1 #!/bin/env python
2 #
3 # File: PyMOLInfoMacromolecules.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 ListInfo()
79
80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
82
83 def ListInfo():
84 """List information for macromolecules."""
85
86 for Infile in OptionsInfo["InfilesNames"]:
87 MiscUtil.PrintInfo("\nProcessing file %s..." % Infile)
88 ListFileInfo(Infile)
89
90 def ListFileInfo(Infile):
91 """List information for macromolecules in a file."""
92
93 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
94 MolName = FileName
95
96 # Load infile...
97 pymol.cmd.load(Infile, MolName)
98
99 ChainIDs = PyMOLUtil.GetChains(MolName)
100 ListHeaderInfo(Infile)
101
102 ListChainsInfo(MolName, ChainIDs)
103 ListChainsResiduesInfo(MolName, ChainIDs)
104
105 ListLigandsInfo(MolName, ChainIDs)
106 ListSolventsInfo(MolName, ChainIDs)
107 ListInorganicsInfo(MolName, ChainIDs)
108
109 ListPocketsInfo(MolName, ChainIDs)
110
111 ListInterfaceResiduesInfo(MolName, ChainIDs)
112 ListSurfaceResiduesInfo(MolName, ChainIDs)
113 ListPhiPsiAnglesInfo(MolName, ChainIDs)
114
115 ListBoundingBoxInfo(MolName)
116 ListCentroid(MolName)
117
118 # Delete infile object...
119 pymol.cmd.delete(MolName)
120
121 ListFileSizeAndModificationInfo(Infile)
122
123 def ListHeaderInfo(Infile):
124 """List header information."""
125
126 if not (OptionsInfo["All"] or OptionsInfo["Header"]):
127 return
128
129 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
130
131 Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = ["Not Available"] * 5
132 if re.match("^pdb$", FileExt, re.I):
133 Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = RetriveHeadAndExperimentalInfoFromPDBFile(Infile)
134 elif re.match("^cif$", FileExt, re.I):
135 Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = RetriveHeadAndExperimentalInfoFromCIFFile(Infile)
136
137 MiscUtil.PrintInfo("\nID: %s\nClassification: %s\nDeposition date: %s" % (IDCode, Classification, DepositionDate))
138 MiscUtil.PrintInfo("\nExperimental technique: %s\nResolution: %s" % (ExperimentalTechnique, Resolution))
139
140 def RetriveHeadAndExperimentalInfoFromPDBFile(Infile):
141 """Retrieve header and experimental information from PDB file."""
142
143 Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = ["Not Available"] * 5
144
145 Lines = MiscUtil.GetTextLines(Infile)
146
147 # Retrieve header info...
148 for Line in Lines:
149 if re.match("^HEADER", Line, re.I):
150 # Format: 10x40s9s3x4s
151 FormatSize = 66
152 Line = PrepareLineForFormatSize(Line, FormatSize)
153
154 Classification = Line[10:50]
155 DepositionDate = Line[50:59]
156 IDCode = Line[62:66]
157
158 Classification = Classification.strip() if len(Classification.strip()) else "Not Available"
159 DepositionDate = DepositionDate.strip() if len(DepositionDate.strip()) else "Not Available"
160 IDCode = IDCode.strip() if len(IDCode.strip()) else "Not Available"
161
162 break
163
164 # Retrieve experimental info...
165 for Line in Lines:
166 if re.match("^EXPDTA", Line, re.I):
167 ExperimentalTechnique = re.sub("^EXPDTA", "", Line, re.I)
168 ExperimentalTechnique = ExperimentalTechnique.strip()
169 elif re.match("^REMARK 2 RESOLUTION.", Line, re.I):
170 if re.search("NOT APPLICABLE", Line, re.I):
171 Resolution = "NOT APPLICABLE"
172 else:
173 FormatSize = 70
174 Line = PrepareLineForFormatSize(Line, FormatSize)
175 Resolution = Line[22:70]
176 Resolution = Resolution.strip() if len(Resolution.strip()) else "Not Available"
177 elif re.match("^(ATOM|HETATM)", Line, re.I):
178 break
179
180 return Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution
181
182 def RetriveHeadAndExperimentalInfoFromCIFFile(Infile):
183 """Retrieve header information from CIF file."""
184
185 Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution = ["Not Available"] * 5
186
187 Lines = MiscUtil.GetTextLines(Infile)
188
189 # IDCode...
190 for Line in Lines:
191 if re.match("^_struct_keywords.entry_id", Line, re.I):
192 IDCode = re.sub("^_struct_keywords.entry_id", "", Line, re.I)
193 IDCode = IDCode.strip() if len(IDCode.strip()) else "Not Available"
194 break
195
196 # Classification...
197 for Line in Lines:
198 if re.match("^_struct_keywords.pdbx_keywords", Line, re.I):
199 Classification = re.sub("^_struct_keywords.pdbx_keywords", "", Line, re.I)
200 Classification = Classification.strip() if len(Classification.strip()) else "Not Available"
201 break
202
203 # Deposition date...
204 for Line in Lines:
205 if re.match("^_pdbx_database_status.recvd_initial_deposition_date", Line, re.I):
206 DepositionDate = re.sub("^_pdbx_database_status.recvd_initial_deposition_date", "", Line, re.I)
207 DepositionDate = DepositionDate.strip() if len(DepositionDate.strip()) else "Not Available"
208 break
209
210 # Experimental technique...
211 for Line in Lines:
212 if re.match("^_exptl.method", Line, re.I):
213 ExperimentalTechnique = re.sub("(_exptl.method|')", "", Line, flags = re.I)
214 ExperimentalTechnique = ExperimentalTechnique.strip() if len(ExperimentalTechnique.strip()) else "Not Available"
215 break
216
217 # Resolution...
218 for Line in Lines:
219 if re.match("^_reflns.d_resolution_high", Line, re.I):
220 Resolution = re.sub("^_reflns.d_resolution_high", "", Line, re.I)
221 Resolution = Resolution.strip() if len(Resolution.strip()) else "Not Available"
222 break
223
224 return Classification, DepositionDate, IDCode, ExperimentalTechnique, Resolution
225
226 def PrepareLineForFormatSize(Text, FormatSize):
227 """Prepare text string for format size padding or truncation to
228 alter its size.
229 """
230
231 TextLen = len(Text)
232 if TextLen < FormatSize:
233 PaddingLen = FormatSize - TextLen
234 TextPadding = " " * PaddingLen
235 Text = Text + TextPadding
236 elif TextLen > FormatSize:
237 Text = Text[:FormatSize]
238
239 return Text
240
241 def ListChainsInfo(MolName, ChainIDs):
242 """List chains information across all chains."""
243
244 if not (OptionsInfo["All"] or OptionsInfo["Chains"]):
245 return
246
247 ChainsInfo = ", ".join(ChainIDs) if len(ChainIDs) else "None"
248
249 MiscUtil.PrintInfo("\nNumber of chains: %s" % len(ChainIDs))
250 MiscUtil.PrintInfo("ChainIDs: %s" % ChainsInfo)
251
252 def ListChainsResiduesInfo(MolName, ChainIDs):
253 """List polymer chain residue information across all chains."""
254
255 if not (OptionsInfo["All"] or OptionsInfo["CountResidues"]):
256 return
257
258 ListSelectionResiduesInfo(MolName, ChainIDs, "Chains")
259
260 # List information for non-standard amino acids...
261 ListSelectionResiduesInfo(MolName, ChainIDs, "NonStandardAminoAcids")
262
263 def ListLigandsInfo(MolName, ChainIDs):
264 """List ligand information across all chains."""
265
266 if not (OptionsInfo["All"] or OptionsInfo["Ligands"]):
267 return
268
269 ListSelectionResiduesInfo(MolName, ChainIDs, "Ligands")
270
271 def ListSolventsInfo(MolName, ChainIDs):
272 """List solvents information across all chains."""
273
274 if not (OptionsInfo["All"] or OptionsInfo["Solvents"]):
275 return
276
277 ListSelectionResiduesInfo(MolName, ChainIDs, "Solvents")
278
279 def ListInorganicsInfo(MolName, ChainIDs):
280 """List inorganics information across all chains."""
281
282 if not (OptionsInfo["All"] or OptionsInfo["Inorganics"]):
283 return
284
285 ListSelectionResiduesInfo(MolName, ChainIDs, "Inorganics")
286
287 def ListSelectionResiduesInfo(MolName, ChainIDs, SelectionType):
288 """List residues information for a specified selection type."""
289
290 Lines = []
291 TotalResCount = 0
292 SelectionLabel = None
293
294 if not len(ChainIDs):
295 SelectionInfo, SelectionLabel = GetSelectionResiduesInfo(MolName, None, SelectionType)
296 MiscUtil.PrintInfo("\nNumber of %s residues: %s" % (SelectionLabel, TotalResCount))
297 return
298
299 for ChainID in ChainIDs:
300 SelectionInfo, SelectionLabel = GetSelectionResiduesInfo(MolName, ChainID, SelectionType)
301
302 ChainResCount = 0
303 LineWords = []
304
305 SortedResNames = sorted(SelectionInfo["ResNames"], key = lambda ResName: SelectionInfo["ResCount"][ResName], reverse = True)
306 for ResName in SortedResNames:
307 ResCount = SelectionInfo["ResCount"][ResName]
308 LineWords.append("%s - %s" % (ResName, ResCount))
309
310 ChainResCount += ResCount
311 TotalResCount += ResCount
312
313 Line = "; ".join(LineWords) if len(LineWords) else None
314 Lines.append("Chain ID: %s; Count: %s; Names: %s" % (ChainID, ChainResCount, Line))
315
316 MiscUtil.PrintInfo("\nNumber of %s residues: %s" % (SelectionLabel, TotalResCount))
317 for Line in Lines:
318 MiscUtil.PrintInfo("%s" % Line)
319
320 def GetSelectionResiduesInfo(MolName, ChainID, SelectionType):
321 """Get residues info for a specified selection type."""
322
323 SelectionInfo = None
324 SelectionLabel = None
325
326 if re.match("^Ligands$", SelectionType, re.I):
327 SelectionLabel = "ligand"
328 SelectionInfo = PyMOLUtil.GetLigandResiduesInfo(MolName, ChainID) if ChainID is not None else None
329 elif re.match("^Solvents$", SelectionType, re.I):
330 SelectionLabel = "solvent"
331 SelectionInfo = PyMOLUtil.GetSolventResiduesInfo(MolName, ChainID) if ChainID is not None else None
332 elif re.match("^Inorganics$", SelectionType, re.I):
333 SelectionLabel = "inorganic"
334 SelectionInfo = PyMOLUtil.GetInorganicResiduesInfo(MolName, ChainID) if ChainID is not None else None
335 elif re.match("^Chains$", SelectionType, re.I):
336 SelectionLabel = "polymer chain"
337 SelectionInfo = PyMOLUtil.GetPolymerResiduesInfo(MolName, ChainID) if ChainID is not None else None
338 elif re.match("^NonStandardAminoAcids$", SelectionType, re.I):
339 SelectionLabel = "non-standard amino acids"
340 SelectionInfo = PyMOLUtil.GetAminoAcidResiduesInfo(MolName, ChainID, "NonStandard") if ChainID is not None else None
341 else:
342 MiscUtil.PrintError("Failed to retrieve residues information: Selection type %s is not valid..." % SelectionType)
343
344 return SelectionInfo, SelectionLabel
345
346 def ListPocketsInfo(MolName, ChainIDs):
347 """List pockect residues information across all chains."""
348
349 if not (OptionsInfo["All"] or OptionsInfo["PocketLigands"] or OptionsInfo["PocketSolvents"] or OptionsInfo["PocketInorganics"]) :
350 return
351
352 for ChainID in ChainIDs:
353 MiscUtil.PrintInfo("\nListing ligand pockets information for chain %s..." % (ChainID))
354
355 LigandsInfo = PyMOLUtil.GetLigandResiduesInfo(MolName, ChainID)
356 if not len(LigandsInfo["ResNames"]):
357 MiscUtil.PrintInfo("\nNumber of residues in ligand pocket: None")
358 MiscUtil.PrintInfo("Chain ID: %s; Ligands: None" % (ChainID))
359 continue
360
361 for LigandResName in sorted(LigandsInfo["ResNames"]):
362 for LigandResNum in LigandsInfo["ResNum"][LigandResName]:
363 ListPocketsPolymerInfo(MolName, ChainID, LigandResName, LigandResNum)
364 ListPocketsSolventsInfo(MolName, ChainID, LigandResName, LigandResNum)
365 ListPocketsInorganicsInfo(MolName, ChainID, LigandResName, LigandResNum)
366
367 def ListPocketsPolymerInfo(MolName, ChainID, LigandResName, LigandResNum):
368 """List pockect residues information across all chains."""
369
370 if not (OptionsInfo["All"] or OptionsInfo["PocketLigands"]):
371 return
372
373 ListPocketSelectionResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, "Pockets")
374
375 def ListPocketsSolventsInfo(MolName, ChainID, LigandResName, LigandResNum):
376 """List pockect solvent residues information across all chains."""
377
378 if not (OptionsInfo["All"] or OptionsInfo["PocketSolvents"]):
379 return
380
381 ListPocketSelectionResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, "PocketSolvents")
382
383 def ListPocketsInorganicsInfo(MolName, ChainID, LigandResName, LigandResNum):
384 """List pockect inorganic residues information across all chains."""
385
386 if not (OptionsInfo["All"] or OptionsInfo["PocketInorganics"]):
387 return
388
389 ListPocketSelectionResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, "PocketInorganics")
390
391 def ListPocketSelectionResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, SelectionType):
392 """List residues information for a specified pocket selection type."""
393
394 PocketDistanceCutoff = OptionsInfo["PocketDistanceCutoff"]
395 SelectionLabel = GetPocketSelectionResiduesInfoLabel(SelectionType)
396
397 SelectionInfo = GetPocketSelectionResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, PocketDistanceCutoff, SelectionType)
398
399 ResiduesCount, ResiduesDistribution, ResiduesIDs = SetupSelectionResiduesInfo(SelectionInfo)
400 MiscUtil.PrintInfo("\nNumber of %s residues in ligand pocket: %s" % (SelectionLabel, ResiduesCount))
401 MiscUtil.PrintInfo("Chain ID: %s; Ligand ID: %s_%s\nResidue distribution: %s\nResidue IDs: %s" % (ChainID, LigandResName, LigandResNum, ResiduesDistribution, ResiduesIDs))
402
403 def GetPocketSelectionResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, PocketDistanceCutoff, SelectionType):
404 """Get pocket residues info for a specified selection type."""
405
406 SelectionInfo = None
407
408 if re.match("^Pockets$", SelectionType, re.I):
409 SelectionInfo = PyMOLUtil.GetPocketPolymerResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, PocketDistanceCutoff)
410 elif re.match("^PocketSolvents$", SelectionType, re.I):
411 SelectionInfo = PyMOLUtil.GetPocketSolventResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, PocketDistanceCutoff)
412 elif re.match("^PocketInorganics$", SelectionType, re.I):
413 SelectionInfo = PyMOLUtil.GetPocketInorganicResiduesInfo(MolName, ChainID, LigandResName, LigandResNum, PocketDistanceCutoff)
414 else:
415 MiscUtil.PrintError("Failed to retrieve pocket residues information: Selection type %s is not valid..." % SelectionType)
416
417 return SelectionInfo
418
419 def ListSurfaceResiduesInfo(MolName, ChainIDs):
420 """List surface and buried residues for polymer chains with in a molecule."""
421
422 if not (OptionsInfo["All"] or OptionsInfo["SurfaceResidues"]):
423 return
424
425 MiscUtil.PrintInfo("\nListing surface and buried residues information...")
426 if not len(ChainIDs):
427 MiscUtil.PrintInfo("\nNumber of surface residues: None\nNumber of buried residues: None")
428 return
429
430 TotalSurfaceResidues, TotalBuriedResidues = [0] * 2
431
432 for ChainID in ChainIDs:
433 SurfaceResiduesSelectionInfo, BuriedResiduesSelectionInfo = PyMOLUtil.GetSurfaceAndBuriedResiduesInfo(MolName, ChainID, OptionsInfo["SurfaceResiduesCutoff"])
434
435 SurfaceResiduesCount, SurfaceResiduesDistribution, SurfaceResiduesIDs = SetupSelectionResiduesInfo(SurfaceResiduesSelectionInfo)
436 BuriedResiduesCount, BuriedResiduesDistribution, BuriedResiduesIDs = SetupSelectionResiduesInfo(BuriedResiduesSelectionInfo)
437
438 TotalSurfaceResidues += SurfaceResiduesCount
439 MiscUtil.PrintInfo("\nChainID: %s; Number of surface residues: %d" % (ChainID, SurfaceResiduesCount))
440 MiscUtil.PrintInfo("Residue distribution: %s" % (SurfaceResiduesDistribution))
441 if OptionsInfo["SurfaceResiduesIDs"]:
442 MiscUtil.PrintInfo("Residue IDs: %s" % (SurfaceResiduesIDs))
443
444 TotalBuriedResidues += BuriedResiduesCount
445 MiscUtil.PrintInfo("\nChainID: %s; Number of buried residues: %d" % (ChainID, BuriedResiduesCount))
446 MiscUtil.PrintInfo("Residue distribution: %s" % (BuriedResiduesDistribution))
447 if OptionsInfo["SurfaceResiduesIDs"]:
448 MiscUtil.PrintInfo("Residue IDs: %s" % (BuriedResiduesIDs))
449
450 MiscUtil.PrintInfo("\nTotal number of surface residues: %d\nTotal number of buried residues: %s" % (TotalSurfaceResidues, TotalBuriedResidues))
451
452 def ListPhiPsiAnglesInfo(MolName, ChainIDs):
453 """List phi and psi torsion angles for polymer chains with in a molecule."""
454
455 if not (OptionsInfo["All"] or OptionsInfo["PhiPsi"]):
456 return
457
458 MiscUtil.PrintInfo("\nListing phi and psi angles information...")
459
460 if not len(ChainIDs):
461 MiscUtil.PrintInfo("\nNumber of phi and psi angles: None\n")
462 return
463
464 for ChainID in ChainIDs:
465 if re.match("^Categories$", OptionsInfo["PhiPsiMode"], re.I):
466 # Retrieve phi and psi angles by categories used for Ramachandran plots
467 GeneralPhiPsiInfo, GlyPhiPsiInfo, ProPhiPsiInfo, PreProPhiPsiInfo = PyMOLUtil.GetPhiPsiCategoriesResiduesInfo(MolName, ChainID)
468
469 SetupAndListPhiPsiResiduesInfo(GeneralPhiPsiInfo, "General (All residues except glycine, proline, or pre-proline)", ChainID)
470 SetupAndListPhiPsiResiduesInfo(GlyPhiPsiInfo, "Glycine (Only glycine residues)", ChainID)
471 SetupAndListPhiPsiResiduesInfo(ProPhiPsiInfo, "Proline (Only proline residues)", ChainID)
472 SetupAndListPhiPsiResiduesInfo(PreProPhiPsiInfo, "Pre-Proline (Only residues before proline not including glycine or proline)", ChainID)
473 else:
474 PhiPsiResiduesInfo = PyMOLUtil.GetPhiPsiResiduesInfo(MolName, ChainID, Categorize = True)
475 SetupAndListPhiPsiResiduesInfo(PhiPsiResiduesInfo, "All", ChainID)
476
477 def SetupAndListPhiPsiResiduesInfo(PhiPsiResiduesInfo, AnglesType, ChainID):
478 """Setup and list information for phi and psi torsion angles."""
479
480 MiscUtil.PrintInfo("\nChainID: %s; Phi and Psi angles: %s" %(ChainID, AnglesType))
481
482 PhiPsiCount = len(PhiPsiResiduesInfo["ResNums"])
483 if not PhiPsiCount:
484 MiscUtil.PrintInfo("Number of angles: None")
485 return
486
487 MiscUtil.PrintInfo("Number of phi and psi angles: %d" % PhiPsiCount)
488
489 CategoriesMode = True if re.match("^Categories$", OptionsInfo["PhiPsiMode"], re.I) else False
490
491 if CategoriesMode:
492 MiscUtil.PrintInfo("\nResNum, ResName, Phi, Psi")
493 else:
494 MiscUtil.PrintInfo("\nResNum, ResName, Phi, Psi, Category")
495
496 Precision = OptionsInfo["PhiPsiPrecision"]
497 for ResNum in PhiPsiResiduesInfo["ResNums"]:
498 ResName = PhiPsiResiduesInfo["ResName"][ResNum]
499 Phi = PhiPsiResiduesInfo["Phi"][ResNum]
500 Psi = PhiPsiResiduesInfo["Psi"][ResNum]
501 if CategoriesMode:
502 MiscUtil.PrintInfo("%s, %s, %.*f, %.*f" % (ResNum, ResName, Precision, Phi, Precision, Psi))
503 else:
504 Category = PhiPsiResiduesInfo["Category"][ResNum]
505 MiscUtil.PrintInfo("%s, %s, %.*f, %.*f, %s " % (ResNum, ResName, Precision, Phi, Precision, Psi, Category))
506
507 def ListInterfaceResiduesInfo(MolName, ChainIDs):
508 """List interface residues between all unique pairs of polymer chains
509 with in a molecule."""
510
511 if not (OptionsInfo["All"] or OptionsInfo["InterfaceResidues"]):
512 return
513
514 MiscUtil.PrintInfo("\nListing interface residues information...")
515
516 # Get chain ID pairs for identifying interface residues...
517 ChainIDsPairs = GetChainIDsPairsForInterfaceResidues(ChainIDs)
518 if not len(ChainIDsPairs):
519 MiscUtil.PrintInfo("Valid interface chain ID pairs: None")
520 return
521
522 InterfaceResiduesMethod = OptionsInfo["InterfaceResiduesMethod"]
523 InterfaceResiduesCutoff = OptionsInfo["InterfaceResiduesCutoff"]
524 MiscUtil.PrintInfo("Methodology: %s; Cutoff: %.2f" % (InterfaceResiduesMethod, InterfaceResiduesCutoff))
525
526 for ChainIDsPair in ChainIDsPairs:
527 InterfaceChainIDs1, InterfaceChainIDs2 = ChainIDsPair
528 InterfaceID = "%s-%s" % ("+".join(InterfaceChainIDs1), "+".join(InterfaceChainIDs2))
529
530 InterfaceResiduesInfo1, InterfaceResiduesInfo2 = GetInterfaceChainsAndResiduesInfo(MolName, InterfaceChainIDs1, MolName, InterfaceChainIDs2, InterfaceResiduesMethod, InterfaceResiduesCutoff)
531
532 ChainNames1, ResiduesInfo1 = SetupSelectionChainsResiduesInfo(InterfaceResiduesInfo1)
533 ChainNames2, ResiduesInfo2 = SetupSelectionChainsResiduesInfo(InterfaceResiduesInfo2)
534
535 if len(ChainNames1) and len(ChainNames2):
536 MiscUtil.PrintInfo("\nListing interface residues for interface chain IDs: %s" % (InterfaceID))
537
538 ListInterfaceChainsAndResiduesInfo(InterfaceID, InterfaceChainIDs1, ChainNames1, ResiduesInfo1)
539 ListInterfaceChainsAndResiduesInfo(InterfaceID, InterfaceChainIDs2, ChainNames2, ResiduesInfo2)
540 else:
541 MiscUtil.PrintInfo("\nListing interface residues for interface chain IDs: %s" % (InterfaceID))
542 MiscUtil.PrintInfo("Interface chain IDs: None; ChainID: None; Number of interface residues: 0")
543
544 def ListInterfaceChainsAndResiduesInfo(InterfaceID, InterfaceChainIDs, ChainNames, ResiduesInfo):
545 """List interface chains and residues."""
546
547 for ChainID in InterfaceChainIDs:
548 if not ChainID in ChainNames:
549 MiscUtil.PrintInfo("\nInterface chain IDs: %s; ChainID: %s; Number of interface residues: 0" % (InterfaceID, ChainID))
550 continue
551
552 for Index in range(0, len(ChainNames)):
553 ChainName = ChainNames[Index]
554 ChainResiduesInfo = ResiduesInfo[Index]
555 if re.match(ChainID, ChainName, re.I):
556 MiscUtil.PrintInfo("\nInterface chain IDs: %s; ChainID: %s; Number of interface residues: %d" % (InterfaceID, ChainName, ChainResiduesInfo[0]))
557 MiscUtil.PrintInfo("Residue distribution: %s\nResidue IDs: %s" % (ChainResiduesInfo[1], ChainResiduesInfo[2]))
558 continue
559
560 def GetInterfaceChainsAndResiduesInfo(MolName1, ChainIDs1, MolName2, ChainIDs2, Method, Cutoff):
561 """Get interface chains and residues info for chains using a specified methodology."""
562
563 InterfaceChainsResiduesInfo1 = None
564 InterfaceChainsResiduesInfo2 = None
565
566 ChainNames1 = ",".join(ChainIDs1)
567 ChainNames2 = ",".join(ChainIDs2)
568
569 if re.match("^BySASAChange$", Method, re.I):
570 InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesBySASAChange(MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
571 elif re.match("^ByHeavyAtomsDistance$", Method, re.I):
572 InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesByHeavyAtomsDistance(MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
573 elif re.match("^ByCAlphaAtomsDistance$", Method, re.I):
574 InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesByCAlphaAtomsDistance(MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
575 else:
576 MiscUtil.PrintError("Failed to retrieve interface residues information: Method %s is not valid..." % Method)
577
578 return InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2
579
580 def GetChainIDsPairsForInterfaceResidues(ChainIDs):
581 """Get chain IDs pairs for identifying interface residues."""
582
583 ChainIDsPairsList = []
584
585 InterfaceResiduesChainsList = OptionsInfo["InterfaceResiduesChainsList"]
586 if not len(InterfaceResiduesChainsList):
587 # Use first two chain IDs...
588 if len(ChainIDs) >= 2:
589 ChainIDsPair = [ChainIDs[0], ChainIDs[1]]
590 ChainIDsPairsList.append(ChainIDsPair)
591 return ChainIDsPairsList
592
593 # Validate specified pairwise chain IDs...
594 for Index in range(0, len(InterfaceResiduesChainsList), 2):
595 ChainIDs1 = InterfaceResiduesChainsList[Index]
596 ChainIDs2 = InterfaceResiduesChainsList[Index + 1]
597
598 ValidChainIDs = True
599 SpecifiedChainIDs = []
600 SpecifiedChainIDs.extend(ChainIDs1)
601 SpecifiedChainIDs.extend(ChainIDs2)
602
603 for ChainID in (SpecifiedChainIDs):
604 if not ChainID in ChainIDs:
605 ValidChainIDs = False
606 MiscUtil.PrintWarning("The chain ID, %s, specified using \"--interfaceResiduesChains\" for a chain IDs pairs is not a valid chain ID." % (ChainID))
607
608 if not ValidChainIDs:
609 MiscUtil.PrintWarning("Ignoring chain IDs pair: %s, %s" % ("+".join(ChainIDs1), "+".join(ChainIDs2)))
610 continue
611
612 ChainIDsPair = [ChainIDs1, ChainIDs2]
613 ChainIDsPairsList.append(ChainIDsPair)
614
615 return ChainIDsPairsList
616
617 def SetupSelectionResiduesInfo(SelectionInfo):
618 """Setup residues info."""
619
620 # Setup distribution of residues...
621 LineWords = []
622 ResiduesCount = 0
623 SortedResNames = sorted(SelectionInfo["ResNames"], key = lambda ResName: SelectionInfo["ResCount"][ResName], reverse = True)
624 for ResName in SortedResNames:
625 ResCount = SelectionInfo["ResCount"][ResName]
626 LineWords.append("%s - %s" % (ResName, ResCount))
627 ResiduesCount += ResCount
628
629 ResiduesDistribution = "; ".join(LineWords) if len(LineWords) else None
630
631 # Setup residue IDs sorted by residue numbers...
632 ResNumMap = {}
633 for ResName in SelectionInfo["ResNames"]:
634 for ResNum in SelectionInfo["ResNum"][ResName]:
635 ResNumMap[ResNum] = ResName
636
637 LineWords = []
638 for ResNum in sorted(ResNumMap, key = int):
639 ResName = ResNumMap[ResNum]
640 ResID = "%s_%s" % (ResName, ResNum)
641 LineWords.append(ResID)
642 ResiduesIDs = ", ".join(LineWords) if len(LineWords) else None
643
644 return ResiduesCount, ResiduesDistribution, ResiduesIDs
645
646 def SetupSelectionChainsResiduesInfo(SelectionInfo):
647 """Setup chains and residues info."""
648
649 ChainNames = []
650 ResiduesInfo = []
651
652 for ChainID in SelectionInfo["ChainIDs"]:
653 ChainNames.append(ChainID)
654
655 # Setup distribution of residues...
656 LineWords = []
657 ResiduesCount = 0
658 SortedResNames = sorted(SelectionInfo["ResNames"][ChainID], key = lambda ResName: SelectionInfo["ResCount"][ChainID][ResName], reverse = True)
659 for ResName in SortedResNames:
660 ResCount = SelectionInfo["ResCount"][ChainID][ResName]
661 LineWords.append("%s - %s" % (ResName, ResCount))
662 ResiduesCount += ResCount
663
664 ResiduesDistribution = "; ".join(LineWords) if len(LineWords) else None
665
666 # Setup residue IDs sorted by residue numbers...
667 ResNumMap = {}
668 for ResName in SelectionInfo["ResNames"][ChainID]:
669 for ResNum in SelectionInfo["ResNum"][ChainID][ResName]:
670 ResNumMap[ResNum] = ResName
671
672 LineWords = []
673 for ResNum in sorted(ResNumMap, key = int):
674 ResName = ResNumMap[ResNum]
675 ResID = "%s_%s" % (ResName, ResNum)
676 LineWords.append(ResID)
677 ResiduesIDs = ", ".join(LineWords) if len(LineWords) else None
678
679 ResiduesInfo.append([ResiduesCount, ResiduesDistribution, ResiduesIDs])
680
681 return ChainNames, ResiduesInfo
682
683 def ListBoundingBoxInfo(MolName):
684 """List bounding box information."""
685
686 if not (OptionsInfo["All"] or OptionsInfo["BoundingBox"]):
687 return
688
689 MolSelection = "(%s)" % MolName
690 MolExtents = pymol.cmd.get_extent(MolSelection)
691
692 XMin, YMin, ZMin = MolExtents[0]
693 XMax, YMax, ZMax = MolExtents[1]
694
695 XSize = abs(XMax - XMin)
696 YSize = abs(YMax - YMin)
697 ZSize = abs(ZMax - ZMin)
698
699 MiscUtil.PrintInfo("\nBounding box coordinates: <XMin, XMax> - <%.3f, %.3f>; <YMin, YMax> - <%.3f, %.3f>; <ZMin, ZMax> - <%.3f, %.3f>" % (XMin, XMax, YMin, YMax, ZMin, ZMax))
700 MiscUtil.PrintInfo("Bounding box size in Angstroms: XSize - %.3f; YSize - %.3f; ZSize - %.3f" % (XSize, YSize, ZSize))
701
702 def ListCentroid(MolName):
703 """List centroid information."""
704
705 if not (OptionsInfo["All"] or OptionsInfo["Centroid"]):
706 return
707
708 MolSelection = "(%s)" % MolName
709 Centroid = PyMOLUtil.GetCentroid(MolSelection)
710
711 MiscUtil.PrintInfo("\nCentroid: <%.3f, %.3f, %.3f>" % (Centroid[0], Centroid[1], Centroid[2]))
712
713 def ListFileSizeAndModificationInfo(Infile):
714 """List file size and modification time info."""
715
716 MiscUtil.PrintInfo("\nFile size: %s" % MiscUtil.GetFormattedFileSize(Infile))
717 MiscUtil.PrintInfo("Last modified: %s" % time.ctime(os.path.getmtime(Infile)))
718 MiscUtil.PrintInfo("Created: %s" % time.ctime(os.path.getctime(Infile)))
719
720 def GetPocketSelectionResiduesInfoLabel(SelectionType):
721 """Get pocket residues info label for a specified selection type."""
722
723 SelectionLabel = None
724
725 if re.match("^Pockets$", SelectionType, re.I):
726 SelectionLabel = "polymer"
727 elif re.match("^PocketSolvents$", SelectionType, re.I):
728 SelectionLabel = "solvent"
729 elif re.match("^PocketInorganics$", SelectionType, re.I):
730 SelectionLabel = "inorganic"
731 else:
732 MiscUtil.PrintError("Failed to retrieve pocket residues label information: Selection type %s is not valid..." % SelectionType)
733
734 return SelectionLabel
735
736 def ProcessOptions():
737 """Process and validate command line arguments and options."""
738
739 MiscUtil.PrintInfo("Processing options...")
740
741 # Validate options...
742 ValidateOptions()
743
744 OptionsInfo["All"] = Options["--all"]
745 OptionsInfo["BoundingBox"] = Options["--boundingBox"]
746 OptionsInfo["Centroid"] = Options["--centroid"]
747
748 OptionsInfo["Chains"] = Options["--chains"]
749
750 OptionsInfo["CountResidues"] = Options["--countResidues"]
751 OptionsInfo["Header"] = Options["--header"]
752
753 OptionsInfo["Infiles"] = Options["--infiles"]
754 OptionsInfo["InfilesNames"] = Options["--infilesNames"]
755
756 OptionsInfo["Inorganics"] = Options["--inorganics"]
757
758 OptionsInfo["InterfaceResidues"] = Options["--interfaceResidues"]
759 OptionsInfo["InterfaceResiduesMethod"] = Options["--interfaceResiduesMethod"]
760
761 InterfaceResiduesChains = Options["--interfaceResiduesChains"]
762 InterfaceResiduesChainsList = []
763 if not re.match("^auto$", InterfaceResiduesChains, re.I):
764 InterfaceResiduesChains = re.sub(" ", "", Options["--interfaceResiduesChains"])
765 InterfaceResiduesChainsWords = InterfaceResiduesChains.split(",")
766 if len(InterfaceResiduesChainsWords) % 2:
767 MiscUtil.PrintError("The number of comma delimited chain IDs, %d, specified using \"--interfaceResiduesChains\" option, \"%s\", must be a multple of 2." % (len(InterfaceResiduesChainsWords), Options["--interfaceResiduesChains"]))
768 for ChainID in InterfaceResiduesChainsWords:
769 ChainIDWords = ChainID.split("+")
770 InterfaceResiduesChainsList.append(ChainIDWords)
771 OptionsInfo["InterfaceResiduesChains"] = InterfaceResiduesChains
772 OptionsInfo["InterfaceResiduesChainsList"] = InterfaceResiduesChainsList
773
774 InterfaceResiduesCutoff = Options["--interfaceResiduesCutoff"]
775 InterfaceResiduesMethod = OptionsInfo["InterfaceResiduesMethod"]
776 if re.match("^auto$", InterfaceResiduesCutoff, re.I):
777 if re.match("^BySASAChange$", InterfaceResiduesMethod, re.I):
778 InterfaceResiduesCutoff = 1.0
779 elif re.match("^ByHeavyAtomsDistance$", InterfaceResiduesMethod, re.I):
780 InterfaceResiduesCutoff = 5.0
781 elif re.match("^ByCAlphaAtomsDistance$", InterfaceResiduesMethod, re.I):
782 InterfaceResiduesCutoff = 8.0
783 else:
784 MiscUtil.PrintError("The specified value, %s, for option \"--interfaceResiduesMethod\" is not supported." % (InterfaceResiduesMethod))
785 else:
786 InterfaceResiduesCutoff = float(InterfaceResiduesCutoff)
787 OptionsInfo["InterfaceResiduesCutoff"] = InterfaceResiduesCutoff
788
789 OptionsInfo["Ligands"] = Options["--ligands"]
790
791 OptionsInfo["PocketLigands"] = Options["--pocketLigands"]
792 OptionsInfo["PocketDistanceCutoff"] = float(Options["--pocketDistanceCutoff"])
793 OptionsInfo["PocketSolvents"] = Options["--pocketSolvents"]
794 OptionsInfo["PocketInorganics"] = Options["--pocketInorganics"]
795
796 OptionsInfo["PhiPsi"] = Options["--phiPsi"]
797 OptionsInfo["PhiPsiMode"] = Options["--phiPsiMode"]
798 OptionsInfo["PhiPsiPrecision"] = int(Options["--phiPsiPrecision"])
799
800 OptionsInfo["Solvents"] = Options["--solvents"]
801
802 OptionsInfo["SurfaceResidues"] = Options["--surfaceResidues"]
803 OptionsInfo["SurfaceResiduesCutoff"] = float(Options["--surfaceResiduesCutoff"])
804 OptionsInfo["SurfaceResiduesIDs"] = True if re.match("^Yes$", Options["--surfaceResiduesIDs"], re.I) else False
805
806 # Always list header, chains, and ligands...
807 OptionNames = ["Chains", "Header", "Ligands"]
808 for Name in OptionNames:
809 if Name in OptionsInfo:
810 OptionsInfo[Name] = True
811 else:
812 MiscUtil.PrintError("Option name %s is not a valid name..." % s)
813
814 def RetrieveOptions():
815 """Retrieve command line arguments and options."""
816
817 # Get options...
818 global Options
819 Options = docopt(_docoptUsage_)
820
821 # Set current working directory to the specified directory...
822 WorkingDir = Options["--workingdir"]
823 if WorkingDir:
824 os.chdir(WorkingDir)
825
826 # Handle examples option...
827 if "--examples" in Options and Options["--examples"]:
828 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
829 sys.exit(0)
830
831 def ValidateOptions():
832 """Validate option values."""
833
834 # Expand infile names..
835 InfilesNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
836
837 # Validate file extensions...
838 for Infile in InfilesNames:
839 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
840 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
841 Options["--infilesNames"] = InfilesNames
842
843 if not re.match("^auto$", Options["--interfaceResiduesCutoff"], re.I):
844 MiscUtil.ValidateOptionFloatValue("--interfaceResiduesCutoff", Options["--interfaceResiduesCutoff"], {">": 0.0})
845 MiscUtil.ValidateOptionTextValue("--interfaceResiduesMethod", Options["--interfaceResiduesMethod"], "BySASAChange ByHeavyAtomsDistance ByCAlphaAtomsDistance")
846
847 MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0})
848 MiscUtil.ValidateOptionTextValue("--phiPsiMode", Options["--phiPsiMode"], "All Categories")
849 MiscUtil.ValidateOptionIntegerValue("--phiPsiPrecision", Options["--phiPsiPrecision"], {">": 0})
850 MiscUtil.ValidateOptionFloatValue("--surfaceResiduesCutoff", Options["--surfaceResiduesCutoff"], {">": 0.0})
851 MiscUtil.ValidateOptionTextValue("--surfaceResiduesIDs", Options["--surfaceResiduesIDs"], "Yes No")
852
853 # Setup a usage string for docopt...
854 _docoptUsage_ = """
855 PyMOLInfoMacromolecules.py - List information about macromolecules
856
857 Usage:
858 PyMOLInfoMacromolecules.py [--all] [--boundingBox] [--centroid] [--chains]
859 [--countResidues] [--header] [--inorganics] [--interfaceResidues]
860 [--interfaceResiduesChains <ChainID1,ChainD2,...>] [--interfaceResiduesMethod <text>]
861 [--interfaceResiduesCutoff <number>] [--ligands] [--pocketLigands]
862 [--pocketDistanceCutoff <number>] [--pocketSolvents] [--pocketInorganics]
863 [--phiPsi] [--phiPsiMode <All or Categories>] [--phiPsiPrecision <number>]
864 [--surfaceResidues] [--surfaceResiduesCutoff <number>] [--surfaceResiduesIDs <yes or no>]
865 [--solvents] [-w <dir>] -i <infile1,infile2,infile3...>
866 PyMOLInfoMacromolecules.py -h | --help | -e | --examples
867
868 Description:
869 List information regarding ID, classification, experimental technique, chains,
870 solvents, inorganics, ligands, and ligand binding pockets in macromolecules
871 present including proteins and nucleic acids.
872
873 The supported input file format are: PDB (.pdb), mmCIF (.cif)
874
875 Options:
876 -a, --all
877 All available information.
878 -b, --boundingBox
879 Min and max coordinates for bounding box along with its size.
880 -c, --chains
881 Number of chains and their IDs. This is also default behavior.
882 --centroid
883 Centroid of atomic coordinates. It corresponds to the mean of all 3D
884 coordinates in input file.
885 --countResidues
886 Number of residues across chains. The chain residues are identified
887 using polymer selection operator available in PyMOL. In addition,
888 the non-standard amino acid residues are listed.
889 -e, --examples
890 Print examples.
891 -h, --help
892 Print this help message.
893 --header
894 Header information including experimental technique information
895 along with any available resolution. This is also default behavior.
896 -i, --infiles <infile1,infile2,infile3...>
897 A comma delimited list of input files. The wildcards are also allowed
898 in file names.
899 --inorganics
900 Inorganic residues across chains. The inorganic residues are identified
901 using inorganic selection operator available in PyMOL.
902 --interfaceResidues
903 Interface residues between specified pairs of chains.
904 --interfaceResiduesChains <ChainID1,Chain1D2,...> [default: Auto]
905 Pairwise comma delimited list of chain IDs for the identification of
906 interface residues. Each chain ID may contain mutiple chain IDs
907 delimited by a plus sign. For example: A+B,C+D chain pair specifies
908 interface between chain complexes A+B and C+D.
909
910 The interface residues are identified between first two chains in
911 input files by default.
912 --interfaceResiduesMethod <text> [default: BySASAChange]
913 Methodology for the identification of interface residues between a pair
914 of chains in an input file. The interface residues may be identified by
915 change in solvent accessible surface area (SASA) for a residue between
916 a chain and chains complex, distance between heavy atoms
917 in two chains, or distance between CAlpha atoms. Possible values:
918 BySASAChange, ByHeavyAtomsDistance, or ByCAlphaAtomsDistance.
919 --interfaceResiduesCutoff <number> [default: auto]
920 Cutoff value used by different methodologies during identification of
921 interface residues between a pair of chains. The default values are
922 shown below:
923
924 BySASAChange: 1.0; Units: Angstrom**2 [ Ref 141 ]
925 ByHeavyAtomsDistance: 5.0; Units: Angstrom [ Ref 142 ]
926 ByCAlphaAtomsDistance: 8.0; Units: Angstrom [ Ref 143 ]
927
928 -l, --ligands
929 Ligands across chains. This is also default behavior. The ligands
930 residues are identified using organic selection operator available
931 in PyMOL.
932 -p, --pocketLigands
933 Chain residues in ligand pockets.
934 --pocketDistanceCutoff <number> [default: 5.0]
935 Distance in Angstroms for identifying pocket residues around ligands.
936 --pocketSolvents
937 Solvent residues in ligand pockets. The solvent residues are identified
938 using solvent selection operator available in PyMOL.
939 --pocketInorganics
940 Inorganic residues in ligand pockets. The inorganic residues are identified
941 using Inorganic selection operator available in PyMOL.
942 --phiPsi
943 Phi and psi torsion angles across chains in macromolecules containing
944 amino acids.
945 --phiPsiMode <All or Categories> [default: Categories]
946 List all phi and psi torsion angles for residues as a single group or split
947 them into the following categories corresponding to four types of
948 Ramachandran plots:
949
950 General: All residues except glycine, proline, or pre-proline
951 Glycine: Only glycine residues
952 Proline: Only proline residues
953 Pre-Proline: Only residues before proline not including glycine
954 or proline
955
956 --phiPsiPrecision <number> [default: 2]
957 Precision for listing phi and psi torsion angles.
958 -s, --solvents
959 Solvent residues across chains. The solvent residues are identified
960 using solvent selection operator available in PyMOL.
961 --surfaceResidues
962 Surface and buried residues in chains.
963 --surfaceResiduesCutoff <number> [default: 2.5]
964 Solvenet Accessible Surface Area (SASA) cutoff value in Angstroms**2
965 for surface and buried resiudes in chains. The residues with SASA less than
966 the cutoff value correspond to burried residues.
967 --surfaceResiduesIDs <yes or no> [default: No]
968 List residue IDs for surface and buried residues during listing of the
969 distribution of these residues for '--surfaceResidues' option.
970 -w, --workingdir <dir>
971 Location of working directory which defaults to the current directory.
972
973 Examples:
974 To list header, chains, and ligand information for macromolecules in input
975 file, type:
976
977 % PyMOLInfoMacromolecules.py -i Sample3.pdb
978
979 To list all available information for macromolecules in input files, type:
980
981 % PyMOLInfoMacromolecules.py -a -i "Sample3.pdb,Sample4.pdb"
982
983 To list pockets residues information along with other default information
984 for marcomolecules in input file, type:
985
986 % PyMOLInfoMacromolecules.py -p --pocketDistanceCutoff 4.5
987 --pocketSolvents --pocketInorganics -i Sample3.pdb
988
989 To list chain residues information along with other default information
990 for marcomolecules in input file, type:
991
992 % PyMOLInfoMacromolecules.py -c --countResidues --solvents
993 --inorganics -i "Sample3.pdb,Sample4.pdb"
994
995 To list interface residues between first two chains by SASA change for
996 marcomolecules in input file, type:
997
998 % PyMOLInfoMacromolecules.py --interfaceResidues
999 -i Sample3.pdb
1000
1001 To list interface residues between chains E and I by heay atoms
1002 distance for marcomolecules in input file, type:
1003
1004 % PyMOLInfoMacromolecules.py --interfaceResidues
1005 --interfaceResiduesChains E,I --interfaceResiduesMethod
1006 ByHeavyAtomsDistance --interfaceResiduesCutoff 5 -i Sample3.pdb
1007
1008 To list interface residues between two sets of chains by SASA change for
1009 marcomolecules in input file, type:
1010
1011 % PyMOLInfoMacromolecules.py --interfaceResidues
1012 --interfaceResiduesChains "A+B,C+D" -i Sample8.pdb
1013
1014 Author:
1015 Manish Sud(msud@san.rr.com)
1016
1017 See also:
1018 DownloadPDBFiles.pl, PyMOLSplitChainsAndLigands.py,
1019 PyMOLVisualizeMacromolecules.py
1020
1021 Copyright:
1022 Copyright (C) 2024 Manish Sud. All rights reserved.
1023
1024 The functionality available in this script is implemented using PyMOL, a
1025 molecular visualization system on an open source foundation originally
1026 developed by Warren DeLano.
1027
1028 This file is part of MayaChemTools.
1029
1030 MayaChemTools is free software; you can redistribute it and/or modify it under
1031 the terms of the GNU Lesser General Public License as published by the Free
1032 Software Foundation; either version 3 of the License, or (at your option) any
1033 later version.
1034
1035 """
1036
1037 if __name__ == "__main__":
1038 main()
