Merge pull request #406 from choderalab/tripos-mol2

Add property accessors for retrieving HostGuest* molecules as OEMols

.travis.yml

@@ -40,13 +40,7 @@ env:
     - ORGNAME="omnia" # the name of the organization
     - PACKAGENAME="openmmtools" # the name of your package
     - OPENMM_CPU_THREADS="1" # only use one CPU thread for determinism
-    # encrypted BINSTAR_TOKEN for push of dev package to binstar
-    - secure: "DP5heLvW3wnHvw6d2tinSHcyAxe0EWEsoL4X3lrGC+BSSy3Fd60pb90zSibK/hcxzV7Cb/x4mC4C7KPgGZEXzvVFH/iF7tg2Yy41XgyuZ5vxacfXICdryoTAlGxrbwACvO/ak+OHEYTtkX3OyFM/f8zV0z7Shz/rOSbSvcEKmpQ="
 
 matrix:
   allow_failures:
   - env: python=3.7 CONDA_PY=37 DEVOMNIA=true
-
-after_success:
-  - echo "after_success"
-  - if [ "$TRAVIS_SECURE_ENV_VARS" == true ]; then source devtools/travis-ci/after_success.sh; fi

devtools/conda-recipe/meta.yaml

@@ -13,15 +13,15 @@ requirements:
   build:
     - python
     - setuptools
-    - openmm >=7.3
+    - openmm >=7.3.1
     - cython
 
   run:
     - python
     - numpy
     - scipy
     - six
-    - openmm >=7.3
+    - openmm >=7.3.1
     - parmed
     - mdtraj
     - netcdf4 >=1.4.2 # after bugfix: "always return masked array by default, even if there are no masked values"

docs/releasehistory.rst

@@ -1,6 +1,19 @@
 Release History
 ***************
 
+0.19.0 -
+==================================
+
+New features
+------------
+- Improvements for ``HostGuest*`` classes
+  - add ``oemols``, ``host_oemol``, and ``guest_oemol`` properties to retrieve OpenEye Toolkit ``OEMol`` objects (requires toolkit license and installation)
+  - these classes can now accept overriding ``kwargs``ss
+
+Bugfixes
+--------
+- ``openmmtools.multistate`` experimental API warning is only issued when ``openmmtools.multistate`` is imported
+
 0.18.0 - Added multistate samplers
 ==================================
 
@@ -12,7 +25,6 @@ New features
   - ``SAMSSampler``: self-adjusted mixture sampling (SAMS) sampling
 - All samplers can use MPI via the ``mpiplus <https://github.com/choderalab/mpiplus>`_ package
 
-
 0.17.0 - Removed Py2 support, faster exact PME treatment
 ========================================================
 

openmmtools/__init__.py

@@ -9,5 +9,4 @@
 from openmmtools import version
 __version__ = version.version
 
-# Import modules.
 from openmmtools import testsystems, integrators, alchemy, mcmc, states, cache, utils, constants, forces, forcefactories, storage, multistate

openmmtools/data/cb7-b2/b2_tripos.mol2

@@ -0,0 +1,72 @@
+@<TRIPOS>MOLECULE
+B2
+   30    31     1     0     0
+SMALL
+No Charge or Current Charge
+
+
+@<TRIPOS>ATOM
+      1 C1           5.6530     6.9290    18.9420 C.3        2 B2       -0.066400
+      2 C2           4.2520     6.9700    18.3070 C.3        2 B2       -0.066400
+      3 C3           4.3590     6.6600    16.7920 C.3        2 B2       -0.092000
+      4 C4           6.7210     6.9720    17.8190 C.3        2 B2       -0.092000
+      5 C5           6.3870     8.1520    16.8670 C.3        2 B2       -0.066400
+      6 C6           5.0960     7.8360    16.0970 C.3        2 B2       -0.066400
+      7 C7           6.6540     5.6500    17.0130 C.3        2 B2       -0.066400
+      8 C8           5.1990     5.3700    16.5990 C.3        2 B2       -0.066400
+      9 C9           8.1110     7.1550    18.4530 C.3        2 B2        0.136400
+     10 O1           9.1270     7.4280    17.4610 O.3        2 B2       -0.596800
+     11 C10          2.9650     6.4430    16.1760 C.3        2 B2        0.136400
+     12 O2           2.1980     7.6680    16.1310 O.3        2 B2       -0.596800
+     13 H1           5.7740     6.0080    19.5410 H          2 B2        0.043533
+     14 H2           5.7820     7.7750    19.6400 H          2 B2        0.043533
+     15 H3           3.5790     6.2520    18.8090 H          2 B2        0.043533
+     16 H4           3.7940     7.9670    18.4490 H          2 B2        0.043533
+     17 H5           7.2250     8.3270    16.1630 H          2 B2        0.043533
+     18 H6           6.2680     9.0820    17.4510 H          2 B2        0.043533
+     19 H7           4.4410     8.7290    16.0550 H          2 B2        0.043533
+     20 H8           5.3280     7.5670    15.0510 H          2 B2        0.043533
+     21 H9           7.0570     4.8080    17.6050 H          2 B2        0.043533
+     22 H10          7.3010     5.7300    16.1180 H          2 B2        0.043533
+     23 H11          5.1570     5.0270    15.5510 H          2 B2        0.043533
+     24 H12          4.7780     4.5530    17.2130 H          2 B2        0.043533
+     25 H13          8.1310     7.9890    19.1820 H          2 B2        0.046200
+     26 H14          8.4620     6.2320    18.9460 H          2 B2        0.046200
+     27 H15          8.8150     8.1730    16.8730 H          2 B2        0.397000
+     28 H16          3.0220     6.0520    15.1410 H          2 B2        0.046200
+     29 H17          2.3460     5.7640    16.7880 H          2 B2        0.046200
+     30 H18          2.7500     8.3790    15.7000 H          2 B2        0.397000
+@<TRIPOS>BOND
+     1     1     2 1   
+     2     1     4 1   
+     3     1    13 1   
+     4     1    14 1   
+     5     2     3 1   
+     6     2    15 1   
+     7     2    16 1   
+     8     3     6 1   
+     9     3     8 1   
+    10     3    11 1   
+    11     4     5 1   
+    12     4     7 1   
+    13     4     9 1   
+    14     5     6 1   
+    15     5    17 1   
+    16     5    18 1   
+    17     6    19 1   
+    18     6    20 1   
+    19     7     8 1   
+    20     7    21 1   
+    21     7    22 1   
+    22     8    23 1   
+    23     8    24 1   
+    24     9    10 1   
+    25     9    25 1   
+    26     9    26 1   
+    27    10    27 1   
+    28    11    12 1   
+    29    11    28 1   
+    30    11    29 1   
+    31    12    30 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 B2          1 TEMP              0 ****  ****    0 ROOT