1 #!/bin/env python 2 # 3 # File: PyMOLConvertLigandFileFormat.py 4 # Author: Manish Sud <msud@san.rr.com> 5 # 6 # Copyright (C) 2024 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 # Add local python path to the global path and import standard library modules... 33 import os 34 import sys; sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "..", "lib", "Python")) 35 import time 36 import re 37 38 # PyMOL imports... 39 try: 40 import pymol 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 try: 52 from docopt import docopt 53 import MiscUtil 54 import PyMOLUtil 55 except ImportError as ErrMsg: 56 sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg) 57 sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n") 58 sys.exit(1) 59 60 ScriptName = os.path.basename(sys.argv[0]) 61 Options = {} 62 OptionsInfo = {} 63 64 def main(): 65 """Start execution of the script.""" 66 67 MiscUtil.PrintInfo("\n%s (PyMOL v%s; MayaChemTools v%s; %s): Starting...\n" % (ScriptName, pymol.cmd.get_version()[0], MiscUtil.GetMayaChemToolsVersion(), time.asctime())) 68 69 (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime() 70 71 # Retrieve command line arguments and options... 72 RetrieveOptions() 73 74 # Process and validate command line arguments and options... 75 ProcessOptions() 76 77 # Perform actions required by the script... 78 ConvertLigandFileFormat() 79 80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName) 81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime)) 82 83 def ConvertLigandFileFormat(): 84 """Comvert ligand file format.""" 85 86 Infile = OptionsInfo["Infile"] 87 Outfile = OptionsInfo["Outfile"] 88 89 MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile) 90 91 PyMOLUtil.ConvertFileFormat(Infile, Outfile) 92 93 if not os.path.exists(Outfile): 94 MiscUtil.PrintWarning("Failed to generate Outfile file, %s..." % (Outfile)) 95 96 def ProcessOptions(): 97 """Process and validate command line arguments and options.""" 98 99 MiscUtil.PrintInfo("Processing options...") 100 101 # Validate options... 102 ValidateOptions() 103 104 OptionsInfo["Infile"] = Options["--infile"] 105 OptionsInfo["Outfile"] = Options["--outfile"] 106 107 def RetrieveOptions(): 108 """Retrieve command line arguments and options.""" 109 110 # Get options... 111 global Options 112 Options = docopt(_docoptUsage_) 113 114 # Set current working directory to the specified directory... 115 WorkingDir = Options["--workingdir"] 116 if WorkingDir: 117 os.chdir(WorkingDir) 118 119 # Handle examples option... 120 if "--examples" in Options and Options["--examples"]: 121 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_)) 122 sys.exit(0) 123 124 def ValidateOptions(): 125 """Validate option values.""" 126 127 MiscUtil.ValidateOptionFilePath("-i, --infile", Options["--infile"]) 128 MiscUtil.ValidateOptionFileExt("-i, --infile", Options["--infile"], "mol mol2 pdb") 129 130 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "mol mol2 pdb") 131 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"]) 132 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infile", Options["--infile"], "-o, --outfile", Options["--outfile"]) 133 134 # Setup a usage string for docopt... 135 _docoptUsage_ = """ 136 PyMOLConvertLigandFileFormat.py.py - Convert between ligand file formats 137 138 Usage: 139 PyMOLConvertLigandFileFormat.py.py [--overwrite] 140 [-w <dir>] -i <infile> -o <outfile> 141 PyMOLConvertLigandFileFormat.py.py -h | --help | -e | --examples 142 143 Description: 144 Convert between ligand file formats. 145 146 The supported input and output file formats are: MDLMOL (.mol), MOL2 (.mol2), 147 and PDB (.pdb). 148 149 Options: 150 -e, --examples 151 Print examples. 152 -h, --help 153 Print this help message. 154 -i, --infile <infile> 155 Input file name. 156 -o, --outfile <outfile> 157 Output file name. 158 --overwrite 159 Overwrite existing files. 160 -w, --workingdir <dir> 161 Location of working directory which defaults to the current directory. 162 163 Examples: 164 To convert MDLMOL file format to MOL2 file format, type: 165 166 % PyMOLConvertLigandFileFormat.py -i caffeine.mol -o caffeine.mol2 167 168 To convert MDLMOL file format to PDB file format, type: 169 170 % PyMOLConvertLigandFileFormat.py -i caffeine.mol -o caffeine.pdb 171 172 Author: 173 Manish Sud(msud@san.rr.com) 174 175 See also: 176 PyMOLConvertPMLToPSE.py, PyMOLSplitChainsAndLigands.py, 177 PyMOLVisualizeMacromolecules.py 178 179 Copyright: 180 Copyright (C) 2024 Manish Sud. All rights reserved. 181 182 The functionality available in this script is implemented using PyMOL, a 183 molecular visualization system on an open source foundation originally 184 developed by Warren DeLano. 185 186 This file is part of MayaChemTools. 187 188 MayaChemTools is free software; you can redistribute it and/or modify it under 189 the terms of the GNU Lesser General Public License as published by the Free 190 Software Foundation; either version 3 of the License, or (at your option) any 191 later version. 192 193 """ 194 195 if __name__ == "__main__": 196 main()
