1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeMacromolecules.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 GenerateMacromolecularVisualization()
84
85 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
86 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
87
88
89 def GenerateMacromolecularVisualization():
90 """Generate macromolecular visualization."""
91
92 Outfile = OptionsInfo["PMLOutfile"]
93 OutFH = open(Outfile, "w")
94 if OutFH is None:
95 MiscUtil.PrintError("Failed to open output fie %s " % Outfile)
96
97 MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
98
99 # Setup header...
100 WritePMLHeader(OutFH, ScriptName)
101 WritePyMOLParameters(OutFH)
102
103 # Load reffile for alignment..
104 if OptionsInfo["Align"]:
105 WriteAlignReference(OutFH)
106
107 # Setup view for each input file...
108 FirstComplex = True
109 FirstComplexFirstChainName = None
110 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
111 # Setup PyMOL object names...
112 PyMOLObjectNames = SetupPyMOLObjectNames(FileIndex)
113
114 # Setup complex view...
115 WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex)
116
117 # Setup trajectories views...
118 if GetTrajectoriesStatus(FileIndex):
119 WriteTrajectoriesView(OutFH, FileIndex, PyMOLObjectNames)
120
121 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
122 FirstChain = True
123 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
124 if FirstComplex and FirstChain:
125 FirstComplexFirstChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
126
127 WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
128
129 # Setup ligand views...
130 FirstLigand = True
131 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
132 WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID)
133
134 # Set up ligand level group...
135 Enable, Action = [False, "close"]
136 if FirstLigand:
137 FirstLigand = False
138 Enable, Action = [True, "open"]
139 GenerateAndWritePMLForGroup(
140 OutFH,
141 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"],
142 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"],
143 Enable,
144 Action,
145 )
146
147 # Setup docked poses views...
148 if GetChainAloneDockedPosesStatus(FileIndex, ChainID):
149 WriteChainDockedPosesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
150
151 # Setup Chain level group...
152 Enable, Action = [False, "close"]
153 if FirstChain:
154 FirstChain = False
155 Enable, Action = [True, "open"]
156 GenerateAndWritePMLForGroup(
157 OutFH,
158 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"],
159 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"],
160 Enable,
161 Action,
162 )
163
164 # Set up complex level group...
165 Enable, Action = [False, "close"]
166 if FirstComplex:
167 FirstComplex = False
168 Enable, Action = [True, "open"]
169 GenerateAndWritePMLForGroup(
170 OutFH, PyMOLObjectNames["PDBGroup"], PyMOLObjectNames["PDBGroupMembers"], Enable, Action
171 )
172
173 # Delete empty PyMOL objects...
174 DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames)
175
176 if OptionsInfo["Align"]:
177 DeleteAlignReference(OutFH)
178
179 if FirstComplexFirstChainName is not None:
180 OutFH.write("""\ncmd.orient("%s", animate = -1)\n""" % FirstComplexFirstChainName)
181 else:
182 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
183
184 OutFH.close()
185
186 # Generate PSE file as needed...
187 if OptionsInfo["PSEOut"]:
188 GeneratePyMOLSessionFile()
189
190
191 def WritePMLHeader(OutFH, ScriptName):
192 """Write out PML header."""
193
194 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
195 OutFH.write("%s\n" % HeaderInfo)
196
197
198 def WritePyMOLParameters(OutFH):
199 """Write out PyMOL global parameters."""
200
201 PMLCmds = []
202 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
203 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
204 PML = "\n".join(PMLCmds)
205
206 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
207 OutFH.write("%s\n" % PML)
208
209
210 def WriteAlignReference(OutFH):
211 """Setup object for alignment reference."""
212
213 RefFileInfo = OptionsInfo["RefFileInfo"]
214 RefFile = RefFileInfo["RefFileName"]
215 RefName = RefFileInfo["PyMOLObjectName"]
216
217 PMLCmds = []
218 PMLCmds.append("""cmd.load("%s", "%s")""" % (RefFile, RefName))
219 PMLCmds.append("""cmd.hide("everything", "%s")""" % (RefName))
220 PMLCmds.append("""cmd.disable("%s")""" % (RefName))
221 PML = "\n".join(PMLCmds)
222
223 OutFH.write("""\n""\n"Loading %s and setting up view for align reference..."\n""\n""" % RefFile)
224 OutFH.write("%s\n" % PML)
225
226
227 def WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames):
228 """Setup alignment of complex to reference."""
229
230 RefFileInfo = OptionsInfo["RefFileInfo"]
231 RefName = RefFileInfo["PyMOLObjectName"]
232
233 ComplexName = PyMOLObjectNames["Complex"]
234
235 if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
236 RefFirstChainID = RefFileInfo["ChainsAndLigandsInfo"]["ChainIDs"][0]
237 RefAlignSelection = "%s and chain %s" % (RefName, RefFirstChainID)
238
239 ComplexFirstChainID = RetrieveFirstChainID(FileIndex)
240 ComplexAlignSelection = "%s and chain %s" % (ComplexName, ComplexFirstChainID)
241 else:
242 RefAlignSelection = RefName
243 ComplexAlignSelection = ComplexName
244
245 PML = PyMOLUtil.SetupPMLForAlignment(OptionsInfo["AlignMethod"], RefAlignSelection, ComplexAlignSelection)
246 OutFH.write("""\n""\n"Aligning %s against reference %s ..."\n""\n""" % (ComplexAlignSelection, RefAlignSelection))
247 OutFH.write("%s\n" % PML)
248
249
250 def DeleteAlignReference(OutFH):
251 """Delete alignment reference object."""
252
253 RefName = OptionsInfo["RefFileInfo"]["PyMOLObjectName"]
254 OutFH.write("""\n""\n"Deleting alignment reference object %s..."\n""\n""" % RefName)
255 OutFH.write("""cmd.delete("%s")\n""" % RefName)
256
257
258 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex):
259 """Write out PML for viewing polymer complex."""
260
261 # Setup complex...
262 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
263 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["Complex"], Infile, True)
264 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
265 OutFH.write("%s\n" % PML)
266
267 if OptionsInfo["Align"]:
268 # No need to align complex on to itself...
269 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
270 WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames)
271
272 if OptionsInfo["SurfaceComplex"]:
273 # Setup hydrophobic surface...
274 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(
275 PyMOLObjectNames["ComplexHydrophobicSurface"],
276 PyMOLObjectNames["Complex"],
277 ColorPalette=OptionsInfo["SurfaceColorPalette"],
278 Enable=False,
279 )
280 OutFH.write("\n%s\n" % PML)
281
282 # Setup complex group...
283 GenerateAndWritePMLForGroup(
284 OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close"
285 )
286
287
288 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
289 """Write out PML for viewing chain."""
290
291 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
292
293 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
294
295 # Setup chain complex group view...
296 WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
297
298 # Setup chain view...
299 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
300
301 # Setup chain solvent view...
302 PML = PyMOLUtil.SetupPMLForSolventView(PyMOLObjectNames["Chains"][ChainID]["Solvent"], ChainComplexName, False)
303 OutFH.write("\n%s\n" % PML)
304
305 # Setup chain inorganic view...
306 PML = PyMOLUtil.SetupPMLForInorganicView(PyMOLObjectNames["Chains"][ChainID]["Inorganic"], ChainComplexName, False)
307 OutFH.write("\n%s\n" % PML)
308
309
310 def WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
311 """Write chain complex views."""
312
313 # Setup chain complex...
314 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
315 PML = PyMOLUtil.SetupPMLForPolymerChainComplexView(ChainComplexName, PyMOLObjectNames["Complex"], ChainID, True)
316 OutFH.write("%s\n" % PML)
317
318 if OptionsInfo["SurfaceChainComplex"]:
319 # Setup hydrophobic surface...
320 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(
321 PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"],
322 ChainComplexName,
323 ColorPalette=OptionsInfo["SurfaceColorPalette"],
324 Enable=False,
325 )
326 OutFH.write("\n%s\n" % PML)
327
328 # Setup chain complex group...
329 GenerateAndWritePMLForGroup(
330 OutFH,
331 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"],
332 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"],
333 False,
334 "close",
335 )
336
337
338 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
339 """Write individual chain views."""
340
341 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
342
343 # Setup chain view...
344 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
345 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, True)
346 OutFH.write("\n%s\n" % PML)
347
348 WriteChainAloneBFactorViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
349
350 WriteChainAloneChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
351 WriteChainAloneResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
352
353 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
354 # Setup a generic color surface...
355 PML = PyMOLUtil.SetupPMLForSurfaceView(
356 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"],
357 ChainName,
358 Enable=False,
359 Color=OptionsInfo["SurfaceColor"],
360 )
361 OutFH.write("\n%s\n" % PML)
362
363 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
364 # Setup surface colored by hydrophobicity...
365 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(
366 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"],
367 ChainName,
368 ColorPalette=OptionsInfo["SurfaceColorPalette"],
369 Enable=False,
370 )
371 OutFH.write("\n%s\n" % PML)
372
373 # Setup surface colored by hyrdophobicity and charge...
374 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(
375 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"],
376 ChainName,
377 OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"],
378 OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"],
379 OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"],
380 OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"],
381 Enable=False,
382 DisplayAs=None,
383 )
384 OutFH.write("\n%s\n" % PML)
385
386 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
387 # Setup electrostatics surface...
388 SelectionObjectName = ChainName
389 ElectrostaticsGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroup"]
390 ElectrostaticsGroupMembers = PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"]
391 WriteSurfaceElectrostaticsView(
392 "Surface",
393 OutFH,
394 SelectionObjectName,
395 ElectrostaticsGroupName,
396 ElectrostaticsGroupMembers,
397 DisplayAs="cartoon",
398 )
399
400 # Setup surface group...
401 GenerateAndWritePMLForGroup(
402 OutFH,
403 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"],
404 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"],
405 True,
406 "open",
407 )
408
409 # Setup disulfide group...
410 WriteChainAloneDisulfideBondsView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
411
412 # Setup salt bridges group...
413 WriteChainAloneSaltBridgesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
414
415 # Setup chain group...
416 GenerateAndWritePMLForGroup(
417 OutFH,
418 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"],
419 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"],
420 True,
421 "close",
422 )
423
424
425 def WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID):
426 """Write out PML for viewing ligand in a chain."""
427
428 for GroupID in ["Ligand", "Pocket", "PocketSolvent", "PocketInorganic"]:
429 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
430 LigandName = PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
431
432 # Setup main object...
433 GroupTypeObjectID = "%s" % (GroupID)
434 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
435
436 if re.match("^Ligand$", GroupID, re.I):
437 OutFH.write("""\n""\n"Setting up views for ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
438 PML = PyMOLUtil.SetupPMLForLigandView(
439 GroupTypeObjectName, ComplexName, LigandID, Enable=True, IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"]
440 )
441 OutFH.write("%s\n" % PML)
442 elif re.match("^Pocket$", GroupID, re.I):
443 OutFH.write(
444 """\n""\n"Setting up views for pocket around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID)
445 )
446 PML = PyMOLUtil.SetupPMLForLigandPocketView(
447 GroupTypeObjectName,
448 ComplexName,
449 LigandName,
450 OptionsInfo["PocketDistanceCutoff"],
451 Enable=True,
452 IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"],
453 )
454 OutFH.write("%s\n" % PML)
455 OutFH.write(
456 """cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], GroupTypeObjectName)
457 )
458 elif re.match("^PocketSolvent$", GroupID, re.I):
459 OutFH.write(
460 """\n""\n"Setting up views for solvent in pockect around ligand %s in chain %s..."\n""\n"""
461 % (LigandID, ChainID)
462 )
463 PML = PyMOLUtil.SetupPMLForLigandPocketSolventView(
464 GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable=True
465 )
466 OutFH.write("%s\n" % PML)
467 elif re.match("^PocketInorganic$", GroupID, re.I):
468 OutFH.write(
469 """\n""\n"Setting up views for inorganic in pockect around ligand %s in chain %s..."\n""\n"""
470 % (LigandID, ChainID)
471 )
472 PML = PyMOLUtil.SetupPMLForLigandPocketInorganicView(
473 GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable=True
474 )
475 OutFH.write("%s\n" % PML)
476
477 # Set up polar contacts...
478 if re.match("^(Pocket|PocketSolvent|PocketInorganic)$", GroupID, re.I):
479 PolarContactsID = "%sPolarContacts" % (GroupID)
480 PolarContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID]
481
482 PolarContactsColor = OptionsInfo["PocketContactsLigandColor"]
483 if re.match("^PocketSolvent$", GroupID, re.I):
484 PolarContactsColor = OptionsInfo["PocketContactsSolventColor"]
485 elif re.match("^PocketInorganic$", GroupID, re.I):
486 PolarContactsColor = OptionsInfo["PocketContactsInorganicColor"]
487
488 PML = PyMOLUtil.SetupPMLForPolarContactsView(
489 PolarContactsName,
490 LigandName,
491 GroupTypeObjectName,
492 Enable=False,
493 Color=PolarContactsColor,
494 Cutoff=OptionsInfo["PocketContactsCutoff"],
495 )
496 OutFH.write("\n%s\n" % PML)
497
498 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PolarContactsColor, PolarContactsName))
499
500 if re.match("^PocketInorganic$", GroupID, re.I):
501 # Setup pi cation contacts...
502 PiCationContactsID = "%sPiCationContacts" % (GroupID)
503 PiCationContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID]
504 PiCationContactsColor = OptionsInfo["PocketContactsInorganicPiCationColor"]
505
506 PML = PyMOLUtil.SetupPMLForPiCationContactsView(
507 PiCationContactsName,
508 LigandName,
509 GroupTypeObjectName,
510 Enable=False,
511 Color=PiCationContactsColor,
512 Cutoff=OptionsInfo["PocketContactsCutoff"],
513 )
514 OutFH.write("\n%s\n" % PML)
515 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
516
517 if re.match("^Pocket$", GroupID, re.I):
518 # Setup hydrophobic contacts...
519 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
520 HydrophobicContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID]
521 HydrophobicContactsColor = OptionsInfo["PocketContactsLigandHydrophobicColor"]
522
523 PML = PyMOLUtil.SetupPMLForHydrophobicContactsView(
524 HydrophobicContactsName,
525 LigandName,
526 GroupTypeObjectName,
527 Enable=False,
528 Color=HydrophobicContactsColor,
529 Cutoff=OptionsInfo["PocketContactsCutoff"],
530 )
531 OutFH.write("\n%s\n" % PML)
532 OutFH.write(
533 """cmd.set("label_color", "%s", "%s")\n""" % (HydrophobicContactsColor, HydrophobicContactsName)
534 )
535
536 # Setup pi pi contacts...
537 PiPiContactsID = "%sPiPiContacts" % (GroupID)
538 PiPiContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PiPiContactsID]
539 PiPiContactsColor = OptionsInfo["PocketContactsLigandPiPiColor"]
540
541 PML = PyMOLUtil.SetupPMLForPiPiContactsView(
542 PiPiContactsName,
543 LigandName,
544 GroupTypeObjectName,
545 Enable=False,
546 Color=PiPiContactsColor,
547 Cutoff=OptionsInfo["PocketContactsCutoff"],
548 )
549 OutFH.write("\n%s\n" % PML)
550 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiPiContactsColor, PiPiContactsName))
551
552 # Setup pi cation contacts...
553 PiCationContactsID = "%sPiCationContacts" % (GroupID)
554 PiCationContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID]
555 PiCationContactsColor = OptionsInfo["PocketContactsLigandPiCationColor"]
556
557 PML = PyMOLUtil.SetupPMLForPiCationContactsView(
558 PiCationContactsName,
559 LigandName,
560 GroupTypeObjectName,
561 Enable=False,
562 Color=PiCationContactsColor,
563 Cutoff=OptionsInfo["PocketContactsCutoff"],
564 )
565 OutFH.write("\n%s\n" % PML)
566 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
567
568 # Setup halogen contacts...
569 HalogenContactsID = "%sHalogenContacts" % (GroupID)
570 HalogenContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HalogenContactsID]
571 HalogenContactsColor = OptionsInfo["PocketContactsLigandHalogenColor"]
572
573 PML = PyMOLUtil.SetupPMLForHalogenContactsView(
574 HalogenContactsName,
575 LigandName,
576 GroupTypeObjectName,
577 Enable=False,
578 Color=HalogenContactsColor,
579 Cutoff=OptionsInfo["PocketContactsCutoff"],
580 )
581 OutFH.write("\n%s\n" % PML)
582 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HalogenContactsColor, HalogenContactsName))
583
584 # Setup pocket selections...
585 WritePocketSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
586
587 # Setup pocket residues...
588 WritePocketResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
589 WritePocketSurfacesTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
590
591 if re.match("^Ligand$", GroupID, re.I):
592 # Setup ball and stick view...
593 BallAndStickNameID = "%sBallAndStick" % (GroupID)
594 BallAndStickName = PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickNameID]
595 PML = PyMOLUtil.SetupPMLForBallAndStickView(BallAndStickName, GroupTypeObjectName, Enable=False)
596 OutFH.write("\n%s\n" % PML)
597
598 # Setup group...
599 GroupNameID = "%sGroup" % (GroupID)
600 GroupMembersID = "%sGroupMembers" % (GroupID)
601 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
602 GroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID]
603
604 Action = "close"
605 Enable = False
606 if re.match("^(Ligand|Pocket)$", GroupID, re.I):
607 Action = "open"
608 Enable = True
609 GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable, Action)
610
611
612 def WriteChainDockedPosesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
613 """Write out PML for viewing docked poses for input files in a chain."""
614
615 if not GetChainAloneDockedPosesStatus(FileIndex, ChainID):
616 return
617
618 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
619 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
620 WriteChainDockedPosesViewForInputFile(OutFH, FileIndex, PyMOLObjectNames, ChainID, InputFileIndex)
621
622 GenerateAndWritePMLForGroup(
623 OutFH,
624 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"],
625 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"],
626 False,
627 "close",
628 )
629
630
631 def WriteChainDockedPosesViewForInputFile(OutFH, PDBFileIndex, PyMOLObjectNames, ChainID, InputFileIndex):
632 """Write out PML for viewing docked poses for an input file in a chain."""
633
634 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
635 DockedPosesDistanceContactsInfo = OptionsInfo["DockedPosesDistanceContactsInfo"]
636
637 LigandID = DockedPosesInfo["LigandID"][PDBFileIndex]
638 UseInputFileAsLigandID = DockedPosesInfo["UseInputFileAsLigandID"][PDBFileIndex]
639 InputFile = DockedPosesInfo["InputFiles"][PDBFileIndex][InputFileIndex]
640 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
641
642 OutFH.write(
643 """\n""\n"Setting up views for docked poses in input file ID %s for chain %s..."\n""\n"""
644 % (InputFileID, ChainID)
645 )
646
647 # Setup poses view...
648 PosesName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["Poses"]
649 PML = PyMOLUtil.SetupPMLForLigandsInputFileView(
650 PosesName, InputFile, Enable=True, IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"]
651 )
652 OutFH.write("%s\n" % PML)
653
654 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
655 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
656 LigandName = PosesName if UseInputFileAsLigandID else PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
657
658 # Setup pocket object...
659 PocketID = "%sPocket" % (GroupID)
660 PocketName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PocketID]
661
662 if re.match("^Pocket$", GroupID, re.I):
663 PML = PyMOLUtil.SetupPMLForLigandPocketView(
664 PocketName,
665 ComplexName,
666 LigandName,
667 OptionsInfo["PocketDistanceCutoff"],
668 Enable=True,
669 IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"],
670 )
671 OutFH.write("%s\n" % PML)
672 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], PocketName))
673 elif re.match("^PocketSolvent$", GroupID, re.I):
674 PML = PyMOLUtil.SetupPMLForLigandPocketSolventView(
675 PocketName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable=True
676 )
677 OutFH.write("%s\n" % PML)
678 elif re.match("^PocketInorganic$", GroupID, re.I):
679 PML = PyMOLUtil.SetupPMLForLigandPocketInorganicView(
680 PocketName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable=True
681 )
682 OutFH.write("%s\n" % PML)
683
684 if DockedPosesInfo["DistanceContacts"] and re.match("^Pocket$", GroupID, re.I):
685 # Setup distance contacts...
686 for ContactIndex, ContactID in enumerate(DockedPosesDistanceContactsInfo["ContactIDs"]):
687 ContactCutoff = DockedPosesDistanceContactsInfo["ContactCutoff"][ContactID]
688
689 DistanceContactID = "%sPocketDistanceContacts%s" % (GroupID, ContactID)
690 DistanceContactName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactID]
691
692 DistanceContactsColor = OptionsInfo["DockedPosesDistanceContactsColor"]
693 EnableContact = True if ContactIndex == 0 else False
694 PML = PyMOLUtil.SetupPMLForDistanceContactsView(
695 DistanceContactName,
696 PosesName,
697 PocketName,
698 Enable=EnableContact,
699 Color=DistanceContactsColor,
700 Cutoff=ContactCutoff,
701 IgnoreHydrogens=True,
702 )
703 OutFH.write("\n%s\n" % PML)
704
705 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (DistanceContactsColor, DistanceContactName))
706
707 # Setup distance conatcts group...
708 DistanceContactGroupNameID = "%sDistanceContactsGroup" % GroupID
709 DistanceContactGroupMembersID = "%sDistanceContactsGroupMembers" % GroupID
710
711 GenerateAndWritePMLForGroup(
712 OutFH,
713 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupNameID],
714 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID],
715 True,
716 "open",
717 )
718
719 # Setup polar contacts...
720 if re.match("^(Pocket|PocketSolvent|PocketInorganic)$", GroupID, re.I):
721 PolarContactsID = "%sPolarContacts" % (GroupID)
722 PolarContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PolarContactsID]
723
724 PolarContactsColor = OptionsInfo["PocketContactsLigandColor"]
725 if re.match("^PocketSolvent$", GroupID, re.I):
726 PolarContactsColor = OptionsInfo["PocketContactsSolventColor"]
727 elif re.match("^PocketInorganic$", GroupID, re.I):
728 PolarContactsColor = OptionsInfo["PocketContactsInorganicColor"]
729
730 PML = PyMOLUtil.SetupPMLForPolarContactsView(
731 PolarContactsName,
732 PosesName,
733 PocketName,
734 Enable=False,
735 Color=PolarContactsColor,
736 Cutoff=OptionsInfo["PocketContactsCutoff"],
737 )
738 OutFH.write("\n%s\n" % PML)
739
740 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PolarContactsColor, PolarContactsName))
741
742 if re.match("^PocketInorganic$", GroupID, re.I):
743 # Setup pi cation contacts...
744 PiCationContactsID = "%sPiCationContacts" % (GroupID)
745 PiCationContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID]
746 PiCationContactsColor = OptionsInfo["PocketContactsInorganicPiCationColor"]
747
748 PML = PyMOLUtil.SetupPMLForPiCationContactsView(
749 PiCationContactsName,
750 PosesName,
751 PocketName,
752 Enable=False,
753 Color=PiCationContactsColor,
754 Cutoff=OptionsInfo["PocketContactsCutoff"],
755 )
756 OutFH.write("\n%s\n" % PML)
757
758 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
759
760 if re.match("^Pocket$", GroupID, re.I):
761 # Setup hydrophobic contacts...
762 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
763 HydrophobicContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][
764 HydrophobicContactsID
765 ]
766 HydrophobicContactsColor = OptionsInfo["PocketContactsLigandHydrophobicColor"]
767
768 PML = PyMOLUtil.SetupPMLForHydrophobicContactsView(
769 HydrophobicContactsName,
770 PosesName,
771 PocketName,
772 Enable=False,
773 Color=HydrophobicContactsColor,
774 Cutoff=OptionsInfo["PocketContactsCutoff"],
775 )
776 OutFH.write("\n%s\n" % PML)
777 OutFH.write(
778 """cmd.set("label_color", "%s", "%s")\n""" % (HydrophobicContactsColor, HydrophobicContactsName)
779 )
780
781 # Setup pi pi contacts...
782 PiPiContactsID = "%sPiPiContacts" % (GroupID)
783 PiPiContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiPiContactsID]
784 PiPiContactsColor = OptionsInfo["PocketContactsLigandPiPiColor"]
785
786 PML = PyMOLUtil.SetupPMLForPiPiContactsView(
787 PiPiContactsName,
788 PosesName,
789 PocketName,
790 Enable=False,
791 Color=PiPiContactsColor,
792 Cutoff=OptionsInfo["PocketContactsCutoff"],
793 )
794 OutFH.write("\n%s\n" % PML)
795 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiPiContactsColor, PiPiContactsName))
796
797 # Setup pi cation contacts...
798 PiCationContactsID = "%sPiCationContacts" % (GroupID)
799 PiCationContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID]
800 PiCationContactsColor = OptionsInfo["PocketContactsLigandPiCationColor"]
801
802 PML = PyMOLUtil.SetupPMLForPiCationContactsView(
803 PiCationContactsName,
804 PosesName,
805 PocketName,
806 Enable=False,
807 Color=PiCationContactsColor,
808 Cutoff=OptionsInfo["PocketContactsCutoff"],
809 )
810 OutFH.write("\n%s\n" % PML)
811 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
812
813 # Setup halogen contacts...
814 HalogenContactsID = "%sHalogenContacts" % (GroupID)
815 HalogenContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HalogenContactsID]
816 HalogenContactsColor = OptionsInfo["PocketContactsLigandHalogenColor"]
817
818 PML = PyMOLUtil.SetupPMLForHalogenContactsView(
819 HalogenContactsName,
820 LigandName,
821 PocketName,
822 Enable=False,
823 Color=HalogenContactsColor,
824 Cutoff=OptionsInfo["PocketContactsCutoff"],
825 )
826 OutFH.write("\n%s\n" % PML)
827 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HalogenContactsColor, HalogenContactsName))
828
829 # Setup group for an input file...
830 GroupNameID = "%sGroup" % (GroupID)
831 GroupMembersID = "%sGroupMembers" % (GroupID)
832 Enable = True if re.match("^Pocket$", GroupID, re.I) else False
833 Action = "open" if re.match("^Pocket$", GroupID, re.I) else "close"
834
835 GenerateAndWritePMLForGroup(
836 OutFH,
837 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID],
838 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID],
839 Enable,
840 Action,
841 )
842
843 # Setup docked poses group for an input file...
844 Action = "open" if InputFileIndex == 0 else "close"
845 Enable = True if InputFileIndex == 0 else False
846 GenerateAndWritePMLForGroup(
847 OutFH,
848 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupName"],
849 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"],
850 Enable,
851 Action,
852 )
853
854
855 def WritePocketSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
856 """Write out PML for viewing selections for a lgand pocket."""
857
858 if not GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
859 return
860
861 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
862 SelectionsGroupIDPrefix = "PocketSelectionsGroup"
863
864 for Index in range(0, len(OptionsInfo["PocketChainSelectionsInfo"]["Names"])):
865 SelectionName = OptionsInfo["PocketChainSelectionsInfo"]["Names"][Index]
866 Selection = OptionsInfo["PocketChainSelectionsInfo"]["Selections"][Index]
867
868 SelectionNameGroupID = SelectionName
869
870 # Setup a selection object...
871 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
872 SelectionObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionObjectID]
873 SelectionCmd = "(%s and (%s))" % (PocketObjectName, Selection)
874 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(
875 SelectionObjectName,
876 SelectionCmd,
877 OptionsInfo["SelectionsPocketStyle"],
878 Enable=True,
879 IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"],
880 )
881 OutFH.write("\n%s\n" % PML)
882
883 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
884 # Display style for selection objects in surfaces...
885 DisplayStyle = "lines"
886
887 # Setup a generic color surface...
888 SurfaceID = "%s%s%sSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface")
889 SurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceID]
890 PML = PyMOLUtil.SetupPMLForSurfaceView(
891 SurfaceName,
892 SelectionObjectName,
893 Enable=False,
894 Color=OptionsInfo["SurfaceColor"],
895 DisplayAs=DisplayStyle,
896 )
897 OutFH.write("\n%s\n" % PML)
898
899 # Setup a surface colored by hydrphobicity...
900 HydrophobicSurfaceID = "%s%sSurfaceHydrophobicity" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
901 HydrophobicSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID]
902 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(
903 HydrophobicSurfaceName,
904 SelectionObjectName,
905 ColorPalette=OptionsInfo["SurfaceColorPalette"],
906 Enable=False,
907 DisplayAs=DisplayStyle,
908 )
909 OutFH.write("\n%s\n" % PML)
910
911 # Setup a surface colored by hydrphobicity and charge...
912 HydrophobicChargeSurfaceID = "%s%sSurfaceHydrophobicityCharge" % (
913 SelectionsGroupIDPrefix,
914 SelectionNameGroupID,
915 )
916 HydrophobicChargeSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicChargeSurfaceID]
917 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(
918 HydrophobicChargeSurfaceName,
919 SelectionObjectName,
920 OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"],
921 OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"],
922 OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"],
923 OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"],
924 Enable=False,
925 DisplayAs=DisplayStyle,
926 )
927 OutFH.write("\n%s\n" % PML)
928
929 # Setup group for surfaces...
930 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
931 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
932 GenerateAndWritePMLForGroup(
933 OutFH,
934 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupID],
935 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupMembersID],
936 True,
937 "open",
938 )
939
940 # Setup groups for named selections...
941 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
942 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
943 GenerateAndWritePMLForGroup(
944 OutFH,
945 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupID],
946 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID],
947 True,
948 "open",
949 )
950
951 # Setup a group for selections...
952 SelectionsGroupID = "%s" % (SelectionsGroupIDPrefix)
953 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupIDPrefix)
954 GenerateAndWritePMLForGroup(
955 OutFH,
956 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID],
957 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID],
958 True,
959 "close",
960 )
961
962
963 def WritePocketSurfacesTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
964 """Write out PML for viewing surfaces for a ligand pocket."""
965
966 if not GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
967 return
968
969 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
970
971 SurfacesGroupID = "%sSurfacesGroup" % (PocketObjectID)
972 SurfacesGroupMembersID = "%sSurfacesGroupMembers" % (PocketObjectID)
973
974 # Cavity modes: 1 or 2. 1: Cavity surfaces; 2: Culled cavity surfaces...
975 CavityMode = 2
976
977 # Setup surfaces subgroup and its members...
978 for SubGroupType in ["Surface", "Cavity"]:
979 ProcessingCavity = True if re.match("^Cavity$", SubGroupType, re.I) else False
980
981 SubGroupID = re.sub("_", "", SubGroupType)
982 SurfacesSubGroupID = "%s%sGroup" % (SurfacesGroupID, SubGroupID)
983 SurfacesSubGroupMembersID = "%sMembers" % (SurfacesSubGroupID)
984
985 # Turn off lines display for cavity surfaces...
986 DisplayStyle = None if ProcessingCavity else "lines"
987
988 # Setup a generic color surface...
989 SurfaceID = "%sSurface" % (SurfacesSubGroupID)
990 SurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceID]
991 PML = PyMOLUtil.SetupPMLForSurfaceView(
992 SurfaceName, PocketObjectName, Enable=False, Color=OptionsInfo["SurfaceColor"], DisplayAs=DisplayStyle
993 )
994 OutFH.write("\n%s\n" % PML)
995
996 if ProcessingCavity:
997 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (CavityMode, SurfaceName))
998
999 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], SurfaceName))
1000
1001 if GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
1002 # Setup a surface colored by hydrphobicity...
1003 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SurfacesSubGroupID)
1004 HydrophobicSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID]
1005 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(
1006 HydrophobicSurfaceName,
1007 PocketObjectName,
1008 ColorPalette=OptionsInfo["SurfaceColorPalette"],
1009 Enable=False,
1010 DisplayAs=DisplayStyle,
1011 )
1012 OutFH.write("\n%s\n" % PML)
1013
1014 if ProcessingCavity:
1015 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (CavityMode, HydrophobicSurfaceName))
1016
1017 OutFH.write(
1018 """cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], HydrophobicSurfaceName)
1019 )
1020
1021 # Setup a surface colored by hydrphobicity and charge...
1022 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SurfacesSubGroupID)
1023 HydrophobicChargeSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicChargeSurfaceID]
1024 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(
1025 HydrophobicChargeSurfaceName,
1026 PocketObjectName,
1027 OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"],
1028 OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"],
1029 OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"],
1030 OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"],
1031 Enable=False,
1032 DisplayAs=DisplayStyle,
1033 )
1034 OutFH.write("\n%s\n" % PML)
1035
1036 if ProcessingCavity:
1037 OutFH.write(
1038 """cmd.set("surface_cavity_mode", %d, "%s")\n""" % (CavityMode, HydrophobicChargeSurfaceName)
1039 )
1040
1041 OutFH.write(
1042 """cmd.set("label_color", "%s", "%s")\n"""
1043 % (OptionsInfo["PocketLabelColor"], HydrophobicChargeSurfaceName)
1044 )
1045
1046 if GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
1047 # Set up a electrostatics surface...
1048 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SurfacesSubGroupID)
1049 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SurfacesSubGroupID)
1050 ElectrostaticsGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupID]
1051 ElectrostaticsGroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][
1052 ElectrostaticsGroupMembersID
1053 ]
1054 WriteSurfaceElectrostaticsView(
1055 SubGroupType,
1056 OutFH,
1057 PocketObjectName,
1058 ElectrostaticsGroupName,
1059 ElectrostaticsGroupMembers,
1060 DisplayAs=DisplayStyle,
1061 SurfaceCavityMode=CavityMode,
1062 )
1063
1064 # Setup surfaces sub group...
1065 GenerateAndWritePMLForGroup(
1066 OutFH,
1067 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupID],
1068 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID],
1069 True,
1070 "open",
1071 )
1072
1073 # Setup surface group...
1074 GenerateAndWritePMLForGroup(
1075 OutFH,
1076 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupID],
1077 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID],
1078 True,
1079 "open",
1080 )
1081
1082
1083 def WritePocketResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
1084 """Write out PML for viewing residue types for a ligand pocket."""
1085
1086 if not GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
1087 return
1088
1089 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
1090
1091 ResiduesGroupID = "%sResiduesGroup" % (PocketObjectID)
1092 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
1093
1094 # Setup residue types objects...
1095 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1096 SubGroupID = re.sub("_", "", SubGroupType)
1097
1098 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
1099 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
1100
1101 SubGroupMemberID = "%sResidues" % (ResiduesSubGroupID)
1102 ResiduesObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID]
1103
1104 SubGroupMemberID = "%sSurface" % (ResiduesSubGroupID)
1105 ResiduesSurfaceObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID]
1106
1107 ResiduesColor = OptionsInfo["ResidueTypesParams"][SubGroupType]["Color"]
1108 ResiduesNames = OptionsInfo["ResidueTypesParams"][SubGroupType]["Residues"]
1109
1110 NegateResidueNames = True if re.match("^Other$", SubGroupType, re.I) else False
1111 WriteResidueTypesResiduesAndSurfaceView(
1112 OutFH,
1113 PocketObjectName,
1114 ResiduesObjectName,
1115 ResiduesSurfaceObjectName,
1116 ResiduesColor,
1117 ResiduesNames,
1118 NegateResidueNames,
1119 )
1120
1121 # Setup residue type sub groups...
1122 GenerateAndWritePMLForGroup(
1123 OutFH,
1124 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID],
1125 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID],
1126 True,
1127 "close",
1128 )
1129
1130 # Setup residue types group...
1131 GenerateAndWritePMLForGroup(
1132 OutFH,
1133 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupID],
1134 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID],
1135 False,
1136 "close",
1137 )
1138
1139
1140 def WriteChainAloneChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1141 """Write out PML for viewing selections for a chain."""
1142
1143 if not GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
1144 return
1145
1146 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
1147 SelectionsGroupIDPrefix = "ChainAloneSelections"
1148
1149 for Index in range(0, len(OptionsInfo["ChainSelectionsInfo"]["Names"])):
1150 SelectionName = OptionsInfo["ChainSelectionsInfo"]["Names"][Index]
1151 Selection = OptionsInfo["ChainSelectionsInfo"]["Selections"][Index]
1152
1153 SelectionNameGroupID = SelectionName
1154
1155 # Setup a selection object...
1156 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1157 SelectionObjectName = PyMOLObjectNames["Chains"][ChainID][SelectionObjectID]
1158 SelectionCmd = "(%s and (%s))" % (ChainName, Selection)
1159 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(
1160 SelectionObjectName,
1161 SelectionCmd,
1162 OptionsInfo["SelectionsChainStyle"],
1163 Enable=True,
1164 IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"],
1165 )
1166 OutFH.write("\n%s\n" % PML)
1167
1168 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
1169 # Display style for selection objects in surfaces...
1170 DisplayStyle = "lines"
1171
1172 # Setup a generic color surface...
1173 SurfaceID = "%s%s%sSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface")
1174 SurfaceName = PyMOLObjectNames["Chains"][ChainID][SurfaceID]
1175 PML = PyMOLUtil.SetupPMLForSurfaceView(
1176 SurfaceName,
1177 SelectionObjectName,
1178 Enable=False,
1179 Color=OptionsInfo["SurfaceColor"],
1180 DisplayAs=DisplayStyle,
1181 )
1182 OutFH.write("\n%s\n" % PML)
1183
1184 if GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
1185 # Setup a surface colored by hydrphobicity...
1186 HydrophobicSurfaceID = "%s%sSurfaceHydrophobicity" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1187 HydrophobicSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicSurfaceID]
1188 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(
1189 HydrophobicSurfaceName,
1190 SelectionObjectName,
1191 ColorPalette=OptionsInfo["SurfaceColorPalette"],
1192 Enable=False,
1193 DisplayAs=DisplayStyle,
1194 )
1195 OutFH.write("\n%s\n" % PML)
1196
1197 # Setup a surface colored by hydrphobicity and charge...
1198 HydrophobicChargeSurfaceID = "%s%sSurfaceHydrophobicityCharge" % (
1199 SelectionsGroupIDPrefix,
1200 SelectionNameGroupID,
1201 )
1202 HydrophobicChargeSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicChargeSurfaceID]
1203 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(
1204 HydrophobicChargeSurfaceName,
1205 SelectionObjectName,
1206 OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"],
1207 OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"],
1208 OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"],
1209 OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"],
1210 Enable=False,
1211 DisplayAs=DisplayStyle,
1212 )
1213 OutFH.write("\n%s\n" % PML)
1214
1215 # Setup group for surfaces...
1216 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1217 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1218 GenerateAndWritePMLForGroup(
1219 OutFH,
1220 PyMOLObjectNames["Chains"][ChainID][SurfaceGroupID],
1221 PyMOLObjectNames["Chains"][ChainID][SurfaceGroupMembersID],
1222 True,
1223 "close",
1224 )
1225
1226 # Setup groups for named selections...
1227 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1228 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1229 GenerateAndWritePMLForGroup(
1230 OutFH,
1231 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID],
1232 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID],
1233 True,
1234 "open",
1235 )
1236
1237 # Setup a group for selections...
1238 SelectionsGroupID = "%sGroup" % (SelectionsGroupIDPrefix)
1239 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupIDPrefix)
1240 GenerateAndWritePMLForGroup(
1241 OutFH,
1242 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID],
1243 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID],
1244 False,
1245 "close",
1246 )
1247
1248
1249 def WriteChainAloneResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1250 """Write out PML for viewing residue types for a chain."""
1251
1252 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
1253 return
1254
1255 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
1256
1257 # Setup residue types objects...
1258 ResiduesGroupIDPrefix = "ChainAloneResidues"
1259 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1260 SubGroupID = re.sub("_", "", SubGroupType)
1261
1262 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, SubGroupID)
1263 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
1264
1265 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, SubGroupID)
1266 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
1267
1268 ResiduesColor = OptionsInfo["ResidueTypesParams"][SubGroupType]["Color"]
1269 ResiduesNames = OptionsInfo["ResidueTypesParams"][SubGroupType]["Residues"]
1270
1271 NegateResidueNames = True if re.match("^Other$", SubGroupType, re.I) else False
1272 WriteResidueTypesResiduesAndSurfaceView(
1273 OutFH,
1274 ChainName,
1275 ResiduesObjectName,
1276 ResiduesSurfaceObjectName,
1277 ResiduesColor,
1278 ResiduesNames,
1279 NegateResidueNames,
1280 )
1281
1282 # Setup sub groups for residue types..
1283 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
1284 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
1285
1286 # Setup residue type sub groups...
1287 GenerateAndWritePMLForGroup(
1288 OutFH,
1289 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID],
1290 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID],
1291 True,
1292 "close",
1293 )
1294
1295 # Setup residue types group...
1296 GenerateAndWritePMLForGroup(
1297 OutFH,
1298 PyMOLObjectNames["Chains"][ChainID]["ChainAloneResiduesGroup"],
1299 PyMOLObjectNames["Chains"][ChainID]["ChainAloneResiduesGroupMembers"],
1300 False,
1301 "close",
1302 )
1303
1304
1305 def WriteChainAloneBFactorViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1306 """Write out PML for viewing B factor values for a chain."""
1307
1308 if not GetChainAloneBFactorStatus(FileIndex, ChainID):
1309 return
1310
1311 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
1312
1313 # Setup cartoon...
1314 Name = PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorCartoon"]
1315 PML = PyMOLUtil.SetupPMLForBFactorCartoonView(
1316 Name, ChainName, ColorPalette=OptionsInfo["BFactorColorPalette"], Enable=False
1317 )
1318 OutFH.write("\n%s\n" % PML)
1319
1320 # Setup putty...
1321 Name = PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"]
1322 PML = PyMOLUtil.SetupPMLForBFactorPuttyView(
1323 Name, ChainName, ColorPalette=OptionsInfo["BFactorColorPalette"], Enable=True
1324 )
1325 OutFH.write("\n%s\n" % PML)
1326
1327 # Setup B factor group...
1328 GenerateAndWritePMLForGroup(
1329 OutFH,
1330 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroup"],
1331 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"],
1332 False,
1333 "close",
1334 )
1335
1336
1337 def WriteChainAloneDisulfideBondsView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1338 """Write out PML for viewing disulfide bonds for a chain."""
1339
1340 if not GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
1341 return
1342
1343 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
1344 Name = PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"]
1345
1346 PML = PyMOLUtil.SetupPMLForDisulfideBondsView(Name, ChainName, "sticks", Enable=True)
1347 OutFH.write("\n%s\n" % PML)
1348
1349 # Setup disulfide bonds group...
1350 GenerateAndWritePMLForGroup(
1351 OutFH,
1352 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"],
1353 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"],
1354 True,
1355 "close",
1356 )
1357
1358
1359 def WriteChainAloneSaltBridgesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1360 """Write out PML for viewing salt bridges for a chain."""
1361
1362 if not GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
1363 return
1364
1365 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
1366
1367 # Seup salt bridges resiudes group...
1368 PositivelyChargedResiduesName = PyMOLObjectNames["Chains"][ChainID][
1369 "ChainAloneSaltBridgesResiduesPositivelyCharged"
1370 ]
1371 PML = PyMOLUtil.SetupPMLForSaltBridgesResiduesView(
1372 PositivelyChargedResiduesName,
1373 ChainName,
1374 OptionsInfo["SaltBridgesChainResiduesInfo"]["Positively_Charged"],
1375 "lines",
1376 Enable=True,
1377 )
1378 OutFH.write("\n%s\n" % PML)
1379
1380 NegativelyChargedResiduesName = PyMOLObjectNames["Chains"][ChainID][
1381 "ChainAloneSaltBridgesResiduesNegativelyCharged"
1382 ]
1383 PML = PyMOLUtil.SetupPMLForSaltBridgesResiduesView(
1384 NegativelyChargedResiduesName,
1385 ChainName,
1386 OptionsInfo["SaltBridgesChainResiduesInfo"]["Negatively_Charged"],
1387 "lines",
1388 Enable=True,
1389 )
1390 OutFH.write("\n%s\n" % PML)
1391
1392 GenerateAndWritePMLForGroup(
1393 OutFH,
1394 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroup"],
1395 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"],
1396 True,
1397 "open",
1398 )
1399
1400 # Setup salt bridges contacts...
1401 ContactsColor = OptionsInfo["SaltBridgesChainContactsColor"]
1402 ContactsName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesContacts"]
1403 PML = PyMOLUtil.SetupPMLForPolarContactsView(
1404 ContactsName,
1405 PositivelyChargedResiduesName,
1406 NegativelyChargedResiduesName,
1407 Enable=True,
1408 Color=ContactsColor,
1409 Cutoff=OptionsInfo["SaltBridgesChainCutoff"],
1410 )
1411 OutFH.write("\n%s\n" % PML)
1412
1413 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (ContactsColor, ContactsName))
1414
1415 # Setup salt bridges group...
1416 GenerateAndWritePMLForGroup(
1417 OutFH,
1418 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"],
1419 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"],
1420 False,
1421 "close",
1422 )
1423
1424
1425 def WriteResidueTypesResiduesAndSurfaceView(
1426 OutFH, SelectionObjectName, Name, SurfaceName, ResiduesColor, ResiduesNames, NegateResidueNames
1427 ):
1428 """Write residue types residues and surface view."""
1429
1430 ResidueNamesSelection = "+".join(ResiduesNames)
1431 if NegateResidueNames:
1432 Selection = "%s and (not resn %s)" % (SelectionObjectName, ResidueNamesSelection)
1433 else:
1434 Selection = "%s and (resn %s)" % (SelectionObjectName, ResidueNamesSelection)
1435
1436 # Setup residues...
1437 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(
1438 Name, Selection, "lines", ResiduesColor, True, IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"]
1439 )
1440 OutFH.write("\n%s\n" % PML)
1441
1442 # Setup surface...
1443 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(
1444 SurfaceName, Selection, "surface", ResiduesColor, True, IgnoreHydrogens=OptionsInfo["IgnoreHydrogens"]
1445 )
1446 OutFH.write("\n%s\n" % PML)
1447
1448
1449 def WriteSurfaceElectrostaticsView(
1450 Mode,
1451 OutFH,
1452 SelectionObjectName,
1453 ElectrostaticsGroupName,
1454 ElectrostaticsGroupMembers,
1455 DisplayAs=None,
1456 SurfaceCavityMode=2,
1457 ):
1458 """Write out PML for viewing surface electrostatics."""
1459
1460 if len(ElectrostaticsGroupMembers) == 5:
1461 Name, ContactPotentialName, MapName, LegendName, VolumeName = ElectrostaticsGroupMembers
1462 else:
1463 Name, ContactPotentialName, MapName, LegendName = ElectrostaticsGroupMembers
1464 VolumeName = None
1465
1466 PMLCmds = []
1467
1468 # Setup chain...
1469 PMLCmds.append("""cmd.create("%s", "(%s)")""" % (Name, SelectionObjectName))
1470
1471 # Setup vacuum electrostatics surface along with associated objects...
1472 PMLCmds.append("""util.protein_vacuum_esp("%s", mode=2, quiet=0, _self=cmd)""" % (Name))
1473 PMLCmds.append("""cmd.set_name("%s_e_chg", "%s")""" % (Name, ContactPotentialName))
1474
1475 if DisplayAs is not None:
1476 PMLCmds.append("""cmd.show("%s", "(%s)")""" % (DisplayAs, ContactPotentialName))
1477
1478 if re.match("^Cavity$", Mode, re.I):
1479 if SurfaceCavityMode is not None:
1480 PMLCmds.append("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (SurfaceCavityMode, ContactPotentialName))
1481
1482 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(ContactPotentialName, Enable=True))
1483
1484 PMLCmds.append("""cmd.set_name("%s_e_map", "%s")""" % (Name, MapName))
1485 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MapName, Enable=False))
1486
1487 PMLCmds.append("""cmd.set_name("%s_e_pot", "%s")""" % (Name, LegendName))
1488 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(LegendName, Enable=False))
1489
1490 if VolumeName is not None:
1491 PMLCmds.append("""cmd.volume("%s", "%s", "%s", "(%s)")""" % (VolumeName, MapName, "esp", Name))
1492 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(VolumeName, Enable=False))
1493
1494 # Delete name and take it out from the group membership. It is
1495 # is already part of ContactPotential object.
1496 PMLCmds.append("""cmd.delete("%s")""" % (Name))
1497 ElectrostaticsGroupMembers.pop(0)
1498
1499 PML = "\n".join(PMLCmds)
1500
1501 OutFH.write("\n%s\n" % PML)
1502
1503 # Setup group...
1504 GenerateAndWritePMLForGroup(OutFH, ElectrostaticsGroupName, ElectrostaticsGroupMembers, False, "close")
1505
1506
1507 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable=False, Action="close"):
1508 """Generate and write PML for group."""
1509
1510 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
1511 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
1512 OutFH.write("%s\n" % PML)
1513
1514
1515 def WriteTrajectoriesView(OutFH, FileIndex, PyMOLObjectNames):
1516 """Write out PML for viewing trajectories for a PDB file."""
1517
1518 if not GetTrajectoriesStatus(FileIndex):
1519 return
1520
1521 # Setup topology view...
1522 Name = PyMOLObjectNames["Trajectories"]["Topology"]
1523
1524 PMLCmds = []
1525 PMLCmds.append("""cmd.load("%s", "%s")""" % (OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex], Name))
1526 PMLCmds.append("""cmd.show("cartoon", "%s")""" % (Name))
1527 PMLCmds.append("""util.cba(33, "%s", _self = cmd)""" % (Name))
1528 PMLCmds.append("""cmd.show("sticks", "(organic and (%s))")""" % (Name))
1529 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable=False))
1530
1531 PML = "\n".join(PMLCmds)
1532 OutFH.write("\n%s\n" % PML)
1533
1534 # Write view for each trajectory file...
1535 for TrajFileIndex, TrajFile in enumerate(OptionsInfo["TrajectoriesInfo"]["TrajFiles"][FileIndex]):
1536 WriteTrajectoryViewTrajectoryFile(OutFH, FileIndex, PyMOLObjectNames, TrajFileIndex)
1537
1538 GenerateAndWritePMLForGroup(
1539 OutFH,
1540 PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"],
1541 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"],
1542 False,
1543 "close",
1544 )
1545
1546
1547 def WriteTrajectoryViewTrajectoryFile(OutFH, PDBFileIndex, PyMOLObjectNames, TrajFileIndex):
1548 """Write out PML for viewing a trajectory file."""
1549
1550 TrajFile = OptionsInfo["TrajectoriesInfo"]["TrajFiles"][PDBFileIndex][TrajFileIndex]
1551 TrajFileID = OptionsInfo["TrajectoriesInfo"]["TrajFilesIDs"][PDBFileIndex][TrajFileIndex]
1552
1553 OutFH.write("""\n""\n"Setting up views for trajectory file ID %s..."\n""\n""" % (TrajFileID))
1554
1555 # Setup trajectory view...
1556 Name = PyMOLObjectNames["Trajectories"][TrajFileID]["Trajectory"]
1557 PDBFile = OptionsInfo["InfilesInfo"]["InfilesNames"][PDBFileIndex]
1558
1559 PMLCmds = []
1560 PMLCmds.append("""cmd.load("%s", "%s")""" % (PDBFile, Name))
1561 PMLCmds.append("""cmd.load_traj("%s", "%s", state = 1)""" % (TrajFile, Name))
1562 PMLCmds.append("""cmd.show("cartoon", "%s")""" % (Name))
1563 PMLCmds.append("""util.cba(33, "%s", _self = cmd)""" % (Name))
1564 PMLCmds.append("""cmd.show("sticks", "(organic and (%s))")""" % (Name))
1565 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable=True))
1566
1567 PML = "\n".join(PMLCmds)
1568 OutFH.write("%s\n" % PML)
1569
1570 # Setup group for a trajectory file...
1571 Action = "open" if TrajFileIndex == 0 else "close"
1572 Enable = True if TrajFileIndex == 0 else False
1573 GenerateAndWritePMLForGroup(
1574 OutFH,
1575 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroup"],
1576 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"],
1577 Enable,
1578 Action,
1579 )
1580
1581
1582 def GeneratePyMOLSessionFile():
1583 """Generate PME file from PML file."""
1584
1585 PSEOutfile = OptionsInfo["PSEOutfile"]
1586 PMLOutfile = OptionsInfo["PMLOutfile"]
1587
1588 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
1589
1590 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
1591
1592 if not os.path.exists(PSEOutfile):
1593 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
1594
1595 if not OptionsInfo["PMLOut"]:
1596 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
1597 os.remove(PMLOutfile)
1598
1599
1600 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
1601 """Delete empty PyMOL objects."""
1602
1603 if OptionsInfo["AllowEmptyObjects"]:
1604 return
1605
1606 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1607 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1608 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
1609
1610 # Delete any chain level objects...
1611 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
1612 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
1613
1614 # Delete chain selection objects...
1615 DeleteEmptyChainSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1616
1617 # Delete residue type objects...
1618 DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1619
1620 # Delete disulfide bonds objects...
1621 DeleteEmptyChainDisulfideBondsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1622
1623 # Delete salt bridges objects...
1624 DeleteEmptyChainSaltBridgesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1625
1626 # Delete ligand objects...
1627 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
1628 # Delete ligand level objects...
1629 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
1630 GroupNameID = "%sGroup" % (GroupID)
1631 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
1632
1633 GroupTypeObjectID = "%s" % (GroupID)
1634 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
1635
1636 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
1637
1638 if re.match("^Pocket$", GroupID, re.I):
1639 DeleteEmptyPocketSelectionsObjects(
1640 OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID
1641 )
1642 DeleteEmptyPocketResidueTypesObjects(
1643 OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID
1644 )
1645
1646 # Delete docked poses objects...
1647 DeleteEmptyChainDockedPosesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1648
1649
1650 def DeleteEmptyChainSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1651 """Delete empty chain selection objects"""
1652
1653 if not GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
1654 return
1655
1656 SelectionsGroupIDPrefix = "ChainAloneSelections"
1657
1658 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
1659 SelectionNameGroupID = SelectionName
1660
1661 # Delete surface objects and surface group...
1662 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
1663 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1664 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1665 WritePMLToCheckAndDeleteEmptyObjects(
1666 OutFH,
1667 ",".join(PyMOLObjectNames["Chains"][ChainID][SurfaceGroupMembersID]),
1668 PyMOLObjectNames["Chains"][ChainID][SurfaceGroupID],
1669 )
1670
1671 # Delete Selection object and selection name group...
1672 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1673 SelectionsGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1674 WritePMLToCheckAndDeleteEmptyObjects(
1675 OutFH,
1676 PyMOLObjectNames["Chains"][ChainID][SelectionObjectID],
1677 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID],
1678 )
1679
1680
1681 def DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1682 """Delete empty chain residue objects."""
1683
1684 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
1685 return
1686
1687 ResiduesGroupIDPrefix = "ChainAloneResidues"
1688 for GroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1689 GroupID = re.sub("_", "", GroupType)
1690
1691 ResiduesGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, GroupID)
1692 GroupName = PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID]
1693
1694 GroupObjectNamesList = []
1695
1696 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, GroupID)
1697 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
1698 GroupObjectNamesList.append(ResiduesObjectName)
1699
1700 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, GroupID)
1701 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
1702 GroupObjectNamesList.append(ResiduesSurfaceObjectName)
1703
1704 GroupObjectNames = ",".join(GroupObjectNamesList)
1705 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupObjectNames, GroupName)
1706
1707
1708 def DeleteEmptyChainDisulfideBondsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1709 """Delete empty chain disulfide bonds objects."""
1710
1711 if not GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
1712 return
1713
1714 WritePMLToCheckAndDeleteEmptyObjects(
1715 OutFH,
1716 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"],
1717 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"],
1718 )
1719
1720
1721 def DeleteEmptyChainSaltBridgesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1722 """Delete empty chain salt bridges objects."""
1723
1724 if not GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
1725 return
1726
1727 Names = []
1728 Names.append(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesPositivelyCharged"])
1729 Names.append(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesNegativelyCharged"])
1730
1731 WritePMLToCheckAndDeleteEmptyObjects(
1732 OutFH, ",".join(Names), PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"]
1733 )
1734
1735
1736 def DeleteEmptyPocketSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
1737 """Delete empty pocket selection objects."""
1738
1739 if not GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
1740 return
1741
1742 SelectionsGroupIDPrefix = "PocketSelectionsGroup"
1743
1744 for SelectionName in OptionsInfo["PocketChainSelectionsInfo"]["Names"]:
1745 SelectionNameGroupID = SelectionName
1746
1747 # Delete surface objects and surface group...
1748 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
1749 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1750 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1751 WritePMLToCheckAndDeleteEmptyObjects(
1752 OutFH,
1753 ",".join(PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupMembersID]),
1754 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupID],
1755 )
1756
1757 # Delete Selection object and selection name group...
1758 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1759 SelectionsGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1760 WritePMLToCheckAndDeleteEmptyObjects(
1761 OutFH,
1762 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionObjectID],
1763 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID],
1764 )
1765
1766
1767 def DeleteEmptyPocketResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
1768 """Delete empty chain residue objects."""
1769
1770 if not GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
1771 return
1772
1773 ResiduesGroupID = "%sResiduesGroup" % (PocketObjectID)
1774
1775 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1776 SubGroupID = re.sub("_", "", SubGroupType)
1777
1778 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
1779 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
1780
1781 SubGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID]
1782 SubGroupObjectNames = ",".join(PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID])
1783
1784 WritePMLToCheckAndDeleteEmptyObjects(OutFH, SubGroupObjectNames, SubGroupName)
1785
1786
1787 def DeleteEmptyChainDockedPosesObjects(OutFH, PDBFileIndex, PyMOLObjectNames, ChainID):
1788 """Delete empty chain docked poses objest."""
1789
1790 if not GetChainAloneDockedPosesStatus(PDBFileIndex, ChainID):
1791 return
1792
1793 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][PDBFileIndex]
1794 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
1795
1796 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
1797 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
1798 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
1799 GroupNameID = "%sGroup" % (GroupID)
1800 GroupName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID]
1801
1802 GroupTypeObjectID = "%sPocket" % (GroupID)
1803 GroupTypeObjectName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupTypeObjectID]
1804
1805 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
1806
1807
1808 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName=None):
1809 """Write PML to check and delete empty PyMOL objects."""
1810
1811 if ParentObjectName is None:
1812 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
1813 else:
1814 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
1815
1816 OutFH.write("%s\n" % PML)
1817
1818
1819 def SetupPyMOLObjectNames(FileIndex):
1820 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
1821 chains and ligands present in input file.
1822 """
1823
1824 PyMOLObjectNames = {}
1825 PyMOLObjectNames["Chains"] = {}
1826 PyMOLObjectNames["Ligands"] = {}
1827 PyMOLObjectNames["DockedPosesInputFile"] = {}
1828 PyMOLObjectNames["Trajectories"] = {}
1829
1830 # Setup groups and objects for complex...
1831 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
1832
1833 # Setup groups and object for trajectories...
1834 if GetTrajectoriesStatus(FileIndex):
1835 SetupPyMOLObjectNamesForTrajectories(FileIndex, PyMOLObjectNames)
1836
1837 # Setup groups and objects for chain...
1838 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1839 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1840 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
1841
1842 # Setup groups and objects for ligand...
1843 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
1844 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
1845
1846 # Setup group and objects for docked poses...
1847 if GetChainAloneDockedPosesStatus(FileIndex, ChainID):
1848 SetupPyMOLObjectNamesForDockedPoses(FileIndex, PyMOLObjectNames, ChainID)
1849
1850 return PyMOLObjectNames
1851
1852
1853 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
1854 """Setup groups and objects for complex."""
1855
1856 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
1857
1858 PDBGroupName = "%s" % PDBFileRoot
1859 PyMOLObjectNames["PDBGroup"] = PDBGroupName
1860 PyMOLObjectNames["PDBGroupMembers"] = []
1861
1862 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
1863 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
1864 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
1865
1866 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
1867 if OptionsInfo["SurfaceComplex"]:
1868 PyMOLObjectNames["ComplexHydrophobicSurface"] = "%s.Surface" % ComplexGroupName
1869
1870 PyMOLObjectNames["ComplexGroupMembers"] = []
1871 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
1872 if OptionsInfo["SurfaceComplex"]:
1873 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexHydrophobicSurface"])
1874
1875
1876 def SetupPyMOLObjectNamesForTrajectories(FileIndex, PyMOLObjectNames):
1877 """Setup groups and objects for a PDB file."""
1878
1879 if not GetTrajectoriesStatus(FileIndex):
1880 return
1881
1882 # Setup a group for trajectories....
1883 TrajectoriesGroupName = "%s.Trajectories" % PyMOLObjectNames["PDBGroup"]
1884 PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"] = TrajectoriesGroupName
1885 PyMOLObjectNames["PDBGroupMembers"].append(TrajectoriesGroupName)
1886
1887 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"] = []
1888
1889 # Setup a topolgy object...
1890 TopologyName = "%s.Topology" % TrajectoriesGroupName
1891 PyMOLObjectNames["Trajectories"]["Topology"] = TopologyName
1892 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"].append(TopologyName)
1893
1894 # Setup trajectory objects...
1895 for TrajFileIndex, TrajFile in enumerate(OptionsInfo["TrajectoriesInfo"]["TrajFiles"][FileIndex]):
1896 SetupPyMOLObjectNamesForTrajectoryFile(FileIndex, PyMOLObjectNames, TrajFileIndex)
1897
1898
1899 def SetupPyMOLObjectNamesForTrajectoryFile(PDBFileIndex, PyMOLObjectNames, TrajFileIndex):
1900 """Setup groups and objest for a trajectory file for a PDB file."""
1901
1902 TrajFileID = OptionsInfo["TrajectoriesInfo"]["TrajFilesIDs"][PDBFileIndex][TrajFileIndex]
1903
1904 PyMOLObjectNames["Trajectories"][TrajFileID] = {}
1905
1906 TrajectoriesGroupName = PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"]
1907
1908 # Setup a trajectories level trajectory file group...
1909 TrajectoryFileGroupName = "%s.%s" % (TrajectoriesGroupName, TrajFileID)
1910 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroup"] = TrajectoryFileGroupName
1911 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"].append(TrajectoryFileGroupName)
1912
1913 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"] = []
1914
1915 # Setup object for a trajectory file...
1916 TrajectoryName = "%s.Trajectory" % (TrajectoryFileGroupName)
1917 PyMOLObjectNames["Trajectories"][TrajFileID]["Trajectory"] = TrajectoryName
1918 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"].append(TrajectoryName)
1919
1920
1921 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
1922 """Setup groups and objects for chain."""
1923
1924 PDBGroupName = PyMOLObjectNames["PDBGroup"]
1925
1926 PyMOLObjectNames["Chains"][ChainID] = {}
1927 PyMOLObjectNames["Ligands"][ChainID] = {}
1928
1929 # Set up chain group and chain objects...
1930 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
1931 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
1932 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
1933 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
1934
1935 # Setup chain complex group and objects...
1936 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
1937 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
1938 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
1939
1940 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
1941
1942 Name = "%s.Complex" % (ChainComplexGroupName)
1943 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = Name
1944 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1945
1946 if OptionsInfo["SurfaceChainComplex"]:
1947 Name = "%s.Surface" % (ChainComplexGroupName)
1948 PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"] = Name
1949 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1950
1951 # Setup up a group for individual chains...
1952 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
1953 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
1954 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
1955
1956 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
1957
1958 Name = "%s.Chain" % (ChainAloneGroupName)
1959 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
1960 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
1961
1962 if GetChainAloneBFactorStatus(FileIndex, ChainID):
1963 # Setup B factor group and add it to chain alone group...
1964 BFactorGroupName = "%s.BFactor" % (ChainAloneGroupName)
1965 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroup"] = BFactorGroupName
1966 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(BFactorGroupName)
1967
1968 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"] = []
1969
1970 # Setup cartoon...
1971 Name = "%s.Cartoon" % (BFactorGroupName)
1972 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorCartoon"] = Name
1973 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"].append(Name)
1974
1975 # Setup putty...
1976 Name = "%s.Putty" % (BFactorGroupName)
1977 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"] = Name
1978 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"].append(Name)
1979
1980 if GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
1981 # Setup selections group and its subgroups..
1982 SelectionsGroupName = "%s.Selections" % (ChainAloneGroupName)
1983
1984 SelectionsGroupIDPrefix = "ChainAloneSelections"
1985 SelectionsGroupID = "%sGroup" % SelectionsGroupIDPrefix
1986
1987 # Add selections group to chain alone group...
1988 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID] = SelectionsGroupName
1989 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SelectionsGroupName)
1990
1991 # Initialize selections group members...
1992 SelectionsGroupMembersID = "%sGroupMembers" % SelectionsGroupIDPrefix
1993 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID] = []
1994
1995 # Setup selections name sub group and its members...
1996 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
1997 SelectionNameGroupID = SelectionName
1998
1999 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
2000 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
2001
2002 # Add selections name sub group to selections group...
2003 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID] = SelectionsNameGroupName
2004 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID].append(SelectionsNameGroupName)
2005
2006 # Initialize selections names sub group members...
2007 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
2008 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID] = []
2009
2010 # Add selection member to selections name group...
2011 SubGroupMemberName = "%s.Selection" % (SelectionsNameGroupName)
2012 SubGroupMemberID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
2013
2014 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
2015 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SubGroupMemberName)
2016
2017 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
2018 # Setup a surface sub group and add it to selections name group...
2019
2020 SelectionsNameSurfaceGroupName = "%s.Surface" % (SelectionsNameGroupName)
2021 SelectionsNameSurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
2022
2023 # Add selection surface group to selection name group...
2024 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupID] = SelectionsNameSurfaceGroupName
2025 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SelectionsNameSurfaceGroupName)
2026
2027 # Initialize surface names sub group members...
2028 SelectionsNameSurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (
2029 SelectionsGroupIDPrefix,
2030 SelectionNameGroupID,
2031 )
2032 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID] = []
2033
2034 # Setup a generic color surface...
2035 SubGroupMemberName = "%s.Surface" % (SelectionsNameSurfaceGroupName)
2036 SubGroupMemberID = "%s%s%sSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface")
2037 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
2038 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID].append(SubGroupMemberName)
2039
2040 if GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
2041 # Setup surfaces...
2042 for MemberType in ["Hydrophobicity", "Hydrophobicity_Charge"]:
2043 MemberID = re.sub("_", "", MemberType)
2044
2045 SubGroupMemberName = "%s.%s" % (SelectionsNameSurfaceGroupName, MemberType)
2046 SubGroupMemberID = "%s%s%s%s" % (
2047 SelectionsGroupIDPrefix,
2048 SelectionNameGroupID,
2049 "Surface",
2050 MemberID,
2051 )
2052
2053 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
2054 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID].append(
2055 SubGroupMemberName
2056 )
2057
2058 if GetChainAloneResidueTypesStatus(FileIndex, ChainID):
2059 # Setup residue type group and its subgroups...
2060 ResiduesGroupName = "%s.Residues" % (ChainAloneGroupName)
2061
2062 ResiduesGroupIDPrefix = "ChainAloneResidues"
2063 ResiduesGroupID = "%sGroup" % ResiduesGroupIDPrefix
2064
2065 # Add residue group to chain alone group...
2066 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID] = ResiduesGroupName
2067 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(ResiduesGroupName)
2068
2069 # Initialize residue group members...
2070 ResiduesGroupMembersID = "%sGroupMembers" % ResiduesGroupIDPrefix
2071 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID] = []
2072
2073 # Setup residues sub groups and its members...
2074 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
2075 SubGroupID = re.sub("_", "", SubGroupType)
2076
2077 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
2078 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
2079
2080 # Add sub group to residues group...
2081 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID] = ResiduesSubGroupName
2082 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
2083
2084 # Initialize sub group members...
2085 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
2086 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID] = []
2087
2088 # Add sub group members to subgroup...
2089 for MemberType in ["Residues", "Surface"]:
2090 MemberID = re.sub("_", "", MemberType)
2091
2092 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
2093 SubGroupMemberID = "%s%s%s" % (ResiduesGroupIDPrefix, SubGroupID, MemberID)
2094
2095 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
2096 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID].append(SubGroupMemberName)
2097
2098 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
2099 # Setup a surface group and add it to chain alone group...
2100 SurfaceGroupName = "%s.Surface" % (ChainAloneGroupName)
2101 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"] = SurfaceGroupName
2102 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SurfaceGroupName)
2103
2104 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"] = []
2105
2106 # Setup a generic color surface...
2107 Name = "%s.Surface" % (SurfaceGroupName)
2108 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"] = Name
2109 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
2110
2111 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
2112 # Setup hydrophobicity surface...
2113 Name = "%s.Hydrophobicity" % (SurfaceGroupName)
2114 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"] = Name
2115 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
2116
2117 # Setup hydrophobicity and charge surface...
2118 Name = "%s.Hydrophobicity_Charge" % (SurfaceGroupName)
2119 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"] = Name
2120 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
2121
2122 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
2123 # Setup electrostatics group...
2124 GroupName = "%s.Vacuum_Electrostatics" % (SurfaceGroupName)
2125 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroup"] = GroupName
2126 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(GroupName)
2127
2128 # Setup electrostatics group members...
2129 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"] = []
2130
2131 for MemberType in ["Chain", "Contact_Potential", "Map", "Legend", "Volume"]:
2132 MemberID = re.sub("_", "", MemberType)
2133
2134 Name = "%s.%s" % (GroupName, MemberType)
2135 NameID = "ChainAloneElectrostaticsSurface%s" % MemberID
2136
2137 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
2138 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"].append(Name)
2139
2140 if GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
2141 # Setup disulfide bonds group and add it to chain alone group...
2142 DisulfideBondsGroupName = "%s.Disulfide_Bonds" % (ChainAloneGroupName)
2143 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"] = DisulfideBondsGroupName
2144 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(DisulfideBondsGroupName)
2145
2146 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"] = []
2147
2148 # Setup a residues object for disulfide bonds...
2149 Name = "%s.Residues" % (DisulfideBondsGroupName)
2150 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"] = Name
2151 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"].append(Name)
2152
2153 if GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
2154 # Setup salt bridges group and add it to chain alone group...
2155 SaltBridgesGroupName = "%s.Salt_Bridges" % (ChainAloneGroupName)
2156 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"] = SaltBridgesGroupName
2157 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SaltBridgesGroupName)
2158
2159 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"] = []
2160
2161 # Setup residues group and add it to salt bridges group...
2162 ResiduesGroupName = "%s.Residues" % (SaltBridgesGroupName)
2163 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroup"] = ResiduesGroupName
2164 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"].append(ResiduesGroupName)
2165
2166 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"] = []
2167
2168 # Setup objects for residues group...
2169 Name = "%s.Positively_Charged" % (ResiduesGroupName)
2170 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesPositivelyCharged"] = Name
2171 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"].append(Name)
2172
2173 Name = "%s.Negatively_Charged" % (ResiduesGroupName)
2174 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesNegativelyCharged"] = Name
2175 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"].append(Name)
2176
2177 # Add contacts object to salt bridges group...
2178 Name = "%s.Contacts" % (SaltBridgesGroupName)
2179 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesContacts"] = Name
2180 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"].append(Name)
2181
2182 # Setup solvent and inorganic objects for chain...
2183 for NameID in ["Solvent", "Inorganic"]:
2184 Name = "%s.%s" % (ChainGroupName, NameID)
2185 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
2186 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
2187
2188
2189 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
2190 """Stetup groups and objects for ligand."""
2191
2192 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
2193
2194 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
2195
2196 # Setup a chain level ligand group...
2197 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
2198 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
2199 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
2200
2201 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
2202
2203 # Set up groups and objects for a specific ligand group...
2204 for GroupType in ["Ligand", "Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
2205 GroupID = re.sub("_", "", GroupType)
2206 GroupName = "%s.%s" % (ChainLigandGroupName, GroupType)
2207
2208 GroupNameID = "%sGroup" % (GroupID)
2209 GroupMembersID = "%sGroupMembers" % (GroupID)
2210
2211 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
2212 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
2213
2214 GroupTypeObjectName = "%s.%s" % (GroupName, GroupType)
2215 GroupTypeObjectID = "%s" % (GroupID)
2216 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID] = GroupTypeObjectName
2217
2218 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
2219 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(GroupTypeObjectName)
2220
2221 if re.match("^Ligand$", GroupType, re.I):
2222 # Only need to add ball and stick...
2223 BallAndStickName = "%s.BallAndStick" % (GroupName)
2224 BallAndStickID = "%sBallAndStick" % (GroupID)
2225 PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickID] = BallAndStickName
2226 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(BallAndStickName)
2227
2228 if re.match("^(Pocket|Pocket_Solvent|Pocket_Inorganic)$", GroupType, re.I):
2229 PolarContactsName = "%s.Polar_Contacts" % (GroupName)
2230 PolarContactsID = "%sPolarContacts" % (GroupID)
2231 PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID] = PolarContactsName
2232 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PolarContactsName)
2233
2234 if re.match("^Pocket_Inorganic$", GroupType, re.I):
2235 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
2236 PiCationContactsID = "%sPiCationContacts" % (GroupID)
2237 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
2238 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
2239
2240 if re.match("^Pocket$", GroupType, re.I):
2241 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % (GroupName)
2242 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
2243 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID] = HydrophobicContactsName
2244 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HydrophobicContactsName)
2245
2246 PiPiContactsName = "%s.Pi_Pi_Contacts" % (GroupName)
2247 PiPiContactsID = "%sPiPiContacts" % (GroupID)
2248 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiPiContactsID] = PiPiContactsName
2249 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiPiContactsName)
2250
2251 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
2252 PiCationContactsID = "%sPiCationContacts" % (GroupID)
2253 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
2254 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
2255
2256 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
2257 PiCationContactsID = "%sPiCationContacts" % (GroupID)
2258 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
2259 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
2260
2261 HalogenContactsName = "%s.Halogen_Contacts" % (GroupName)
2262 HalogenContactsID = "%sHalogenContacts" % (GroupID)
2263 PyMOLObjectNames["Ligands"][ChainID][LigandID][HalogenContactsID] = HalogenContactsName
2264 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HalogenContactsName)
2265
2266 if GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
2267 # Setup selections group and its subgroups..
2268 SelectionsGroupName = "%s.Selections" % (GroupName)
2269 SelectionsGroupID = "%sSelectionsGroup" % (GroupID)
2270 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupID)
2271
2272 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID] = SelectionsGroupName
2273 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(SelectionsGroupName)
2274
2275 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID] = []
2276
2277 # Setup selections name sub group and its members...
2278 for SelectionName in OptionsInfo["PocketChainSelectionsInfo"]["Names"]:
2279 SelectionNameGroupID = SelectionName
2280
2281 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
2282 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupID, SelectionNameGroupID)
2283 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupID, SelectionNameGroupID)
2284
2285 # Add selections name sub group to selections group...
2286 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupID] = SelectionsNameGroupName
2287 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID].append(
2288 SelectionsNameGroupName
2289 )
2290
2291 # Initialize selections names sub group members...
2292 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID] = []
2293
2294 # Add selection member to selections name group...
2295 SubGroupMemberName = "%s.Selection" % (SelectionsNameGroupName)
2296 SubGroupMemberID = "%s%sSelection" % (SelectionsGroupID, SelectionNameGroupID)
2297
2298 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
2299 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID].append(
2300 SubGroupMemberName
2301 )
2302
2303 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
2304 # Setup a surface sub group and add it to selections name group...
2305 SelectionsNameSurfaceGroupName = "%s.Surface" % (SelectionsNameGroupName)
2306 SelectionsNameSurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupID, SelectionNameGroupID)
2307
2308 # Add selection surface group to selection name group...
2309 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupID] = (
2310 SelectionsNameSurfaceGroupName
2311 )
2312 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID].append(
2313 SelectionsNameSurfaceGroupName
2314 )
2315
2316 # Initialize surface names sub group members...
2317 SelectionsNameSurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (
2318 SelectionsGroupID,
2319 SelectionNameGroupID,
2320 )
2321 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupMembersID] = []
2322
2323 # Setup surfaces...
2324 for MemberType in ["Surface", "Hydrophobicity", "Hydrophobicity_Charge"]:
2325 MemberID = re.sub("_", "", MemberType)
2326
2327 SubGroupMemberName = "%s.%s" % (SelectionsNameSurfaceGroupName, MemberType)
2328 SubGroupMemberID = "%s%s%s%s" % (
2329 SelectionsGroupID,
2330 SelectionNameGroupID,
2331 "Surface",
2332 MemberID,
2333 )
2334
2335 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
2336 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupMembersID].append(
2337 SubGroupMemberName
2338 )
2339
2340 if GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
2341 # Setup residue type group and add to pocket group...
2342 ResiduesGroupName = "%s.Residues" % (GroupName)
2343 ResiduesGroupID = "%sResiduesGroup" % (GroupID)
2344 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
2345
2346 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupID] = ResiduesGroupName
2347 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(ResiduesGroupName)
2348 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID] = []
2349
2350 # Setup residue group subgroup and its members...
2351 for SubGroupType in [
2352 "Aromatic",
2353 "Hydrophobic",
2354 "Polar",
2355 "Positively_Charged",
2356 "Negatively_Charged",
2357 "Other",
2358 ]:
2359 SubGroupID = re.sub("_", "", SubGroupType)
2360 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
2361 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
2362 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
2363
2364 # Add sub group to residues group...
2365 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID] = ResiduesSubGroupName
2366 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
2367 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID] = []
2368
2369 # Add sub group members to subgroup...
2370 for MemberType in ["Residues", "Surface"]:
2371 MemberID = re.sub("_", "", MemberType)
2372 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
2373 SubGroupMemberID = "%s%s" % (ResiduesSubGroupID, MemberID)
2374
2375 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
2376 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID].append(
2377 SubGroupMemberName
2378 )
2379
2380 if GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
2381 # Setup a surfaces group and add it to pocket group...
2382 SurfacesGroupName = "%s.Surfaces" % (GroupName)
2383 SurfacesGroupID = "%sSurfacesGroup" % (GroupID)
2384 SurfacesGroupMembersID = "%sMembers" % (SurfacesGroupID)
2385
2386 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupID] = SurfacesGroupName
2387 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(SurfacesGroupName)
2388 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID] = []
2389
2390 # Setup surfaces subgroup and its members...
2391 for SubGroupType in ["Surface", "Cavity"]:
2392 SubGroupID = re.sub("_", "", SubGroupType)
2393 SurfacesSubGroupName = "%s.%s" % (SurfacesGroupName, SubGroupType)
2394 SurfacesSubGroupID = "%s%sGroup" % (SurfacesGroupID, SubGroupID)
2395 SurfacesSubGroupMembersID = "%sMembers" % (SurfacesSubGroupID)
2396
2397 # Add sub group to surfaces group...
2398 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupID] = SurfacesSubGroupName
2399 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID].append(SurfacesSubGroupName)
2400 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID] = []
2401
2402 # Setup a generic color surface...
2403 SurfaceName = "%s.Surface" % (SurfacesSubGroupName)
2404 SurfaceID = "%sSurface" % (SurfacesSubGroupID)
2405 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceID] = SurfaceName
2406 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(SurfaceName)
2407
2408 if GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
2409 # Surface colored by hydrophobicity...
2410 HydrophobicSurfaceName = "%s.Hydrophobicity" % (SurfacesSubGroupName)
2411 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SurfacesSubGroupID)
2412 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID] = HydrophobicSurfaceName
2413 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(
2414 HydrophobicSurfaceName
2415 )
2416
2417 # Surface colored by hydrophobicity and charge...
2418 HydrophobicChargeSurfaceName = "%s.Hydrophobicity_Charge" % (SurfacesSubGroupName)
2419 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SurfacesSubGroupID)
2420 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicChargeSurfaceID] = (
2421 HydrophobicChargeSurfaceName
2422 )
2423 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(
2424 HydrophobicChargeSurfaceName
2425 )
2426
2427 if GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
2428 ElectrostaticsGroupName = "%s.Vacuum_Electrostatics" % (SurfacesSubGroupName)
2429 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SurfacesSubGroupID)
2430 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SurfacesSubGroupID)
2431
2432 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupID] = ElectrostaticsGroupName
2433 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(
2434 ElectrostaticsGroupName
2435 )
2436
2437 # Setup electrostatics group members without the volume object...
2438 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupMembersID] = []
2439
2440 for MemberType in ["Pocket", "Contact_Potential", "Map", "Legend"]:
2441 MemberID = re.sub("_", "", MemberType)
2442
2443 Name = "%s.%s" % (ElectrostaticsGroupName, MemberType)
2444 NameID = "%s%s" % (ElectrostaticsGroupID, MemberID)
2445
2446 PyMOLObjectNames["Ligands"][ChainID][LigandID][NameID] = Name
2447 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupMembersID].append(Name)
2448
2449
2450 def SetupPyMOLObjectNamesForDockedPoses(FileIndex, PyMOLObjectNames, ChainID):
2451 """Stetup groups and objects for docked poses in input files for a chain."""
2452
2453 PyMOLObjectNames["DockedPosesInputFile"][ChainID] = {}
2454
2455 if not GetChainAloneDockedPosesStatus(FileIndex, ChainID):
2456 return
2457
2458 # Setup group for docked poses...
2459 if "DockedPosesGroup" not in PyMOLObjectNames["Chains"][ChainID]:
2460 # Setup docked poses group at a chain level...
2461 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
2462 DockedPosesGroupName = "%s.%s" % (ChainGroupName, OptionsInfo["DockedPosesGroupName"])
2463
2464 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"] = DockedPosesGroupName
2465 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(DockedPosesGroupName)
2466 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"] = []
2467
2468 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
2469 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
2470 SetupPyMOLObjectNamesForDockedPosesInputFile(FileIndex, PyMOLObjectNames, ChainID, InputFileIndex)
2471
2472
2473 def SetupPyMOLObjectNamesForDockedPosesInputFile(PDBFileIndex, PyMOLObjectNames, ChainID, InputFileIndex):
2474 """Stetup groups and objects for docked poses in an input file for a chain."""
2475
2476 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
2477 DockedPosesDistanceContactsInfo = OptionsInfo["DockedPosesDistanceContactsInfo"]
2478
2479 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
2480
2481 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID] = {}
2482
2483 DockedPosesGroupName = PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"]
2484
2485 # Setup a docked poses level InputFile group...
2486 DockedPosesInputFileGroupName = "%s.%s" % (DockedPosesGroupName, InputFileID)
2487 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupName"] = (
2488 DockedPosesInputFileGroupName
2489 )
2490 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"].append(DockedPosesInputFileGroupName)
2491
2492 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"] = []
2493
2494 # Setup objects for docked poses...
2495 PosesName = "%s.%s" % (DockedPosesInputFileGroupName, OptionsInfo["DockedPosesName"])
2496 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["Poses"] = PosesName
2497 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"].append(PosesName)
2498
2499 for GroupType in ["Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
2500 GroupID = re.sub("_", "", GroupType)
2501 GroupName = "%s.%s" % (DockedPosesInputFileGroupName, GroupType)
2502
2503 GroupNameID = "%sGroup" % (GroupID)
2504 GroupMembersID = "%sGroupMembers" % (GroupID)
2505
2506 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID] = GroupName
2507 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"].append(GroupName)
2508
2509 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID] = []
2510
2511 PocketID = "%sPocket" % GroupID
2512 PocketName = "%s.Pocket" % GroupName
2513 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PocketID] = PocketName
2514 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PocketName)
2515
2516 if DockedPosesInfo["DistanceContacts"] and re.match("^Pocket$", GroupType, re.I):
2517 # Setup distance contacts group and add it to pocket group...
2518 DistanceContactGroupName = "%s.Distance_Contacts" % GroupName
2519
2520 DistanceContactGroupNameID = "%sDistanceContactsGroup" % GroupID
2521 DistanceContactGroupMembersID = "%sDistanceContactsGroupMembers" % GroupID
2522
2523 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupNameID] = (
2524 DistanceContactGroupName
2525 )
2526 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(
2527 DistanceContactGroupName
2528 )
2529
2530 # Setup distance contacts group members...
2531 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID] = []
2532
2533 for ContactID in DockedPosesDistanceContactsInfo["ContactIDs"]:
2534 DistanceContactID = "%sPocketDistanceContacts%s" % (GroupID, ContactID)
2535 DistanceContactName = "%s.Distance_Contacts.%s" % (GroupName, ContactID)
2536
2537 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactID] = DistanceContactName
2538 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID].append(
2539 DistanceContactName
2540 )
2541
2542 PolarContactsID = "%sPolarContacts" % GroupID
2543 PolarContactsName = "%s.Polar_Contacts" % GroupName
2544 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PolarContactsID] = PolarContactsName
2545 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PolarContactsName)
2546
2547 if re.match("^Pocket_Inorganic$", GroupType, re.I):
2548 PiCationContactsID = "%sPiCationContacts" % GroupID
2549 PiCationContactsName = "%s.Pi_Cation_Contacts" % GroupName
2550 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID] = PiCationContactsName
2551 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiCationContactsName)
2552
2553 if re.match("^Pocket$", GroupType, re.I):
2554 HydrophobicContactsID = "%sHydrophobicContacts" % GroupID
2555 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % GroupName
2556 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HydrophobicContactsID] = (
2557 HydrophobicContactsName
2558 )
2559 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(
2560 HydrophobicContactsName
2561 )
2562
2563 PiPiContactsID = "%sPiPiContacts" % GroupID
2564 PiPiContactsName = "%s.Pi_Pi_Contacts" % GroupName
2565 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiPiContactsID] = PiPiContactsName
2566 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiPiContactsName)
2567
2568 PiCationContactsID = "%sPiCationContacts" % GroupID
2569 PiCationContactsName = "%s.Pi_Cation_Contacts" % GroupName
2570 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID] = PiCationContactsName
2571 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiCationContactsName)
2572
2573 HalogenContactsID = "%sHalogenContacts" % GroupID
2574 HalogenContactsName = "%s.Halogen_Contacts" % GroupName
2575 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HalogenContactsID] = HalogenContactsName
2576 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(HalogenContactsName)
2577
2578
2579 def RetrieveInfilesInfo():
2580 """Retrieve information for input files."""
2581
2582 InfilesInfo = {}
2583
2584 InfilesInfo["InfilesNames"] = []
2585 InfilesInfo["InfilesRoots"] = []
2586 InfilesInfo["ChainsAndLigandsInfo"] = []
2587
2588 for Infile in OptionsInfo["InfilesNames"]:
2589 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
2590 InfileRoot = FileName
2591
2592 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
2593
2594 InfilesInfo["InfilesNames"].append(Infile)
2595 InfilesInfo["InfilesRoots"].append(InfileRoot)
2596 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
2597
2598 OptionsInfo["InfilesInfo"] = InfilesInfo
2599
2600
2601 def RetrieveRefFileInfo():
2602 """Retrieve information for ref file."""
2603
2604 RefFileInfo = {}
2605 if not OptionsInfo["Align"]:
2606 OptionsInfo["RefFileInfo"] = RefFileInfo
2607 return
2608
2609 RefFile = OptionsInfo["RefFileName"]
2610
2611 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
2612 RefFileRoot = FileName
2613
2614 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
2615 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
2616 else:
2617 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
2618 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
2619
2620 RefFileInfo["RefFileName"] = RefFile
2621 RefFileInfo["RefFileRoot"] = RefFileRoot
2622 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
2623 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
2624
2625 OptionsInfo["RefFileInfo"] = RefFileInfo
2626
2627
2628 def ProcessChainAndLigandIDs():
2629 """Process specified chain and ligand IDs for infiles."""
2630
2631 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
2632
2633 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2634 MiscUtil.PrintInfo(
2635 "\nProcessing specified chain and ligand IDs for input file %s..."
2636 % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2637 )
2638
2639 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
2640 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(
2641 ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], "-l, --ligandIDs", OptionsInfo["LigandIDs"]
2642 )
2643 ProcessResidueTypesAndSurfaceAndChainSelectionsOptions(FileIndex, SpecifiedChainsAndLigandsInfo)
2644
2645 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
2646
2647 CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo)
2648
2649
2650 def ProcessResidueTypesAndSurfaceAndChainSelectionsOptions(FileIndex, SpecifiedChainsAndLigandsInfo):
2651 """Process residue types, surface, and chian selections options for chains and pockets."""
2652
2653 SpecifiedChainsAndLigandsInfo["ChainSurfaces"] = {}
2654 SpecifiedChainsAndLigandsInfo["SurfaceChain"] = {}
2655 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"] = {}
2656
2657 SpecifiedChainsAndLigandsInfo["PocketChainSelections"] = {}
2658 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"] = {}
2659 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"] = {}
2660
2661 SpecifiedChainsAndLigandsInfo["PocketSurfaces"] = {}
2662 SpecifiedChainsAndLigandsInfo["SurfacePocket"] = {}
2663 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"] = {}
2664
2665 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"] = {}
2666 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"] = {}
2667
2668 SpecifiedChainsAndLigandsInfo["ChainSelections"] = {}
2669 SpecifiedChainsAndLigandsInfo["ChainSelectionsSurfaces"] = {}
2670 SpecifiedChainsAndLigandsInfo["SurfaceChainSelections"] = {}
2671
2672 SpecifiedChainsAndLigandsInfo["DisulfideBondsChain"] = {}
2673 SpecifiedChainsAndLigandsInfo["SaltBridgesChain"] = {}
2674
2675 SpecifiedChainsAndLigandsInfo["BFactorChain"] = {}
2676
2677 # Load infile...
2678 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2679 MolName = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
2680 pymol.cmd.load(Infile, MolName)
2681
2682 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2683 AminoAcidsPresent = PyMOLUtil.AreAminoAcidResiduesPresent(MolName, ChainID)
2684
2685 # Process BFactors for chains...
2686 BFactorChain = True if re.match("^yes$", OptionsInfo["BFactorChain"], re.I) else False
2687 SpecifiedChainsAndLigandsInfo["BFactorChain"][ChainID] = BFactorChain
2688
2689 # Process surfaces for chains...
2690 if re.match("^auto$", OptionsInfo["SurfaceChain"], re.I):
2691 SurfaceChain = True if AminoAcidsPresent else False
2692 else:
2693 SurfaceChain = True if re.match("^yes$", OptionsInfo["SurfaceChain"], re.I) else False
2694 SpecifiedChainsAndLigandsInfo["SurfaceChain"][ChainID] = SurfaceChain
2695
2696 if re.match("^auto$", OptionsInfo["SurfaceChainElectrostatics"], re.I):
2697 SurfaceChainElectrostatics = True if AminoAcidsPresent else False
2698 else:
2699 SurfaceChainElectrostatics = (
2700 True if re.match("^yes$", OptionsInfo["SurfaceChainElectrostatics"], re.I) else False
2701 )
2702 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"][ChainID] = SurfaceChainElectrostatics
2703
2704 SpecifiedChainsAndLigandsInfo["ChainSurfaces"][ChainID] = SurfaceChain
2705
2706 # Process disulfide bonds for chains...
2707 if re.match("^auto$", OptionsInfo["DisulfideBondsChain"], re.I):
2708 DisulfideBondsChain = True if AminoAcidsPresent else False
2709 else:
2710 DisulfideBondsChain = True if re.match("^yes$", OptionsInfo["DisulfideBondsChain"], re.I) else False
2711 SpecifiedChainsAndLigandsInfo["DisulfideBondsChain"][ChainID] = DisulfideBondsChain
2712
2713 # Process salt bridges bonds for chains...
2714 if re.match("^auto$", OptionsInfo["SaltBridgesChain"], re.I):
2715 SaltBridgesChain = True if AminoAcidsPresent else False
2716 else:
2717 SaltBridgesChain = True if re.match("^yes$", OptionsInfo["SaltBridgesChain"], re.I) else False
2718 SpecifiedChainsAndLigandsInfo["SaltBridgesChain"][ChainID] = SaltBridgesChain
2719
2720 # Process residue types for chains...
2721 if re.match("^auto$", OptionsInfo["ResidueTypesChain"], re.I):
2722 ResidueTypesChain = True if AminoAcidsPresent else False
2723 else:
2724 ResidueTypesChain = True if re.match("^yes$", OptionsInfo["ResidueTypesChain"], re.I) else False
2725 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"][ChainID] = ResidueTypesChain
2726
2727 # Process chain selections...
2728 ChainSelections = True if len(OptionsInfo["ChainSelectionsInfo"]["Names"]) else False
2729 SpecifiedChainsAndLigandsInfo["ChainSelections"][ChainID] = ChainSelections
2730
2731 # Process surfaces for chain selections...
2732 if re.match("^auto$", OptionsInfo["SelectionsChainSurface"], re.I):
2733 SurfaceChainSelections = True if AminoAcidsPresent else False
2734 else:
2735 SurfaceChainSelections = True if re.match("^yes$", OptionsInfo["SelectionsChainSurface"], re.I) else False
2736 SpecifiedChainsAndLigandsInfo["SurfaceChainSelections"][ChainID] = SurfaceChainSelections
2737
2738 SpecifiedChainsAndLigandsInfo["ChainSelectionsSurfaces"][ChainID] = SurfaceChainSelections
2739
2740 # Process selections, residue types and surfaces for pockets...
2741 SpecifiedChainsAndLigandsInfo["PocketChainSelections"][ChainID] = {}
2742 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"][ChainID] = {}
2743 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"][ChainID] = {}
2744
2745 SpecifiedChainsAndLigandsInfo["PocketSurfaces"][ChainID] = {}
2746 SpecifiedChainsAndLigandsInfo["SurfacePocket"][ChainID] = {}
2747 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"][ChainID] = {}
2748
2749 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"][ChainID] = {}
2750
2751 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
2752 # Process pocket chain selections and surfaces...
2753 PocketChainSelections = True if len(OptionsInfo["PocketChainSelectionsInfo"]["Names"]) else False
2754 SpecifiedChainsAndLigandsInfo["PocketChainSelections"][ChainID][LigandID] = PocketChainSelections
2755
2756 # Process surfaces for chain selections...
2757 if re.match("^auto$", OptionsInfo["SelectionsPocketSurface"], re.I):
2758 PocketChainSelectionsSurface = True if AminoAcidsPresent else False
2759 else:
2760 PocketChainSelectionsSurface = (
2761 True if re.match("^yes$", OptionsInfo["SelectionsPocketSurface"], re.I) else False
2762 )
2763
2764 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"][ChainID][LigandID] = (
2765 PocketChainSelectionsSurface
2766 )
2767
2768 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"][ChainID][LigandID] = (
2769 PocketChainSelectionsSurface
2770 )
2771
2772 # Process pocket surfaces...
2773 if re.match("^auto$", OptionsInfo["PocketSurface"], re.I):
2774 PocketSurface = True if AminoAcidsPresent else False
2775 else:
2776 PocketSurface = True if re.match("^yes$", OptionsInfo["PocketSurface"], re.I) else False
2777 SpecifiedChainsAndLigandsInfo["SurfacePocket"][ChainID][LigandID] = PocketSurface
2778
2779 if re.match("^auto$", OptionsInfo["PocketSurfaceElectrostatics"], re.I):
2780 PocketSurfaceElectrostatics = True if AminoAcidsPresent else False
2781 else:
2782 PocketSurfaceElectrostatics = (
2783 True if re.match("^yes$", OptionsInfo["PocketSurfaceElectrostatics"], re.I) else False
2784 )
2785 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"][ChainID][LigandID] = (
2786 PocketSurfaceElectrostatics
2787 )
2788
2789 # Process pocket residue types...
2790 SpecifiedChainsAndLigandsInfo["PocketSurfaces"][ChainID][LigandID] = PocketSurface
2791
2792 if re.match("^auto$", OptionsInfo["PocketResidueTypes"], re.I):
2793 PocketResidueTypes = True if AminoAcidsPresent else False
2794 else:
2795 PocketResidueTypes = True if re.match("^yes$", OptionsInfo["PocketResidueTypes"], re.I) else False
2796 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"][ChainID][LigandID] = PocketResidueTypes
2797
2798 # Delete loaded object...
2799 pymol.cmd.delete(MolName)
2800
2801
2802 def GetChainAloneResidueTypesStatus(FileIndex, ChainID):
2803 """Get status of residue types for chain alone object."""
2804
2805 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesChain"][ChainID]
2806
2807 return Status
2808
2809
2810 def GetChainAloneBFactorStatus(FileIndex, ChainID):
2811 """Get status of B factors for chain alone object."""
2812
2813 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["BFactorChain"][ChainID]
2814
2815 return Status
2816
2817
2818 def GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
2819 """Get status of disulfide bonds for chain alone object."""
2820
2821 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["DisulfideBondsChain"][ChainID]
2822
2823 return Status
2824
2825
2826 def GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
2827 """Get status of salt bridges for chain alone object."""
2828
2829 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SaltBridgesChain"][ChainID]
2830
2831 return Status
2832
2833
2834 def GetChainAloneDockedPosesStatus(FileIndex, ChainID):
2835 """Get status of docked for chain alone object."""
2836
2837 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["DockedPoses"][ChainID]
2838
2839 return Status
2840
2841
2842 def GetTrajectoriesStatus(FileIndex):
2843 """Get status of trajectories for a PDB object."""
2844
2845 if OptionsInfo["TrajectoriesInfo"] is None:
2846 return False
2847
2848 Status = True if FileIndex in OptionsInfo["TrajectoriesInfo"]["PDBFileIndices"] else False
2849
2850 return Status
2851
2852
2853 def GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
2854 """Get status of residue types for a pocket."""
2855
2856 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesPocket"][ChainID][
2857 LigandID
2858 ]
2859
2860
2861 def GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
2862 """Get status of surfaces present in chain alone object."""
2863
2864 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSurfaces"][ChainID]
2865
2866
2867 def GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
2868 """Get status of selections present in a pocket."""
2869
2870 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["PocketChainSelections"][ChainID][
2871 LigandID
2872 ]
2873
2874
2875 def GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
2876 """Get status of surfaces present in a pocket."""
2877
2878 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["PocketSurfaces"][ChainID][LigandID]
2879
2880
2881 def GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
2882 """Get status of hydrophobic surfaces for chain alone object."""
2883
2884 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChain"][ChainID]
2885
2886
2887 def GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
2888 """Get status of electrostatics surfaces for chain alone object."""
2889
2890 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainElectrostatics"][ChainID]
2891
2892
2893 def GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
2894 """Get status of surfaces for a pocket selection in a chain."""
2895
2896 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocketChainSelections"][
2897 ChainID
2898 ][LigandID]
2899
2900
2901 def GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
2902 """Get status of hydrophobic surfaces for a pocket."""
2903
2904 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocket"][ChainID][LigandID]
2905
2906
2907 def GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
2908 """Get status of hydrophobic surfaces for a pocket."""
2909
2910 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocketElectrostatics"][
2911 ChainID
2912 ][LigandID]
2913
2914
2915 def GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
2916 """Get status of selections present in chain alone object."""
2917 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSelections"][ChainID]
2918
2919
2920 def GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
2921 """Get status of chain selections surfaces present in chain alone object."""
2922 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSelectionsSurfaces"][ChainID]
2923
2924
2925 def GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
2926 """Get status of hydrophobic surfaces for chain alone object."""
2927 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainSelections"][ChainID]
2928
2929
2930 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
2931 """Check presence of valid ligand IDs."""
2932
2933 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
2934
2935 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2936 if len(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
2937 MiscUtil.PrintInfo(
2938 "Chain ID: %s; Specified LigandIDs: %s"
2939 % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]))
2940 )
2941 else:
2942 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
2943 MiscUtil.PrintWarning(
2944 "No valid ligand IDs found for chain ID, %s. PyMOL groups and objects related to ligand and binding pockect won't be created."
2945 % (ChainID)
2946 )
2947
2948
2949 def RetrieveFirstChainID(FileIndex):
2950 """Get first chain ID."""
2951
2952 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
2953
2954 FirstChainID = None
2955 if len(ChainsAndLigandsInfo["ChainIDs"]):
2956 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
2957
2958 return FirstChainID
2959
2960
2961 def ProcessDockedPoses():
2962 """Process docked poses."""
2963
2964 OptionsInfo["DockedPosesGroupName"] = Options["--dockedPosesGroupName"]
2965 OptionsInfo["DockedPosesName"] = Options["--dockedPosesName"]
2966
2967 DockedPosesInfo = ProcessDockedPosesOptionsInfo("--dockedPoses", OptionsInfo["DockedPoses"])
2968 OptionsInfo["DockedPosesInfo"] = DockedPosesInfo
2969
2970 ProcessDockedPosesInfoForInfiles()
2971
2972 OptionsInfo["DockedPosesDistanceContactsCutoffs"] = Options["--dockedPosesDistanceContactsCutoffs"]
2973 OptionsInfo["DockedPosesDistanceContactsColor"] = Options["--dockedPosesDistanceContactsColor"]
2974
2975 DockedPosesDistanceContactsInfo = ProcessDockedPosesDistanceContactsOptionsInfo()
2976 OptionsInfo["DockedPosesDistanceContactsInfo"] = DockedPosesDistanceContactsInfo
2977
2978 # Setup distance conatcts status for dockes poses...
2979 if DockedPosesInfo is not None:
2980 DockedPosesInfo["DistanceContacts"] = False
2981 if DockedPosesDistanceContactsInfo is not None:
2982 if len(DockedPosesDistanceContactsInfo["ContactIDs"]):
2983 DockedPosesInfo["DistanceContacts"] = True
2984
2985
2986 def ProcessDockedPosesInfoForInfiles():
2987 """Process docked poses info for infiles."""
2988
2989 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
2990 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2991 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
2992 ProcessDockedPosesInfoForInfileAndChains(FileIndex, SpecifiedChainsAndLigandsInfo, DockedPosesInfo)
2993
2994
2995 def ProcessDockedPosesInfoForInfileAndChains(FileIndex, SpecifiedChainsAndLigandsInfo, DockedPosesInfo):
2996 """Process docked poses info for a specific infile."""
2997
2998 SpecifiedChainsAndLigandsInfo["DockedPoses"] = {}
2999 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"] = {}
3000
3001 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
3002 DockedPoses = False
3003 if DockedPosesInfo is not None:
3004 if FileIndex in DockedPosesInfo["PDBFileIndices"]:
3005 if ChainID == DockedPosesInfo["ChainID"][FileIndex]:
3006 DockedPoses = True
3007
3008 SpecifiedChainsAndLigandsInfo["DockedPoses"][ChainID] = DockedPoses
3009
3010 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID] = []
3011 if DockedPoses:
3012 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID].extend(
3013 DockedPosesInfo["InputFiles"][FileIndex]
3014 )
3015
3016
3017 def ProcessDockedPosesOptionsInfo(DockedPosesOptionName, DockedPosesOptionValue):
3018 """Process docked poses options info."""
3019
3020 DockedPoses = DockedPosesOptionValue
3021 if re.match("^none$", DockedPoses, re.I):
3022 return None
3023
3024 MiscUtil.PrintInfo("\nProcessing docked poses...")
3025
3026 # Initialize docked poses info...
3027 DockedPosesInfo = {}
3028 DockedPosesInfo["PDBFileIndices"] = []
3029
3030 DockedPosesInfo["PDBFile"] = {}
3031 DockedPosesInfo["ChainID"] = {}
3032 DockedPosesInfo["LigandID"] = {}
3033 DockedPosesInfo["UseInputFileAsLigandID"] = {}
3034 DockedPosesInfo["InputFiles"] = {}
3035 DockedPosesInfo["InputFilesRoots"] = {}
3036 DockedPosesInfo["InputFilesIDs"] = {}
3037
3038 # Parse docked poses values...
3039 DockedPosesWords = DockedPoses.split(",")
3040 if len(DockedPosesWords) % 4:
3041 MiscUtil.PrintError(
3042 'The number of comma delimited docked poses values, %d, specified using "%s" option must be a multple of 4.'
3043 % (len(DockedPosesWords), DockedPosesOptionName)
3044 )
3045
3046 # Validate and process specified values...
3047 for Index in range(0, len(DockedPosesWords), 4):
3048 PDBFile = DockedPosesWords[Index].strip()
3049 ChainID = DockedPosesWords[Index + 1].strip()
3050 LigandID = DockedPosesWords[Index + 2].strip()
3051 InputFiles = DockedPosesWords[Index + 3].strip()
3052
3053 InputFiles = re.sub("[ ]+", " ", InputFiles)
3054 InputFiles = InputFiles.split(" ")
3055
3056 # Process PDB file...
3057 MiscUtil.ValidateOptionFilePath("--dockedPoses", PDBFile)
3058
3059 PDBFileIndex = None
3060 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
3061 PDBInfile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
3062 if PDBFile == PDBInfile:
3063 PDBFileIndex = FileIndex
3064 break
3065 if PDBFileIndex is None:
3066 MiscUtil.PrintError(
3067 'The PDB file specified, %s, using option "--dockedPoses" is not valid. It must be specified as an input file.'
3068 % (PDBFile)
3069 )
3070
3071 if PDBFileIndex in DockedPosesInfo["PDBFileIndices"]:
3072 MiscUtil.PrintError(
3073 'The PDB file specified, %s, using option "--dockedPoses" is not valid. It is a duplicate and has already been specified.'
3074 % (PDBFile)
3075 )
3076
3077 # Process chain ID...
3078 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][PDBFileIndex]
3079 if ChainID not in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
3080 MiscUtil.PrintError(
3081 'The chain ID, %s, specified for PDB file, %s, using option "--dockedPoses" is not valid. It must be present in valid chain IDs corresponding to option "-c, --chainIDs" .'
3082 % (ChainID, PDBFile)
3083 )
3084
3085 # Process ligand ID...
3086 UseInputFileAsLigandID = True if re.match("^UseInputFile$", LigandID, re.I) else False
3087 if not UseInputFileAsLigandID:
3088 if LigandID not in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
3089 MiscUtil.PrintError(
3090 'The ligand ID, %s, specified for chain ID, %s, and PDB file, %s, using option "--dockedPoses" is not valid. It must be present in valid ligand IDs corresponding to option "-l, --ligandIDs" .'
3091 % (LigandID, ChainID, PDBFile)
3092 )
3093
3094 # Process input files...
3095 InputFilesRoots = []
3096 InputFilesIDs = []
3097 for InputFile in InputFiles:
3098 MiscUtil.ValidateOptionFilePath("--dockedPoses", InputFile)
3099 MiscUtil.ValidateOptionFileExt("--dockedPoses", InputFile, "sdf sd")
3100
3101 FileDir, FileName, FileExt = MiscUtil.ParseFileName(InputFile)
3102 InputFileRoot = FileName
3103
3104 # Clean up input file names for generating PyMOL object names...
3105 InputFileID = re.sub("[^a-zA-Z0-9]", "_", FileName)
3106
3107 if InputFileRoot in InputFilesRoots:
3108 MiscUtil.PrintError(
3109 'The input file specified, %s, using option "--dockedPoses" is not valid. It is a duplicate and has already been specified for a PDB file.'
3110 % (InputFile)
3111 )
3112
3113 InputFilesRoots.append(InputFileRoot)
3114 InputFilesIDs.append(InputFileID)
3115
3116 # Track values...
3117 DockedPosesInfo["PDBFileIndices"].append(PDBFileIndex)
3118
3119 DockedPosesInfo["PDBFile"][PDBFileIndex] = PDBFile
3120 DockedPosesInfo["ChainID"][PDBFileIndex] = ChainID
3121
3122 DockedPosesInfo["LigandID"][PDBFileIndex] = LigandID
3123 DockedPosesInfo["UseInputFileAsLigandID"][PDBFileIndex] = UseInputFileAsLigandID
3124
3125 DockedPosesInfo["InputFiles"][PDBFileIndex] = InputFiles
3126 DockedPosesInfo["InputFilesRoots"][PDBFileIndex] = InputFilesRoots
3127 DockedPosesInfo["InputFilesIDs"][PDBFileIndex] = InputFilesIDs
3128
3129 return DockedPosesInfo
3130
3131
3132 def ProcessDockedPosesDistanceContactsOptionsInfo():
3133 """Process dockes poses distance contacts info."""
3134
3135 DistanceContactsCutoffs = OptionsInfo["DockedPosesDistanceContactsCutoffs"]
3136 if re.match("^none$", DistanceContactsCutoffs):
3137 return None
3138
3139 DistanceContactsInfo = {}
3140 DistanceContactsInfo["ContactIDs"] = []
3141 DistanceContactsInfo["ContactCutoff"] = {}
3142
3143 DistanceContactsCutoffs = re.sub(" ", "", DistanceContactsCutoffs)
3144 if not DistanceContactsCutoffs:
3145 MiscUtil.PrintError('No value specified using "--dockedPosesDistanceContactsCutoffs" option.')
3146
3147 ContactCutoffValues = DistanceContactsCutoffs.split(",")
3148 for Index, ContactCutoff in enumerate(ContactCutoffValues):
3149 MiscUtil.ValidateOptionFloatValue(
3150 "--dockedPosesDistanceContactsCutoffs", ContactCutoff, {">": 0.0, "<=": OptionsInfo["PocketDistanceCutoff"]}
3151 )
3152 ContactCutoff = float(ContactCutoff.strip())
3153
3154 ContactID = "Contact%s_At_%s" % ((Index + 1), ContactCutoff)
3155 ContactID = re.sub(r"\.", "pt", ContactID)
3156
3157 DistanceContactsInfo["ContactIDs"].append(ContactID)
3158 DistanceContactsInfo["ContactCutoff"][ContactID] = ContactCutoff
3159
3160 return DistanceContactsInfo
3161
3162
3163 def ProcessTrajectories():
3164 """Process trajectories."""
3165
3166 TrajectoriesInfo = ProcessTrajectoriesOptionsInfo("--Trajectories", OptionsInfo["Trajectories"])
3167 OptionsInfo["TrajectoriesInfo"] = TrajectoriesInfo
3168
3169
3170 def ProcessTrajectoriesOptionsInfo(TrajectoriesOptionName, TrajectoriesOptionValue):
3171 """Process trajectories options info."""
3172
3173 Trajectories = TrajectoriesOptionValue
3174 if re.match("^none$", Trajectories, re.I):
3175 return None
3176
3177 MiscUtil.PrintInfo("\nProcessing trajectories...")
3178
3179 # Initialize trajectories info...
3180 TrajectoriesInfo = {}
3181 TrajectoriesInfo["PDBFileIndices"] = []
3182
3183 TrajectoriesInfo["PDBFile"] = {}
3184 TrajectoriesInfo["TrajFiles"] = {}
3185 TrajectoriesInfo["TrajFilesRoots"] = {}
3186 TrajectoriesInfo["TrajFilesIDs"] = {}
3187
3188 # Parse trajectories values...
3189 TrajectoriesWords = Trajectories.split(",")
3190 if len(TrajectoriesWords) % 2:
3191 MiscUtil.PrintError(
3192 'The number of comma delimited trajectories values, %d, specified using "%s" option must be a multple of 2.'
3193 % (len(TrajectoriesWords), TrajectoriesOptionName)
3194 )
3195
3196 # Validate and process specified values...
3197 for Index in range(0, len(TrajectoriesWords), 2):
3198 PDBFile = TrajectoriesWords[Index].strip()
3199 TrajFiles = TrajectoriesWords[Index + 1].strip()
3200
3201 TrajFiles = re.sub("[ ]+", " ", TrajFiles)
3202 TrajFiles = TrajFiles.split(" ")
3203
3204 # Process PDB file...
3205 MiscUtil.ValidateOptionFilePath(TrajectoriesOptionName, PDBFile)
3206
3207 PDBFileIndex = None
3208 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
3209 PDBInfile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
3210 if PDBFile == PDBInfile:
3211 PDBFileIndex = FileIndex
3212 break
3213 if PDBFileIndex is None:
3214 MiscUtil.PrintError(
3215 'The topology PDB file specified, %s, using option "%s" is not valid. It must be specified as an input file.'
3216 % (PDBFile, TrajectoriesOptionName)
3217 )
3218
3219 if PDBFileIndex in TrajectoriesInfo["PDBFileIndices"]:
3220 MiscUtil.PrintError(
3221 'The topology PDB file specified, %s, using option "%s" is not valid. It is a duplicate and has already been specified.'
3222 % (PDBFile, TrajectoriesOptionName)
3223 )
3224
3225 # Process trajectory files...
3226 TrajFilesRoots = []
3227 TrajFilesIDs = []
3228 for TrajFile in TrajFiles:
3229 MiscUtil.ValidateOptionFilePath(TrajectoriesOptionName, TrajFile)
3230
3231 FileDir, FileName, FileExt = MiscUtil.ParseFileName(TrajFile)
3232 TrajFileRoot = FileName
3233
3234 # Clean up trajectory file names for generating PyMOL object names...
3235 TrajFileID = re.sub("[^a-zA-Z0-9]", "_", FileName)
3236
3237 if TrajFileRoot in TrajFilesRoots:
3238 MiscUtil.PrintError(
3239 'The trajectory file specified, %s, using option "%s" is not valid. It is a duplicate and has already been specified for a PDB file.'
3240 % (TrajFile, TrajectoriesOptionName)
3241 )
3242
3243 TrajFilesRoots.append(TrajFileRoot)
3244 TrajFilesIDs.append(TrajFileID)
3245
3246 # Track values...
3247 TrajectoriesInfo["PDBFileIndices"].append(PDBFileIndex)
3248
3249 TrajectoriesInfo["PDBFile"][PDBFileIndex] = PDBFile
3250
3251 TrajectoriesInfo["TrajFiles"][PDBFileIndex] = TrajFiles
3252 TrajectoriesInfo["TrajFilesRoots"][PDBFileIndex] = TrajFilesRoots
3253 TrajectoriesInfo["TrajFilesIDs"][PDBFileIndex] = TrajFilesIDs
3254
3255 return TrajectoriesInfo
3256
3257
3258 def ProcessResidueTypes():
3259 """Process residue types."""
3260
3261 ResidueTypesNamesInfo, ResidueTypesParamsInfo = PyMOLUtil.ProcessResidueTypesOptionsInfo(
3262 "-r, --residueTypes", OptionsInfo["ResidueTypes"]
3263 )
3264 OptionsInfo["ResidueTypesNames"] = ResidueTypesNamesInfo
3265 OptionsInfo["ResidueTypesParams"] = ResidueTypesParamsInfo
3266
3267
3268 def ProcessSaltBridgesChainResidues():
3269 """Process salt bridges chain residues."""
3270
3271 SaltBridgesChainResiduesInfo = PyMOLUtil.ProcessSaltBridgesChainResiduesOptionsInfo(
3272 "--saltBridgesChainResidues", OptionsInfo["SaltBridgesChainResidues"]
3273 )
3274 OptionsInfo["SaltBridgesChainResiduesInfo"] = SaltBridgesChainResiduesInfo
3275
3276
3277 def ProcessSurfaceAtomTypesColors():
3278 """Process surface atom types colors."""
3279
3280 AtomTypesColorNamesInfo = PyMOLUtil.ProcessSurfaceAtomTypesColorsOptionsInfo(
3281 "--surfaceAtomTypesColors", OptionsInfo["SurfaceAtomTypesColors"]
3282 )
3283 OptionsInfo["AtomTypesColorNames"] = AtomTypesColorNamesInfo
3284
3285
3286 def ProcessPockectChainSelections():
3287 """Process custom selections for pocket chains."""
3288
3289 PocketChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo(
3290 "--selectionsPocket", OptionsInfo["SelectionsPocket"]
3291 )
3292 OptionsInfo["PocketChainSelectionsInfo"] = PocketChainSelectionsInfo
3293
3294
3295 def ProcessChainSelections():
3296 """Process custom selections for chains."""
3297
3298 ChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo(
3299 "--selectionsChain", OptionsInfo["SelectionsChain"]
3300 )
3301 OptionsInfo["ChainSelectionsInfo"] = ChainSelectionsInfo
3302
3303
3304 def ProcessOptions():
3305 """Process and validate command line arguments and options."""
3306
3307 MiscUtil.PrintInfo("Processing options...")
3308
3309 # Validate options...
3310 ValidateOptions()
3311
3312 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
3313 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
3314 OptionsInfo["AlignMode"] = Options["--alignMode"]
3315
3316 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
3317
3318 OptionsInfo["BFactorChain"] = Options["--BFactorChain"]
3319 OptionsInfo["BFactorColorPalette"] = Options["--BFactorColorPalette"]
3320
3321 OptionsInfo["Infiles"] = Options["--infiles"]
3322 OptionsInfo["InfilesNames"] = Options["--infileNames"]
3323
3324 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
3325 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
3326 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
3327 else:
3328 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
3329
3330 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
3331
3332 OptionsInfo["Overwrite"] = Options["--overwrite"]
3333 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
3334
3335 OptionsInfo["Outfile"] = Options["--outfile"]
3336 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
3337 OptionsInfo["PSEOut"] = False
3338 if re.match("^pml$", FileExt, re.I):
3339 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
3340 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
3341 elif re.match("^pse$", FileExt, re.I):
3342 OptionsInfo["PSEOut"] = True
3343 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
3344 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
3345 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
3346 MiscUtil.PrintError(
3347 'The intermediate output file to be generated, %s, already exist. Use option "--ov" or "--overwrite" and try again.'
3348 % OptionsInfo["PMLOutfile"]
3349 )
3350
3351 OptionsInfo["DisulfideBondsChain"] = Options["--disulfideBondsChain"]
3352
3353 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
3354
3355 OptionsInfo["PocketContactsLigandColor"] = Options["--pocketContactsLigandColor"]
3356 OptionsInfo["PocketContactsLigandHydrophobicColor"] = Options["--pocketContactsLigandHydrophobicColor"]
3357 OptionsInfo["PocketContactsLigandPiPiColor"] = Options["--pocketContactsLigandPiPiColor"]
3358 OptionsInfo["PocketContactsLigandPiCationColor"] = Options["--pocketContactsLigandPiCationColor"]
3359 OptionsInfo["PocketContactsLigandHalogenColor"] = Options["--pocketContactsLigandHalogenColor"]
3360
3361 OptionsInfo["PocketContactsSolventColor"] = Options["--pocketContactsSolventColor"]
3362
3363 OptionsInfo["PocketContactsInorganicColor"] = Options["--pocketContactsInorganicColor"]
3364 OptionsInfo["PocketContactsInorganicPiCationColor"] = Options["--pocketContactsInorganicPiCationColor"]
3365
3366 OptionsInfo["PocketContactsCutoff"] = float(Options["--pocketContactsCutoff"])
3367 OptionsInfo["PocketDistanceCutoff"] = float(Options["--pocketDistanceCutoff"])
3368
3369 OptionsInfo["PocketLabelColor"] = Options["--pocketLabelColor"]
3370
3371 OptionsInfo["PocketResidueTypes"] = Options["--pocketResidueTypes"]
3372 OptionsInfo["PocketSurface"] = Options["--pocketSurface"]
3373 OptionsInfo["PocketSurfaceElectrostatics"] = Options["--pocketSurfaceElectrostatics"]
3374
3375 OptionsInfo["ResidueTypesChain"] = Options["--residueTypesChain"]
3376 OptionsInfo["ResidueTypes"] = Options["--residueTypes"]
3377 ProcessResidueTypes()
3378
3379 OptionsInfo["SaltBridgesChain"] = Options["--saltBridgesChain"]
3380 OptionsInfo["SaltBridgesChainContactsColor"] = Options["--saltBridgesChainContactsColor"]
3381 OptionsInfo["SaltBridgesChainCutoff"] = float(Options["--saltBridgesChainCutoff"])
3382 OptionsInfo["SaltBridgesChainResidues"] = Options["--saltBridgesChainResidues"]
3383 ProcessSaltBridgesChainResidues()
3384
3385 OptionsInfo["SelectionsChain"] = Options["--selectionsChain"]
3386 OptionsInfo["SelectionsChainSurface"] = Options["--selectionsChainSurface"]
3387 OptionsInfo["SelectionsChainStyle"] = Options["--selectionsChainStyle"]
3388 ProcessChainSelections()
3389
3390 OptionsInfo["SelectionsPocket"] = Options["--selectionsPocket"]
3391 OptionsInfo["SelectionsPocketSurface"] = Options["--selectionsPocketSurface"]
3392 OptionsInfo["SelectionsPocketStyle"] = Options["--selectionsPocketStyle"]
3393 ProcessPockectChainSelections()
3394
3395 OptionsInfo["SurfaceChain"] = Options["--surfaceChain"]
3396 OptionsInfo["SurfaceChainElectrostatics"] = Options["--surfaceChainElectrostatics"]
3397
3398 OptionsInfo["SurfaceChainComplex"] = True if re.match("^Yes$", Options["--surfaceChainComplex"], re.I) else False
3399 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
3400
3401 OptionsInfo["SurfaceColor"] = Options["--surfaceColor"]
3402 OptionsInfo["SurfaceColorPalette"] = Options["--surfaceColorPalette"]
3403 OptionsInfo["SurfaceAtomTypesColors"] = Options["--surfaceAtomTypesColors"]
3404 ProcessSurfaceAtomTypesColors()
3405
3406 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
3407
3408 RetrieveInfilesInfo()
3409 RetrieveRefFileInfo()
3410
3411 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
3412 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
3413
3414 ProcessChainAndLigandIDs()
3415
3416 OptionsInfo["DockedPoses"] = Options["--dockedPoses"]
3417 ProcessDockedPoses()
3418
3419 OptionsInfo["Trajectories"] = Options["--trajectories"]
3420 ProcessTrajectories()
3421
3422
3423 def RetrieveOptions():
3424 """Retrieve command line arguments and options."""
3425
3426 # Get options...
3427 global Options
3428 Options = docopt(_docoptUsage_)
3429
3430 # Set current working directory to the specified directory...
3431 WorkingDir = Options["--workingdir"]
3432 if WorkingDir:
3433 os.chdir(WorkingDir)
3434
3435 # Handle examples option...
3436 if "--examples" in Options and Options["--examples"]:
3437 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
3438 sys.exit(0)
3439
3440
3441 def ValidateOptions():
3442 """Validate option values."""
3443
3444 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
3445 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
3446 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
3447
3448 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
3449
3450 MiscUtil.ValidateOptionTextValue("--BFactorChain", Options["--BFactorChain"], "yes no")
3451
3452 # Expand infiles to handle presence of multiple input files...
3453 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
3454 if not len(InfileNames):
3455 MiscUtil.PrintError('No input files specified for "-i, --infiles" option')
3456
3457 # Validate file extensions...
3458 for Infile in InfileNames:
3459 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
3460 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
3461 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
3462 Options["--infileNames"] = InfileNames
3463
3464 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
3465 MiscUtil.ValidateOptionsOutputFileOverwrite(
3466 "-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"]
3467 )
3468
3469 if re.match("^yes$", Options["--align"], re.I):
3470 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
3471 AlignRefFile = Options["--alignRefFile"]
3472 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
3473 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
3474 MiscUtil.ValidateOptionsDistinctFileNames(
3475 "--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"]
3476 )
3477
3478 MiscUtil.ValidateOptionTextValue("--disulfideBondsChain", Options["--disulfideBondsChain"], "yes no auto")
3479
3480 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
3481
3482 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
3483 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
3484
3485 MiscUtil.ValidateOptionFloatValue("--pocketContactsCutoff", Options["--pocketContactsCutoff"], {">": 0.0})
3486 MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0})
3487 if float(Options["--pocketContactsCutoff"]) > float(Options["--pocketDistanceCutoff"]):
3488 MiscUtil.PrintError(
3489 'The value, %s, specified using option "--pocketContactsCutoff" must be less than value, %s, specified using "-pocketDistanceCutoff" option.'
3490 % (Options["--pocketContactsCutoff"], Options["--pocketDistanceCutoff"])
3491 )
3492
3493 MiscUtil.ValidateOptionTextValue("--pocketResidueTypes", Options["--pocketResidueTypes"], "yes no auto")
3494 MiscUtil.ValidateOptionTextValue("--pocketSurface", Options["--pocketSurface"], "yes no auto")
3495 MiscUtil.ValidateOptionTextValue(
3496 "--pocketSurfaceElectrostatics", Options["--pocketSurfaceElectrostatics"], "yes no auto"
3497 )
3498
3499 MiscUtil.ValidateOptionTextValue("--residueTypesChain", Options["--residueTypesChain"], "yes no auto")
3500
3501 MiscUtil.ValidateOptionTextValue("--saltBridgesChain", Options["--saltBridgesChain"], "yes no auto")
3502 MiscUtil.ValidateOptionFloatValue("--saltBridgesChainCutoff", Options["--saltBridgesChainCutoff"], {">": 0.0})
3503
3504 MiscUtil.ValidateOptionTextValue("--selectionsChainSurface", Options["--selectionsChainSurface"], "yes no auto")
3505 MiscUtil.ValidateOptionTextValue("--selectionsPocketSurface", Options["--selectionsPocketSurface"], "yes no auto")
3506
3507 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
3508 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no")
3509 MiscUtil.ValidateOptionTextValue("--surfaceChain", Options["--surfaceChain"], "yes no auto")
3510 MiscUtil.ValidateOptionTextValue(
3511 "--surfaceChainElectrostatics", Options["--surfaceChainElectrostatics"], "yes no auto"
3512 )
3513
3514 MiscUtil.ValidateOptionTextValue(
3515 "--surfaceColorPalette", Options["--surfaceColorPalette"], "RedToWhite WhiteToGreen"
3516 )
3517 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
3518
3519
3520 # Setup a usage string for docopt...
3521 _docoptUsage_ = """
3522 PyMOLVisualizeMacromolecules.py - Visualize macromolecules
3523
3524 Usage:
3525 PyMOLVisualizeMacromolecules.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
3526 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
3527 [--allowEmptyObjects <yes or no>] [--BFactorChain <yes or no>] [--BFactorColorPalette <text>]
3528 [--chainIDs <First, All or ID1,ID2...>] [--disulfideBondsChain <yes or no>]
3529 [--dockedPoses <PDBFile,ChainID,LigandID,InputFiles,...>] [--dockedPosesDistanceContactsCutoffs <number1,number2...>]
3530 [--dockedPosesDistanceContactsColor <text>] [--dockedPosesGroupName <text>]
3531 [--dockedPosesName <text>] [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All or ID1,ID2...>]
3532 [--labelFontID <number>] [--PMLOut <yes or no>] [--pocketContactsInorganicColor <text>]
3533 [--pocketContactsInorganicPiCationColor <text>] [--pocketContactsLigandColor <text>]
3534 [--pocketContactsLigandHydrophobicColor <text>] [--pocketContactsLigandHalogenColor <text>]
3535 [--pocketContactsLigandPiCationColor <text>] [--pocketContactsLigandPiPiColor <text>]
3536 [--pocketContactsSolventColor <text>] [--pocketContactsCutoff <number>]
3537 [--pocketDistanceCutoff <number>] [--pocketLabelColor <text>] [--pocketResidueTypes <yes or no>]
3538 [--pocketSurface <yes or no>] [--pocketSurfaceElectrostatics <yes or no>]
3539 [--residueTypes <Type,Color,ResNames,...>] [--residueTypesChain <yes or no>]
3540 [--saltBridgesChain <yes or no>] [--saltBridgesChainContactsColor <text>]
3541 [--saltBridgesChainCutoff <number>] [--saltBridgesChainResidues <Type, ResNames,...>]
3542 [--selectionsChain <ObjectName,SelectionSpec,...>] [--selectionsChainSurface <yes or no>]
3543 [--selectionsChainStyle <DisplayStyle>] [--selectionsPocket <ObjectName,SelectionSpec,...>]
3544 [--selectionsPocketSurface <yes or no>] [--selectionsPocketStyle <DisplayStyle>]
3545 [--surfaceChain <yes or no>] [--surfaceChainElectrostatics <yes or no>]
3546 [--surfaceChainComplex <yes or no>] [--surfaceComplex <yes or no>]
3547 [--surfaceColor <ColorName>] [--surfaceColorPalette <RedToWhite or WhiteToGreen>]
3548 [--surfaceAtomTypesColors <ColorType,ColorSpec,...>]
3549 [--surfaceTransparency <number>] [--trajectories <PDBToplogyFile,TrajFiles,...> ]
3550 [--overwrite] [-w <dir>] -i <infile1,infile2,infile3...> -o <outfile>
3551 PyMOLVisualizeMacromolecules.py -h | --help | -e | --examples
3552
3553 Description:
3554 Generate PyMOL visualization files for viewing surfaces, chains, ligands, ligand
3555 binding pockets, and interactions between ligands and binding pockets in
3556 macromolecules including proteins and nucleic acids.
3557
3558 The supported input file format are: PDB (.pdb), CIF (.cif)
3559
3560 The supported output file formats are: PyMOL script file (.pml), PyMOL session
3561 file (.pse)
3562
3563 A variety of PyMOL groups and objects may be created for visualization of
3564 macromolecules. These groups and objects correspond to complexes, surfaces,
3565 chains, ligands, inorganics, ligand binding pockets, pocket, polar interactions,
3566 and pocket hydrophobic surfaces. A complete hierarchy of all possible PyMOL
3567 groups and objects is shown below:
3568
3569 <PDBFileRoot>
3570 .Complex
3571 .Complex
3572 .Surface
3573 .Trajectories
3574 .Topology
3575 .<TrajFileID>
3576 .Trajectory
3577 .<TrajFileID>
3578 ... ... ...
3579 .<TrajFileID>
3580 ... ... ...
3581 .Chain<ID>
3582 .Complex
3583 .Complex
3584 .Surface
3585 .Chain
3586 .Chain
3587 .BFactor
3588 .Putty
3589 .Cartoon
3590 .Selections
3591 .<Name>
3592 .Selection
3593 .Surface
3594 .Surface
3595 .Hydrophobicity
3596 .Hydrophobicity_Charge
3597 .<Name>
3598 ... ... ..
3599 .Residues
3600 .Aromatic
3601 .Residues
3602 .Surface
3603 .Hydrophobic
3604 .Residues
3605 .Surface
3606 .Polar
3607 .Residues
3608 .Surface
3609 .Positively_Charged
3610 .Residues
3611 .Surface
3612 .Negatively_Charged
3613 .Residues
3614 .Surface
3615 .Other
3616 .Residues
3617 .Surface
3618 .Surface
3619 .Surface
3620 .Hydrophobicity
3621 .Hydrophobicity_Charge
3622 .Vacuum_Electrostatics
3623 .Contact_Potentials
3624 .Map
3625 .Legend
3626 .Volume
3627 .Disulfide_Bonds
3628 .Residues
3629 .Salt_Bridges
3630 .Residues
3631 .Positively_Charged
3632 .Negatively_Charged
3633 .Contacts
3634 .Solvent
3635 .Inorganic
3636 .Ligand<ID>
3637 .Ligand
3638 .Ligand
3639 .BallAndStick
3640 .Pocket
3641 .Pocket
3642 .Polar_Contacts
3643 .Hydrophobic_Contacts
3644 .Pi_Pi_Contacts
3645 .Pi_Cation_Contacts
3646 .Halogen_Contacts
3647 .Selections
3648 .<Name>
3649 .Selection
3650 .Surface
3651 .Surface
3652 .Hydrophobicity
3653 .Hydrophobicity_Charge
3654 .<Name>
3655 ... ... ..
3656 .Residues
3657 .Aromatic
3658 .Residues
3659 .Surface
3660 .Hydrophobic
3661 .Residues
3662 .Surface
3663 .Polar
3664 .Residues
3665 .Surface
3666 .Positively_Charged
3667 .Residues
3668 .Surface
3669 .Negatively_Charged
3670 .Residues
3671 .Surface
3672 .Other
3673 .Residues
3674 .Surface
3675 .Surfaces
3676 .Surface
3677 .Surface
3678 .Hydrophobicity
3679 .Hydrophobicity_Charge
3680 .Vacuum_Electrostatics
3681 .Contact_Potentials
3682 .Map
3683 .Legend
3684 .Cavity
3685 .Surface
3686 .Hydrophobicity
3687 .Hydrophobicity_Charge
3688 .Vacuum_Electrostatics
3689 .Contact_Potentials
3690 .Map
3691 .Legend
3692 .Pocket_Solvent
3693 .Pocket_Solvent
3694 .Polar_Contacts
3695 .Pocket_Inorganic
3696 .Pocket_Inorganic
3697 .Polar_Contacts
3698 .Pi_Cation_Contacts
3699 .Ligand<ID>
3700 .Ligand
3701 ... ... ...
3702 .Pocket
3703 ... ... ...
3704 .Pocket_Solvent
3705 ... ... ...
3706 .Pocket_Inorganic
3707 ... ... ...
3708 .Docked_Poses or <CustomLabel>
3709 .<InputFileID>
3710 .Poses or <CustomLabel>
3711 .Pocket
3712 .Pocket
3713 .Distance_Contacts
3714 .Contact1_At_<Distance>
3715 .Contact1_At_<Distance>
3716 ... ... ...
3717 .Polar_Contacts
3718 .Hydrophobic_Contacts
3719 .Pi_Pi_Contacts
3720 .Pi_Cation_Contacts
3721 .Halogen_Contacts
3722 .Pocket_Solvent
3723 .Pocket_Solvent
3724 .Polar_Contacts
3725 .Pocket_Inorganic
3726 .Polar_Contacts
3727 .Pi_Cation_Contacts
3728 .<InputFileID>
3729 ... ... ...
3730 .<InputFileID>
3731 ... ... ...
3732 .Chain<ID>
3733 ... ... ...
3734 .Ligand<ID>
3735 ... ... ...
3736 .Ligand<ID>
3737 ... ... ...
3738 .Chain<ID>
3739 ... ... ...
3740 <PDBFileRoot>
3741 .Complex
3742 ... ... ...
3743 .Chain<ID>
3744 ... ... ...
3745 .Ligand<ID>
3746 ... ... ...
3747 .Ligand<ID>
3748 ... ... ...
3749 .Chain<ID>
3750 ... ... ...
3751
3752 The hydrophobic and electrostatic surfaces are not created for complete complex
3753 and chain complex in input file(s) by default. A word to the wise: The creation of
3754 surface objects may slow down loading of PML file and generation of PSE file, based
3755 on the size of input complexes. The generation of PSE file may also fail.
3756
3757 Options:
3758 -a, --align <yes or no> [default: no]
3759 Align input files to a reference file before visualization. The docked poses
3760 and trajectories are not aligned.
3761 --alignMethod <align, cealign, super> [default: super]
3762 Alignment methodology to use for aligning input files to a
3763 reference file.
3764 --alignMode <FirstChain or Complex> [default: FirstChain]
3765 Portion of input and reference files to use for spatial alignment of
3766 input files against reference file. Possible values: FirstChain or
3767 Complex.
3768
3769 The FirstChain mode allows alignment of the first chain in each input
3770 file to the first chain in the reference file along with moving the rest
3771 of the complex to coordinate space of the reference file. The complete
3772 complex in each input file is aligned to the complete complex in reference
3773 file for the Complex mode.
3774 --alignRefFile <filename> [default: FirstInputFile]
3775 Reference input file name. The default is to use the first input file
3776 name specified using '-i, --infiles' option.
3777 --allowEmptyObjects <yes or no> [default: no]
3778 Allow creation of empty PyMOL objects corresponding to solvent and
3779 inorganic atom selections across chains and ligands in input file(s). By
3780 default, the empty objects are marked for deletion.
3781 -b, --BFactorChain <yes or no> [default: yes]
3782 A cartoon and putty around individual chains colored by an arbitrary set
3783 of B factor values. The minimum and maximum values for B factors are
3784 automatically detected. These values may indicate spread of electron
3785 density around atoms or correspond to any other property mapped to
3786 B factors in input file.
3787 --BFactorColorPalette <text> [default: blue_white_red]
3788 Color palette for coloring cartoon and putty around chains generated using B
3789 factor values. Any valid PyMOL color palette name is allowed. No validation is
3790 performed. The complete list of valid color palette names is a available
3791 at: pymolwiki.org/index.php/Spectrum. Examples: blue_white_red,
3792 blue_white_magenta, blue_red, green_white_red, green_red.
3793 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
3794 List of chain IDs to use for visualizing macromolecules. Possible values:
3795 First, All, or a comma delimited list of chain IDs. The default is to use the
3796 chain ID for the first chain in each input file.
3797 -d --disulfideBondsChain <yes or no> [default: auto]
3798 Disulfide bonds for chains. By default, the disulfide bonds group is
3799 automatically created for chains containing amino acids and skipped for
3800 chains only containing nucleic acids.
3801 --dockedPoses <PDBFile,ChainID,LigandID,InputFiles,...> [default: none]
3802 PDB file name, pocket chain ID, ligand specification, and input files to use
3803 for creating pockets to visualize docked poses or any arbitrary set of
3804 molecules. Any valid PyMOL input file format is allowed.
3805
3806 It's a quartet of comma limited values corresponding to PDF file name,
3807 pocket chain ID, ligand ID, and input files. Multiple input file names are
3808 delimited by spaces.
3809
3810 The supported values for docked poses are shown below:
3811
3812 PDBFile: A valid PDB file name
3813 ChainID: A valid Chain ID
3814 LigandID: A valid Ligand ID or UseInputFile
3815 InputFiles: A space delimited list of input file names
3816
3817 All docked pose values must be specified. No default values are assigned.
3818
3819 The 'ChainID' and 'LigandID' are used for creating pocket to visualize docked
3820 poses.
3821
3822 The 'LigandID' must be a valid ligand ID in 'ChainID'. Alternatively, you may use
3823 input files by specifying 'UseInputFile' to select residues in 'ChainID' for creating
3824 pockets to visualize docked poses.
3825 --dockedPosesDistanceContactsCutoffs <number1,number2...> [default: none]
3826 A comma delimited list of distances in Angstroms for identifying and displaying
3827 distance contacts between heavy atoms in pocket residues and docked poses. A
3828 PyMOL distance contact object is created for each specified distance. You may
3829 find it helpful for identifying steric clashes between docked poses and pocket
3830 residues. The maximum distance cutoff value must be less than the specified
3831 value for '--pocketDistanceCutoff' option.
3832 --dockedPosesDistanceContactsColor <text> [default: red]
3833 Color for drawing distance contacts between docked poses and pocket residues.
3834 The specified value must be valid color. No validation is performed.
3835 --dockedPosesGroupName <text> [default: Docked_Poses]
3836 PyMOL object name for docked poses group. You may use an artbitray name
3837 to reflect data in input file(s) specified in '--dockedPoses' option. It must be a valid
3838 PyMOL object name. No validation is performed.
3839 --dockedPosesName <text> [default: Poses]
3840 PyMOL object name for docked poses object. You may use an artbitray name
3841 to reflect data in input file(s) specified in '--dockedPoses' option. It must be a
3842 valid PyMOL object name. No validation is performed.
3843 -e, --examples
3844 Print examples.
3845 -h, --help
3846 Print this help message.
3847 -i, --infiles <infile1,infile2,infile3...>
3848 Input file names.
3849 --ignoreHydrogens <yes or no> [default: yes]
3850 Ignore hydrogens for ligand, pocket, selection, and residue type views.
3851 -l, --ligandIDs <Largest, All or ID1,ID2...> [default: Largest]
3852 List of ligand IDs present in chains for visualizing macromolecules to
3853 highlight ligand interactions. Possible values: Largest, All, or a comma
3854 delimited list of ligand IDs. The default is to use the largest ligand present
3855 in all or specified chains in each input file.
3856
3857 Ligands are identified using organic selection operator available in PyMOL.
3858 It'll also identify buffer molecules as ligands. The largest ligand contains
3859 the highest number of heavy atoms.
3860 --labelFontID <number> [default: 7]
3861 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
3862 The specified value must be a valid PyMOL font ID. No validation is
3863 performed. The complete lists of valid font IDs is available at:
3864 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
3865 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
3866 -o, --outfile <outfile>
3867 Output file name.
3868 -p, --PMLOut <yes or no> [default: yes]
3869 Save PML file during generation of PSE file.
3870 --pocketContactsInorganicColor <text> [default: deepsalmon]
3871 Color for drawing polar contacts between inorganic and pocket residues.
3872 The specified value must be valid color. No validation is performed.
3873 --pocketContactsInorganicPiCationColor <text> [default: limon]
3874 Color for drawing pi cation contacts between inorganic and pocket residues.
3875 The specified value must be valid color. No validation is performed. The pi
3876 cation contacts are drawn using PyMOL distance command with support for
3877 mode 7 and may require incentive version of PyMOL.
3878 --pocketContactsLigandColor <text> [default: orange]
3879 Color for drawing polar contacts between ligand and pocket residues.
3880 The specified value must be valid color. No validation is performed.
3881 --pocketContactsLigandHalogenColor <text> [default: magenta]
3882 Color for drawing halogen contacts between ligand and pocket residues.
3883 The specified value must be valid color. No validation is performed.
3884 --pocketContactsLigandHydrophobicColor <text> [default: purpleblue]
3885 Color for drawing hydrophobic contacts between ligand and pocket residues.
3886 The specified value must be valid color. No validation is performed. The
3887 hydrophobic contacts are shown between pairs of carbon atoms not
3888 connected to hydrogen bond donor or acceptors atoms as identified
3889 by PyMOL.
3890 --pocketContactsLigandPiCationColor <text> [default: yelloworange]
3891 Color for drawing pi cation contacts between ligand and pocket residues.
3892 The specified value must be valid color. No validation is performed. The pi
3893 cation contacts are drawn using PyMOL distance command with support for
3894 mode 7 and may require incentive version of PyMOL.
3895 --pocketContactsLigandPiPiColor <text> [default: cyan]
3896 Color for drawing pi pi contacts between ligand and pocket residues.
3897 The specified value must be valid color. No validation is performed. The pi
3898 pi contacts are drawn using PyMOL distance command with support for
3899 mode 6 and may require incentive version of PyMOL.
3900 --pocketContactsSolventColor <text> [default: marine]
3901 Color for drawing polar contacts between solvent and pocket residues..
3902 The specified value must be valid color. No validation is performed.
3903 --pocketContactsCutoff <number> [default: 4.0]
3904 Distance in Angstroms for identifying polar, hyrdophobic contacts, pi pi,
3905 pi cation, and halogen contacts between atoms in pocket residues and
3906 ligands.
3907 --pocketDistanceCutoff <number> [default: 5.0]
3908 Distance in Angstroms for identifying pocket residues around ligands.
3909 --pocketLabelColor <text> [default: magenta]
3910 Color for drawing residue or atom level labels for a pocket. The specified
3911 value must be valid color. No validation is performed.
3912 --pocketResidueTypes <yes or no> [default: auto]
3913 Pocket residue types. The residue groups are generated using residue types,
3914 colors, and names specified by '--residueTypes' option. It is only valid for
3915 amino acids. By default, the residue type groups are automatically created
3916 for pockets containing amino acids and skipped for chains only containing
3917 nucleic acids.
3918 --pocketSurface <yes or no> [default: auto]
3919 Surfaces around pocket residues colored by hydrophobicity alone and
3920 both hydrophobicity and charge. The hydrophobicity surface is colored
3921 at residue level using Eisenberg hydrophobicity scale for residues and color
3922 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
3923 charge surface is colored [ Ref 140 ] at atom level using colors specified for
3924 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
3925 simultaneous mapping of hyrophobicity and charge values on the surfaces.
3926
3927 The cavity surfaces around ligands are also generated. These surfaces are
3928 colored by hydrophobicity along and both hydrophobicity and charge.
3929
3930 This option is only valid for amino acids. By default, both surfaces are
3931 automatically created for pockets containing amino acids and skipped for
3932 pockets containing only nucleic acids.
3933 --pocketSurfaceElectrostatics <yes or no> [default: no]
3934 Vacuum electrostatics contact potential surface around pocket residues.
3935 A word to the wise from PyMOL documentation: The computed protein
3936 contact potentials are only qualitatively useful, due to short cutoffs,
3937 truncation, and lack of solvent "screening".
3938
3939 The cavity surface around ligands is also generated. This surface is
3940 colored by vacuum electrostatics contact potential.
3941
3942 This option is only valid for amino acids. By default, the electrostatics surface
3943 is automatically created for chains containing amino acids and skipped for chains
3944 containing only nucleic acids.
3945 -r, --residueTypes <Type,Color,ResNames,...> [default: auto]
3946 Residue types, colors, and names to generate for residue groups during
3947 '--pocketResidueTypes' and '--residueTypesChain' option. It is only
3948 valid for amino acids.
3949
3950 It is a triplet of comma delimited list of amino acid residues type, residues
3951 color, and a space delimited list three letter residue names.
3952
3953 The default values for residue type, color, and name triplets are shown
3954 below:
3955
3956 Aromatic,brightorange,HIS PHE TRP TYR,
3957 Hydrophobic,orange,ALA GLY VAL LEU ILE PRO MET,
3958 Polar,palegreen,ASN GLN SER THR CYS,
3959 Positively_Charged,marine,ARG LYS,
3960 Negatively_Charged,red,ASP GLU
3961
3962 The color name must be a valid PyMOL name. No validation is performed.
3963 An amino acid name may appear across multiple residue types. All other
3964 residues are grouped under 'Other'.
3965 --residueTypesChain <yes or no> [default: auto]
3966 Chain residue types. The residue groups are generated using residue types,
3967 colors, and names specified by '--residueTypes' option. It is only valid for
3968 amino acids. By default, the residue type groups are automatically created
3969 for chains containing amino acids and skipped for chains only containing
3970 nucleic acids.
3971 --saltBridgesChain <yes or no> [default: auto]
3972 Salt bridges for chains. By default, the salt bridges group is automatically
3973 created for chains containing amino acids and skipped for chains only
3974 containing nucleic acids. The salt bridges correspond to polar contacts
3975 between positively and negatively charges residues in a chain.
3976 --saltBridgesChainContactsColor <text> [default: brightorange]
3977 Color for drawing polar contacts between positively and negatively
3978 charged residues involved in salt bridges. The specified value must
3979 be valid color. No validation is performed.
3980 --saltBridgesChainCutoff <number> [default: 4.0]
3981 Distance in Angstroms for identifying polar contacts between positively
3982 and negatively charged residues involved in salt bridges in a chain.
3983 --saltBridgesChainResidues <Type, ResNames,...> [default: auto]
3984 Residue types and names to use for identifying positively and negatively
3985 charged residues involved in salt bridges.
3986
3987 It is a pair of comma delimited list of amino acid residue types and a space
3988 delimited list three letter residue names.
3989
3990 The default values for residue type and name pairs are shown below:
3991
3992 Positively_Charged,ARG LYS HIS HSP
3993 Negatively_Charged,ASP GLU
3994
3995 The residue names must be valid names. No validation is performed.
3996 --selectionsChain <ObjectName,SelectionSpec,...> [default: none]
3997 Custom selections for chains. It is a pairwise list of comma delimited values
3998 corresponding to PyMOL object names and selection specifications. The
3999 selection specification must be a valid PyMOL specification. No validation is
4000 performed.
4001
4002 The PyMOL objects are created for each chain corresponding to the
4003 specified selections. The display style for PyMOL objects is set using
4004 value of '--selectionsChainStyle' option.
4005
4006 The specified selection specification is automatically appended to appropriate
4007 chain specification before creating PyMOL objects.
4008
4009 For example, the following specification for '--selectionsChain' option will
4010 generate PyMOL objects for chains containing Cysteines and Serines:
4011
4012 Cysteines,resn CYS,Serines,resn SER
4013
4014 --selectionsChainSurface <yes or no> [default: auto]
4015 Surfaces around individual chain selections colored by hydrophobicity alone
4016 and both hydrophobicity and charge. This option is similar to '--surfaceChain'
4017 options for creating surfaces for chain. Additional details are available in the
4018 documentation section for '--surfaceChain' options.
4019 --selectionsChainStyle <DisplayStyle> [default: sticks]
4020 Display style for PyMOL objects created for '--selectionsChain' option. It
4021 must be a valid PyMOL display style. No validation is performed.
4022 --selectionsPocket <ObjectName,SelectionSpec,...> [default: none]
4023 Custom selections for pocket residues. It is a pairwise list of comma delimited
4024 values corresponding to PyMOL object names and selection specifications. The
4025 selection specification must be a valid PyMOL specification. No validation is
4026 performed.
4027
4028 The PyMOL objects are created for each pocket corresponding to the
4029 specified selections. The display style for PyMOL objects is set using
4030 value of '--selectionsChainStyle' option.
4031
4032 The specified selection specification is automatically appended to appropriate
4033 pocket specification before creating PyMOL objects.
4034
4035 For example, the following specification for '--selectionsPocket' option will
4036 generate PyMOL objects for pockets containing Tyrosines and Serines:
4037
4038 Tyrosines,resn TYR,Serines,resn SER
4039
4040 --selectionsPocketSurface <yes or no> [default: auto]
4041 Surfaces around individual pocket chain selections colored by hydrophobicity
4042 alone and both hydrophobicity and charge. This option is similar to '--surfaceChain'
4043 options for creating surfaces for chain. Additional details are available in the
4044 documentation section for '--surfaceChain' options.
4045 --selectionsPocketStyle <DisplayStyle> [default: sticks]
4046 Display style for PyMOL objects created for '--selectionsPocket' option. It
4047 must be a valid PyMOL display style. No validation is performed.
4048 --surfaceChain <yes or no> [default: auto]
4049 Surfaces around individual chain colored by hydrophobicity alone and
4050 both hydrophobicity and charge. The hydrophobicity surface is colored
4051 at residue level using Eisenberg hydrophobicity scale for residues and color
4052 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
4053 charge surface is colored [ Ref 140 ] at atom level using colors specified for
4054 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
4055 simultaneous mapping of hyrophobicity and charge values on the surfaces.
4056
4057 This option is only valid for amino acids. By default, both surfaces are
4058 automatically created for chains containing amino acids and skipped for
4059 chains containing only nucleic acids.
4060 --surfaceChainElectrostatics <yes or no> [default: no]
4061 Vacuum electrostatics contact potential surface and volume around individual
4062 chain. A word to the wise from PyMOL documentation: The computed protein
4063 contact potentials are only qualitatively useful, due to short cutoffs,
4064 truncation, and lack of solvent "screening".
4065
4066 This option is only valid for amino acids. By default, the electrostatics surface
4067 and volume are automatically created for chains containing amino acids and
4068 skipped for chains containing only nucleic acids.
4069 --surfaceChainComplex <yes or no> [default: no]
4070 Hydrophobic surface around chain complex. The surface is colored by
4071 hydrophobicity. It is only valid for amino acids.
4072 --surfaceComplex <yes or no> [default: no]
4073 Hydrophobic surface around complete complex. The surface is colored by
4074 hydrophobicity. It is only valid for amino acids.
4075 --surfaceAtomTypesColors <ColorType,ColorSpec,...> [default: auto]
4076 Atom colors for generating surfaces colored by hyrophobicity and charge
4077 around chains and pockets in proteins. It's a pairwise comma delimited list
4078 of atom color type and color specification for goups of atoms.
4079
4080 The default values for color types [ Ref 140 ] along wth color specifications
4081 are shown below:
4082
4083 HydrophobicAtomsColor, yellow,
4084 NegativelyChargedAtomsColor, red,
4085 PositivelyChargedAtomsColor, blue,
4086 OtherAtomsColor, gray90
4087
4088 The color names must be valid PyMOL names.
4089
4090 The color values may also be specified as space delimited RGB triplets:
4091
4092 HydrophobicAtomsColor, 0.95 0.78 0.0,
4093 NegativelyChargedAtomsColor, 1.0 0.4 0.4,
4094 PositivelyChargedAtomsColor, 0.2 0.5 0.8,
4095 OtherAtomsColor, 0.95 0.95 0.95
4096
4097 --surfaceColor <ColorName> [default: lightblue]
4098 Color name for surfaces around chains and pockets. This color is not used
4099 for surfaces colored by hydrophobicity and charge. The color name must be
4100 a valid PyMOL name.
4101 --surfaceColorPalette <RedToWhite or WhiteToGreen> [default: RedToWhite]
4102 Color palette for hydrophobic surfaces around chains and pockets in proteins.
4103 Possible values: RedToWhite or WhiteToGreen from most hydrophobic amino
4104 acid to least hydrophobic. The colors values for amino acids are taken from
4105 color_h script available as part of the Script Library at PyMOL Wiki.
4106 --surfaceTransparency <number> [default: 0.25]
4107 Surface transparency for molecular surfaces.
4108 -t, --trajectories <PDBToplogyFile,TrajFiles,...> [default: none]
4109 PDB topology file name and MD trajectories files for visualizing trajectories
4110 for PDB files.
4111
4112 It's a pair of comma limited values corresponding to a PDB file name and
4113 MD trajectory files. Multiple trajectory file names are delimited by spaces.
4114
4115 The supported values for trajectories are shown below:
4116
4117 PDBTopologyFile: A valid PDB file name
4118 TrajFiles: A space delimited list of MD trajectory file names
4119
4120 The trajectory files must correspond to the specified PDB topology file. In
4121 addition, the format of trajectory files must be a valid PyMOL format. PyMOL
4122 uses Molfile Plugin, which supports a variety of trajectory file formats. For
4123 example: HARMM, NAMD, X-PLOR (.dcd), Gromacs TRR/XTC (.trr, .xtc),
4124 XYZ (.xyz) etc.
4125 --overwrite
4126 Overwrite existing files.
4127 -w, --workingdir <dir>
4128 Location of working directory which defaults to the current directory.
4129
4130 Examples:
4131 To visualize the first chain, the largest ligand in the first chain, and ligand
4132 binding pockets to highlight ligand interaction with pocket resiudes, solvents
4133 and inorganics, in a PDB file, and generate a PML file, type:
4134
4135 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
4136
4137 To visualize the first chain along with all cysteines and serines, the largest
4138 ligand in the first chain, and ligand binding pockets to highlight ligand
4139 interaction with pocket resiudes, solvents and inorganics, in a PDB file,
4140 and generate a PML file, type:
4141
4142 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
4143 --selectionsChain "Cysteines,resn cys,Serines,resn ser"
4144
4145 To visualize the first chain along with all serines and tyrosines in binding
4146 pockets, the largest ligand in the first chain, and ligand binding pockets
4147 to highlight ligand interaction with pocket resiudes, solvents and inorganics,
4148 in a PDB file, and generate a PML file, type:
4149
4150 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
4151 --selectionsPocket "Serines,resn ser,Tyrosines,resn tyr"
4152
4153 To visualize docking poses from a SD file in a pocket corresponding to a SD file
4154 for a chain, along with visualization of other information, in a PDB file,
4155 and generate a PML file, type:
4156
4157 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
4158 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
4159 SampleMproDockedPosesTop100.sdf"
4160
4161 To visualize docking poses from a SD file in a pocket corresponding to SD file
4162 for a chain, along with visualization of distance contacts at 3.0 and 3.5 Angstroms,
4163 in a PDB file, and generate a PML file, type:
4164
4165 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
4166 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
4167 SampleMproDockedPosesTop100.sdf"
4168 --dockedPosesDistanceContactsCutoffs "3.0, 3.5"
4169
4170 To visualize docking poses from a SD file in a pocket corresponding to a specific
4171 ligand a chain, along with visualization of other information, in a PDB file,
4172 and generate a PML file, type:
4173
4174 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
4175 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,N3,
4176 SampleMproDockedPosesTop100.sdf"
4177
4178 To visualize docking poses from multiple SDs file in a pocket corresponding SD file
4179 a for a chain, along with visualization of other information, in a PDB file, and
4180 generate a PML file, type:
4181
4182 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
4183 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
4184 SampleMproDockedPosesTop100.sdf SampleMproDockedPosesDiverse100.sdf"
4185
4186 To visualize trajectory from a DCD file, along with visualization of other
4187 information, corresponding to a PDB topology file and generate a PML file,
4188 type:
4189
4190 % PyMOLVisualizeMacromolecules.py -t "Sample10.pdb, Sample10.dcd"
4191 -i Sample10.pdb -o Sample10.pml
4192
4193 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
4194 highlight ligand interaction with pocket resiudes, solvents and inorganics, in a
4195 PDB file, and generate a PML file, type:
4196
4197 % PyMOLVisualizeMacromolecules.py -c All -l All -i Sample4.pdb -o
4198 Sample4.pml
4199
4200 To visualize all chains, ligands, and ligand binding pockets along with displaying
4201 all hydrophibic surfaces and chain electrostatic surface, in a PDB file, and
4202 generate a PML file, type:
4203
4204 % PyMOLVisualizeMacromolecules.py -c All -l All
4205 --surfaceChainElectrostatics yes --surfaceChainComplex yes
4206 --surfaceComplex yes -i Sample4.pdb -o Sample4.pml
4207
4208 To visualize chain E, ligand ADP in chain E, and ligand binding pockets to
4209 highlight ligand interaction with pocket resiudes, solvents and inorganics,
4210 in a PDB file, and generate a PML file, type:
4211
4212 % PyMOLVisualizeMacromolecules.py -c E -l ADP -i Sample3.pdb
4213 -o Sample3.pml
4214
4215 To visualize chain E, ligand ADP in chain E, and ligand binding pockets to
4216 highlight ligand interaction with pocket resiudes, solvents and inorganics,
4217 in a PDB file, and generate a PSE file, type:
4218
4219 % PyMOLVisualizeMacromolecules.py -c E -l ADP -i Sample3.pdb
4220 -o Sample3.pse
4221
4222 To visualize the first chain, the largest ligand in the first chain, and ligand
4223 binding pockets to highlight ligand interaction with pocket resiudes, solvents
4224 and inorganics, in PDB files, along with aligning first chain in each input file to
4225 the first chain in first input file, and generate a PML file, type:
4226
4227 % PyMOLVisualizeMacromolecules.py --align yes -i
4228 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
4229
4230 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
4231 highlight ligand interaction with pocket resiudes, solvents and inorganics, in
4232 PDB files, along with aligning first chain in each input file to the first chain in
4233 first input file, and generate a PML file, type:
4234
4235 % PyMOLVisualizeMacromolecules.py --align yes -c All -l All -i
4236 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
4237
4238 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
4239 highlight ligand interaction with pocket resiudes, solvents and inorganics, in
4240 PDB files, along with aligning first chain in each input file to the first chain in a
4241 specified PDB file using a specified alignment method, and generate a PML
4242 file, type:
4243
4244 % PyMOLVisualizeMacromolecules.py --align yes --alignMode FirstChain
4245 --alignRefFile Sample5.pdb --alignMethod super -c All -l All -i
4246 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
4247
4248 Author:
4249 Manish Sud(msud@san.rr.com)
4250
4251 See also:
4252 DownloadPDBFiles.pl, PyMOLVisualizeCavities.py,
4253 PyMOLVisualizeCryoEMDensity.py, PyMOLVisualizeElectronDensity.py,
4254 PyMOLVisualizeInterfaces.py, PyMOLVisualizeSurfaceAndBuriedResidues.py
4255
4256 Copyright:
4257 Copyright (C) 2026 Manish Sud. All rights reserved.
4258
4259 The functionality available in this script is implemented using PyMOL, a
4260 molecular visualization system on an open source foundation originally
4261 developed by Warren DeLano.
4262
4263 This file is part of MayaChemTools.
4264
4265 MayaChemTools is free software; you can redistribute it and/or modify it under
4266 the terms of the GNU Lesser General Public License as published by the Free
4267 Software Foundation; either version 3 of the License, or (at your option) any
4268 later version.
4269
4270 """
4271
4272 if __name__ == "__main__":
4273 main()
