1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeSurfaceAndBuriedResidues.py
4 # Author: Manish Sud <msud@san.rr.com>
5 #
6 # Copyright (C) 2024 Manish Sud. All rights reserved.
7 #
8 # The functionality available in this script is implemented using PyMOL, a
9 # molecular visualization system on an open source foundation originally
10 # developed by Warren DeLano.
11 #
12 # This file is part of MayaChemTools.
13 #
14 # MayaChemTools is free software; you can redistribute it and/or modify it under
15 # the terms of the GNU Lesser General Public License as published by the Free
16 # Software Foundation; either version 3 of the License, or (at your option) any
17 # later version.
18 #
19 # MayaChemTools is distributed in the hope that it will be useful, but without
20 # any warranty; without even the implied warranty of merchantability of fitness
21 # for a particular purpose. See the GNU Lesser General Public License for more
22 # details.
23 #
24 # You should have received a copy of the GNU Lesser General Public License
25 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
26 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
27 # Boston, MA, 02111-1307, USA.
28 #
29
30 from __future__ import print_function
31
32 # Add local python path to the global path and import standard library modules...
33 import os
34 import sys; sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "..", "lib", "Python"))
35 import time
36 import re
37
38 # PyMOL imports...
39 try:
40 import pymol
41 # Finish launching PyMOL in a command line mode for batch processing (-c)
42 # along with the following options: disable loading of pymolrc and plugins (-k);
43 # suppress start up messages (-q)
44 pymol.finish_launching(['pymol', '-ckq'])
45 except ImportError as ErrMsg:
46 sys.stderr.write("\nFailed to import PyMOL module/package: %s\n" % ErrMsg)
47 sys.stderr.write("Check/update your PyMOL environment and try again.\n\n")
48 sys.exit(1)
49
50 # MayaChemTools imports...
51 try:
52 from docopt import docopt
53 import MiscUtil
54 import PyMOLUtil
55 except ImportError as ErrMsg:
56 sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg)
57 sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n")
58 sys.exit(1)
59
60 ScriptName = os.path.basename(sys.argv[0])
61 Options = {}
62 OptionsInfo = {}
63
64 def main():
65 """Start execution of the script."""
66
67 MiscUtil.PrintInfo("\n%s (PyMOL v%s; MayaChemTools v%s; %s): Starting...\n" % (ScriptName, pymol.cmd.get_version()[0], MiscUtil.GetMayaChemToolsVersion(), time.asctime()))
68
69 (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
70
71 # Retrieve command line arguments and options...
72 RetrieveOptions()
73
74 # Process and validate command line arguments and options...
75 ProcessOptions()
76
77 # Perform actions required by the script...
78 GenerateSurfaceAndBuriedResiduesVisualization()
79
80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
82
83 def GenerateSurfaceAndBuriedResiduesVisualization():
84 """Generate visualization for surface and buried residues."""
85
86 Outfile = OptionsInfo["PMLOutfile"]
87 OutFH = open(Outfile, "w")
88 if OutFH is None:
89 MiscUtil.PrintError("Failed to open output fie %s " % Outfile)
90
91 MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
92
93 # Setup header...
94 WritePMLHeader(OutFH, ScriptName)
95 WritePyMOLParameters(OutFH)
96
97 # Load reffile for alignment..
98 if OptionsInfo["Align"]:
99 WriteAlignReference(OutFH)
100
101 # Setup view for each input file...
102 FirstComplex = True
103 FirstComplexFirstChainName = None
104 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
105 # Setup PyMOL object names...
106 PyMOLObjectNames = SetupPyMOLObjectNames(FileIndex)
107
108 # Setup complex view...
109 WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex)
110
111 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
112 FirstChain = True
113 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
114 if FirstComplex and FirstChain:
115 FirstComplexFirstChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
116
117 WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
118
119 # Setup ligand views...
120 FirstLigand = True
121 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
122 WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID)
123
124 # Set up ligand level group...
125 Enable, Action = [False, "close"]
126 if FirstLigand:
127 FirstLigand = False
128 Enable, Action = [True, "open"]
129 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"], PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"], Enable, Action)
130
131 # Setup Chain level group...
132 Enable, Action = [False, "close"]
133 if FirstChain:
134 FirstChain = False
135 Enable, Action = [True, "open"]
136 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"], Enable, Action)
137
138 # Set up complex level group...
139 Enable, Action = [False, "close"]
140 if FirstComplex:
141 FirstComplex = False
142 Enable, Action = [True, "open"]
143 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["PDBGroup"], PyMOLObjectNames["PDBGroupMembers"], Enable, Action)
144
145 # Delete empty PyMOL objects...
146 DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames)
147
148 if OptionsInfo["Align"]:
149 DeleteAlignReference(OutFH)
150
151 if FirstComplexFirstChainName is not None:
152 OutFH.write("""\ncmd.orient("%s", animate = -1)\n""" % FirstComplexFirstChainName)
153 else:
154 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
155
156 OutFH.close()
157
158 # Generate PSE file as needed...
159 if OptionsInfo["PSEOut"]:
160 GeneratePyMOLSessionFile()
161
162 def WritePMLHeader(OutFH, ScriptName):
163 """Write out PML setting up complex view."""
164
165 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
166 OutFH.write("%s\n" % HeaderInfo)
167
168 def WritePyMOLParameters(OutFH):
169 """Write out PyMOL global parameters."""
170
171 PMLCmds = []
172 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
173 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
174
175 PML = "\n".join(PMLCmds)
176
177 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
178 OutFH.write("%s\n" % PML)
179
180 def WriteAlignReference(OutFH):
181 """Setup object for alignment reference."""
182
183 RefFileInfo = OptionsInfo["RefFileInfo"]
184 RefFile = RefFileInfo["RefFileName"]
185 RefName = RefFileInfo["PyMOLObjectName"]
186
187 PMLCmds = []
188 PMLCmds.append("""cmd.load("%s", "%s")""" % (RefFile, RefName))
189 PMLCmds.append("""cmd.hide("everything", "%s")""" % (RefName))
190 PMLCmds.append("""cmd.disable("%s")""" % (RefName))
191 PML = "\n".join(PMLCmds)
192
193 OutFH.write("""\n""\n"Loading %s and setting up view for align reference..."\n""\n""" % RefFile)
194 OutFH.write("%s\n" % PML)
195
196 def WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames):
197 """Setup alignment of complex to reference."""
198
199 RefFileInfo = OptionsInfo["RefFileInfo"]
200 RefName = RefFileInfo["PyMOLObjectName"]
201
202 ComplexName = PyMOLObjectNames["Complex"]
203
204 if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
205 RefFirstChainID = RefFileInfo["ChainsAndLigandsInfo"]["ChainIDs"][0]
206 RefAlignSelection = "%s and chain %s" % (RefName, RefFirstChainID)
207
208 ComplexFirstChainID = RetrieveFirstChainID(FileIndex)
209 ComplexAlignSelection = "%s and chain %s" % (ComplexName, ComplexFirstChainID)
210 else:
211 RefAlignSelection = RefName
212 ComplexAlignSelection = ComplexName
213
214 PML = PyMOLUtil.SetupPMLForAlignment(OptionsInfo["AlignMethod"], RefAlignSelection, ComplexAlignSelection)
215 OutFH.write("""\n""\n"Aligning %s against reference %s ..."\n""\n""" % (ComplexAlignSelection, RefAlignSelection))
216 OutFH.write("%s\n" % PML)
217
218 def DeleteAlignReference(OutFH):
219 """Delete alignment reference object."""
220
221 RefName = OptionsInfo["RefFileInfo"]["PyMOLObjectName"]
222 OutFH.write("""\n""\n"Deleting alignment reference object %s..."\n""\n""" % RefName)
223 OutFH.write("""cmd.delete("%s")\n""" % RefName)
224
225 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex):
226 """Write out PML for viewing polymer complex."""
227
228 # Setup complex...
229 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
230 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["Complex"], Infile, True)
231 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
232 OutFH.write("%s\n" % PML)
233
234 if OptionsInfo["Align"]:
235 # No need to align complex on to itself...
236 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
237 WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames)
238
239 if OptionsInfo["SurfaceComplex"]:
240 # Setup hydrophobic surface...
241 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["ComplexHydrophobicSurface"], PyMOLObjectNames["Complex"], ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
242 OutFH.write("\n%s\n" % PML)
243
244 # Setup complex group...
245 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close")
246
247 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
248 """Write out PML for viewing chain."""
249
250 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
251
252 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
253
254 # Setup chain complex group view...
255 WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
256
257 # Setup chain view...
258 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
259
260 # Setup chain solvent view...
261 PML = PyMOLUtil.SetupPMLForSolventView(PyMOLObjectNames["Chains"][ChainID]["Solvent"], ChainComplexName, False)
262 OutFH.write("\n%s\n" % PML)
263
264 # Setup chain inorganic view...
265 PML = PyMOLUtil.SetupPMLForInorganicView(PyMOLObjectNames["Chains"][ChainID]["Inorganic"], ChainComplexName, False)
266 OutFH.write("\n%s\n" % PML)
267
268 def WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
269 """Write chain complex views."""
270
271 # Setup chain complex...
272 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
273 PML = PyMOLUtil.SetupPMLForPolymerChainComplexView(ChainComplexName, PyMOLObjectNames["Complex"], ChainID, True)
274 OutFH.write("%s\n" % PML)
275
276 if OptionsInfo["SurfaceChainComplex"]:
277 # Setup hydrophobic surface...
278 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"], ChainComplexName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
279 OutFH.write("\n%s\n" % PML)
280
281 # Setup chain complex group...
282 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"], False, "close")
283
284 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
285 """Write individual chain views."""
286
287 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
288
289 # Setup a chain view...
290 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
291 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, True)
292 OutFH.write("\n%s\n" % PML)
293
294 ChainAloneGroupID = "ChainAloneGroup"
295 ChainAloneGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"]
296
297 for GroupType in ["Surface_Residues", "Buried_Residues"]:
298 GroupID = re.sub("_", "", GroupType)
299
300 ResiduesGroupID = "%s%sGroup" % (ChainAloneGroupID, GroupID)
301 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
302
303 # Setup a chain view using residues selection...
304 ResiduesChainNameID = "%sChain" % (ResiduesGroupID)
305 ResiduesChainName = PyMOLObjectNames["Chains"][ChainID][ResiduesChainNameID]
306 ChainResiduesSelection = GetChainResiduesSelection(FileIndex, ChainID, GroupType)
307
308 Selection = "%s and chain %s and polymer and (%s)" % (ChainComplexName, ChainID, ChainResiduesSelection)
309 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(ResiduesChainName, Selection, "cartoon", Enable = False)
310 OutFH.write("\n%s\n" % PML)
311
312 WriteChainAloneResiduesGroupResiduesTypesView(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, ResiduesGroupID)
313 WriteChainAloneResiduesGroupResiduesSurfacesView(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, ResiduesGroupID)
314
315 # Setup residues group...
316 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID], PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID], True, "open")
317
318 # Setup chain group...
319 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"], True, "open")
320
321 def WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID):
322 """Write out PML for viewing ligand in a chain."""
323
324 GroupID = "Ligand"
325 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
326 LigandName = PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
327
328 # Setup main object...
329 GroupTypeObjectID = "%s" % (GroupID)
330 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
331
332 OutFH.write("""\n""\n"Setting up views for ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
333 PML = PyMOLUtil.SetupPMLForLigandView(GroupTypeObjectName, ComplexName, LigandID, Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
334 OutFH.write("%s\n" % PML)
335
336 # Setup ball and stick view...
337 BallAndStickNameID = "%sBallAndStick" % (GroupID)
338 BallAndStickName = PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickNameID]
339 PML = PyMOLUtil.SetupPMLForBallAndStickView(BallAndStickName, GroupTypeObjectName, Enable = False)
340 OutFH.write("\n%s\n" % PML)
341
342 # Setup group....
343 GroupNameID = "%sGroup" % (GroupID)
344 GroupMembersID = "%sGroupMembers" % (GroupID)
345 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
346 GroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID]
347
348 Action = "close"
349 Enable = True
350 GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable, Action)
351
352 def GetChainResiduesSelection(FileIndex, ChainID, GroupType):
353 """Get residue selection for surface or buried residues for a chain."""
354
355 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
356 ResiduesSelection = SpecifiedChainsAndLigandsInfo["SurfaceResiduesSelection"][ChainID] if re.match("^Surface_Residues$", GroupType, re.I) else SpecifiedChainsAndLigandsInfo["BuriedResiduesSelection"][ChainID]
357
358 return ResiduesSelection
359
360 def WriteChainAloneResiduesGroupResiduesTypesView(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, MainGroupID):
361 """Write out PML for viewing residue types for surface or buried residues in a chain."""
362
363 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
364 return
365
366 NameID = "%sChain" % (MainGroupID)
367 ChainName = PyMOLObjectNames["Chains"][ChainID][NameID]
368
369 ResiduesGroupID = "%sResiduesGroup" % MainGroupID
370 ResiduesGroupMembersID = "%sMembers" % ResiduesGroupID
371
372 # Setup residue types objects...
373 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
374 SubGroupID = re.sub("_", "", SubGroupType)
375
376 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
377 ResiduesSubGroupMembersID = "%sMembers" % (ResiduesSubGroupID)
378
379 ResiduesObjectID = "%sResidues" % (ResiduesSubGroupID)
380 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
381
382 ResiduesSurfaceObjectID = "%sSurface" % (ResiduesSubGroupID)
383 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
384
385 ResiduesColor = OptionsInfo["ResidueTypesParams"][SubGroupType]["Color"]
386 ResiduesNames = OptionsInfo["ResidueTypesParams"][SubGroupType]["Residues"]
387
388 NegateResidueNames = True if re.match("^Other$", SubGroupType, re.I) else False
389 WriteResidueTypesResiduesAndSurfaceView(OutFH, ChainName, ResiduesObjectName, ResiduesSurfaceObjectName, ResiduesColor, ResiduesNames, NegateResidueNames)
390
391 # Setup sub groups for residue types..
392 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID], PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID], True, "close")
393
394 # Setup residues group...
395 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID], PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID], False, "close")
396
397 def WriteResidueTypesResiduesAndSurfaceView(OutFH, SelectionObjectName, Name, SurfaceName, ResiduesColor, ResiduesNames, NegateResidueNames):
398 """Write residue types residues and surface view."""
399
400 ResidueNamesSelection = "+".join(ResiduesNames)
401 if NegateResidueNames:
402 Selection = "%s and (not resn %s)" % (SelectionObjectName, ResidueNamesSelection)
403 else:
404 Selection = "%s and (resn %s)" % (SelectionObjectName, ResidueNamesSelection)
405
406 # Setup residues...
407 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(Name, Selection, "lines", ResiduesColor, True)
408 OutFH.write("\n%s\n" % PML)
409
410 # Setup surface...
411 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SurfaceName, Selection, "surface", ResiduesColor, True)
412 OutFH.write("\n%s\n" % PML)
413
414 def WriteChainAloneResiduesGroupResiduesSurfacesView(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, MainGroupID):
415 """Write out PML for viewing surfaces for surface and buried residues in chains."""
416
417 if not GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
418 return
419
420 NameID = "%sChain" % (MainGroupID)
421 ChainName = PyMOLObjectNames["Chains"][ChainID][NameID]
422
423 SurfacesGroupID = "%sSurfaceGroup" % MainGroupID
424 SurfacesGroupMembersID = "%sMembers" % SurfacesGroupID
425
426 ProcessingBuriedResidues = True if re.match("^Buried_Residues$", GroupType, re.I) else False
427
428 # Setup a generic color surface...
429 SurfaceID = "%sSurface" % (SurfacesGroupID)
430 SurfaceName = PyMOLObjectNames["Chains"][ChainID][SurfaceID]
431 ColorName = OptionsInfo["SurfaceBuriedResiduesColor"] if ProcessingBuriedResidues else OptionsInfo["SurfaceColor"]
432 PML = PyMOLUtil.SetupPMLForSurfaceView(SurfaceName, ChainName, Enable = True, DisplayAs = None, Color = ColorName)
433 OutFH.write("\n%s\n" % PML)
434
435 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
436 # Setup surface colored by hydrophobicity...
437 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SurfacesGroupID)
438 HydrophobicSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicSurfaceID]
439 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(HydrophobicSurfaceName, ChainName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False, DisplayAs = None)
440 OutFH.write("\n%s\n" % PML)
441
442 # Setup surface colored by hyrdophobicity and charge...
443 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SurfacesGroupID)
444 HydrophobicChargeSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicChargeSurfaceID]
445 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(HydrophobicChargeSurfaceName, ChainName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = None)
446 OutFH.write("\n%s\n" % PML)
447
448 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
449 # Setup electrostatics surface...
450 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SurfacesGroupID)
451 ElectrostaticsGroupMembersID = "%sMembers" % (ElectrostaticsGroupID)
452 ElectrostaticsGroupName = PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupID]
453 ElectrostaticsGroupMembers = PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupMembersID]
454 WriteSurfaceElectrostaticsView(OutFH, ChainName, ElectrostaticsGroupName, ElectrostaticsGroupMembers, DisplayAs = None)
455
456 # Setup surfaces group...
457 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SurfacesGroupID], PyMOLObjectNames["Chains"][ChainID][SurfacesGroupMembersID], True, "close")
458
459 def WriteSurfaceElectrostaticsView(OutFH, SelectionObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers, DisplayAs = "lines"):
460 """Write out PML for viewing surface electrostatics."""
461
462 if len(ElectrostaticsGroupMembers) == 5:
463 Name, ContactPotentialName, MapName, LegendName, VolumeName = ElectrostaticsGroupMembers
464 else:
465 Name, ContactPotentialName, MapName, LegendName = ElectrostaticsGroupMembers
466 VolumeName = None
467
468 PMLCmds = []
469
470 # Setup chain...
471 PMLCmds.append("""cmd.create("%s", "(%s)")""" % (Name, SelectionObjectName))
472
473 # Setup vacuum electrostatics surface along with associated objects...
474 PMLCmds.append("""util.protein_vacuum_esp("%s", mode=2, quiet=0, _self=cmd)""" % (Name))
475 PMLCmds.append("""cmd.set_name("%s_e_chg", "%s")""" % (Name, ContactPotentialName))
476
477 if DisplayAs is not None:
478 PMLCmds.append("""cmd.show("%s", "(%s)")""" % (DisplayAs, ContactPotentialName))
479
480 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(ContactPotentialName, Enable = True))
481
482 PMLCmds.append("""cmd.set_name("%s_e_map", "%s")""" % (Name, MapName))
483 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MapName, Enable = False))
484
485 PMLCmds.append("""cmd.set_name("%s_e_pot", "%s")""" % (Name, LegendName))
486 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(LegendName, Enable = False))
487
488 if VolumeName is not None:
489 PMLCmds.append("""cmd.volume("%s", "%s", "%s", "(%s)")""" % (VolumeName, MapName, "esp", Name))
490 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(VolumeName, Enable = False))
491
492 # Delete name and take it out from the group membership. It is
493 # is already part of ContactPotential object.
494 PMLCmds.append("""cmd.delete("%s")""" % (Name))
495 ElectrostaticsGroupMembers.pop(0)
496
497 PML = "\n".join(PMLCmds)
498
499 OutFH.write("\n%s\n" % PML)
500
501 # Setup group...
502 GenerateAndWritePMLForGroup(OutFH, ElectrostaticsGroupName, ElectrostaticsGroupMembers, False, "close")
503
504 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable = False, Action = "close"):
505 """Generate and write PML for group."""
506
507 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
508 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
509 OutFH.write("%s\n" % PML)
510
511 def GeneratePyMOLSessionFile():
512 """Generate PME file from PML file."""
513
514 PSEOutfile = OptionsInfo["PSEOutfile"]
515 PMLOutfile = OptionsInfo["PMLOutfile"]
516
517 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
518
519 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
520
521 if not os.path.exists(PSEOutfile):
522 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
523
524 if not OptionsInfo["PMLOut"]:
525 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
526 os.remove(PMLOutfile)
527
528 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
529 """Delete empty PyMOL objects."""
530
531 if OptionsInfo["AllowEmptyObjects"]:
532 return
533
534 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
535 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
536 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
537
538 # Delete any chain level objects...
539 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
540 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
541
542 # Delete any chain alone level objects
543 ChainAloneGroupID = "ChainAloneGroup"
544
545 for GroupType in ["Surface_Residues", "Buried_Residues"]:
546 GroupID = re.sub("_", "", GroupType)
547 ResiduesGroupID = "%s%sGroup" % (ChainAloneGroupID, GroupID)
548
549 # Delete empty chain object...
550 ResiduesChainNameID = "%sChain" % (ResiduesGroupID)
551 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID][ResiduesChainNameID])
552
553 # Delete empty residue type objects...
554 DeleteEmptyChainAloneResiduesGroupResiduesTypesObjects(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, ResiduesGroupID)
555
556 # Delete empty surface objects...
557 DeleteEmptyAloneResiduesGroupResiduesSurfacesObjects(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, ResiduesGroupID)
558
559 def DeleteEmptyChainAloneResiduesGroupResiduesTypesObjects(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, MainGroupID):
560 """Delete empty residue type objects for surface or buried residues in a chain."""
561
562 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
563 return
564
565 ResiduesGroupID = "%sResiduesGroup" % MainGroupID
566 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
567 SubGroupID = re.sub("_", "", SubGroupType)
568
569 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
570 SubGroupName = PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID]
571
572 SubGroupObjectNamesList = []
573
574 ResiduesObjectID = "%sResidues" % (ResiduesSubGroupID)
575 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
576 SubGroupObjectNamesList.append(ResiduesObjectName)
577
578 ResiduesSurfaceObjectID = "%sSurface" % (ResiduesSubGroupID)
579 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
580 SubGroupObjectNamesList.append(ResiduesSurfaceObjectName)
581
582 SubGroupObjectNames = ",".join(SubGroupObjectNamesList)
583 WritePMLToCheckAndDeleteEmptyObjects(OutFH, SubGroupObjectNames, SubGroupName)
584
585 # Delete residues group object...
586 DeleteResiduesGroup = False if AreGroupTypeResiduesPresent(GroupType, FileIndex, PyMOLObjectNames, ChainID) else True
587 if DeleteResiduesGroup:
588 OutFH.write("""cmd.delete("%s")\n""" % PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID])
589
590 def DeleteEmptyAloneResiduesGroupResiduesSurfacesObjects(GroupType, OutFH, FileIndex, PyMOLObjectNames, ChainID, MainGroupID):
591 """Delete empty surfaces objects for surface or buried residues in a chain."""
592
593 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
594 return
595
596 if AreGroupTypeResiduesPresent(GroupType, FileIndex, PyMOLObjectNames, ChainID):
597 return
598
599 SurfacesGroupID = "%sSurfaceGroup" % MainGroupID
600
601 # Delete plain surface...
602 SurfaceID = "%sSurface" % (SurfacesGroupID)
603 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID][SurfaceID])
604
605 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
606 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SurfacesGroupID)
607 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID][HydrophobicSurfaceID])
608
609 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SurfacesGroupID)
610 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID][HydrophobicChargeSurfaceID])
611
612 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
613 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SurfacesGroupID)
614 ElectrostaticsGroupMembersID = "%sMembers" % (ElectrostaticsGroupID)
615
616 ElectrostaticsGroupName = PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupID]
617 ElectrostaticsGroupMembers = PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupMembersID]
618 ElectrostaticsGroupMembersNames = ",".join(ElectrostaticsGroupMembers)
619 WritePMLToCheckAndDeleteEmptyObjects(OutFH, ElectrostaticsGroupMembersNames, ElectrostaticsGroupName)
620
621 # Delete surface group...
622 OutFH.write("""cmd.delete("%s")\n""" % PyMOLObjectNames["Chains"][ChainID][SurfacesGroupID])
623
624 def AreGroupTypeResiduesPresent(GroupType, FileIndex, PyMOLObjectNames, ChainID):
625 """Check presence of surface or buries residue groups in a chain."""
626
627 GroupTypeResiduesPresent = True
628
629 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
630
631 if re.match("^Surface_Residues$", GroupType, re.I):
632 GroupTypeResiduesPresent = SpecifiedChainsAndLigandsInfo["SurfaceResiduesPresent"][ChainID]
633 elif re.match("^Buried_Residues$", GroupType, re.I):
634 GroupTypeResiduesPresent = SpecifiedChainsAndLigandsInfo["BuriedResiduesPresent"][ChainID]
635
636 return GroupTypeResiduesPresent
637
638 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
639 """Write PML to check and delete empty PyMOL objects."""
640
641 if ParentObjectName is None:
642 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
643 else:
644 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
645
646 OutFH.write("%s\n" % PML)
647
648 def SetupPyMOLObjectNames(FileIndex):
649 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
650 chains and ligands present in input file.
651 """
652
653 PyMOLObjectNames = {}
654 PyMOLObjectNames["Chains"] = {}
655 PyMOLObjectNames["Ligands"] = {}
656
657 # Setup groups and objects for complex...
658 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
659
660 # Setup groups and objects for chain...
661 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
662 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
663 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
664
665 # Setup groups and objects for ligand...
666 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
667 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
668
669 return PyMOLObjectNames
670
671 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
672 """Setup groups and objects for complex."""
673
674 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
675
676 PDBGroupName = "%s" % PDBFileRoot
677 PyMOLObjectNames["PDBGroup"] = PDBGroupName
678 PyMOLObjectNames["PDBGroupMembers"] = []
679
680 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
681 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
682 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
683
684 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
685 if OptionsInfo["SurfaceComplex"]:
686 PyMOLObjectNames["ComplexHydrophobicSurface"] = "%s.Surface" % ComplexGroupName
687
688 PyMOLObjectNames["ComplexGroupMembers"] = []
689 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
690 if OptionsInfo["SurfaceComplex"]:
691 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexHydrophobicSurface"])
692
693 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
694 """Setup groups and objects for chain."""
695
696 PDBGroupName = PyMOLObjectNames["PDBGroup"]
697
698 PyMOLObjectNames["Chains"][ChainID] = {}
699 PyMOLObjectNames["Ligands"][ChainID] = {}
700
701 # Set up chain group and chain objects...
702 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
703 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
704 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
705 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
706
707 # Setup chain complex group and objects...
708 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
709 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
710 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
711
712 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
713
714 Name = "%s.Complex" % (ChainComplexGroupName)
715 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = Name
716 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
717
718 if OptionsInfo["SurfaceChainComplex"]:
719 Name = "%s.Surface" % (ChainComplexGroupName)
720 PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"] = Name
721 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
722
723 # Setup up a group for individual chains...
724 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
725 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
726 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
727
728 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
729
730 Name = "%s.Chain" % (ChainAloneGroupName)
731 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
732 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
733
734 # Setup groups and their members for surface and buried residues...
735 ChainAloneGroupID = "ChainAloneGroup"
736 for GroupType in ["Surface_Residues", "Buried_Residues"]:
737 GroupID = re.sub("_", "", GroupType)
738
739 ResiduesGroupName = "%s.%s" % (ChainAloneGroupName, GroupType)
740 ResiduesGroupID = "%s%sGroup" % (ChainAloneGroupID, GroupID)
741 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
742
743 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID] = ResiduesGroupName
744 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(ResiduesGroupName)
745
746 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID] = []
747
748 # Add a chain for surface and buried residues...
749 Name = "%s.Chain" % (ResiduesGroupName)
750 NameID = "%sChain" % (ResiduesGroupID)
751 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
752 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID].append(Name)
753
754 SetupPyMOLObjectNamesForChainResiduesTypes(FileIndex, PyMOLObjectNames, ChainID, ResiduesGroupName, ResiduesGroupID, ResiduesGroupMembersID)
755 SetupPyMOLObjectNamesForChainResiduesSurfaces(FileIndex, PyMOLObjectNames, ChainID, ResiduesGroupName, ResiduesGroupID, ResiduesGroupMembersID)
756
757 # Setup solvent and inorganic objects for chain...
758 for NameID in ["Solvent", "Inorganic"]:
759 Name = "%s.%s" % (ChainGroupName, NameID)
760 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
761 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
762
763 def SetupPyMOLObjectNamesForChainResiduesTypes(FileIndex, PyMOLObjectNames, ChainID, MainGroupName, MainGroupID, MainGroupMembersID):
764 """Setup residue type groups and its objects for residues."""
765
766 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
767 return
768
769 ResiduesGroupName = "%s.Residues" % (MainGroupName)
770 ResiduesGroupID = "%sResiduesGroup" % MainGroupID
771 ResiduesGroupMembersID = "%sMembers" % ResiduesGroupID
772
773 # Add residue type group to residues group...
774 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID] = ResiduesGroupName
775 PyMOLObjectNames["Chains"][ChainID][MainGroupMembersID].append(ResiduesGroupName)
776
777 # Initialize residue type group members...
778 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID] = []
779
780 # Setup residues sub groups and its members...
781 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
782 SubGroupID = re.sub("_", "", SubGroupType)
783
784 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
785 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
786 ResiduesSubGroupMembersID = "%sMembers" % (ResiduesSubGroupID)
787
788 # Add sub group to residues group...
789 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID] = ResiduesSubGroupName
790 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
791
792 # Initialize sub group members...
793 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID] = []
794
795 # Add sub group members to subgroup...
796 for MemberType in ["Residues", "Surface"]:
797 MemberID = re.sub("_", "", MemberType)
798
799 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
800 SubGroupMemberID = "%s%s" % (ResiduesSubGroupID, MemberID)
801
802 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
803 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID].append(SubGroupMemberName)
804
805 def SetupPyMOLObjectNamesForChainResiduesSurfaces(FileIndex, PyMOLObjectNames, ChainID, MainGroupName, MainGroupID, MainGroupMembersID):
806 """Setup residue surface groups and its objects for residues."""
807
808 if not GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
809 return
810
811 SubGroupName = "%s.Surface" % (MainGroupName)
812 SubGroupID = "%sSurfaceGroup" % MainGroupID
813 SubGroupMembersID = "%sMembers" % SubGroupID
814
815 # Add surface group to main group...
816 PyMOLObjectNames["Chains"][ChainID][SubGroupID] = SubGroupName
817 PyMOLObjectNames["Chains"][ChainID][MainGroupMembersID].append(SubGroupName)
818
819 # Initialize surface group members...
820 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID] = []
821
822 # Setup a generic color surface...
823 SurfaceName = "%s.Surface" % (SubGroupName)
824 SurfaceID = "%sSurface" % (SubGroupID)
825 PyMOLObjectNames["Chains"][ChainID][SurfaceID] = SurfaceName
826 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(SurfaceName)
827
828 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
829 # Setup hydrophobicity surface...
830 HydrophobicSurfaceName = "%s.Hydrophobicity" % (SubGroupName)
831 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SubGroupID)
832 PyMOLObjectNames["Chains"][ChainID][HydrophobicSurfaceID] = HydrophobicSurfaceName
833 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(HydrophobicSurfaceName)
834
835 # Setup hydrophobicity and charge surface...
836 HydrophobicChargeSurfaceName = "%s.Hydrophobicity_Charge" % (SubGroupName)
837 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SubGroupID)
838 PyMOLObjectNames["Chains"][ChainID][HydrophobicChargeSurfaceID] = HydrophobicChargeSurfaceName
839 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(HydrophobicChargeSurfaceName)
840
841 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
842 # Setup electrostatics group...
843 ElectrostaticsGroupName = "%s.Vacuum_Electrostatics" % (SubGroupName)
844 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SubGroupID)
845 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SubGroupID)
846
847 PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupID] = ElectrostaticsGroupName
848 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(ElectrostaticsGroupName)
849
850 # Setup electrostatics group members...
851 PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupMembersID] = []
852
853 for MemberType in ["Chain", "Contact_Potential", "Map", "Legend"]:
854 MemberID = re.sub("_", "", MemberType)
855
856 Name = "%s.%s" % (ElectrostaticsGroupName, MemberType)
857 NameID = "%s%s" % (ElectrostaticsGroupID, MemberID)
858
859 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
860 PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupMembersID].append(Name)
861
862 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
863 """Stetup groups and objects for ligand."""
864
865 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
866
867 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
868
869 # Setup a chain level ligand group...
870 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
871 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
872 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
873
874 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
875
876 # Set up ligand group and its members...
877 GroupName = "%s.Ligand" % (ChainLigandGroupName)
878 GroupNameID = "LigandGroup"
879 GroupMembersID = "LigandGroupMembers"
880
881 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
882 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
883
884 LigandName = "%s.Ligand" % (GroupName)
885 LigandNameID = "Ligand"
886 PyMOLObjectNames["Ligands"][ChainID][LigandID][LigandNameID] = LigandName
887
888 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
889 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(LigandName)
890
891 # Add ball and stick...
892 BallAndStickName = "%s.BallAndStick" % (GroupName)
893 BallAndStickID = "LigandBallAndStick"
894 PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickID] = BallAndStickName
895 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(BallAndStickName)
896
897 def RetrieveInfilesInfo():
898 """Retrieve information for input files."""
899
900 InfilesInfo = {}
901
902 InfilesInfo["InfilesNames"] = []
903 InfilesInfo["InfilesRoots"] = []
904 InfilesInfo["ChainsAndLigandsInfo"] = []
905
906 for Infile in OptionsInfo["InfilesNames"]:
907 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
908 InfileRoot = FileName
909
910 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
911
912 InfilesInfo["InfilesNames"].append(Infile)
913 InfilesInfo["InfilesRoots"].append(InfileRoot)
914 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
915
916 OptionsInfo["InfilesInfo"] = InfilesInfo
917
918 def RetrieveRefFileInfo():
919 """Retrieve information for ref file."""
920
921 RefFileInfo = {}
922 if not OptionsInfo["Align"]:
923 OptionsInfo["RefFileInfo"] = RefFileInfo
924 return
925
926 RefFile = OptionsInfo["RefFileName"]
927
928 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
929 RefFileRoot = FileName
930
931 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
932 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
933 else:
934 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
935 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
936
937 RefFileInfo["RefFileName"] = RefFile
938 RefFileInfo["RefFileRoot"] = RefFileRoot
939 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
940 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
941
942 OptionsInfo["RefFileInfo"] = RefFileInfo
943
944 def ProcessChainAndLigandIDs():
945 """Process specified chain and ligand IDs for infiles."""
946
947 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
948
949 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
950 MiscUtil.PrintInfo("\nProcessing specified chain and ligand IDs for input file %s..." % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex])
951
952 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
953 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], "-l, --ligandIDs", OptionsInfo["LigandIDs"])
954 ProcessResidueTypesAndSurfaceOptions(FileIndex, SpecifiedChainsAndLigandsInfo)
955 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
956
957 CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo)
958
959 def RetrieveSurfaceAndBuriedResiduesInfo():
960 """Setup surface and buried residues for specified chains."""
961
962 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
963 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
964 MolName = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
965
966 MiscUtil.PrintInfo("\nRetrieving surface and buried residues from input file %s..." % Infile)
967
968 # Load infile...
969 pymol.cmd.load(Infile, MolName)
970
971 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
972
973 # Initialize surface and buried residues selection...
974 SpecifiedChainsAndLigandsInfo["SurfaceResiduesPresent"] = {}
975 SpecifiedChainsAndLigandsInfo["SurfaceResiduesSelection"] = {}
976 SpecifiedChainsAndLigandsInfo["BuriedResiduesSelection"] = {}
977 SpecifiedChainsAndLigandsInfo["BuriedResiduesPresent"] = {}
978
979 # Go over all specified chains...
980 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
981 SurfaceResiduesInfo, BuriedResiduesInfo = PyMOLUtil.GetSurfaceAndBuriedResiduesInfo(MolName, ChainID, OptionsInfo["CutoffSASA"])
982
983 # Retrieve surface and buried residue numbers...
984 SurfaceResiduesNums = RetrieveResiduesNumbers(SurfaceResiduesInfo)
985 BuriedResiduesNums = RetrieveResiduesNumbers(BuriedResiduesInfo)
986
987 # Setup PyMOL selection for surface and buried residue numbers...
988 SurfaceResiduesSelection, BuriedResiduesSelection = SetupSurfaceAndBuriedResiduesSelection(SurfaceResiduesNums, BuriedResiduesNums)
989
990 # Track surface and buried residues...
991 SpecifiedChainsAndLigandsInfo["SurfaceResiduesPresent"][ChainID] = True if len(SurfaceResiduesNums) else False
992 SpecifiedChainsAndLigandsInfo["SurfaceResiduesSelection"][ChainID] = SurfaceResiduesSelection
993
994 SpecifiedChainsAndLigandsInfo["BuriedResiduesPresent"][ChainID] = True if len(BuriedResiduesNums) else False
995 SpecifiedChainsAndLigandsInfo["BuriedResiduesSelection"][ChainID] = BuriedResiduesSelection
996
997 # List surface residues...
998 SurfaceResiduesCount, SurfaceResiduesDistribution, SurfaceResiduesIDs = FormatResiduesInfo(SurfaceResiduesInfo)
999 MiscUtil.PrintInfo("\nInput file: %s; ChainID: %s\nNumber of surface residues: %d" % (Infile, ChainID, SurfaceResiduesCount))
1000 MiscUtil.PrintInfo("Residue distribution: %s" % (SurfaceResiduesDistribution))
1001 if OptionsInfo["ResidueIDs"]:
1002 MiscUtil.PrintInfo("Residue IDs: %s" % (SurfaceResiduesIDs))
1003
1004 # List buried residues...
1005 BuriedResiduesCount, BuriedResiduesDistribution, BuriedResiduesIDs = FormatResiduesInfo(BuriedResiduesInfo)
1006 MiscUtil.PrintInfo("\nInput file: %s;ChainID: %s\nNumber of buried residues: %d" % (Infile, ChainID, BuriedResiduesCount))
1007 MiscUtil.PrintInfo("Residue distribution: %s" % (BuriedResiduesDistribution))
1008 if OptionsInfo["ResidueIDs"]:
1009 MiscUtil.PrintInfo("Residue IDs: %s" % (BuriedResiduesIDs))
1010
1011 # Delete loaded object...
1012 pymol.cmd.delete(MolName)
1013
1014 def RetrieveResiduesNumbers(ResiduesInfo):
1015 """Retrieve residue numbers."""
1016
1017 # Setup residue IDs sorted by residue numbers...
1018 ResNumMap = {}
1019 for ResName in ResiduesInfo["ResNames"]:
1020 for ResNum in ResiduesInfo["ResNum"][ResName]:
1021 ResNumMap[ResNum] = ResName
1022
1023 ResNumsList = []
1024 if len(ResNumMap):
1025 ResNumsList = sorted(ResNumMap, key = int)
1026
1027 return ResNumsList
1028
1029 def SetupSurfaceAndBuriedResiduesSelection(SurfaceResiduesNums, BuriedResiduesNums):
1030 """Setup PyMOL selection for surface and buried residues."""
1031
1032 SurfaceResiduesSelection, BuriedResiduesSelection = [None] * 2
1033 UseSurfaceResidueNums, UseBuriedResidueNums = [False] * 2
1034
1035 SurfaceResiduesCount = len(SurfaceResiduesNums)
1036 BuriedResiduesCount = len(BuriedResiduesNums)
1037
1038 # Setup selections using the residue list containing lower number of residues for
1039 # ease of read in PML file...
1040 if SurfaceResiduesCount and BuriedResiduesCount:
1041 if SurfaceResiduesCount < BuriedResiduesCount:
1042 UseSurfaceResidueNums = True
1043 else:
1044 UseBuriedResidueNums = True
1045 elif SurfaceResiduesCount:
1046 UseSurfaceResidueNums = True
1047 elif BuriedResiduesCount:
1048 UseBuriedResidueNums = True
1049
1050 if UseSurfaceResidueNums:
1051 SurfaceResiduesSelection = "resi %s" % ("+".join(SurfaceResiduesNums))
1052 BuriedResiduesSelection = "not %s" % SurfaceResiduesSelection
1053 elif UseBuriedResidueNums:
1054 BuriedResiduesSelection = "resi %s" % ("+".join(BuriedResiduesNums))
1055 SurfaceResiduesSelection = "not %s" % BuriedResiduesSelection
1056
1057 return SurfaceResiduesSelection, BuriedResiduesSelection
1058
1059 def FormatResiduesInfo(SelectionInfo):
1060 """Format residues info."""
1061
1062 # Setup distribution of residues...
1063 LineWords = []
1064 ResiduesCount = 0
1065 SortedResNames = sorted(SelectionInfo["ResNames"], key = lambda ResName: SelectionInfo["ResCount"][ResName], reverse = True)
1066 for ResName in SortedResNames:
1067 ResCount = SelectionInfo["ResCount"][ResName]
1068 LineWords.append("%s - %s" % (ResName, ResCount))
1069 ResiduesCount += ResCount
1070
1071 ResiduesDistribution = "; ".join(LineWords) if len(LineWords) else None
1072
1073 # Setup residue IDs sorted by residue numbers...
1074 ResNumMap = {}
1075 for ResName in SelectionInfo["ResNames"]:
1076 for ResNum in SelectionInfo["ResNum"][ResName]:
1077 ResNumMap[ResNum] = ResName
1078
1079 ResNumsList = []
1080 if len(ResNumMap):
1081 ResNumsList = sorted(ResNumMap, key = int)
1082
1083 LineWords = []
1084 for ResNum in ResNumsList:
1085 ResName = ResNumMap[ResNum]
1086 ResID = "%s_%s" % (ResName, ResNum)
1087 LineWords.append(ResID)
1088 ResiduesIDs = ", ".join(LineWords) if len(LineWords) else None
1089
1090 return ResiduesCount, ResiduesDistribution, ResiduesIDs
1091
1092 def ProcessResidueTypesAndSurfaceOptions(FileIndex, SpecifiedChainsAndLigandsInfo):
1093 """Process residue types and surface options for chains."""
1094
1095 SpecifiedChainsAndLigandsInfo["ChainSurfaces"] = {}
1096 SpecifiedChainsAndLigandsInfo["SurfaceChain"] = {}
1097 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"] = {}
1098
1099 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"] = {}
1100
1101 # Load infile...
1102 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
1103 MolName = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
1104 pymol.cmd.load(Infile, MolName)
1105
1106 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1107 AminoAcidsPresent = PyMOLUtil.AreAminoAcidResiduesPresent(MolName, ChainID)
1108
1109 # Process surfaces for chains...
1110 if re.match("^auto$", OptionsInfo["SurfaceChain"], re.I):
1111 SurfaceChain = True if AminoAcidsPresent else False
1112 else:
1113 SurfaceChain = True if re.match("^yes$", OptionsInfo["SurfaceChain"], re.I) else False
1114 SpecifiedChainsAndLigandsInfo["SurfaceChain"][ChainID] = SurfaceChain
1115
1116 if re.match("^auto$", OptionsInfo["SurfaceChainElectrostatics"], re.I):
1117 SurfaceChainElectrostatics = True if AminoAcidsPresent else False
1118 else:
1119 SurfaceChainElectrostatics = True if re.match("^yes$", OptionsInfo["SurfaceChainElectrostatics"], re.I) else False
1120 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"][ChainID] = SurfaceChainElectrostatics
1121
1122 # A generic color surface is always created...
1123 ChainSurfaces = True
1124 SpecifiedChainsAndLigandsInfo["ChainSurfaces"][ChainID] = ChainSurfaces
1125
1126 # Process residue types for chains...
1127 if re.match("^auto$", OptionsInfo["ResidueTypesChain"], re.I):
1128 ResidueTypesChain = True if AminoAcidsPresent else False
1129 else:
1130 ResidueTypesChain = True if re.match("^yes$", OptionsInfo["ResidueTypesChain"], re.I) else False
1131 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"][ChainID] = ResidueTypesChain
1132
1133 # Delete loaded object...
1134 pymol.cmd.delete(MolName)
1135
1136 def GetChainAloneResidueTypesStatus(FileIndex, ChainID):
1137 """Get status of residue types for chain alone object."""
1138
1139 # o Need to handle Surface_Residues and Buried residues group based detection...
1140 Status = True if OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesChain"][ChainID] else False
1141
1142 return Status
1143
1144 def GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
1145 """Get status of surfaces present in chain alone object."""
1146
1147 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSurfaces"][ChainID]
1148
1149 def GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
1150 """Get status of hydrophobic surfaces for chain alone object."""
1151
1152 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChain"][ChainID]
1153
1154 def GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
1155 """Get status of electrostatics surfaces for chain alone object."""
1156
1157 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainElectrostatics"][ChainID]
1158
1159 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
1160 """Check presence of valid ligand IDs."""
1161
1162 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
1163
1164 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1165 if len (SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
1166 MiscUtil.PrintInfo("Chain ID: %s; Specified LigandIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID])))
1167 else:
1168 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
1169 MiscUtil.PrintWarning("No valid ligand IDs found for chain ID, %s. PyMOL groups and objects related to ligand and binding pockect won't be created." % (ChainID))
1170
1171 def RetrieveFirstChainID(FileIndex):
1172 """Get first chain ID."""
1173
1174 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
1175
1176 FirstChainID = None
1177 if len(ChainsAndLigandsInfo["ChainIDs"]):
1178 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
1179
1180 return FirstChainID
1181
1182 def ProcessResidueTypes():
1183 """Process residue types."""
1184
1185 ResidueTypesNamesInfo, ResidueTypesParamsInfo = PyMOLUtil.ProcessResidueTypesOptionsInfo("-r, --residueTypes", OptionsInfo["ResidueTypes"])
1186 OptionsInfo["ResidueTypesNames"] = ResidueTypesNamesInfo
1187 OptionsInfo["ResidueTypesParams"] = ResidueTypesParamsInfo
1188
1189 def ProcessSurfaceAtomTypesColors():
1190 """Process surface atom types colors."""
1191
1192 AtomTypesColorNamesInfo = PyMOLUtil.ProcessSurfaceAtomTypesColorsOptionsInfo("--surfaceAtomTypesColors", OptionsInfo["SurfaceAtomTypesColors"])
1193 OptionsInfo["AtomTypesColorNames"] = AtomTypesColorNamesInfo
1194
1195 def ProcessOptions():
1196 """Process and validate command line arguments and options."""
1197
1198 MiscUtil.PrintInfo("Processing options...")
1199
1200 # Validate options...
1201 ValidateOptions()
1202
1203 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
1204 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
1205 OptionsInfo["AlignMode"] = Options["--alignMode"]
1206
1207 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
1208
1209 OptionsInfo["CutoffSASA"] = float(Options["--cutoffSASA"])
1210
1211 OptionsInfo["Infiles"] = Options["--infiles"]
1212 OptionsInfo["InfilesNames"] = Options["--infileNames"]
1213
1214 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
1215 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1216 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
1217 else:
1218 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
1219
1220 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
1221
1222 OptionsInfo["Overwrite"] = Options["--overwrite"]
1223 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
1224
1225 OptionsInfo["Outfile"] = Options["--outfile"]
1226 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
1227 OptionsInfo["PSEOut"] = False
1228 if re.match("^pml$", FileExt, re.I):
1229 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
1230 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
1231 elif re.match("^pse$", FileExt, re.I):
1232 OptionsInfo["PSEOut"] = True
1233 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
1234 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
1235 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
1236 MiscUtil.PrintError("The intermediate output file to be generated, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again." % OptionsInfo["PMLOutfile"] )
1237
1238 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
1239
1240 OptionsInfo["ResidueIDs"] = True if re.match("^Yes$", Options["--residueIDs"], re.I) else False
1241
1242 OptionsInfo["ResidueTypesChain"] = Options["--residueTypesChain"]
1243 OptionsInfo["ResidueTypes"] = Options["--residueTypes"]
1244 ProcessResidueTypes()
1245
1246 OptionsInfo["SurfaceChain"] = Options["--surfaceChain"]
1247 OptionsInfo["SurfaceChainElectrostatics"] = Options["--surfaceChainElectrostatics"]
1248
1249 OptionsInfo["SurfaceChainComplex"] = True if re.match("^Yes$", Options["--surfaceChainComplex"], re.I) else False
1250 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
1251
1252 # Retrieve surface colors for generic surfaces..
1253 SurfaceColors = re.sub(" ", "", Options["--surfaceColors"])
1254 SurfaceColorsWords = SurfaceColors.split(",")
1255 if len(SurfaceColorsWords) != 2:
1256 MiscUtil.PrintError("The number of comma delimited color names, %d, specified using \"--surfaceColors\" option, \"%s\", must be a 2." % (len(SurfaceColorsWords), Options["--surfaceColors"]))
1257 OptionsInfo["SurfaceColors"] = SurfaceColors
1258 OptionsInfo["SurfaceColor"] = SurfaceColorsWords[0]
1259 OptionsInfo["SurfaceBuriedResiduesColor"] = SurfaceColorsWords[1]
1260
1261 OptionsInfo["SurfaceColorPalette"] = Options["--surfaceColorPalette"]
1262 OptionsInfo["SurfaceAtomTypesColors"] = Options["--surfaceAtomTypesColors"]
1263 ProcessSurfaceAtomTypesColors()
1264
1265 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
1266
1267 RetrieveInfilesInfo()
1268 RetrieveRefFileInfo()
1269
1270 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
1271 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
1272 ProcessChainAndLigandIDs()
1273
1274 RetrieveSurfaceAndBuriedResiduesInfo()
1275
1276 def RetrieveOptions():
1277 """Retrieve command line arguments and options."""
1278
1279 # Get options...
1280 global Options
1281 Options = docopt(_docoptUsage_)
1282
1283 # Set current working directory to the specified directory...
1284 WorkingDir = Options["--workingdir"]
1285 if WorkingDir:
1286 os.chdir(WorkingDir)
1287
1288 # Handle examples option...
1289 if "--examples" in Options and Options["--examples"]:
1290 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
1291 sys.exit(0)
1292
1293 def ValidateOptions():
1294 """Validate option values."""
1295
1296 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
1297 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
1298 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
1299
1300 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
1301
1302 MiscUtil.ValidateOptionFloatValue("--cutoffSASA", Options["--cutoffSASA"], {">": 0.0})
1303
1304 # Expand infiles to handle presence of multiple input files...
1305 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
1306 if not len(InfileNames):
1307 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
1308
1309 # Validate file extensions...
1310 for Infile in InfileNames:
1311 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
1312 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
1313 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
1314 Options["--infileNames"] = InfileNames
1315
1316 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
1317 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
1318
1319 if re.match("^yes$", Options["--align"], re.I):
1320 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1321 AlignRefFile = Options["--alignRefFile"]
1322 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
1323 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
1324 MiscUtil.ValidateOptionsDistinctFileNames("--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"])
1325
1326 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
1327
1328 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
1329 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
1330
1331 MiscUtil.ValidateOptionTextValue("--residueIDs", Options["--residueIDs"], "yes no")
1332
1333 MiscUtil.ValidateOptionTextValue("--residueTypesChain", Options["--residueTypesChain"], "yes no auto")
1334
1335 MiscUtil.ValidateOptionTextValue("--surfaceChain", Options["--surfaceChain"], "yes no auto")
1336 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
1337 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no")
1338 MiscUtil.ValidateOptionTextValue("--surfaceChainElectrostatics", Options["--surfaceChainElectrostatics"], "yes no auto")
1339
1340 MiscUtil.ValidateOptionTextValue("--surfaceColorPalette", Options["--surfaceColorPalette"], "RedToWhite WhiteToGreen")
1341 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
1342
1343 # Setup a usage string for docopt...
1344 _docoptUsage_ = """
1345 PyMOLVisualizeSurfaceAndBuriedResidues.py - Visualize surface and buried residues in macromolecules
1346
1347 Usage:
1348 PyMOLVisualizeSurfaceAndBuriedResidues.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
1349 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
1350 [--allowEmptyObjects <yes or no>] [--chainIDs <First, All or ID1,ID2...>]
1351 [--cutoffSASA <number> ] [--labelFontID <number>]
1352 [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All or ID1,ID2...> ] [--PMLOut <yes or no>]
1353 [--residueIDs <yes or no> ] [--residueTypes <Type,Color,ResNames,...>] [--residueTypesChain <yes or no>]
1354 [--surfaceChain <yes or no>] [--surfaceChainElectrostatics <yes or no>]
1355 [--surfaceChainComplex <yes or no>] [--surfaceComplex <yes or no>]
1356 [--surfaceAtomTypesColors <ColorType,ColorSpec,...>]
1357 [--surfaceColors <ColorName1,ColorName2>] [--surfaceColorPalette <RedToWhite or WhiteToGreen>]
1358 [--surfaceTransparency <number>] [--overwrite] [-w <dir>] -i <infile1,infile2,infile3...> -o <outfile>
1359 PyMOLVisualizeSurfaceAndBuriedResidues.py -h | --help | -e | --examples
1360
1361 Description:
1362 Generate PyMOL visualization files for viewing surface and buried residues
1363 in macromolecules including proteins and nucleic acids.
1364
1365 The supported input file format are: PDB (.pdb), CIF (.cif)
1366
1367 The supported output file formats are: PyMOL script file (.pml), PyMOL session
1368 file (.pse)
1369
1370 A variety of PyMOL groups and objects may be created for visualization of
1371 surface and buried residues in macromolecules. These groups and objects
1372 correspond to complexes, surfaces, chains, ligands, and inorganics. A complete
1373 hierarchy of all possible PyMOL groups and objects is shown below:
1374
1375 <PDBFileRoot>
1376 .Complex
1377 .Complex
1378 .Surface
1379 .Chain<ID>
1380 .Complex
1381 .Complex
1382 .Surface
1383 .Chain
1384 .Chain
1385 .Surface_Residues
1386 .Chain
1387 .Residues
1388 .Aromatic
1389 .Residues
1390 .Surface
1391 .Hydrophobic
1392 .Residues
1393 .Surface
1394 .Polar
1395 .Residues
1396 .Surface
1397 .Positively_Charged
1398 .Residues
1399 .Surface
1400 .Negatively_Charged
1401 .Residues
1402 .Surface
1403 .Other
1404 .Residues
1405 .Surface
1406 .Surface
1407 .Surface
1408 .Hydrophobicity
1409 .Hydrophobicity_Charge
1410 .Vacuum_Electrostatics
1411 .Contact_Potentials
1412 .Map
1413 .Legend
1414 .Buried_Residues
1415 .Chain
1416 .Residues
1417 .Aromatic
1418 .Residues
1419 .Surface
1420 .Hydrophobic
1421 .Residues
1422 .Surface
1423 .Polar
1424 .Residues
1425 .Surface
1426 .Positively_Charged
1427 .Residues
1428 .Surface
1429 .Negatively_Charged
1430 .Residues
1431 .Surface
1432 .Other
1433 .Residues
1434 .Surface
1435 .Surface
1436 .Surface
1437 .Hydrophobicity
1438 .Hydrophobicity_Charge
1439 .Vacuum_Electrostatics
1440 .Contact_Potentials
1441 .Map
1442 .Legend
1443 .Solvent
1444 .Inorganic
1445 .Ligand<ID>
1446 .Ligand
1447 .Ligand
1448 .BallAndStick
1449 .Ligand<ID>
1450 .Ligand
1451 ... ... ...
1452 .Chain<ID>
1453 ... ... ...
1454 .Ligand<ID>
1455 ... ... ...
1456 .Ligand<ID>
1457 ... ... ...
1458 .Chain<ID>
1459 ... ... ...
1460 <PDBFileRoot>
1461 .Complex
1462 ... ... ...
1463 .Chain<ID>
1464 ... ... ...
1465 .Ligand<ID>
1466 ... ... ...
1467 .Ligand<ID>
1468 ... ... ...
1469 .Chain<ID>
1470 ... ... ...
1471
1472 The hydrophobic and electrostatic surfaces are not created for complete complex
1473 and chain complex in input file(s) by default. A word to the wise: The creation of
1474 surface objects may slow down loading of PML file and generation of PSE file, based
1475 on the size of input complexes. The generation of PSE file may also fail.
1476
1477 Options:
1478 -a, --align <yes or no> [default: no]
1479 Align input files to a reference file before visualization.
1480 --alignMethod <align, cealign, super> [default: super]
1481 Alignment methodology to use for aligning input files to a
1482 reference file.
1483 --alignMode <FirstChain or Complex> [default: FirstChain]
1484 Portion of input and reference files to use for spatial alignment of
1485 input files against reference file. Possible values: FirstChain or
1486 Complex.
1487
1488 The FirstChain mode allows alignment of the first chain in each input
1489 file to the first chain in the reference file along with moving the rest
1490 of the complex to coordinate space of the reference file. The complete
1491 complex in each input file is aligned to the complete complex in reference
1492 file for the Complex mode.
1493 --alignRefFile <filename> [default: FirstInputFile]
1494 Reference input file name. The default is to use the first input file
1495 name specified using '-i, --infiles' option.
1496 --allowEmptyObjects <yes or no> [default: no]
1497 Allow creation of empty PyMOL objects corresponding to solvent and
1498 inorganic atom selections across chains and ligands in input file(s). By
1499 default, the empty objects are marked for deletion.
1500 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
1501 List of chain IDs to use for visualizing surface and buried residues in
1502 macromolecules. Possible values: First, All, or a comma delimited
1503 list of chain IDs. The default is to use the chain ID for the first chain
1504 in each input file.
1505 --cutoffSASA <number> [default: 2.5]
1506 Solvent Accessible Surface Area (SASA) cutoff value in Angstroms**2
1507 for identification of surface and buried residues in chains. The residues
1508 with SASA less than the cutoff value are considered buried residues.
1509 -e, --examples
1510 Print examples.
1511 -h, --help
1512 Print this help message.
1513 -i, --infiles <infile1,infile2,infile3...>
1514 Input file names.
1515 --ignoreHydrogens <yes or no> [default: yes]
1516 Ignore hydrogens for ligand views.
1517 --labelFontID <number> [default: 7]
1518 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
1519 The specified value must be a valid PyMOL font ID. No validation is
1520 performed. The complete lists of valid font IDs is available at:
1521 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
1522 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
1523 -l, --ligandIDs <Largest, All or ID1,ID2...> [default: All]
1524 List of ligand IDs to show in chains during visualizing of surface and buried
1525 residues in macromolecules. Possible values: Largest, All, or a comma delimited
1526 list of ligand IDs. The default is to show all ligands present in all or
1527 specified chains in each input file.
1528
1529 Ligands are identified using organic selection operator available in PyMOL.
1530 It'll also identify buffer molecules as ligands. The largest ligand contains
1531 the highest number of heavy atoms.
1532 -o, --outfile <outfile>
1533 Output file name.
1534 -p, --PMLOut <yes or no> [default: yes]
1535 Save PML file during generation of PSE file.
1536 --residueIDs <yes or no> [default: no]
1537 List residue IDs (ResName_ResNum) corresponding to surface and buried
1538 residues. The count and residue distribution for these residues is always
1539 listed.
1540 -r, --residueTypes <Type,Color,ResNames,...> [default: auto]
1541 Residue types, colors, and names to generate for residue groups during
1542 '--residueTypesChain' option. It is only valid for amino acids.
1543
1544 It is a triplet of comma delimited list of amino acid residues type, residues
1545 color, and a space delimited list three letter residue names.
1546
1547 The default values for residue type, color, and name triplets are shown
1548 below:
1549
1550 Aromatic,brightorange,HIS PHE TRP TYR,
1551 Hydrophobic,orange,ALA GLY VAL LEU ILE PRO MET,
1552 Polar,palegreen,ASN GLN SER THR CYS,
1553 Positively_Charged,marine,ARG LYS,
1554 Negatively_Charged,red,ASP GLU
1555
1556 The color name must be a valid PyMOL name. No validation is performed.
1557 An amino acid name may appear across multiple residue types. All other
1558 residues are grouped under 'Other'.
1559 --residueTypesChain <yes or no> [default: auto]
1560 Chain residue types. The residue groups are generated using residue types,
1561 colors, and names specified by '--residueTypes' option. It is only valid for
1562 amino acids. By default, the residue type groups are automatically created
1563 for chains containing amino acids and skipped for chains only containing
1564 nucleic acids.
1565 --surfaceChain <yes or no> [default: auto]
1566 Surfaces around individual chain colored by hydrophobicity alone and
1567 both hydrophobicity and charge. The hydrophobicity surface is colored
1568 at residue level using Eisenberg hydrophobicity scale for residues and color
1569 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
1570 charge surface is colored [ Ref 140 ] at atom level using colors specified for
1571 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
1572 simultaneous mapping of hyrophobicity and charge values on the surfaces.
1573
1574 This option is only valid for amino acids. By default, both surfaces are
1575 automatically created for chains containing amino acids and skipped for
1576 chains containing only nucleic acids.
1577
1578 In addition, generic surfaces colored by '--surfaceColor' are always created
1579 for chain residues containing amino acids and nucleic acids.
1580 --surfaceChainElectrostatics <yes or no> [default: no]
1581 Vacuum electrostatics contact potential surface around individual
1582 chain. A word to the wise from PyMOL documentation: The computed protein
1583 contact potentials are only qualitatively useful, due to short cutoffs,
1584 truncation, and lack of solvent "screening".
1585
1586 This option is only valid for amino acids. By default, the electrostatics surface
1587 is automatically created for chains containing amino acids and
1588 skipped for chains containing only nucleic acids.
1589 --surfaceChainComplex <yes or no> [default: no]
1590 Hydrophobic surface around chain complex. The surface is colored by
1591 hydrophobicity. It is only valid for amino acids.
1592 --surfaceComplex <yes or no> [default: no]
1593 Hydrophobic surface around complete complex. The surface is colored by
1594 hydrophobicity. It is only valid for amino acids.
1595 --surfaceAtomTypesColors <ColorType,ColorSpec,...> [default: auto]
1596 Atom colors for generating surfaces colored by hyrophobicity and charge
1597 around chains and pockets in proteins. It's a pairwise comma delimited list
1598 of atom color type and color specification for goups of atoms.
1599
1600 The default values for color types [ Ref 140 ] along wth color specifications
1601 are shown below:
1602
1603 HydrophobicAtomsColor, yellow,
1604 NegativelyChargedAtomsColor, red,
1605 PositivelyChargedAtomsColor, blue,
1606 OtherAtomsColor, gray90
1607
1608 The color names must be valid PyMOL names.
1609
1610 The color values may also be specified as space delimited RGB triplets:
1611
1612 HydrophobicAtomsColor, 0.95 0.78 0.0,
1613 NegativelyChargedAtomsColor, 1.0 0.4 0.4,
1614 PositivelyChargedAtomsColor, 0.2 0.5 0.8,
1615 OtherAtomsColor, 0.95 0.95 0.95
1616
1617 --surfaceColors <ColorName1,ColorName2> [default: lightblue,salmon]
1618 Color names for surface and burieds residues in chains. These colors are not
1619 used for surfaces colored by hydrophobicity and charge. The color names
1620 must be valid PyMOL names.
1621 --surfaceColorPalette <RedToWhite or WhiteToGreen> [default: RedToWhite]
1622 Color palette for hydrophobic surfaces around chains and pockets in proteins.
1623 Possible values: RedToWhite or WhiteToGreen from most hydrophobic amino
1624 acid to least hydrophobic. The colors values for amino acids are taken from
1625 color_h script available as part of the Script Library at PyMOL Wiki.
1626 --surfaceTransparency <number> [default: 0.25]
1627 Surface transparency for molecular surfaces.
1628 --overwrite
1629 Overwrite existing files.
1630 -w, --workingdir <dir>
1631 Location of working directory which defaults to the current directory.
1632
1633 Examples:
1634 To visualize surface and buried residues in the first chain along with the
1635 largest ligand in the first chain, solvents, and inorganics, in a PDB file, and
1636 generate a PML file, type:
1637
1638 % PyMOLVisualizeSurfaceAndBuriedResidues.py -i Sample4.pdb
1639 -o Sample4.pml
1640
1641 To visualize surface and buries residues in all chain along with all ligands,
1642 solvents, and inorganics, in a PDB file, and generate a PML file, type:
1643
1644 % PyMOLVisualizeSurfaceAndBuriedResidues.py -c All -l All
1645 -i Sample4.pdb -o Sample4.pml
1646
1647 To visualize surface and buried residues in the first chain at a specific
1648 cutoff using specifc colors for surfaces corresponding to surface and
1649 buried residues, and generate a PML file, type:
1650
1651 % PyMOLVisualizeSurfaceAndBuriedResidues.py --cutoffSASA 3
1652 --surfaceColors "blue,red" -i Sample4.pdb -o Sample4.pml
1653
1654 To visualize surface and buried residues in the first chain along with the
1655 largest ligand in the first chain, solvents, and inorganics, in PDB files, along
1656 with aligning first chain in each input file to the first chain inand generate a
1657 PML file, type:
1658
1659 % PyMOLVisualizeSurfaceAndBuriedResidues.py --align yes
1660 -i "Sample5.pdb,Sample6.pdb,Sample7.pdb"
1661 -o SampleOut.pml
1662
1663 Author:
1664 Manish Sud(msud@san.rr.com)
1665
1666 See also:
1667 DownloadPDBFiles.pl, PyMOLVisualizeCavities.py,
1668 PyMOLVisualizeCryoEMDensity.py, PyMOLVisualizeElectronDensity.py,
1669 PyMOLVisualizeInterfaces.py, PyMOLVisualizeMacromolecules.py
1670
1671 Copyright:
1672 Copyright (C) 2024 Manish Sud. All rights reserved.
1673
1674 The functionality available in this script is implemented using PyMOL, a
1675 molecular visualization system on an open source foundation originally
1676 developed by Warren DeLano.
1677
1678 This file is part of MayaChemTools.
1679
1680 MayaChemTools is free software; you can redistribute it and/or modify it under
1681 the terms of the GNU Lesser General Public License as published by the Free
1682 Software Foundation; either version 3 of the License, or (at your option) any
1683 later version.
1684
1685 """
1686
1687 if __name__ == "__main__":
1688 main()
