1 #!/bin/env python
   2 #
   3 # File: PyMOLConvertPMLToPSE.py
   4 # Author: Manish Sud <msud@san.rr.com>
   5 #
   6 # Copyright (C) 2026 Manish Sud. All rights reserved.
   7 #
   8 # The functionality available in this script is implemented using PyMOL, a
   9 # molecular visualization system on an open source foundation originally
  10 # developed by Warren DeLano.
  11 #
  12 # This file is part of MayaChemTools.
  13 #
  14 # MayaChemTools is free software; you can redistribute it and/or modify it under
  15 # the terms of the GNU Lesser General Public License as published by the Free
  16 # Software Foundation; either version 3 of the License, or (at your option) any
  17 # later version.
  18 #
  19 # MayaChemTools is distributed in the hope that it will be useful, but without
  20 # any warranty; without even the implied warranty of merchantability of fitness
  21 # for a particular purpose.  See the GNU Lesser General Public License for more
  22 # details.
  23 #
  24 # You should have received a copy of the GNU Lesser General Public License
  25 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
  26 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
  27 # Boston, MA, 02111-1307, USA.
  28 #
  29 
  30 from __future__ import print_function
  31 
  32 import os
  33 import sys
  34 import time
  35 import re
  36 
  37 # PyMOL imports...
  38 try:
  39     import pymol
  40 
  41     # Finish launching PyMOL in  a command line mode for batch processing (-c)
  42     # along with the following options:  disable loading of pymolrc and plugins (-k);
  43     # suppress start up messages (-q)
  44     pymol.finish_launching(["pymol", "-ckq"])
  45 except ImportError as ErrMsg:
  46     sys.stderr.write("\nFailed to import PyMOL module/package: %s\n" % ErrMsg)
  47     sys.stderr.write("Check/update your PyMOL environment and try again.\n\n")
  48     sys.exit(1)
  49 
  50 # MayaChemTools imports...
  51 sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "..", "lib", "Python"))
  52 try:
  53     from docopt import docopt
  54     import MiscUtil
  55     import PyMOLUtil
  56 except ImportError as ErrMsg:
  57     sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg)
  58     sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n")
  59     sys.exit(1)
  60 
  61 ScriptName = os.path.basename(sys.argv[0])
  62 Options = {}
  63 OptionsInfo = {}
  64 
  65 
  66 def main():
  67     """Start execution of the script."""
  68 
  69     MiscUtil.PrintInfo(
  70         "\n%s (PyMOL v%s; MayaChemTools v%s; %s): Starting...\n"
  71         % (ScriptName, pymol.cmd.get_version()[0], MiscUtil.GetMayaChemToolsVersion(), time.asctime())
  72     )
  73 
  74     (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
  75 
  76     # Retrieve command line arguments and options...
  77     RetrieveOptions()
  78 
  79     # Process and validate command line arguments and options...
  80     ProcessOptions()
  81 
  82     # Perform actions required by the script...
  83     GeneratePSEFile()
  84 
  85     MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
  86     MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
  87 
  88 
  89 def GeneratePSEFile():
  90     """Comvert PML file to PSE file."""
  91 
  92     PMLFile = OptionsInfo["Infile"]
  93     PSEFile = OptionsInfo["Outfile"]
  94 
  95     MiscUtil.PrintInfo("\nGenerating file %s..." % PSEFile)
  96 
  97     PyMOLUtil.ConvertPMLFileToPSEFile(PMLFile, PSEFile, OutputFeedback=OptionsInfo["Feedback"])
  98 
  99     if not os.path.exists(PSEFile):
 100         MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEFile))
 101 
 102 
 103 def ProcessOptions():
 104     """Process and validate command line arguments and options."""
 105 
 106     MiscUtil.PrintInfo("Processing options...")
 107 
 108     # Validate options...
 109     ValidateOptions()
 110 
 111     OptionsInfo["Feedback"] = True if re.match("^Yes$", Options["--feedback"], re.I) else False
 112 
 113     OptionsInfo["Infile"] = Options["--infile"]
 114     OptionsInfo["Outfile"] = Options["--outfile"]
 115 
 116 
 117 def RetrieveOptions():
 118     """Retrieve command line arguments and options."""
 119 
 120     # Get options...
 121     global Options
 122     Options = docopt(_docoptUsage_)
 123 
 124     # Set current working directory to the specified directory...
 125     WorkingDir = Options["--workingdir"]
 126     if WorkingDir:
 127         os.chdir(WorkingDir)
 128 
 129     # Handle examples option...
 130     if "--examples" in Options and Options["--examples"]:
 131         MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
 132         sys.exit(0)
 133 
 134 
 135 def ValidateOptions():
 136     """Validate option values."""
 137 
 138     MiscUtil.ValidateOptionTextValue("-f, --feedback", Options["--feedback"], "yes no")
 139 
 140     MiscUtil.ValidateOptionFilePath("-i, --infile", Options["--infile"])
 141     MiscUtil.ValidateOptionFileExt("-i, --infile", Options["--infile"], "pml")
 142 
 143     MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pse")
 144     MiscUtil.ValidateOptionsOutputFileOverwrite(
 145         "-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"]
 146     )
 147     MiscUtil.ValidateOptionsDistinctFileNames(
 148         "-i, --infile", Options["--infile"], "-o, --outfile", Options["--outfile"]
 149     )
 150 
 151 
 152 # Setup a usage string for docopt...
 153 _docoptUsage_ = """
 154 PyMOLConvertPMLToPSE.py - Convert PML to PSE
 155 
 156 Usage:
 157     PyMOLConvertPMLToPSE.py [--feedback <yes or no>] [--overwrite]
 158                             [-w <dir>] -i <infile> -o <outfile>
 159     PyMOLConvertPMLToPSE.py -h | --help | -e | --examples
 160 
 161 Description:
 162     Convert PyMOL script language (PML) file to PyMOL session (PSE) file.
 163 
 164     The supported input and output file formats are PML (.pml) and PSE (.pse).
 165 
 166 Options:
 167     -f, --feedback <yes or no>  [default: yes]
 168         PyMOL output feedback during loading of PML file. This option may not
 169         work in all versions of PyMOL across various platforms.
 170     -e, --examples
 171         Print examples.
 172     -h, --help
 173         Print this help message.
 174     -i, --infile <infile>
 175         Input file name.
 176     -o, --outfile <outfile>
 177         Output file name.
 178     --overwrite
 179         Overwrite existing files.
 180     -w, --workingdir <dir>
 181         Location of working directory which defaults to the current directory.
 182 
 183 Examples:
 184     To convert a PML file to a PSE file, type:
 185 
 186         % PyMOLConvertPMLToPSE.py -i Sample.pml -o Sample.pse
 187 
 188     To convert a PML file to a PSE file along with turning off PyMOL feedback
 189     during loading of PML file, type:
 190 
 191         % PyMOLConvertPMLToPSE.py -f no -i Sample.pml -o Sample.pse
 192 
 193 Author:
 194     Manish Sud(msud@san.rr.com)
 195 
 196 See also:
 197     PyMOLConvertLigandFileFormat.py, PyMOLSplitChainsAndLigands.py,
 198     PyMOLVisualizeMacromolecules.py
 199 
 200 Copyright:
 201     Copyright (C) 2026 Manish Sud. All rights reserved.
 202 
 203     The functionality available in this script is implemented using PyMOL, a
 204     molecular visualization system on an open source foundation originally
 205     developed by Warren DeLano.
 206 
 207     This file is part of MayaChemTools.
 208 
 209     MayaChemTools is free software; you can redistribute it and/or modify it under
 210     the terms of the GNU Lesser General Public License as published by the Free
 211     Software Foundation; either version 3 of the License, or (at your option) any
 212     later version.
 213 
 214 """
 215 
 216 if __name__ == "__main__":
 217     main()