1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeInterfaces.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 GenerateMacromolecularInterfacesVisualization()
79
80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
82
83 def GenerateMacromolecularInterfacesVisualization():
84 """Generate visualization for macromolecular interfaces."""
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 WriteComplexesAndChainsViews(OutFH)
98 WriteInterfaceViews(OutFH)
99
100 OutFH.close()
101
102 # Generate PSE file as needed...
103 if OptionsInfo["PSEOut"]:
104 GeneratePyMOLSessionFile()
105
106 def WriteComplexesAndChainsViews(OutFH):
107 """Write out PML for viewing complexes and chains in input files."""
108
109 # Setup views for input file(s)...
110 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
111 # Setup PyMOL object names...
112 PyMOLObjectNamesInfo = OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"][FileIndex]
113
114 # Setup complex view...
115 WriteComplexView(OutFH, FileIndex, PyMOLObjectNamesInfo)
116
117 # Setup chain views...
118 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
119
120 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
121 WriteChainView(OutFH, FileIndex, PyMOLObjectNamesInfo, ChainID)
122
123 # Setup ligand views...
124 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
125 WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNamesInfo, ChainID, LigandID)
126
127 # Set up ligand level group...
128 Enable, Action = [True, "close"]
129 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNamesInfo["Ligands"][ChainID][LigandID]["ChainLigandGroup"], PyMOLObjectNamesInfo["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"], Enable, Action)
130
131 # Setup Chain level group...
132 Enable, Action = [True, "open"]
133 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNamesInfo["Chains"][ChainID]["ChainGroup"], PyMOLObjectNamesInfo["Chains"][ChainID]["ChainGroupMembers"], Enable, Action)
134
135 # Set up complex level group...
136 Enable, Action = [True, "close"]
137 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNamesInfo["PDBGroup"], PyMOLObjectNamesInfo["PDBGroupMembers"], Enable, Action)
138
139 # Delete empty PyMOL objects...
140 DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNamesInfo)
141
142 def WriteInterfaceViews(OutFH):
143 """Write out PML for viewing macromolecular interfaces among specified chains."""
144
145 InterfaceChainsAndResiduesInfo = OptionsInfo["InfilesInfo"]["InterfaceChainsAndResiduesInfo"]
146 if InterfaceChainsAndResiduesInfo is None:
147 return
148
149 PyMOLInterfaceObjectNamesInfo = OptionsInfo["InfilesInfo"]["PyMOLInterfaceObjectNamesInfo"]
150 InterfaceChainPairsAndResiduesInfo = OptionsInfo["InfilesInfo"]["InterfaceChainPairsAndResiduesInfo"]
151
152 FirstInterfaceID = True
153 for InterfaceID in InterfaceChainsAndResiduesInfo["InterfaceIDs"]:
154 WriteInterfacePolarContactsView(OutFH, InterfaceID, InterfaceChainPairsAndResiduesInfo, PyMOLInterfaceObjectNamesInfo)
155 WriteInterfaceHydrophobicContactsView(OutFH, InterfaceID, InterfaceChainPairsAndResiduesInfo, PyMOLInterfaceObjectNamesInfo)
156
157 for InterfaceChainID in InterfaceChainsAndResiduesInfo["InterfaceChainIDs"][InterfaceID]:
158 ChainID = InterfaceChainsAndResiduesInfo["ChainIDs"][InterfaceID][InterfaceChainID]
159 ResNums = InterfaceChainsAndResiduesInfo["ChainIDsResNums"][InterfaceID][InterfaceChainID]
160 ComplexName = InterfaceChainsAndResiduesInfo["ChainIDsComplexNames"][InterfaceID][InterfaceChainID]
161 FileIndex = InterfaceChainsAndResiduesInfo["ChainIDsInfileIndices"][InterfaceID][InterfaceChainID]
162
163 WriteInterfaceChainView(OutFH, FileIndex, InterfaceID, InterfaceChainID, ChainID, ResNums, ComplexName, PyMOLInterfaceObjectNamesInfo)
164
165 # Setup interface Chain level group...
166 Enable, Action = [True, "open"]
167 GenerateAndWritePMLForGroup(OutFH, PyMOLInterfaceObjectNamesInfo["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroup"], PyMOLInterfaceObjectNamesInfo["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroupMembers"], Enable, Action)
168
169 if FirstInterfaceID:
170 FirstInterfaceID = False
171 Enable, Action = [True, "open"]
172 else:
173 Enable, Action = [True, "close"]
174
175 GenerateAndWritePMLForGroup(OutFH, PyMOLInterfaceObjectNamesInfo["InterfaceIDs"][InterfaceID]["InterfaceIDGroup"], PyMOLInterfaceObjectNamesInfo["InterfaceIDs"][InterfaceID]["InterfaceIDGroupMembers"], Enable, Action)
176
177 # Setup interfaces level group...
178 Enable, Action = [True, "open"]
179 GenerateAndWritePMLForGroup(OutFH, PyMOLInterfaceObjectNamesInfo["InterfacesGroup"], PyMOLInterfaceObjectNamesInfo["InterfacesGroupMembers"], Enable, Action)
180
181 DeleteEmptyPyMOLInterfaceObjects(OutFH)
182
183 # Setup orientation...
184 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
185
186 def WritePMLHeader(OutFH, ScriptName):
187 """Write out PML setting up complex view."""
188
189 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
190 OutFH.write("%s\n" % HeaderInfo)
191
192 def WritePyMOLParameters(OutFH):
193 """Write out PyMOL global parameters."""
194
195 PMLCmds = []
196 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
197 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
198 PML = "\n".join(PMLCmds)
199
200 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
201 OutFH.write("%s\n" % PML)
202
203 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames):
204 """Write out PML for viewing polymer complex."""
205
206 # Setup complex...
207 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
208 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["Complex"], Infile, True)
209 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
210 OutFH.write("%s\n" % PML)
211
212 if OptionsInfo["SurfaceComplex"]:
213 # Setup hydrophobic surface...
214 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["ComplexHydrophobicSurface"], PyMOLObjectNames["Complex"], ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
215 OutFH.write("\n%s\n" % PML)
216
217 # Setup complex group...
218 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close")
219
220 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
221 """Write out PML for viewing chain."""
222
223 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
224
225 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
226
227 # Setup chain complex group view...
228 WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
229
230 # Setup chain view...
231 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
232
233 # Setup chain solvent view...
234 PML = PyMOLUtil.SetupPMLForSolventView(PyMOLObjectNames["Chains"][ChainID]["Solvent"], ChainComplexName, False)
235 OutFH.write("\n%s\n" % PML)
236
237 # Setup chain inorganic view...
238 PML = PyMOLUtil.SetupPMLForInorganicView(PyMOLObjectNames["Chains"][ChainID]["Inorganic"], ChainComplexName, False)
239 OutFH.write("\n%s\n" % PML)
240
241 def WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
242 """Write chain complex views."""
243
244 # Setup chain complex...
245 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
246 PML = PyMOLUtil.SetupPMLForPolymerChainComplexView(ChainComplexName, PyMOLObjectNames["Complex"], ChainID, True)
247 OutFH.write("%s\n" % PML)
248
249 if OptionsInfo["SurfaceChainComplex"]:
250 # Setup hydrophobic surface...
251 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"], ChainComplexName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
252 OutFH.write("\n%s\n" % PML)
253
254 # Setup chain complex group...
255 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"], False, "close")
256
257 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
258 """Write individual chain views."""
259
260 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
261
262 # Setup chain view...
263 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
264 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, True)
265 OutFH.write("\n%s\n" % PML)
266
267 # Setup a non-interface chain view...
268 NonInterfaceChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterface"]
269
270 InterfaceResNums = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["InterfaceResNums"][ChainID]
271 InterfaceResNumsSelection = "+".join(InterfaceResNums)
272
273 Selection = "%s and chain %s and polymer and (not (resi %s))" % (ChainComplexName, ChainID, InterfaceResNumsSelection)
274 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(NonInterfaceChainName, Selection, "cartoon", Enable = False)
275 OutFH.write("\n%s\n" % PML)
276
277 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
278 # Setup a generic colored surface...
279 PML = PyMOLUtil.SetupPMLForSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"], NonInterfaceChainName, Enable = False, Color = OptionsInfo["SurfaceNonInterfaceColor"])
280 OutFH.write("\n%s\n" % PML)
281
282 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
283 # Setup surface colored by hydrophobicity...
284 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"], NonInterfaceChainName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
285 OutFH.write("\n%s\n" % PML)
286
287 # Setup surface colored by hyrdophobicity and charge...
288 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"], NonInterfaceChainName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = None)
289 OutFH.write("\n%s\n" % PML)
290
291 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
292 # Setup electrostatics surface...
293 SelectionObjectName = NonInterfaceChainName
294 ElectrostaticsGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroup"]
295 ElectrostaticsGroupMembers = PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"]
296 WriteSurfaceElectrostaticsView("Chain", OutFH, SelectionObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers)
297
298 # Setup surface group...
299 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"], True, "open")
300
301 # Setup a non-interface group...
302 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterfaceGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterfaceGroupMembers"], True, "open")
303
304 # Setup chain group...
305 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"], True, "close")
306
307 def WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID):
308 """Write out PML for viewing ligand in a chain."""
309
310 GroupID = "Ligand"
311 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
312 LigandName = PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
313
314 # Setup main object...
315 GroupTypeObjectID = "%s" % (GroupID)
316 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
317
318 OutFH.write("""\n""\n"Setting up views for ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
319 PML = PyMOLUtil.SetupPMLForLigandView(GroupTypeObjectName, ComplexName, LigandID, Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
320 OutFH.write("%s\n" % PML)
321
322 # Setup ball and stick view...
323 BallAndStickNameID = "%sBallAndStick" % (GroupID)
324 BallAndStickName = PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickNameID]
325 PML = PyMOLUtil.SetupPMLForBallAndStickView(BallAndStickName, GroupTypeObjectName, Enable = False)
326 OutFH.write("\n%s\n" % PML)
327
328 # Setup group....
329 GroupNameID = "%sGroup" % (GroupID)
330 GroupMembersID = "%sGroupMembers" % (GroupID)
331 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
332 GroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID]
333
334 Action = "open"
335 Enable = True
336 GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable, Action)
337
338 def WriteInterfacePolarContactsView(OutFH, InterfaceID, InterfaceChainPairsAndResiduesInfo, PyMOLObjectNames):
339 """Write out PML for viewing polar contacts between interface residues."""
340
341 if not OptionsInfo["InterfacePolarContacts"]:
342 return
343
344 WriteInterfaceContactsView("InterfacePolarConatcts", OutFH, InterfaceID, InterfaceChainPairsAndResiduesInfo, PyMOLObjectNames)
345
346 def WriteInterfaceHydrophobicContactsView(OutFH, InterfaceID, InterfaceChainPairsAndResiduesInfo, PyMOLObjectNames):
347 """Write out PML for viewing hydrophobic contacts between interface residues."""
348
349 if not OptionsInfo["InterfaceHydrophobicContacts"]:
350 return
351
352 WriteInterfaceContactsView("InterfaceHydrophobicContacts", OutFH, InterfaceID, InterfaceChainPairsAndResiduesInfo, PyMOLObjectNames)
353
354 def WriteInterfaceContactsView(Mode, OutFH, InterfaceID, InterfaceChainPairsAndResiduesInfo, PyMOLObjectNames):
355 """Write out PML for viewing polar or hydrophobic contacts between interface residues."""
356
357 InterfacePolarContacts = True if re.match("^InterfacePolarConatcts$", Mode, re.I) else False
358
359 ChainIDs1, ChainIDs2 = InterfaceChainPairsAndResiduesInfo["ChainIDsPairs"][InterfaceID]
360 ResNums1, ResNums2 = InterfaceChainPairsAndResiduesInfo["ChainIDsResNumsPairs"][InterfaceID]
361
362 FileIndex1, FileIndex2 = InterfaceChainPairsAndResiduesInfo["InfileIndicesPairs"][InterfaceID]
363 ComplexName1 = OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"][FileIndex1]["Complex"]
364 ComplexName2 = OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"][FileIndex2]["Complex"]
365
366 Selection1 = SetupSelectionForInterfaceContactsView(ComplexName1, ChainIDs1, ResNums1)
367 Selection2 = SetupSelectionForInterfaceContactsView(ComplexName2, ChainIDs2, ResNums2)
368
369 if InterfacePolarContacts:
370 ContactsName = PyMOLObjectNames["InterfaceIDs"][InterfaceID]["PolarContacts"]
371 ContactsColor = OptionsInfo["InterfacePolarContactsColor"]
372 ContactsCutoff = OptionsInfo["InterfaceContactsCutoff"]
373
374 PML = PyMOLUtil.SetupPMLForPolarContactsView(ContactsName, Selection1, Selection2, Enable = False, Color = ContactsColor, Cutoff = ContactsCutoff)
375 else:
376 ContactsName = PyMOLObjectNames["InterfaceIDs"][InterfaceID]["HydrophobicContacts"]
377 ContactsColor = OptionsInfo["InterfaceHydrophobicContactsColor"]
378 ContactsCutoff = OptionsInfo["InterfaceContactsCutoff"]
379
380 PML = PyMOLUtil.SetupPMLForHydrophobicContactsView(ContactsName, Selection1, Selection2, Enable = False, Color = ContactsColor, Cutoff = ContactsCutoff)
381
382 OutFH.write("\n%s\n" % PML)
383
384 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (ContactsColor, ContactsName))
385
386 def SetupSelectionForInterfaceContactsView(ComplexName, ChainIDs, ResNums):
387 """Setup a selection for generating polar or hyrophobic contacts for an interface."""
388
389 ChainSelections = []
390
391 for ChainID in ChainIDs:
392 ChainResNumsSelection = "+".join(ResNums["ResNums"][ChainID])
393 Selection = "(%s and chain %s and polymer and (resi %s))" % (ComplexName, ChainID, ChainResNumsSelection)
394 ChainSelections.append(Selection)
395
396 Selection = " or ".join(ChainSelections)
397
398 return Selection
399
400 def WriteInterfaceChainView(OutFH, FileIndex, InterfaceID, InterfaceChainID, ChainID, ResiduesNums, ComplexName, PyMOLObjectNames):
401 """Write out PML for viewing interface residues in a chain."""
402
403 OutFH.write("""\n""\n"Setting up interface views for interface in %s..."\n""\n""" % InterfaceChainID)
404
405 ResiduesNumsSelection = "+".join(ResiduesNums)
406
407 # Setup a chain for interface residues...
408 ChainName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["Chain"]
409 Selection = "%s and chain %s and polymer and (resi %s)" % (ComplexName, ChainID, ResiduesNumsSelection)
410
411 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(ChainName, Selection, "lines", Enable = True)
412 OutFH.write("\n%s\n" % PML)
413
414 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["InterfaceLabelColor"], ChainName))
415
416 WriteInterfaceChainResidueTypesView(OutFH, FileIndex, InterfaceID, InterfaceChainID, ChainID, PyMOLObjectNames)
417
418 if GetInterfaceContainsSurfacesStatus(FileIndex, ChainID):
419 # Setup generic colored surface...
420 PML = PyMOLUtil.SetupPMLForSurfaceView(PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurface"], ChainName, Color = OptionsInfo["SurfaceInterfaceColor"], Enable = True, DisplayAs = "lines")
421 OutFH.write("\n%s\n" % PML)
422
423 if GetInterfaceSurfaceChainStatus(FileIndex, ChainID):
424 # Setup surface colored by hydrophobicity...
425 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainHydrophobicSurface"], ChainName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False, DisplayAs = "lines")
426 OutFH.write("\n%s\n" % PML)
427
428 # Setup surface colored by hyrdophobicity and charge...
429 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainHydrophobicChargeSurface"], ChainName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = "lines")
430 OutFH.write("\n%s\n" % PML)
431
432 if GetInterfaceSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
433 # Setup electrostatics surface...
434 SelectionObjectName = ChainName
435 ElectrostaticsGroupName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainElectrostaticsGroup"]
436 ElectrostaticsGroupMembers = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainElectrostaticsGroupMembers"]
437 WriteSurfaceElectrostaticsView("InterfaceResidues", OutFH, SelectionObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers)
438
439 # Setup surface group...
440 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroup"], PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroupMembers"], True, "open")
441
442 # Setup chain group...
443 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroup"], PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroupMembers"], True, "close")
444
445 def WriteInterfaceChainResidueTypesView(OutFH, FileIndex, InterfaceID, InterfaceChainID, ChainID, PyMOLObjectNames):
446 """Write out PML for viewing interface residue types for a chain."""
447
448 if not GetInterfaceResidueTypesStatus(FileIndex, ChainID):
449 return
450
451 ChainName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["Chain"]
452
453 # Setup residue types objects...
454 ResiduesGroupIDPrefix = "ChainResidues"
455 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
456 SubGroupID = re.sub("_", "", SubGroupType)
457
458 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, SubGroupID)
459 ResiduesObjectName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesObjectID]
460
461 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, SubGroupID)
462 ResiduesSurfaceObjectName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesSurfaceObjectID]
463
464 ResiduesColor = OptionsInfo["ResidueTypesParams"][SubGroupType]["Color"]
465 ResiduesNames = OptionsInfo["ResidueTypesParams"][SubGroupType]["Residues"]
466
467 NegateResidueNames = True if re.match("^Other$", SubGroupType, re.I) else False
468 WriteResidueTypesResiduesAndSurfaceView(OutFH, ChainName, ResiduesObjectName, ResiduesSurfaceObjectName, ResiduesColor, ResiduesNames, NegateResidueNames)
469
470 # Setup residue type sub groups...
471 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
472 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
473
474 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesSubGroupID], PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesSubGroupMembersID], True, "close")
475
476 # Setup residue types group...
477 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainResiduesGroup"], PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainResiduesGroupMembers"], False, "close")
478
479 def WriteResidueTypesResiduesAndSurfaceView(OutFH, SelectionObjectName, Name, SurfaceName, ResiduesColor, ResiduesNames, NegateResidueNames):
480 """Write residue types residues and surface view."""
481
482 ResidueNamesSelection = "+".join(ResiduesNames)
483 if NegateResidueNames:
484 Selection = "%s and (not resn %s)" % (SelectionObjectName, ResidueNamesSelection)
485 else:
486 Selection = "%s and (resn %s)" % (SelectionObjectName, ResidueNamesSelection)
487
488 # Setup residues...
489 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(Name, Selection, "lines", ResiduesColor, True)
490 OutFH.write("\n%s\n" % PML)
491
492 # Setup surface...
493 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SurfaceName, Selection, "surface", ResiduesColor, True)
494 OutFH.write("\n%s\n" % PML)
495
496 def WriteSurfaceElectrostaticsView(Mode, OutFH, SelectionObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers):
497 """Write out PML for viewing surface electrostatics."""
498
499 if len(ElectrostaticsGroupMembers) == 5:
500 Name, ContactPotentialName, MapName, LegendName, VolumeName = ElectrostaticsGroupMembers
501 else:
502 Name, ContactPotentialName, MapName, LegendName = ElectrostaticsGroupMembers
503 VolumeName = None
504
505 PMLCmds = []
506
507 # Setup chain...
508 PMLCmds.append("""cmd.create("%s", "(%s)")""" % (Name, SelectionObjectName))
509
510 # Setup vacuum electrostatics surface along with associated objects...
511 PMLCmds.append("""util.protein_vacuum_esp("%s", mode=2, quiet=0, _self=cmd)""" % (Name))
512
513 PMLCmds.append("""cmd.set_name("%s_e_chg", "%s")""" % (Name, ContactPotentialName))
514 if re.match("^Chain$", Mode, re.I):
515 DisplayStyle = "cartoon"
516 else:
517 DisplayStyle = "lines"
518 PMLCmds.append("""cmd.show("%s", "(%s)")""" % (DisplayStyle, ContactPotentialName))
519 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(ContactPotentialName, Enable = True))
520
521 PMLCmds.append("""cmd.set_name("%s_e_map", "%s")""" % (Name, MapName))
522 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MapName, Enable = False))
523
524 PMLCmds.append("""cmd.set_name("%s_e_pot", "%s")""" % (Name, LegendName))
525 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(LegendName, Enable = False))
526
527 if VolumeName is not None:
528 PMLCmds.append("""cmd.volume("%s", "%s", "%s", "(%s)")""" % (VolumeName, MapName, "esp", Name))
529 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(VolumeName, Enable = False))
530
531 # Delete name and take it out from the group membership. It is
532 # is already part of ContactPotential object.
533 PMLCmds.append("""cmd.delete("%s")""" % (Name))
534 ElectrostaticsGroupMembers.pop(0)
535
536 PML = "\n".join(PMLCmds)
537
538 OutFH.write("\n%s\n" % PML)
539
540 # Setup group...
541 GenerateAndWritePMLForGroup(OutFH, ElectrostaticsGroupName, ElectrostaticsGroupMembers, False, "close")
542
543 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable = False, Action = "close"):
544 """Generate and write PML for group."""
545
546 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
547 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
548 OutFH.write("%s\n" % PML)
549
550 def GeneratePyMOLSessionFile():
551 """Generate PME file from PML file."""
552
553 PSEOutfile = OptionsInfo["PSEOutfile"]
554 PMLOutfile = OptionsInfo["PMLOutfile"]
555
556 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
557
558 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
559
560 if not os.path.exists(PSEOutfile):
561 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
562
563 if not OptionsInfo["PMLOut"]:
564 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
565 os.remove(PMLOutfile)
566
567 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
568 """Delete empty PyMOL objects."""
569
570 if OptionsInfo["AllowEmptyObjects"]:
571 return
572
573 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
574 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
575 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
576
577 # Delete any chain level objects...
578 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
579 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
580
581 def DeleteEmptyPyMOLInterfaceObjects(OutFH):
582 """Delete empty PyMOL interface objects."""
583
584 if OptionsInfo["AllowEmptyObjects"]:
585 return
586
587 InterfaceChainsAndResiduesInfo = OptionsInfo["InfilesInfo"]["InterfaceChainsAndResiduesInfo"]
588 PyMOLInterfaceObjectNamesInfo = OptionsInfo["InfilesInfo"]["PyMOLInterfaceObjectNamesInfo"]
589
590 if InterfaceChainsAndResiduesInfo is None:
591 return
592
593 for InterfaceID in InterfaceChainsAndResiduesInfo["InterfaceIDs"]:
594 for InterfaceChainID in InterfaceChainsAndResiduesInfo["InterfaceChainIDs"][InterfaceID]:
595 ChainID = InterfaceChainsAndResiduesInfo["ChainIDs"][InterfaceID][InterfaceChainID]
596 FileIndex = InterfaceChainsAndResiduesInfo["ChainIDsInfileIndices"][InterfaceID][InterfaceChainID]
597
598 # Delete interface residue type objects...
599 DeleteEmptyInterfaceChainResidueTypesObjects(OutFH, FileIndex, InterfaceID, InterfaceChainID, ChainID, PyMOLInterfaceObjectNamesInfo)
600
601 def DeleteEmptyInterfaceChainResidueTypesObjects(OutFH, FileIndex, InterfaceID, InterfaceChainID, ChainID, PyMOLObjectNames):
602 """Delete empty interface chain residue objects."""
603
604 if not GetInterfaceResidueTypesStatus(FileIndex, ChainID):
605 return
606
607 ResiduesGroupIDPrefix = "ChainResidues"
608 for GroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
609 GroupID = re.sub("_", "", GroupType)
610
611 ResiduesGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, GroupID)
612 GroupName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesGroupID]
613
614 GroupObjectNamesList = []
615
616 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, GroupID)
617 ResiduesObjectName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesObjectID]
618 GroupObjectNamesList.append(ResiduesObjectName)
619
620 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, GroupID)
621 ResiduesSurfaceObjectName = PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesSurfaceObjectID]
622 GroupObjectNamesList.append(ResiduesSurfaceObjectName)
623
624 GroupObjectNames = ",".join(GroupObjectNamesList)
625 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupObjectNames, GroupName)
626
627 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
628 """Write PML to check and delete empty PyMOL objects."""
629
630 if ParentObjectName is None:
631 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
632 else:
633 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
634
635 OutFH.write("%s\n" % PML)
636
637 def RetrieveInfilesInfo():
638 """Retrieve information for input files."""
639
640 InfilesInfo = {}
641
642 InfilesInfo["InfilesNames"] = []
643 InfilesInfo["InfilesRoots"] = []
644 InfilesInfo["ChainsAndLigandsInfo"] = []
645 InfilesInfo["SpecifiedChainsAndLigandsInfo"] = []
646
647 InfilesInfo["PyMOLObjectNamesInfo"] = []
648
649 InfilesInfo["SingleInfileMode"] = False
650 InfilesInfo["InterfaceChainsAndResiduesInfo"] = None
651 InfilesInfo["InterfaceChainPairsAndResiduesInfo"] = None
652
653 InfilesInfo["PyMOLInterfaceObjectNamesInfo"] = None
654
655 InfilesCount = 0
656 for Infile in OptionsInfo["InfilesNames"]:
657 InfilesCount += 1
658 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
659 InfileRoot = FileName
660
661 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
662
663 InfilesInfo["InfilesNames"].append(Infile)
664 InfilesInfo["InfilesRoots"].append(InfileRoot)
665 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
666
667 if InfilesCount > 2:
668 MiscUtil.PrintError("Number of input files, %s, specified using \"-i, --infiles\" option is not valid. Number of allowed files: 1 or 2" % (InfilesCount))
669
670 InfilesInfo["SingleInfileMode"] = True if InfilesCount == 1 else False
671
672 OptionsInfo["InfilesInfo"] = InfilesInfo
673
674 def ProcessInterfaceChainIDs():
675 """Process specified interface chain IDs for input files."""
676
677 ValidateInterfaceChainIDs()
678
679 SetupChainsAndLigandsInfo()
680 SetupPyMOLObjectNamesInfo()
681
682 SetupInterfaceChainPairsAndResiduesInfo()
683 ProcessInterfaceChainPairsAndResiduesInfo()
684
685 SetupPyMOLInterfaceObjectNamesInfo()
686
687 def ValidateInterfaceChainIDs():
688 """Check for the presence of interface IDs in input file(s)."""
689
690 if re.match("^auto$", OptionsInfo["InterfaceChainIDs"], re.I):
691 AutoAssignInterfaceChainIDs()
692 SetupInfilesInterfaceChainIDsLists()
693 return
694
695 MiscUtil.PrintInfo("\nValidating interface chain IDs...")
696
697 # Check for the presences of interface chain IDs across input files..
698 SingleInfileMode = OptionsInfo["InfilesInfo"]["SingleInfileMode"]
699 Infile1ChainIDs = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]["ChainIDs"]
700 Infile2ChainIDs = []
701 if not SingleInfileMode:
702 Infile2ChainIDs = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][1]["ChainIDs"]
703
704 InterfaceChainIDsList = OptionsInfo["InterfaceChainIDsList"]
705
706 for Index in range(0, len(InterfaceChainIDsList), 2):
707 ChainIDs1 = InterfaceChainIDsList[Index]
708 ChainIDs2 = InterfaceChainIDsList[Index + 1]
709
710 for ChainID in ChainIDs1:
711 if not ChainID in Infile1ChainIDs:
712 MiscUtil.PrintError("The chain ID, %s, specified using \"-c, --chainIDs\" for a chain IDs pairs, \"%s,%s\", must be present in first input file." % (ChainID, "+".join(ChainIDs1), "+".join(ChainIDs2)))
713
714 for ChainID in ChainIDs2:
715 if SingleInfileMode:
716 if not ChainID in Infile1ChainIDs:
717 MiscUtil.PrintError("The chain ID, %s, specified using \"-c, --chainIDs\" for a chain IDs pairs, \"%s,%s\", must be present in first input file." % (ChainID, "+".join(ChainIDs1), "+".join(ChainIDs2)))
718 else:
719 if not ChainID in Infile2ChainIDs:
720 MiscUtil.PrintError("The chain ID, %s, specified using \"-c, --chainIDs\" for a chain IDs pairs, \"%s,%s\", must be present in second input file." % (ChainID, "+".join(ChainIDs1), "+".join(ChainIDs2)))
721
722 # Check for any duplicate interface chain IDs specifications...
723 CanonicalInterfaceIDsMap = {}
724
725 for Index in range(0, len(InterfaceChainIDsList), 2):
726 ChainIDs1 = InterfaceChainIDsList[Index]
727 ChainIDs2 = InterfaceChainIDsList[Index + 1]
728 InterfaceID = "%s,%s" % ("+".join(ChainIDs1), "+".join(ChainIDs2))
729
730 SortedChainIDs1 = sorted(ChainIDs1)
731 SortedChainIDs2 = sorted(ChainIDs2)
732 CanonicalInterfaceID = "%s,%s" % ("+".join(SortedChainIDs1), "+".join(SortedChainIDs2))
733
734 if CanonicalInterfaceID in CanonicalInterfaceIDsMap:
735 MiscUtil.PrintError("The chain ID pair, \"%s\", using \"-c, --chainIDs\", option has been specified multiple times, \"%s\"." % (CanonicalInterfaceIDsMap[CanonicalInterfaceID], OptionsInfo["InterfaceChainIDs"]))
736 else:
737 CanonicalInterfaceIDsMap[CanonicalInterfaceID] = InterfaceID
738
739 SetupInfilesInterfaceChainIDsLists()
740
741 def SetupInfilesInterfaceChainIDsLists():
742 """Setup interface chain IDs list for infiles."""
743
744 Infie1InterfaceChainIDsList = []
745 Infie2InterfaceChainIDsList = []
746
747 SingleInfileMode = OptionsInfo["InfilesInfo"]["SingleInfileMode"]
748 InterfaceChainIDsList = OptionsInfo["InterfaceChainIDsList"]
749
750 for Index in range(0, len(InterfaceChainIDsList), 2):
751 ChainIDs1 = InterfaceChainIDsList[Index]
752 ChainIDs2 = InterfaceChainIDsList[Index + 1]
753
754 Infie1InterfaceChainIDsList.extend(ChainIDs1)
755 if SingleInfileMode:
756 Infie1InterfaceChainIDsList.extend(ChainIDs2)
757 else:
758 Infie2InterfaceChainIDsList.extend(ChainIDs2)
759
760 Infie1InterfaceChainIDsList = sorted(Infie1InterfaceChainIDsList)
761 Infie2InterfaceChainIDsList = sorted(Infie2InterfaceChainIDsList)
762
763 OptionsInfo["InfilesInterfaceChainIDsList"] = [Infie1InterfaceChainIDsList, Infie2InterfaceChainIDsList]
764
765 def AutoAssignInterfaceChainIDs():
766 """Handle automatic assignment of interface chain IDs."""
767
768 Infile1ChainIDs = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]["ChainIDs"]
769 Infile2ChainIDs = []
770 if not OptionsInfo["InfilesInfo"]["SingleInfileMode"]:
771 Infile2ChainIDs = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][1]["ChainIDs"]
772
773 InterfaceChainIDsList = []
774 if OptionsInfo["InfilesInfo"]["SingleInfileMode"]:
775 # Take first two chains from first input file...
776 if len(Infile1ChainIDs) < 2:
777 MiscUtil.PrintError("Failed to automatically set interface chain IDs. Number of chains, %s, in input file specified using \"-i, --infiles\" option must be >= 2. " % (len(Infile1ChainIDs)))
778 InterfaceChainIDsList.append([Infile1ChainIDs[0]])
779 InterfaceChainIDsList.append([Infile1ChainIDs[1]])
780 else:
781 # Take first chain from each input file...
782 if len(Infile1ChainIDs) < 1:
783 MiscUtil.PrintError("Failed to automatically set interface chain IDs. Number of chains, %s, in first input file specified using \"-i, --infiles\" option must be >= 1. " % (len(Infile1ChainIDs)))
784 if len(Infile2ChainIDs) < 1:
785 MiscUtil.PrintError("Failed to automatically set interface chain IDs. Number of chains, %s, in second input file specified using \"-i, --infiles\" option must be >= 1. " % (len(Infile1ChainIDs)))
786 InterfaceChainIDsList.append([Infile1ChainIDs[0]])
787 InterfaceChainIDsList.append([Infile2ChainIDs[1]])
788
789 OptionsInfo["InterfaceChainIDsList"] = []
790 OptionsInfo["InterfaceChainIDsList"].extend(InterfaceChainIDsList)
791
792 return
793
794 def SetupChainsAndLigandsInfo():
795 """Setup chains and ligands info for input files to visualize macromolecules."""
796
797 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
798 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
799 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
800 MiscUtil.PrintInfo("\nSetting up chain and ligand information for input file %s..." % Infile)
801
802 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
803 InfilesInterfaceChainIDsList = OptionsInfo["InfilesInterfaceChainIDsList"][FileIndex]
804
805 SpecifiedChainsAndLigandsInfo = {}
806 SpecifiedChainsAndLigandsInfo["ChainIDs"] = []
807 SpecifiedChainsAndLigandsInfo["InterfaceResNums"] = {}
808 SpecifiedChainsAndLigandsInfo["LigandIDs"] = {}
809
810 if len(InfilesInterfaceChainIDsList):
811 # Add unique interface IDs to the chain IDs list for visualization. Interface chain IDs
812 # may contain duplicate chain IDs due to the presence # of same chain in multiple
813 # interfaces.
814 for ChainID in InfilesInterfaceChainIDsList:
815 if not ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
816 SpecifiedChainsAndLigandsInfo["ChainIDs"].append(ChainID)
817
818 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
819 # Initialize interface residue numbers to be assigned later...
820 SpecifiedChainsAndLigandsInfo["InterfaceResNums"][ChainID] = []
821
822 # Setup ligand IDs...
823 SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID] = SetupSpecifiedLigandIDs(FileIndex, ChainID, ChainsAndLigandsInfo)
824
825 ProcessResidueTypesAndSurfaceOptions(FileIndex, SpecifiedChainsAndLigandsInfo)
826
827 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
828
829 def SetupSpecifiedLigandIDs(FileIndex, ChainID, ChainsAndLigandsInfo):
830 """Setup specified ligand IDs for input file."""
831
832 LigandIDs = []
833
834 if re.match("^All$", OptionsInfo["LigandIDs"], re.I):
835 LigandIDs = ChainsAndLigandsInfo["LigandIDs"][ChainID]
836 return LigandIDs
837 elif re.match("^Largest|Auto$", OptionsInfo["LigandIDs"], re.I):
838 LargestLigandID = ChainsAndLigandsInfo["LigandIDs"][ChainID][0] if (len(ChainsAndLigandsInfo["LigandIDs"][ChainID])) else None
839 if LargestLigandID is not None:
840 LigandIDs.append(LargestLigandID)
841 return LigandIDs
842 elif re.match("^None$", OptionsInfo["LigandIDs"], re.I):
843 return LigandIDs
844
845 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
846 ValidLigandIDs = ChainsAndLigandsInfo["LigandIDs"][ChainID]
847
848 SpecifiedLigandIDs = re.sub(" ", "", OptionsInfo["LigandIDs"])
849 if not SpecifiedLigandIDs:
850 MiscUtil.PrintError("No valid value specified using \-l, --ligandIDs\" option.")
851
852 LigandIDsWords = SpecifiedLigandIDs.split(",")
853 for LigandID in LigandIDsWords:
854 if not LigandID in ValidLigandIDs:
855 LigandIDsListNames = ",".join(ValidLigandIDs) if len(ValidLigandIDs) else "None"
856 MiscUtil.PrintWarning("The ligand ID, %s, specified using \"-l, --ligandiIDs\" option is not valid for chain, %s, in input file, %s. It'll be ignored. Valid ligand IDs: %s" % (LigandID, ChainID, Infile, LigandIDsListNames))
857 continue
858
859 if LigandID in LigandIDs:
860 MiscUtil.PrintWarning("The ligand ID, %s, has already been specified using \"-l, --ligandIDs\" option for chain, %s, in input file, %s. It'll be ignored." % (LigandID, ChainID, Infile))
861 continue
862
863 LigandIDs.append(LigandID)
864
865 if not len(LigandIDs):
866 MiscUtil.PrintWarning("No valid ligand IDs \"%s\" specified using \"-l, --ligandIDs\" option for chain ID, %s, in input file, %s." % (OptionsInfo["LigandIDs"], ChainID, Infile))
867
868 return LigandIDs
869
870 def SetupInterfaceChainPairsAndResiduesInfo():
871 """Setup chain and residue pairs corresponding to interfaces."""
872
873 MiscUtil.PrintInfo("\nIdentifying interface residues...")
874
875 SingleInfileMode = OptionsInfo["InfilesInfo"]["SingleInfileMode"]
876 InterfaceChainIDsList = OptionsInfo["InterfaceChainIDsList"]
877
878 if not len(InterfaceChainIDsList):
879 MiscUtil.PrintError("Failed to identify interface residues: No valid chain ID pairs available for interfaces")
880
881 # Load infiles to identify interface residues...
882 Infile1 = OptionsInfo["InfilesInfo"]["InfilesNames"][0]
883 MolName1 = OptionsInfo["InfilesInfo"]["InfilesRoots"][0]
884 pymol.cmd.load(Infile1, MolName1)
885 if SingleInfileMode:
886 MolName2 = MolName1
887 else:
888 Infile2 = OptionsInfo["InfilesInfo"]["InfilesNames"][1]
889 MolName2 = OptionsInfo["InfilesInfo"]["InfilesRoots"][1]
890 pymol.cmd.load(Infile2, MolName2)
891
892 # Initialize data...
893 InterfaceChainPairsAndResiduesInfo = {}
894 InterfaceChainPairsAndResiduesInfo["InterfaceIDs"] = []
895 InterfaceChainPairsAndResiduesInfo["ChainIDsPairs"] = {}
896 InterfaceChainPairsAndResiduesInfo["ChainIDsResNumsPairs"] = {}
897 InterfaceChainPairsAndResiduesInfo["InfileIndicesPairs"] = {}
898
899 Method = OptionsInfo["Method"]
900 MethodCutoff = OptionsInfo["MethodCutoff"]
901 MiscUtil.PrintInfo("Methodology: %s; Cutoff: %.2f" % (Method, MethodCutoff))
902
903 for Index in range(0, len(InterfaceChainIDsList), 2):
904 ChainIDs1 = sorted(InterfaceChainIDsList[Index])
905 ChainIDs2 = sorted(InterfaceChainIDsList[Index + 1])
906
907 ChainIDs1Prefix = "Chains" if len(ChainIDs1) > 1 else "Chain"
908 ChainIDs2Prefix = "Chains" if len(ChainIDs2) > 1 else "Chain"
909 InterfaceID = "%s%s_%s%s" % (ChainIDs1Prefix, "+".join(ChainIDs1), ChainIDs2Prefix, "+".join(ChainIDs2))
910
911 ListInterfaceID = "%s_%s" % ("+".join(ChainIDs1), "+".join(ChainIDs2))
912
913 FileIndex1 = 0
914 FileIndex2 = 0 if SingleInfileMode else 1
915
916 if InterfaceID in InterfaceChainPairsAndResiduesInfo["InterfaceIDs"]:
917 MiscUtil.PrintInfo("Ignoring interface ID %s: It has already been defined" % InterfaceID)
918 continue
919
920 # Identify and list interface chains and residues...
921 ChainsAndResiduesInfo1, ChainsAndResiduesInfo2 = GetInterfaceChainsAndResiduesInfo(MolName1, ChainIDs1, MolName2, ChainIDs2, Method, MethodCutoff)
922 ListInterfaceChainsAndResidues(ListInterfaceID, MolName1, ChainIDs1, ChainsAndResiduesInfo1, MolName2, ChainIDs2, ChainsAndResiduesInfo2)
923
924 # Check presence of interface residues...
925 if (not (len(ChainsAndResiduesInfo1["ChainIDs"]) and len(ChainsAndResiduesInfo2["ChainIDs"]))):
926 MiscUtil.PrintWarning("Ignoring interface ID %s: Failed to identify any interface residues. PyMOL groups and objects won't be created." % InterfaceID)
927 continue
928
929 # Collect residue numbers for set of interface residues in each chain...
930 InterfaceChainIDs1, InterfaceChainResidueNums1 = GetInterfaceChainsAndResidueNumbers(ChainIDs1, ChainsAndResiduesInfo1)
931 InterfaceChainIDs2, InterfaceChainResidueNums2 = GetInterfaceChainsAndResidueNumbers(ChainIDs2, ChainsAndResiduesInfo2)
932
933 InterfaceChainPairsAndResiduesInfo["InterfaceIDs"].append(InterfaceID)
934 InterfaceChainPairsAndResiduesInfo["ChainIDsPairs"][InterfaceID] = [InterfaceChainIDs1, InterfaceChainIDs2]
935 InterfaceChainPairsAndResiduesInfo["ChainIDsResNumsPairs"][InterfaceID] = [InterfaceChainResidueNums1, InterfaceChainResidueNums2]
936 InterfaceChainPairsAndResiduesInfo["InfileIndicesPairs"][InterfaceID] = [FileIndex1, FileIndex2]
937
938 InterfaceChainPairsAndResiduesInfo["InterfaceIDs"] = sorted(InterfaceChainPairsAndResiduesInfo["InterfaceIDs"])
939 OptionsInfo["InfilesInfo"]["InterfaceChainPairsAndResiduesInfo"] = InterfaceChainPairsAndResiduesInfo
940
941 # Delete loaded objects...
942 pymol.cmd.delete(MolName1)
943 if not SingleInfileMode:
944 pymol.cmd.delete(MolName2)
945
946 def ProcessInterfaceChainPairsAndResiduesInfo():
947 """Process chain and residue pairs for visualizing interfaces."""
948
949 InterfaceChainsAndResiduesInfo = {}
950 InterfaceChainsAndResiduesInfo["InterfaceIDs"] = []
951 InterfaceChainsAndResiduesInfo["InterfaceChainIDs"] = {}
952 InterfaceChainsAndResiduesInfo["ChainIDs"] = {}
953 InterfaceChainsAndResiduesInfo["ChainIDsResNums"] = {}
954 InterfaceChainsAndResiduesInfo["ChainIDsComplexNames"] = {}
955 InterfaceChainsAndResiduesInfo["ChainIDsInfileIndices"] = {}
956
957 InterfaceChainPairsAndResiduesInfo = OptionsInfo["InfilesInfo"]["InterfaceChainPairsAndResiduesInfo"]
958
959 for InterfaceID in InterfaceChainPairsAndResiduesInfo["InterfaceIDs"]:
960 # Flatten pairwise interface chain and residues info...
961 FlattenedInterfaceChainIDs, FlattenedChainIDs, FlattenedResNums, FlattenedComplexNames, FlattenedInfileIndices = FlattenIntferfaceChainPairsAndResiduesInfo(InterfaceChainPairsAndResiduesInfo, InterfaceID)
962
963 if not InterfaceID in InterfaceChainsAndResiduesInfo["InterfaceIDs"]:
964 InterfaceChainsAndResiduesInfo["InterfaceIDs"].append(InterfaceID)
965
966 InterfaceChainsAndResiduesInfo["InterfaceChainIDs"][InterfaceID] = []
967 InterfaceChainsAndResiduesInfo["ChainIDs"][InterfaceID] = {}
968 InterfaceChainsAndResiduesInfo["ChainIDsResNums"][InterfaceID] = {}
969 InterfaceChainsAndResiduesInfo["ChainIDsComplexNames"][InterfaceID] = {}
970 InterfaceChainsAndResiduesInfo["ChainIDsInfileIndices"][InterfaceID] = {}
971
972 # Track interface information for visualization...
973 for Index in range(0, len(FlattenedInterfaceChainIDs)):
974 InterfaceChainID = FlattenedInterfaceChainIDs[Index]
975 ChainID = FlattenedChainIDs[Index]
976 ResNums = FlattenedResNums[Index]
977 ComplexName = FlattenedComplexNames[Index]
978 FileIndex = FlattenedInfileIndices[Index]
979
980 if not len(ResNums):
981 continue
982
983 InterfaceChainsAndResiduesInfo["InterfaceChainIDs"][InterfaceID].append(InterfaceChainID)
984 InterfaceChainsAndResiduesInfo["ChainIDs"][InterfaceID][InterfaceChainID] = ChainID
985 InterfaceChainsAndResiduesInfo["ChainIDsResNums"][InterfaceID][InterfaceChainID] = ResNums
986 InterfaceChainsAndResiduesInfo["ChainIDsComplexNames"][InterfaceID][InterfaceChainID] = ComplexName
987 InterfaceChainsAndResiduesInfo["ChainIDsInfileIndices"][InterfaceID][InterfaceChainID] = FileIndex
988
989 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["InterfaceResNums"][ChainID].extend(ResNums)
990
991 OptionsInfo["InfilesInfo"]["InterfaceChainsAndResiduesInfo"] = InterfaceChainsAndResiduesInfo
992
993 def FlattenIntferfaceChainPairsAndResiduesInfo(InterfaceChainPairsAndResiduesInfo, InterfaceID):
994 """Flatten interface chain and residues info."""
995
996 SingleInfileMode = OptionsInfo["InfilesInfo"]["SingleInfileMode"]
997
998 ChainIDs1, ChainIDs2 = InterfaceChainPairsAndResiduesInfo["ChainIDsPairs"][InterfaceID]
999 ResNums1, ResNums2 = InterfaceChainPairsAndResiduesInfo["ChainIDsResNumsPairs"][InterfaceID]
1000 FileIndex1, FileIndex2 = InterfaceChainPairsAndResiduesInfo["InfileIndicesPairs"][InterfaceID]
1001
1002 # Set complex names..
1003 PDBGroup1 = OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"][FileIndex1]["PDBGroup"]
1004 ComplexName1 = OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"][FileIndex1]["Complex"]
1005
1006 PDBGroup2 = OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"][FileIndex2]["PDBGroup"]
1007 ComplexName2 = OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"][FileIndex2]["Complex"]
1008
1009 ChainIDs = []
1010 InterfaceChainIDs = []
1011 ResNums = []
1012 ComplexNames = []
1013 FileIndices = []
1014
1015 for ChainID in ChainIDs1:
1016 ChainIDs.append(ChainID)
1017 InterfaceChainID = ("Chain%s" % ChainID) if SingleInfileMode else ("Chain%s_%s" % (ChainID, PDBGroup1))
1018 InterfaceChainIDs.append(InterfaceChainID)
1019 ResNums.append(ResNums1["ResNums"][ChainID])
1020 ComplexNames.append(ComplexName1)
1021 FileIndices.append(FileIndex1)
1022
1023 for ChainID in ChainIDs2:
1024 ChainIDs.append(ChainID)
1025 InterfaceChainID = ("Chain%s" % ChainID) if SingleInfileMode else ("Chain%s_%s" % (ChainID, PDBGroup2))
1026 InterfaceChainIDs.append(InterfaceChainID)
1027 ResNums.append(ResNums2["ResNums"][ChainID])
1028 ComplexNames.append(ComplexName2)
1029 FileIndices.append(FileIndex2)
1030
1031 return InterfaceChainIDs, ChainIDs, ResNums, ComplexNames, FileIndices
1032
1033 def GetInterfaceChainsAndResiduesInfo(MolName1, ChainIDs1, MolName2, ChainIDs2, Method, Cutoff):
1034 """Get interface chains and residues info for chains using a specified methodology."""
1035
1036 InterfaceChainsResiduesInfo1 = None
1037 InterfaceChainsResiduesInfo2 = None
1038
1039 ChainNames1 = ",".join(ChainIDs1)
1040 ChainNames2 = ",".join(ChainIDs2)
1041
1042 if re.match("^BySASAChange$", Method, re.I):
1043 InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesBySASAChange(MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
1044 elif re.match("^ByHeavyAtomsDistance$", Method, re.I):
1045 InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesByHeavyAtomsDistance(MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
1046 elif re.match("^ByCAlphaAtomsDistance$", Method, re.I):
1047 InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2 = PyMOLUtil.GetInterfaceChainsResiduesByCAlphaAtomsDistance(MolName1, ChainNames1, MolName2, ChainNames2, Cutoff)
1048 else:
1049 MiscUtil.PrintError("Failed to retrieve interface residues information: Method %s is not valid..." % Method)
1050
1051 return InterfaceChainsResiduesInfo1, InterfaceChainsResiduesInfo2
1052
1053 def ListInterfaceChainsAndResidues(InterfaceID, MolName1, ChainIDs1, ChainsAndResiduesInfo1, MolName2, ChainIDs2, ChainsAndResiduesInfo2):
1054 """List interface chains and residues for an interface."""
1055
1056 ChainNames1, ResiduesInfo1 = PrepareInterfaceChainsAndResiduesInfo(ChainsAndResiduesInfo1)
1057 ChainNames2, ResiduesInfo2 = PrepareInterfaceChainsAndResiduesInfo(ChainsAndResiduesInfo2)
1058
1059 if len(ChainNames1) and len(ChainNames2):
1060 MiscUtil.PrintInfo("\nListing interface residues for interface chain IDs: %s" % (InterfaceID))
1061
1062 ListInterfaceChainsAndResiduesInfo(InterfaceID, MolName1, ChainIDs1, ChainNames1, ResiduesInfo1)
1063 ListInterfaceChainsAndResiduesInfo(InterfaceID, MolName2, ChainIDs2, ChainNames2, ResiduesInfo2)
1064 else:
1065 MiscUtil.PrintInfo("\nListing interface residues for interface chain IDs: %s" % (InterfaceID))
1066 MiscUtil.PrintInfo("Interface chain IDs: None; ChainID: None; Number of interface residues: 0")
1067
1068 def PrepareInterfaceChainsAndResiduesInfo(ChainsAndResiduesInfo):
1069 """Prepare interface chains and residues info for listing."""
1070
1071 ChainNames = []
1072 ResiduesInfo = []
1073
1074 for ChainID in ChainsAndResiduesInfo["ChainIDs"]:
1075 ChainNames.append(ChainID)
1076
1077 # Setup distribution of residues...
1078 LineWords = []
1079 ResiduesCount = 0
1080 SortedResNames = sorted(ChainsAndResiduesInfo["ResNames"][ChainID], key = lambda ResName: ChainsAndResiduesInfo["ResCount"][ChainID][ResName], reverse = True)
1081 for ResName in SortedResNames:
1082 ResCount = ChainsAndResiduesInfo["ResCount"][ChainID][ResName]
1083 LineWords.append("%s - %s" % (ResName, ResCount))
1084 ResiduesCount += ResCount
1085
1086 ResiduesDistribution = "; ".join(LineWords) if len(LineWords) else None
1087
1088 # Setup residue IDs sorted by residue numbers...
1089 ResNumMap = {}
1090 for ResName in ChainsAndResiduesInfo["ResNames"][ChainID]:
1091 for ResNum in ChainsAndResiduesInfo["ResNum"][ChainID][ResName]:
1092 ResNumMap[ResNum] = ResName
1093
1094 LineWords = []
1095 for ResNum in sorted(ResNumMap, key = int):
1096 ResName = ResNumMap[ResNum]
1097 ResID = "%s_%s" % (ResName, ResNum)
1098 LineWords.append(ResID)
1099 ResiduesIDs = ", ".join(LineWords) if len(LineWords) else None
1100
1101 ResiduesInfo.append([ResiduesCount, ResiduesDistribution, ResiduesIDs])
1102
1103 return ChainNames, ResiduesInfo
1104
1105 def ListInterfaceChainsAndResiduesInfo(InterfaceID, MolName, InterfaceChainIDs, ChainNames, ResiduesInfo):
1106 """List interface chains and residues."""
1107
1108 for ChainID in InterfaceChainIDs:
1109 if not ChainID in ChainNames:
1110 MiscUtil.PrintWarning("Interface chain IDs: %s; MoleculeID: %s; ChainID: %s; Number of interface residues: 0. PyMOL groups and objects related to chain won't be created." % (InterfaceID, MolName, ChainID))
1111 continue
1112
1113 for Index in range(0, len(ChainNames)):
1114 ChainName = ChainNames[Index]
1115 ChainResiduesInfo = ResiduesInfo[Index]
1116 if re.match(ChainID, ChainName, re.I):
1117 MiscUtil.PrintInfo("\nInterface chain IDs: %s; MoleculeID: %s; ChainID: %s; Number of interface residues: %d" % (InterfaceID, MolName, ChainName, ChainResiduesInfo[0]))
1118 MiscUtil.PrintInfo("Residue distribution: %s\nResidue IDs: %s" % (ChainResiduesInfo[1], ChainResiduesInfo[2]))
1119 continue
1120
1121 def GetInterfaceChainsAndResidueNumbers(ChainIDs, ChainsAndResiduesInfo):
1122 """Collect interface residue numbers for chains."""
1123
1124 ChainResidueNums = {}
1125 ChainResidueNums["ChainIDs"] = []
1126 ChainResidueNums["ResNums"] = {}
1127
1128 for ChainID in ChainIDs:
1129 if not ChainID in ChainsAndResiduesInfo["ChainIDs"]:
1130 continue
1131
1132 ChainResidueNums["ChainIDs"].append(ChainID)
1133 ChainResidueNums["ResNums"][ChainID] = []
1134
1135 ResNums = []
1136 for ResName in ChainsAndResiduesInfo["ResNames"][ChainID]:
1137 ResNums.extend(ChainsAndResiduesInfo["ResNum"][ChainID][ResName])
1138
1139 ChainResidueNums["ResNums"][ChainID] = sorted(ResNums, key = int)
1140
1141 InterfaceChainIDs = ChainResidueNums["ChainIDs"]
1142
1143 return InterfaceChainIDs, ChainResidueNums
1144
1145 def SetupPyMOLObjectNamesInfo():
1146 """Setup PyMOL object names for displaying macromolecules."""
1147
1148 OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"] = []
1149
1150 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
1151 PyMOLObjectNamesInfo = SetupPyMOLObjectNames(FileIndex)
1152 OptionsInfo["InfilesInfo"]["PyMOLObjectNamesInfo"].append(PyMOLObjectNamesInfo)
1153
1154 def SetupPyMOLObjectNames(FileIndex):
1155 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
1156 chains and ligands present in input file.
1157 """
1158
1159 PyMOLObjectNames = {}
1160 PyMOLObjectNames["Chains"] = {}
1161 PyMOLObjectNames["Ligands"] = {}
1162
1163 # Setup groups and objects for complex...
1164 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
1165
1166 # Setup groups and objects for chain...
1167 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1168 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1169 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
1170
1171 # Setup groups and objects for ligand...
1172 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
1173 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
1174
1175 return PyMOLObjectNames
1176
1177 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
1178 """Setup groups and objects for complex."""
1179
1180 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
1181
1182 PDBGroupName = "%s" % PDBFileRoot
1183 PyMOLObjectNames["PDBGroup"] = PDBGroupName
1184 PyMOLObjectNames["PDBGroupMembers"] = []
1185
1186 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
1187 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
1188 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
1189
1190 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
1191 if OptionsInfo["SurfaceComplex"]:
1192 PyMOLObjectNames["ComplexHydrophobicSurface"] = "%s.Surface" % ComplexGroupName
1193
1194 PyMOLObjectNames["ComplexGroupMembers"] = []
1195 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
1196 if OptionsInfo["SurfaceComplex"]:
1197 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexHydrophobicSurface"])
1198
1199 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
1200 """Setup groups and objects for chain."""
1201
1202 PDBGroupName = PyMOLObjectNames["PDBGroup"]
1203
1204 PyMOLObjectNames["Chains"][ChainID] = {}
1205 PyMOLObjectNames["Ligands"][ChainID] = {}
1206
1207 # Set up chain group and chain objects...
1208 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
1209 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
1210 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
1211 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
1212
1213 # Setup chain complex group and objects...
1214 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
1215 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
1216 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
1217
1218 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
1219
1220 Name = "%s.Complex" % (ChainComplexGroupName)
1221 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = Name
1222 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1223
1224 if OptionsInfo["SurfaceChainComplex"]:
1225 Name = "%s.Surface" % (ChainComplexGroupName)
1226 PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"] = Name
1227 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1228
1229 # Setup up a group for individual chains...
1230 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
1231 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
1232 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
1233
1234 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
1235
1236 Name = "%s.Chain" % (ChainAloneGroupName)
1237 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
1238 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
1239
1240 # Setup a group for non-interface residues...
1241 NonInterfaceGroupName = "%s.NonInterface" % (ChainAloneGroupName)
1242 PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterfaceGroup"] = NonInterfaceGroupName
1243 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(NonInterfaceGroupName)
1244
1245 PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterfaceGroupMembers"] = []
1246
1247 # Setup a chain for non-interface residues...
1248 Name = "%s.Chain" % (NonInterfaceGroupName)
1249 PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterface"] = Name
1250 PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterfaceGroupMembers"].append(Name)
1251
1252 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
1253 # Setup a surface group and add it to chain alone non-interface group...
1254 SurfaceGroupName = "%s.Surface" % (NonInterfaceGroupName)
1255 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"] = SurfaceGroupName
1256 PyMOLObjectNames["Chains"][ChainID]["ChainAloneNonInterfaceGroupMembers"].append(SurfaceGroupName)
1257
1258 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"] = []
1259
1260 # Setup a generic colored surface...
1261 Name = "%s.Surface" % (SurfaceGroupName)
1262 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"] = Name
1263 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1264
1265 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
1266 # Setup hydrophobicity surface...
1267 Name = "%s.Hydrophobicity" % (SurfaceGroupName)
1268 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"] = Name
1269 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1270
1271 # Setup hydrophobicity and charge surface...
1272 Name = "%s.Hydrophobicity_Charge" % (SurfaceGroupName)
1273 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"] = Name
1274 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1275
1276 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
1277 # Setup electrostatics group...
1278 GroupName = "%s.Vacuum_Electrostatics" % (SurfaceGroupName)
1279 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroup"] = GroupName
1280 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(GroupName)
1281
1282 # Setup electrostatics group members...
1283 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"] = []
1284
1285 for MemberType in ["Chain", "Contact_Potential", "Map", "Legend", "Volume"]:
1286 MemberID = re.sub("_", "", MemberType)
1287
1288 Name = "%s.%s" % (GroupName, MemberType)
1289 NameID = "ChainAloneElectrostaticsSurface%s" % MemberID
1290
1291 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
1292 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"].append(Name)
1293
1294 # Setup solvent and inorganic objects for chain...
1295 for NameID in ["Solvent", "Inorganic"]:
1296 Name = "%s.%s" % (ChainGroupName, NameID)
1297 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
1298 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
1299
1300 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
1301 """Stetup groups and objects for ligand."""
1302
1303 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
1304
1305 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
1306
1307 # Setup a chain level ligand group...
1308 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
1309 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
1310 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
1311
1312 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
1313
1314 # Set up ligand group and its members...
1315 GroupName = "%s.Ligand" % (ChainLigandGroupName)
1316 GroupNameID = "LigandGroup"
1317 GroupMembersID = "LigandGroupMembers"
1318
1319 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
1320 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
1321
1322 LigandName = "%s.Ligand" % (GroupName)
1323 LigandNameID = "Ligand"
1324 PyMOLObjectNames["Ligands"][ChainID][LigandID][LigandNameID] = LigandName
1325
1326 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
1327 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(LigandName)
1328
1329 # Add ball and stick...
1330 BallAndStickName = "%s.BallAndStick" % (GroupName)
1331 BallAndStickID = "LigandBallAndStick"
1332 PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickID] = BallAndStickName
1333 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(BallAndStickName)
1334
1335 def SetupPyMOLInterfaceObjectNamesInfo():
1336 """Setup PyMOL object names for displaying macromolecular interfaces."""
1337
1338 InterfaceChainsAndResiduesInfo = OptionsInfo["InfilesInfo"]["InterfaceChainsAndResiduesInfo"]
1339
1340 PyMOLObjectNames = {}
1341 PyMOLObjectNames["InterfaceIDs"] = {}
1342 PyMOLObjectNames["InterfaceChainIDs"] = {}
1343
1344 # Setup top level interfaces group...
1345 InterfacesGroupName = "Interfaces"
1346 PyMOLObjectNames["InterfacesGroup"] = InterfacesGroupName
1347 PyMOLObjectNames["InterfacesGroupMembers"] = []
1348
1349 for InterfaceID in InterfaceChainsAndResiduesInfo["InterfaceIDs"]:
1350 PyMOLObjectNames["InterfaceIDs"][InterfaceID] = {}
1351 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID] = {}
1352
1353 # Setup an interface group...
1354 InterfaceIDGroupName = "%s.%s" % (InterfacesGroupName, InterfaceID)
1355 PyMOLObjectNames["InterfaceIDs"][InterfaceID]["InterfaceIDGroup"] = InterfaceIDGroupName
1356 PyMOLObjectNames["InterfacesGroupMembers"].append(InterfaceIDGroupName)
1357 PyMOLObjectNames["InterfaceIDs"][InterfaceID]["InterfaceIDGroupMembers"] = []
1358
1359 # Setup a polar contact group...
1360 if OptionsInfo["InterfacePolarContacts"]:
1361 PolarContactName = "%s.Polar_Contacts" % (InterfaceIDGroupName)
1362 PyMOLObjectNames["InterfaceIDs"][InterfaceID]["PolarContacts"] = PolarContactName
1363 PyMOLObjectNames["InterfaceIDs"][InterfaceID]["InterfaceIDGroupMembers"].append(PolarContactName)
1364
1365 # Setup a hydrophobic contact group...
1366 if OptionsInfo["InterfaceHydrophobicContacts"]:
1367 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % (InterfaceIDGroupName)
1368 PyMOLObjectNames["InterfaceIDs"][InterfaceID]["HydrophobicContacts"] = HydrophobicContactsName
1369 PyMOLObjectNames["InterfaceIDs"][InterfaceID]["InterfaceIDGroupMembers"].append(HydrophobicContactsName)
1370
1371 for InterfaceChainID in InterfaceChainsAndResiduesInfo["InterfaceChainIDs"][InterfaceID]:
1372 SetupPyMOLInterfaceObjectNamesForChain(PyMOLObjectNames, InterfaceID, InterfaceChainID)
1373
1374 OptionsInfo["InfilesInfo"]["PyMOLInterfaceObjectNamesInfo"] = PyMOLObjectNames
1375
1376 def SetupPyMOLInterfaceObjectNamesForChain(PyMOLObjectNames, InterfaceID, InterfaceChainID):
1377 """Setup PyMOL interface object names for a chain."""
1378
1379 InterfaceChainsAndResiduesInfo = OptionsInfo["InfilesInfo"]["InterfaceChainsAndResiduesInfo"]
1380 FileIndex = InterfaceChainsAndResiduesInfo["ChainIDsInfileIndices"][InterfaceID][InterfaceChainID]
1381 ChainID = InterfaceChainsAndResiduesInfo["ChainIDs"][InterfaceID][InterfaceChainID]
1382
1383 InterfaceIDGroupName = PyMOLObjectNames["InterfaceIDs"][InterfaceID]["InterfaceIDGroup"]
1384
1385 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID] = {}
1386
1387 # Setup a chain group...
1388 ChainGroupName = "%s.%s" % (InterfaceIDGroupName, InterfaceChainID)
1389 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroup"] = ChainGroupName
1390 PyMOLObjectNames["InterfaceIDs"][InterfaceID]["InterfaceIDGroupMembers"].append(ChainGroupName)
1391 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroupMembers"] = []
1392
1393 # Setup chain...
1394 Name = "%s.Chain" % (ChainGroupName)
1395 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["Chain"] = Name
1396 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroupMembers"].append(Name)
1397
1398 if GetInterfaceResidueTypesStatus(FileIndex, ChainID):
1399 # Setup residue type group and its subgroups...
1400 ResiduesGroupName = "%s.Residues" % (ChainGroupName)
1401
1402 ResiduesGroupIDPrefix = "ChainResidues"
1403 ResiduesGroupID = "%sGroup" % ResiduesGroupIDPrefix
1404
1405 # Add residue group to chain group...
1406 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesGroupID] = ResiduesGroupName
1407 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroupMembers"].append(ResiduesGroupName)
1408
1409 # Initialize residue group members...
1410 ResiduesGroupMembersID = "%sGroupMembers" % ResiduesGroupIDPrefix
1411 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesGroupMembersID] = []
1412
1413 # Setup residues sub groups and its members...
1414 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1415 SubGroupID = re.sub("_", "", SubGroupType)
1416
1417 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
1418 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
1419
1420 # Add sub group to residues group...
1421 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesSubGroupID] = ResiduesSubGroupName
1422 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
1423
1424 # Initialize sub group members...
1425 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
1426 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesSubGroupMembersID] = []
1427
1428 # Add sub group members to subgroup...
1429 for MemberType in ["Residues", "Surface"]:
1430 MemberID = re.sub("_", "", MemberType)
1431
1432 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
1433 SubGroupMemberID = "%s%s%s" % (ResiduesGroupIDPrefix, SubGroupID, MemberID)
1434
1435 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][SubGroupMemberID] = SubGroupMemberName
1436 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][ResiduesSubGroupMembersID].append(SubGroupMemberName)
1437
1438 if GetInterfaceContainsSurfacesStatus(FileIndex, ChainID):
1439 # Setup a surface group and add it to chain group...
1440 SurfaceGroupName = "%s.Surface" % (ChainGroupName)
1441 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroup"] = SurfaceGroupName
1442 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainGroupMembers"].append(SurfaceGroupName)
1443
1444 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroupMembers"] = []
1445
1446 # Setup a generic colored surface...
1447 Name = "%s.Surface" % (SurfaceGroupName)
1448 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurface"] = Name
1449 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroupMembers"].append(Name)
1450
1451 if GetInterfaceSurfaceChainStatus(FileIndex, ChainID):
1452 # Setup hydrophobicity surface...
1453 Name = "%s.Hydrophobicity" % (SurfaceGroupName)
1454 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainHydrophobicSurface"] = Name
1455 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroupMembers"].append(Name)
1456
1457 # Setup hydrophobicity and charge surface...
1458 Name = "%s.Hydrophobicity_Charge" % (SurfaceGroupName)
1459 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainHydrophobicChargeSurface"] = Name
1460 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroupMembers"].append(Name)
1461
1462 if GetInterfaceSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
1463 # Setup electrostatics group...
1464 GroupName = "%s.Vacuum_Electrostatics" % (SurfaceGroupName)
1465 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainElectrostaticsGroup"] = GroupName
1466 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainSurfaceGroupMembers"].append(GroupName)
1467
1468 # Setup electrostatics group members...
1469 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainElectrostaticsGroupMembers"] = []
1470
1471 for MemberType in ["Chain", "Contact_Potential", "Map", "Legend", "Volume"]:
1472 MemberID = re.sub("_", "", MemberType)
1473
1474 Name = "%s.%s" % (GroupName, MemberType)
1475 NameID = "ChainElectrostaticsSurface%s" % MemberID
1476
1477 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID][NameID] = Name
1478 PyMOLObjectNames["InterfaceChainIDs"][InterfaceID][InterfaceChainID]["ChainElectrostaticsGroupMembers"].append(Name)
1479
1480 def ProcessResidueTypesAndSurfaceOptions(FileIndex, SpecifiedChainsAndLigandsInfo):
1481 """Process residue types and surface options for chains and interfaces."""
1482
1483 SpecifiedChainsAndLigandsInfo["ChainSurfaces"] = {}
1484 SpecifiedChainsAndLigandsInfo["SurfaceChain"] = {}
1485 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"] = {}
1486
1487 SpecifiedChainsAndLigandsInfo["InterfaceSurfaces"] = {}
1488 SpecifiedChainsAndLigandsInfo["SurfaceInterface"] = {}
1489 SpecifiedChainsAndLigandsInfo["SurfaceInterfaceElectrostatics"] = {}
1490
1491 SpecifiedChainsAndLigandsInfo["ResidueTypesInterface"] = {}
1492
1493 # Load infile...
1494 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
1495 MolName = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
1496 pymol.cmd.load(Infile, MolName)
1497
1498 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1499 AminoAcidsPresent = PyMOLUtil.AreAminoAcidResiduesPresent(MolName, ChainID)
1500
1501 # Process surfaces for chains...
1502 if re.match("^auto$", OptionsInfo["SurfaceChain"], re.I):
1503 SurfaceChain = True if AminoAcidsPresent else False
1504 else:
1505 SurfaceChain = True if re.match("^yes$", OptionsInfo["SurfaceChain"], re.I) else False
1506 SpecifiedChainsAndLigandsInfo["SurfaceChain"][ChainID] = SurfaceChain
1507
1508 if re.match("^auto$", OptionsInfo["SurfaceChainElectrostatics"], re.I):
1509 SurfaceChainElectrostatics = True if AminoAcidsPresent else False
1510 else:
1511 SurfaceChainElectrostatics = True if re.match("^yes$", OptionsInfo["SurfaceChainElectrostatics"], re.I) else False
1512 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"][ChainID] = SurfaceChainElectrostatics
1513
1514 # A colored surface is always created by default...
1515 ChainSurfaces = True
1516 SpecifiedChainsAndLigandsInfo["ChainSurfaces"][ChainID] = ChainSurfaces
1517
1518 # Process residue types and surfaces for interfaces...
1519 if re.match("^auto$", OptionsInfo["InterfaceSurface"], re.I):
1520 InterfaceSurface = True if AminoAcidsPresent else False
1521 else:
1522 InterfaceSurface = True if re.match("^yes$", OptionsInfo["InterfaceSurface"], re.I) else False
1523 SpecifiedChainsAndLigandsInfo["SurfaceInterface"][ChainID] = InterfaceSurface
1524
1525 if re.match("^auto$", OptionsInfo["InterfaceSurfaceElectrostatics"], re.I):
1526 InterfaceSurfaceElectrostatics = True if AminoAcidsPresent else False
1527 else:
1528 InterfaceSurfaceElectrostatics = True if re.match("^yes$", OptionsInfo["InterfaceSurfaceElectrostatics"], re.I) else False
1529 SpecifiedChainsAndLigandsInfo["SurfaceInterfaceElectrostatics"][ChainID] = InterfaceSurfaceElectrostatics
1530
1531 # A colored surface is always created by default...
1532 InterfaceSurfaces = True
1533 SpecifiedChainsAndLigandsInfo["InterfaceSurfaces"][ChainID] = InterfaceSurfaces
1534
1535 if re.match("^auto$", OptionsInfo["InterfaceResidueTypes"], re.I):
1536 InterfaceResidueTypes = True if AminoAcidsPresent else False
1537 else:
1538 InterfaceResidueTypes = True if re.match("^yes$", OptionsInfo["InterfaceResidueTypes"], re.I) else False
1539 SpecifiedChainsAndLigandsInfo["ResidueTypesInterface"][ChainID] = InterfaceResidueTypes
1540
1541 # Delete loaded object...
1542 pymol.cmd.delete(MolName)
1543
1544 def GetInterfaceResidueTypesStatus(FileIndex, ChainID):
1545 """Get status of residue types for an interface."""
1546
1547 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesInterface"][ChainID]
1548
1549 def GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
1550 """Get status of surfaces present in chain alone object."""
1551
1552 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSurfaces"][ChainID]
1553
1554 def GetInterfaceContainsSurfacesStatus(FileIndex, ChainID):
1555 """Get status of surfaces present in an interface."""
1556
1557 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["InterfaceSurfaces"][ChainID]
1558
1559 def GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
1560 """Get status of hydrophobic surfaces for chain alone object."""
1561
1562 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChain"][ChainID]
1563
1564 def GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
1565 """Get status of electrostatics surfaces for chain alone object."""
1566
1567 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainElectrostatics"][ChainID]
1568
1569 def GetInterfaceSurfaceChainStatus(FileIndex, ChainID):
1570 """Get status of hydrophobic surfaces for an interface."""
1571
1572 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceInterface"][ChainID]
1573
1574 def GetInterfaceSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
1575 """Get status of hydrophobic surfaces for an interface."""
1576
1577 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceInterfaceElectrostatics"][ChainID]
1578
1579 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
1580 """Check presence of valid ligand IDs."""
1581
1582 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
1583
1584 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1585 if len (SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
1586 MiscUtil.PrintInfo("Chain ID: %s; Specified LigandIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID])))
1587 else:
1588 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
1589 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))
1590
1591 def RetrieveFirstChainID(FileIndex):
1592 """Get first chain ID."""
1593
1594 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
1595
1596 FirstChainID = None
1597 if len(ChainsAndLigandsInfo["ChainIDs"]):
1598 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
1599
1600 return FirstChainID
1601
1602 def ProcessResidueTypes():
1603 """Process residue types."""
1604
1605 ResidueTypesNamesInfo, ResidueTypesParamsInfo = PyMOLUtil.ProcessResidueTypesOptionsInfo("-r, --residueTypes", OptionsInfo["ResidueTypes"])
1606 OptionsInfo["ResidueTypesNames"] = ResidueTypesNamesInfo
1607 OptionsInfo["ResidueTypesParams"] = ResidueTypesParamsInfo
1608
1609 def ProcessSurfaceAtomTypesColors():
1610 """Process surface atom types colors. """
1611
1612 AtomTypesColorNamesInfo = PyMOLUtil.ProcessSurfaceAtomTypesColorsOptionsInfo("--surfaceAtomTypesColors", OptionsInfo["SurfaceAtomTypesColors"])
1613 OptionsInfo["AtomTypesColorNames"] = AtomTypesColorNamesInfo
1614
1615 def ProcessOptions():
1616 """Process and validate command line arguments and options."""
1617
1618 MiscUtil.PrintInfo("Processing options...")
1619
1620 # Validate options...
1621 ValidateOptions()
1622
1623 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
1624
1625 OptionsInfo["Infiles"] = Options["--infiles"]
1626 OptionsInfo["InfilesNames"] = Options["--infileNames"]
1627
1628 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
1629
1630 OptionsInfo["Overwrite"] = Options["--overwrite"]
1631 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
1632
1633 OptionsInfo["Outfile"] = Options["--outfile"]
1634 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
1635 OptionsInfo["PSEOut"] = False
1636 if re.match("^pml$", FileExt, re.I):
1637 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
1638 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
1639 elif re.match("^pse$", FileExt, re.I):
1640 OptionsInfo["PSEOut"] = True
1641 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
1642 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
1643 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
1644 MiscUtil.PrintError("The intermediate output file to be generated, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again." % OptionsInfo["PMLOutfile"] )
1645
1646 OptionsInfo["InterfaceLabelColor"] = Options["--interfaceLabelColor"]
1647
1648 OptionsInfo["InterfaceContactsCutoff"] = float(Options["--interfaceContactsCutoff"])
1649
1650 OptionsInfo["InterfaceHydrophobicContactsColor"] = Options["--interfaceHydrophobicContactsColor"]
1651 OptionsInfo["InterfaceHydrophobicContacts"] = True if re.match("^Yes$", Options["--interfaceHydrophobicContacts"], re.I) else False
1652
1653 OptionsInfo["InterfacePolarContactsColor"] = Options["--interfacePolarContactsColor"]
1654 OptionsInfo["InterfacePolarContacts"] = True if re.match("^Yes$", Options["--interfacePolarContacts"], re.I) else False
1655
1656 OptionsInfo["InterfaceResidueTypes"] = Options["--interfaceResidueTypes"]
1657 OptionsInfo["InterfaceSurface"] = Options["--interfaceSurface"]
1658 OptionsInfo["InterfaceSurfaceElectrostatics"] = Options["--interfaceSurfaceElectrostatics"]
1659
1660 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
1661
1662 Method = Options["--method"]
1663 MethodCutoff = Options["--methodCutoff"]
1664 if re.match("^auto$", MethodCutoff, re.I):
1665 if re.match("BySASAChange", Method, re.I):
1666 MethodCutoff = 1.0
1667 elif re.match("ByHeavyAtomsDistance", Method, re.I):
1668 MethodCutoff = 5.0
1669 elif re.match("ByCAlphaAtomsDistance", Method, re.I):
1670 MethodCutoff = 8.0
1671 else:
1672 MiscUtil.PrintError("The method, %s, specified using \"-m, --method\" option is not a valid method." % (Method))
1673 else:
1674 MethodCutoff = float(Options["--methodCutoff"])
1675 OptionsInfo["Method"] = Method
1676 OptionsInfo["MethodCutoff"] = MethodCutoff
1677
1678 OptionsInfo["ResidueTypes"] = Options["--residueTypes"]
1679 ProcessResidueTypes()
1680
1681 OptionsInfo["SurfaceChain"] = Options["--surfaceChain"]
1682 OptionsInfo["SurfaceChainElectrostatics"] = Options["--surfaceChainElectrostatics"]
1683
1684 OptionsInfo["SurfaceChainComplex"] = True if re.match("^Yes$", Options["--surfaceChainComplex"], re.I) else False
1685 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
1686
1687 # Retrieve surface colors...
1688 SurfaceColors = re.sub(" ", "", Options["--surfaceColors"])
1689 SurfaceColorsWords = SurfaceColors.split(",")
1690 if len(SurfaceColorsWords) != 2:
1691 MiscUtil.PrintError("The number of comma delinited color names, %d, specified using \"--surfaceColors\" option, \"%s\", must be a 2." % (len(SurfaceColorsWords), Options["--surfaceColors"]))
1692 OptionsInfo["SurfaceColors"] = SurfaceColors
1693 OptionsInfo["SurfaceInterfaceColor"] = SurfaceColorsWords[0]
1694 OptionsInfo["SurfaceNonInterfaceColor"] = SurfaceColorsWords[1]
1695
1696 OptionsInfo["SurfaceColorPalette"] = Options["--surfaceColorPalette"]
1697 OptionsInfo["SurfaceAtomTypesColors"] = Options["--surfaceAtomTypesColors"]
1698 ProcessSurfaceAtomTypesColors()
1699
1700 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
1701
1702 RetrieveInfilesInfo()
1703
1704 # Retrieve interface chain IDs...
1705 InterfaceChainIDs = re.sub(" ", "", Options["--chainIDs"])
1706 InterfaceChainIDsList = []
1707 CanonicalInterfaceChainIDsMap = {}
1708 if not re.match("^auto$", InterfaceChainIDs, re.I):
1709 InterfaceChainIDsWords = InterfaceChainIDs.split(",")
1710 if len(InterfaceChainIDsWords) % 2:
1711 MiscUtil.PrintError("The number of comma delimited chain IDs, %d, specified using \"-c, --chainIDs\" option, \"%s\", must be a multple of 2." % (len(InterfaceChainIDsWords), Options["--chainIDs"]))
1712 for ChainID in InterfaceChainIDsWords:
1713 if not len(ChainID):
1714 MiscUtil.PrintError("A chain ID specified, \"%s\" using \"-c, --chainIDs\" option is empty." % (Options["--chainIDs"]))
1715 ChainIDWords = ChainID.split("+")
1716 InterfaceChainIDsList.append(ChainIDWords)
1717 OptionsInfo["InterfaceChainIDs"] = InterfaceChainIDs
1718 OptionsInfo["InterfaceChainIDsList"] = InterfaceChainIDsList
1719
1720 # Process interface chain IDs...
1721 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
1722 ProcessInterfaceChainIDs()
1723
1724 def RetrieveOptions():
1725 """Retrieve command line arguments and options."""
1726
1727 # Get options...
1728 global Options
1729 Options = docopt(_docoptUsage_)
1730
1731 # Set current working directory to the specified directory...
1732 WorkingDir = Options["--workingdir"]
1733 if WorkingDir:
1734 os.chdir(WorkingDir)
1735
1736 # Handle examples option...
1737 if "--examples" in Options and Options["--examples"]:
1738 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
1739 sys.exit(0)
1740
1741 def ValidateOptions():
1742 """Validate option values."""
1743
1744 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
1745
1746 # Expand infiles to handle presence of multiple input files...
1747 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
1748 InfilesCount = len(InfileNames)
1749 if not InfilesCount:
1750 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
1751
1752 # Validate file extensions...
1753 for Infile in InfileNames:
1754 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
1755 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
1756 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
1757
1758 # Validate file count...
1759 if InfilesCount > 2:
1760 MiscUtil.PrintError("Number of input files, %s, specified using \"-i, --infiles\" option is not valid. Number of allowed files: 1 or 2" % (InfilesCount))
1761
1762 # Validate distinct file names...
1763 if InfilesCount == 2:
1764 Infile1Name, Infile2Name = InfileNames
1765 Infile1Pattern = r"^" + re.escape(Infile1Name) + r"$";
1766 if re.match(Infile1Pattern, Infile2Name, re.I):
1767 MiscUtil.PrintError("The file names specified, \"%s\", for option \"-i, --infiles\" must be different.\n" % (Options["--infiles"]))
1768
1769 Options["--infileNames"] = InfileNames
1770
1771 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
1772 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
1773
1774 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
1775
1776 MiscUtil.ValidateOptionFloatValue("--interfaceContactsCutoff", Options["--interfaceContactsCutoff"], {">": 0.0})
1777 MiscUtil.ValidateOptionTextValue("--interfaceHydrophobicContacts", Options["--interfaceHydrophobicContacts"], "yes no")
1778 MiscUtil.ValidateOptionTextValue("--interfacePolarContacts", Options["--interfacePolarContacts"], "yes no")
1779
1780 MiscUtil.ValidateOptionTextValue("--interfaceResidueTypes", Options["--interfaceResidueTypes"], "yes no auto")
1781 MiscUtil.ValidateOptionTextValue("--interfaceSurface", Options["--interfaceSurface"], "yes no auto")
1782 MiscUtil.ValidateOptionTextValue("--interfaceSurfaceElectrostatics", Options["--interfaceSurfaceElectrostatics"], "yes no auto")
1783
1784 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
1785
1786 MiscUtil.ValidateOptionTextValue("--method", Options["--method"], "BySASAChange ByHeavyAtomsDistance ByCAlphaAtomsDistance")
1787 if not re.match("^auto$", Options["--methodCutoff"], re.I):
1788 MiscUtil.ValidateOptionFloatValue("--methodCutoff", Options["--methodCutoff"], {">": 0.0})
1789
1790 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
1791
1792 MiscUtil.ValidateOptionTextValue("--surfaceChain", Options["--surfaceChain"], "yes no auto")
1793 MiscUtil.ValidateOptionTextValue("--surfaceChainElectrostatics", Options["--surfaceChainElectrostatics"], "yes no auto")
1794 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
1795 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no")
1796
1797 MiscUtil.ValidateOptionTextValue("--surfaceColorPalette", Options["--surfaceColorPalette"], "RedToWhite WhiteToGreen")
1798 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
1799
1800 # Setup a usage string for docopt...
1801 _docoptUsage_ = """
1802 PyMOLVisualizeInterfaces.py - Visualize macromolecular interfaces
1803
1804 Usage:
1805 PyMOLVisualizeInterfaces.py [--allowEmptyObjects <yes or no>] [--chainIDs <ChainID1 or ChainID1,ChainID2>]
1806 [--interfaceLabelColor <text>] [ --interfaceContactsCutoff <number>]
1807 [--interfaceHydrophobicContacts <yes or no>] [--interfaceHydrophobicContactsColor <text>]
1808 [--interfacePolarContacts <yes or no>] [--interfacePolarContactsColor <text>]
1809 [--interfaceResidueTypes <yes or no>] [--interfaceSurface <yes or no>]
1810 [--interfaceSurfaceElectrostatics <yes or no>] [--labelFontID <number>]
1811 [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All, None or ID1,ID2...>]
1812 [--method <text>] [--methodCutoff <number>]
1813 [--PMLOut <yes or no>] [--residueTypes <Type,Color,ResNames,...>] [--surfaceChain <yes or no>]
1814 [--surfaceChainElectrostatics <yes or no>] [--surfaceChainComplex <yes or no>]
1815 [--surfaceComplex <yes or no>] [--surfaceColors <ColorName1,ColorName2>]
1816 [--surfaceColorPalette <RedToWhite or WhiteToGreen>]
1817 [--surfaceAtomTypesColors <ColorType,ColorSpec,...>] [--surfaceTransparency <number>]
1818 [--overwrite] [-w <dir>] -i <infile1,...> -o <outfile>
1819 PyMOLVisualizeInterfaces.py -h | --help | -e | --examples
1820
1821 Description:
1822 Generate PyMOL visualization files for viewing interfaces between macromolecules
1823 including proteins and nucleic acids. The interfaces may be generated between
1824 pairs of chains in a single file or across two different files.
1825
1826 The supported input file format are: PDB (.pdb), CIF (.cif)
1827
1828 The supported output file formats are: PyMOL script file (.pml), PyMOL session
1829 file (.pse)
1830
1831 A variety of PyMOL groups and objects may be created for visualization of
1832 macromolecular interfaces. These groups and objects correspond to complexes,
1833 surfaces, chains, ligands, and interfaces. A complete hierarchy of all possible
1834 PyMOL groups and objects is shown below:
1835
1836 <PDBFileRoot>
1837 .Complex
1838 .Complex
1839 .Surface
1840 .Chain<ID>
1841 .Complex
1842 .Complex
1843 .Surface
1844 .Chain
1845 .Chain
1846 .NonInterface
1847 .Chain
1848 .Surface
1849 .Surface
1850 .Hydrophobicity
1851 .Hydrophobicity_Charge
1852 .Vacuum_Electrostatics
1853 .Contact_Potentials
1854 .Map
1855 .Legend
1856 .Volume
1857 .Solvent
1858 .Inorganic
1859 .Ligand<ID>
1860 .Ligand
1861 .Ligand
1862 .BallAndStick
1863 .Ligand<ID>
1864 .Ligand
1865 ... ... ...
1866 .Chain<ID>
1867 ... ... ...
1868 .Ligand<ID>
1869 ... ... ...
1870 .Ligand<ID>
1871 ... ... ...
1872 .Chain<ID>
1873 ... ... ...
1874 <PDBFileRoot>
1875 .Complex
1876 ... ... ...
1877 .Chain<ID>
1878 ... ... ...
1879 .Ligand<ID>
1880 ... ... ...
1881 .Ligand<ID>
1882 ... ... ...
1883 .Chain<ID>
1884 ... ... ...
1885 <Interfaces>
1886 .Chain<IDs1>_Chain<IDs2>
1887 .Polar_Contacts
1888 .Hydrophobic_Contacts
1889 .Chain<ID> or Chain<ID>_<PDBFileRoot>
1890 .Chain
1891 .Residues
1892 .Aromatic
1893 .Residues
1894 .Surface
1895 .Hydrophobic
1896 .Residues
1897 .Surface
1898 .Polar
1899 .Residues
1900 .Surface
1901 .Positively_Charged
1902 .Residues
1903 .Surface
1904 .Negatively_Charged
1905 .Residues
1906 .Surface
1907 .Other
1908 .Residues
1909 .Surface
1910 .Surface
1911 .Surface
1912 .Hydrophobicity
1913 .Hydrophobicity_Charge
1914 .Vacuum_Electrostatics
1915 .Contact_Potentials
1916 .Map
1917 .Legend
1918 .Volume
1919 .Chain<ID> or <PDBFileRoot>_Chain<ID>
1920 .Chain
1921 .Residues
1922 ... ... ...
1923 .Surface
1924 ... ... ...
1925 .Chain<IDs>_Chain<IDs>
1926 .Polar_Contacts
1927 .Hydrophobic_Contacts
1928 .Chain<ID> or Chain<ID>_<PDBFileRoot>
1929 .Chain
1930 .Residues
1931 ... ... ...
1932 .Surface
1933 ... ... ...
1934 .Chain<ID> or Chain<ID>_<PDBFileRoot>
1935 .Chain
1936 .Residues
1937 ... ... ...
1938 .Surface
1939 ... ... ...
1940
1941 The hydrophobic and electrostatic surfaces are not created for complete complex
1942 and chain complex in input file(s) by default. A word to the wise: The creation of
1943 surface objects may slow down loading of PML file and generation of PSE file, based
1944 on the size of input complexes. The generation of PSE file may also fail.
1945
1946 Options:
1947 --allowEmptyObjects <yes or no> [default: no]
1948 Allow creation of empty PyMOL objects corresponding to interface,
1949 solvent, and inorganic atom selections across chains and ligands in
1950 input file(s). By default, the empty objects are marked for deletion.
1951 -c, --chainIDs <ChainID1,ChainD2,...> [default: Auto]
1952 Pairwise comma delimited list of chain IDs for the identification of
1953 macromolecular interfaces. All chain IDs must be present in the
1954 same file for a single input file. Otherwise, the first and second
1955 chain ID(s) in a pair belong to the first and second input file.
1956
1957 The default values for interface chain IDs depend on the number
1958 of input files as shown below:
1959
1960 One input file: First two chains
1961 Two input files: First chain in each input file
1962
1963 Each chain may contain multiple chain IDs delimited by a plus sign. For
1964 example, A+B,C+D chain pair specifies interface between chain complexes
1965 A+B and C+D in first input file or across two input files.
1966 -e, --examples
1967 Print examples.
1968 -h, --help
1969 Print this help message.
1970 -i, --infiles <infile or infile1,infile2>
1971 Name of an input file or a comma delmited list of names for two input
1972 files.
1973 --ignoreHydrogens <yes or no> [default: yes]
1974 Ignore hydrogens for ligand views.
1975 --interfaceLabelColor <text> [default: magenta]
1976 Color for drawing residue or atom level labels for residues in an interface.
1977 The specified value must be valid color. No validation is performed.
1978 --interfaceContactsCutoff <number> [default: 4.0]
1979 Distance in Angstroms for identifying polar and hyrdophobic contacts
1980 between atoms in interface reisudes.
1981 --interfaceHydrophobicContacts <yes or no> [default: yes]
1982 Hydrophobic contacts between residues in an interface. The hydrophobic
1983 contacts are shown between pairs of carbon atoms not connected to
1984 hydrogen bond donor or acceptors atoms as identified by PyMOL.
1985 --interfaceHydrophobicContactsColor <text> [default: purpleblue]
1986 Color for drawing hydrophobic contacts between residues in an interface.
1987 The specified value must be valid color. No validation is performed.
1988 --interfacePolarContacts <yes or no> [default: yes]
1989 Polar contacts between residues in an interface.
1990 --interfacePolarContactsColor <text> [default: orange]
1991 Color for drawing polar contacts between residues in an interface.
1992 The specified value must be valid color. No validation is performed.
1993 --interfaceResidueTypes <yes or no> [default: auto]
1994 Interface residue types. The residue groups are generated using residue types,
1995 colors, and names specified by '--residueTypes' option. It is only valid for
1996 amino acids. By default, the residue type groups are automatically created
1997 for interfaces containing amino acids and skipped for chains only containing
1998 nucleic acids.
1999 --interfaceSurface <yes or no> [default: auto]
2000 Surfaces around interface residues colored by hydrophobicity alone and
2001 both hydrophobicity and charge. The hydrophobicity surface is colored
2002 at residue level using Eisenberg hydrophobicity scale for residues and color
2003 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
2004 charge surface is colored [ Ref 140 ] at atom level using colors specified for
2005 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
2006 simultaneous mapping of hyrophobicity and charge values on the surfaces.
2007
2008 This option is only valid for amino acids. By default, both surfaces are
2009 automatically created for pockets containing amino acids and skipped for
2010 pockets containing only nucleic acids.
2011
2012 In addition, generic surfaces colored by '--surfaceColors' are always created
2013 for interface residues containing amino acids and nucleic acids.
2014 --interfaceSurfaceElectrostatics <yes or no> [default: no]
2015 Vacuum electrostatics contact potential surface around interface residues.
2016 A word to the wise from PyMOL documentation: The computed protein
2017 contact potentials are only qualitatively useful, due to short cutoffs,
2018 truncation, and lack of solvent "screening".
2019
2020 This option is only valid for amino acids. By default, the electrostatics surface
2021 is automatically created for chains containing amino acids and skipped for chains
2022 containing only nucleic acids.
2023 --labelFontID <number> [default: 7]
2024 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
2025 The specified value must be a valid PyMOL font ID. No validation is
2026 performed. The complete lists of valid font IDs is available at:
2027 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
2028 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
2029 -l, --ligandIDs <Largest, All, None or ID1,ID2...> [default: All]
2030 List of ligand IDs to show in chains during visualization of interfaces. Possible
2031 values: Largest, All, None, or a comma delimited list of ligand IDs. The
2032 default is to show all ligands present in chains involved in interfaces.
2033
2034 Ligands are identified using organic selection operator available in PyMOL.
2035 It'll also identify buffer molecules as ligands. The largest ligand contains
2036 the highest number of heavy atoms.
2037 -m, --method <text> [default: BySASAChange]
2038 Methodology for the identification of interface residues between a pair
2039 of chains in an input file. The interface residues may be identified by
2040 change in solvent accessible surface area (SASA) for a residue between
2041 a chain and chains complex, distance between heavy atoms
2042 in two chains, or distance between CAlpha atoms. Possible values:
2043 BySASAChange, ByHeavyAtomsDistance, or ByCAlphaAtomsDistance.
2044 --methodCutoff <number> [default: auto]
2045 Cutoff value used by different methodologies during the identification of
2046 interface residues between a pair of chains. The default values are
2047 shown below:
2048
2049 BySASAChange: 1.0; Units: Angstrom**2 [ Ref 141 ]
2050 ByHeavyAtomsDistance: 5.0; Units: Angstrom [ Ref 142 ]
2051 ByCAlphaAtomsDistance: 8.0; Units: Angstrom [ Ref 143 ]
2052
2053 -o, --outfile <outfile>
2054 Output file name.
2055 -p, --PMLOut <yes or no> [default: yes]
2056 Save PML file during generation of PSE file.
2057 -r, --residueTypes <Type,Color,ResNames,...> [default: auto]
2058 Residue types, colors, and names to generate for residue groups during
2059 and '--residueTypesChain' option. It is only valid for amino acids.
2060
2061 It is a triplet of comma delimited list of amino acid residues type, residues
2062 color, and a space delimited list three letter residue names.
2063
2064 The default values for residue type, color, and name triplets are shown
2065 below:
2066
2067 Aromatic,brightorange,HIS PHE TRP TYR,
2068 Hydrophobic,orange,ALA GLY VAL LEU ILE PRO MET,
2069 Polar,palegreen,ASN GLN SER THR CYS,
2070 Positively_Charged,marine,ARG LYS,
2071 Negatively_Charged,red,ASP GLU
2072
2073 The color name must be a valid PyMOL name. No validation is performed.
2074 An amino acid name may appear across multiple residue types. All other
2075 residues are grouped under 'Other'.
2076 --surfaceChain <yes or no> [default: auto]
2077 Surfaces around non-interface residues in individual chain colored by
2078 hydrophobicity alone and both hydrophobicity and charge. The hydrophobicity
2079 surface is colored at residue level using Eisenberg hydrophobicity scale for residues
2080 and color gradient specified by '--surfaceColorPalette' option. The hydrophobicity
2081 and charge surface is colored [ Ref 140 ] at atom level using colors specified for
2082 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
2083 simultaneous mapping of hyrophobicity and charge values on the surfaces.
2084
2085 This option is only valid for amino acids. By default, both surfaces are
2086 automatically created for chains containing amino acids and skipped for
2087 chains containing only nucleic acids.
2088
2089 In addition, generic surfaces colored by '--surfaceColors' are always created
2090 for non-interface residues containing amino acids and nucleic acids.
2091 --surfaceChainElectrostatics <yes or no> [default: no]
2092 Vacuum electrostatics contact potential surface and volume around non-interface
2093 residues in individual chain. A word to the wise from PyMOL documentation: The
2094 computed protein contact potentials are only qualitatively useful, due to short cutoffs,
2095 truncation, and lack of solvent "screening".
2096
2097 This option is only valid for amino acids. By default, the electrostatics surface
2098 and volume are automatically created for chains containing amino acids and
2099 skipped for chains containing only nucleic acids.
2100 --surfaceChainComplex <yes or no> [default: no]
2101 Hydrophobic surface around chain complex. The surface is colored by
2102 hydrophobicity. It is only valid for amino acids.
2103 --surfaceComplex <yes or no> [default: no]
2104 Hydrophobic surface around complete complex. The surface is colored by
2105 hydrophobicity. It is only valid for amino acids.
2106 --surfaceColors <ColorName1,ColorName2> [default: salmon,lightblue]
2107 Color names for surfaces around interface residues and non-interface
2108 residues in chains. These colors are not used for surfaces colored by
2109 hydrophobicity and charge. The color names must be valid PyMOL names.
2110 --surfaceColorPalette <RedToWhite or WhiteToGreen> [default: RedToWhite]
2111 Color palette for hydrophobic surfaces around chains and interface residues
2112 in proteins. Possible values: RedToWhite or WhiteToGreen from most
2113 hydrophobic amino acid to least hydrophobic. The colors values for amino
2114 acids are taken from color_h script available as part of the Script Library at
2115 PyMOL Wiki.
2116 --surfaceAtomTypesColors <ColorType,ColorSpec,...> [default: auto]
2117 Atom colors for generating surfaces colored by hyrophobicity and charge
2118 around chains and interface residues in proteins. It's a pairwise comma
2119 delimited list of atom color type and color specification for goups of atoms.
2120
2121 The default values for color types [ Ref 140 ] along wth color specifications
2122 are shown below:
2123
2124 HydrophobicAtomsColor, yellow,
2125 NegativelyChargedAtomsColor, red,
2126 PositivelyChargedAtomsColor, blue,
2127 OtherAtomsColor, gray90
2128
2129 The color names must be valid PyMOL names.
2130
2131 The color values may also be specified as space delimited RGB triplets:
2132
2133 HydrophobicAtomsColor, 0.95 0.78 0.0,
2134 NegativelyChargedAtomsColor, 1.0 0.4 0.4,
2135 PositivelyChargedAtomsColor, 0.2 0.5 0.8,
2136 OtherAtomsColor, 0.95 0.95 0.95
2137
2138 --surfaceTransparency <number> [default: 0.25]
2139 Surface transparency for molecular surfaces.
2140 --overwrite
2141 Overwrite existing files.
2142 -w, --workingdir <dir>
2143 Location of working directory which defaults to the current directory.
2144
2145 Examples:
2146 To visualize interface residues between the first two chains in a PDB file,
2147 using default methodology to identify interfaces, and and generate a PML
2148 file, type:
2149
2150 % PyMOLVisualizeInterfaces.py -i Sample8.pdb -o Sample8.pml
2151
2152 To visualize interface residues between a pair of specific chains in a PDB
2153 file using a specific methodology and cutoff value to identify interfaces, and
2154 generate a PML file, type:
2155
2156 % PyMOLVisualizeInterfaces.py -m BySASAChange --methodCutoff 1.0
2157 -c "A,B" -i Sample8.pdb -o Sample8.pml
2158
2159 To visualize interface residues between multiple pairs of specified chains in
2160 a PDB file using a specific methodology and cutoff value to identify interfaces,
2161 and generate a PML file, type:
2162
2163 % PyMOLVisualizeInterfaces.py -m ByHeavyAtomsDistance
2164 --methodCutoff 5.0 -c "A,B,B,D" -i Sample8.pdb -o Sample8.pml
2165
2166 To visualize interface residues between a pair of specified chains, each member
2167 containing multiple chains, a PDB file using a specific methodology and cutoff
2168 value to identify interfaces, and generate a PML file, type:
2169
2170 % PyMOLVisualizeInterfaces.py -m ByCAlphaAtomsDistance
2171 --methodCutoff 8.0 -c "A+C,B+D" -i Sample8.pdb -o Sample8.pml
2172
2173 To visualize interface residues between a pair of specific chains across two PDB
2174 files using a specific methodology and cutoff value to identify interfaces, and
2175 generate a PML file, type:
2176
2177 % PyMOLVisualizeInterfaces.py -m BySASAChange --methodCutoff 1.0
2178 -c "A,B" -i Sample8Part1.pdb,Sample8Part2.pdb
2179 -o Sample8.pml
2180
2181 To visualize interface residues between multiple pairs of specified chains across
2182 two PDB files using a specific methodology and cutoff value to identify interfaces,
2183 and generate a PML file, type:
2184
2185 % PyMOLVisualizeInterfaces.py -m ByHeavyAtomsDistance
2186 --methodCutoff 5.0 -c "A,B,C,B" -i Sample8Part1.pdb,Sample8Part2.pdb
2187 -o Sample8.pml
2188
2189 To visualize interface residues between a pair of specified chains, each member
2190 containing multiple chains, across two PDB files using a specific methodology
2191 and cutoff value to identify interfaces, and generate a PML file, type:
2192
2193 % PyMOLVisualizeInterfaces.py -m ByCAlphaAtomsDistance
2194 --methodCutoff 8.0 -c "A+C,B+D" -i "Sample8Part1.pdb,Sample8Part2.pdb"
2195 -o Sample8.pml
2196
2197 Author:
2198 Manish Sud(msud@san.rr.com)
2199
2200 See also:
2201 DownloadPDBFiles.pl, PyMOLVisualizeCryoEMDensity.py,
2202 PyMOLVisualizeElectronDensity.py, PyMOLVisualizeMacromolecules.py,
2203 PyMOLVisualizeSurfaceAndBuriedResidues.py
2204
2205 Copyright:
2206 Copyright (C) 2024 Manish Sud. All rights reserved.
2207
2208 The functionality available in this script is implemented using PyMOL, a
2209 molecular visualization system on an open source foundation originally
2210 developed by Warren DeLano.
2211
2212 This file is part of MayaChemTools.
2213
2214 MayaChemTools is free software; you can redistribute it and/or modify it under
2215 the terms of the GNU Lesser General Public License as published by the Free
2216 Software Foundation; either version 3 of the License, or (at your option) any
2217 later version.
2218
2219 """
2220
2221 if __name__ == "__main__":
2222 main()
