# lrcd-vmd.tcl (Jun 17, 2020)
Tcl scripts and utilities for calculating the LRCD parameter

Repository started from personal libraries (lrcd.tcl, version 1.0.5) and
refering to the published work in Journal of Molecular Recognition (2019).

Below the original readme.

# reference: Gómez-Castro CZ, López-Martínez M, Hernández-Pineda J,
#            Trujillo-Ferrara JG, Padilla-Martínez II. Profiling the
#            interaction of 1-phenylbenzimidazoles to cyclooxygenases.
#            J Mol Recognit. 2019; 32:e2801. https://doi.org/10.1002/jmr.2801
#
# lrcd.tcl v-1.0.8:
#
# Tcl script for VMD to calculate the Ligand-Receptor Contact Distance (LRCD)
# parameter that compares the interaction profile of two complexes involving
# small molecules as the ligands and macromolecules as the receptors.
#
# Several variants of the LRCD parameter are implemented:
#  LRCD   - Ligand-Receptor Contact Distance.
#  LRCND  - Ligand-Receptor Contact Normalized Distance.
#  LRCDI  - Ligand-Receptor Contact Distance Index [= 1/(1 + LRCND)].
#  LRCMD  - Ligand-Receptor Contact Manhattan Distance.
#  LRCMDI - Ligand-Receptor Contact Manhattan Distance Index [= 1/(1 + LRCMD)].
#  LRCP   - Ligand-Receptor Contact Projection.
#
# This script should be sourced within the program VMD either in the TkConsole,
# in the VMD's command line or from a .vmdrc file:
#
# i.e.
# # from the VMD's TkConsole:
# source lrcd.tcl
# # from the command line:
# vmd -e lrcd.tcl
#
# Instructions:
#
#   -This library was created to be used within the TkConsole of VMD, with
#    the molecules forming ligand-receptor complexes already loaded. The
#    ligand and receptor moieties of a complex may either be part of the
#    same molecule or come from different molecules, i.e., they may be
#    provided as separated files.
#
#   -This library requires prior definition by the user of the atom selections
#    specifying at least two complexes (A and B), each involving a ligand
#    (ligA and ligB) and a receptor (recA and recB) moieties. Each of this
#    four atom selections have to specify also the Id assigned by VMD when the
#    molecule containing the atom selections was loaded.
#
#   -The atom selections and Ids are stored in a Tcl array called selInfo.
#    The array keys follow the format: selInfo(<UserLabel>,<Keyword>).
#    The user specifies a label to identify a complex (<UserLabel>) and,
#    separated by a comma, one of the following keywords: 'ligId', 'ligSelTxt',
#    'recId', 'recSelTxt', and 'title'. Some examples below:
#      set selInfo(MyComplex,ligId) 0
#      set selInfo(MyComplex,ligSelTxt) "noh"
#      set selInfo(MyComplex,recId) 1
#      set selInfo(MyComplex,recSelTxt) "protein and chain A and noh"
#      set selInfo(MyComplex,title) "First lig-rec complex declared"
#
#   -Note that the ligId and recId correspond to the Ids in VMD of already
#    loaded molecules. ligSelTxt and recSelTxt are text (enclosed by "")
#    in VMD's atom selection language. See Selection Methods in the VMD
#    user's guide.
#
#   -Once declared two or more complexes in the selInfo array, the procedures
#    lrcdMat_dct, lrcdMat_cmd, and lrcdMat_lapa may be used in sequence to
#    calculate the lrcd matrix that stores lig-rec interaction measurements.
#    Then the lrcdVec_sum procedure is used to calculate the lrcd vectors
#    for each complex with sums over each interaction type. Finally, the
#    lrcd procedure uses two lrcd vectors to calculate the LRCD parameter.
#    See lrcd_test1 procedure below for an example on these steps.
#
#   -Alternatively, the procedures lrcd_pwMat and lrcd_dlgTab perform the
#    whole sequence of steps to calculate the LRCD parameter for several
#    complexes. These procedures also show the usage of lower-level procedures.
#    The lrcd_pwMat procedure calculate all pairs in a set of complexes
#    declared in the selInfo array, and specified by a list of <UserLabel>
#    identifiers. See lrcd_test2 below for an usage example. The lrcd_dlgTab
#    procedure calculate the LRCD parameter for all the complexes in a .dlg
#    file obtained from an AutoDock (version 3 or 4) molecular docking
#    calculation. In this case, the .dlg file is loaded into VMD specifying
#    PDB format. The best binding poses from the cluster analysis performed
#    by AutoDock are loaded as frames in a single molecule. Thus, the
#    procedure runs over these frames and calculate the LRCD against a
#    common reference complex. Obviously, all poses consider the same receptor.
#    See lrcd_test3 procedure below for an usage example. Several .dlg files
#    may be processed with the proper set up of the selInfo array.
#
#   -Note that the lrcd_dlgTab does not actually use any information from the
#    .dlg file, but rather only the poses of a ligand taken from a .dlg file
#    are loaded into VMD as a PDB file with several frames. Thus, the procedure
#    is independent from the docking program used to generate the complexes 
#    whenever the resulting poses may be loaded into VMD in a single molecule.
#
#   -The procedures lrcd_test* provide examples of different ways of performing
#    the LRCD calculation:
#      -lrcd_test1: performs the whole calculation for a single
#       pair of complexes taken from two PDB structures.
#      -lrcd_test2: calculates a pairwise matrix of LRCD for a set of 16
#       COX-1/2 - ligand complexes, downloading the files
#       from the repository using the internet.
#      -lrcd_test3: calculate the LRCD for the best binding poses obtained
#       from a .dlg AutoDock molecular docking calculation taken the lowest-
#       energy pose as reference for the rest.
#      -lrcd_test4: calculate the LRCD for a list of complexes or a list
#       of docking poses (.dlg file) taking as reference LRC vectors
#       pre-calculated for a set of PDB complexes (as a data base).
#
#   -In order to run the test procedures it may be neccessary to change to
#    the directory containing the lrcd.tcl script and the subdirectories
#    test1, ..., test4 with the 'cd' command in the TkConsole of VMD.
#