1 #!/bin/env python 2 # 3 # File: PyMOLExtractSelection.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 ExtractSelection() 79 80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName) 81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime)) 82 83 def ExtractSelection(): 84 """Extract selection from input file and write it out.""" 85 86 MiscUtil.PrintInfo("\nGenerating output files...") 87 88 # Load macromolecule from input file... 89 MolName = OptionsInfo["InfileRoot"] 90 pymol.cmd.load(OptionsInfo["Infile"], MolName) 91 92 # Extract and write selection... 93 ExtractAndWriteSelection(MolName) 94 95 # Delete macromolecule... 96 pymol.cmd.delete(MolName) 97 98 def ExtractAndWriteSelection(MolName): 99 """Extract selection from an input file and write it out.""" 100 101 Outfile = OptionsInfo["Outfile"] 102 MiscUtil.PrintInfo("\nGenerating output file %s..." % Outfile) 103 104 # Setup selection... 105 if OptionsInfo["SelectionAppend"]: 106 MolSelection = "(%s and (%s))" % (MolName, OptionsInfo["Selection"]) 107 else: 108 MolSelection = "(%s)" % (OptionsInfo["Selection"]) 109 110 MolSelectionName = OptionsInfo["SelectionName"] 111 112 # Create selection object and write it out... 113 MiscUtil.PrintInfo("Extracting selection: %s" % MolSelection) 114 115 pymol.cmd.create(MolSelectionName, MolSelection) 116 pymol.cmd.save(Outfile, MolSelectionName) 117 pymol.cmd.delete(MolSelectionName) 118 119 if not os.path.exists(Outfile): 120 MiscUtil.PrintWarning("Failed to generate output file, %s..." % (Outfile)) 121 122 def ProcessOptions(): 123 """Process and validate command line arguments and options.""" 124 125 MiscUtil.PrintInfo("Processing options...") 126 127 # Validate options... 128 ValidateOptions() 129 130 OptionsInfo["Infile"] = Options["--infile"] 131 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Infile"]) 132 OptionsInfo["InfileRoot"] = FileName 133 134 OptionsInfo["Outfile"] = Options["--outfile"] 135 136 OptionsInfo["Selection"] = Options["--selection"] 137 OptionsInfo["SelectionName"] = "%s_Selection" % OptionsInfo["InfileRoot"] 138 139 OptionsInfo["SelectionAppend"] = True if re.match("^Yes$", Options["--selectionAppend"], re.I) else False 140 141 OptionsInfo["Overwrite"] = Options["--overwrite"] 142 143 def RetrieveOptions(): 144 """Retrieve command line arguments and options.""" 145 146 # Get options... 147 global Options 148 Options = docopt(_docoptUsage_) 149 150 # Set current working directory to the specified directory... 151 WorkingDir = Options["--workingdir"] 152 if WorkingDir: 153 os.chdir(WorkingDir) 154 155 # Handle examples option... 156 if "--examples" in Options and Options["--examples"]: 157 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_)) 158 sys.exit(0) 159 160 def ValidateOptions(): 161 """Validate option values.""" 162 163 MiscUtil.ValidateOptionFilePath("-i, --infile", Options["--infile"]) 164 MiscUtil.ValidateOptionFileExt("-i, --infile", Options["--infile"], "pdb cif") 165 166 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pdb cif") 167 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"]) 168 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infile", Options["--infile"], "-o, --outfile", Options["--outfile"]) 169 170 MiscUtil.ValidateOptionTextValue("--selectionAppend", Options["--selectionAppend"], "yes no") 171 172 # Setup a usage string for docopt... 173 _docoptUsage_ = """ 174 PyMOLExtractSelection.py - Extract selection from a macromolecule 175 176 Usage: 177 PyMOLExtractSelection.py [--overwrite] [--selectionAppend <yes or no>] 178 [-w <dir>] -i <infile> -o <outfile> -s <selection> 179 PyMOLExtractSelection.py -h | --help | -e | --examples 180 181 Description: 182 Extract data corresponding to a PyMOL selection specification from a 183 macromolecule in an input file and write it out to an output file. 184 185 The selection specification must be a valid PyMOL specification. No 186 validation is performed. 187 188 The supported input file format are: PDB (.pdb) and CIF (.cif) 189 190 The supported output file formats are: PDB (.pdb) and CIF (.cif) 191 192 Options: 193 -e, --examples 194 Print examples. 195 -h, --help 196 Print this help message. 197 -i, --infile <infile> 198 Input file name. 199 -o, --outfile <infile> 200 Output file name. 201 -s, --selection <PyMOL SelectionSpec> 202 Selection specification for extracting data from a macromolecule in an 203 input file. The selection specification must be a valid PyMOL specification. 204 No Validation is performed. 205 206 The specified selection specification is optionally appended to PyMOL 207 object name for input file. 208 --selectionAppend <yes or no> [default: yes] 209 Append specified selection specification to PyMOL object name for input 210 file before creating PyMOL object for a specified selection specification. 211 The PyMOL object name for input file is <InfileRoot>. 212 213 You may choose to explicitly specify PyMOL object name in the selection 214 specification instead of automatically appending it to the selection. 215 --overwrite 216 Overwrite existing files. 217 -w, --workingdir <dir> 218 Location of working directory which defaults to the current directory. 219 220 Examples: 221 To extract all data corresponding to chain E in a macromolecule and write 222 out to a PDB file, type: 223 224 % PyMOLExtractSelection.py -i Sample3.cif -o Sample3Out.pdb -s "chain E" --ov 225 226 To extract only polymer chain data for chains E and I in a macromolecule and 227 write out to a PDB file, type: 228 229 % PyMOLExtractSelection.py -i Sample3.cif -o Sample3Out.pdb 230 -s "((chain E) or (chain I)) and polymer" --ov 231 232 To extract only polymer chain data for chain E in a macromolecule and write 233 out to a PDB file, type: 234 235 % PyMOLExtractSelection.py -i Sample3.pdb -o Sample3Out.pdb 236 -s "(chain E) and polymer" --ov 237 238 To extract only polymer chain data for chain E in a macromolecule by explicitly 239 ignoring non-polymer chain data and write out to a CIF file, type: 240 241 % PyMOLExtractSelection.py -i Sample3.pdb -o Sample3Out.cif 242 -s "(chain E) and (not organic) and (not solvent) and 243 (not inorganic)" --ov 244 245 To extract solvent data corresponding to chain E in a macromolecule and write 246 out to a PDB file, type: 247 248 % PyMOLExtractSelection.py -i Sample3.pdb -o Sample3Out.pdb 249 -s "(chain E) and solvent" --ov 250 251 To extract ligand data corresponding to chain E in a macromolecule and write 252 out to a PDB file, type: 253 254 % PyMOLExtractSelection.py -i Sample3.pdb -o Sample3Out.pdb 255 -s "(chain E) and organic" --ov 256 257 To extract binding pocket residues with 5.0 of ligand ID ADP in chain E and write 258 out a PDB file, type: 259 260 % PyMOLExtractSelection.py -i Sample3.pdb -o Sample3Out.pdb 261 --selectionAppend no -s "(byresidue (Sample3 and chain E) 262 within 5.0 of (Sample3 and chain E and organic and resn ADP)) 263 and polymer" --ov 264 265 Author: 266 Manish Sud(msud@san.rr.com) 267 268 See also: 269 PyMOLAlignChains.py, PyMOLSplitChainsAndLigands.py, 270 PyMOLVisualizeMacromolecules.py 271 272 Copyright: 273 Copyright (C) 2024 Manish Sud. All rights reserved. 274 275 The functionality available in this script is implemented using PyMOL, a 276 molecular visualization system on an open source foundation originally 277 developed by Warren DeLano. 278 279 This file is part of MayaChemTools. 280 281 MayaChemTools is free software; you can redistribute it and/or modify it under 282 the terms of the GNU Lesser General Public License as published by the Free 283 Software Foundation; either version 3 of the License, or (at your option) any 284 later version. 285 286 """ 287 288 if __name__ == "__main__": 289 main()
