ----------------- msmtools/analysis/tests/test_fingerprints.py | 25 ----------------- msmtools/analysis/tests/test_mfpt.py | 25 ----------------- msmtools/analysis/tests/test_sensitivity.py | 25 ----------------- msmtools/dtraj/__init__.py | 25 ----------------- msmtools/estimation/api.py | 25 ----------------- .../estimation/dense/_mle_trev_given_pi.c | 25 ----------------- .../estimation/dense/_mle_trev_given_pi.h | 25 ----------------- msmtools/estimation/dense/bootstrapping.py | 25 ----------------- msmtools/estimation/dense/covariance.py | 25 ----------------- msmtools/estimation/dense/covariance_test.py | 25 ----------------- msmtools/estimation/dense/sample_rev.c | 25 ----------------- msmtools/estimation/dense/sample_rev.h | 25 ----------------- msmtools/estimation/dense/sample_revpi.c | 25 ----------------- msmtools/estimation/dense/sample_revpi.h | 25 ----------------- .../estimation/dense/transition_matrix.py | 25 ----------------- msmtools/estimation/sparse/_mle_trev.c | 25 ----------------- msmtools/estimation/sparse/_mle_trev.h | 25 ----------------- .../estimation/sparse/_mle_trev_given_pi.c | 25 ----------------- .../estimation/sparse/_mle_trev_given_pi.h | 25 ----------------- msmtools/estimation/sparse/connectivity.py | 25 ----------------- .../estimation/sparse/connectivity_test.py | 25 ----------------- msmtools/estimation/sparse/count_matrix.py | 25 ----------------- .../estimation/sparse/count_matrix_test.py | 25 ----------------- msmtools/estimation/sparse/likelihood.py | 25 ----------------- msmtools/estimation/sparse/likelihood_test.py | 25 ----------------- msmtools/estimation/sparse/prior.py | 25 ----------------- msmtools/estimation/sparse/prior_test.py | 25 ----------------- .../estimation/sparse/transition_matrix.py | 25 ----------------- .../sparse/transition_matrix_test.py | 25 ----------------- .../estimation/tests/test_bootstrapping.py | 25 ----------------- .../estimation/tests/test_connectivity.py | 25 ----------------- .../estimation/tests/test_count_matrix.py | 25 ----------------- .../tests/test_effective_count_matrix.py | 25 ----------------- msmtools/estimation/tests/test_likelihood.py | 25 ----------------- msmtools/estimation/tests/test_mle_trev.py | 25 ----------------- .../tests/test_mle_trev_given_pi.py | 25 ----------------- msmtools/estimation/tests/test_prior.py | 25 ----------------- .../estimation/tests/test_tmatrix_sampling.py | 27 +------------------ .../tests/test_transition_matrix.py | 25 ----------------- msmtools/flux/api.py | 25 ----------------- msmtools/flux/dense/tpt.py | 25 ----------------- msmtools/flux/dense/tpt_test.py | 25 ----------------- msmtools/flux/reactive_flux.py | 25 ----------------- msmtools/flux/reactive_flux_test.py | 25 ----------------- msmtools/flux/sparse/pathways.py | 25 ----------------- msmtools/flux/sparse/tpt.py | 25 ----------------- msmtools/flux/tests/birth_death_chain.py | 25 ----------------- msmtools/flux/tests/test_pathways.py | 25 ----------------- msmtools/flux/tests/test_tpt.py | 25 ----------------- msmtools/util/matrix/__init__.py | 25 ----------------- msmtools/util/matrix/matrix_test.py | 25 ----------------- msmtools/util/statistics.py | 25 ----------------- msmtools/util/types.py | 25 ----------------- setup.py | 25 ----------------- setup_util.py | 26 +----------------- 86 files changed, 2 insertions(+), 2151 deletions(-) diff --git a/msmtools/analysis/__init__.py b/msmtools/analysis/__init__.py index 415da2f8..0d03ed33 100644 --- a/msmtools/analysis/__init__.py +++ b/msmtools/analysis/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" ============================================================== diff --git a/msmtools/analysis/dense/assessment_test.py b/msmtools/analysis/dense/assessment_test.py index deac1b77..8db00c3b 100644 --- a/msmtools/analysis/dense/assessment_test.py +++ b/msmtools/analysis/dense/assessment_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on 07.10.2013 diff --git a/msmtools/analysis/dense/birth_death_chain.py b/msmtools/analysis/dense/birth_death_chain.py index 8d5ad699..96fcf1db 100644 --- a/msmtools/analysis/dense/birth_death_chain.py +++ b/msmtools/analysis/dense/birth_death_chain.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/committor.py b/msmtools/analysis/dense/committor.py index 9570e3a7..361ac9de 100644 --- a/msmtools/analysis/dense/committor.py +++ b/msmtools/analysis/dense/committor.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides functions for the computation of forward and backward comittors using dense linear algebra. diff --git a/msmtools/analysis/dense/committor_test.py b/msmtools/analysis/dense/committor_test.py index aa73b3ca..694f2252 100644 --- a/msmtools/analysis/dense/committor_test.py +++ b/msmtools/analysis/dense/committor_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the committor module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/correlations.py b/msmtools/analysis/dense/correlations.py index f9ada3e9..95d17d2f 100644 --- a/msmtools/analysis/dense/correlations.py +++ b/msmtools/analysis/dense/correlations.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on 29.11.2013 diff --git a/msmtools/analysis/dense/correlations_test.py b/msmtools/analysis/dense/correlations_test.py index 19fa31f1..bc93650b 100644 --- a/msmtools/analysis/dense/correlations_test.py +++ b/msmtools/analysis/dense/correlations_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on Jun 3, 2014 diff --git a/msmtools/analysis/dense/expectations.py b/msmtools/analysis/dense/expectations.py index 4083498c..01c902af 100644 --- a/msmtools/analysis/dense/expectations.py +++ b/msmtools/analysis/dense/expectations.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides dense implementations for the computation of expectation values for a given transition matrix. diff --git a/msmtools/analysis/dense/expectations_test.py b/msmtools/analysis/dense/expectations_test.py index 347f63d2..15cdc4e7 100644 --- a/msmtools/analysis/dense/expectations_test.py +++ b/msmtools/analysis/dense/expectations_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides unit tests for the expectations module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/fingerprints.py b/msmtools/analysis/dense/fingerprints.py index 38e10b29..0820f7c1 100644 --- a/msmtools/analysis/dense/fingerprints.py +++ b/msmtools/analysis/dense/fingerprints.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides dense implementation for the computation of dynamical fingerprints, expectations and correlations diff --git a/msmtools/analysis/dense/fingerprints_test.py b/msmtools/analysis/dense/fingerprints_test.py index 04194b0d..a703c504 100644 --- a/msmtools/analysis/dense/fingerprints_test.py +++ b/msmtools/analysis/dense/fingerprints_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the fingerprint module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/hitting_probability.py b/msmtools/analysis/dense/hitting_probability.py index 779d535d..95a1101a 100644 --- a/msmtools/analysis/dense/hitting_probability.py +++ b/msmtools/analysis/dense/hitting_probability.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Dense implementation of hitting probabilities .. moduleauthor:: F.Noe diff --git a/msmtools/analysis/dense/hitting_probability_test.py b/msmtools/analysis/dense/hitting_probability_test.py index 6ea1390e..06d0b4a8 100644 --- a/msmtools/analysis/dense/hitting_probability_test.py +++ b/msmtools/analysis/dense/hitting_probability_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test, dense implementation of hitting probabilities .. moduleauthor:: F.Noe diff --git a/msmtools/analysis/dense/mean_first_passage_time.py b/msmtools/analysis/dense/mean_first_passage_time.py index 24b7756d..179d1ff8 100644 --- a/msmtools/analysis/dense/mean_first_passage_time.py +++ b/msmtools/analysis/dense/mean_first_passage_time.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Dense implementation of mean first passage time computation .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/mean_first_passage_time_test.py b/msmtools/analysis/dense/mean_first_passage_time_test.py index 79e147e5..78774338 100644 --- a/msmtools/analysis/dense/mean_first_passage_time_test.py +++ b/msmtools/analysis/dense/mean_first_passage_time_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the mean first passage time module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/pcca.py b/msmtools/analysis/dense/pcca.py index 736cd2e2..62e4b64e 100644 --- a/msmtools/analysis/dense/pcca.py +++ b/msmtools/analysis/dense/pcca.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' @author: Susanna Roeblitz, Marcus Weber, Frank Noe diff --git a/msmtools/analysis/dense/pcca_test.py b/msmtools/analysis/dense/pcca_test.py index 0a45ef3b..b69d8e69 100644 --- a/msmtools/analysis/dense/pcca_test.py +++ b/msmtools/analysis/dense/pcca_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on 06.12.2013 diff --git a/msmtools/analysis/dense/sensitivity.py b/msmtools/analysis/dense/sensitivity.py index 06704504..72b9cdd4 100644 --- a/msmtools/analysis/dense/sensitivity.py +++ b/msmtools/analysis/dense/sensitivity.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on 22.11.2013 diff --git a/msmtools/analysis/dense/sensitivity_test.py b/msmtools/analysis/dense/sensitivity_test.py index 6c77d4f7..7d6c2819 100644 --- a/msmtools/analysis/dense/sensitivity_test.py +++ b/msmtools/analysis/dense/sensitivity_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on 06.12.2013 diff --git a/msmtools/analysis/sparse/assessment_test.py b/msmtools/analysis/sparse/assessment_test.py index 877478b2..658ca1c3 100644 --- a/msmtools/analysis/sparse/assessment_test.py +++ b/msmtools/analysis/sparse/assessment_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """This module provides unit tests for the assessment module""" from __future__ import absolute_import from __future__ import division diff --git a/msmtools/analysis/sparse/birth_death_chain.py b/msmtools/analysis/sparse/birth_death_chain.py index 8d5ad699..96fcf1db 100644 --- a/msmtools/analysis/sparse/birth_death_chain.py +++ b/msmtools/analysis/sparse/birth_death_chain.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/committor.py b/msmtools/analysis/sparse/committor.py index 198c7732..c45ddfde 100644 --- a/msmtools/analysis/sparse/committor.py +++ b/msmtools/analysis/sparse/committor.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides functions for the computation of forward and backward comittors using sparse linear algebra. diff --git a/msmtools/analysis/sparse/committor_test.py b/msmtools/analysis/sparse/committor_test.py index b2ecb423..075f2a1c 100644 --- a/msmtools/analysis/sparse/committor_test.py +++ b/msmtools/analysis/sparse/committor_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the committor module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/fingerprints.py b/msmtools/analysis/sparse/fingerprints.py index a611a3c8..95e90ceb 100644 --- a/msmtools/analysis/sparse/fingerprints.py +++ b/msmtools/analysis/sparse/fingerprints.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module contains sparse implementation of the fingerprint module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/fingerprints_test.py b/msmtools/analysis/sparse/fingerprints_test.py index c9d3d976..98455227 100644 --- a/msmtools/analysis/sparse/fingerprints_test.py +++ b/msmtools/analysis/sparse/fingerprints_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the fingerprint module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/mean_first_passage_time.py b/msmtools/analysis/sparse/mean_first_passage_time.py index d66215f7..c3ae159e 100644 --- a/msmtools/analysis/sparse/mean_first_passage_time.py +++ b/msmtools/analysis/sparse/mean_first_passage_time.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Sparse implementation of mean first passage time computation .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/mean_first_passage_time_test.py b/msmtools/analysis/sparse/mean_first_passage_time_test.py index 495b5b9b..85786d7c 100644 --- a/msmtools/analysis/sparse/mean_first_passage_time_test.py +++ b/msmtools/analysis/sparse/mean_first_passage_time_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the mean first passage time module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/birth_death_chain.py b/msmtools/analysis/tests/birth_death_chain.py index 8d5ad699..96fcf1db 100644 --- a/msmtools/analysis/tests/birth_death_chain.py +++ b/msmtools/analysis/tests/birth_death_chain.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_assessment.py b/msmtools/analysis/tests/test_assessment.py index 162a2560..90003a8c 100644 --- a/msmtools/analysis/tests/test_assessment.py +++ b/msmtools/analysis/tests/test_assessment.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """This module provides unit tests for the assessment functions of the analysis API .. moduleauthor:: Martin Scherer diff --git a/msmtools/analysis/tests/test_committor.py b/msmtools/analysis/tests/test_committor.py index fdf243e1..d54b6f1a 100644 --- a/msmtools/analysis/tests/test_committor.py +++ b/msmtools/analysis/tests/test_committor.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the committor API-function .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_decomposition.py b/msmtools/analysis/tests/test_decomposition.py index ce952cb5..2cb5c784 100644 --- a/msmtools/analysis/tests/test_decomposition.py +++ b/msmtools/analysis/tests/test_decomposition.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for decomposition functions in api.py .. moduleauthor:: Benjamin Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_fingerprints.py b/msmtools/analysis/tests/test_fingerprints.py index bc064598..105868a9 100644 --- a/msmtools/analysis/tests/test_fingerprints.py +++ b/msmtools/analysis/tests/test_fingerprints.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the fingerprint API-functions .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_mfpt.py b/msmtools/analysis/tests/test_mfpt.py index c98c6468..f8258dbb 100644 --- a/msmtools/analysis/tests/test_mfpt.py +++ b/msmtools/analysis/tests/test_mfpt.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the mean first passage time API-functions .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_sensitivity.py b/msmtools/analysis/tests/test_sensitivity.py index e8f1f6c1..7e7eb77e 100644 --- a/msmtools/analysis/tests/test_sensitivity.py +++ b/msmtools/analysis/tests/test_sensitivity.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on 06.12.2013 diff --git a/msmtools/dtraj/__init__.py b/msmtools/dtraj/__init__.py index 5bb5b9be..01e2b4dc 100644 --- a/msmtools/dtraj/__init__.py +++ b/msmtools/dtraj/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" =============================================================== diff --git a/msmtools/estimation/api.py b/msmtools/estimation/api.py index ad338deb..9ce8d247 100644 --- a/msmtools/estimation/api.py +++ b/msmtools/estimation/api.py @@ -1,29 +1,4 @@ # -*- coding: utf-8 -*- - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" ========================= Estimation API diff --git a/msmtools/estimation/dense/_mle_trev_given_pi.c b/msmtools/estimation/dense/_mle_trev_given_pi.c index a912db0a..82c40e27 100644 --- a/msmtools/estimation/dense/_mle_trev_given_pi.c +++ b/msmtools/estimation/dense/_mle_trev_given_pi.c @@ -1,28 +1,3 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - /* moduleauthor:: F. Paul */ #include #include diff --git a/msmtools/estimation/dense/_mle_trev_given_pi.h b/msmtools/estimation/dense/_mle_trev_given_pi.h index 88934392..874c9106 100644 --- a/msmtools/estimation/dense/_mle_trev_given_pi.h +++ b/msmtools/estimation/dense/_mle_trev_given_pi.h @@ -1,27 +1,2 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - int _mle_trev_given_pi_dense(double * const T, const double * const C, const double * const mu, const int n, const double maxerr, const int maxiter); diff --git a/msmtools/estimation/dense/bootstrapping.py b/msmtools/estimation/dense/bootstrapping.py index 2b71f7bd..3e35eb18 100644 --- a/msmtools/estimation/dense/bootstrapping.py +++ b/msmtools/estimation/dense/bootstrapping.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on Jul 23, 2014 diff --git a/msmtools/estimation/dense/covariance.py b/msmtools/estimation/dense/covariance.py index 8aab19aa..479b483a 100644 --- a/msmtools/estimation/dense/covariance.py +++ b/msmtools/estimation/dense/covariance.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module implements the transition matrix covariance function .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/dense/covariance_test.py b/msmtools/estimation/dense/covariance_test.py index fc6c67d9..c1ee7535 100644 --- a/msmtools/estimation/dense/covariance_test.py +++ b/msmtools/estimation/dense/covariance_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the covariance module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/dense/sample_rev.c b/msmtools/estimation/dense/sample_rev.c index 7d89be80..c1ddc308 100644 --- a/msmtools/estimation/dense/sample_rev.c +++ b/msmtools/estimation/dense/sample_rev.c @@ -1,28 +1,3 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - /* * moduleauthor:: F. Noe */ #include diff --git a/msmtools/estimation/dense/sample_rev.h b/msmtools/estimation/dense/sample_rev.h index e8d743e7..85394352 100644 --- a/msmtools/estimation/dense/sample_rev.h +++ b/msmtools/estimation/dense/sample_rev.h @@ -1,28 +1,3 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - /* * moduleauthor:: F. Noe */ diff --git a/msmtools/estimation/dense/sample_revpi.c b/msmtools/estimation/dense/sample_revpi.c index 98ae255c..d58fa278 100644 --- a/msmtools/estimation/dense/sample_revpi.c +++ b/msmtools/estimation/dense/sample_revpi.c @@ -1,28 +1,3 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - /* * moduleauthor:: B. Trendelkamp-Schroer * */ diff --git a/msmtools/estimation/dense/sample_revpi.h b/msmtools/estimation/dense/sample_revpi.h index f2c3bda1..5a0a90a2 100644 --- a/msmtools/estimation/dense/sample_revpi.h +++ b/msmtools/estimation/dense/sample_revpi.h @@ -1,28 +1,3 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - /* * moduleauthor:: B. Trendelkamp-Schroer * */ diff --git a/msmtools/estimation/dense/transition_matrix.py b/msmtools/estimation/dense/transition_matrix.py index 9472daac..eec4e3c1 100644 --- a/msmtools/estimation/dense/transition_matrix.py +++ b/msmtools/estimation/dense/transition_matrix.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on Jan 13, 2014 diff --git a/msmtools/estimation/sparse/_mle_trev.c b/msmtools/estimation/sparse/_mle_trev.c index 5c4cac2d..86f15864 100644 --- a/msmtools/estimation/sparse/_mle_trev.c +++ b/msmtools/estimation/sparse/_mle_trev.c @@ -1,28 +1,3 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - /* moduleauthor:: F. Paul */ #include #include diff --git a/msmtools/estimation/sparse/_mle_trev.h b/msmtools/estimation/sparse/_mle_trev.h index b76ce8bf..56f0eedc 100644 --- a/msmtools/estimation/sparse/_mle_trev.h +++ b/msmtools/estimation/sparse/_mle_trev.h @@ -1,26 +1 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - int _mle_trev_sparse(double * const T_data, const double * const CCt_data, const int * const i_indices, const int * const j_indices, const int len_CCt, const double * const sum_C, const int dim, const double maxerr, const int maxiter); diff --git a/msmtools/estimation/sparse/_mle_trev_given_pi.c b/msmtools/estimation/sparse/_mle_trev_given_pi.c index 7488b82d..3f7fd5bd 100644 --- a/msmtools/estimation/sparse/_mle_trev_given_pi.c +++ b/msmtools/estimation/sparse/_mle_trev_given_pi.c @@ -1,28 +1,3 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - /* moduleauthor:: F. Paul */ #include #include diff --git a/msmtools/estimation/sparse/_mle_trev_given_pi.h b/msmtools/estimation/sparse/_mle_trev_given_pi.h index 882ec9c8..0d34206a 100644 --- a/msmtools/estimation/sparse/_mle_trev_given_pi.h +++ b/msmtools/estimation/sparse/_mle_trev_given_pi.h @@ -1,26 +1 @@ -/* * Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University - * Berlin, 14195 Berlin, Germany. - * All rights reserved. - * - * Redistribution and use in source and binary forms, with or without modification, - * are permitted provided that the following conditions are met: - * - * * Redistributions of source code must retain the above copyright notice, this - * list of conditions and the following disclaimer. - * * Redistributions in binary form must reproduce the above copyright notice, - * this list of conditions and the following disclaimer in the documentation and/or - * other materials provided with the distribution. - * - * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' - * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR - * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; - * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON - * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS - * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - */ - int _mle_trev_given_pi_sparse(double * const T_unnormalized_data, const double * const CCt_data, const int * const i_indices, const int * const j_indices, const int len_CCt, const double * const mu, const int len_mu, const double maxerr, const int maxiter); diff --git a/msmtools/estimation/sparse/connectivity.py b/msmtools/estimation/sparse/connectivity.py index 115a04a9..f4c681ce 100644 --- a/msmtools/estimation/sparse/connectivity.py +++ b/msmtools/estimation/sparse/connectivity.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module implements the connectivity functionality .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/connectivity_test.py b/msmtools/estimation/sparse/connectivity_test.py index 7e82e832..8c017f6b 100644 --- a/msmtools/estimation/sparse/connectivity_test.py +++ b/msmtools/estimation/sparse/connectivity_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the connectivity module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/count_matrix.py b/msmtools/estimation/sparse/count_matrix.py index 7428cbb6..a10ee6ea 100644 --- a/msmtools/estimation/sparse/count_matrix.py +++ b/msmtools/estimation/sparse/count_matrix.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module implements the countmatrix estimation functionality .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/count_matrix_test.py b/msmtools/estimation/sparse/count_matrix_test.py index a5bb6c73..2b178027 100644 --- a/msmtools/estimation/sparse/count_matrix_test.py +++ b/msmtools/estimation/sparse/count_matrix_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """Unit tests for the count_matrix module""" from __future__ import absolute_import diff --git a/msmtools/estimation/sparse/likelihood.py b/msmtools/estimation/sparse/likelihood.py index 40c79653..b0351daf 100644 --- a/msmtools/estimation/sparse/likelihood.py +++ b/msmtools/estimation/sparse/likelihood.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """This module implements the transition matrix functionality""" from __future__ import absolute_import diff --git a/msmtools/estimation/sparse/likelihood_test.py b/msmtools/estimation/sparse/likelihood_test.py index 587e6d69..29ca32e6 100644 --- a/msmtools/estimation/sparse/likelihood_test.py +++ b/msmtools/estimation/sparse/likelihood_test.py @@ -1,29 +1,4 @@ from __future__ import absolute_import - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - import unittest import numpy as np diff --git a/msmtools/estimation/sparse/prior.py b/msmtools/estimation/sparse/prior.py index e2983131..bc849a02 100644 --- a/msmtools/estimation/sparse/prior.py +++ b/msmtools/estimation/sparse/prior.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides functions for computation of prior count matrices .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/prior_test.py b/msmtools/estimation/sparse/prior_test.py index b5b943d1..f379e281 100644 --- a/msmtools/estimation/sparse/prior_test.py +++ b/msmtools/estimation/sparse/prior_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the prior module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/transition_matrix.py b/msmtools/estimation/sparse/transition_matrix.py index 292abd80..9b5761a2 100644 --- a/msmtools/estimation/sparse/transition_matrix.py +++ b/msmtools/estimation/sparse/transition_matrix.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """This module implements the transition matrix functionality""" from __future__ import absolute_import from __future__ import division diff --git a/msmtools/estimation/sparse/transition_matrix_test.py b/msmtools/estimation/sparse/transition_matrix_test.py index cf0576e3..ac86cef5 100644 --- a/msmtools/estimation/sparse/transition_matrix_test.py +++ b/msmtools/estimation/sparse/transition_matrix_test.py @@ -1,29 +1,4 @@ from __future__ import absolute_import - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - import unittest from msmtools.util.numeric import assert_allclose diff --git a/msmtools/estimation/tests/test_bootstrapping.py b/msmtools/estimation/tests/test_bootstrapping.py index a7aded88..22361ff1 100644 --- a/msmtools/estimation/tests/test_bootstrapping.py +++ b/msmtools/estimation/tests/test_bootstrapping.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on Jul 25, 2014 diff --git a/msmtools/estimation/tests/test_connectivity.py b/msmtools/estimation/tests/test_connectivity.py index 5aeffffd..1aec8dd2 100644 --- a/msmtools/estimation/tests/test_connectivity.py +++ b/msmtools/estimation/tests/test_connectivity.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the connectivity API functions .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/tests/test_count_matrix.py b/msmtools/estimation/tests/test_count_matrix.py index 36ad3b9e..0719d736 100644 --- a/msmtools/estimation/tests/test_count_matrix.py +++ b/msmtools/estimation/tests/test_count_matrix.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """Unit tests for the count_matrix module""" from __future__ import absolute_import diff --git a/msmtools/estimation/tests/test_effective_count_matrix.py b/msmtools/estimation/tests/test_effective_count_matrix.py index 053f9a84..31ed8a21 100644 --- a/msmtools/estimation/tests/test_effective_count_matrix.py +++ b/msmtools/estimation/tests/test_effective_count_matrix.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - import unittest import numpy as np diff --git a/msmtools/estimation/tests/test_likelihood.py b/msmtools/estimation/tests/test_likelihood.py index d78db429..7dc04634 100644 --- a/msmtools/estimation/tests/test_likelihood.py +++ b/msmtools/estimation/tests/test_likelihood.py @@ -1,29 +1,4 @@ from __future__ import absolute_import - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - import unittest import numpy as np diff --git a/msmtools/estimation/tests/test_mle_trev.py b/msmtools/estimation/tests/test_mle_trev.py index aee75f04..bd00a9e4 100644 --- a/msmtools/estimation/tests/test_mle_trev.py +++ b/msmtools/estimation/tests/test_mle_trev.py @@ -1,29 +1,4 @@ from __future__ import absolute_import - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - import unittest import numpy as np from msmtools.util.numeric import assert_allclose diff --git a/msmtools/estimation/tests/test_mle_trev_given_pi.py b/msmtools/estimation/tests/test_mle_trev_given_pi.py index c422a0e9..77172cb5 100644 --- a/msmtools/estimation/tests/test_mle_trev_given_pi.py +++ b/msmtools/estimation/tests/test_mle_trev_given_pi.py @@ -1,29 +1,4 @@ from __future__ import absolute_import - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - import unittest import numpy as np from msmtools.util.numeric import assert_allclose diff --git a/msmtools/estimation/tests/test_prior.py b/msmtools/estimation/tests/test_prior.py index 3a2986f0..4db0976b 100644 --- a/msmtools/estimation/tests/test_prior.py +++ b/msmtools/estimation/tests/test_prior.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the prior module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/tests/test_tmatrix_sampling.py b/msmtools/estimation/tests/test_tmatrix_sampling.py index 53d21f2f..d83d1045 100644 --- a/msmtools/estimation/tests/test_tmatrix_sampling.py +++ b/msmtools/estimation/tests/test_tmatrix_sampling.py @@ -1,30 +1,5 @@ from __future__ import absolute_import -from six.moves import range -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -r"""Unit tests for the transition_matrix module +from six.moves import ranger"""Unit tests for the transition_matrix module .. moduleauthor:: B.Trendelkamp-Schroer .. moduleauthor:: Frank Noe diff --git a/msmtools/estimation/tests/test_transition_matrix.py b/msmtools/estimation/tests/test_transition_matrix.py index 48d60c2e..3e22e683 100644 --- a/msmtools/estimation/tests/test_transition_matrix.py +++ b/msmtools/estimation/tests/test_transition_matrix.py @@ -1,30 +1,5 @@ from __future__ import absolute_import from __future__ import division - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - import unittest import warnings diff --git a/msmtools/flux/api.py b/msmtools/flux/api.py index 99d5f231..af52d8f8 100644 --- a/msmtools/flux/api.py +++ b/msmtools/flux/api.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" =================== Flux API diff --git a/msmtools/flux/dense/tpt.py b/msmtools/flux/dense/tpt.py index f5849c80..45b92342 100644 --- a/msmtools/flux/dense/tpt.py +++ b/msmtools/flux/dense/tpt.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module contains function for the Transition Path Theory (TPT) analysis of Markov models. diff --git a/msmtools/flux/dense/tpt_test.py b/msmtools/flux/dense/tpt_test.py index a5b8fa1e..0affc733 100644 --- a/msmtools/flux/dense/tpt_test.py +++ b/msmtools/flux/dense/tpt_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the TPT-module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/reactive_flux.py b/msmtools/flux/reactive_flux.py index 206dcb3c..f1e4df39 100644 --- a/msmtools/flux/reactive_flux.py +++ b/msmtools/flux/reactive_flux.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module contains function for the Transition Path Theory (TPT) analysis of Markov models. diff --git a/msmtools/flux/reactive_flux_test.py b/msmtools/flux/reactive_flux_test.py index cdf0db45..131a1179 100644 --- a/msmtools/flux/reactive_flux_test.py +++ b/msmtools/flux/reactive_flux_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the ReactiveFlux object .. moduleauthor:: F.Noe diff --git a/msmtools/flux/sparse/pathways.py b/msmtools/flux/sparse/pathways.py index 4aa3cf79..48372bc7 100644 --- a/msmtools/flux/sparse/pathways.py +++ b/msmtools/flux/sparse/pathways.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Decomposition of a netflux network into its dominant reaction pathways .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/sparse/tpt.py b/msmtools/flux/sparse/tpt.py index c75c518a..bc9130f9 100644 --- a/msmtools/flux/sparse/tpt.py +++ b/msmtools/flux/sparse/tpt.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module contains function for the Transition Path Theory (TPT) analysis of Markov models. diff --git a/msmtools/flux/tests/birth_death_chain.py b/msmtools/flux/tests/birth_death_chain.py index 8d5ad699..96fcf1db 100644 --- a/msmtools/flux/tests/birth_death_chain.py +++ b/msmtools/flux/tests/birth_death_chain.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/tests/test_pathways.py b/msmtools/flux/tests/test_pathways.py index f7d7462b..7f36c5e3 100644 --- a/msmtools/flux/tests/test_pathways.py +++ b/msmtools/flux/tests/test_pathways.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """Unit test for the reaction pathway decomposition .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/tests/test_tpt.py b/msmtools/flux/tests/test_tpt.py index 994d92d6..2b4302bf 100644 --- a/msmtools/flux/tests/test_tpt.py +++ b/msmtools/flux/tests/test_tpt.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the TPT-functions of the analysis API .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/util/matrix/__init__.py b/msmtools/util/matrix/__init__.py index 51c8b12c..e69de29b 100644 --- a/msmtools/util/matrix/__init__.py +++ b/msmtools/util/matrix/__init__.py @@ -1,25 +0,0 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - diff --git a/msmtools/util/matrix/matrix_test.py b/msmtools/util/matrix/matrix_test.py index c93a4454..17e64b3e 100644 --- a/msmtools/util/matrix/matrix_test.py +++ b/msmtools/util/matrix/matrix_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for matrix io implementations .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/util/statistics.py b/msmtools/util/statistics.py index c6b4d968..5acaaad9 100644 --- a/msmtools/util/statistics.py +++ b/msmtools/util/statistics.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on Jul 25, 2014 diff --git a/msmtools/util/types.py b/msmtools/util/types.py index 0281cd16..d196a77b 100644 --- a/msmtools/util/types.py +++ b/msmtools/util/types.py @@ -2,31 +2,6 @@ from __future__ import print_function import six from six.moves import range - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - __author__ = 'noe' import numpy as np diff --git a/setup.py b/setup.py index b41ea11c..858532d3 100755 --- a/setup.py +++ b/setup.py @@ -1,29 +1,4 @@ #!/usr/bin/env python - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """ MSMTools MSMTools contains an API to estimate and analyze Markov state models. diff --git a/setup_util.py b/setup_util.py index ffd9e13b..838136b5 100644 --- a/setup_util.py +++ b/setup_util.py @@ -1,28 +1,4 @@ -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """ utility functions for python setup """ @@ -97,4 +73,4 @@ def c_list(self): def __iter__(self): for e in self.c_list(): yield e def __getitem__(self, ii): return self.c_list()[ii] - def __len__(self): return len(self.c_list()) \ No newline at end of file + def __len__(self): return len(self.c_list()) From 2acd02986a8b9f44f1620bf62e58e802194b2ae7 Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 20:59:42 +0200 Subject: [PATCH 02/11] changed license text to full text LGPLv3 --- LICENSE.txt | 190 +++++++++++++++++++++++++++++++++++++++++++++------- 1 file changed, 165 insertions(+), 25 deletions(-) diff --git a/LICENSE.txt b/LICENSE.txt index b3ab2bc0..65c5ca88 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,25 +1,165 @@ -Copyright (c) 2015, 2014 Computational Molecular Biology Group, - FU Berlin, 14195 Berlin, Germany. - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions -are met: - -1. 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From 75f1d446fcc0b6a69d0e8a1bcfdf43bd0d1f8b90 Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 21:29:07 +0200 Subject: [PATCH 03/11] added first line separator --- msmtools/__init__.py | 1 + msmtools/analysis/api.py | 1 + msmtools/analysis/dense/__init__.py | 1 + msmtools/analysis/dense/decomposition.py | 1 + msmtools/analysis/dense/decomposition_test.py | 1 + msmtools/analysis/dense/stationary_vector.py | 1 + msmtools/analysis/sparse/__init__.py | 1 + msmtools/analysis/sparse/assessment.py | 1 + msmtools/analysis/sparse/decomposition.py | 1 + msmtools/analysis/sparse/decomposition_test.py | 1 + msmtools/analysis/sparse/expectations.py | 1 + msmtools/analysis/sparse/expectations_test.py | 1 + msmtools/analysis/sparse/stationary_vector.py | 1 + msmtools/analysis/sparse/stationary_vector_test.py | 1 + msmtools/analysis/tests/test_expectations.py | 1 + msmtools/dtraj/api.py | 1 + msmtools/dtraj/tests/test_trajectory.py | 1 + msmtools/estimation/__init__.py | 1 + msmtools/estimation/api.py | 1 + msmtools/estimation/dense/__init__.py | 1 + msmtools/estimation/dense/sampler_nrev.py | 1 + msmtools/estimation/dense/tmatrix_sampler.py | 1 + msmtools/estimation/dense/tmatrix_sampler_test.py | 1 + msmtools/estimation/sparse/__init__.py | 1 + msmtools/estimation/sparse/effective_counts.py | 1 + msmtools/flux/__init__.py | 1 + msmtools/flux/dense/__init__.py | 1 + msmtools/flux/sparse/__init__.py | 1 + msmtools/flux/sparse/pathways_test.py | 1 + msmtools/flux/sparse/tpt_test.py | 1 + msmtools/generation/__init__.py | 1 + msmtools/generation/api.py | 1 + msmtools/generation/tests/test_generation.py | 1 + msmtools/util/annotators.py | 1 + msmtools/util/exceptions.py | 1 + msmtools/util/matrix/matrix.py | 1 + msmtools/util/numeric.py | 1 + setup.py | 1 + 38 files changed, 38 insertions(+) diff --git a/msmtools/__init__.py b/msmtools/__init__.py index 4dbe9b06..85611ad4 100644 --- a/msmtools/__init__.py +++ b/msmtools/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/api.py b/msmtools/analysis/api.py index df1e44bf..56dcfdf4 100644 --- a/msmtools/analysis/api.py +++ b/msmtools/analysis/api.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/dense/__init__.py b/msmtools/analysis/dense/__init__.py index 8811c6fa..3f1c02f4 100644 --- a/msmtools/analysis/dense/__init__.py +++ b/msmtools/analysis/dense/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/dense/decomposition.py b/msmtools/analysis/dense/decomposition.py index b5336456..f636fe07 100644 --- a/msmtools/analysis/dense/decomposition.py +++ b/msmtools/analysis/dense/decomposition.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/dense/decomposition_test.py b/msmtools/analysis/dense/decomposition_test.py index f5a517e5..2315ece9 100644 --- a/msmtools/analysis/dense/decomposition_test.py +++ b/msmtools/analysis/dense/decomposition_test.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/dense/stationary_vector.py b/msmtools/analysis/dense/stationary_vector.py index cd171769..723b0e59 100644 --- a/msmtools/analysis/dense/stationary_vector.py +++ b/msmtools/analysis/dense/stationary_vector.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/__init__.py b/msmtools/analysis/sparse/__init__.py index b95f2c61..fdf3e972 100644 --- a/msmtools/analysis/sparse/__init__.py +++ b/msmtools/analysis/sparse/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/assessment.py b/msmtools/analysis/sparse/assessment.py index dd544305..ed2f847e 100644 --- a/msmtools/analysis/sparse/assessment.py +++ b/msmtools/analysis/sparse/assessment.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/decomposition.py b/msmtools/analysis/sparse/decomposition.py index ffdd6a07..e640597d 100644 --- a/msmtools/analysis/sparse/decomposition.py +++ b/msmtools/analysis/sparse/decomposition.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/decomposition_test.py b/msmtools/analysis/sparse/decomposition_test.py index 8fc2a1d0..92f4dc8d 100644 --- a/msmtools/analysis/sparse/decomposition_test.py +++ b/msmtools/analysis/sparse/decomposition_test.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/expectations.py b/msmtools/analysis/sparse/expectations.py index 93867589..a4c8a725 100644 --- a/msmtools/analysis/sparse/expectations.py +++ b/msmtools/analysis/sparse/expectations.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/expectations_test.py b/msmtools/analysis/sparse/expectations_test.py index be2ab654..0c9be3cc 100644 --- a/msmtools/analysis/sparse/expectations_test.py +++ b/msmtools/analysis/sparse/expectations_test.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/stationary_vector.py b/msmtools/analysis/sparse/stationary_vector.py index 834e40e6..36f86935 100644 --- a/msmtools/analysis/sparse/stationary_vector.py +++ b/msmtools/analysis/sparse/stationary_vector.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/sparse/stationary_vector_test.py b/msmtools/analysis/sparse/stationary_vector_test.py index 08a66c71..954f621b 100644 --- a/msmtools/analysis/sparse/stationary_vector_test.py +++ b/msmtools/analysis/sparse/stationary_vector_test.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/analysis/tests/test_expectations.py b/msmtools/analysis/tests/test_expectations.py index f9242fcd..78ac475c 100644 --- a/msmtools/analysis/tests/test_expectations.py +++ b/msmtools/analysis/tests/test_expectations.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/dtraj/api.py b/msmtools/dtraj/api.py index c8716928..e54dbe5c 100644 --- a/msmtools/dtraj/api.py +++ b/msmtools/dtraj/api.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/dtraj/tests/test_trajectory.py b/msmtools/dtraj/tests/test_trajectory.py index a2599066..c0300900 100644 --- a/msmtools/dtraj/tests/test_trajectory.py +++ b/msmtools/dtraj/tests/test_trajectory.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/estimation/__init__.py b/msmtools/estimation/__init__.py index 86ee88f3..d34e0c21 100644 --- a/msmtools/estimation/__init__.py +++ b/msmtools/estimation/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/estimation/api.py b/msmtools/estimation/api.py index 9ce8d247..f66d04c9 100644 --- a/msmtools/estimation/api.py +++ b/msmtools/estimation/api.py @@ -1,3 +1,4 @@ + # -*- coding: utf-8 -*- r""" ========================= diff --git a/msmtools/estimation/dense/__init__.py b/msmtools/estimation/dense/__init__.py index c51007e5..82620ed4 100644 --- a/msmtools/estimation/dense/__init__.py +++ b/msmtools/estimation/dense/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/estimation/dense/sampler_nrev.py b/msmtools/estimation/dense/sampler_nrev.py index bdaf759e..206c3f27 100644 --- a/msmtools/estimation/dense/sampler_nrev.py +++ b/msmtools/estimation/dense/sampler_nrev.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/estimation/dense/tmatrix_sampler.py b/msmtools/estimation/dense/tmatrix_sampler.py index e16eda7c..74e4fbc1 100644 --- a/msmtools/estimation/dense/tmatrix_sampler.py +++ b/msmtools/estimation/dense/tmatrix_sampler.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/estimation/dense/tmatrix_sampler_test.py b/msmtools/estimation/dense/tmatrix_sampler_test.py index 7dfa59f5..ceb9bce0 100644 --- a/msmtools/estimation/dense/tmatrix_sampler_test.py +++ b/msmtools/estimation/dense/tmatrix_sampler_test.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/estimation/sparse/__init__.py b/msmtools/estimation/sparse/__init__.py index 2ecab03c..c357f1e4 100644 --- a/msmtools/estimation/sparse/__init__.py +++ b/msmtools/estimation/sparse/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/estimation/sparse/effective_counts.py b/msmtools/estimation/sparse/effective_counts.py index ae62d89a..7ff76ae8 100644 --- a/msmtools/estimation/sparse/effective_counts.py +++ b/msmtools/estimation/sparse/effective_counts.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/flux/__init__.py b/msmtools/flux/__init__.py index 39109ad8..aaa69477 100644 --- a/msmtools/flux/__init__.py +++ b/msmtools/flux/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/flux/dense/__init__.py b/msmtools/flux/dense/__init__.py index d5909312..e74b65c1 100644 --- a/msmtools/flux/dense/__init__.py +++ b/msmtools/flux/dense/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/flux/sparse/__init__.py b/msmtools/flux/sparse/__init__.py index 91bc47b6..913b1642 100644 --- a/msmtools/flux/sparse/__init__.py +++ b/msmtools/flux/sparse/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/flux/sparse/pathways_test.py b/msmtools/flux/sparse/pathways_test.py index e8785775..82808451 100644 --- a/msmtools/flux/sparse/pathways_test.py +++ b/msmtools/flux/sparse/pathways_test.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/flux/sparse/tpt_test.py b/msmtools/flux/sparse/tpt_test.py index d1162fe3..ef325447 100644 --- a/msmtools/flux/sparse/tpt_test.py +++ b/msmtools/flux/sparse/tpt_test.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/generation/__init__.py b/msmtools/generation/__init__.py index 318cab9d..735015ac 100644 --- a/msmtools/generation/__init__.py +++ b/msmtools/generation/__init__.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/generation/api.py b/msmtools/generation/api.py index 5ef8a891..08868ca9 100644 --- a/msmtools/generation/api.py +++ b/msmtools/generation/api.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/generation/tests/test_generation.py b/msmtools/generation/tests/test_generation.py index cdd460be..a92c381b 100644 --- a/msmtools/generation/tests/test_generation.py +++ b/msmtools/generation/tests/test_generation.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/util/annotators.py b/msmtools/util/annotators.py index a451268d..99fac69b 100644 --- a/msmtools/util/annotators.py +++ b/msmtools/util/annotators.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/util/exceptions.py b/msmtools/util/exceptions.py index c7225be8..672b8f43 100644 --- a/msmtools/util/exceptions.py +++ b/msmtools/util/exceptions.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/util/matrix/matrix.py b/msmtools/util/matrix/matrix.py index b52bfa33..f8dcc503 100644 --- a/msmtools/util/matrix/matrix.py +++ b/msmtools/util/matrix/matrix.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/msmtools/util/numeric.py b/msmtools/util/numeric.py index d2a3c393..5dfcc15e 100644 --- a/msmtools/util/numeric.py +++ b/msmtools/util/numeric.py @@ -1,3 +1,4 @@ + # Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University # Berlin, 14195 Berlin, Germany. # All rights reserved. diff --git a/setup.py b/setup.py index 858532d3..2af3819f 100755 --- a/setup.py +++ b/setup.py @@ -1,3 +1,4 @@ + #!/usr/bin/env python """ MSMTools From 60214dd66fe777703c7060fd91b20201be4bdaab Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 21:29:44 +0200 Subject: [PATCH 04/11] removed bsd --- msmtools/analysis/dense/decomposition.py | 25 ------------------- msmtools/analysis/dense/decomposition_test.py | 25 ------------------- msmtools/analysis/dense/stationary_vector.py | 25 ------------------- msmtools/analysis/sparse/assessment.py | 25 ------------------- msmtools/analysis/sparse/decomposition.py | 25 ------------------- .../analysis/sparse/decomposition_test.py | 25 ------------------- msmtools/analysis/sparse/expectations.py | 25 ------------------- msmtools/analysis/sparse/expectations_test.py | 25 ------------------- msmtools/analysis/sparse/stationary_vector.py | 25 ------------------- .../analysis/sparse/stationary_vector_test.py | 25 ------------------- msmtools/analysis/tests/test_expectations.py | 25 ------------------- msmtools/dtraj/tests/test_trajectory.py | 25 ------------------- msmtools/estimation/__init__.py | 25 ------------------- msmtools/estimation/dense/__init__.py | 25 ------------------- msmtools/estimation/dense/sampler_nrev.py | 25 ------------------- msmtools/estimation/dense/tmatrix_sampler.py | 25 ------------------- msmtools/flux/dense/__init__.py | 25 ------------------- msmtools/flux/sparse/pathways_test.py | 25 ------------------- msmtools/flux/sparse/tpt_test.py | 25 ------------------- msmtools/generation/api.py | 25 ------------------- msmtools/generation/tests/test_generation.py | 25 ------------------- 21 files changed, 525 deletions(-) diff --git a/msmtools/analysis/dense/decomposition.py b/msmtools/analysis/dense/decomposition.py index f636fe07..332c20e6 100644 --- a/msmtools/analysis/dense/decomposition.py +++ b/msmtools/analysis/dense/decomposition.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides matrix-decomposition based functions for the analysis of stochastic matrices diff --git a/msmtools/analysis/dense/decomposition_test.py b/msmtools/analysis/dense/decomposition_test.py index 2315ece9..90b9bba8 100644 --- a/msmtools/analysis/dense/decomposition_test.py +++ b/msmtools/analysis/dense/decomposition_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides unit tests for the decomposition module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/stationary_vector.py b/msmtools/analysis/dense/stationary_vector.py index 723b0e59..71590030 100644 --- a/msmtools/analysis/dense/stationary_vector.py +++ b/msmtools/analysis/dense/stationary_vector.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides functions for the coputation of stationary vectors of stochastic matrices diff --git a/msmtools/analysis/sparse/assessment.py b/msmtools/analysis/sparse/assessment.py index ed2f847e..b2adf879 100644 --- a/msmtools/analysis/sparse/assessment.py +++ b/msmtools/analysis/sparse/assessment.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """ Sparse assessment module of msm analysis package """ diff --git a/msmtools/analysis/sparse/decomposition.py b/msmtools/analysis/sparse/decomposition.py index e640597d..73bc5f3c 100644 --- a/msmtools/analysis/sparse/decomposition.py +++ b/msmtools/analysis/sparse/decomposition.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides matrix-decomposition based functions for the analysis of stochastic matrices diff --git a/msmtools/analysis/sparse/decomposition_test.py b/msmtools/analysis/sparse/decomposition_test.py index 92f4dc8d..c341dff1 100644 --- a/msmtools/analysis/sparse/decomposition_test.py +++ b/msmtools/analysis/sparse/decomposition_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Test package for the decomposition module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/expectations.py b/msmtools/analysis/sparse/expectations.py index a4c8a725..3af14871 100644 --- a/msmtools/analysis/sparse/expectations.py +++ b/msmtools/analysis/sparse/expectations.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides sparse implementations for the computation of expectation values for a given transition matrix. diff --git a/msmtools/analysis/sparse/expectations_test.py b/msmtools/analysis/sparse/expectations_test.py index 0c9be3cc..297698cc 100644 --- a/msmtools/analysis/sparse/expectations_test.py +++ b/msmtools/analysis/sparse/expectations_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Test package for the expectations module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/stationary_vector.py b/msmtools/analysis/sparse/stationary_vector.py index 36f86935..12c3a57b 100644 --- a/msmtools/analysis/sparse/stationary_vector.py +++ b/msmtools/analysis/sparse/stationary_vector.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides functions for the computation of stationary vectors of stochastic matrices. diff --git a/msmtools/analysis/sparse/stationary_vector_test.py b/msmtools/analysis/sparse/stationary_vector_test.py index 954f621b..bf7104be 100644 --- a/msmtools/analysis/sparse/stationary_vector_test.py +++ b/msmtools/analysis/sparse/stationary_vector_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Test package for the decomposition module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_expectations.py b/msmtools/analysis/tests/test_expectations.py index 78ac475c..8a579972 100644 --- a/msmtools/analysis/tests/test_expectations.py +++ b/msmtools/analysis/tests/test_expectations.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides unit tests for the expectations function in API .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/dtraj/tests/test_trajectory.py b/msmtools/dtraj/tests/test_trajectory.py index c0300900..af8f49fb 100644 --- a/msmtools/dtraj/tests/test_trajectory.py +++ b/msmtools/dtraj/tests/test_trajectory.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module contains unit tests for the trajectory module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/__init__.py b/msmtools/estimation/__init__.py index d34e0c21..889fbb63 100644 --- a/msmtools/estimation/__init__.py +++ b/msmtools/estimation/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" ==================================================================== diff --git a/msmtools/estimation/dense/__init__.py b/msmtools/estimation/dense/__init__.py index 82620ed4..f1d5cc7c 100644 --- a/msmtools/estimation/dense/__init__.py +++ b/msmtools/estimation/dense/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - from __future__ import absolute_import from . import bootstrapping diff --git a/msmtools/estimation/dense/sampler_nrev.py b/msmtools/estimation/dense/sampler_nrev.py index 206c3f27..b53f12c0 100644 --- a/msmtools/estimation/dense/sampler_nrev.py +++ b/msmtools/estimation/dense/sampler_nrev.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Transition matrix sampling for non-reversible stochastic matrices. .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/dense/tmatrix_sampler.py b/msmtools/estimation/dense/tmatrix_sampler.py index 74e4fbc1..bcc42e38 100644 --- a/msmtools/estimation/dense/tmatrix_sampler.py +++ b/msmtools/estimation/dense/tmatrix_sampler.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Transition matrix sampling module. Provides a common class for sampling of i) non-reversible transition matrices diff --git a/msmtools/flux/dense/__init__.py b/msmtools/flux/dense/__init__.py index e74b65c1..b675fef3 100644 --- a/msmtools/flux/dense/__init__.py +++ b/msmtools/flux/dense/__init__.py @@ -1,27 +1,2 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - from __future__ import absolute_import from . import tpt diff --git a/msmtools/flux/sparse/pathways_test.py b/msmtools/flux/sparse/pathways_test.py index 82808451..d61422fa 100644 --- a/msmtools/flux/sparse/pathways_test.py +++ b/msmtools/flux/sparse/pathways_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the pathways-module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/sparse/tpt_test.py b/msmtools/flux/sparse/tpt_test.py index ef325447..38204ef2 100644 --- a/msmtools/flux/sparse/tpt_test.py +++ b/msmtools/flux/sparse/tpt_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit test for the TPT-module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/generation/api.py b/msmtools/generation/api.py index 08868ca9..60ab743d 100644 --- a/msmtools/generation/api.py +++ b/msmtools/generation/api.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on Jan 8, 2014 diff --git a/msmtools/generation/tests/test_generation.py b/msmtools/generation/tests/test_generation.py index a92c381b..6437a816 100644 --- a/msmtools/generation/tests/test_generation.py +++ b/msmtools/generation/tests/test_generation.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' @author: noe, trendelkampschroer ''' From b1b855397f1bfccfb9bb6ab7b323a9eb69824264 Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 21:31:19 +0200 Subject: [PATCH 05/11] partially added lgpl... --- msmtools/_version.py | 20 ++++++++++++- msmtools/analysis/__init__.py | 20 ++++++++++++- msmtools/analysis/dense/assessment_test.py | 18 +++++++++++ msmtools/analysis/dense/birth_death_chain.py | 18 +++++++++++ msmtools/analysis/dense/committor.py | 20 ++++++++++++- msmtools/analysis/dense/committor_test.py | 18 +++++++++++ msmtools/analysis/dense/correlations.py | 18 +++++++++++ msmtools/analysis/dense/correlations_test.py | 18 +++++++++++ msmtools/analysis/dense/decomposition.py | 21 +++++++++++-- msmtools/analysis/dense/decomposition_test.py | 21 +++++++++++-- msmtools/analysis/dense/expectations.py | 21 +++++++++++-- msmtools/analysis/dense/expectations_test.py | 18 +++++++++++ msmtools/analysis/dense/fingerprints.py | 20 ++++++++++++- msmtools/analysis/dense/fingerprints_test.py | 18 +++++++++++ .../analysis/dense/hitting_probability.py | 18 +++++++++++ .../dense/hitting_probability_test.py | 18 +++++++++++ .../analysis/dense/mean_first_passage_time.py | 23 +++++++++++--- .../dense/mean_first_passage_time_test.py | 18 +++++++++++ msmtools/analysis/dense/pcca.py | 18 +++++++++++ msmtools/analysis/dense/pcca_test.py | 18 +++++++++++ msmtools/analysis/dense/sensitivity.py | 20 ++++++++++++- msmtools/analysis/dense/sensitivity_test.py | 18 +++++++++++ msmtools/analysis/dense/stationary_vector.py | 20 ++++++++++++- .../analysis/dense/stationary_vector_test.py | 20 ++++++++++++- msmtools/analysis/sparse/assessment.py | 18 +++++++++++ msmtools/analysis/sparse/assessment_test.py | 18 +++++++++++ msmtools/analysis/sparse/birth_death_chain.py | 18 +++++++++++ msmtools/analysis/sparse/committor.py | 18 +++++++++++ msmtools/analysis/sparse/committor_test.py | 18 +++++++++++ msmtools/analysis/sparse/decomposition.py | 20 ++++++++++++- .../analysis/sparse/decomposition_test.py | 26 +++++++++++----- msmtools/analysis/sparse/expectations.py | 20 ++++++++++++- msmtools/analysis/sparse/expectations_test.py | 18 +++++++++++ msmtools/analysis/sparse/fingerprints.py | 18 +++++++++++ msmtools/analysis/sparse/fingerprints_test.py | 18 +++++++++++ .../sparse/mean_first_passage_time.py | 18 +++++++++++ .../sparse/mean_first_passage_time_test.py | 18 +++++++++++ msmtools/analysis/sparse/stationary_vector.py | 18 +++++++++++ .../analysis/sparse/stationary_vector_test.py | 20 ++++++++++++- msmtools/analysis/tests/birth_death_chain.py | 18 +++++++++++ msmtools/analysis/tests/test_assessment.py | 18 +++++++++++ msmtools/analysis/tests/test_committor.py | 18 +++++++++++ msmtools/analysis/tests/test_decomposition.py | 20 ++++++++++++- msmtools/analysis/tests/test_expectations.py | 18 +++++++++++ msmtools/analysis/tests/test_fingerprints.py | 18 +++++++++++ msmtools/analysis/tests/test_mfpt.py | 18 +++++++++++ msmtools/analysis/tests/test_sensitivity.py | 18 +++++++++++ msmtools/dtraj/__init__.py | 20 ++++++++++++- msmtools/dtraj/tests/test_trajectory.py | 20 ++++++++++++- msmtools/estimation/__init__.py | 20 ++++++++++++- msmtools/estimation/api.py | 20 ++++++++++++- msmtools/estimation/dense/__init__.py | 20 ++++++++++++- .../estimation/dense/_mle_trev_given_pi.c | 18 +++++++++++ .../estimation/dense/_mle_trev_given_pi.h | 18 +++++++++++ msmtools/estimation/dense/_ranlib.c | 18 +++++++++++ msmtools/estimation/dense/_ranlib.h | 18 +++++++++++ msmtools/estimation/dense/_rnglib.c | 18 +++++++++++ msmtools/estimation/dense/_rnglib.h | 18 +++++++++++ msmtools/estimation/dense/bootstrapping.py | 18 +++++++++++ msmtools/estimation/dense/covariance.py | 18 +++++++++++ msmtools/estimation/dense/covariance_test.py | 18 +++++++++++ msmtools/estimation/dense/sample_rev.c | 18 +++++++++++ msmtools/estimation/dense/sample_rev.h | 18 +++++++++++ msmtools/estimation/dense/sample_revpi.c | 18 +++++++++++ msmtools/estimation/dense/sample_revpi.h | 18 +++++++++++ msmtools/estimation/dense/sampler_nrev.py | 20 ++++++++++++- msmtools/estimation/dense/tmatrix_sampler.py | 20 ++++++++++++- .../estimation/dense/transition_matrix.py | 20 ++++++++++++- msmtools/estimation/dense/util.h | 18 +++++++++++ msmtools/estimation/sparse/_mle_trev.c | 18 +++++++++++ msmtools/estimation/sparse/_mle_trev.h | 18 +++++++++++ .../estimation/sparse/_mle_trev_given_pi.c | 18 +++++++++++ .../estimation/sparse/_mle_trev_given_pi.h | 18 +++++++++++ msmtools/estimation/sparse/connectivity.py | 18 +++++++++++ .../estimation/sparse/connectivity_test.py | 18 +++++++++++ msmtools/estimation/sparse/count_matrix.py | 18 +++++++++++ .../estimation/sparse/count_matrix_test.py | 18 +++++++++++ msmtools/estimation/sparse/likelihood.py | 18 +++++++++++ msmtools/estimation/sparse/likelihood_test.py | 18 +++++++++++ msmtools/estimation/sparse/prior.py | 18 +++++++++++ msmtools/estimation/sparse/prior_test.py | 18 +++++++++++ .../estimation/sparse/transition_matrix.py | 18 +++++++++++ .../sparse/transition_matrix_test.py | 18 +++++++++++ .../estimation/tests/test_bootstrapping.py | 18 +++++++++++ .../estimation/tests/test_connectivity.py | 18 +++++++++++ .../estimation/tests/test_count_matrix.py | 18 +++++++++++ .../tests/test_effective_count_matrix.py | 18 +++++++++++ msmtools/estimation/tests/test_likelihood.py | 18 +++++++++++ msmtools/estimation/tests/test_mle_trev.py | 20 ++++++++++++- .../tests/test_mle_trev_given_pi.py | 20 ++++++++++++- msmtools/estimation/tests/test_prior.py | 18 +++++++++++ .../estimation/tests/test_tmatrix_sampling.py | 20 ++++++++++++- .../tests/test_transition_matrix.py | 18 +++++++++++ msmtools/flux/api.py | 18 +++++++++++ msmtools/flux/dense/__init__.py | 18 +++++++++++ msmtools/flux/dense/tpt.py | 18 +++++++++++ msmtools/flux/dense/tpt_test.py | 18 +++++++++++ msmtools/flux/reactive_flux.py | 18 +++++++++++ msmtools/flux/reactive_flux_test.py | 20 ++++++++++++- msmtools/flux/sparse/pathways.py | 30 ++++++++++++------- msmtools/flux/sparse/pathways_test.py | 21 +++++++++++-- msmtools/flux/sparse/tpt.py | 18 +++++++++++ msmtools/flux/sparse/tpt_test.py | 20 ++++++++++++- msmtools/flux/tests/birth_death_chain.py | 18 +++++++++++ msmtools/flux/tests/test_pathways.py | 18 +++++++++++ msmtools/flux/tests/test_tpt.py | 18 +++++++++++ msmtools/generation/api.py | 20 ++++++++++++- msmtools/generation/tests/test_generation.py | 20 ++++++++++++- msmtools/util/__init__.py | 18 +++++++++++ msmtools/util/matrix/__init__.py | 18 +++++++++++ msmtools/util/matrix/matrix_test.py | 18 +++++++++++ msmtools/util/sigint_handler.h | 18 +++++++++++ msmtools/util/statistics.py | 20 ++++++++++++- msmtools/util/types.py | 18 +++++++++++ 114 files changed, 2086 insertions(+), 57 deletions(-) diff --git a/msmtools/_version.py b/msmtools/_version.py index 3ff764a0..b484d491 100644 --- a/msmtools/_version.py +++ b/msmtools/_version.py @@ -1,4 +1,22 @@ +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + + # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build @@ -457,4 +475,4 @@ def get_versions(): return {"version": "0+unknown", "full-revisionid": None, "dirty": None, - "error": "unable to compute version"} + "error": "unable to compute version"} \ No newline at end of file diff --git a/msmtools/analysis/__init__.py b/msmtools/analysis/__init__.py index 0d03ed33..9867a388 100644 --- a/msmtools/analysis/__init__.py +++ b/msmtools/analysis/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" ============================================================== @@ -92,4 +110,4 @@ """ from __future__ import absolute_import -from .api import * +from .api import * \ No newline at end of file diff --git a/msmtools/analysis/dense/assessment_test.py b/msmtools/analysis/dense/assessment_test.py index 8db00c3b..7cbc363d 100644 --- a/msmtools/analysis/dense/assessment_test.py +++ b/msmtools/analysis/dense/assessment_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on 07.10.2013 diff --git a/msmtools/analysis/dense/birth_death_chain.py b/msmtools/analysis/dense/birth_death_chain.py index 96fcf1db..35053c2d 100644 --- a/msmtools/analysis/dense/birth_death_chain.py +++ b/msmtools/analysis/dense/birth_death_chain.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/committor.py b/msmtools/analysis/dense/committor.py index 361ac9de..dfaa547a 100644 --- a/msmtools/analysis/dense/committor.py +++ b/msmtools/analysis/dense/committor.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides functions for the computation of forward and backward comittors using dense linear algebra. @@ -142,4 +160,4 @@ def backward_committor(T, A, B, mu=None): u = solve(W, r) - return u + return u \ No newline at end of file diff --git a/msmtools/analysis/dense/committor_test.py b/msmtools/analysis/dense/committor_test.py index 694f2252..cc3c86b7 100644 --- a/msmtools/analysis/dense/committor_test.py +++ b/msmtools/analysis/dense/committor_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the committor module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/correlations.py b/msmtools/analysis/dense/correlations.py index 95d17d2f..3ba304a7 100644 --- a/msmtools/analysis/dense/correlations.py +++ b/msmtools/analysis/dense/correlations.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on 29.11.2013 diff --git a/msmtools/analysis/dense/correlations_test.py b/msmtools/analysis/dense/correlations_test.py index bc93650b..db1dd541 100644 --- a/msmtools/analysis/dense/correlations_test.py +++ b/msmtools/analysis/dense/correlations_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on Jun 3, 2014 diff --git a/msmtools/analysis/dense/decomposition.py b/msmtools/analysis/dense/decomposition.py index 332c20e6..117f36b9 100644 --- a/msmtools/analysis/dense/decomposition.py +++ b/msmtools/analysis/dense/decomposition.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides matrix-decomposition based functions for the analysis of stochastic matrices @@ -525,5 +543,4 @@ def timescales_from_eigenvalues(evals, tau=1): """All other eigenvalues give rise to finite timescales""" ts[np.logical_not(ind_abs_one)] = \ -1.0 * tau / np.log(np.abs(evals[np.logical_not(ind_abs_one)])) - return ts - + return ts \ No newline at end of file diff --git a/msmtools/analysis/dense/decomposition_test.py b/msmtools/analysis/dense/decomposition_test.py index 90b9bba8..09bdd2a2 100644 --- a/msmtools/analysis/dense/decomposition_test.py +++ b/msmtools/analysis/dense/decomposition_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides unit tests for the decomposition module .. moduleauthor:: B.Trendelkamp-Schroer @@ -353,5 +371,4 @@ def test_timescales_2(self): assert issubclass(w[-1].category, ImaginaryEigenValueWarning) if __name__ == "__main__": - unittest.main() - + unittest.main() \ No newline at end of file diff --git a/msmtools/analysis/dense/expectations.py b/msmtools/analysis/dense/expectations.py index 01c902af..610b1ef9 100644 --- a/msmtools/analysis/dense/expectations.py +++ b/msmtools/analysis/dense/expectations.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides dense implementations for the computation of expectation values for a given transition matrix. @@ -226,5 +244,4 @@ def ec_geometric_series(p0, T, n): """Truncate imginary part - which is zero, but we want real return values""" EC = EC.real - return EC - + return EC \ No newline at end of file diff --git a/msmtools/analysis/dense/expectations_test.py b/msmtools/analysis/dense/expectations_test.py index 15cdc4e7..8bee6e84 100644 --- a/msmtools/analysis/dense/expectations_test.py +++ b/msmtools/analysis/dense/expectations_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides unit tests for the expectations module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/fingerprints.py b/msmtools/analysis/dense/fingerprints.py index 0820f7c1..3ada55c9 100644 --- a/msmtools/analysis/dense/fingerprints.py +++ b/msmtools/analysis/dense/fingerprints.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides dense implementation for the computation of dynamical fingerprints, expectations and correlations @@ -435,4 +453,4 @@ def propagate(A, x, N): y = 1.0 * x for i in range(N): y = np.dot(A, y) - return y + return y \ No newline at end of file diff --git a/msmtools/analysis/dense/fingerprints_test.py b/msmtools/analysis/dense/fingerprints_test.py index a703c504..4e39af22 100644 --- a/msmtools/analysis/dense/fingerprints_test.py +++ b/msmtools/analysis/dense/fingerprints_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the fingerprint module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/hitting_probability.py b/msmtools/analysis/dense/hitting_probability.py index 95a1101a..3aea154b 100644 --- a/msmtools/analysis/dense/hitting_probability.py +++ b/msmtools/analysis/dense/hitting_probability.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Dense implementation of hitting probabilities .. moduleauthor:: F.Noe diff --git a/msmtools/analysis/dense/hitting_probability_test.py b/msmtools/analysis/dense/hitting_probability_test.py index 06d0b4a8..43d51915 100644 --- a/msmtools/analysis/dense/hitting_probability_test.py +++ b/msmtools/analysis/dense/hitting_probability_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test, dense implementation of hitting probabilities .. moduleauthor:: F.Noe diff --git a/msmtools/analysis/dense/mean_first_passage_time.py b/msmtools/analysis/dense/mean_first_passage_time.py index 179d1ff8..a5ddec9d 100644 --- a/msmtools/analysis/dense/mean_first_passage_time.py +++ b/msmtools/analysis/dense/mean_first_passage_time.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Dense implementation of mean first passage time computation .. moduleauthor:: B.Trendelkamp-Schroer @@ -112,7 +130,4 @@ def mfpt_between_sets(T, target, origin, mu=None): """Mean first-passage time from X to Y""" tXY = np.dot(muX, tY[origin]) - return tXY - - - + return tXY \ No newline at end of file diff --git a/msmtools/analysis/dense/mean_first_passage_time_test.py b/msmtools/analysis/dense/mean_first_passage_time_test.py index 78774338..1503c185 100644 --- a/msmtools/analysis/dense/mean_first_passage_time_test.py +++ b/msmtools/analysis/dense/mean_first_passage_time_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the mean first passage time module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/dense/pcca.py b/msmtools/analysis/dense/pcca.py index 62e4b64e..5c1ee21b 100644 --- a/msmtools/analysis/dense/pcca.py +++ b/msmtools/analysis/dense/pcca.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' @author: Susanna Roeblitz, Marcus Weber, Frank Noe diff --git a/msmtools/analysis/dense/pcca_test.py b/msmtools/analysis/dense/pcca_test.py index b69d8e69..77341dd7 100644 --- a/msmtools/analysis/dense/pcca_test.py +++ b/msmtools/analysis/dense/pcca_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on 06.12.2013 diff --git a/msmtools/analysis/dense/sensitivity.py b/msmtools/analysis/dense/sensitivity.py index 72b9cdd4..8d105519 100644 --- a/msmtools/analysis/dense/sensitivity.py +++ b/msmtools/analysis/dense/sensitivity.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on 22.11.2013 @@ -386,4 +404,4 @@ def expectation_sensitivity(T, a): S = numpy.zeros((M, M)) for i in range(M): S += a[i] * stationary_distribution_sensitivity(T, i) - return S + return S \ No newline at end of file diff --git a/msmtools/analysis/dense/sensitivity_test.py b/msmtools/analysis/dense/sensitivity_test.py index 7d6c2819..3db6b3ff 100644 --- a/msmtools/analysis/dense/sensitivity_test.py +++ b/msmtools/analysis/dense/sensitivity_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on 06.12.2013 diff --git a/msmtools/analysis/dense/stationary_vector.py b/msmtools/analysis/dense/stationary_vector.py index 71590030..3d8b5176 100644 --- a/msmtools/analysis/dense/stationary_vector.py +++ b/msmtools/analysis/dense/stationary_vector.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides functions for the coputation of stationary vectors of stochastic matrices @@ -130,4 +148,4 @@ def stationary_distribution(T): if fallback: mu = stationary_distribution_from_eigenvector(T) - return mu + return mu \ No newline at end of file diff --git a/msmtools/analysis/dense/stationary_vector_test.py b/msmtools/analysis/dense/stationary_vector_test.py index a4da9631..0765170f 100644 --- a/msmtools/analysis/dense/stationary_vector_test.py +++ b/msmtools/analysis/dense/stationary_vector_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import, division import unittest @@ -40,4 +58,4 @@ def test_statdist_iteration(self): assert_allclose(mu, mun) if __name__ == "__main__": - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/analysis/sparse/assessment.py b/msmtools/analysis/sparse/assessment.py index b2adf879..e26e990d 100644 --- a/msmtools/analysis/sparse/assessment.py +++ b/msmtools/analysis/sparse/assessment.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """ Sparse assessment module of msm analysis package """ diff --git a/msmtools/analysis/sparse/assessment_test.py b/msmtools/analysis/sparse/assessment_test.py index 658ca1c3..58a938dd 100644 --- a/msmtools/analysis/sparse/assessment_test.py +++ b/msmtools/analysis/sparse/assessment_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """This module provides unit tests for the assessment module""" from __future__ import absolute_import from __future__ import division diff --git a/msmtools/analysis/sparse/birth_death_chain.py b/msmtools/analysis/sparse/birth_death_chain.py index 96fcf1db..35053c2d 100644 --- a/msmtools/analysis/sparse/birth_death_chain.py +++ b/msmtools/analysis/sparse/birth_death_chain.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/committor.py b/msmtools/analysis/sparse/committor.py index c45ddfde..43daacc6 100644 --- a/msmtools/analysis/sparse/committor.py +++ b/msmtools/analysis/sparse/committor.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides functions for the computation of forward and backward comittors using sparse linear algebra. diff --git a/msmtools/analysis/sparse/committor_test.py b/msmtools/analysis/sparse/committor_test.py index 075f2a1c..490d4c30 100644 --- a/msmtools/analysis/sparse/committor_test.py +++ b/msmtools/analysis/sparse/committor_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the committor module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/decomposition.py b/msmtools/analysis/sparse/decomposition.py index 73bc5f3c..da425a63 100644 --- a/msmtools/analysis/sparse/decomposition.py +++ b/msmtools/analysis/sparse/decomposition.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides matrix-decomposition based functions for the analysis of stochastic matrices @@ -522,4 +540,4 @@ def timescales_from_eigenvalues(ev, tau=1): """All other eigenvalues give rise to finite timescales""" ts[np.logical_not(ind_abs_one)] = \ -1.0 * tau / np.log(np.abs(ev[np.logical_not(ind_abs_one)])) - return ts + return ts \ No newline at end of file diff --git a/msmtools/analysis/sparse/decomposition_test.py b/msmtools/analysis/sparse/decomposition_test.py index c341dff1..ce917a73 100644 --- a/msmtools/analysis/sparse/decomposition_test.py +++ b/msmtools/analysis/sparse/decomposition_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Test package for the decomposition module .. moduleauthor:: B.Trendelkamp-Schroer @@ -436,10 +454,4 @@ def test_timescales_rev(self): if __name__ == "__main__": - unittest.main() - - - - - - + unittest.main() \ No newline at end of file diff --git a/msmtools/analysis/sparse/expectations.py b/msmtools/analysis/sparse/expectations.py index 3af14871..51340fd1 100644 --- a/msmtools/analysis/sparse/expectations.py +++ b/msmtools/analysis/sparse/expectations.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides sparse implementations for the computation of expectation values for a given transition matrix. @@ -89,4 +107,4 @@ def expected_counts_stationary(T, n, mu=None): mu = stationary_distribution(T) D_mu = diags(mu, 0) EC = n * D_mu.dot(T) - return EC + return EC \ No newline at end of file diff --git a/msmtools/analysis/sparse/expectations_test.py b/msmtools/analysis/sparse/expectations_test.py index 297698cc..f6bcd14e 100644 --- a/msmtools/analysis/sparse/expectations_test.py +++ b/msmtools/analysis/sparse/expectations_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Test package for the expectations module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/fingerprints.py b/msmtools/analysis/sparse/fingerprints.py index 95e90ceb..63423442 100644 --- a/msmtools/analysis/sparse/fingerprints.py +++ b/msmtools/analysis/sparse/fingerprints.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module contains sparse implementation of the fingerprint module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/fingerprints_test.py b/msmtools/analysis/sparse/fingerprints_test.py index 98455227..f1bef0ab 100644 --- a/msmtools/analysis/sparse/fingerprints_test.py +++ b/msmtools/analysis/sparse/fingerprints_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the fingerprint module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/mean_first_passage_time.py b/msmtools/analysis/sparse/mean_first_passage_time.py index c3ae159e..be27daf1 100644 --- a/msmtools/analysis/sparse/mean_first_passage_time.py +++ b/msmtools/analysis/sparse/mean_first_passage_time.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Sparse implementation of mean first passage time computation .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/mean_first_passage_time_test.py b/msmtools/analysis/sparse/mean_first_passage_time_test.py index 85786d7c..bb28635d 100644 --- a/msmtools/analysis/sparse/mean_first_passage_time_test.py +++ b/msmtools/analysis/sparse/mean_first_passage_time_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the mean first passage time module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/sparse/stationary_vector.py b/msmtools/analysis/sparse/stationary_vector.py index 12c3a57b..ab244e17 100644 --- a/msmtools/analysis/sparse/stationary_vector.py +++ b/msmtools/analysis/sparse/stationary_vector.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides functions for the computation of stationary vectors of stochastic matrices. diff --git a/msmtools/analysis/sparse/stationary_vector_test.py b/msmtools/analysis/sparse/stationary_vector_test.py index bf7104be..ee163041 100644 --- a/msmtools/analysis/sparse/stationary_vector_test.py +++ b/msmtools/analysis/sparse/stationary_vector_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Test package for the decomposition module .. moduleauthor:: B.Trendelkamp-Schroer @@ -48,4 +66,4 @@ def test_statdist_iteration(self): assert_allclose(mu, mun) if __name__ == "__main__": - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/analysis/tests/birth_death_chain.py b/msmtools/analysis/tests/birth_death_chain.py index 96fcf1db..35053c2d 100644 --- a/msmtools/analysis/tests/birth_death_chain.py +++ b/msmtools/analysis/tests/birth_death_chain.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_assessment.py b/msmtools/analysis/tests/test_assessment.py index 90003a8c..170085f4 100644 --- a/msmtools/analysis/tests/test_assessment.py +++ b/msmtools/analysis/tests/test_assessment.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """This module provides unit tests for the assessment functions of the analysis API .. moduleauthor:: Martin Scherer diff --git a/msmtools/analysis/tests/test_committor.py b/msmtools/analysis/tests/test_committor.py index d54b6f1a..7a7d6645 100644 --- a/msmtools/analysis/tests/test_committor.py +++ b/msmtools/analysis/tests/test_committor.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the committor API-function .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_decomposition.py b/msmtools/analysis/tests/test_decomposition.py index 2cb5c784..ab7645fe 100644 --- a/msmtools/analysis/tests/test_decomposition.py +++ b/msmtools/analysis/tests/test_decomposition.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for decomposition functions in api.py .. moduleauthor:: Benjamin Trendelkamp-Schroer @@ -783,4 +801,4 @@ def test_timescales_rev(self): if __name__ == "__main__": - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/analysis/tests/test_expectations.py b/msmtools/analysis/tests/test_expectations.py index 8a579972..97f31ef7 100644 --- a/msmtools/analysis/tests/test_expectations.py +++ b/msmtools/analysis/tests/test_expectations.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides unit tests for the expectations function in API .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_fingerprints.py b/msmtools/analysis/tests/test_fingerprints.py index 105868a9..09eb4cde 100644 --- a/msmtools/analysis/tests/test_fingerprints.py +++ b/msmtools/analysis/tests/test_fingerprints.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the fingerprint API-functions .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_mfpt.py b/msmtools/analysis/tests/test_mfpt.py index f8258dbb..1c57c8f6 100644 --- a/msmtools/analysis/tests/test_mfpt.py +++ b/msmtools/analysis/tests/test_mfpt.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the mean first passage time API-functions .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/analysis/tests/test_sensitivity.py b/msmtools/analysis/tests/test_sensitivity.py index 7e7eb77e..f934e37c 100644 --- a/msmtools/analysis/tests/test_sensitivity.py +++ b/msmtools/analysis/tests/test_sensitivity.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on 06.12.2013 diff --git a/msmtools/dtraj/__init__.py b/msmtools/dtraj/__init__.py index 01e2b4dc..0dd11503 100644 --- a/msmtools/dtraj/__init__.py +++ b/msmtools/dtraj/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" =============================================================== @@ -44,4 +62,4 @@ """ from __future__ import absolute_import -from .api import * +from .api import * \ No newline at end of file diff --git a/msmtools/dtraj/tests/test_trajectory.py b/msmtools/dtraj/tests/test_trajectory.py index af8f49fb..4bfaeb3a 100644 --- a/msmtools/dtraj/tests/test_trajectory.py +++ b/msmtools/dtraj/tests/test_trajectory.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module contains unit tests for the trajectory module .. moduleauthor:: B.Trendelkamp-Schroer @@ -73,4 +91,4 @@ def test_save_discrete_trajectory(self): if __name__ == "__main__": - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/estimation/__init__.py b/msmtools/estimation/__init__.py index 889fbb63..3bc678dd 100644 --- a/msmtools/estimation/__init__.py +++ b/msmtools/estimation/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" ==================================================================== @@ -70,4 +88,4 @@ """ from __future__ import absolute_import -from .api import * +from .api import * \ No newline at end of file diff --git a/msmtools/estimation/api.py b/msmtools/estimation/api.py index f66d04c9..b658282c 100644 --- a/msmtools/estimation/api.py +++ b/msmtools/estimation/api.py @@ -1,5 +1,23 @@ # -*- coding: utf-8 -*- + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" ========================= Estimation API @@ -1242,4 +1260,4 @@ def tmatrix_sampler(C, reversible=False, mu=None, T0=None, nsteps=None, prior='s from .dense.tmatrix_sampler import TransitionMatrixSampler sampler = TransitionMatrixSampler(C, reversible=reversible, mu=mu, P0=T0, nsteps=nsteps, prior=prior) - return sampler + return sampler \ No newline at end of file diff --git a/msmtools/estimation/dense/__init__.py b/msmtools/estimation/dense/__init__.py index f1d5cc7c..922a4841 100644 --- a/msmtools/estimation/dense/__init__.py +++ b/msmtools/estimation/dense/__init__.py @@ -1,7 +1,25 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from . import bootstrapping from . import transition_matrix from . import covariance from . import mle_trev_given_pi -from . import tmatrix_sampler \ No newline at end of file +from . import tmatrix_sampler diff --git a/msmtools/estimation/dense/_mle_trev_given_pi.c b/msmtools/estimation/dense/_mle_trev_given_pi.c index 82c40e27..0b09f4fe 100644 --- a/msmtools/estimation/dense/_mle_trev_given_pi.c +++ b/msmtools/estimation/dense/_mle_trev_given_pi.c @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + /* moduleauthor:: F. Paul */ #include #include diff --git a/msmtools/estimation/dense/_mle_trev_given_pi.h b/msmtools/estimation/dense/_mle_trev_given_pi.h index 874c9106..4014a03e 100644 --- a/msmtools/estimation/dense/_mle_trev_given_pi.h +++ b/msmtools/estimation/dense/_mle_trev_given_pi.h @@ -1,2 +1,20 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + int _mle_trev_given_pi_dense(double * const T, const double * const C, const double * const mu, const int n, const double maxerr, const int maxiter); diff --git a/msmtools/estimation/dense/_ranlib.c b/msmtools/estimation/dense/_ranlib.c index abe8010e..62367c38 100644 --- a/msmtools/estimation/dense/_ranlib.c +++ b/msmtools/estimation/dense/_ranlib.c @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + # include # include # include diff --git a/msmtools/estimation/dense/_ranlib.h b/msmtools/estimation/dense/_ranlib.h index 711a1ff3..589a4125 100644 --- a/msmtools/estimation/dense/_ranlib.h +++ b/msmtools/estimation/dense/_ranlib.h @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + #ifndef _RANLIB_ #define _RANLIB_ diff --git a/msmtools/estimation/dense/_rnglib.c b/msmtools/estimation/dense/_rnglib.c index ebc28622..55e1ce17 100644 --- a/msmtools/estimation/dense/_rnglib.c +++ b/msmtools/estimation/dense/_rnglib.c @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + # include # include # include diff --git a/msmtools/estimation/dense/_rnglib.h b/msmtools/estimation/dense/_rnglib.h index 9278bcc7..22a91969 100644 --- a/msmtools/estimation/dense/_rnglib.h +++ b/msmtools/estimation/dense/_rnglib.h @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + #ifndef _RNGLIB_ #define _RNGLIB_ diff --git a/msmtools/estimation/dense/bootstrapping.py b/msmtools/estimation/dense/bootstrapping.py index 3e35eb18..88d948ef 100644 --- a/msmtools/estimation/dense/bootstrapping.py +++ b/msmtools/estimation/dense/bootstrapping.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on Jul 23, 2014 diff --git a/msmtools/estimation/dense/covariance.py b/msmtools/estimation/dense/covariance.py index 479b483a..ddbb4767 100644 --- a/msmtools/estimation/dense/covariance.py +++ b/msmtools/estimation/dense/covariance.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module implements the transition matrix covariance function .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/dense/covariance_test.py b/msmtools/estimation/dense/covariance_test.py index c1ee7535..f11c7cfb 100644 --- a/msmtools/estimation/dense/covariance_test.py +++ b/msmtools/estimation/dense/covariance_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the covariance module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/dense/sample_rev.c b/msmtools/estimation/dense/sample_rev.c index c1ddc308..852a65ab 100644 --- a/msmtools/estimation/dense/sample_rev.c +++ b/msmtools/estimation/dense/sample_rev.c @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + /* * moduleauthor:: F. Noe */ #include diff --git a/msmtools/estimation/dense/sample_rev.h b/msmtools/estimation/dense/sample_rev.h index 85394352..aa098e97 100644 --- a/msmtools/estimation/dense/sample_rev.h +++ b/msmtools/estimation/dense/sample_rev.h @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + /* * moduleauthor:: F. Noe */ diff --git a/msmtools/estimation/dense/sample_revpi.c b/msmtools/estimation/dense/sample_revpi.c index d58fa278..6539f07d 100644 --- a/msmtools/estimation/dense/sample_revpi.c +++ b/msmtools/estimation/dense/sample_revpi.c @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + /* * moduleauthor:: B. Trendelkamp-Schroer * */ diff --git a/msmtools/estimation/dense/sample_revpi.h b/msmtools/estimation/dense/sample_revpi.h index 5a0a90a2..19069d76 100644 --- a/msmtools/estimation/dense/sample_revpi.h +++ b/msmtools/estimation/dense/sample_revpi.h @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + /* * moduleauthor:: B. Trendelkamp-Schroer * */ diff --git a/msmtools/estimation/dense/sampler_nrev.py b/msmtools/estimation/dense/sampler_nrev.py index b53f12c0..94a7ecee 100644 --- a/msmtools/estimation/dense/sampler_nrev.py +++ b/msmtools/estimation/dense/sampler_nrev.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Transition matrix sampling for non-reversible stochastic matrices. .. moduleauthor:: B.Trendelkamp-Schroer @@ -35,4 +53,4 @@ def sample(self, N=1, return_statdist=False): else: return self.P - + \ No newline at end of file diff --git a/msmtools/estimation/dense/tmatrix_sampler.py b/msmtools/estimation/dense/tmatrix_sampler.py index bcc42e38..f1e955a9 100644 --- a/msmtools/estimation/dense/tmatrix_sampler.py +++ b/msmtools/estimation/dense/tmatrix_sampler.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Transition matrix sampling module. Provides a common class for sampling of i) non-reversible transition matrices @@ -69,4 +87,4 @@ def sample(self, nsamples=1, return_statdist=False, call_back=None): P_samples[i, :, :] = self.sampler.sample(N=self.nsteps, return_statdist=False) if call_back is not None: call_back() - return P_samples + return P_samples \ No newline at end of file diff --git a/msmtools/estimation/dense/transition_matrix.py b/msmtools/estimation/dense/transition_matrix.py index eec4e3c1..1148b2c2 100644 --- a/msmtools/estimation/dense/transition_matrix.py +++ b/msmtools/estimation/dense/transition_matrix.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on Jan 13, 2014 @@ -258,4 +276,4 @@ def transition_matrix_reversible_fixpi(Z, mu, maxerr=1e-10, maxiter=10000, retur if return_iterations: return T, it else: - return T + return T \ No newline at end of file diff --git a/msmtools/estimation/dense/util.h b/msmtools/estimation/dense/util.h index 9b0baf7f..46e82992 100644 --- a/msmtools/estimation/dense/util.h +++ b/msmtools/estimation/dense/util.h @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + #ifndef __util_h_ #define __util_h_ diff --git a/msmtools/estimation/sparse/_mle_trev.c b/msmtools/estimation/sparse/_mle_trev.c index 86f15864..140a2c94 100644 --- a/msmtools/estimation/sparse/_mle_trev.c +++ b/msmtools/estimation/sparse/_mle_trev.c @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + /* moduleauthor:: F. Paul */ #include #include diff --git a/msmtools/estimation/sparse/_mle_trev.h b/msmtools/estimation/sparse/_mle_trev.h index 56f0eedc..43247de6 100644 --- a/msmtools/estimation/sparse/_mle_trev.h +++ b/msmtools/estimation/sparse/_mle_trev.h @@ -1 +1,19 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + int _mle_trev_sparse(double * const T_data, const double * const CCt_data, const int * const i_indices, const int * const j_indices, const int len_CCt, const double * const sum_C, const int dim, const double maxerr, const int maxiter); diff --git a/msmtools/estimation/sparse/_mle_trev_given_pi.c b/msmtools/estimation/sparse/_mle_trev_given_pi.c index 3f7fd5bd..c66781f0 100644 --- a/msmtools/estimation/sparse/_mle_trev_given_pi.c +++ b/msmtools/estimation/sparse/_mle_trev_given_pi.c @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + /* moduleauthor:: F. Paul */ #include #include diff --git a/msmtools/estimation/sparse/_mle_trev_given_pi.h b/msmtools/estimation/sparse/_mle_trev_given_pi.h index 0d34206a..fe5fa7a0 100644 --- a/msmtools/estimation/sparse/_mle_trev_given_pi.h +++ b/msmtools/estimation/sparse/_mle_trev_given_pi.h @@ -1 +1,19 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + int _mle_trev_given_pi_sparse(double * const T_unnormalized_data, const double * const CCt_data, const int * const i_indices, const int * const j_indices, const int len_CCt, const double * const mu, const int len_mu, const double maxerr, const int maxiter); diff --git a/msmtools/estimation/sparse/connectivity.py b/msmtools/estimation/sparse/connectivity.py index f4c681ce..54aad0e2 100644 --- a/msmtools/estimation/sparse/connectivity.py +++ b/msmtools/estimation/sparse/connectivity.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module implements the connectivity functionality .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/connectivity_test.py b/msmtools/estimation/sparse/connectivity_test.py index 8c017f6b..73fcd3c1 100644 --- a/msmtools/estimation/sparse/connectivity_test.py +++ b/msmtools/estimation/sparse/connectivity_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the connectivity module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/count_matrix.py b/msmtools/estimation/sparse/count_matrix.py index a10ee6ea..a4c404d3 100644 --- a/msmtools/estimation/sparse/count_matrix.py +++ b/msmtools/estimation/sparse/count_matrix.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module implements the countmatrix estimation functionality .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/count_matrix_test.py b/msmtools/estimation/sparse/count_matrix_test.py index 2b178027..f670c0e7 100644 --- a/msmtools/estimation/sparse/count_matrix_test.py +++ b/msmtools/estimation/sparse/count_matrix_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """Unit tests for the count_matrix module""" from __future__ import absolute_import diff --git a/msmtools/estimation/sparse/likelihood.py b/msmtools/estimation/sparse/likelihood.py index b0351daf..aecd3e7e 100644 --- a/msmtools/estimation/sparse/likelihood.py +++ b/msmtools/estimation/sparse/likelihood.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """This module implements the transition matrix functionality""" from __future__ import absolute_import diff --git a/msmtools/estimation/sparse/likelihood_test.py b/msmtools/estimation/sparse/likelihood_test.py index 29ca32e6..d921c6aa 100644 --- a/msmtools/estimation/sparse/likelihood_test.py +++ b/msmtools/estimation/sparse/likelihood_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import import unittest diff --git a/msmtools/estimation/sparse/prior.py b/msmtools/estimation/sparse/prior.py index bc849a02..2990c3aa 100644 --- a/msmtools/estimation/sparse/prior.py +++ b/msmtools/estimation/sparse/prior.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides functions for computation of prior count matrices .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/prior_test.py b/msmtools/estimation/sparse/prior_test.py index f379e281..359358a7 100644 --- a/msmtools/estimation/sparse/prior_test.py +++ b/msmtools/estimation/sparse/prior_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the prior module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/transition_matrix.py b/msmtools/estimation/sparse/transition_matrix.py index 9b5761a2..b230ab40 100644 --- a/msmtools/estimation/sparse/transition_matrix.py +++ b/msmtools/estimation/sparse/transition_matrix.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """This module implements the transition matrix functionality""" from __future__ import absolute_import from __future__ import division diff --git a/msmtools/estimation/sparse/transition_matrix_test.py b/msmtools/estimation/sparse/transition_matrix_test.py index ac86cef5..1e251720 100644 --- a/msmtools/estimation/sparse/transition_matrix_test.py +++ b/msmtools/estimation/sparse/transition_matrix_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import import unittest diff --git a/msmtools/estimation/tests/test_bootstrapping.py b/msmtools/estimation/tests/test_bootstrapping.py index 22361ff1..400852fe 100644 --- a/msmtools/estimation/tests/test_bootstrapping.py +++ b/msmtools/estimation/tests/test_bootstrapping.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on Jul 25, 2014 diff --git a/msmtools/estimation/tests/test_connectivity.py b/msmtools/estimation/tests/test_connectivity.py index 1aec8dd2..fa6ef5c1 100644 --- a/msmtools/estimation/tests/test_connectivity.py +++ b/msmtools/estimation/tests/test_connectivity.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the connectivity API functions .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/tests/test_count_matrix.py b/msmtools/estimation/tests/test_count_matrix.py index 0719d736..b8cf2fe7 100644 --- a/msmtools/estimation/tests/test_count_matrix.py +++ b/msmtools/estimation/tests/test_count_matrix.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """Unit tests for the count_matrix module""" from __future__ import absolute_import diff --git a/msmtools/estimation/tests/test_effective_count_matrix.py b/msmtools/estimation/tests/test_effective_count_matrix.py index 31ed8a21..cf620c8b 100644 --- a/msmtools/estimation/tests/test_effective_count_matrix.py +++ b/msmtools/estimation/tests/test_effective_count_matrix.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + import unittest import numpy as np diff --git a/msmtools/estimation/tests/test_likelihood.py b/msmtools/estimation/tests/test_likelihood.py index 7dc04634..e37f04a6 100644 --- a/msmtools/estimation/tests/test_likelihood.py +++ b/msmtools/estimation/tests/test_likelihood.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import import unittest diff --git a/msmtools/estimation/tests/test_mle_trev.py b/msmtools/estimation/tests/test_mle_trev.py index bd00a9e4..eede6085 100644 --- a/msmtools/estimation/tests/test_mle_trev.py +++ b/msmtools/estimation/tests/test_mle_trev.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import import unittest import numpy as np @@ -71,4 +89,4 @@ def test_noninteger_counts_dense(self): if __name__ == '__main__': - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/estimation/tests/test_mle_trev_given_pi.py b/msmtools/estimation/tests/test_mle_trev_given_pi.py index 77172cb5..e87642f7 100644 --- a/msmtools/estimation/tests/test_mle_trev_given_pi.py +++ b/msmtools/estimation/tests/test_mle_trev_given_pi.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import import unittest import numpy as np @@ -84,4 +102,4 @@ def test_warnings(self): if __name__ == '__main__': - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/estimation/tests/test_prior.py b/msmtools/estimation/tests/test_prior.py index 4db0976b..8c8653b7 100644 --- a/msmtools/estimation/tests/test_prior.py +++ b/msmtools/estimation/tests/test_prior.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the prior module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/tests/test_tmatrix_sampling.py b/msmtools/estimation/tests/test_tmatrix_sampling.py index d83d1045..d59094c6 100644 --- a/msmtools/estimation/tests/test_tmatrix_sampling.py +++ b/msmtools/estimation/tests/test_tmatrix_sampling.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from six.moves import ranger"""Unit tests for the transition_matrix module @@ -119,4 +137,4 @@ def test_revpi(self): if __name__ == "__main__": - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/estimation/tests/test_transition_matrix.py b/msmtools/estimation/tests/test_transition_matrix.py index 3e22e683..508d4c39 100644 --- a/msmtools/estimation/tests/test_transition_matrix.py +++ b/msmtools/estimation/tests/test_transition_matrix.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from __future__ import division import unittest diff --git a/msmtools/flux/api.py b/msmtools/flux/api.py index af52d8f8..ad25dafb 100644 --- a/msmtools/flux/api.py +++ b/msmtools/flux/api.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" =================== Flux API diff --git a/msmtools/flux/dense/__init__.py b/msmtools/flux/dense/__init__.py index b675fef3..67e44cfe 100644 --- a/msmtools/flux/dense/__init__.py +++ b/msmtools/flux/dense/__init__.py @@ -1,2 +1,20 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from . import tpt diff --git a/msmtools/flux/dense/tpt.py b/msmtools/flux/dense/tpt.py index 45b92342..f1ede3fc 100644 --- a/msmtools/flux/dense/tpt.py +++ b/msmtools/flux/dense/tpt.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module contains function for the Transition Path Theory (TPT) analysis of Markov models. diff --git a/msmtools/flux/dense/tpt_test.py b/msmtools/flux/dense/tpt_test.py index 0affc733..e3fec6c4 100644 --- a/msmtools/flux/dense/tpt_test.py +++ b/msmtools/flux/dense/tpt_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the TPT-module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/reactive_flux.py b/msmtools/flux/reactive_flux.py index f1e4df39..1bf67edd 100644 --- a/msmtools/flux/reactive_flux.py +++ b/msmtools/flux/reactive_flux.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module contains function for the Transition Path Theory (TPT) analysis of Markov models. diff --git a/msmtools/flux/reactive_flux_test.py b/msmtools/flux/reactive_flux_test.py index 131a1179..879151df 100644 --- a/msmtools/flux/reactive_flux_test.py +++ b/msmtools/flux/reactive_flux_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the ReactiveFlux object .. moduleauthor:: F.Noe @@ -184,4 +202,4 @@ def test_coarse_grain(self): if __name__ == "__main__": - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/flux/sparse/pathways.py b/msmtools/flux/sparse/pathways.py index 48372bc7..ddfbe531 100644 --- a/msmtools/flux/sparse/pathways.py +++ b/msmtools/flux/sparse/pathways.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Decomposition of a netflux network into its dominant reaction pathways .. moduleauthor:: B.Trendelkamp-Schroer @@ -351,14 +369,4 @@ def add_endstates(F, A, B): """New netflux matrix""" F_new = coo_matrix((data, (row, col)), shape=(M + 2, M + 2)) - return F_new, M, M + 1 - - - - - - - - - - + return F_new, M, M + 1 \ No newline at end of file diff --git a/msmtools/flux/sparse/pathways_test.py b/msmtools/flux/sparse/pathways_test.py index d61422fa..6ac6a54e 100644 --- a/msmtools/flux/sparse/pathways_test.py +++ b/msmtools/flux/sparse/pathways_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the pathways-module .. moduleauthor:: B.Trendelkamp-Schroer @@ -45,5 +63,4 @@ def test_pathways(self): if __name__=="__main__": unittest.main() - - + \ No newline at end of file diff --git a/msmtools/flux/sparse/tpt.py b/msmtools/flux/sparse/tpt.py index bc9130f9..ba71793b 100644 --- a/msmtools/flux/sparse/tpt.py +++ b/msmtools/flux/sparse/tpt.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module contains function for the Transition Path Theory (TPT) analysis of Markov models. diff --git a/msmtools/flux/sparse/tpt_test.py b/msmtools/flux/sparse/tpt_test.py index 38204ef2..1194dfb7 100644 --- a/msmtools/flux/sparse/tpt_test.py +++ b/msmtools/flux/sparse/tpt_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the TPT-module .. moduleauthor:: B.Trendelkamp-Schroer @@ -308,4 +326,4 @@ def test_netflux(self): if __name__ == "__main__": - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/flux/tests/birth_death_chain.py b/msmtools/flux/tests/birth_death_chain.py index 96fcf1db..35053c2d 100644 --- a/msmtools/flux/tests/birth_death_chain.py +++ b/msmtools/flux/tests/birth_death_chain.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Birth death chain for testing .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/tests/test_pathways.py b/msmtools/flux/tests/test_pathways.py index 7f36c5e3..880fa223 100644 --- a/msmtools/flux/tests/test_pathways.py +++ b/msmtools/flux/tests/test_pathways.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """Unit test for the reaction pathway decomposition .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/flux/tests/test_tpt.py b/msmtools/flux/tests/test_tpt.py index 2b4302bf..743fc825 100644 --- a/msmtools/flux/tests/test_tpt.py +++ b/msmtools/flux/tests/test_tpt.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit test for the TPT-functions of the analysis API .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/generation/api.py b/msmtools/generation/api.py index 60ab743d..bfa3bcab 100644 --- a/msmtools/generation/api.py +++ b/msmtools/generation/api.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on Jan 8, 2014 @@ -232,4 +250,4 @@ def transition_matrix_metropolis_1d(E, d=1.0): # normalize P += np.diag(1.0 - np.sum(P, axis=1)) # done - return P + return P \ No newline at end of file diff --git a/msmtools/generation/tests/test_generation.py b/msmtools/generation/tests/test_generation.py index 6437a816..5655e7b3 100644 --- a/msmtools/generation/tests/test_generation.py +++ b/msmtools/generation/tests/test_generation.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' @author: noe, trendelkampschroer ''' @@ -71,4 +89,4 @@ def test_trajectories(self): if __name__ == "__main__": # import sys;sys.argv = ['', 'Test.testName'] - unittest.main() + unittest.main() \ No newline at end of file diff --git a/msmtools/util/__init__.py b/msmtools/util/__init__.py index e69de29b..b91292c5 100644 --- a/msmtools/util/__init__.py +++ b/msmtools/util/__init__.py @@ -0,0 +1,18 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + diff --git a/msmtools/util/matrix/__init__.py b/msmtools/util/matrix/__init__.py index e69de29b..b91292c5 100644 --- a/msmtools/util/matrix/__init__.py +++ b/msmtools/util/matrix/__init__.py @@ -0,0 +1,18 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + diff --git a/msmtools/util/matrix/matrix_test.py b/msmtools/util/matrix/matrix_test.py index 17e64b3e..53263c75 100644 --- a/msmtools/util/matrix/matrix_test.py +++ b/msmtools/util/matrix/matrix_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for matrix io implementations .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/util/sigint_handler.h b/msmtools/util/sigint_handler.h index 58e215d0..da7dc84d 100644 --- a/msmtools/util/sigint_handler.h +++ b/msmtools/util/sigint_handler.h @@ -1,3 +1,21 @@ +/* * This file is part of MSMTools. + * + * Copyright (c) 2015, 2014 Computational Molecular Biology Group + * + * MSMTools is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program. If not, see . + */ + #ifndef SIGINT_HANDLER_H #define SIGINT_HANDLER_H diff --git a/msmtools/util/statistics.py b/msmtools/util/statistics.py index 5acaaad9..868b554d 100644 --- a/msmtools/util/statistics.py +++ b/msmtools/util/statistics.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on Jul 25, 2014 @@ -214,4 +232,4 @@ def statistical_inefficiency(X, truncate_acf=True, mact=1.0): # compute damped correlation time corrtime = 0.5 + mact * corrsum / x2m # return statistical inefficiency - return 1.0 / (2 * corrtime) + return 1.0 / (2 * corrtime) \ No newline at end of file diff --git a/msmtools/util/types.py b/msmtools/util/types.py index d196a77b..5bd263fc 100644 --- a/msmtools/util/types.py +++ b/msmtools/util/types.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from __future__ import print_function import six From 5516527a6c64b5c9ad62c86f564d2b0317410cbb Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 21:37:22 +0200 Subject: [PATCH 06/11] added newline after bsd lic --- msmtools/__init__.py | 1 + msmtools/analysis/api.py | 1 + msmtools/analysis/dense/__init__.py | 1 + msmtools/analysis/dense/assessment.py | 1 + msmtools/analysis/sparse/__init__.py | 1 + msmtools/dtraj/api.py | 1 + msmtools/estimation/dense/tmatrix_sampler_test.py | 1 + msmtools/estimation/sparse/__init__.py | 1 + msmtools/estimation/sparse/effective_counts.py | 1 + msmtools/flux/__init__.py | 1 + msmtools/flux/sparse/__init__.py | 1 + msmtools/generation/__init__.py | 1 + msmtools/util/annotators.py | 1 + msmtools/util/exceptions.py | 1 + msmtools/util/matrix/matrix.py | 1 + msmtools/util/numeric.py | 1 + 16 files changed, 16 insertions(+) diff --git a/msmtools/__init__.py b/msmtools/__init__.py index 85611ad4..9d854ebe 100644 --- a/msmtools/__init__.py +++ b/msmtools/__init__.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r""" .. currentmodule:: msmtools diff --git a/msmtools/analysis/api.py b/msmtools/analysis/api.py index 56dcfdf4..228f24cc 100644 --- a/msmtools/analysis/api.py +++ b/msmtools/analysis/api.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r""" ======================= diff --git a/msmtools/analysis/dense/__init__.py b/msmtools/analysis/dense/__init__.py index 3f1c02f4..a084d267 100644 --- a/msmtools/analysis/dense/__init__.py +++ b/msmtools/analysis/dense/__init__.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + from __future__ import absolute_import from . import assessment diff --git a/msmtools/analysis/dense/assessment.py b/msmtools/analysis/dense/assessment.py index ff36517b..597d18e6 100644 --- a/msmtools/analysis/dense/assessment.py +++ b/msmtools/analysis/dense/assessment.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + from __future__ import absolute_import import numpy as np diff --git a/msmtools/analysis/sparse/__init__.py b/msmtools/analysis/sparse/__init__.py index fdf3e972..89045f92 100644 --- a/msmtools/analysis/sparse/__init__.py +++ b/msmtools/analysis/sparse/__init__.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + from __future__ import absolute_import from . import assessment diff --git a/msmtools/dtraj/api.py b/msmtools/dtraj/api.py index e54dbe5c..6e9156ea 100644 --- a/msmtools/dtraj/api.py +++ b/msmtools/dtraj/api.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r"""This module implements IO and manipulation function for discrete trajectories ================= diff --git a/msmtools/estimation/dense/tmatrix_sampler_test.py b/msmtools/estimation/dense/tmatrix_sampler_test.py index ceb9bce0..f670af50 100644 --- a/msmtools/estimation/dense/tmatrix_sampler_test.py +++ b/msmtools/estimation/dense/tmatrix_sampler_test.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r"""Unit tests for the covariance module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/__init__.py b/msmtools/estimation/sparse/__init__.py index c357f1e4..600d0ce8 100644 --- a/msmtools/estimation/sparse/__init__.py +++ b/msmtools/estimation/sparse/__init__.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r"""This module provides implementations for the estimation package .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/effective_counts.py b/msmtools/estimation/sparse/effective_counts.py index 7ff76ae8..ae27a4b8 100644 --- a/msmtools/estimation/sparse/effective_counts.py +++ b/msmtools/estimation/sparse/effective_counts.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r"""This module implements effective transition counts .. moduleauthor:: F. Noe diff --git a/msmtools/flux/__init__.py b/msmtools/flux/__init__.py index aaa69477..2e089481 100644 --- a/msmtools/flux/__init__.py +++ b/msmtools/flux/__init__.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r""" ==================================================================== diff --git a/msmtools/flux/sparse/__init__.py b/msmtools/flux/sparse/__init__.py index 913b1642..e475b5f7 100644 --- a/msmtools/flux/sparse/__init__.py +++ b/msmtools/flux/sparse/__init__.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + from __future__ import absolute_import from . import tpt diff --git a/msmtools/generation/__init__.py b/msmtools/generation/__init__.py index 735015ac..dda9bafc 100644 --- a/msmtools/generation/__init__.py +++ b/msmtools/generation/__init__.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r""" ================================================================ diff --git a/msmtools/util/annotators.py b/msmtools/util/annotators.py index 99fac69b..8908b54d 100644 --- a/msmtools/util/annotators.py +++ b/msmtools/util/annotators.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + """ doc_inherit decorator diff --git a/msmtools/util/exceptions.py b/msmtools/util/exceptions.py index 672b8f43..62d09562 100644 --- a/msmtools/util/exceptions.py +++ b/msmtools/util/exceptions.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + ''' Created on May 26, 2014 diff --git a/msmtools/util/matrix/matrix.py b/msmtools/util/matrix/matrix.py index f8dcc503..c6a3e14f 100644 --- a/msmtools/util/matrix/matrix.py +++ b/msmtools/util/matrix/matrix.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + r"""Implementation of IO for dense and sparse matrices .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/util/numeric.py b/msmtools/util/numeric.py index 5dfcc15e..7dc6ab93 100644 --- a/msmtools/util/numeric.py +++ b/msmtools/util/numeric.py @@ -22,6 +22,7 @@ # ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + ''' Created on 28.10.2013 From 1bd819c21e9cabd0977924a8776cd1c2a13f84a8 Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 21:38:13 +0200 Subject: [PATCH 07/11] removed bsd --- msmtools/__init__.py | 25 ------------------- msmtools/analysis/api.py | 25 ------------------- msmtools/analysis/dense/__init__.py | 25 ------------------- msmtools/analysis/dense/assessment.py | 25 ------------------- msmtools/analysis/sparse/__init__.py | 25 ------------------- msmtools/dtraj/api.py | 25 ------------------- .../estimation/dense/tmatrix_sampler_test.py | 25 ------------------- msmtools/estimation/sparse/__init__.py | 25 ------------------- .../estimation/sparse/effective_counts.py | 25 ------------------- msmtools/flux/__init__.py | 25 ------------------- msmtools/flux/sparse/__init__.py | 25 ------------------- msmtools/generation/__init__.py | 25 ------------------- msmtools/util/annotators.py | 25 ------------------- msmtools/util/exceptions.py | 25 ------------------- msmtools/util/matrix/matrix.py | 25 ------------------- msmtools/util/numeric.py | 25 ------------------- 16 files changed, 400 deletions(-) diff --git a/msmtools/__init__.py b/msmtools/__init__.py index 9d854ebe..93c18618 100644 --- a/msmtools/__init__.py +++ b/msmtools/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" .. currentmodule:: msmtools diff --git a/msmtools/analysis/api.py b/msmtools/analysis/api.py index 228f24cc..4bcd48b1 100644 --- a/msmtools/analysis/api.py +++ b/msmtools/analysis/api.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" ======================= diff --git a/msmtools/analysis/dense/__init__.py b/msmtools/analysis/dense/__init__.py index a084d267..05866bb1 100644 --- a/msmtools/analysis/dense/__init__.py +++ b/msmtools/analysis/dense/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - from __future__ import absolute_import from . import assessment diff --git a/msmtools/analysis/dense/assessment.py b/msmtools/analysis/dense/assessment.py index 597d18e6..8b19abce 100644 --- a/msmtools/analysis/dense/assessment.py +++ b/msmtools/analysis/dense/assessment.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - from __future__ import absolute_import import numpy as np diff --git a/msmtools/analysis/sparse/__init__.py b/msmtools/analysis/sparse/__init__.py index 89045f92..fb920e00 100644 --- a/msmtools/analysis/sparse/__init__.py +++ b/msmtools/analysis/sparse/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - from __future__ import absolute_import from . import assessment diff --git a/msmtools/dtraj/api.py b/msmtools/dtraj/api.py index 6e9156ea..9bfbeb7e 100644 --- a/msmtools/dtraj/api.py +++ b/msmtools/dtraj/api.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module implements IO and manipulation function for discrete trajectories ================= diff --git a/msmtools/estimation/dense/tmatrix_sampler_test.py b/msmtools/estimation/dense/tmatrix_sampler_test.py index f670af50..223345c2 100644 --- a/msmtools/estimation/dense/tmatrix_sampler_test.py +++ b/msmtools/estimation/dense/tmatrix_sampler_test.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Unit tests for the covariance module .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/__init__.py b/msmtools/estimation/sparse/__init__.py index 600d0ce8..4aee0160 100644 --- a/msmtools/estimation/sparse/__init__.py +++ b/msmtools/estimation/sparse/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module provides implementations for the estimation package .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/estimation/sparse/effective_counts.py b/msmtools/estimation/sparse/effective_counts.py index ae27a4b8..9b658bd7 100644 --- a/msmtools/estimation/sparse/effective_counts.py +++ b/msmtools/estimation/sparse/effective_counts.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""This module implements effective transition counts .. moduleauthor:: F. Noe diff --git a/msmtools/flux/__init__.py b/msmtools/flux/__init__.py index 2e089481..e801ea8a 100644 --- a/msmtools/flux/__init__.py +++ b/msmtools/flux/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" ==================================================================== diff --git a/msmtools/flux/sparse/__init__.py b/msmtools/flux/sparse/__init__.py index e475b5f7..8285517c 100644 --- a/msmtools/flux/sparse/__init__.py +++ b/msmtools/flux/sparse/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - from __future__ import absolute_import from . import tpt diff --git a/msmtools/generation/__init__.py b/msmtools/generation/__init__.py index dda9bafc..87a56dd6 100644 --- a/msmtools/generation/__init__.py +++ b/msmtools/generation/__init__.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r""" ================================================================ diff --git a/msmtools/util/annotators.py b/msmtools/util/annotators.py index 8908b54d..08f9afd8 100644 --- a/msmtools/util/annotators.py +++ b/msmtools/util/annotators.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - """ doc_inherit decorator diff --git a/msmtools/util/exceptions.py b/msmtools/util/exceptions.py index 62d09562..a2093e65 100644 --- a/msmtools/util/exceptions.py +++ b/msmtools/util/exceptions.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on May 26, 2014 diff --git a/msmtools/util/matrix/matrix.py b/msmtools/util/matrix/matrix.py index c6a3e14f..2cb0211e 100644 --- a/msmtools/util/matrix/matrix.py +++ b/msmtools/util/matrix/matrix.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - r"""Implementation of IO for dense and sparse matrices .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/util/numeric.py b/msmtools/util/numeric.py index 7dc6ab93..47ce5130 100644 --- a/msmtools/util/numeric.py +++ b/msmtools/util/numeric.py @@ -1,28 +1,3 @@ - -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. -# -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: -# -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - ''' Created on 28.10.2013 From 73a9e6cd01039b9f7439ee5907a29721c07ad597 Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 21:38:41 +0200 Subject: [PATCH 08/11] added lgpl --- msmtools/__init__.py | 20 ++++++++++++++++- msmtools/analysis/api.py | 20 ++++++++++++++++- msmtools/analysis/dense/__init__.py | 21 ++++++++++++++++-- msmtools/analysis/dense/assessment.py | 20 ++++++++++++++++- msmtools/analysis/sparse/__init__.py | 18 +++++++++++++++ msmtools/dtraj/api.py | 20 ++++++++++++++++- .../estimation/dense/tmatrix_sampler_test.py | 22 ++++++++++++++++--- msmtools/estimation/sparse/__init__.py | 20 ++++++++++++++++- .../estimation/sparse/effective_counts.py | 20 ++++++++++++++++- msmtools/flux/__init__.py | 20 ++++++++++++++++- msmtools/flux/sparse/__init__.py | 18 +++++++++++++++ msmtools/generation/__init__.py | 20 ++++++++++++++++- msmtools/util/annotators.py | 20 ++++++++++++++++- msmtools/util/exceptions.py | 20 ++++++++++++++++- msmtools/util/matrix/matrix.py | 18 +++++++++++++++ msmtools/util/numeric.py | 20 ++++++++++++++++- 16 files changed, 301 insertions(+), 16 deletions(-) diff --git a/msmtools/__init__.py b/msmtools/__init__.py index 93c18618..f72441b0 100644 --- a/msmtools/__init__.py +++ b/msmtools/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" .. currentmodule:: msmtools @@ -28,4 +46,4 @@ from ._version import get_versions __version__ = get_versions()['version'] -del get_versions +del get_versions \ No newline at end of file diff --git a/msmtools/analysis/api.py b/msmtools/analysis/api.py index 4bcd48b1..40d4e9cb 100644 --- a/msmtools/analysis/api.py +++ b/msmtools/analysis/api.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" ======================= @@ -1828,4 +1846,4 @@ def expectation_sensitivity(T, a): _showSparseConversionWarning() return dense.sensitivity.expectation_sensitivity(T.toarray(), a) else: - return dense.sensitivity.expectation_sensitivity(T, a) + return dense.sensitivity.expectation_sensitivity(T, a) \ No newline at end of file diff --git a/msmtools/analysis/dense/__init__.py b/msmtools/analysis/dense/__init__.py index 05866bb1..737cb9cf 100644 --- a/msmtools/analysis/dense/__init__.py +++ b/msmtools/analysis/dense/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from . import assessment @@ -8,5 +26,4 @@ from . import fingerprints from . import hitting_probability from . import mean_first_passage_time -from . import pcca - +from . import pcca \ No newline at end of file diff --git a/msmtools/analysis/dense/assessment.py b/msmtools/analysis/dense/assessment.py index 8b19abce..5391ae02 100644 --- a/msmtools/analysis/dense/assessment.py +++ b/msmtools/analysis/dense/assessment.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import import numpy as np @@ -86,4 +104,4 @@ def is_reversible(T, mu=None, tol=1e-10): X = mu[:, np.newaxis] * T return np.allclose(X, np.transpose(X), atol=tol) else: - raise ValueError("given matrix is not a valid transition matrix.") + raise ValueError("given matrix is not a valid transition matrix.") \ No newline at end of file diff --git a/msmtools/analysis/sparse/__init__.py b/msmtools/analysis/sparse/__init__.py index fb920e00..b491da5f 100644 --- a/msmtools/analysis/sparse/__init__.py +++ b/msmtools/analysis/sparse/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from . import assessment diff --git a/msmtools/dtraj/api.py b/msmtools/dtraj/api.py index 9bfbeb7e..5a624968 100644 --- a/msmtools/dtraj/api.py +++ b/msmtools/dtraj/api.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module implements IO and manipulation function for discrete trajectories ================= @@ -540,4 +558,4 @@ def sample_indexes_by_distribution(indexes, distributions, nsample): sequence = np.random.choice(n, size=nsample, p=distributions[i]) res[i] = sample_indexes_by_sequence(indexes, sequence) # - return res + return res \ No newline at end of file diff --git a/msmtools/estimation/dense/tmatrix_sampler_test.py b/msmtools/estimation/dense/tmatrix_sampler_test.py index 223345c2..50050466 100644 --- a/msmtools/estimation/dense/tmatrix_sampler_test.py +++ b/msmtools/estimation/dense/tmatrix_sampler_test.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Unit tests for the covariance module .. moduleauthor:: B.Trendelkamp-Schroer @@ -101,6 +119,4 @@ def test_mean(self): self.assertTrue(np.all( np.abs(mean - self.P_mle) <= std) ) if __name__=="__main__": - unittest.main() - - + unittest.main() \ No newline at end of file diff --git a/msmtools/estimation/sparse/__init__.py b/msmtools/estimation/sparse/__init__.py index 4aee0160..5cffcb06 100644 --- a/msmtools/estimation/sparse/__init__.py +++ b/msmtools/estimation/sparse/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module provides implementations for the estimation package .. moduleauthor:: B.Trendelkamp-Schroer @@ -12,4 +30,4 @@ from . import transition_matrix from . import prior from . import mle_trev_given_pi -from . import mle_trev +from . import mle_trev \ No newline at end of file diff --git a/msmtools/estimation/sparse/effective_counts.py b/msmtools/estimation/sparse/effective_counts.py index 9b658bd7..215935d6 100644 --- a/msmtools/estimation/sparse/effective_counts.py +++ b/msmtools/estimation/sparse/effective_counts.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""This module implements effective transition counts .. moduleauthor:: F. Noe @@ -219,4 +237,4 @@ def effective_count_matrix(dtrajs, lag, average='row', truncate_acf=True, mact=1 Ceff = scipy.sparse.csr_matrix(C.multiply(factor)) # else: by element, we're done. - return Ceff + return Ceff \ No newline at end of file diff --git a/msmtools/flux/__init__.py b/msmtools/flux/__init__.py index e801ea8a..380cdd4b 100644 --- a/msmtools/flux/__init__.py +++ b/msmtools/flux/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" ==================================================================== @@ -54,4 +72,4 @@ from __future__ import absolute_import from .api import * -from .reactive_flux import * +from .reactive_flux import * \ No newline at end of file diff --git a/msmtools/flux/sparse/__init__.py b/msmtools/flux/sparse/__init__.py index 8285517c..aa815dd4 100644 --- a/msmtools/flux/sparse/__init__.py +++ b/msmtools/flux/sparse/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + from __future__ import absolute_import from . import tpt diff --git a/msmtools/generation/__init__.py b/msmtools/generation/__init__.py index 87a56dd6..10429e49 100644 --- a/msmtools/generation/__init__.py +++ b/msmtools/generation/__init__.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r""" ================================================================ @@ -19,4 +37,4 @@ """ from __future__ import absolute_import -from .api import * +from .api import * \ No newline at end of file diff --git a/msmtools/util/annotators.py b/msmtools/util/annotators.py index 08f9afd8..1b17b468 100644 --- a/msmtools/util/annotators.py +++ b/msmtools/util/annotators.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """ doc_inherit decorator @@ -145,4 +163,4 @@ def wrap(f): if name not in frame.f_globals['__all__']: frame.f_globals['__all__'].append(name) return f - return wrap + return wrap \ No newline at end of file diff --git a/msmtools/util/exceptions.py b/msmtools/util/exceptions.py index a2093e65..767a2268 100644 --- a/msmtools/util/exceptions.py +++ b/msmtools/util/exceptions.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on May 26, 2014 @@ -30,4 +48,4 @@ class NotConvergedWarning(RuntimeWarning): as a safe guard to prevent arbitrary many iterations in loops with a conditional termination criterion. - """ + """ \ No newline at end of file diff --git a/msmtools/util/matrix/matrix.py b/msmtools/util/matrix/matrix.py index 2cb0211e..93f94668 100644 --- a/msmtools/util/matrix/matrix.py +++ b/msmtools/util/matrix/matrix.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Implementation of IO for dense and sparse matrices .. moduleauthor:: B.Trendelkamp-Schroer diff --git a/msmtools/util/numeric.py b/msmtools/util/numeric.py index 47ce5130..28c81766 100644 --- a/msmtools/util/numeric.py +++ b/msmtools/util/numeric.py @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + ''' Created on 28.10.2013 @@ -63,4 +81,4 @@ def allclose_sparse(A, B, rtol=1e-5, atol=1e-8): return same_data else: - return False + return False \ No newline at end of file From 2cd85e788f34b95a4f01e7722329eb7c0fad685e Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 21:44:55 +0200 Subject: [PATCH 09/11] some missing files --- .../estimation/dense/mle_trev_given_pi.pyx | 18 ++++++++++ msmtools/estimation/dense/sample_rev.c | 1 + msmtools/estimation/dense/sampler_rev.pyx | 34 ++++++++----------- msmtools/estimation/dense/sampler_revpi.pyx | 34 ++++++++----------- .../estimation/sparse/mle_trev_given_pi.pyx | 18 ++++++++++ 5 files changed, 65 insertions(+), 40 deletions(-) diff --git a/msmtools/estimation/dense/mle_trev_given_pi.pyx b/msmtools/estimation/dense/mle_trev_given_pi.pyx index a68b4391..4ebf0e86 100644 --- a/msmtools/estimation/dense/mle_trev_given_pi.pyx +++ b/msmtools/estimation/dense/mle_trev_given_pi.pyx @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Cython implementation of iterative likelihood maximization. .. moduleauthor:: F. Paul diff --git a/msmtools/estimation/dense/sample_rev.c b/msmtools/estimation/dense/sample_rev.c index 852a65ab..77fa67c9 100644 --- a/msmtools/estimation/dense/sample_rev.c +++ b/msmtools/estimation/dense/sample_rev.c @@ -1,3 +1,4 @@ + /* * This file is part of MSMTools. * * Copyright (c) 2015, 2014 Computational Molecular Biology Group diff --git a/msmtools/estimation/dense/sampler_rev.pyx b/msmtools/estimation/dense/sampler_rev.pyx index bf3f21ec..dfb009d5 100644 --- a/msmtools/estimation/dense/sampler_rev.pyx +++ b/msmtools/estimation/dense/sampler_rev.pyx @@ -1,26 +1,20 @@ -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group # -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. # -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. # -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . r"""Transition matrix sampling for revrsible stochastic matrices. diff --git a/msmtools/estimation/dense/sampler_revpi.pyx b/msmtools/estimation/dense/sampler_revpi.pyx index 0a76ea6a..a5cd5d05 100644 --- a/msmtools/estimation/dense/sampler_revpi.pyx +++ b/msmtools/estimation/dense/sampler_revpi.pyx @@ -1,26 +1,20 @@ -# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University -# Berlin, 14195 Berlin, Germany. -# All rights reserved. + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group # -# Redistribution and use in source and binary forms, with or without modification, -# are permitted provided that the following conditions are met: +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. # -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation and/or -# other materials provided with the distribution. +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. # -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS ``AS IS'' -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR -# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . r"""Transition matrix sampling for revrsible stochastic matrices with fixed stationary vector. diff --git a/msmtools/estimation/sparse/mle_trev_given_pi.pyx b/msmtools/estimation/sparse/mle_trev_given_pi.pyx index 353c62b5..230e45fc 100644 --- a/msmtools/estimation/sparse/mle_trev_given_pi.pyx +++ b/msmtools/estimation/sparse/mle_trev_given_pi.pyx @@ -1,3 +1,21 @@ + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + r"""Cython implementation of iterative likelihood maximization. .. moduleauthor:: F. Paul From bb23b009ac715d94f5907cc8be4a295b00d4a1ff Mon Sep 17 00:00:00 2001 From: marscher Date: Sun, 30 Aug 2015 23:11:05 +0200 Subject: [PATCH 10/11] added location to copyright notice --- msmtools/__init__.py | 2 +- msmtools/_version.py | 2 +- msmtools/analysis/__init__.py | 2 +- msmtools/analysis/api.py | 2 +- msmtools/analysis/dense/__init__.py | 2 +- msmtools/analysis/dense/assessment.py | 2 +- msmtools/analysis/dense/assessment_test.py | 2 +- msmtools/analysis/dense/birth_death_chain.py | 2 +- msmtools/analysis/dense/committor.py | 2 +- msmtools/analysis/dense/committor_test.py | 2 +- msmtools/analysis/dense/correlations.py | 2 +- msmtools/analysis/dense/correlations_test.py | 2 +- msmtools/analysis/dense/decomposition.py | 2 +- msmtools/analysis/dense/decomposition_test.py | 2 +- msmtools/analysis/dense/expectations.py | 2 +- msmtools/analysis/dense/expectations_test.py | 2 +- msmtools/analysis/dense/fingerprints.py | 2 +- msmtools/analysis/dense/fingerprints_test.py | 2 +- .../analysis/dense/hitting_probability.py | 2 +- .../dense/hitting_probability_test.py | 2 +- .../analysis/dense/mean_first_passage_time.py | 2 +- .../dense/mean_first_passage_time_test.py | 2 +- msmtools/analysis/dense/pcca.py | 2 +- msmtools/analysis/dense/pcca_test.py | 2 +- msmtools/analysis/dense/sensitivity.py | 2 +- msmtools/analysis/dense/sensitivity_test.py | 2 +- msmtools/analysis/dense/stationary_vector.py | 2 +- .../analysis/dense/stationary_vector_test.py | 2 +- msmtools/analysis/sparse/__init__.py | 2 +- msmtools/analysis/sparse/assessment.py | 2 +- msmtools/analysis/sparse/assessment_test.py | 2 +- msmtools/analysis/sparse/birth_death_chain.py | 2 +- msmtools/analysis/sparse/committor.py | 2 +- msmtools/analysis/sparse/committor_test.py | 2 +- msmtools/analysis/sparse/decomposition.py | 2 +- .../analysis/sparse/decomposition_test.py | 2 +- msmtools/analysis/sparse/expectations.py | 2 +- msmtools/analysis/sparse/expectations_test.py | 2 +- msmtools/analysis/sparse/fingerprints.py | 2 +- msmtools/analysis/sparse/fingerprints_test.py | 2 +- .../sparse/mean_first_passage_time.py | 2 +- .../sparse/mean_first_passage_time_test.py | 2 +- msmtools/analysis/sparse/stationary_vector.py | 2 +- .../analysis/sparse/stationary_vector_test.py | 2 +- msmtools/dtraj/__init__.py | 2 +- msmtools/dtraj/api.py | 2 +- msmtools/estimation/__init__.py | 2 +- msmtools/estimation/api.py | 2 +- msmtools/estimation/dense/__init__.py | 2 +- msmtools/estimation/dense/bootstrapping.py | 2 +- msmtools/estimation/dense/covariance.py | 2 +- msmtools/estimation/dense/covariance_test.py | 2 +- .../estimation/dense/mle_trev_given_pi.pyx | 2 +- msmtools/estimation/dense/sampler_nrev.py | 2 +- msmtools/estimation/dense/sampler_rev.pyx | 2 +- msmtools/estimation/dense/sampler_revpi.pyx | 2 +- msmtools/estimation/dense/tmatrix_sampler.py | 2 +- .../estimation/dense/tmatrix_sampler_test.py | 2 +- .../estimation/dense/transition_matrix.py | 2 +- msmtools/estimation/sparse/__init__.py | 2 +- msmtools/estimation/sparse/connectivity.py | 2 +- .../estimation/sparse/connectivity_test.py | 2 +- msmtools/estimation/sparse/count_matrix.py | 2 +- .../estimation/sparse/count_matrix_test.py | 2 +- .../estimation/sparse/effective_counts.py | 2 +- msmtools/estimation/sparse/likelihood.py | 2 +- msmtools/estimation/sparse/likelihood_test.py | 2 +- .../estimation/sparse/mle_trev_given_pi.pyx | 2 +- msmtools/estimation/sparse/prior.py | 2 +- msmtools/estimation/sparse/prior_test.py | 2 +- .../estimation/sparse/transition_matrix.py | 2 +- .../sparse/transition_matrix_test.py | 2 +- msmtools/flux/__init__.py | 2 +- msmtools/flux/api.py | 2 +- msmtools/flux/dense/__init__.py | 2 +- msmtools/flux/dense/tpt.py | 2 +- msmtools/flux/dense/tpt_test.py | 2 +- msmtools/flux/reactive_flux.py | 2 +- msmtools/flux/reactive_flux_test.py | 2 +- msmtools/flux/sparse/__init__.py | 2 +- msmtools/flux/sparse/pathways.py | 2 +- msmtools/flux/sparse/pathways_test.py | 2 +- msmtools/flux/sparse/tpt.py | 2 +- msmtools/flux/sparse/tpt_test.py | 2 +- msmtools/generation/__init__.py | 2 +- msmtools/generation/api.py | 2 +- msmtools/util/__init__.py | 2 +- msmtools/util/annotators.py | 2 +- msmtools/util/exceptions.py | 2 +- msmtools/util/matrix/__init__.py | 2 +- msmtools/util/matrix/matrix.py | 2 +- msmtools/util/matrix/matrix_test.py | 2 +- msmtools/util/numeric.py | 2 +- msmtools/util/statistics.py | 2 +- msmtools/util/types.py | 2 +- setup.py | 19 ++++++++++++++++++- setup_util.py | 17 +++++++++++++++++ 97 files changed, 130 insertions(+), 96 deletions(-) diff --git a/msmtools/__init__.py b/msmtools/__init__.py index f72441b0..4951f323 100644 --- a/msmtools/__init__.py +++ b/msmtools/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/_version.py b/msmtools/_version.py index b484d491..97592e83 100644 --- a/msmtools/_version.py +++ b/msmtools/_version.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/__init__.py b/msmtools/analysis/__init__.py index 9867a388..5868fe46 100644 --- a/msmtools/analysis/__init__.py +++ b/msmtools/analysis/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/api.py b/msmtools/analysis/api.py index 40d4e9cb..6afe637b 100644 --- a/msmtools/analysis/api.py +++ b/msmtools/analysis/api.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/__init__.py b/msmtools/analysis/dense/__init__.py index 737cb9cf..82e8e4d0 100644 --- a/msmtools/analysis/dense/__init__.py +++ b/msmtools/analysis/dense/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/assessment.py b/msmtools/analysis/dense/assessment.py index 5391ae02..058e8845 100644 --- a/msmtools/analysis/dense/assessment.py +++ b/msmtools/analysis/dense/assessment.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/assessment_test.py b/msmtools/analysis/dense/assessment_test.py index 7cbc363d..b84b06dd 100644 --- a/msmtools/analysis/dense/assessment_test.py +++ b/msmtools/analysis/dense/assessment_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/birth_death_chain.py b/msmtools/analysis/dense/birth_death_chain.py index 35053c2d..d1efe246 100644 --- a/msmtools/analysis/dense/birth_death_chain.py +++ b/msmtools/analysis/dense/birth_death_chain.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/committor.py b/msmtools/analysis/dense/committor.py index dfaa547a..43b3f646 100644 --- a/msmtools/analysis/dense/committor.py +++ b/msmtools/analysis/dense/committor.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/committor_test.py b/msmtools/analysis/dense/committor_test.py index cc3c86b7..09e3974c 100644 --- a/msmtools/analysis/dense/committor_test.py +++ b/msmtools/analysis/dense/committor_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/correlations.py b/msmtools/analysis/dense/correlations.py index 3ba304a7..51569f7d 100644 --- a/msmtools/analysis/dense/correlations.py +++ b/msmtools/analysis/dense/correlations.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/correlations_test.py b/msmtools/analysis/dense/correlations_test.py index db1dd541..37d246e5 100644 --- a/msmtools/analysis/dense/correlations_test.py +++ b/msmtools/analysis/dense/correlations_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/decomposition.py b/msmtools/analysis/dense/decomposition.py index 117f36b9..7b60ed99 100644 --- a/msmtools/analysis/dense/decomposition.py +++ b/msmtools/analysis/dense/decomposition.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/decomposition_test.py b/msmtools/analysis/dense/decomposition_test.py index 09bdd2a2..20df3c73 100644 --- a/msmtools/analysis/dense/decomposition_test.py +++ b/msmtools/analysis/dense/decomposition_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/expectations.py b/msmtools/analysis/dense/expectations.py index 610b1ef9..bfdf1bc5 100644 --- a/msmtools/analysis/dense/expectations.py +++ b/msmtools/analysis/dense/expectations.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/expectations_test.py b/msmtools/analysis/dense/expectations_test.py index 8bee6e84..8d7280fc 100644 --- a/msmtools/analysis/dense/expectations_test.py +++ b/msmtools/analysis/dense/expectations_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/fingerprints.py b/msmtools/analysis/dense/fingerprints.py index 3ada55c9..8ab88157 100644 --- a/msmtools/analysis/dense/fingerprints.py +++ b/msmtools/analysis/dense/fingerprints.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/fingerprints_test.py b/msmtools/analysis/dense/fingerprints_test.py index 4e39af22..96f365dd 100644 --- a/msmtools/analysis/dense/fingerprints_test.py +++ b/msmtools/analysis/dense/fingerprints_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/hitting_probability.py b/msmtools/analysis/dense/hitting_probability.py index 3aea154b..070862e3 100644 --- a/msmtools/analysis/dense/hitting_probability.py +++ b/msmtools/analysis/dense/hitting_probability.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/hitting_probability_test.py b/msmtools/analysis/dense/hitting_probability_test.py index 43d51915..55bdf8e2 100644 --- a/msmtools/analysis/dense/hitting_probability_test.py +++ b/msmtools/analysis/dense/hitting_probability_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/mean_first_passage_time.py b/msmtools/analysis/dense/mean_first_passage_time.py index a5ddec9d..16f29732 100644 --- a/msmtools/analysis/dense/mean_first_passage_time.py +++ b/msmtools/analysis/dense/mean_first_passage_time.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/mean_first_passage_time_test.py b/msmtools/analysis/dense/mean_first_passage_time_test.py index 1503c185..ae0d44e7 100644 --- a/msmtools/analysis/dense/mean_first_passage_time_test.py +++ b/msmtools/analysis/dense/mean_first_passage_time_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/pcca.py b/msmtools/analysis/dense/pcca.py index 5c1ee21b..f4d562ed 100644 --- a/msmtools/analysis/dense/pcca.py +++ b/msmtools/analysis/dense/pcca.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/pcca_test.py b/msmtools/analysis/dense/pcca_test.py index 77341dd7..dfe856a3 100644 --- a/msmtools/analysis/dense/pcca_test.py +++ b/msmtools/analysis/dense/pcca_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/sensitivity.py b/msmtools/analysis/dense/sensitivity.py index 8d105519..d7715a4a 100644 --- a/msmtools/analysis/dense/sensitivity.py +++ b/msmtools/analysis/dense/sensitivity.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/sensitivity_test.py b/msmtools/analysis/dense/sensitivity_test.py index 3db6b3ff..2ab6369c 100644 --- a/msmtools/analysis/dense/sensitivity_test.py +++ b/msmtools/analysis/dense/sensitivity_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/stationary_vector.py b/msmtools/analysis/dense/stationary_vector.py index 3d8b5176..bc723d18 100644 --- a/msmtools/analysis/dense/stationary_vector.py +++ b/msmtools/analysis/dense/stationary_vector.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/dense/stationary_vector_test.py b/msmtools/analysis/dense/stationary_vector_test.py index 0765170f..e3cd50a3 100644 --- a/msmtools/analysis/dense/stationary_vector_test.py +++ b/msmtools/analysis/dense/stationary_vector_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/__init__.py b/msmtools/analysis/sparse/__init__.py index b491da5f..dc334fa3 100644 --- a/msmtools/analysis/sparse/__init__.py +++ b/msmtools/analysis/sparse/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/assessment.py b/msmtools/analysis/sparse/assessment.py index e26e990d..0ebdd6fc 100644 --- a/msmtools/analysis/sparse/assessment.py +++ b/msmtools/analysis/sparse/assessment.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/assessment_test.py b/msmtools/analysis/sparse/assessment_test.py index 58a938dd..04e9bd3b 100644 --- a/msmtools/analysis/sparse/assessment_test.py +++ b/msmtools/analysis/sparse/assessment_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/birth_death_chain.py b/msmtools/analysis/sparse/birth_death_chain.py index 35053c2d..d1efe246 100644 --- a/msmtools/analysis/sparse/birth_death_chain.py +++ b/msmtools/analysis/sparse/birth_death_chain.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/committor.py b/msmtools/analysis/sparse/committor.py index 43daacc6..2df7cd93 100644 --- a/msmtools/analysis/sparse/committor.py +++ b/msmtools/analysis/sparse/committor.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/committor_test.py b/msmtools/analysis/sparse/committor_test.py index 490d4c30..83a9c659 100644 --- a/msmtools/analysis/sparse/committor_test.py +++ b/msmtools/analysis/sparse/committor_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/decomposition.py b/msmtools/analysis/sparse/decomposition.py index da425a63..f5ea6f36 100644 --- a/msmtools/analysis/sparse/decomposition.py +++ b/msmtools/analysis/sparse/decomposition.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/decomposition_test.py b/msmtools/analysis/sparse/decomposition_test.py index ce917a73..d4138208 100644 --- a/msmtools/analysis/sparse/decomposition_test.py +++ b/msmtools/analysis/sparse/decomposition_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/expectations.py b/msmtools/analysis/sparse/expectations.py index 51340fd1..41f1dbd1 100644 --- a/msmtools/analysis/sparse/expectations.py +++ b/msmtools/analysis/sparse/expectations.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/expectations_test.py b/msmtools/analysis/sparse/expectations_test.py index f6bcd14e..a0885933 100644 --- a/msmtools/analysis/sparse/expectations_test.py +++ b/msmtools/analysis/sparse/expectations_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/fingerprints.py b/msmtools/analysis/sparse/fingerprints.py index 63423442..2578e9b2 100644 --- a/msmtools/analysis/sparse/fingerprints.py +++ b/msmtools/analysis/sparse/fingerprints.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/fingerprints_test.py b/msmtools/analysis/sparse/fingerprints_test.py index f1bef0ab..34655c32 100644 --- a/msmtools/analysis/sparse/fingerprints_test.py +++ b/msmtools/analysis/sparse/fingerprints_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/mean_first_passage_time.py b/msmtools/analysis/sparse/mean_first_passage_time.py index be27daf1..ba1e6183 100644 --- a/msmtools/analysis/sparse/mean_first_passage_time.py +++ b/msmtools/analysis/sparse/mean_first_passage_time.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/mean_first_passage_time_test.py b/msmtools/analysis/sparse/mean_first_passage_time_test.py index bb28635d..d83453ff 100644 --- a/msmtools/analysis/sparse/mean_first_passage_time_test.py +++ b/msmtools/analysis/sparse/mean_first_passage_time_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/stationary_vector.py b/msmtools/analysis/sparse/stationary_vector.py index ab244e17..a7fc76b0 100644 --- a/msmtools/analysis/sparse/stationary_vector.py +++ b/msmtools/analysis/sparse/stationary_vector.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/analysis/sparse/stationary_vector_test.py b/msmtools/analysis/sparse/stationary_vector_test.py index ee163041..a464d45d 100644 --- a/msmtools/analysis/sparse/stationary_vector_test.py +++ b/msmtools/analysis/sparse/stationary_vector_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/dtraj/__init__.py b/msmtools/dtraj/__init__.py index 0dd11503..d26e2bc9 100644 --- a/msmtools/dtraj/__init__.py +++ b/msmtools/dtraj/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/dtraj/api.py b/msmtools/dtraj/api.py index 5a624968..fe49c5fb 100644 --- a/msmtools/dtraj/api.py +++ b/msmtools/dtraj/api.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/__init__.py b/msmtools/estimation/__init__.py index 3bc678dd..6e9792b7 100644 --- a/msmtools/estimation/__init__.py +++ b/msmtools/estimation/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/api.py b/msmtools/estimation/api.py index b658282c..0b6cedad 100644 --- a/msmtools/estimation/api.py +++ b/msmtools/estimation/api.py @@ -3,7 +3,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/__init__.py b/msmtools/estimation/dense/__init__.py index 922a4841..f1939d83 100644 --- a/msmtools/estimation/dense/__init__.py +++ b/msmtools/estimation/dense/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/bootstrapping.py b/msmtools/estimation/dense/bootstrapping.py index 88d948ef..4558b9e1 100644 --- a/msmtools/estimation/dense/bootstrapping.py +++ b/msmtools/estimation/dense/bootstrapping.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/covariance.py b/msmtools/estimation/dense/covariance.py index ddbb4767..8b401cfd 100644 --- a/msmtools/estimation/dense/covariance.py +++ b/msmtools/estimation/dense/covariance.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/covariance_test.py b/msmtools/estimation/dense/covariance_test.py index f11c7cfb..e3eef90f 100644 --- a/msmtools/estimation/dense/covariance_test.py +++ b/msmtools/estimation/dense/covariance_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/mle_trev_given_pi.pyx b/msmtools/estimation/dense/mle_trev_given_pi.pyx index 4ebf0e86..60d1e082 100644 --- a/msmtools/estimation/dense/mle_trev_given_pi.pyx +++ b/msmtools/estimation/dense/mle_trev_given_pi.pyx @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/sampler_nrev.py b/msmtools/estimation/dense/sampler_nrev.py index 94a7ecee..b41126a3 100644 --- a/msmtools/estimation/dense/sampler_nrev.py +++ b/msmtools/estimation/dense/sampler_nrev.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/sampler_rev.pyx b/msmtools/estimation/dense/sampler_rev.pyx index dfb009d5..d4630184 100644 --- a/msmtools/estimation/dense/sampler_rev.pyx +++ b/msmtools/estimation/dense/sampler_rev.pyx @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/sampler_revpi.pyx b/msmtools/estimation/dense/sampler_revpi.pyx index a5cd5d05..90528dcd 100644 --- a/msmtools/estimation/dense/sampler_revpi.pyx +++ b/msmtools/estimation/dense/sampler_revpi.pyx @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/tmatrix_sampler.py b/msmtools/estimation/dense/tmatrix_sampler.py index f1e955a9..2b873dac 100644 --- a/msmtools/estimation/dense/tmatrix_sampler.py +++ b/msmtools/estimation/dense/tmatrix_sampler.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/tmatrix_sampler_test.py b/msmtools/estimation/dense/tmatrix_sampler_test.py index 50050466..d0f27c7e 100644 --- a/msmtools/estimation/dense/tmatrix_sampler_test.py +++ b/msmtools/estimation/dense/tmatrix_sampler_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/dense/transition_matrix.py b/msmtools/estimation/dense/transition_matrix.py index 1148b2c2..d036d46f 100644 --- a/msmtools/estimation/dense/transition_matrix.py +++ b/msmtools/estimation/dense/transition_matrix.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/__init__.py b/msmtools/estimation/sparse/__init__.py index 5cffcb06..54b63ae0 100644 --- a/msmtools/estimation/sparse/__init__.py +++ b/msmtools/estimation/sparse/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/connectivity.py b/msmtools/estimation/sparse/connectivity.py index 54aad0e2..59eb4a87 100644 --- a/msmtools/estimation/sparse/connectivity.py +++ b/msmtools/estimation/sparse/connectivity.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/connectivity_test.py b/msmtools/estimation/sparse/connectivity_test.py index 73fcd3c1..4f0832a5 100644 --- a/msmtools/estimation/sparse/connectivity_test.py +++ b/msmtools/estimation/sparse/connectivity_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/count_matrix.py b/msmtools/estimation/sparse/count_matrix.py index a4c404d3..d9118fba 100644 --- a/msmtools/estimation/sparse/count_matrix.py +++ b/msmtools/estimation/sparse/count_matrix.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/count_matrix_test.py b/msmtools/estimation/sparse/count_matrix_test.py index f670c0e7..32e22523 100644 --- a/msmtools/estimation/sparse/count_matrix_test.py +++ b/msmtools/estimation/sparse/count_matrix_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/effective_counts.py b/msmtools/estimation/sparse/effective_counts.py index 215935d6..afc31feb 100644 --- a/msmtools/estimation/sparse/effective_counts.py +++ b/msmtools/estimation/sparse/effective_counts.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/likelihood.py b/msmtools/estimation/sparse/likelihood.py index aecd3e7e..950fef7e 100644 --- a/msmtools/estimation/sparse/likelihood.py +++ b/msmtools/estimation/sparse/likelihood.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/likelihood_test.py b/msmtools/estimation/sparse/likelihood_test.py index d921c6aa..8b5fcc01 100644 --- a/msmtools/estimation/sparse/likelihood_test.py +++ b/msmtools/estimation/sparse/likelihood_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/mle_trev_given_pi.pyx b/msmtools/estimation/sparse/mle_trev_given_pi.pyx index 230e45fc..9b72148f 100644 --- a/msmtools/estimation/sparse/mle_trev_given_pi.pyx +++ b/msmtools/estimation/sparse/mle_trev_given_pi.pyx @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/prior.py b/msmtools/estimation/sparse/prior.py index 2990c3aa..954615fb 100644 --- a/msmtools/estimation/sparse/prior.py +++ b/msmtools/estimation/sparse/prior.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/prior_test.py b/msmtools/estimation/sparse/prior_test.py index 359358a7..792ba6d8 100644 --- a/msmtools/estimation/sparse/prior_test.py +++ b/msmtools/estimation/sparse/prior_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/transition_matrix.py b/msmtools/estimation/sparse/transition_matrix.py index b230ab40..3158293d 100644 --- a/msmtools/estimation/sparse/transition_matrix.py +++ b/msmtools/estimation/sparse/transition_matrix.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/estimation/sparse/transition_matrix_test.py b/msmtools/estimation/sparse/transition_matrix_test.py index 1e251720..4672d815 100644 --- a/msmtools/estimation/sparse/transition_matrix_test.py +++ b/msmtools/estimation/sparse/transition_matrix_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/__init__.py b/msmtools/flux/__init__.py index 380cdd4b..947b162a 100644 --- a/msmtools/flux/__init__.py +++ b/msmtools/flux/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/api.py b/msmtools/flux/api.py index ad25dafb..e5370905 100644 --- a/msmtools/flux/api.py +++ b/msmtools/flux/api.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/dense/__init__.py b/msmtools/flux/dense/__init__.py index 67e44cfe..919b1ad3 100644 --- a/msmtools/flux/dense/__init__.py +++ b/msmtools/flux/dense/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/dense/tpt.py b/msmtools/flux/dense/tpt.py index f1ede3fc..15aa9301 100644 --- a/msmtools/flux/dense/tpt.py +++ b/msmtools/flux/dense/tpt.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/dense/tpt_test.py b/msmtools/flux/dense/tpt_test.py index e3fec6c4..355cf0af 100644 --- a/msmtools/flux/dense/tpt_test.py +++ b/msmtools/flux/dense/tpt_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/reactive_flux.py b/msmtools/flux/reactive_flux.py index 1bf67edd..0692127a 100644 --- a/msmtools/flux/reactive_flux.py +++ b/msmtools/flux/reactive_flux.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/reactive_flux_test.py b/msmtools/flux/reactive_flux_test.py index 879151df..adeb1068 100644 --- a/msmtools/flux/reactive_flux_test.py +++ b/msmtools/flux/reactive_flux_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/sparse/__init__.py b/msmtools/flux/sparse/__init__.py index aa815dd4..a806a385 100644 --- a/msmtools/flux/sparse/__init__.py +++ b/msmtools/flux/sparse/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/sparse/pathways.py b/msmtools/flux/sparse/pathways.py index ddfbe531..274c735f 100644 --- a/msmtools/flux/sparse/pathways.py +++ b/msmtools/flux/sparse/pathways.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/sparse/pathways_test.py b/msmtools/flux/sparse/pathways_test.py index 6ac6a54e..54531609 100644 --- a/msmtools/flux/sparse/pathways_test.py +++ b/msmtools/flux/sparse/pathways_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/sparse/tpt.py b/msmtools/flux/sparse/tpt.py index ba71793b..4617c633 100644 --- a/msmtools/flux/sparse/tpt.py +++ b/msmtools/flux/sparse/tpt.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/flux/sparse/tpt_test.py b/msmtools/flux/sparse/tpt_test.py index 1194dfb7..da21680e 100644 --- a/msmtools/flux/sparse/tpt_test.py +++ b/msmtools/flux/sparse/tpt_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/generation/__init__.py b/msmtools/generation/__init__.py index 10429e49..d1164d95 100644 --- a/msmtools/generation/__init__.py +++ b/msmtools/generation/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/generation/api.py b/msmtools/generation/api.py index bfa3bcab..66685960 100644 --- a/msmtools/generation/api.py +++ b/msmtools/generation/api.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/__init__.py b/msmtools/util/__init__.py index b91292c5..42c3818b 100644 --- a/msmtools/util/__init__.py +++ b/msmtools/util/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/annotators.py b/msmtools/util/annotators.py index 1b17b468..26717ed7 100644 --- a/msmtools/util/annotators.py +++ b/msmtools/util/annotators.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/exceptions.py b/msmtools/util/exceptions.py index 767a2268..dc51d832 100644 --- a/msmtools/util/exceptions.py +++ b/msmtools/util/exceptions.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/matrix/__init__.py b/msmtools/util/matrix/__init__.py index b91292c5..42c3818b 100644 --- a/msmtools/util/matrix/__init__.py +++ b/msmtools/util/matrix/__init__.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/matrix/matrix.py b/msmtools/util/matrix/matrix.py index 93f94668..21f0255e 100644 --- a/msmtools/util/matrix/matrix.py +++ b/msmtools/util/matrix/matrix.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/matrix/matrix_test.py b/msmtools/util/matrix/matrix_test.py index 53263c75..4e3c8b90 100644 --- a/msmtools/util/matrix/matrix_test.py +++ b/msmtools/util/matrix/matrix_test.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/numeric.py b/msmtools/util/numeric.py index 28c81766..9235805b 100644 --- a/msmtools/util/numeric.py +++ b/msmtools/util/numeric.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/statistics.py b/msmtools/util/statistics.py index 868b554d..f6c75cb0 100644 --- a/msmtools/util/statistics.py +++ b/msmtools/util/statistics.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/msmtools/util/types.py b/msmtools/util/types.py index 5bd263fc..18bc8c82 100644 --- a/msmtools/util/types.py +++ b/msmtools/util/types.py @@ -1,7 +1,7 @@ # This file is part of MSMTools. # -# Copyright (c) 2015, 2014 Computational Molecular Biology Group +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) # # MSMTools is free software: you can redistribute it and/or modify # it under the terms of the GNU Lesser General Public License as published by diff --git a/setup.py b/setup.py index 2af3819f..e027f554 100755 --- a/setup.py +++ b/setup.py @@ -1,5 +1,22 @@ - #!/usr/bin/env python + +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """ MSMTools MSMTools contains an API to estimate and analyze Markov state models. diff --git a/setup_util.py b/setup_util.py index 838136b5..6a201865 100644 --- a/setup_util.py +++ b/setup_util.py @@ -1,4 +1,21 @@ +# This file is part of MSMTools. +# +# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER) +# +# MSMTools is free software: you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program. If not, see . + """ utility functions for python setup """ From 3f7ee1c87f9afeff2d9ecaeed9909ca8591b85c5 Mon Sep 17 00:00:00 2001 From: marscher Date: Mon, 31 Aug 2015 01:02:06 +0200 Subject: [PATCH 11/11] fix --- .../estimation/tests/test_tmatrix_sampling.py | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/msmtools/estimation/tests/test_tmatrix_sampling.py b/msmtools/estimation/tests/test_tmatrix_sampling.py index d59094c6..23caa2ed 100644 --- a/msmtools/estimation/tests/test_tmatrix_sampling.py +++ b/msmtools/estimation/tests/test_tmatrix_sampling.py @@ -16,16 +16,17 @@ # You should have received a copy of the GNU Lesser General Public License # along with this program. If not, see . -from __future__ import absolute_import -from six.moves import ranger"""Unit tests for the transition_matrix module + +r"""Unit tests for the transition_matrix module .. moduleauthor:: B.Trendelkamp-Schroer .. moduleauthor:: Frank Noe """ +from __future__ import absolute_import +from six.moves import range import unittest -import warnings import numpy as np from msmtools.util.numeric import assert_allclose @@ -68,7 +69,6 @@ def setUp(self): self.state = np.random.get_state() """Set seed to enforce deterministic behavior""" np.random.seed(42) - self.C = np.array([[5, 2], [3, 10]]) self.pi = np.array([0.25, 0.75]) @@ -96,7 +96,7 @@ def probabilities_rev(self, xedges, yedges): def posterior_revpi(self, x, C, pi): z = (1.0-x)**C[0, 0] * x**C[0, 1] * pi[0]/pi[1] *x**C[1, 0] *\ - (1.0 - pi[0]/pi[1] * x)**C[1, 1] + (1.0 - pi[0]/pi[1] * x)**C[1, 1] return z def probabilities_revpi(self, xedges): @@ -106,7 +106,7 @@ def probabilities_revpi(self, xedges): w = np.zeros(N-1) for i in range(N-1): w[i] = quad(self.posterior_revpi, xedges[i], xedges[i+1], args=(Cp, pi))[0] - return w/w.sum() + return w/w.sum() def test_rev(self): N = self.N @@ -117,12 +117,12 @@ def test_rev(self): T_sample[i, :, :] = sampler.sample() p_12 = T_sample[:, 0, 1] p_21 = T_sample[:, 1, 0] - H, xed, yed = np.histogram2d(p_12, p_21, bins=(self.xedges, self.yedges)) - P_sampled = H/self.N + H, xed, yed = np.histogram2d(p_12, p_21, bins=(self.xedges, self.yedges)) + P_sampled = H/self.N P_analytical = self.probabilities_rev(self.xedges, self.yedges) - + self.assertTrue(np.all(np.abs(P_sampled - P_analytical) < 0.01)) - + def test_revpi(self): N = self.N sampler = tmatrix_sampler(self.C, reversible=True, mu=self.pi)