1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeCavities.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 GenerateCavitiesVisualization()
79
80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
82
83 def GenerateCavitiesVisualization():
84 """Generate visualization for cavities."""
85
86 Outfile = OptionsInfo["PMLOutfile"]
87 OutFH = open(Outfile, "w")
88 if OutFH is None:
89 MiscUtil.PrintError("Failed to open output fie %s " % Outfile)
90
91 MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
92
93 # Setup header...
94 WritePMLHeader(OutFH, ScriptName)
95 WritePyMOLParameters(OutFH)
96
97 # Load reffile for alignment..
98 if OptionsInfo["Align"]:
99 WriteAlignReference(OutFH)
100
101 # Setup view for each input file...
102 FirstComplex = True
103 FirstComplexFirstChainName = None
104 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
105 # Setup PyMOL object names...
106 PyMOLObjectNames = SetupPyMOLObjectNames(FileIndex)
107
108 # Setup complex view...
109 WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex)
110
111 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
112 FirstChain = True
113 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
114 if FirstComplex and FirstChain:
115 FirstComplexFirstChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
116
117 WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
118
119 # Setup ligand views...
120 FirstLigand = True
121 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
122 WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID)
123
124 # Set up ligand level group...
125 Enable, Action = [False, "close"]
126 if FirstLigand:
127 FirstLigand = False
128 Enable, Action = [True, "open"]
129 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"], PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"], Enable, Action)
130
131 # Setup Chain level group...
132 Enable, Action = [False, "close"]
133 if FirstChain:
134 FirstChain = False
135 Enable, Action = [True, "open"]
136 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"], Enable, Action)
137
138 # Set up complex level group...
139 Enable, Action = [False, "close"]
140 if FirstComplex:
141 FirstComplex = False
142 Enable, Action = [True, "open"]
143 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["PDBGroup"], PyMOLObjectNames["PDBGroupMembers"], Enable, Action)
144
145 # Delete empty PyMOL objects...
146 DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames)
147
148 if OptionsInfo["Align"]:
149 DeleteAlignReference(OutFH)
150
151 if FirstComplexFirstChainName is not None:
152 OutFH.write("""\ncmd.orient("%s", animate = -1)\n""" % FirstComplexFirstChainName)
153 else:
154 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
155
156 OutFH.close()
157
158 # Generate PSE file as needed...
159 if OptionsInfo["PSEOut"]:
160 GeneratePyMOLSessionFile()
161
162 def WritePMLHeader(OutFH, ScriptName):
163 """Write out PML setting up complex view."""
164
165 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
166 OutFH.write("%s\n" % HeaderInfo)
167
168 def WritePyMOLParameters(OutFH):
169 """Write out PyMOL global parameters."""
170
171 PMLCmds = []
172 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
173 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
174
175 PMLCmds.append("""cmd.set("cavity_cull", %.1f, "", 0)""" % (OptionsInfo["CavityCullSize"]))
176 PMLCmds.append("""cmd.set("surface_cavity_radius", -%.1f, "", 0)""" % (OptionsInfo["CavityRadius"]))
177 PMLCmds.append("""cmd.set("surface_cavity_cutoff", -%.1f, "", 0)""" % (OptionsInfo["CavityCutoff"]))
178
179 PML = "\n".join(PMLCmds)
180
181 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
182 OutFH.write("%s\n" % PML)
183
184 def WriteAlignReference(OutFH):
185 """Setup object for alignment reference."""
186
187 RefFileInfo = OptionsInfo["RefFileInfo"]
188 RefFile = RefFileInfo["RefFileName"]
189 RefName = RefFileInfo["PyMOLObjectName"]
190
191 PMLCmds = []
192 PMLCmds.append("""cmd.load("%s", "%s")""" % (RefFile, RefName))
193 PMLCmds.append("""cmd.hide("everything", "%s")""" % (RefName))
194 PMLCmds.append("""cmd.disable("%s")""" % (RefName))
195 PML = "\n".join(PMLCmds)
196
197 OutFH.write("""\n""\n"Loading %s and setting up view for align reference..."\n""\n""" % RefFile)
198 OutFH.write("%s\n" % PML)
199
200 def WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames):
201 """Setup alignment of complex to reference."""
202
203 RefFileInfo = OptionsInfo["RefFileInfo"]
204 RefName = RefFileInfo["PyMOLObjectName"]
205
206 ComplexName = PyMOLObjectNames["Complex"]
207
208 if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
209 RefFirstChainID = RefFileInfo["ChainsAndLigandsInfo"]["ChainIDs"][0]
210 RefAlignSelection = "%s and chain %s" % (RefName, RefFirstChainID)
211
212 ComplexFirstChainID = RetrieveFirstChainID(FileIndex)
213 ComplexAlignSelection = "%s and chain %s" % (ComplexName, ComplexFirstChainID)
214 else:
215 RefAlignSelection = RefName
216 ComplexAlignSelection = ComplexName
217
218 PML = PyMOLUtil.SetupPMLForAlignment(OptionsInfo["AlignMethod"], RefAlignSelection, ComplexAlignSelection)
219 OutFH.write("""\n""\n"Aligning %s against reference %s ..."\n""\n""" % (ComplexAlignSelection, RefAlignSelection))
220 OutFH.write("%s\n" % PML)
221
222 def DeleteAlignReference(OutFH):
223 """Delete alignment reference object."""
224
225 RefName = OptionsInfo["RefFileInfo"]["PyMOLObjectName"]
226 OutFH.write("""\n""\n"Deleting alignment reference object %s..."\n""\n""" % RefName)
227 OutFH.write("""cmd.delete("%s")\n""" % RefName)
228
229 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex):
230 """Write out PML for viewing polymer complex."""
231
232 # Setup complex...
233 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
234 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["Complex"], Infile, True)
235 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
236 OutFH.write("%s\n" % PML)
237
238 if OptionsInfo["Align"]:
239 # No need to align complex on to itself...
240 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
241 WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames)
242
243 if OptionsInfo["SurfaceComplex"]:
244 # Setup hydrophobic surface...
245 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["ComplexHydrophobicSurface"], PyMOLObjectNames["Complex"], ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
246 OutFH.write("\n%s\n" % PML)
247
248 # Setup complex group...
249 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close")
250
251 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
252 """Write out PML for viewing chain."""
253
254 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
255
256 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
257
258 # Setup chain complex group view...
259 WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
260
261 # Setup chain view...
262 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
263
264 # Setup chain solvent view...
265 PML = PyMOLUtil.SetupPMLForSolventView(PyMOLObjectNames["Chains"][ChainID]["Solvent"], ChainComplexName, False)
266 OutFH.write("\n%s\n" % PML)
267
268 # Setup chain inorganic view...
269 PML = PyMOLUtil.SetupPMLForInorganicView(PyMOLObjectNames["Chains"][ChainID]["Inorganic"], ChainComplexName, False)
270 OutFH.write("\n%s\n" % PML)
271
272 def WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
273 """Write chain complex views."""
274
275 # Setup chain complex...
276 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
277 PML = PyMOLUtil.SetupPMLForPolymerChainComplexView(ChainComplexName, PyMOLObjectNames["Complex"], ChainID, True)
278 OutFH.write("%s\n" % PML)
279
280 if OptionsInfo["SurfaceChainComplex"]:
281 # Setup hydrophobic surface...
282 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"], ChainComplexName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
283 OutFH.write("\n%s\n" % PML)
284
285 # Setup chain complex group...
286 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"], False, "close")
287
288 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
289 """Write individual chain views."""
290
291 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
292
293 # Setup chain view...
294 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
295 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, True)
296 OutFH.write("\n%s\n" % PML)
297
298 WriteChainAloneResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
299 WriteChainAloneCavitiesAndSurfacesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
300
301 # Setup chain group...
302 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"], True, "open")
303
304 def WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID):
305 """Write out PML for viewing ligand in a chain."""
306
307 GroupID = "Ligand"
308 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
309 LigandName = PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
310
311 # Setup main object...
312 GroupTypeObjectID = "%s" % (GroupID)
313 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
314
315 OutFH.write("""\n""\n"Setting up views for ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
316 PML = PyMOLUtil.SetupPMLForLigandView(GroupTypeObjectName, ComplexName, LigandID, Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
317 OutFH.write("%s\n" % PML)
318
319 # Setup ball and stick view...
320 BallAndStickNameID = "%sBallAndStick" % (GroupID)
321 BallAndStickName = PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickNameID]
322 PML = PyMOLUtil.SetupPMLForBallAndStickView(BallAndStickName, GroupTypeObjectName, Enable = False)
323 OutFH.write("\n%s\n" % PML)
324
325 # Setup group....
326 GroupNameID = "%sGroup" % (GroupID)
327 GroupMembersID = "%sGroupMembers" % (GroupID)
328 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
329 GroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID]
330
331 Action = "close"
332 Enable = True
333 GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable, Action)
334
335 def WriteChainAloneCavitiesAndSurfacesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
336 """Write out PML for viewing cavities and pockets in chains."""
337
338 if not GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
339 return
340
341 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
342
343 for SubGroupType in ["Cavities", "Surface"]:
344 SubGroupID = "ChainAlone%sGroup" % (SubGroupType)
345 SubGroupMembersID = "%sMembers" % (SubGroupID)
346
347 ProcessingCavities = True if re.match("^Cavities$", SubGroupType, re.I) else False
348
349 # Turn off lines display for cavity surfaces...
350 DisplayStyle = None if ProcessingCavities else "cartoon"
351
352 # Setup a generic color surface...
353 SurfaceID = "%sSurface" % (SubGroupID)
354 SurfaceName = PyMOLObjectNames["Chains"][ChainID][SurfaceID]
355 ColorName = OptionsInfo["SurfaceCavityColor"] if ProcessingCavities else OptionsInfo["SurfaceColor"]
356 EnableStatus = True if ProcessingCavities else False
357 PML = PyMOLUtil.SetupPMLForSurfaceView(SurfaceName, ChainName, Enable = EnableStatus, Color = ColorName)
358 OutFH.write("\n%s\n" % PML)
359
360 if ProcessingCavities:
361 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (OptionsInfo["SurfaceCavityMode"], SurfaceName))
362
363 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
364 # Setup surface colored by hydrophobicity...
365 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SubGroupID)
366 HydrophobicSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicSurfaceID]
367 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(HydrophobicSurfaceName, ChainName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
368 OutFH.write("\n%s\n" % PML)
369
370 if ProcessingCavities:
371 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (OptionsInfo["SurfaceCavityMode"], HydrophobicSurfaceName))
372
373 # Setup surface colored by hyrdophobicity and charge...
374 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SubGroupID)
375 HydrophobicChargeSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicChargeSurfaceID]
376 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(HydrophobicChargeSurfaceName, ChainName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = None)
377 OutFH.write("\n%s\n" % PML)
378
379 if ProcessingCavities:
380 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (OptionsInfo["SurfaceCavityMode"], HydrophobicChargeSurfaceName))
381
382 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
383 # Setup electrostatics surface...
384 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SubGroupID)
385 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SubGroupID)
386 ElectrostaticsGroupName = PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupID]
387 ElectrostaticsGroupMembers = PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupMembersID]
388 WriteSurfaceElectrostaticsView(SubGroupType, OutFH, ChainName, ElectrostaticsGroupName, ElectrostaticsGroupMembers, DisplayAs = DisplayStyle, SurfaceCavityMode = OptionsInfo["SurfaceCavityMode"])
389
390 # Setup surface group...
391 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SubGroupID], PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID], True, "open")
392
393 def WriteChainAloneResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
394 """Write out PML for viewing residue types for a chain."""
395
396 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
397 return
398
399 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
400
401 # Setup residue types objects...
402 ResiduesGroupIDPrefix = "ChainAloneResidues"
403 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
404 SubGroupID = re.sub("_", "", SubGroupType)
405
406 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, SubGroupID)
407 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
408
409 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, SubGroupID)
410 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
411
412 ResiduesColor = OptionsInfo["ResidueTypesParams"][SubGroupType]["Color"]
413 ResiduesNames = OptionsInfo["ResidueTypesParams"][SubGroupType]["Residues"]
414
415 NegateResidueNames = True if re.match("^Other$", SubGroupType, re.I) else False
416 WriteResidueTypesResiduesAndSurfaceView(OutFH, ChainName, ResiduesObjectName, ResiduesSurfaceObjectName, ResiduesColor, ResiduesNames, NegateResidueNames)
417
418 # Setup sub groups for residue types..
419 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
420 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
421
422 # Setup residue type sub groups...
423 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID], PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID], True, "close")
424
425 # Setup residue types group...
426 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneResiduesGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneResiduesGroupMembers"], False, "close")
427
428 def WriteResidueTypesResiduesAndSurfaceView(OutFH, SelectionObjectName, Name, SurfaceName, ResiduesColor, ResiduesNames, NegateResidueNames):
429 """Write residue types residues and surface view."""
430
431 ResidueNamesSelection = "+".join(ResiduesNames)
432 if NegateResidueNames:
433 Selection = "%s and (not resn %s)" % (SelectionObjectName, ResidueNamesSelection)
434 else:
435 Selection = "%s and (resn %s)" % (SelectionObjectName, ResidueNamesSelection)
436
437 # Setup residues...
438 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(Name, Selection, "lines", ResiduesColor, True)
439 OutFH.write("\n%s\n" % PML)
440
441 # Setup surface...
442 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SurfaceName, Selection, "surface", ResiduesColor, True)
443 OutFH.write("\n%s\n" % PML)
444
445 def WriteSurfaceElectrostaticsView(Mode, OutFH, SelectionObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers, DisplayAs = None, SurfaceCavityMode = 2):
446 """Write out PML for viewing surface electrostatics."""
447
448 if len(ElectrostaticsGroupMembers) == 5:
449 Name, ContactPotentialName, MapName, LegendName, VolumeName = ElectrostaticsGroupMembers
450 else:
451 Name, ContactPotentialName, MapName, LegendName = ElectrostaticsGroupMembers
452 VolumeName = None
453
454 PMLCmds = []
455
456 # Setup chain...
457 PMLCmds.append("""cmd.create("%s", "(%s)")""" % (Name, SelectionObjectName))
458
459 # Setup vacuum electrostatics surface along with associated objects...
460 PMLCmds.append("""util.protein_vacuum_esp("%s", mode=2, quiet=0, _self=cmd)""" % (Name))
461 PMLCmds.append("""cmd.set_name("%s_e_chg", "%s")""" % (Name, ContactPotentialName))
462
463 if DisplayAs is not None:
464 PMLCmds.append("""cmd.show("%s", "(%s)")""" % (DisplayAs, ContactPotentialName))
465
466 if re.match("^Cavities$", Mode, re.I):
467 if SurfaceCavityMode is not None:
468 PMLCmds.append("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (SurfaceCavityMode, ContactPotentialName))
469
470 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(ContactPotentialName, Enable = True))
471
472 PMLCmds.append("""cmd.set_name("%s_e_map", "%s")""" % (Name, MapName))
473 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MapName, Enable = False))
474
475 PMLCmds.append("""cmd.set_name("%s_e_pot", "%s")""" % (Name, LegendName))
476 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(LegendName, Enable = False))
477
478 if VolumeName is not None:
479 PMLCmds.append("""cmd.volume("%s", "%s", "%s", "(%s)")""" % (VolumeName, MapName, "esp", Name))
480 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(VolumeName, Enable = False))
481
482 # Delete name and take it out from the group membership. It is
483 # is already part of ContactPotential object.
484 PMLCmds.append("""cmd.delete("%s")""" % (Name))
485 ElectrostaticsGroupMembers.pop(0)
486
487 PML = "\n".join(PMLCmds)
488
489 OutFH.write("\n%s\n" % PML)
490
491 # Setup group...
492 GenerateAndWritePMLForGroup(OutFH, ElectrostaticsGroupName, ElectrostaticsGroupMembers, False, "close")
493
494 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable = False, Action = "close"):
495 """Generate and write PML for group."""
496
497 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
498 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
499 OutFH.write("%s\n" % PML)
500
501 def GeneratePyMOLSessionFile():
502 """Generate PME file from PML file."""
503
504 PSEOutfile = OptionsInfo["PSEOutfile"]
505 PMLOutfile = OptionsInfo["PMLOutfile"]
506
507 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
508
509 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
510
511 if not os.path.exists(PSEOutfile):
512 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
513
514 if not OptionsInfo["PMLOut"]:
515 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
516 os.remove(PMLOutfile)
517
518 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
519 """Delete empty PyMOL objects."""
520
521 if OptionsInfo["AllowEmptyObjects"]:
522 return
523
524 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
525 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
526 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
527
528 # Delete any chain level objects...
529 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
530 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
531
532 # Delete residue type objects...
533 DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
534
535 def DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
536 """Delete empty chain residue objects."""
537
538 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
539 return
540
541 ResiduesGroupIDPrefix = "ChainAloneResidues"
542 for GroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
543 GroupID = re.sub("_", "", GroupType)
544
545 ResiduesGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, GroupID)
546 GroupName = PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID]
547
548 GroupObjectNamesList = []
549
550 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, GroupID)
551 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
552 GroupObjectNamesList.append(ResiduesObjectName)
553
554 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, GroupID)
555 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
556 GroupObjectNamesList.append(ResiduesSurfaceObjectName)
557
558 GroupObjectNames = ",".join(GroupObjectNamesList)
559 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupObjectNames, GroupName)
560
561 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
562 """Write PML to check and delete empty PyMOL objects."""
563
564 if ParentObjectName is None:
565 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
566 else:
567 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
568
569 OutFH.write("%s\n" % PML)
570
571 def SetupPyMOLObjectNames(FileIndex):
572 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
573 chains and ligands present in input file.
574 """
575
576 PyMOLObjectNames = {}
577 PyMOLObjectNames["Chains"] = {}
578 PyMOLObjectNames["Ligands"] = {}
579
580 # Setup groups and objects for complex...
581 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
582
583 # Setup groups and objects for chain...
584 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
585 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
586 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
587
588 # Setup groups and objects for ligand...
589 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
590 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
591
592 return PyMOLObjectNames
593
594 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
595 """Setup groups and objects for complex."""
596
597 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
598
599 PDBGroupName = "%s" % PDBFileRoot
600 PyMOLObjectNames["PDBGroup"] = PDBGroupName
601 PyMOLObjectNames["PDBGroupMembers"] = []
602
603 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
604 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
605 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
606
607 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
608 if OptionsInfo["SurfaceComplex"]:
609 PyMOLObjectNames["ComplexHydrophobicSurface"] = "%s.Surface" % ComplexGroupName
610
611 PyMOLObjectNames["ComplexGroupMembers"] = []
612 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
613 if OptionsInfo["SurfaceComplex"]:
614 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexHydrophobicSurface"])
615
616 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
617 """Setup groups and objects for chain."""
618
619 PDBGroupName = PyMOLObjectNames["PDBGroup"]
620
621 PyMOLObjectNames["Chains"][ChainID] = {}
622 PyMOLObjectNames["Ligands"][ChainID] = {}
623
624 # Set up chain group and chain objects...
625 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
626 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
627 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
628 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
629
630 # Setup chain complex group and objects...
631 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
632 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
633 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
634
635 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
636
637 Name = "%s.Complex" % (ChainComplexGroupName)
638 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = Name
639 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
640
641 if OptionsInfo["SurfaceChainComplex"]:
642 Name = "%s.Surface" % (ChainComplexGroupName)
643 PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"] = Name
644 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
645
646 # Setup up a group for individual chains...
647 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
648 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
649 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
650
651 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
652
653 Name = "%s.Chain" % (ChainAloneGroupName)
654 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
655 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
656
657 if GetChainAloneResidueTypesStatus(FileIndex, ChainID):
658 # Setup residue type group and its subgroups...
659 ResiduesGroupName = "%s.Residues" % (ChainAloneGroupName)
660
661 ResiduesGroupIDPrefix = "ChainAloneResidues"
662 ResiduesGroupID = "%sGroup" % ResiduesGroupIDPrefix
663
664 # Add residue group to chain alone group...
665 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID] = ResiduesGroupName
666 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(ResiduesGroupName)
667
668 # Initialize residue group members...
669 ResiduesGroupMembersID = "%sGroupMembers" % ResiduesGroupIDPrefix
670 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID] = []
671
672 # Setup residues sub groups and its members...
673 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
674 SubGroupID = re.sub("_", "", SubGroupType)
675
676 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
677 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
678
679 # Add sub group to residues group...
680 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID] = ResiduesSubGroupName
681 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
682
683 # Initialize sub group members...
684 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
685 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID] = []
686
687 # Add sub group members to subgroup...
688 for MemberType in ["Residues", "Surface"]:
689 MemberID = re.sub("_", "", MemberType)
690
691 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
692 SubGroupMemberID = "%s%s%s" % (ResiduesGroupIDPrefix, SubGroupID, MemberID)
693
694 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
695 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID].append(SubGroupMemberName)
696
697 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
698 # Setup cavity and surface groups...
699 for SubGroupType in ["Cavities", "Surface"]:
700 SubGroupName = "%s.%s" % (ChainAloneGroupName, SubGroupType)
701 SubGroupID = "ChainAlone%sGroup" % (SubGroupType)
702 SubGroupMembersID = "%sMembers" % (SubGroupID)
703
704 PyMOLObjectNames["Chains"][ChainID][SubGroupID] = SubGroupName
705 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SubGroupName)
706
707 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID] = []
708
709 # Setup a generic color surface...
710 SurfaceName = "%s.Surface" % (SubGroupName)
711 SurfaceID = "%sSurface" % (SubGroupID)
712 PyMOLObjectNames["Chains"][ChainID][SurfaceID] = SurfaceName
713 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(SurfaceName)
714
715 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
716 # Setup hydrophobicity surface...
717 HydrophobicSurfaceName = "%s.Hydrophobicity" % (SubGroupName)
718 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SubGroupID)
719 PyMOLObjectNames["Chains"][ChainID][HydrophobicSurfaceID] = HydrophobicSurfaceName
720 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(HydrophobicSurfaceName)
721
722 # Setup hydrophobicity and charge surface...
723 HydrophobicChargeSurfaceName = "%s.Hydrophobicity_Charge" % (SubGroupName)
724 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SubGroupID)
725 PyMOLObjectNames["Chains"][ChainID][HydrophobicChargeSurfaceID] = HydrophobicChargeSurfaceName
726 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(HydrophobicChargeSurfaceName)
727
728 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
729 # Setup electrostatics group...
730 ElectrostaticsGroupName = "%s.Vacuum_Electrostatics" % (SubGroupName)
731 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SubGroupID)
732 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SubGroupID)
733
734 PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupID] = ElectrostaticsGroupName
735 PyMOLObjectNames["Chains"][ChainID][SubGroupMembersID].append(ElectrostaticsGroupName)
736
737 # Setup electrostatics group members...
738 PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupMembersID] = []
739
740 for MemberType in ["Chain", "Contact_Potential", "Map", "Legend"]:
741 MemberID = re.sub("_", "", MemberType)
742
743 Name = "%s.%s" % (ElectrostaticsGroupName, MemberType)
744 NameID = "%s%s" % (ElectrostaticsGroupID, MemberID)
745
746 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
747 PyMOLObjectNames["Chains"][ChainID][ElectrostaticsGroupMembersID].append(Name)
748
749 # Setup solvent and inorganic objects for chain...
750 for NameID in ["Solvent", "Inorganic"]:
751 Name = "%s.%s" % (ChainGroupName, NameID)
752 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
753 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
754
755 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
756 """Stetup groups and objects for ligand."""
757
758 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
759
760 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
761
762 # Setup a chain level ligand group...
763 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
764 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
765 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
766
767 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
768
769 # Set up ligand group and its members...
770 GroupName = "%s.Ligand" % (ChainLigandGroupName)
771 GroupNameID = "LigandGroup"
772 GroupMembersID = "LigandGroupMembers"
773
774 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
775 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
776
777 LigandName = "%s.Ligand" % (GroupName)
778 LigandNameID = "Ligand"
779 PyMOLObjectNames["Ligands"][ChainID][LigandID][LigandNameID] = LigandName
780
781 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
782 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(LigandName)
783
784 # Add ball and stick...
785 BallAndStickName = "%s.BallAndStick" % (GroupName)
786 BallAndStickID = "LigandBallAndStick"
787 PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickID] = BallAndStickName
788 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(BallAndStickName)
789
790 def RetrieveInfilesInfo():
791 """Retrieve information for input files."""
792
793 InfilesInfo = {}
794
795 InfilesInfo["InfilesNames"] = []
796 InfilesInfo["InfilesRoots"] = []
797 InfilesInfo["ChainsAndLigandsInfo"] = []
798
799 for Infile in OptionsInfo["InfilesNames"]:
800 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
801 InfileRoot = FileName
802
803 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
804
805 InfilesInfo["InfilesNames"].append(Infile)
806 InfilesInfo["InfilesRoots"].append(InfileRoot)
807 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
808
809 OptionsInfo["InfilesInfo"] = InfilesInfo
810
811 def RetrieveRefFileInfo():
812 """Retrieve information for ref file."""
813
814 RefFileInfo = {}
815 if not OptionsInfo["Align"]:
816 OptionsInfo["RefFileInfo"] = RefFileInfo
817 return
818
819 RefFile = OptionsInfo["RefFileName"]
820
821 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
822 RefFileRoot = FileName
823
824 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
825 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
826 else:
827 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
828 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
829
830 RefFileInfo["RefFileName"] = RefFile
831 RefFileInfo["RefFileRoot"] = RefFileRoot
832 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
833 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
834
835 OptionsInfo["RefFileInfo"] = RefFileInfo
836
837 def ProcessChainAndLigandIDs():
838 """Process specified chain and ligand IDs for infiles."""
839
840 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
841
842 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
843 MiscUtil.PrintInfo("\nProcessing specified chain and ligand IDs for input file %s..." % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex])
844
845 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
846 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], "-l, --ligandIDs", OptionsInfo["LigandIDs"])
847 ProcessResidueTypesAndSurfaceOptions(FileIndex, SpecifiedChainsAndLigandsInfo)
848 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
849
850 CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo)
851
852 def ProcessResidueTypesAndSurfaceOptions(FileIndex, SpecifiedChainsAndLigandsInfo):
853 """Process residue types and surface options for chains."""
854
855 SpecifiedChainsAndLigandsInfo["ChainSurfaces"] = {}
856 SpecifiedChainsAndLigandsInfo["SurfaceChain"] = {}
857 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"] = {}
858
859 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"] = {}
860
861 # Load infile...
862 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
863 MolName = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
864 pymol.cmd.load(Infile, MolName)
865
866 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
867 AminoAcidsPresent = PyMOLUtil.AreAminoAcidResiduesPresent(MolName, ChainID)
868
869 # Process surfaces for chains...
870 if re.match("^auto$", OptionsInfo["SurfaceChain"], re.I):
871 SurfaceChain = True if AminoAcidsPresent else False
872 else:
873 SurfaceChain = True if re.match("^yes$", OptionsInfo["SurfaceChain"], re.I) else False
874 SpecifiedChainsAndLigandsInfo["SurfaceChain"][ChainID] = SurfaceChain
875
876 if re.match("^auto$", OptionsInfo["SurfaceChainElectrostatics"], re.I):
877 SurfaceChainElectrostatics = True if AminoAcidsPresent else False
878 else:
879 SurfaceChainElectrostatics = True if re.match("^yes$", OptionsInfo["SurfaceChainElectrostatics"], re.I) else False
880 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"][ChainID] = SurfaceChainElectrostatics
881
882 # A generic color surface is always created...
883 ChainSurfaces = True
884 SpecifiedChainsAndLigandsInfo["ChainSurfaces"][ChainID] = ChainSurfaces
885
886 # Process residue types for chains...
887 if re.match("^auto$", OptionsInfo["ResidueTypesChain"], re.I):
888 ResidueTypesChain = True if AminoAcidsPresent else False
889 else:
890 ResidueTypesChain = True if re.match("^yes$", OptionsInfo["ResidueTypesChain"], re.I) else False
891 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"][ChainID] = ResidueTypesChain
892
893 # Delete loaded object...
894 pymol.cmd.delete(MolName)
895
896 def GetChainAloneResidueTypesStatus(FileIndex, ChainID):
897 """Get status of residue types for chain alone object."""
898
899 Status = True if OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesChain"][ChainID] else False
900
901 return Status
902
903 def GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
904 """Get status of surfaces present in chain alone object."""
905
906 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSurfaces"][ChainID]
907
908 def GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
909 """Get status of hydrophobic surfaces for chain alone object."""
910
911 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChain"][ChainID]
912
913 def GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
914 """Get status of electrostatics surfaces for chain alone object."""
915
916 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainElectrostatics"][ChainID]
917
918 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
919 """Check presence of valid ligand IDs."""
920
921 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
922
923 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
924 if len (SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
925 MiscUtil.PrintInfo("Chain ID: %s; Specified LigandIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID])))
926 else:
927 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
928 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))
929
930 def RetrieveFirstChainID(FileIndex):
931 """Get first chain ID."""
932
933 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
934
935 FirstChainID = None
936 if len(ChainsAndLigandsInfo["ChainIDs"]):
937 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
938
939 return FirstChainID
940
941 def ProcessResidueTypes():
942 """Process residue types."""
943
944 ResidueTypesNamesInfo, ResidueTypesParamsInfo = PyMOLUtil.ProcessResidueTypesOptionsInfo("-r, --residueTypes", OptionsInfo["ResidueTypes"])
945 OptionsInfo["ResidueTypesNames"] = ResidueTypesNamesInfo
946 OptionsInfo["ResidueTypesParams"] = ResidueTypesParamsInfo
947
948 def ProcessSurfaceAtomTypesColors():
949 """Process surface atom types colors."""
950
951 AtomTypesColorNamesInfo = PyMOLUtil.ProcessSurfaceAtomTypesColorsOptionsInfo("--surfaceAtomTypesColors", OptionsInfo["SurfaceAtomTypesColors"])
952 OptionsInfo["AtomTypesColorNames"] = AtomTypesColorNamesInfo
953
954 def ProcessOptions():
955 """Process and validate command line arguments and options."""
956
957 MiscUtil.PrintInfo("Processing options...")
958
959 # Validate options...
960 ValidateOptions()
961
962 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
963 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
964 OptionsInfo["AlignMode"] = Options["--alignMode"]
965
966 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
967
968 OptionsInfo["CavityCulled"] = True if re.match("^Yes$", Options["--cavityCulled"], re.I) else False
969 OptionsInfo["SurfaceCavityMode"] = 2 if OptionsInfo["CavityCulled"] else 1
970
971 OptionsInfo["CavityCullSize"] = float(Options["--cavityCullSize"])
972 OptionsInfo["CavityCutoff"] = float(Options["--cavityCutoff"])
973 OptionsInfo["CavityRadius"] = float(Options["--cavityRadius"])
974
975 OptionsInfo["Infiles"] = Options["--infiles"]
976 OptionsInfo["InfilesNames"] = Options["--infileNames"]
977
978 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
979 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
980 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
981 else:
982 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
983
984 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
985
986 OptionsInfo["Overwrite"] = Options["--overwrite"]
987 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
988
989 OptionsInfo["Outfile"] = Options["--outfile"]
990 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
991 OptionsInfo["PSEOut"] = False
992 if re.match("^pml$", FileExt, re.I):
993 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
994 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
995 elif re.match("^pse$", FileExt, re.I):
996 OptionsInfo["PSEOut"] = True
997 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
998 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
999 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
1000 MiscUtil.PrintError("The intermediate output file to be generated, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again." % OptionsInfo["PMLOutfile"] )
1001
1002 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
1003
1004 OptionsInfo["ResidueTypesChain"] = Options["--residueTypesChain"]
1005 OptionsInfo["ResidueTypes"] = Options["--residueTypes"]
1006 ProcessResidueTypes()
1007
1008 OptionsInfo["SurfaceChain"] = Options["--surfaceChain"]
1009 OptionsInfo["SurfaceChainElectrostatics"] = Options["--surfaceChainElectrostatics"]
1010
1011 OptionsInfo["SurfaceChainComplex"] = True if re.match("^Yes$", Options["--surfaceChainComplex"], re.I) else False
1012 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
1013
1014 # Retrieve surface colors for generic surfaces..
1015 SurfaceColors = re.sub(" ", "", Options["--surfaceColors"])
1016 SurfaceColorsWords = SurfaceColors.split(",")
1017 if len(SurfaceColorsWords) != 2:
1018 MiscUtil.PrintError("The number of comma delinited color names, %d, specified using \"--surfaceColors\" option, \"%s\", must be a 2." % (len(SurfaceColorsWords), Options["--surfaceColors"]))
1019 OptionsInfo["SurfaceColors"] = SurfaceColors
1020 OptionsInfo["SurfaceCavityColor"] = SurfaceColorsWords[0]
1021 OptionsInfo["SurfaceColor"] = SurfaceColorsWords[1]
1022
1023 OptionsInfo["SurfaceColorPalette"] = Options["--surfaceColorPalette"]
1024 OptionsInfo["SurfaceAtomTypesColors"] = Options["--surfaceAtomTypesColors"]
1025 ProcessSurfaceAtomTypesColors()
1026
1027 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
1028
1029 RetrieveInfilesInfo()
1030 RetrieveRefFileInfo()
1031
1032 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
1033 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
1034
1035 ProcessChainAndLigandIDs()
1036
1037 def RetrieveOptions():
1038 """Retrieve command line arguments and options."""
1039
1040 # Get options...
1041 global Options
1042 Options = docopt(_docoptUsage_)
1043
1044 # Set current working directory to the specified directory...
1045 WorkingDir = Options["--workingdir"]
1046 if WorkingDir:
1047 os.chdir(WorkingDir)
1048
1049 # Handle examples option...
1050 if "--examples" in Options and Options["--examples"]:
1051 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
1052 sys.exit(0)
1053
1054 def ValidateOptions():
1055 """Validate option values."""
1056
1057 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
1058 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
1059 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
1060
1061 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
1062
1063 MiscUtil.ValidateOptionTextValue("--cavityCulled", Options["--cavityCulled"], "yes no")
1064 MiscUtil.ValidateOptionFloatValue("--cavityCullSize", Options["--cavityCullSize"], {">": 0.0})
1065 MiscUtil.ValidateOptionFloatValue("--cavityCutoff", Options["--cavityCutoff"], {">": 0.0})
1066 MiscUtil.ValidateOptionFloatValue("--cavityRadius", Options["--cavityRadius"], {">": 0.0})
1067
1068 # Expand infiles to handle presence of multiple input files...
1069 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
1070 if not len(InfileNames):
1071 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
1072
1073 # Validate file extensions...
1074 for Infile in InfileNames:
1075 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
1076 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
1077 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
1078 Options["--infileNames"] = InfileNames
1079
1080 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
1081 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
1082
1083 if re.match("^yes$", Options["--align"], re.I):
1084 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1085 AlignRefFile = Options["--alignRefFile"]
1086 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
1087 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
1088 MiscUtil.ValidateOptionsDistinctFileNames("--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"])
1089
1090 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
1091
1092 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
1093 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
1094
1095 MiscUtil.ValidateOptionTextValue("--residueTypesChain", Options["--residueTypesChain"], "yes no auto")
1096
1097 MiscUtil.ValidateOptionTextValue("--surfaceChain", Options["--surfaceChain"], "yes no auto")
1098 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
1099 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no")
1100 MiscUtil.ValidateOptionTextValue("--surfaceChainElectrostatics", Options["--surfaceChainElectrostatics"], "yes no auto")
1101
1102 MiscUtil.ValidateOptionTextValue("--surfaceColorPalette", Options["--surfaceColorPalette"], "RedToWhite WhiteToGreen")
1103 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
1104
1105 # Setup a usage string for docopt...
1106 _docoptUsage_ = """
1107 PyMOLVisualizeCavities.py - Visualize cavities and pockets in macromolecules
1108
1109 Usage:
1110 PyMOLVisualizeCavities.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
1111 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
1112 [--allowEmptyObjects <yes or no>] [--cavityCulled <Yes or No>]
1113 [--cavityCullSize <number>] [--cavityCutoff <number>] [--cavityRadius <number>]
1114 [--chainIDs <First, All or ID1,ID2...>] [--labelFontID <number>]
1115 [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All or ID1,ID2...> ] [--PMLOut <yes or no>]
1116 [--residueTypes <Type,Color,ResNames,...>] [--residueTypesChain <yes or no>]
1117 [--surfaceChain <yes or no>] [--surfaceChainElectrostatics <yes or no>]
1118 [--surfaceChainComplex <yes or no>] [--surfaceComplex <yes or no>]
1119 [--surfaceAtomTypesColors <ColorType,ColorSpec,...>]
1120 [--surfaceColors <ColorName1,ColorName2>] [--surfaceColorPalette <RedToWhite or WhiteToGreen>]
1121 [--surfaceTransparency <number>] [--overwrite] [-w <dir>] -i <infile1,infile2,infile3...> -o <outfile>
1122 PyMOLVisualizeCavities.py -h | --help | -e | --examples
1123
1124 Description:
1125 Generate PyMOL visualization files for viewing cavities and pockets in
1126 macromolecules including proteins and nucleic acids.
1127
1128 The supported input file format are: PDB (.pdb), CIF (.cif)
1129
1130 The supported output file formats are: PyMOL script file (.pml), PyMOL session
1131 file (.pse)
1132
1133 A variety of PyMOL groups and objects may be created for visualization of
1134 cavities and pockets in macromolecules. These groups and objects correspond
1135 to complexes, surfaces, chains, ligands, inorganics, cavities, and pockets.
1136 A complete hierarchy of all possible PyMOL groups and objects is shown below:
1137
1138 <PDBFileRoot>
1139 .Complex
1140 .Complex
1141 .Surface
1142 .Chain<ID>
1143 .Complex
1144 .Complex
1145 .Surface
1146 .Chain
1147 .Chain
1148 .Residues
1149 .Aromatic
1150 .Residues
1151 .Surface
1152 .Hydrophobic
1153 .Residues
1154 .Surface
1155 .Polar
1156 .Residues
1157 .Surface
1158 .Positively_Charged
1159 .Residues
1160 .Surface
1161 .Negatively_Charged
1162 .Residues
1163 .Surface
1164 .Other
1165 .Residues
1166 .Surface
1167 .Cavities
1168 .Surface
1169 .Hydrophobicity
1170 .Hydrophobicity_Charge
1171 .Vacuum_Electrostatics
1172 .Contact_Potentials
1173 .Map
1174 .Legend
1175 .Surface
1176 .Surface
1177 .Hydrophobicity
1178 .Hydrophobicity_Charge
1179 .Vacuum_Electrostatics
1180 .Contact_Potentials
1181 .Map
1182 .Legend
1183 .Solvent
1184 .Inorganic
1185 .Ligand<ID>
1186 .Ligand
1187 .Ligand
1188 .BallAndStick
1189 .Ligand<ID>
1190 .Ligand
1191 ... ... ...
1192 .Chain<ID>
1193 ... ... ...
1194 .Ligand<ID>
1195 ... ... ...
1196 .Ligand<ID>
1197 ... ... ...
1198 .Chain<ID>
1199 ... ... ...
1200 <PDBFileRoot>
1201 .Complex
1202 ... ... ...
1203 .Chain<ID>
1204 ... ... ...
1205 .Ligand<ID>
1206 ... ... ...
1207 .Ligand<ID>
1208 ... ... ...
1209 .Chain<ID>
1210 ... ... ...
1211
1212 The hydrophobic and electrostatic surfaces are not created for complete complex
1213 and chain complex in input file(s) by default. A word to the wise: The creation of
1214 surface objects may slow down loading of PML file and generation of PSE file, based
1215 on the size of input complexes. The generation of PSE file may also fail.
1216
1217 Options:
1218 -a, --align <yes or no> [default: no]
1219 Align input files to a reference file before visualization.
1220 --alignMethod <align, cealign, super> [default: super]
1221 Alignment methodology to use for aligning input files to a
1222 reference file.
1223 --alignMode <FirstChain or Complex> [default: FirstChain]
1224 Portion of input and reference files to use for spatial alignment of
1225 input files against reference file. Possible values: FirstChain or
1226 Complex.
1227
1228 The FirstChain mode allows alignment of the first chain in each input
1229 file to the first chain in the reference file along with moving the rest
1230 of the complex to coordinate space of the reference file. The complete
1231 complex in each input file is aligned to the complete complex in reference
1232 file for the Complex mode.
1233 --alignRefFile <filename> [default: FirstInputFile]
1234 Reference input file name. The default is to use the first input file
1235 name specified using '-i, --infiles' option.
1236 --allowEmptyObjects <yes or no> [default: no]
1237 Allow creation of empty PyMOL objects corresponding to solvent and
1238 inorganic atom selections across chains and ligands in input file(s). By
1239 default, the empty objects are marked for deletion.
1240 --cavityCulled <Yes or No> [default: Yes]
1241 Cull cavities and pockets. The cavities and pockets are culled by default.
1242 This value is used to set of PyMOL parameter surface_cavity_mode as
1243 shown below:
1244
1245 No: 1 (Cavities and Pockets Only)
1246 Yes: 2 (Cavities and Pockets Culled)
1247
1248 --cavityCullSize <number> [default: 2.0]
1249 Approximate dimension of the cavity in Angstroms for detecting cavities and
1250 pockets in the interior of a macromolecule. The higher value makes PyMOL less
1251 sensitive to detection of smaller cavities.
1252 --cavityCutoff <number> [default: 3.0]
1253 Cavity cutoff in terms of number of solvent radii for detecting cavities
1254 and pockets. This value is used to set value of PyMOL parameter
1255 surface_cavity_cutoff.
1256 --cavityRadius <number> [default: 5.0]
1257 Cavity detection radius in terms of number of solvent radii for detecting
1258 cavities and pockets. The detection of larger pockets is ignored for lower
1259 value for the cavity radius. This value is used to set of PyMOL parameter
1260 surface_cavity_radius.
1261 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
1262 List of chain IDs to use for visualizing macromolecules. Possible values:
1263 First, All, or a comma delimited list of chain IDs. The default is to use the
1264 chain ID for the first chain in each input file.
1265 -e, --examples
1266 Print examples.
1267 -h, --help
1268 Print this help message.
1269 -i, --infiles <infile1,infile2,infile3...>
1270 Input file names.
1271 --ignoreHydrogens <yes or no> [default: yes]
1272 Ignore hydrogens for ligand views.
1273 --labelFontID <number> [default: 7]
1274 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
1275 The specified value must be a valid PyMOL font ID. No validation is
1276 performed. The complete lists of valid font IDs is available at:
1277 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
1278 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
1279 -l, --ligandIDs <Largest, All or ID1,ID2...> [default: All]
1280 List of ligand IDs to show in chains during visualizing of cavities in
1281 macromolecules. Possible values: Largest, All, or a comma delimited
1282 list of ligand IDs. The default is to show all ligands present in all or
1283 specified chains in each input file.
1284
1285 Ligands are identified using organic selection operator available in PyMOL.
1286 It'll also identify buffer molecules as ligands. The largest ligand contains
1287 the highest number of heavy atoms.
1288 -o, --outfile <outfile>
1289 Output file name.
1290 -p, --PMLOut <yes or no> [default: yes]
1291 Save PML file during generation of PSE file.
1292 -r, --residueTypes <Type,Color,ResNames,...> [default: auto]
1293 Residue types, colors, and names to generate for residue groups during
1294 '--residueTypesChain' option. It is only valid for amino acids.
1295
1296 It is a triplet of comma delimited list of amino acid residues type, residues
1297 color, and a space delimited list three letter residue names.
1298
1299 The default values for residue type, color, and name triplets are shown
1300 below:
1301
1302 Aromatic,brightorange,HIS PHE TRP TYR,
1303 Hydrophobic,orange,ALA GLY VAL LEU ILE PRO MET,
1304 Polar,palegreen,ASN GLN SER THR CYS,
1305 Positively_Charged,marine,ARG LYS,
1306 Negatively_Charged,red,ASP GLU
1307
1308 The color name must be a valid PyMOL name. No validation is performed.
1309 An amino acid name may appear across multiple residue types. All other
1310 residues are grouped under 'Other'.
1311 --residueTypesChain <yes or no> [default: auto]
1312 Chain residue types. The residue groups are generated using residue types,
1313 colors, and names specified by '--residueTypes' option. It is only valid for
1314 amino acids. By default, the residue type groups are automatically created
1315 for chains containing amino acids and skipped for chains only containing
1316 nucleic acids.
1317 --surfaceChain <yes or no> [default: auto]
1318 Surfaces around individual chain colored by hydrophobicity alone and
1319 both hydrophobicity and charge. The hydrophobicity surface is colored
1320 at residue level using Eisenberg hydrophobicity scale for residues and color
1321 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
1322 charge surface is colored [ Ref 140 ] at atom level using colors specified for
1323 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
1324 simultaneous mapping of hyrophobicity and charge values on the surfaces.
1325
1326 This option is only valid for amino acids. By default, both surfaces are
1327 automatically created for chains containing amino acids and skipped for
1328 chains containing only nucleic acids.
1329
1330 In addition, generic surfaces colored by '--surfaceColor' are always created
1331 for chain residues containing amino acids and nucleic acids.
1332 --surfaceChainElectrostatics <yes or no> [default: no]
1333 Vacuum electrostatics contact potential surface around individual
1334 chain. A word to the wise from PyMOL documentation: The computed protein
1335 contact potentials are only qualitatively useful, due to short cutoffs,
1336 truncation, and lack of solvent "screening".
1337
1338 This option is only valid for amino acids. By default, the electrostatics surface
1339 is automatically created for chains containing amino acids and
1340 skipped for chains containing only nucleic acids.
1341 --surfaceChainComplex <yes or no> [default: no]
1342 Hydrophobic surface around chain complex. The surface is colored by
1343 hydrophobicity. It is only valid for amino acids.
1344 --surfaceComplex <yes or no> [default: no]
1345 Hydrophobic surface around complete complex. The surface is colored by
1346 hydrophobicity. It is only valid for amino acids.
1347 --surfaceAtomTypesColors <ColorType,ColorSpec,...> [default: auto]
1348 Atom colors for generating surfaces colored by hyrophobicity and charge
1349 around chains and pockets in proteins. It's a pairwise comma delimited list
1350 of atom color type and color specification for goups of atoms.
1351
1352 The default values for color types [ Ref 140 ] along wth color specifications
1353 are shown below:
1354
1355 HydrophobicAtomsColor, yellow,
1356 NegativelyChargedAtomsColor, red,
1357 PositivelyChargedAtomsColor, blue,
1358 OtherAtomsColor, gray90
1359
1360 The color names must be valid PyMOL names.
1361
1362 The color values may also be specified as space delimited RGB triplets:
1363
1364 HydrophobicAtomsColor, 0.95 0.78 0.0,
1365 NegativelyChargedAtomsColor, 1.0 0.4 0.4,
1366 PositivelyChargedAtomsColor, 0.2 0.5 0.8,
1367 OtherAtomsColor, 0.95 0.95 0.95
1368
1369 --surfaceColors <ColorName1,ColorName2> [default: salmon,lightblue]
1370 Color names for surfaces around cavities and chains. These colors are not
1371 used for surfaces and cavities colored by hydrophobicity and charge. The
1372 color names must be valid PyMOL names.
1373 --surfaceColorPalette <RedToWhite or WhiteToGreen> [default: RedToWhite]
1374 Color palette for hydrophobic surfaces around chains and pockets in proteins.
1375 Possible values: RedToWhite or WhiteToGreen from most hydrophobic amino
1376 acid to least hydrophobic. The colors values for amino acids are taken from
1377 color_h script available as part of the Script Library at PyMOL Wiki.
1378 --surfaceTransparency <number> [default: 0.25]
1379 Surface transparency for molecular surfaces.
1380 --overwrite
1381 Overwrite existing files.
1382 -w, --workingdir <dir>
1383 Location of working directory which defaults to the current directory.
1384
1385 Examples:
1386 To visualize cavities in the first chain along with the largest ligand in the
1387 first chain, solvents, and inorganics, in a PDB file, and generate a PML
1388 file, type:
1389
1390 % PyMOLVisualizeCavities.py -i Sample4.pdb -o Sample4.pml
1391
1392 To visualize cavities in all chain along with all ligands, solvents,
1393 and inorganics, in a PDB file, and generate a PML file, type:
1394
1395 % PyMOLVisualizeCavities.py -c All -l All -i Sample4.pdb
1396 -o Sample4.pml
1397
1398 To visualize cavities in the first chain at a specific cavity radius and cutoff
1399 using specifc colors for surfaces corresponding to cavities and non-cavities,
1400 and generate a PML file, type:
1401
1402 % PyMOLVisualizeCavities.py --cavityRadius 3 --cavityCutoff 5
1403 --surfaceColors "red,blue" -i Sample4.pdb -o Sample4.pml
1404
1405 To visualize cavities in the first chain along with the largest ligand in the
1406 first chain, solvents, and inorganics, in PDB files, along with aligning first
1407 chain in each input file to the first chain inand generate a PML file, type:
1408
1409 % PyMOLVisualizeCavities.py --align yes
1410 -i "Sample5.pdb,Sample6.pdb,Sample7.pdb"
1411 -o SampleOut.pml
1412
1413 Author:
1414 Manish Sud(msud@san.rr.com)
1415
1416 See also:
1417 DownloadPDBFiles.pl, PyMOLVisualizeCryoEMDensity.py,
1418 PyMOLVisualizeElectronDensity.py, PyMOLVisualizeInterfaces.py
1419 PyMOLVisualizeMacromolecules.py, PyMOLVisualizeSurfaceAndBuriedResidues.py
1420
1421 Copyright:
1422 Copyright (C) 2024 Manish Sud. All rights reserved.
1423
1424 The functionality available in this script is implemented using PyMOL, a
1425 molecular visualization system on an open source foundation originally
1426 developed by Warren DeLano.
1427
1428 This file is part of MayaChemTools.
1429
1430 MayaChemTools is free software; you can redistribute it and/or modify it under
1431 the terms of the GNU Lesser General Public License as published by the Free
1432 Software Foundation; either version 3 of the License, or (at your option) any
1433 later version.
1434
1435 """
1436
1437 if __name__ == "__main__":
1438 main()
