1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeMacromolecules.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 GenerateMacromolecularVisualization()
79
80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
82
83 def GenerateMacromolecularVisualization():
84 """Generate macromolecular visualization."""
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 # Setup trajectories views...
112 if GetTrajectoriesStatus(FileIndex):
113 WriteTrajectoriesView(OutFH, FileIndex, PyMOLObjectNames)
114
115 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
116 FirstChain = True
117 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
118 if FirstComplex and FirstChain:
119 FirstComplexFirstChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
120
121 WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
122
123 # Setup ligand views...
124 FirstLigand = True
125 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
126 WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID)
127
128 # Set up ligand level group...
129 Enable, Action = [False, "close"]
130 if FirstLigand:
131 FirstLigand = False
132 Enable, Action = [True, "open"]
133 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"], PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"], Enable, Action)
134
135 # Setup docked poses views...
136 if GetChainAloneDockedPosesStatus(FileIndex, ChainID):
137 WriteChainDockedPosesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
138
139 # Setup Chain level group...
140 Enable, Action = [False, "close"]
141 if FirstChain:
142 FirstChain = False
143 Enable, Action = [True, "open"]
144 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"], Enable, Action)
145
146 # Set up complex level group...
147 Enable, Action = [False, "close"]
148 if FirstComplex:
149 FirstComplex = False
150 Enable, Action = [True, "open"]
151 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["PDBGroup"], PyMOLObjectNames["PDBGroupMembers"], Enable, Action)
152
153 # Delete empty PyMOL objects...
154 DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames)
155
156 if OptionsInfo["Align"]:
157 DeleteAlignReference(OutFH)
158
159 if FirstComplexFirstChainName is not None:
160 OutFH.write("""\ncmd.orient("%s", animate = -1)\n""" % FirstComplexFirstChainName)
161 else:
162 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
163
164 OutFH.close()
165
166 # Generate PSE file as needed...
167 if OptionsInfo["PSEOut"]:
168 GeneratePyMOLSessionFile()
169
170 def WritePMLHeader(OutFH, ScriptName):
171 """Write out PML header."""
172
173 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
174 OutFH.write("%s\n" % HeaderInfo)
175
176 def WritePyMOLParameters(OutFH):
177 """Write out PyMOL global parameters."""
178
179 PMLCmds = []
180 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
181 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
182 PML = "\n".join(PMLCmds)
183
184 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
185 OutFH.write("%s\n" % PML)
186
187 def WriteAlignReference(OutFH):
188 """Setup object for alignment reference."""
189
190 RefFileInfo = OptionsInfo["RefFileInfo"]
191 RefFile = RefFileInfo["RefFileName"]
192 RefName = RefFileInfo["PyMOLObjectName"]
193
194 PMLCmds = []
195 PMLCmds.append("""cmd.load("%s", "%s")""" % (RefFile, RefName))
196 PMLCmds.append("""cmd.hide("everything", "%s")""" % (RefName))
197 PMLCmds.append("""cmd.disable("%s")""" % (RefName))
198 PML = "\n".join(PMLCmds)
199
200 OutFH.write("""\n""\n"Loading %s and setting up view for align reference..."\n""\n""" % RefFile)
201 OutFH.write("%s\n" % PML)
202
203 def WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames):
204 """Setup alignment of complex to reference."""
205
206 RefFileInfo = OptionsInfo["RefFileInfo"]
207 RefName = RefFileInfo["PyMOLObjectName"]
208
209 ComplexName = PyMOLObjectNames["Complex"]
210
211 if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
212 RefFirstChainID = RefFileInfo["ChainsAndLigandsInfo"]["ChainIDs"][0]
213 RefAlignSelection = "%s and chain %s" % (RefName, RefFirstChainID)
214
215 ComplexFirstChainID = RetrieveFirstChainID(FileIndex)
216 ComplexAlignSelection = "%s and chain %s" % (ComplexName, ComplexFirstChainID)
217 else:
218 RefAlignSelection = RefName
219 ComplexAlignSelection = ComplexName
220
221 PML = PyMOLUtil.SetupPMLForAlignment(OptionsInfo["AlignMethod"], RefAlignSelection, ComplexAlignSelection)
222 OutFH.write("""\n""\n"Aligning %s against reference %s ..."\n""\n""" % (ComplexAlignSelection, RefAlignSelection))
223 OutFH.write("%s\n" % PML)
224
225 def DeleteAlignReference(OutFH):
226 """Delete alignment reference object."""
227
228 RefName = OptionsInfo["RefFileInfo"]["PyMOLObjectName"]
229 OutFH.write("""\n""\n"Deleting alignment reference object %s..."\n""\n""" % RefName)
230 OutFH.write("""cmd.delete("%s")\n""" % RefName)
231
232 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex):
233 """Write out PML for viewing polymer complex."""
234
235 # Setup complex...
236 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
237 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["Complex"], Infile, True)
238 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
239 OutFH.write("%s\n" % PML)
240
241 if OptionsInfo["Align"]:
242 # No need to align complex on to itself...
243 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
244 WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames)
245
246 if OptionsInfo["SurfaceComplex"]:
247 # Setup hydrophobic surface...
248 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["ComplexHydrophobicSurface"], PyMOLObjectNames["Complex"], ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
249 OutFH.write("\n%s\n" % PML)
250
251 # Setup complex group...
252 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close")
253
254 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
255 """Write out PML for viewing chain."""
256
257 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
258
259 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
260
261 # Setup chain complex group view...
262 WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
263
264 # Setup chain view...
265 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
266
267 # Setup chain solvent view...
268 PML = PyMOLUtil.SetupPMLForSolventView(PyMOLObjectNames["Chains"][ChainID]["Solvent"], ChainComplexName, False)
269 OutFH.write("\n%s\n" % PML)
270
271 # Setup chain inorganic view...
272 PML = PyMOLUtil.SetupPMLForInorganicView(PyMOLObjectNames["Chains"][ChainID]["Inorganic"], ChainComplexName, False)
273 OutFH.write("\n%s\n" % PML)
274
275 def WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
276 """Write chain complex views."""
277
278 # Setup chain complex...
279 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
280 PML = PyMOLUtil.SetupPMLForPolymerChainComplexView(ChainComplexName, PyMOLObjectNames["Complex"], ChainID, True)
281 OutFH.write("%s\n" % PML)
282
283 if OptionsInfo["SurfaceChainComplex"]:
284 # Setup hydrophobic surface...
285 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"], ChainComplexName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
286 OutFH.write("\n%s\n" % PML)
287
288 # Setup chain complex group...
289 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"], False, "close")
290
291 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
292 """Write individual chain views."""
293
294 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
295
296 # Setup chain view...
297 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
298 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, True)
299 OutFH.write("\n%s\n" % PML)
300
301 WriteChainAloneBFactorViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
302
303 WriteChainAloneChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
304 WriteChainAloneResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
305
306 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
307 # Setup a generic color surface...
308 PML = PyMOLUtil.SetupPMLForSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"], ChainName, Enable = False, Color = OptionsInfo["SurfaceColor"])
309 OutFH.write("\n%s\n" % PML)
310
311 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
312 # Setup surface colored by hydrophobicity...
313 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"], ChainName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
314 OutFH.write("\n%s\n" % PML)
315
316 # Setup surface colored by hyrdophobicity and charge...
317 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"], ChainName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = None)
318 OutFH.write("\n%s\n" % PML)
319
320 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
321 # Setup electrostatics surface...
322 SelectionObjectName = ChainName
323 ElectrostaticsGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroup"]
324 ElectrostaticsGroupMembers = PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"]
325 WriteSurfaceElectrostaticsView("Surface", OutFH, SelectionObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers, DisplayAs = "cartoon")
326
327 # Setup surface group...
328 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"], True, "open")
329
330 # Setup disulfide group...
331 WriteChainAloneDisulfideBondsView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
332
333 # Setup salt bridges group...
334 WriteChainAloneSaltBridgesView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
335
336 # Setup chain group...
337 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"], True, "close")
338
339 def WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID):
340 """Write out PML for viewing ligand in a chain."""
341
342 for GroupID in ["Ligand", "Pocket", "PocketSolvent", "PocketInorganic"]:
343 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
344 LigandName = PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
345
346 # Setup main object...
347 GroupTypeObjectID = "%s" % (GroupID)
348 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
349
350 if re.match("^Ligand$", GroupID, re.I):
351 OutFH.write("""\n""\n"Setting up views for ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
352 PML = PyMOLUtil.SetupPMLForLigandView(GroupTypeObjectName, ComplexName, LigandID, Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
353 OutFH.write("%s\n" % PML)
354 elif re.match("^Pocket$", GroupID, re.I):
355 OutFH.write("""\n""\n"Setting up views for pocket around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
356 PML = PyMOLUtil.SetupPMLForLigandPocketView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
357 OutFH.write("%s\n" % PML)
358 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], GroupTypeObjectName))
359 elif re.match("^PocketSolvent$", GroupID, re.I):
360 OutFH.write("""\n""\n"Setting up views for solvent in pockect around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
361 PML = PyMOLUtil.SetupPMLForLigandPocketSolventView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
362 OutFH.write("%s\n" % PML)
363 elif re.match("^PocketInorganic$", GroupID, re.I):
364 OutFH.write("""\n""\n"Setting up views for inorganic in pockect around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
365 PML = PyMOLUtil.SetupPMLForLigandPocketInorganicView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
366 OutFH.write("%s\n" % PML)
367
368 # Set up polar contacts...
369 if re.match("^(Pocket|PocketSolvent|PocketInorganic)$", GroupID, re.I):
370 PolarContactsID = "%sPolarContacts" % (GroupID)
371 PolarContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID]
372
373 PolarContactsColor = OptionsInfo["PocketContactsLigandColor"]
374 if re.match("^PocketSolvent$", GroupID, re.I):
375 PolarContactsColor = OptionsInfo["PocketContactsSolventColor"]
376 elif re.match("^PocketInorganic$", GroupID, re.I):
377 PolarContactsColor = OptionsInfo["PocketContactsInorganicColor"]
378
379 PML = PyMOLUtil.SetupPMLForPolarContactsView(PolarContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = PolarContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
380 OutFH.write("\n%s\n" % PML)
381
382 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PolarContactsColor, PolarContactsName))
383
384 if re.match("^PocketInorganic$", GroupID, re.I):
385 # Setup pi cation contacts...
386 PiCationContactsID = "%sPiCationContacts" % (GroupID)
387 PiCationContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID]
388 PiCationContactsColor = OptionsInfo["PocketContactsInorganicPiCationColor"]
389
390 PML = PyMOLUtil.SetupPMLForPiCationContactsView(PiCationContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = PiCationContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
391 OutFH.write("\n%s\n" % PML)
392 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
393
394 if re.match("^Pocket$", GroupID, re.I):
395 # Setup hydrophobic contacts...
396 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
397 HydrophobicContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID]
398 HydrophobicContactsColor = OptionsInfo["PocketContactsLigandHydrophobicColor"]
399
400 PML = PyMOLUtil.SetupPMLForHydrophobicContactsView(HydrophobicContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = HydrophobicContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
401 OutFH.write("\n%s\n" % PML)
402 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HydrophobicContactsColor, HydrophobicContactsName))
403
404 # Setup pi pi contacts...
405 PiPiContactsID = "%sPiPiContacts" % (GroupID)
406 PiPiContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PiPiContactsID]
407 PiPiContactsColor = OptionsInfo["PocketContactsLigandPiPiColor"]
408
409 PML = PyMOLUtil.SetupPMLForPiPiContactsView(PiPiContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = PiPiContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
410 OutFH.write("\n%s\n" % PML)
411 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiPiContactsColor, PiPiContactsName))
412
413 # Setup pi cation contacts...
414 PiCationContactsID = "%sPiCationContacts" % (GroupID)
415 PiCationContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID]
416 PiCationContactsColor = OptionsInfo["PocketContactsLigandPiCationColor"]
417
418 PML = PyMOLUtil.SetupPMLForPiCationContactsView(PiCationContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = PiCationContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
419 OutFH.write("\n%s\n" % PML)
420 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
421
422 # Setup halogen contacts...
423 HalogenContactsID = "%sHalogenContacts" % (GroupID)
424 HalogenContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HalogenContactsID]
425 HalogenContactsColor = OptionsInfo["PocketContactsLigandHalogenColor"]
426
427 PML = PyMOLUtil.SetupPMLForHalogenContactsView(HalogenContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = HalogenContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
428 OutFH.write("\n%s\n" % PML)
429 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HalogenContactsColor, HalogenContactsName))
430
431 # Setup pocket selections...
432 WritePocketSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
433
434 # Setup pocket residues...
435 WritePocketResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
436 WritePocketSurfacesTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
437
438 if re.match("^Ligand$", GroupID, re.I):
439 # Setup ball and stick view...
440 BallAndStickNameID = "%sBallAndStick" % (GroupID)
441 BallAndStickName = PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickNameID]
442 PML = PyMOLUtil.SetupPMLForBallAndStickView(BallAndStickName, GroupTypeObjectName, Enable = False)
443 OutFH.write("\n%s\n" % PML)
444
445 # Setup group...
446 GroupNameID = "%sGroup" % (GroupID)
447 GroupMembersID = "%sGroupMembers" % (GroupID)
448 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
449 GroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID]
450
451 Action = "close"
452 Enable = False
453 if re.match("^(Ligand|Pocket)$", GroupID, re.I):
454 Action = "open"
455 Enable = True
456 GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable, Action)
457
458 def WriteChainDockedPosesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
459 """Write out PML for viewing docked poses for input files in a chain."""
460
461 if not GetChainAloneDockedPosesStatus(FileIndex, ChainID):
462 return
463
464 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
465 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
466 WriteChainDockedPosesViewForInputFile(OutFH, FileIndex, PyMOLObjectNames, ChainID, InputFileIndex)
467
468 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"], PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"], False, "close")
469
470 def WriteChainDockedPosesViewForInputFile(OutFH, PDBFileIndex, PyMOLObjectNames, ChainID, InputFileIndex):
471 """Write out PML for viewing docked poses for an input file in a chain."""
472
473 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
474 DockedPosesDistanceContactsInfo = OptionsInfo["DockedPosesDistanceContactsInfo"]
475
476 LigandID = DockedPosesInfo["LigandID"][PDBFileIndex]
477 UseInputFileAsLigandID = DockedPosesInfo["UseInputFileAsLigandID"][PDBFileIndex]
478 InputFile = DockedPosesInfo["InputFiles"][PDBFileIndex][InputFileIndex]
479 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
480
481 OutFH.write("""\n""\n"Setting up views for docked poses in input file ID %s for chain %s..."\n""\n""" % (InputFileID, ChainID))
482
483 # Setup poses view...
484 PosesName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["Poses"]
485 PML = PyMOLUtil.SetupPMLForLigandsInputFileView(PosesName, InputFile, Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
486 OutFH.write("%s\n" % PML)
487
488 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
489 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
490 LigandName = PosesName if UseInputFileAsLigandID else PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
491
492 # Setup pocket object...
493 PocketID = "%sPocket" % (GroupID)
494 PocketName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PocketID]
495
496 if re.match("^Pocket$", GroupID, re.I):
497 PML = PyMOLUtil.SetupPMLForLigandPocketView(PocketName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
498 OutFH.write("%s\n" % PML)
499 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], PocketName))
500 elif re.match("^PocketSolvent$", GroupID, re.I):
501 PML = PyMOLUtil.SetupPMLForLigandPocketSolventView(PocketName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
502 OutFH.write("%s\n" % PML)
503 elif re.match("^PocketInorganic$", GroupID, re.I):
504 PML = PyMOLUtil.SetupPMLForLigandPocketInorganicView(PocketName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
505 OutFH.write("%s\n" % PML)
506
507 if DockedPosesInfo["DistanceContacts"] and re.match("^Pocket$", GroupID, re.I):
508 # Setup distance contacts...
509 for ContactIndex, ContactID in enumerate(DockedPosesDistanceContactsInfo["ContactIDs"]):
510 ContactCutoff = DockedPosesDistanceContactsInfo["ContactCutoff"][ContactID]
511
512 DistanceContactID = "%sPocketDistanceContacts%s" % (GroupID, ContactID)
513 DistanceContactName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactID]
514
515 DistanceContactsColor = OptionsInfo["DockedPosesDistanceContactsColor"]
516 EnableContact = True if ContactIndex == 0 else False
517 PML = PyMOLUtil.SetupPMLForDistanceContactsView(DistanceContactName, PosesName, PocketName, Enable = EnableContact, Color = DistanceContactsColor, Cutoff = ContactCutoff, IgnoreHydrogens = True)
518 OutFH.write("\n%s\n" % PML)
519
520 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (DistanceContactsColor, DistanceContactName))
521
522 # Setup distance conatcts group...
523 DistanceContactGroupNameID = "%sDistanceContactsGroup" % GroupID
524 DistanceContactGroupMembersID = "%sDistanceContactsGroupMembers" % GroupID
525
526 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupNameID], PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID], True, "open")
527
528 # Setup polar contacts...
529 if re.match("^(Pocket|PocketSolvent|PocketInorganic)$", GroupID, re.I):
530 PolarContactsID = "%sPolarContacts" % (GroupID)
531 PolarContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PolarContactsID]
532
533 PolarContactsColor = OptionsInfo["PocketContactsLigandColor"]
534 if re.match("^PocketSolvent$", GroupID, re.I):
535 PolarContactsColor = OptionsInfo["PocketContactsSolventColor"]
536 elif re.match("^PocketInorganic$", GroupID, re.I):
537 PolarContactsColor = OptionsInfo["PocketContactsInorganicColor"]
538
539 PML = PyMOLUtil.SetupPMLForPolarContactsView(PolarContactsName, PosesName, PocketName, Enable = False, Color = PolarContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
540 OutFH.write("\n%s\n" % PML)
541
542 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PolarContactsColor, PolarContactsName))
543
544 if re.match("^PocketInorganic$", GroupID, re.I):
545 # Setup pi cation contacts...
546 PiCationContactsID = "%sPiCationContacts" % (GroupID)
547 PiCationContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID]
548 PiCationContactsColor = OptionsInfo["PocketContactsInorganicPiCationColor"]
549
550 PML = PyMOLUtil.SetupPMLForPiCationContactsView(PiCationContactsName, PosesName, PocketName, Enable = False, Color = PiCationContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
551 OutFH.write("\n%s\n" % PML)
552
553 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
554
555 if re.match("^Pocket$", GroupID, re.I):
556 # Setup hydrophobic contacts...
557 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
558 HydrophobicContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HydrophobicContactsID]
559 HydrophobicContactsColor = OptionsInfo["PocketContactsLigandHydrophobicColor"]
560
561 PML = PyMOLUtil.SetupPMLForHydrophobicContactsView(HydrophobicContactsName, PosesName, PocketName, Enable = False, Color = HydrophobicContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
562 OutFH.write("\n%s\n" % PML)
563 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HydrophobicContactsColor, HydrophobicContactsName))
564
565 # Setup pi pi contacts...
566 PiPiContactsID = "%sPiPiContacts" % (GroupID)
567 PiPiContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiPiContactsID]
568 PiPiContactsColor = OptionsInfo["PocketContactsLigandPiPiColor"]
569
570 PML = PyMOLUtil.SetupPMLForPiPiContactsView(PiPiContactsName, PosesName, PocketName, Enable = False, Color = PiPiContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
571 OutFH.write("\n%s\n" % PML)
572 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiPiContactsColor, PiPiContactsName))
573
574 # Setup pi cation contacts...
575 PiCationContactsID = "%sPiCationContacts" % (GroupID)
576 PiCationContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID]
577 PiCationContactsColor = OptionsInfo["PocketContactsLigandPiCationColor"]
578
579 PML = PyMOLUtil.SetupPMLForPiCationContactsView(PiCationContactsName, PosesName, PocketName, Enable = False, Color = PiCationContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
580 OutFH.write("\n%s\n" % PML)
581 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PiCationContactsColor, PiCationContactsName))
582
583 # Setup halogen contacts...
584 HalogenContactsID = "%sHalogenContacts" % (GroupID)
585 HalogenContactsName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HalogenContactsID]
586 HalogenContactsColor = OptionsInfo["PocketContactsLigandHalogenColor"]
587
588 PML = PyMOLUtil.SetupPMLForHalogenContactsView(HalogenContactsName, LigandName, PocketName, Enable = False, Color = HalogenContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
589 OutFH.write("\n%s\n" % PML)
590 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HalogenContactsColor, HalogenContactsName))
591
592
593 # Setup group for an input file...
594 GroupNameID = "%sGroup" % (GroupID)
595 GroupMembersID = "%sGroupMembers" % (GroupID)
596 Enable = True if re.match("^Pocket$", GroupID, re.I) else False
597 Action = "open" if re.match("^Pocket$", GroupID, re.I) else "close"
598
599 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID], PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID], Enable, Action)
600
601 # Setup docked poses group for an input file...
602 Action = "open" if InputFileIndex == 0 else "close"
603 Enable = True if InputFileIndex == 0 else False
604 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupName"], PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"], Enable, Action)
605
606 def WritePocketSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
607 """Write out PML for viewing selections for a lgand pocket."""
608
609 if not GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
610 return
611
612 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
613 SelectionsGroupIDPrefix = "PocketSelectionsGroup"
614
615 for Index in range(0, len(OptionsInfo["PocketChainSelectionsInfo"]["Names"])):
616 SelectionName = OptionsInfo["PocketChainSelectionsInfo"]["Names"][Index]
617 Selection = OptionsInfo["PocketChainSelectionsInfo"]["Selections"][Index]
618
619 SelectionNameGroupID = SelectionName
620
621 # Setup a selection object...
622 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
623 SelectionObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionObjectID]
624 SelectionCmd = "(%s and (%s))" % (PocketObjectName, Selection)
625 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SelectionObjectName, SelectionCmd, OptionsInfo["SelectionsPocketStyle"], Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
626 OutFH.write("\n%s\n" % PML)
627
628 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
629 # Display style for selection objects in surfaces...
630 DisplayStyle = "lines"
631
632 # Setup a generic color surface...
633 SurfaceID = "%s%s%sSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface")
634 SurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceID]
635 PML = PyMOLUtil.SetupPMLForSurfaceView(SurfaceName, SelectionObjectName, Enable = False, Color = OptionsInfo["SurfaceColor"], DisplayAs = DisplayStyle)
636 OutFH.write("\n%s\n" % PML)
637
638 # Setup a surface colored by hydrphobicity...
639 HydrophobicSurfaceID = "%s%sSurfaceHydrophobicity" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
640 HydrophobicSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID]
641 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(HydrophobicSurfaceName, SelectionObjectName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False, DisplayAs = DisplayStyle)
642 OutFH.write("\n%s\n" % PML)
643
644 # Setup a surface colored by hydrphobicity and charge...
645 HydrophobicChargeSurfaceID = "%s%sSurfaceHydrophobicityCharge" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
646 HydrophobicChargeSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicChargeSurfaceID]
647 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(HydrophobicChargeSurfaceName, SelectionObjectName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = DisplayStyle)
648 OutFH.write("\n%s\n" % PML)
649
650 # Setup group for surfaces...
651 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
652 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
653 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupID], PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupMembersID], True, "open")
654
655 # Setup groups for named selections...
656 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
657 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
658 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupID], PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID], True, "open")
659
660 # Setup a group for selections...
661 SelectionsGroupID = "%s" % (SelectionsGroupIDPrefix)
662 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupIDPrefix)
663 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID], PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID], True, "close")
664
665 def WritePocketSurfacesTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
666 """Write out PML for viewing surfaces for a ligand pocket."""
667
668 if not GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
669 return
670
671 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
672
673 SurfacesGroupID = "%sSurfacesGroup" % (PocketObjectID)
674 SurfacesGroupMembersID = "%sSurfacesGroupMembers" % (PocketObjectID)
675
676 # Cavity modes: 1 or 2. 1: Cavity surfaces; 2: Culled cavity surfaces...
677 CavityMode = 2
678
679 # Setup surfaces subgroup and its members...
680 for SubGroupType in ["Surface", "Cavity"]:
681 ProcessingCavity = True if re.match("^Cavity$", SubGroupType, re.I) else False
682
683 SubGroupID = re.sub("_", "", SubGroupType)
684 SurfacesSubGroupID = "%s%sGroup" % (SurfacesGroupID, SubGroupID)
685 SurfacesSubGroupMembersID = "%sMembers" % (SurfacesSubGroupID)
686
687 # Turn off lines display for cavity surfaces...
688 DisplayStyle = None if ProcessingCavity else "lines"
689
690 # Setup a generic color surface...
691 SurfaceID = "%sSurface" % (SurfacesSubGroupID)
692 SurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceID]
693 PML = PyMOLUtil.SetupPMLForSurfaceView(SurfaceName, PocketObjectName, Enable = False, Color = OptionsInfo["SurfaceColor"], DisplayAs = DisplayStyle)
694 OutFH.write("\n%s\n" % PML)
695
696 if ProcessingCavity:
697 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (CavityMode, SurfaceName))
698
699 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], SurfaceName))
700
701 if GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
702 # Setup a surface colored by hydrphobicity...
703 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SurfacesSubGroupID)
704 HydrophobicSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID]
705 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(HydrophobicSurfaceName, PocketObjectName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False, DisplayAs = DisplayStyle)
706 OutFH.write("\n%s\n" % PML)
707
708 if ProcessingCavity:
709 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (CavityMode, HydrophobicSurfaceName))
710
711 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], HydrophobicSurfaceName))
712
713 # Setup a surface colored by hydrphobicity and charge...
714 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SurfacesSubGroupID)
715 HydrophobicChargeSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicChargeSurfaceID]
716 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(HydrophobicChargeSurfaceName, PocketObjectName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = DisplayStyle)
717 OutFH.write("\n%s\n" % PML)
718
719 if ProcessingCavity:
720 OutFH.write("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (CavityMode, HydrophobicChargeSurfaceName))
721
722 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], HydrophobicChargeSurfaceName))
723
724 if GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
725 # Set up a electrostatics surface...
726 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SurfacesSubGroupID)
727 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SurfacesSubGroupID)
728 ElectrostaticsGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupID]
729 ElectrostaticsGroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupMembersID]
730 WriteSurfaceElectrostaticsView(SubGroupType, OutFH, PocketObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers, DisplayAs = DisplayStyle, SurfaceCavityMode = CavityMode)
731
732 # Setup surfaces sub group...
733 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupID], PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID], True, "open")
734
735 # Setup surface group...
736 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupID], PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID], True, "open")
737
738 def WritePocketResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
739 """Write out PML for viewing residue types for a ligand pocket."""
740
741 if not GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
742 return
743
744 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
745
746 ResiduesGroupID = "%sResiduesGroup" % (PocketObjectID)
747 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
748
749 # Setup residue types objects...
750 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
751 SubGroupID = re.sub("_", "", SubGroupType)
752
753 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
754 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
755
756 SubGroupMemberID = "%sResidues" % (ResiduesSubGroupID)
757 ResiduesObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID]
758
759 SubGroupMemberID = "%sSurface" % (ResiduesSubGroupID)
760 ResiduesSurfaceObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID]
761
762 ResiduesColor = OptionsInfo["ResidueTypesParams"][SubGroupType]["Color"]
763 ResiduesNames = OptionsInfo["ResidueTypesParams"][SubGroupType]["Residues"]
764
765 NegateResidueNames = True if re.match("^Other$", SubGroupType, re.I) else False
766 WriteResidueTypesResiduesAndSurfaceView(OutFH, PocketObjectName, ResiduesObjectName, ResiduesSurfaceObjectName, ResiduesColor, ResiduesNames, NegateResidueNames)
767
768 # Setup residue type sub groups...
769 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID], PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID], True, "close")
770
771 # Setup residue types group...
772 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupID], PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID], False, "close")
773
774 def WriteChainAloneChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
775 """Write out PML for viewing selections for a chain."""
776
777 if not GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
778 return
779
780 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
781 SelectionsGroupIDPrefix = "ChainAloneSelections"
782
783 for Index in range(0, len(OptionsInfo["ChainSelectionsInfo"]["Names"])):
784 SelectionName = OptionsInfo["ChainSelectionsInfo"]["Names"][Index]
785 Selection = OptionsInfo["ChainSelectionsInfo"]["Selections"][Index]
786
787 SelectionNameGroupID = SelectionName
788
789 # Setup a selection object...
790 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
791 SelectionObjectName = PyMOLObjectNames["Chains"][ChainID][SelectionObjectID]
792 SelectionCmd = "(%s and (%s))" % (ChainName, Selection)
793 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SelectionObjectName, SelectionCmd, OptionsInfo["SelectionsChainStyle"], Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
794 OutFH.write("\n%s\n" % PML)
795
796 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
797 # Display style for selection objects in surfaces...
798 DisplayStyle = "lines"
799
800 # Setup a generic color surface...
801 SurfaceID = "%s%s%sSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface")
802 SurfaceName = PyMOLObjectNames["Chains"][ChainID][SurfaceID]
803 PML = PyMOLUtil.SetupPMLForSurfaceView(SurfaceName, SelectionObjectName, Enable = False, Color = OptionsInfo["SurfaceColor"], DisplayAs = DisplayStyle)
804 OutFH.write("\n%s\n" % PML)
805
806 if GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
807 # Setup a surface colored by hydrphobicity...
808 HydrophobicSurfaceID = "%s%sSurfaceHydrophobicity" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
809 HydrophobicSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicSurfaceID]
810 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(HydrophobicSurfaceName, SelectionObjectName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False, DisplayAs = DisplayStyle)
811 OutFH.write("\n%s\n" % PML)
812
813 # Setup a surface colored by hydrphobicity and charge...
814 HydrophobicChargeSurfaceID = "%s%sSurfaceHydrophobicityCharge" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
815 HydrophobicChargeSurfaceName = PyMOLObjectNames["Chains"][ChainID][HydrophobicChargeSurfaceID]
816 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(HydrophobicChargeSurfaceName, SelectionObjectName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = DisplayStyle)
817 OutFH.write("\n%s\n" % PML)
818
819 # Setup group for surfaces...
820 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
821 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
822 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SurfaceGroupID], PyMOLObjectNames["Chains"][ChainID][SurfaceGroupMembersID], True, "close")
823
824 # Setup groups for named selections...
825 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
826 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
827 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID], PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID], True, "open")
828
829 # Setup a group for selections...
830 SelectionsGroupID = "%sGroup" % (SelectionsGroupIDPrefix)
831 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupIDPrefix)
832 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID], PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID], False, "close")
833
834 def WriteChainAloneResidueTypesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
835 """Write out PML for viewing residue types for a chain."""
836
837 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
838 return
839
840 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
841
842 # Setup residue types objects...
843 ResiduesGroupIDPrefix = "ChainAloneResidues"
844 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
845 SubGroupID = re.sub("_", "", SubGroupType)
846
847 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, SubGroupID)
848 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
849
850 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, SubGroupID)
851 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
852
853 ResiduesColor = OptionsInfo["ResidueTypesParams"][SubGroupType]["Color"]
854 ResiduesNames = OptionsInfo["ResidueTypesParams"][SubGroupType]["Residues"]
855
856 NegateResidueNames = True if re.match("^Other$", SubGroupType, re.I) else False
857 WriteResidueTypesResiduesAndSurfaceView(OutFH, ChainName, ResiduesObjectName, ResiduesSurfaceObjectName, ResiduesColor, ResiduesNames, NegateResidueNames)
858
859 # Setup sub groups for residue types..
860 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
861 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
862
863 # Setup residue type sub groups...
864 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID], PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID], True, "close")
865
866 # Setup residue types group...
867 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneResiduesGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneResiduesGroupMembers"], False, "close")
868
869 def WriteChainAloneBFactorViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
870 """Write out PML for viewing B factor values for a chain."""
871
872 if not GetChainAloneBFactorStatus(FileIndex, ChainID):
873 return
874
875 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
876
877 # Setup cartoon...
878 Name = PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorCartoon"]
879 PML = PyMOLUtil.SetupPMLForBFactorCartoonView(Name, ChainName, ColorPalette = OptionsInfo["BFactorColorPalette"], Enable = False)
880 OutFH.write("\n%s\n" % PML)
881
882 # Setup putty...
883 Name = PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"]
884 PML = PyMOLUtil.SetupPMLForBFactorPuttyView(Name, ChainName, ColorPalette = OptionsInfo["BFactorColorPalette"], Enable = True)
885 OutFH.write("\n%s\n" % PML)
886
887 # Setup B factor group...
888 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"], False, "close")
889
890
891 def WriteChainAloneDisulfideBondsView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
892 """Write out PML for viewing disulfide bonds for a chain."""
893
894 if not GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
895 return
896
897 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
898 Name = PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"]
899
900 PML = PyMOLUtil.SetupPMLForDisulfideBondsView(Name, ChainName, "sticks", Enable = True)
901 OutFH.write("\n%s\n" % PML)
902
903 # Setup disulfide bonds group...
904 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"], True, "close")
905
906 def WriteChainAloneSaltBridgesView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
907 """Write out PML for viewing salt bridges for a chain."""
908
909 if not GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
910 return
911
912 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
913
914 # Seup salt bridges resiudes group...
915 PositivelyChargedResiduesName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesPositivelyCharged"]
916 PML = PyMOLUtil.SetupPMLForSaltBridgesResiduesView(PositivelyChargedResiduesName, ChainName, OptionsInfo["SaltBridgesChainResiduesInfo"]["Positively_Charged"], "lines", Enable = True)
917 OutFH.write("\n%s\n" % PML)
918
919 NegativelyChargedResiduesName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesNegativelyCharged"]
920 PML = PyMOLUtil.SetupPMLForSaltBridgesResiduesView(NegativelyChargedResiduesName, ChainName, OptionsInfo["SaltBridgesChainResiduesInfo"]["Negatively_Charged"], "lines", Enable = True)
921 OutFH.write("\n%s\n" % PML)
922
923 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"], True, "open")
924
925 # Setup salt bridges contacts...
926 ContactsColor = OptionsInfo["SaltBridgesChainContactsColor"]
927 ContactsName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesContacts"]
928 PML = PyMOLUtil.SetupPMLForPolarContactsView(ContactsName, PositivelyChargedResiduesName, NegativelyChargedResiduesName, Enable = True, Color = ContactsColor, Cutoff = OptionsInfo["SaltBridgesChainCutoff"])
929 OutFH.write("\n%s\n" % PML)
930
931 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (ContactsColor, ContactsName))
932
933 # Setup salt bridges group...
934 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"], False, "close")
935
936 def WriteResidueTypesResiduesAndSurfaceView(OutFH, SelectionObjectName, Name, SurfaceName, ResiduesColor, ResiduesNames, NegateResidueNames):
937 """Write residue types residues and surface view."""
938
939 ResidueNamesSelection = "+".join(ResiduesNames)
940 if NegateResidueNames:
941 Selection = "%s and (not resn %s)" % (SelectionObjectName, ResidueNamesSelection)
942 else:
943 Selection = "%s and (resn %s)" % (SelectionObjectName, ResidueNamesSelection)
944
945 # Setup residues...
946 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(Name, Selection, "lines", ResiduesColor, True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
947 OutFH.write("\n%s\n" % PML)
948
949 # Setup surface...
950 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SurfaceName, Selection, "surface", ResiduesColor, True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
951 OutFH.write("\n%s\n" % PML)
952
953 def WriteSurfaceElectrostaticsView(Mode, OutFH, SelectionObjectName, ElectrostaticsGroupName, ElectrostaticsGroupMembers, DisplayAs = None, SurfaceCavityMode = 2):
954 """Write out PML for viewing surface electrostatics."""
955
956 if len(ElectrostaticsGroupMembers) == 5:
957 Name, ContactPotentialName, MapName, LegendName, VolumeName = ElectrostaticsGroupMembers
958 else:
959 Name, ContactPotentialName, MapName, LegendName = ElectrostaticsGroupMembers
960 VolumeName = None
961
962 PMLCmds = []
963
964 # Setup chain...
965 PMLCmds.append("""cmd.create("%s", "(%s)")""" % (Name, SelectionObjectName))
966
967 # Setup vacuum electrostatics surface along with associated objects...
968 PMLCmds.append("""util.protein_vacuum_esp("%s", mode=2, quiet=0, _self=cmd)""" % (Name))
969 PMLCmds.append("""cmd.set_name("%s_e_chg", "%s")""" % (Name, ContactPotentialName))
970
971 if DisplayAs is not None:
972 PMLCmds.append("""cmd.show("%s", "(%s)")""" % (DisplayAs, ContactPotentialName))
973
974 if re.match("^Cavity$", Mode, re.I):
975 if SurfaceCavityMode is not None:
976 PMLCmds.append("""cmd.set("surface_cavity_mode", %d, "%s")\n""" % (SurfaceCavityMode, ContactPotentialName))
977
978 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(ContactPotentialName, Enable = True))
979
980 PMLCmds.append("""cmd.set_name("%s_e_map", "%s")""" % (Name, MapName))
981 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MapName, Enable = False))
982
983 PMLCmds.append("""cmd.set_name("%s_e_pot", "%s")""" % (Name, LegendName))
984 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(LegendName, Enable = False))
985
986 if VolumeName is not None:
987 PMLCmds.append("""cmd.volume("%s", "%s", "%s", "(%s)")""" % (VolumeName, MapName, "esp", Name))
988 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(VolumeName, Enable = False))
989
990 # Delete name and take it out from the group membership. It is
991 # is already part of ContactPotential object.
992 PMLCmds.append("""cmd.delete("%s")""" % (Name))
993 ElectrostaticsGroupMembers.pop(0)
994
995 PML = "\n".join(PMLCmds)
996
997 OutFH.write("\n%s\n" % PML)
998
999 # Setup group...
1000 GenerateAndWritePMLForGroup(OutFH, ElectrostaticsGroupName, ElectrostaticsGroupMembers, False, "close")
1001
1002 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable = False, Action = "close"):
1003 """Generate and write PML for group."""
1004
1005 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
1006 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
1007 OutFH.write("%s\n" % PML)
1008
1009 def WriteTrajectoriesView(OutFH, FileIndex, PyMOLObjectNames):
1010 """Write out PML for viewing trajectories for a PDB file."""
1011
1012 if not GetTrajectoriesStatus(FileIndex):
1013 return
1014
1015 # Setup topology view...
1016 Name = PyMOLObjectNames["Trajectories"]["Topology"]
1017
1018 PMLCmds = []
1019 PMLCmds.append("""cmd.load("%s", "%s")""" % (OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex], Name))
1020 PMLCmds.append("""cmd.hide("everything", "%s")""" % (Name))
1021 PMLCmds.append("""cmd.show("cartoon", "%s")""" % (Name))
1022 PMLCmds.append("""util.cba(33, "%s", _self = cmd)""" % (Name))
1023 PMLCmds.append("""cmd.show("sticks", "(organic and (%s))")""" % (Name))
1024 PMLCmds.append("""cmd.hide("(%s and hydro)")""" % (Name))
1025 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable = False))
1026
1027 PML = "\n".join(PMLCmds)
1028 OutFH.write("\n%s\n" % PML)
1029
1030 # Write view for each trajectory file...
1031 for TrajFileIndex, TrajFile in enumerate(OptionsInfo["TrajectoriesInfo"]["TrajFiles"][FileIndex]):
1032 WriteTrajectoryViewTrajectoryFile(OutFH, FileIndex, PyMOLObjectNames, TrajFileIndex)
1033
1034 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"], PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"], False, "close")
1035
1036 def WriteTrajectoryViewTrajectoryFile(OutFH, PDBFileIndex, PyMOLObjectNames, TrajFileIndex):
1037 """Write out PML for viewing a trajectory file."""
1038
1039 TrajFile = OptionsInfo["TrajectoriesInfo"]["TrajFiles"][PDBFileIndex][TrajFileIndex]
1040 TrajFileID = OptionsInfo["TrajectoriesInfo"]["TrajFilesIDs"][PDBFileIndex][TrajFileIndex]
1041
1042 OutFH.write("""\n""\n"Setting up views for trajectory file ID %s..."\n""\n""" % (TrajFileID))
1043
1044 # Setup trajectory view...
1045 Name = PyMOLObjectNames["Trajectories"][TrajFileID]["Trajectory"]
1046 PDBFile = OptionsInfo["InfilesInfo"]["InfilesNames"][PDBFileIndex]
1047
1048 PMLCmds = []
1049 PMLCmds.append("""cmd.load("%s", "%s")""" % (PDBFile, Name))
1050 PMLCmds.append("""cmd.load_traj("%s", "%s", state = 1)""" % (TrajFile, Name))
1051 PMLCmds.append("""cmd.hide("everything", "%s")""" % (Name))
1052 PMLCmds.append("""cmd.show("cartoon", "%s")""" % (Name))
1053 PMLCmds.append("""util.cba(33, "%s", _self = cmd)""" % (Name))
1054 PMLCmds.append("""cmd.show("sticks", "(organic and (%s))")""" % (Name))
1055 PMLCmds.append("""cmd.hide("(%s and hydro)")""" % (Name))
1056 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable = True))
1057
1058 PML = "\n".join(PMLCmds)
1059 OutFH.write("%s\n" % PML)
1060
1061 # Setup group for a trajectory file...
1062 Action = "open" if TrajFileIndex == 0 else "close"
1063 Enable = True if TrajFileIndex == 0 else False
1064 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroup"], PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"], Enable, Action)
1065
1066 def GeneratePyMOLSessionFile():
1067 """Generate PME file from PML file."""
1068
1069 PSEOutfile = OptionsInfo["PSEOutfile"]
1070 PMLOutfile = OptionsInfo["PMLOutfile"]
1071
1072 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
1073
1074 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
1075
1076 if not os.path.exists(PSEOutfile):
1077 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
1078
1079 if not OptionsInfo["PMLOut"]:
1080 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
1081 os.remove(PMLOutfile)
1082
1083 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
1084 """Delete empty PyMOL objects."""
1085
1086 if OptionsInfo["AllowEmptyObjects"]:
1087 return
1088
1089 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1090 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1091 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
1092
1093 # Delete any chain level objects...
1094 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
1095 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
1096
1097 # Delete chain selection objects...
1098 DeleteEmptyChainSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1099
1100 # Delete residue type objects...
1101 DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1102
1103 # Delete disulfide bonds objects...
1104 DeleteEmptyChainDisulfideBondsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1105
1106 # Delete salt bridges objects...
1107 DeleteEmptyChainSaltBridgesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1108
1109 # Delete ligand objects...
1110 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
1111 # Delete ligand level objects...
1112 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
1113 GroupNameID = "%sGroup" % (GroupID)
1114 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
1115
1116 GroupTypeObjectID = "%s" % (GroupID)
1117 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
1118
1119 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
1120
1121 if re.match("^Pocket$", GroupID, re.I):
1122 DeleteEmptyPocketSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
1123 DeleteEmptyPocketResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
1124
1125 # Delete docked poses objects...
1126 DeleteEmptyChainDockedPosesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1127
1128 def DeleteEmptyChainSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1129 """Delete empty chain selection objects """
1130
1131 if not GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
1132 return
1133
1134 SelectionsGroupIDPrefix = "ChainAloneSelections"
1135
1136 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
1137 SelectionNameGroupID = SelectionName
1138
1139 # Delete surface objects and surface group...
1140 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
1141 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1142 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1143 WritePMLToCheckAndDeleteEmptyObjects(OutFH, ",".join(PyMOLObjectNames["Chains"][ChainID][SurfaceGroupMembersID]), PyMOLObjectNames["Chains"][ChainID][SurfaceGroupID])
1144
1145 # Delete Selection object and selection name group...
1146 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1147 SelectionsGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1148 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionObjectID], PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID])
1149
1150 def DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1151 """Delete empty chain residue objects."""
1152
1153 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
1154 return
1155
1156 ResiduesGroupIDPrefix = "ChainAloneResidues"
1157 for GroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1158 GroupID = re.sub("_", "", GroupType)
1159
1160 ResiduesGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, GroupID)
1161 GroupName = PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID]
1162
1163 GroupObjectNamesList = []
1164
1165 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, GroupID)
1166 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
1167 GroupObjectNamesList.append(ResiduesObjectName)
1168
1169 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, GroupID)
1170 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
1171 GroupObjectNamesList.append(ResiduesSurfaceObjectName)
1172
1173 GroupObjectNames = ",".join(GroupObjectNamesList)
1174 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupObjectNames, GroupName)
1175
1176 def DeleteEmptyChainDisulfideBondsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1177 """Delete empty chain disulfide bonds objects."""
1178
1179 if not GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
1180 return
1181
1182 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"])
1183
1184 def DeleteEmptyChainSaltBridgesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1185 """Delete empty chain salt bridges objects."""
1186
1187 if not GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
1188 return
1189
1190 Names = []
1191 Names.append(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesPositivelyCharged"])
1192 Names.append(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesNegativelyCharged"])
1193
1194 WritePMLToCheckAndDeleteEmptyObjects(OutFH, ",".join(Names), PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"])
1195
1196 def DeleteEmptyPocketSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
1197 """Delete empty pocket selection objects."""
1198
1199 if not GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
1200 return
1201
1202 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
1203 SelectionsGroupIDPrefix = "PocketSelectionsGroup"
1204
1205 for SelectionName in OptionsInfo["PocketChainSelectionsInfo"]["Names"]:
1206 SelectionNameGroupID = SelectionName
1207
1208 # Delete surface objects and surface group...
1209 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
1210 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1211 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1212 WritePMLToCheckAndDeleteEmptyObjects(OutFH, ",".join(PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupMembersID]), PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupID])
1213
1214 # Delete Selection object and selection name group...
1215 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1216 SelectionsGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1217 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionObjectID], PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID])
1218
1219 def DeleteEmptyPocketResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
1220 """Delete empty chain residue objects. """
1221
1222 if not GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
1223 return
1224
1225 ResiduesGroupID = "%sResiduesGroup" % (PocketObjectID)
1226 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
1227
1228 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1229 SubGroupID = re.sub("_", "", SubGroupType)
1230
1231 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
1232 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
1233
1234 SubGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID]
1235 SubGroupObjectNames = ",".join(PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID])
1236
1237 WritePMLToCheckAndDeleteEmptyObjects(OutFH, SubGroupObjectNames, SubGroupName)
1238
1239 def DeleteEmptyChainDockedPosesObjects(OutFH, PDBFileIndex, PyMOLObjectNames, ChainID):
1240 """Delete empty chain docked poses objest."""
1241
1242 if not GetChainAloneDockedPosesStatus(PDBFileIndex, ChainID):
1243 return
1244
1245 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][PDBFileIndex]
1246 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
1247
1248 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
1249 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
1250 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
1251 GroupNameID = "%sGroup" % (GroupID)
1252 GroupName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID]
1253
1254 GroupTypeObjectID = "%sPocket" % (GroupID)
1255 GroupTypeObjectName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupTypeObjectID]
1256
1257 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
1258
1259 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
1260 """Write PML to check and delete empty PyMOL objects."""
1261
1262 if ParentObjectName is None:
1263 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
1264 else:
1265 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
1266
1267 OutFH.write("%s\n" % PML)
1268
1269 def SetupPyMOLObjectNames(FileIndex):
1270 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
1271 chains and ligands present in input file.
1272 """
1273
1274 PyMOLObjectNames = {}
1275 PyMOLObjectNames["Chains"] = {}
1276 PyMOLObjectNames["Ligands"] = {}
1277 PyMOLObjectNames["DockedPosesInputFile"] = {}
1278 PyMOLObjectNames["Trajectories"] = {}
1279
1280 # Setup groups and objects for complex...
1281 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
1282
1283 # Setup groups and object for trajectories...
1284 if GetTrajectoriesStatus(FileIndex):
1285 SetupPyMOLObjectNamesForTrajectories(FileIndex, PyMOLObjectNames)
1286
1287 # Setup groups and objects for chain...
1288 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1289 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1290 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
1291
1292 # Setup groups and objects for ligand...
1293 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
1294 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
1295
1296 # Setup group and objects for docked poses...
1297 if GetChainAloneDockedPosesStatus(FileIndex, ChainID):
1298 SetupPyMOLObjectNamesForDockedPoses(FileIndex, PyMOLObjectNames, ChainID)
1299
1300 return PyMOLObjectNames
1301
1302 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
1303 """Setup groups and objects for complex."""
1304
1305 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
1306
1307 PDBGroupName = "%s" % PDBFileRoot
1308 PyMOLObjectNames["PDBGroup"] = PDBGroupName
1309 PyMOLObjectNames["PDBGroupMembers"] = []
1310
1311 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
1312 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
1313 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
1314
1315 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
1316 if OptionsInfo["SurfaceComplex"]:
1317 PyMOLObjectNames["ComplexHydrophobicSurface"] = "%s.Surface" % ComplexGroupName
1318
1319 PyMOLObjectNames["ComplexGroupMembers"] = []
1320 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
1321 if OptionsInfo["SurfaceComplex"]:
1322 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexHydrophobicSurface"])
1323
1324 def SetupPyMOLObjectNamesForTrajectories(FileIndex, PyMOLObjectNames):
1325 """Setup groups and objects for a PDB file."""
1326
1327 if not GetTrajectoriesStatus(FileIndex):
1328 return
1329
1330 # Setup a group for trajectories....
1331 TrajectoriesGroupName = "%s.Trajectories" % PyMOLObjectNames["PDBGroup"]
1332 PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"] = TrajectoriesGroupName
1333 PyMOLObjectNames["PDBGroupMembers"].append(TrajectoriesGroupName)
1334
1335 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"] = []
1336
1337 # Setup a topolgy object...
1338 TopologyName = "%s.Topology" % TrajectoriesGroupName
1339 PyMOLObjectNames["Trajectories"]["Topology"] = TopologyName
1340 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"].append(TopologyName)
1341
1342 # Setup trajectory objects...
1343 for TrajFileIndex, TrajFile in enumerate(OptionsInfo["TrajectoriesInfo"]["TrajFiles"][FileIndex]):
1344 SetupPyMOLObjectNamesForTrajectoryFile(FileIndex, PyMOLObjectNames, TrajFileIndex)
1345
1346 def SetupPyMOLObjectNamesForTrajectoryFile(PDBFileIndex, PyMOLObjectNames, TrajFileIndex):
1347 """Setup groups and objest for a trajectory file for a PDB file."""
1348
1349 TrajFileID = OptionsInfo["TrajectoriesInfo"]["TrajFilesIDs"][PDBFileIndex][TrajFileIndex]
1350
1351 PyMOLObjectNames["Trajectories"][TrajFileID] = {}
1352
1353 TrajectoriesGroupName = PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"]
1354
1355 # Setup a trajectories level trajectory file group...
1356 TrajectoryFileGroupName = "%s.%s" % (TrajectoriesGroupName, TrajFileID)
1357 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroup"] = TrajectoryFileGroupName
1358 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"].append(TrajectoryFileGroupName)
1359
1360 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"] = []
1361
1362 # Setup object for a trajectory file...
1363 TrajectoryName = "%s.Trajectory" % (TrajectoryFileGroupName)
1364 PyMOLObjectNames["Trajectories"][TrajFileID]["Trajectory"] = TrajectoryName
1365 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"].append(TrajectoryName)
1366
1367 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
1368 """Setup groups and objects for chain."""
1369
1370 PDBGroupName = PyMOLObjectNames["PDBGroup"]
1371
1372 PyMOLObjectNames["Chains"][ChainID] = {}
1373 PyMOLObjectNames["Ligands"][ChainID] = {}
1374
1375 # Set up chain group and chain objects...
1376 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
1377 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
1378 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
1379 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
1380
1381 # Setup chain complex group and objects...
1382 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
1383 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
1384 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
1385
1386 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
1387
1388 Name = "%s.Complex" % (ChainComplexGroupName)
1389 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = Name
1390 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1391
1392 if OptionsInfo["SurfaceChainComplex"]:
1393 Name = "%s.Surface" % (ChainComplexGroupName)
1394 PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"] = Name
1395 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1396
1397 # Setup up a group for individual chains...
1398 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
1399 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
1400 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
1401
1402 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
1403
1404 Name = "%s.Chain" % (ChainAloneGroupName)
1405 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
1406 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
1407
1408 if GetChainAloneBFactorStatus(FileIndex, ChainID):
1409 # Setup B factor group and add it to chain alone group...
1410 BFactorGroupName = "%s.BFactor" % (ChainAloneGroupName)
1411 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroup"] = BFactorGroupName
1412 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(BFactorGroupName)
1413
1414 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"] = []
1415
1416 # Setup cartoon...
1417 Name = "%s.Cartoon" % (BFactorGroupName)
1418 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorCartoon"] = Name
1419 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"].append(Name)
1420
1421 # Setup putty...
1422 Name = "%s.Putty" % (BFactorGroupName)
1423 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"] = Name
1424 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"].append(Name)
1425
1426 if GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
1427 # Setup selections group and its subgroups..
1428 SelectionsGroupName = "%s.Selections" % (ChainAloneGroupName)
1429
1430 SelectionsGroupIDPrefix = "ChainAloneSelections"
1431 SelectionsGroupID = "%sGroup" % SelectionsGroupIDPrefix
1432
1433 # Add selections group to chain alone group...
1434 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID] = SelectionsGroupName
1435 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SelectionsGroupName)
1436
1437 # Initialize selections group members...
1438 SelectionsGroupMembersID = "%sGroupMembers" % SelectionsGroupIDPrefix
1439 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID] = []
1440
1441 # Setup selections name sub group and its members...
1442 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
1443 SelectionNameGroupID = SelectionName
1444
1445 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
1446 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1447
1448 # Add selections name sub group to selections group...
1449 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID] = SelectionsNameGroupName
1450 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID].append(SelectionsNameGroupName)
1451
1452 # Initialize selections names sub group members...
1453 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1454 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID] = []
1455
1456 # Add selection member to selections name group...
1457 SubGroupMemberName = "%s.Selection" % (SelectionsNameGroupName)
1458 SubGroupMemberID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1459
1460 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1461 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SubGroupMemberName)
1462
1463 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
1464 # Setup a surface sub group and add it to selections name group...
1465
1466 SelectionsNameSurfaceGroupName = "%s.Surface" % (SelectionsNameGroupName)
1467 SelectionsNameSurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1468
1469 # Add selection surface group to selection name group...
1470 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupID] = SelectionsNameSurfaceGroupName
1471 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SelectionsNameSurfaceGroupName)
1472
1473 # Initialize surface names sub group members...
1474 SelectionsNameSurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1475 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID] = []
1476
1477 # Setup a generic color surface...
1478 SubGroupMemberName = "%s.Surface" % (SelectionsNameSurfaceGroupName)
1479 SubGroupMemberID = "%s%s%sSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface")
1480 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1481 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID].append(SubGroupMemberName)
1482
1483 if GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
1484 # Setup surfaces...
1485 for MemberType in ["Hydrophobicity", "Hydrophobicity_Charge"]:
1486 MemberID = re.sub("_", "", MemberType)
1487
1488 SubGroupMemberName = "%s.%s" % (SelectionsNameSurfaceGroupName, MemberType)
1489 SubGroupMemberID = "%s%s%s%s" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface", MemberID)
1490
1491 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1492 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID].append(SubGroupMemberName)
1493
1494 if GetChainAloneResidueTypesStatus(FileIndex, ChainID):
1495 # Setup residue type group and its subgroups...
1496 ResiduesGroupName = "%s.Residues" % (ChainAloneGroupName)
1497
1498 ResiduesGroupIDPrefix = "ChainAloneResidues"
1499 ResiduesGroupID = "%sGroup" % ResiduesGroupIDPrefix
1500
1501 # Add residue group to chain alone group...
1502 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID] = ResiduesGroupName
1503 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(ResiduesGroupName)
1504
1505 # Initialize residue group members...
1506 ResiduesGroupMembersID = "%sGroupMembers" % ResiduesGroupIDPrefix
1507 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID] = []
1508
1509 # Setup residues sub groups and its members...
1510 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1511 SubGroupID = re.sub("_", "", SubGroupType)
1512
1513 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
1514 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
1515
1516 # Add sub group to residues group...
1517 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID] = ResiduesSubGroupName
1518 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
1519
1520 # Initialize sub group members...
1521 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
1522 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID] = []
1523
1524 # Add sub group members to subgroup...
1525 for MemberType in ["Residues", "Surface"]:
1526 MemberID = re.sub("_", "", MemberType)
1527
1528 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
1529 SubGroupMemberID = "%s%s%s" % (ResiduesGroupIDPrefix, SubGroupID, MemberID)
1530
1531 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1532 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID].append(SubGroupMemberName)
1533
1534 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
1535 # Setup a surface group and add it to chain alone group...
1536 SurfaceGroupName = "%s.Surface" % (ChainAloneGroupName)
1537 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"] = SurfaceGroupName
1538 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SurfaceGroupName)
1539
1540 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"] = []
1541
1542 # Setup a generic color surface...
1543 Name = "%s.Surface" % (SurfaceGroupName)
1544 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"] = Name
1545 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1546
1547 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
1548 # Setup hydrophobicity surface...
1549 Name = "%s.Hydrophobicity" % (SurfaceGroupName)
1550 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"] = Name
1551 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1552
1553 # Setup hydrophobicity and charge surface...
1554 Name = "%s.Hydrophobicity_Charge" % (SurfaceGroupName)
1555 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"] = Name
1556 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1557
1558 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
1559 # Setup electrostatics group...
1560 GroupName = "%s.Vacuum_Electrostatics" % (SurfaceGroupName)
1561 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroup"] = GroupName
1562 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(GroupName)
1563
1564 # Setup electrostatics group members...
1565 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"] = []
1566
1567 for MemberType in ["Chain", "Contact_Potential", "Map", "Legend", "Volume"]:
1568 MemberID = re.sub("_", "", MemberType)
1569
1570 Name = "%s.%s" % (GroupName, MemberType)
1571 NameID = "ChainAloneElectrostaticsSurface%s" % MemberID
1572
1573 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
1574 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"].append(Name)
1575
1576 if GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
1577 # Setup disulfide bonds group and add it to chain alone group...
1578 DisulfideBondsGroupName = "%s.Disulfide_Bonds" % (ChainAloneGroupName)
1579 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"] = DisulfideBondsGroupName
1580 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(DisulfideBondsGroupName)
1581
1582 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"] = []
1583
1584 # Setup a residues object for disulfide bonds...
1585 Name = "%s.Residues" % (DisulfideBondsGroupName)
1586 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"] = Name
1587 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"].append(Name)
1588
1589 if GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
1590 # Setup salt bridges group and add it to chain alone group...
1591 SaltBridgesGroupName = "%s.Salt_Bridges" % (ChainAloneGroupName)
1592 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"] = SaltBridgesGroupName
1593 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SaltBridgesGroupName)
1594
1595 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"] = []
1596
1597 # Setup residues group and add it to salt bridges group...
1598 ResiduesGroupName = "%s.Residues" % (SaltBridgesGroupName)
1599 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroup"] = ResiduesGroupName
1600 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"].append(ResiduesGroupName)
1601
1602 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"] = []
1603
1604 # Setup objects for residues group...
1605 Name = "%s.Positively_Charged" % (ResiduesGroupName)
1606 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesPositivelyCharged"] = Name
1607 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"].append(Name)
1608
1609 Name = "%s.Negatively_Charged" % (ResiduesGroupName)
1610 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesNegativelyCharged"] = Name
1611 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"].append(Name)
1612
1613 # Add contacts object to salt bridges group...
1614 Name = "%s.Contacts" % (SaltBridgesGroupName)
1615 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesContacts"] = Name
1616 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"].append(Name)
1617
1618 # Setup solvent and inorganic objects for chain...
1619 for NameID in ["Solvent", "Inorganic"]:
1620 Name = "%s.%s" % (ChainGroupName, NameID)
1621 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
1622 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
1623
1624 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
1625 """Stetup groups and objects for ligand."""
1626
1627 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
1628
1629 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
1630
1631 # Setup a chain level ligand group...
1632 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
1633 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
1634 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
1635
1636 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
1637
1638 # Set up groups and objects for a specific ligand group...
1639 for GroupType in ["Ligand", "Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
1640 GroupID = re.sub("_", "", GroupType)
1641 GroupName = "%s.%s" % (ChainLigandGroupName, GroupType)
1642
1643 GroupNameID = "%sGroup" % (GroupID)
1644 GroupMembersID = "%sGroupMembers" % (GroupID)
1645
1646 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
1647 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
1648
1649 GroupTypeObjectName = "%s.%s" % (GroupName, GroupType)
1650 GroupTypeObjectID = "%s" % (GroupID)
1651 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID] = GroupTypeObjectName
1652
1653 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
1654 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(GroupTypeObjectName)
1655
1656 if re.match("^Ligand$", GroupType, re.I):
1657 # Only need to add ball and stick...
1658 BallAndStickName = "%s.BallAndStick" % (GroupName)
1659 BallAndStickID = "%sBallAndStick" % (GroupID)
1660 PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickID] = BallAndStickName
1661 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(BallAndStickName)
1662
1663 if re.match("^(Pocket|Pocket_Solvent|Pocket_Inorganic)$", GroupType, re.I):
1664 PolarContactsName = "%s.Polar_Contacts" % (GroupName)
1665 PolarContactsID = "%sPolarContacts" % (GroupID)
1666 PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID] = PolarContactsName
1667 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PolarContactsName)
1668
1669 if re.match("^Pocket_Inorganic$", GroupType, re.I):
1670 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
1671 PiCationContactsID = "%sPiCationContacts" % (GroupID)
1672 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
1673 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
1674
1675 if re.match("^Pocket$", GroupType, re.I):
1676 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % (GroupName)
1677 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
1678 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID] = HydrophobicContactsName
1679 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HydrophobicContactsName)
1680
1681 PiPiContactsName = "%s.Pi_Pi_Contacts" % (GroupName)
1682 PiPiContactsID = "%sPiPiContacts" % (GroupID)
1683 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiPiContactsID] = PiPiContactsName
1684 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiPiContactsName)
1685
1686 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
1687 PiCationContactsID = "%sPiCationContacts" % (GroupID)
1688 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
1689 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
1690
1691 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
1692 PiCationContactsID = "%sPiCationContacts" % (GroupID)
1693 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
1694 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
1695
1696 HalogenContactsName = "%s.Halogen_Contacts" % (GroupName)
1697 HalogenContactsID = "%sHalogenContacts" % (GroupID)
1698 PyMOLObjectNames["Ligands"][ChainID][LigandID][HalogenContactsID] = HalogenContactsName
1699 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HalogenContactsName)
1700
1701 if GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
1702 # Setup selections group and its subgroups..
1703 SelectionsGroupName = "%s.Selections" % (GroupName)
1704 SelectionsGroupID = "%sSelectionsGroup" % (GroupID)
1705 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupID)
1706
1707 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID] = SelectionsGroupName
1708 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(SelectionsGroupName)
1709
1710 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID] = []
1711
1712 # Setup selections name sub group and its members...
1713 for SelectionName in OptionsInfo["PocketChainSelectionsInfo"]["Names"]:
1714 SelectionNameGroupID = SelectionName
1715
1716 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
1717 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupID, SelectionNameGroupID)
1718 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupID, SelectionNameGroupID)
1719
1720 # Add selections name sub group to selections group...
1721 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupID] = SelectionsNameGroupName
1722 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID].append(SelectionsNameGroupName)
1723
1724 # Initialize selections names sub group members...
1725 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID] = []
1726
1727 # Add selection member to selections name group...
1728 SubGroupMemberName = "%s.Selection" % (SelectionsNameGroupName)
1729 SubGroupMemberID = "%s%sSelection" % (SelectionsGroupID, SelectionNameGroupID)
1730
1731 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
1732 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID].append(SubGroupMemberName)
1733
1734 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
1735 # Setup a surface sub group and add it to selections name group...
1736 SelectionsNameSurfaceGroupName = "%s.Surface" % (SelectionsNameGroupName)
1737 SelectionsNameSurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupID, SelectionNameGroupID)
1738
1739 # Add selection surface group to selection name group...
1740 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupID] = SelectionsNameSurfaceGroupName
1741 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID].append(SelectionsNameSurfaceGroupName)
1742
1743 # Initialize surface names sub group members...
1744 SelectionsNameSurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupID, SelectionNameGroupID)
1745 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupMembersID] = []
1746
1747 # Setup surfaces...
1748 for MemberType in ["Surface", "Hydrophobicity", "Hydrophobicity_Charge"]:
1749 MemberID = re.sub("_", "", MemberType)
1750
1751 SubGroupMemberName = "%s.%s" % (SelectionsNameSurfaceGroupName, MemberType)
1752 SubGroupMemberID = "%s%s%s%s" % (SelectionsGroupID, SelectionNameGroupID, "Surface", MemberID)
1753
1754 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
1755 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupMembersID].append(SubGroupMemberName)
1756
1757 if GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
1758 # Setup residue type group and add to pocket group...
1759 ResiduesGroupName = "%s.Residues" % (GroupName)
1760 ResiduesGroupID = "%sResiduesGroup" % (GroupID)
1761 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
1762
1763 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupID] = ResiduesGroupName
1764 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(ResiduesGroupName)
1765 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID] = []
1766
1767 # Setup residue group subgroup and its members...
1768 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1769 SubGroupID = re.sub("_", "", SubGroupType)
1770 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
1771 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
1772 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
1773
1774 # Add sub group to residues group...
1775 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID] = ResiduesSubGroupName
1776 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
1777 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID] = []
1778
1779 # Add sub group members to subgroup...
1780 for MemberType in ["Residues", "Surface"]:
1781 MemberID = re.sub("_", "", MemberType)
1782 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
1783 SubGroupMemberID = "%s%s" % (ResiduesSubGroupID, MemberID)
1784
1785 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
1786 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID].append(SubGroupMemberName)
1787
1788 if GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
1789 # Setup a surfaces group and add it to pocket group...
1790 SurfacesGroupName = "%s.Surfaces" % (GroupName)
1791 SurfacesGroupID = "%sSurfacesGroup" % (GroupID)
1792 SurfacesGroupMembersID = "%sMembers" % (SurfacesGroupID)
1793
1794 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupID] = SurfacesGroupName
1795 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(SurfacesGroupName)
1796 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID] = []
1797
1798 # Setup surfaces subgroup and its members...
1799 for SubGroupType in ["Surface", "Cavity"]:
1800 SubGroupID = re.sub("_", "", SubGroupType)
1801 SurfacesSubGroupName = "%s.%s" % (SurfacesGroupName, SubGroupType)
1802 SurfacesSubGroupID = "%s%sGroup" % (SurfacesGroupID, SubGroupID)
1803 SurfacesSubGroupMembersID = "%sMembers" % (SurfacesSubGroupID)
1804
1805 # Add sub group to surfaces group...
1806 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupID] = SurfacesSubGroupName
1807 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID].append(SurfacesSubGroupName)
1808 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID] = []
1809
1810 # Setup a generic color surface...
1811 SurfaceName = "%s.Surface" % (SurfacesSubGroupName)
1812 SurfaceID = "%sSurface" % (SurfacesSubGroupID)
1813 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceID] = SurfaceName
1814 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(SurfaceName)
1815
1816 if GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
1817 # Surface colored by hydrophobicity...
1818 HydrophobicSurfaceName = "%s.Hydrophobicity" % (SurfacesSubGroupName)
1819 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SurfacesSubGroupID)
1820 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID] = HydrophobicSurfaceName
1821 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(HydrophobicSurfaceName)
1822
1823 # Surface colored by hydrophobicity and charge...
1824 HydrophobicChargeSurfaceName = "%s.Hydrophobicity_Charge" % (SurfacesSubGroupName)
1825 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SurfacesSubGroupID)
1826 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicChargeSurfaceID] = HydrophobicChargeSurfaceName
1827 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(HydrophobicChargeSurfaceName)
1828
1829 if GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
1830 ElectrostaticsGroupName = "%s.Vacuum_Electrostatics" % (SurfacesSubGroupName)
1831 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SurfacesSubGroupID)
1832 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SurfacesSubGroupID)
1833
1834 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupID] = ElectrostaticsGroupName
1835 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(ElectrostaticsGroupName)
1836
1837 # Setup electrostatics group members without the volume object...
1838 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupMembersID] = []
1839
1840 for MemberType in ["Pocket", "Contact_Potential", "Map", "Legend"]:
1841 MemberID = re.sub("_", "", MemberType)
1842
1843 Name = "%s.%s" % (ElectrostaticsGroupName, MemberType)
1844 NameID = "%s%s" % (ElectrostaticsGroupID, MemberID)
1845
1846 PyMOLObjectNames["Ligands"][ChainID][LigandID][NameID] = Name
1847 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupMembersID].append(Name)
1848
1849 def SetupPyMOLObjectNamesForDockedPoses(FileIndex, PyMOLObjectNames, ChainID):
1850 """Stetup groups and objects for docked poses in input files for a chain."""
1851
1852 PyMOLObjectNames["DockedPosesInputFile"][ChainID] = {}
1853
1854 if not GetChainAloneDockedPosesStatus(FileIndex, ChainID):
1855 return
1856
1857 # Setup group for docked poses...
1858 if "DockedPosesGroup" not in PyMOLObjectNames["Chains"][ChainID]:
1859 # Setup docked poses group at a chain level...
1860 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
1861 DockedPosesGroupName = "%s.%s" % (ChainGroupName, OptionsInfo["DockedPosesGroupName"])
1862
1863 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"] = DockedPosesGroupName
1864 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(DockedPosesGroupName)
1865 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"] = []
1866
1867 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1868 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
1869 SetupPyMOLObjectNamesForDockedPosesInputFile(FileIndex, PyMOLObjectNames, ChainID, InputFileIndex)
1870
1871 def SetupPyMOLObjectNamesForDockedPosesInputFile(PDBFileIndex, PyMOLObjectNames, ChainID, InputFileIndex):
1872 """Stetup groups and objects for docked poses in an input file for a chain."""
1873
1874 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
1875 DockedPosesDistanceContactsInfo = OptionsInfo["DockedPosesDistanceContactsInfo"]
1876
1877 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
1878
1879 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID] = {}
1880
1881 DockedPosesGroupName = PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"]
1882
1883 # Setup a docked poses level InputFile group...
1884 DockedPosesInputFileGroupName = "%s.%s" % (DockedPosesGroupName, InputFileID)
1885 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupName"] = DockedPosesInputFileGroupName
1886 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"].append(DockedPosesInputFileGroupName)
1887
1888 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"] = []
1889
1890 # Setup objects for docked poses...
1891 PosesName = "%s.%s" % (DockedPosesInputFileGroupName, OptionsInfo["DockedPosesName"])
1892 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["Poses"] = PosesName
1893 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"].append(PosesName)
1894
1895 for GroupType in ["Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
1896 GroupID = re.sub("_", "", GroupType)
1897 GroupName = "%s.%s" % (DockedPosesInputFileGroupName, GroupType)
1898
1899 GroupNameID = "%sGroup" % (GroupID)
1900 GroupMembersID = "%sGroupMembers" % (GroupID)
1901
1902 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID] = GroupName
1903 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"].append(GroupName)
1904
1905 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID] = []
1906
1907 PocketID = "%sPocket" % GroupID
1908 PocketName = "%s.Pocket" % GroupName
1909 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PocketID] = PocketName
1910 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PocketName)
1911
1912 if DockedPosesInfo["DistanceContacts"] and re.match("^Pocket$", GroupType, re.I):
1913 # Setup distance contacts group and add it to pocket group...
1914 DistanceContactGroupName = "%s.Distance_Contacts" % GroupName
1915
1916 DistanceContactGroupNameID = "%sDistanceContactsGroup" % GroupID
1917 DistanceContactGroupMembersID = "%sDistanceContactsGroupMembers" % GroupID
1918
1919 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupNameID] = DistanceContactGroupName
1920 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(DistanceContactGroupName)
1921
1922 # Setup distance contacts group members...
1923 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID] = []
1924
1925 for ContactID in DockedPosesDistanceContactsInfo["ContactIDs"]:
1926 DistanceContactID = "%sPocketDistanceContacts%s" % (GroupID, ContactID)
1927 DistanceContactName = "%s.Distance_Contacts.%s" % (GroupName, ContactID)
1928
1929 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactID] = DistanceContactName
1930 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID].append(DistanceContactName)
1931
1932 PolarContactsID = "%sPolarContacts" % GroupID
1933 PolarContactsName = "%s.Polar_Contacts" % GroupName
1934 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PolarContactsID] = PolarContactsName
1935 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PolarContactsName)
1936
1937 if re.match("^Pocket_Inorganic$", GroupType, re.I):
1938 PiCationContactsID = "%sPiCationContacts" % GroupID
1939 PiCationContactsName = "%s.Pi_Cation_Contacts" % GroupName
1940 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID] = PiCationContactsName
1941 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiCationContactsName)
1942
1943 if re.match("^Pocket$", GroupType, re.I):
1944 HydrophobicContactsID = "%sHydrophobicContacts" % GroupID
1945 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % GroupName
1946 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HydrophobicContactsID] = HydrophobicContactsName
1947 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(HydrophobicContactsName)
1948
1949 PiPiContactsID = "%sPiPiContacts" % GroupID
1950 PiPiContactsName = "%s.Pi_Pi_Contacts" % GroupName
1951 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiPiContactsID] = PiPiContactsName
1952 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiPiContactsName)
1953
1954 PiCationContactsID = "%sPiCationContacts" % GroupID
1955 PiCationContactsName = "%s.Pi_Cation_Contacts" % GroupName
1956 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID] = PiCationContactsName
1957 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiCationContactsName)
1958
1959 HalogenContactsID = "%sHalogenContacts" % GroupID
1960 HalogenContactsName = "%s.Halogen_Contacts" % GroupName
1961 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HalogenContactsID] = HalogenContactsName
1962 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(HalogenContactsName)
1963
1964 def RetrieveInfilesInfo():
1965 """Retrieve information for input files."""
1966
1967 InfilesInfo = {}
1968
1969 InfilesInfo["InfilesNames"] = []
1970 InfilesInfo["InfilesRoots"] = []
1971 InfilesInfo["ChainsAndLigandsInfo"] = []
1972
1973 for Infile in OptionsInfo["InfilesNames"]:
1974 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
1975 InfileRoot = FileName
1976
1977 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
1978
1979 InfilesInfo["InfilesNames"].append(Infile)
1980 InfilesInfo["InfilesRoots"].append(InfileRoot)
1981 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
1982
1983 OptionsInfo["InfilesInfo"] = InfilesInfo
1984
1985 def RetrieveRefFileInfo():
1986 """Retrieve information for ref file."""
1987
1988 RefFileInfo = {}
1989 if not OptionsInfo["Align"]:
1990 OptionsInfo["RefFileInfo"] = RefFileInfo
1991 return
1992
1993 RefFile = OptionsInfo["RefFileName"]
1994
1995 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
1996 RefFileRoot = FileName
1997
1998 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
1999 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
2000 else:
2001 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
2002 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
2003
2004 RefFileInfo["RefFileName"] = RefFile
2005 RefFileInfo["RefFileRoot"] = RefFileRoot
2006 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
2007 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
2008
2009 OptionsInfo["RefFileInfo"] = RefFileInfo
2010
2011 def ProcessChainAndLigandIDs():
2012 """Process specified chain and ligand IDs for infiles."""
2013
2014 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
2015
2016 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2017 MiscUtil.PrintInfo("\nProcessing specified chain and ligand IDs for input file %s..." % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex])
2018
2019 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
2020 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], "-l, --ligandIDs", OptionsInfo["LigandIDs"])
2021 ProcessResidueTypesAndSurfaceAndChainSelectionsOptions(FileIndex, SpecifiedChainsAndLigandsInfo)
2022
2023 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
2024
2025 CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo)
2026
2027 def ProcessResidueTypesAndSurfaceAndChainSelectionsOptions(FileIndex, SpecifiedChainsAndLigandsInfo):
2028 """Process residue types, surface, and chian selections options for chains and pockets."""
2029
2030 SpecifiedChainsAndLigandsInfo["ChainSurfaces"] = {}
2031 SpecifiedChainsAndLigandsInfo["SurfaceChain"] = {}
2032 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"] = {}
2033
2034 SpecifiedChainsAndLigandsInfo["PocketChainSelections"] = {}
2035 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"] = {}
2036 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"] = {}
2037
2038 SpecifiedChainsAndLigandsInfo["PocketSurfaces"] = {}
2039 SpecifiedChainsAndLigandsInfo["SurfacePocket"] = {}
2040 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"] = {}
2041
2042 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"] = {}
2043 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"] = {}
2044
2045 SpecifiedChainsAndLigandsInfo["ChainSelections"] = {}
2046 SpecifiedChainsAndLigandsInfo["ChainSelectionsSurfaces"] = {}
2047 SpecifiedChainsAndLigandsInfo["SurfaceChainSelections"] = {}
2048
2049 SpecifiedChainsAndLigandsInfo["DisulfideBondsChain"] = {}
2050 SpecifiedChainsAndLigandsInfo["SaltBridgesChain"] = {}
2051
2052 SpecifiedChainsAndLigandsInfo["BFactorChain"] = {}
2053
2054 # Load infile...
2055 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2056 MolName = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
2057 pymol.cmd.load(Infile, MolName)
2058
2059 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2060 AminoAcidsPresent = PyMOLUtil.AreAminoAcidResiduesPresent(MolName, ChainID)
2061
2062 # Process BFactors for chains...
2063 BFactorChain = True if re.match("^yes$", OptionsInfo["BFactorChain"], re.I) else False
2064 SpecifiedChainsAndLigandsInfo["BFactorChain"][ChainID] = BFactorChain
2065
2066 # Process surfaces for chains...
2067 if re.match("^auto$", OptionsInfo["SurfaceChain"], re.I):
2068 SurfaceChain = True if AminoAcidsPresent else False
2069 else:
2070 SurfaceChain = True if re.match("^yes$", OptionsInfo["SurfaceChain"], re.I) else False
2071 SpecifiedChainsAndLigandsInfo["SurfaceChain"][ChainID] = SurfaceChain
2072
2073 if re.match("^auto$", OptionsInfo["SurfaceChainElectrostatics"], re.I):
2074 SurfaceChainElectrostatics = True if AminoAcidsPresent else False
2075 else:
2076 SurfaceChainElectrostatics = True if re.match("^yes$", OptionsInfo["SurfaceChainElectrostatics"], re.I) else False
2077 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"][ChainID] = SurfaceChainElectrostatics
2078
2079 SpecifiedChainsAndLigandsInfo["ChainSurfaces"][ChainID] = SurfaceChain
2080
2081 # Process disulfide bonds for chains...
2082 if re.match("^auto$", OptionsInfo["DisulfideBondsChain"], re.I):
2083 DisulfideBondsChain = True if AminoAcidsPresent else False
2084 else:
2085 DisulfideBondsChain = True if re.match("^yes$", OptionsInfo["DisulfideBondsChain"], re.I) else False
2086 SpecifiedChainsAndLigandsInfo["DisulfideBondsChain"][ChainID] = DisulfideBondsChain
2087
2088 # Process salt bridges bonds for chains...
2089 if re.match("^auto$", OptionsInfo["SaltBridgesChain"], re.I):
2090 SaltBridgesChain = True if AminoAcidsPresent else False
2091 else:
2092 SaltBridgesChain = True if re.match("^yes$", OptionsInfo["SaltBridgesChain"], re.I) else False
2093 SpecifiedChainsAndLigandsInfo["SaltBridgesChain"][ChainID] = SaltBridgesChain
2094
2095 # Process residue types for chains...
2096 if re.match("^auto$", OptionsInfo["ResidueTypesChain"], re.I):
2097 ResidueTypesChain = True if AminoAcidsPresent else False
2098 else:
2099 ResidueTypesChain = True if re.match("^yes$", OptionsInfo["ResidueTypesChain"], re.I) else False
2100 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"][ChainID] = ResidueTypesChain
2101
2102 # Process chain selections...
2103 ChainSelections = True if len(OptionsInfo["ChainSelectionsInfo"]["Names"]) else False
2104 SpecifiedChainsAndLigandsInfo["ChainSelections"][ChainID] = ChainSelections
2105
2106 # Process surfaces for chain selections...
2107 if re.match("^auto$", OptionsInfo["SelectionsChainSurface"], re.I):
2108 SurfaceChainSelections = True if AminoAcidsPresent else False
2109 else:
2110 SurfaceChainSelections = True if re.match("^yes$", OptionsInfo["SelectionsChainSurface"], re.I) else False
2111 SpecifiedChainsAndLigandsInfo["SurfaceChainSelections"][ChainID] = SurfaceChainSelections
2112
2113 SpecifiedChainsAndLigandsInfo["ChainSelectionsSurfaces"][ChainID] = SurfaceChainSelections
2114
2115 # Process selections, residue types and surfaces for pockets...
2116 SpecifiedChainsAndLigandsInfo["PocketChainSelections"][ChainID] = {}
2117 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"][ChainID] = {}
2118 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"][ChainID] = {}
2119
2120 SpecifiedChainsAndLigandsInfo["PocketSurfaces"][ChainID] = {}
2121 SpecifiedChainsAndLigandsInfo["SurfacePocket"][ChainID] = {}
2122 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"][ChainID] = {}
2123
2124 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"][ChainID] = {}
2125
2126 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
2127 #Process pocket chain selections and surfaces...
2128 PocketChainSelections = True if len(OptionsInfo["PocketChainSelectionsInfo"]["Names"]) else False
2129 SpecifiedChainsAndLigandsInfo["PocketChainSelections"][ChainID][LigandID] = PocketChainSelections
2130
2131 # Process surfaces for chain selections...
2132 if re.match("^auto$", OptionsInfo["SelectionsPocketSurface"], re.I):
2133 PocketChainSelectionsSurface = True if AminoAcidsPresent else False
2134 else:
2135 PocketChainSelectionsSurface = True if re.match("^yes$", OptionsInfo["SelectionsPocketSurface"], re.I) else False
2136
2137 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"][ChainID][LigandID] = PocketChainSelectionsSurface
2138
2139 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"][ChainID][LigandID] = PocketChainSelectionsSurface
2140
2141 #Process pocket surfaces...
2142 if re.match("^auto$", OptionsInfo["PocketSurface"], re.I):
2143 PocketSurface = True if AminoAcidsPresent else False
2144 else:
2145 PocketSurface = True if re.match("^yes$", OptionsInfo["PocketSurface"], re.I) else False
2146 SpecifiedChainsAndLigandsInfo["SurfacePocket"][ChainID][LigandID] = PocketSurface
2147
2148 if re.match("^auto$", OptionsInfo["PocketSurfaceElectrostatics"], re.I):
2149 PocketSurfaceElectrostatics = True if AminoAcidsPresent else False
2150 else:
2151 PocketSurfaceElectrostatics = True if re.match("^yes$", OptionsInfo["PocketSurfaceElectrostatics"], re.I) else False
2152 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"][ChainID][LigandID] = PocketSurfaceElectrostatics
2153
2154 #Process pocket residue types...
2155 SpecifiedChainsAndLigandsInfo["PocketSurfaces"][ChainID][LigandID] = PocketSurface
2156
2157 if re.match("^auto$", OptionsInfo["PocketResidueTypes"], re.I):
2158 PocketResidueTypes = True if AminoAcidsPresent else False
2159 else:
2160 PocketResidueTypes = True if re.match("^yes$", OptionsInfo["PocketResidueTypes"], re.I) else False
2161 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"][ChainID][LigandID] = PocketResidueTypes
2162
2163 # Delete loaded object...
2164 pymol.cmd.delete(MolName)
2165
2166 def GetChainAloneResidueTypesStatus(FileIndex, ChainID):
2167 """Get status of residue types for chain alone object."""
2168
2169 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesChain"][ChainID]
2170
2171 return Status
2172
2173 def GetChainAloneBFactorStatus(FileIndex, ChainID):
2174 """Get status of B factors for chain alone object."""
2175
2176 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["BFactorChain"][ChainID]
2177
2178 return Status
2179
2180 def GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
2181 """Get status of disulfide bonds for chain alone object."""
2182
2183 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["DisulfideBondsChain"][ChainID]
2184
2185 return Status
2186
2187 def GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
2188 """Get status of salt bridges for chain alone object."""
2189
2190 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SaltBridgesChain"][ChainID]
2191
2192 return Status
2193
2194 def GetChainAloneDockedPosesStatus(FileIndex, ChainID):
2195 """Get status of docked for chain alone object."""
2196
2197 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["DockedPoses"][ChainID]
2198
2199 return Status
2200
2201 def GetTrajectoriesStatus(FileIndex):
2202 """Get status of trajectories for a PDB object."""
2203
2204 if OptionsInfo["TrajectoriesInfo"] is None:
2205 return False
2206
2207 Status = True if FileIndex in OptionsInfo["TrajectoriesInfo"]["PDBFileIndices"] else False
2208
2209 return Status
2210
2211 def GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
2212 """Get status of residue types for a pocket."""
2213
2214 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesPocket"][ChainID][LigandID]
2215
2216 def GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
2217 """Get status of surfaces present in chain alone object."""
2218
2219 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSurfaces"][ChainID]
2220
2221 def GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
2222 """Get status of selections present in a pocket."""
2223
2224 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["PocketChainSelections"][ChainID][LigandID]
2225
2226 def GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
2227 """Get status of surfaces present in a pocket."""
2228
2229 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["PocketSurfaces"][ChainID][LigandID]
2230
2231 def GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
2232 """Get status of hydrophobic surfaces for chain alone object."""
2233
2234 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChain"][ChainID]
2235
2236 def GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
2237 """Get status of electrostatics surfaces for chain alone object."""
2238
2239 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainElectrostatics"][ChainID]
2240
2241 def GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
2242 """Get status of surfaces for a pocket selection in a chain."""
2243
2244 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocketChainSelections"][ChainID][LigandID]
2245
2246 def GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
2247 """Get status of hydrophobic surfaces for a pocket."""
2248
2249 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocket"][ChainID][LigandID]
2250
2251 def GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
2252 """Get status of hydrophobic surfaces for a pocket."""
2253
2254 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocketElectrostatics"][ChainID][LigandID]
2255
2256 def GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
2257 """Get status of selections present in chain alone object."""
2258 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSelections"][ChainID]
2259
2260 def GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
2261 """Get status of chain selections surfaces present in chain alone object."""
2262 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSelectionsSurfaces"][ChainID]
2263
2264 def GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
2265 """Get status of hydrophobic surfaces for chain alone object."""
2266 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainSelections"][ChainID]
2267
2268 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
2269 """Check presence of valid ligand IDs."""
2270
2271 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
2272
2273 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2274 if len (SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
2275 MiscUtil.PrintInfo("Chain ID: %s; Specified LigandIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID])))
2276 else:
2277 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
2278 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))
2279
2280 def RetrieveFirstChainID(FileIndex):
2281 """Get first chain ID."""
2282
2283 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
2284
2285 FirstChainID = None
2286 if len(ChainsAndLigandsInfo["ChainIDs"]):
2287 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
2288
2289 return FirstChainID
2290
2291 def ProcessDockedPoses():
2292 """Process docked poses."""
2293
2294 OptionsInfo["DockedPosesGroupName"] = Options["--dockedPosesGroupName"]
2295 OptionsInfo["DockedPosesName"] = Options["--dockedPosesName"]
2296
2297 DockedPosesInfo = ProcessDockedPosesOptionsInfo("--dockedPoses", OptionsInfo["DockedPoses"])
2298 OptionsInfo["DockedPosesInfo"] = DockedPosesInfo
2299
2300 ProcessDockedPosesInfoForInfiles()
2301
2302 OptionsInfo["DockedPosesDistanceContactsCutoffs"] = Options["--dockedPosesDistanceContactsCutoffs"]
2303 OptionsInfo["DockedPosesDistanceContactsColor"] = Options["--dockedPosesDistanceContactsColor"]
2304
2305 DockedPosesDistanceContactsInfo = ProcessDockedPosesDistanceContactsOptionsInfo()
2306 OptionsInfo["DockedPosesDistanceContactsInfo"] = DockedPosesDistanceContactsInfo
2307
2308 # Setup distance conatcts status for dockes poses...
2309 if DockedPosesInfo is not None:
2310 DockedPosesInfo["DistanceContacts"] = False
2311 if DockedPosesDistanceContactsInfo is not None:
2312 if len(DockedPosesDistanceContactsInfo["ContactIDs"]):
2313 DockedPosesInfo["DistanceContacts"] = True
2314
2315 def ProcessDockedPosesInfoForInfiles():
2316 """Process docked poses info for infiles."""
2317
2318 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
2319 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2320 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
2321 ProcessDockedPosesInfoForInfileAndChains(FileIndex, SpecifiedChainsAndLigandsInfo, DockedPosesInfo)
2322
2323 def ProcessDockedPosesInfoForInfileAndChains(FileIndex, SpecifiedChainsAndLigandsInfo, DockedPosesInfo):
2324 """Process docked poses info for a specific infile."""
2325
2326 SpecifiedChainsAndLigandsInfo["DockedPoses"] = {}
2327 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"] = {}
2328
2329 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2330 DockedPoses = False
2331 if DockedPosesInfo is not None:
2332 if FileIndex in DockedPosesInfo["PDBFileIndices"]:
2333 if ChainID == DockedPosesInfo['ChainID'][FileIndex]:
2334 DockedPoses = True
2335
2336 SpecifiedChainsAndLigandsInfo["DockedPoses"][ChainID] = DockedPoses
2337
2338 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID] = []
2339 if DockedPoses:
2340 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID].extend(DockedPosesInfo['InputFiles'][FileIndex])
2341
2342 def ProcessDockedPosesOptionsInfo(DockedPosesOptionName, DockedPosesOptionValue):
2343 """Process docked poses options info."""
2344
2345 DockedPoses = DockedPosesOptionValue
2346 if re.match("^none$", DockedPoses, re.I):
2347 return None
2348
2349 MiscUtil.PrintInfo("\nProcessing docked poses...")
2350
2351 # Initialize docked poses info...
2352 DockedPosesInfo = {}
2353 DockedPosesInfo["PDBFileIndices"] = []
2354
2355 DockedPosesInfo["PDBFile"] = {}
2356 DockedPosesInfo["ChainID"] = {}
2357 DockedPosesInfo["LigandID"] = {}
2358 DockedPosesInfo["UseInputFileAsLigandID"] = {}
2359 DockedPosesInfo["InputFiles"] = {}
2360 DockedPosesInfo["InputFilesRoots"] = {}
2361 DockedPosesInfo["InputFilesIDs"] = {}
2362
2363 # Parse docked poses values...
2364 DockedPosesWords = DockedPoses.split(",")
2365 if len(DockedPosesWords) % 4:
2366 MiscUtil.PrintError("The number of comma delimited docked poses values, %d, specified using \"%s\" option must be a multple of 4." % (len(DockedPosesWords), DockedPosesOptionName))
2367
2368 # Validate and process specified values...
2369 for Index in range(0, len(DockedPosesWords), 4):
2370 PDBFile = DockedPosesWords[Index].strip()
2371 ChainID = DockedPosesWords[Index + 1].strip()
2372 LigandID = DockedPosesWords[Index + 2].strip()
2373 InputFiles = DockedPosesWords[Index + 3].strip()
2374
2375 InputFiles = re.sub("[ ]+", " ", InputFiles)
2376 InputFiles = InputFiles.split(" ")
2377
2378 # Process PDB file...
2379 MiscUtil.ValidateOptionFilePath("--dockedPoses", PDBFile)
2380
2381 PDBFileIndex = None
2382 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2383 PDBInfile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2384 if PDBFile == PDBInfile:
2385 PDBFileIndex = FileIndex
2386 break
2387 if PDBFileIndex is None:
2388 MiscUtil.PrintError("The PDB file specified, %s, using option \"--dockedPoses\" is not valid. It must be specified as an input file." % (PDBFile))
2389
2390 if PDBFileIndex in DockedPosesInfo['PDBFileIndices']:
2391 MiscUtil.PrintError("The PDB file specified, %s, using option \"--dockedPoses\" is not valid. It is a duplicate and has already been specified." % (PDBFile))
2392
2393 # Process chain ID...
2394 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][PDBFileIndex]
2395 if ChainID not in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2396 MiscUtil.PrintError("The chain ID, %s, specified for PDB file, %s, using option \"--dockedPoses\" is not valid. It must be present in valid chain IDs corresponding to option \"-c, --chainIDs\" ." % (ChainID, PDBFile))
2397
2398 # Process ligand ID...
2399 UseInputFileAsLigandID = True if re.match("^UseInputFile$", LigandID, re.I) else False
2400 if not UseInputFileAsLigandID:
2401 if LigandID not in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
2402 MiscUtil.PrintError("The ligand ID, %s, specified for chain ID, %s, and PDB file, %s, using option \"--dockedPoses\" is not valid. It must be present in valid ligand IDs corresponding to option \"-l, --ligandIDs\" ." % (LigandID, ChainID, PDBFile))
2403
2404 # Process input files...
2405 InputFilesRoots = []
2406 InputFilesIDs = []
2407 for InputFile in InputFiles:
2408 MiscUtil.ValidateOptionFilePath("--dockedPoses", InputFile)
2409 MiscUtil.ValidateOptionFileExt("--dockedPoses", InputFile, "sdf sd")
2410
2411 FileDir, FileName, FileExt = MiscUtil.ParseFileName(InputFile)
2412 InputFileRoot = FileName
2413
2414 # Clean up input file names for generating PyMOL object names...
2415 InputFileID = re.sub("[^a-zA-Z0-9]", "_", FileName)
2416
2417 if InputFileRoot in InputFilesRoots:
2418 MiscUtil.PrintError("The input file specified, %s, using option \"--dockedPoses\" is not valid. It is a duplicate and has already been specified for a PDB file." % (InputFile))
2419
2420 InputFilesRoots.append(InputFileRoot)
2421 InputFilesIDs.append(InputFileID)
2422
2423 # Track values...
2424 DockedPosesInfo['PDBFileIndices'].append(PDBFileIndex)
2425
2426 DockedPosesInfo["PDBFile"][PDBFileIndex] = PDBFile
2427 DockedPosesInfo["ChainID"][PDBFileIndex] = ChainID
2428
2429 DockedPosesInfo["LigandID"][PDBFileIndex] = LigandID
2430 DockedPosesInfo["UseInputFileAsLigandID"][PDBFileIndex] = UseInputFileAsLigandID
2431
2432 DockedPosesInfo["InputFiles"][PDBFileIndex] = InputFiles
2433 DockedPosesInfo["InputFilesRoots"][PDBFileIndex] = InputFilesRoots
2434 DockedPosesInfo["InputFilesIDs"][PDBFileIndex] = InputFilesIDs
2435
2436 return DockedPosesInfo
2437
2438 def ProcessDockedPosesDistanceContactsOptionsInfo():
2439 """Process dockes poses distance contacts info. """
2440
2441 DistanceContactsCutoffs = OptionsInfo["DockedPosesDistanceContactsCutoffs"]
2442 if re.match("^none$", DistanceContactsCutoffs):
2443 return None
2444
2445 DistanceContactsInfo = {}
2446 DistanceContactsInfo["ContactIDs"] = []
2447 DistanceContactsInfo["ContactCutoff"] = {}
2448
2449 DistanceContactsCutoffs = re.sub(" ", "", DistanceContactsCutoffs)
2450 if not DistanceContactsCutoffs:
2451 MiscUtil.PrintError("No value specified using \"--dockedPosesDistanceContactsCutoffs\" option.")
2452
2453 ContactCutoffValues = DistanceContactsCutoffs.split(",")
2454 for Index, ContactCutoff in enumerate(ContactCutoffValues):
2455 MiscUtil.ValidateOptionFloatValue("--dockedPosesDistanceContactsCutoffs", ContactCutoff, {">" : 0.0, "<=": OptionsInfo["PocketDistanceCutoff"]})
2456 ContactCutoff = float(ContactCutoff.strip())
2457
2458 ContactID = "Contact%s_At_%s" % ((Index + 1),ContactCutoff)
2459 ContactID = re.sub("\.", "pt", ContactID)
2460
2461 DistanceContactsInfo["ContactIDs"].append(ContactID)
2462 DistanceContactsInfo["ContactCutoff"][ContactID] = ContactCutoff
2463
2464 return DistanceContactsInfo
2465
2466 def ProcessTrajectories():
2467 """Process trajectories."""
2468
2469 TrajectoriesInfo = ProcessTrajectoriesOptionsInfo("--Trajectories", OptionsInfo["Trajectories"])
2470 OptionsInfo["TrajectoriesInfo"] = TrajectoriesInfo
2471
2472 def ProcessTrajectoriesOptionsInfo(TrajectoriesOptionName, TrajectoriesOptionValue):
2473 """Process trajectories options info."""
2474
2475 Trajectories = TrajectoriesOptionValue
2476 if re.match("^none$", Trajectories, re.I):
2477 return None
2478
2479 MiscUtil.PrintInfo("\nProcessing trajectories...")
2480
2481 # Initialize trajectories info...
2482 TrajectoriesInfo = {}
2483 TrajectoriesInfo["PDBFileIndices"] = []
2484
2485 TrajectoriesInfo["PDBFile"] = {}
2486 TrajectoriesInfo["TrajFiles"] = {}
2487 TrajectoriesInfo["TrajFilesRoots"] = {}
2488 TrajectoriesInfo["TrajFilesIDs"] = {}
2489
2490 # Parse trajectories values...
2491 TrajectoriesWords = Trajectories.split(",")
2492 if len(TrajectoriesWords) % 2:
2493 MiscUtil.PrintError("The number of comma delimited trajectories values, %d, specified using \"%s\" option must be a multple of 2." % (len(TrajectoriesWords), TrajectoriesOptionName))
2494
2495 # Validate and process specified values...
2496 for Index in range(0, len(TrajectoriesWords), 2):
2497 PDBFile = TrajectoriesWords[Index].strip()
2498 TrajFiles = TrajectoriesWords[Index + 1].strip()
2499
2500 TrajFiles = re.sub("[ ]+", " ", TrajFiles)
2501 TrajFiles = TrajFiles.split(" ")
2502
2503 # Process PDB file...
2504 MiscUtil.ValidateOptionFilePath(TrajectoriesOptionName, PDBFile)
2505
2506 PDBFileIndex = None
2507 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2508 PDBInfile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2509 if PDBFile == PDBInfile:
2510 PDBFileIndex = FileIndex
2511 break
2512 if PDBFileIndex is None:
2513 MiscUtil.PrintError("The topology PDB file specified, %s, using option \"%s\" is not valid. It must be specified as an input file." % (PDBFile, TrajectoriesOptionName))
2514
2515 if PDBFileIndex in TrajectoriesInfo['PDBFileIndices']:
2516 MiscUtil.PrintError("The topology PDB file specified, %s, using option \"%s\" is not valid. It is a duplicate and has already been specified." % (PDBFile, TrajectoriesOptionName))
2517
2518 # Process trajectory files...
2519 TrajFilesRoots = []
2520 TrajFilesIDs = []
2521 for TrajFile in TrajFiles:
2522 MiscUtil.ValidateOptionFilePath(TrajectoriesOptionName, TrajFile)
2523
2524 FileDir, FileName, FileExt = MiscUtil.ParseFileName(TrajFile)
2525 TrajFileRoot = FileName
2526
2527 # Clean up trajectory file names for generating PyMOL object names...
2528 TrajFileID = re.sub("[^a-zA-Z0-9]", "_", FileName)
2529
2530 if TrajFileRoot in TrajFilesRoots:
2531 MiscUtil.PrintError("The trajectory file specified, %s, using option \"%s\" is not valid. It is a duplicate and has already been specified for a PDB file." % (TrajFile, TrajectoriesOptionName))
2532
2533 TrajFilesRoots.append(TrajFileRoot)
2534 TrajFilesIDs.append(TrajFileID)
2535
2536 # Track values...
2537 TrajectoriesInfo['PDBFileIndices'].append(PDBFileIndex)
2538
2539 TrajectoriesInfo["PDBFile"][PDBFileIndex] = PDBFile
2540
2541 TrajectoriesInfo["TrajFiles"][PDBFileIndex] = TrajFiles
2542 TrajectoriesInfo["TrajFilesRoots"][PDBFileIndex] = TrajFilesRoots
2543 TrajectoriesInfo["TrajFilesIDs"][PDBFileIndex] = TrajFilesIDs
2544
2545 return TrajectoriesInfo
2546
2547 def ProcessResidueTypes():
2548 """Process residue types."""
2549
2550 ResidueTypesNamesInfo, ResidueTypesParamsInfo = PyMOLUtil.ProcessResidueTypesOptionsInfo("-r, --residueTypes", OptionsInfo["ResidueTypes"])
2551 OptionsInfo["ResidueTypesNames"] = ResidueTypesNamesInfo
2552 OptionsInfo["ResidueTypesParams"] = ResidueTypesParamsInfo
2553
2554 def ProcessSaltBridgesChainResidues():
2555 """Process salt bridges chain residues."""
2556
2557 SaltBridgesChainResiduesInfo = PyMOLUtil.ProcessSaltBridgesChainResiduesOptionsInfo("--saltBridgesChainResidues", OptionsInfo["SaltBridgesChainResidues"])
2558 OptionsInfo["SaltBridgesChainResiduesInfo"] = SaltBridgesChainResiduesInfo
2559
2560 def ProcessSurfaceAtomTypesColors():
2561 """Process surface atom types colors."""
2562
2563 AtomTypesColorNamesInfo = PyMOLUtil.ProcessSurfaceAtomTypesColorsOptionsInfo("--surfaceAtomTypesColors", OptionsInfo["SurfaceAtomTypesColors"])
2564 OptionsInfo["AtomTypesColorNames"] = AtomTypesColorNamesInfo
2565
2566 def ProcessPockectChainSelections():
2567 """Process custom selections for pocket chains."""
2568
2569 PocketChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo("--selectionsPocket", OptionsInfo["SelectionsPocket"])
2570 OptionsInfo["PocketChainSelectionsInfo"] = PocketChainSelectionsInfo
2571
2572 def ProcessChainSelections():
2573 """Process custom selections for chains."""
2574
2575 ChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo("--selectionsChain", OptionsInfo["SelectionsChain"])
2576 OptionsInfo["ChainSelectionsInfo"] = ChainSelectionsInfo
2577
2578 def ProcessOptions():
2579 """Process and validate command line arguments and options."""
2580
2581 MiscUtil.PrintInfo("Processing options...")
2582
2583 # Validate options...
2584 ValidateOptions()
2585
2586 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
2587 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
2588 OptionsInfo["AlignMode"] = Options["--alignMode"]
2589
2590 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
2591
2592 OptionsInfo["BFactorChain"] = Options["--BFactorChain"]
2593 OptionsInfo["BFactorColorPalette"] = Options["--BFactorColorPalette"]
2594
2595 OptionsInfo["Infiles"] = Options["--infiles"]
2596 OptionsInfo["InfilesNames"] = Options["--infileNames"]
2597
2598 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
2599 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
2600 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
2601 else:
2602 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
2603
2604 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
2605
2606 OptionsInfo["Overwrite"] = Options["--overwrite"]
2607 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
2608
2609 OptionsInfo["Outfile"] = Options["--outfile"]
2610 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
2611 OptionsInfo["PSEOut"] = False
2612 if re.match("^pml$", FileExt, re.I):
2613 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
2614 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
2615 elif re.match("^pse$", FileExt, re.I):
2616 OptionsInfo["PSEOut"] = True
2617 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
2618 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
2619 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
2620 MiscUtil.PrintError("The intermediate output file to be generated, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again." % OptionsInfo["PMLOutfile"] )
2621
2622 OptionsInfo["DisulfideBondsChain"] = Options["--disulfideBondsChain"]
2623
2624 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
2625
2626 OptionsInfo["PocketContactsLigandColor"] = Options["--pocketContactsLigandColor"]
2627 OptionsInfo["PocketContactsLigandHydrophobicColor"] = Options["--pocketContactsLigandHydrophobicColor"]
2628 OptionsInfo["PocketContactsLigandPiPiColor"] = Options["--pocketContactsLigandPiPiColor"]
2629 OptionsInfo["PocketContactsLigandPiCationColor"] = Options["--pocketContactsLigandPiCationColor"]
2630 OptionsInfo["PocketContactsLigandHalogenColor"] = Options["--pocketContactsLigandHalogenColor"]
2631
2632 OptionsInfo["PocketContactsSolventColor"] = Options["--pocketContactsSolventColor"]
2633
2634 OptionsInfo["PocketContactsInorganicColor"] = Options["--pocketContactsInorganicColor"]
2635 OptionsInfo["PocketContactsInorganicPiCationColor"] = Options["--pocketContactsInorganicPiCationColor"]
2636
2637 OptionsInfo["PocketContactsCutoff"] = float(Options["--pocketContactsCutoff"])
2638 OptionsInfo["PocketDistanceCutoff"] = float(Options["--pocketDistanceCutoff"])
2639
2640 OptionsInfo["PocketLabelColor"] = Options["--pocketLabelColor"]
2641
2642 OptionsInfo["PocketResidueTypes"] = Options["--pocketResidueTypes"]
2643 OptionsInfo["PocketSurface"] = Options["--pocketSurface"]
2644 OptionsInfo["PocketSurfaceElectrostatics"] = Options["--pocketSurfaceElectrostatics"]
2645
2646 OptionsInfo["ResidueTypesChain"] = Options["--residueTypesChain"]
2647 OptionsInfo["ResidueTypes"] = Options["--residueTypes"]
2648 ProcessResidueTypes()
2649
2650 OptionsInfo["SaltBridgesChain"] = Options["--saltBridgesChain"]
2651 OptionsInfo["SaltBridgesChainContactsColor"] = Options["--saltBridgesChainContactsColor"]
2652 OptionsInfo["SaltBridgesChainCutoff"] = float(Options["--saltBridgesChainCutoff"])
2653 OptionsInfo["SaltBridgesChainResidues"] = Options["--saltBridgesChainResidues"]
2654 ProcessSaltBridgesChainResidues()
2655
2656 OptionsInfo["SelectionsChain"] = Options["--selectionsChain"]
2657 OptionsInfo["SelectionsChainSurface"] = Options["--selectionsChainSurface"]
2658 OptionsInfo["SelectionsChainStyle"] = Options["--selectionsChainStyle"]
2659 ProcessChainSelections()
2660
2661 OptionsInfo["SelectionsPocket"] = Options["--selectionsPocket"]
2662 OptionsInfo["SelectionsPocketSurface"] = Options["--selectionsPocketSurface"]
2663 OptionsInfo["SelectionsPocketStyle"] = Options["--selectionsPocketStyle"]
2664 ProcessPockectChainSelections()
2665
2666 OptionsInfo["SurfaceChain"] = Options["--surfaceChain"]
2667 OptionsInfo["SurfaceChainElectrostatics"] = Options["--surfaceChainElectrostatics"]
2668
2669 OptionsInfo["SurfaceChainComplex"] = True if re.match("^Yes$", Options["--surfaceChainComplex"], re.I) else False
2670 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
2671
2672 OptionsInfo["SurfaceColor"] = Options["--surfaceColor"]
2673 OptionsInfo["SurfaceColorPalette"] = Options["--surfaceColorPalette"]
2674 OptionsInfo["SurfaceAtomTypesColors"] = Options["--surfaceAtomTypesColors"]
2675 ProcessSurfaceAtomTypesColors()
2676
2677 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
2678
2679 RetrieveInfilesInfo()
2680 RetrieveRefFileInfo()
2681
2682 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
2683 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
2684
2685 ProcessChainAndLigandIDs()
2686
2687 OptionsInfo["DockedPoses"] = Options["--dockedPoses"]
2688 ProcessDockedPoses()
2689
2690 OptionsInfo["Trajectories"] = Options["--trajectories"]
2691 ProcessTrajectories()
2692
2693 def RetrieveOptions():
2694 """Retrieve command line arguments and options."""
2695
2696 # Get options...
2697 global Options
2698 Options = docopt(_docoptUsage_)
2699
2700 # Set current working directory to the specified directory...
2701 WorkingDir = Options["--workingdir"]
2702 if WorkingDir:
2703 os.chdir(WorkingDir)
2704
2705 # Handle examples option...
2706 if "--examples" in Options and Options["--examples"]:
2707 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
2708 sys.exit(0)
2709
2710 def ValidateOptions():
2711 """Validate option values."""
2712
2713 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
2714 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
2715 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
2716
2717 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
2718
2719 MiscUtil.ValidateOptionTextValue("--BFactorChain", Options["--BFactorChain"], "yes no")
2720
2721 # Expand infiles to handle presence of multiple input files...
2722 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
2723 if not len(InfileNames):
2724 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
2725
2726 # Validate file extensions...
2727 for Infile in InfileNames:
2728 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
2729 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
2730 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
2731 Options["--infileNames"] = InfileNames
2732
2733 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
2734 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
2735
2736 if re.match("^yes$", Options["--align"], re.I):
2737 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
2738 AlignRefFile = Options["--alignRefFile"]
2739 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
2740 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
2741 MiscUtil.ValidateOptionsDistinctFileNames("--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"])
2742
2743 MiscUtil.ValidateOptionTextValue("--disulfideBondsChain", Options["--disulfideBondsChain"], "yes no auto")
2744
2745 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
2746
2747 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
2748 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
2749
2750 MiscUtil.ValidateOptionFloatValue("--pocketContactsCutoff", Options["--pocketContactsCutoff"], {">": 0.0})
2751 MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0})
2752 if (float(Options["--pocketContactsCutoff"]) > float(Options["--pocketDistanceCutoff"])):
2753 MiscUtil.PrintError("The value, %s, specified using option \"--pocketContactsCutoff\" must be less than value, %s, specified using \"-pocketDistanceCutoff\" option." % (Options["--pocketContactsCutoff"], Options["--pocketDistanceCutoff"]))
2754
2755 MiscUtil.ValidateOptionTextValue("--pocketResidueTypes", Options["--pocketResidueTypes"], "yes no auto")
2756 MiscUtil.ValidateOptionTextValue("--pocketSurface", Options["--pocketSurface"], "yes no auto")
2757 MiscUtil.ValidateOptionTextValue("--pocketSurfaceElectrostatics", Options["--pocketSurfaceElectrostatics"], "yes no auto")
2758
2759 MiscUtil.ValidateOptionTextValue("--residueTypesChain", Options["--residueTypesChain"], "yes no auto")
2760
2761 MiscUtil.ValidateOptionTextValue("--saltBridgesChain", Options["--saltBridgesChain"], "yes no auto")
2762 MiscUtil.ValidateOptionFloatValue("--saltBridgesChainCutoff", Options["--saltBridgesChainCutoff"], {">": 0.0})
2763
2764 MiscUtil.ValidateOptionTextValue("--selectionsChainSurface", Options["--selectionsChainSurface"], "yes no auto")
2765 MiscUtil.ValidateOptionTextValue("--selectionsPocketSurface", Options["--selectionsPocketSurface"], "yes no auto")
2766
2767 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
2768 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no")
2769 MiscUtil.ValidateOptionTextValue("--surfaceChain", Options["--surfaceChain"], "yes no auto")
2770 MiscUtil.ValidateOptionTextValue("--surfaceChainElectrostatics", Options["--surfaceChainElectrostatics"], "yes no auto")
2771
2772 MiscUtil.ValidateOptionTextValue("--surfaceColorPalette", Options["--surfaceColorPalette"], "RedToWhite WhiteToGreen")
2773 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
2774
2775 # Setup a usage string for docopt...
2776 _docoptUsage_ = """
2777 PyMOLVisualizeMacromolecules.py - Visualize macromolecules
2778
2779 Usage:
2780 PyMOLVisualizeMacromolecules.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
2781 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
2782 [--allowEmptyObjects <yes or no>] [--BFactorChain <yes or no>] [--BFactorColorPalette <text>]
2783 [--chainIDs <First, All or ID1,ID2...>] [--disulfideBondsChain <yes or no>]
2784 [--dockedPoses <PDBFile,ChainID,LigandID,InputFiles,...>] [--dockedPosesDistanceContactsCutoffs <number1,number2...>]
2785 [--dockedPosesDistanceContactsColor <text>] [--dockedPosesGroupName <text>]
2786 [--dockedPosesName <text>] [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All or ID1,ID2...>]
2787 [--labelFontID <number>] [--PMLOut <yes or no>] [--pocketContactsInorganicColor <text>]
2788 [--pocketContactsInorganicPiCationColor <text>] [--pocketContactsLigandColor <text>]
2789 [--pocketContactsLigandHydrophobicColor <text>] [--pocketContactsLigandHalogenColor <text>]
2790 [--pocketContactsLigandPiCationColor <text>] [--pocketContactsLigandPiPiColor <text>]
2791 [--pocketContactsSolventColor <text>] [--pocketContactsCutoff <number>]
2792 [--pocketDistanceCutoff <number>] [--pocketLabelColor <text>] [--pocketResidueTypes <yes or no>]
2793 [--pocketSurface <yes or no>] [--pocketSurfaceElectrostatics <yes or no>]
2794 [--residueTypes <Type,Color,ResNames,...>] [--residueTypesChain <yes or no>]
2795 [--saltBridgesChain <yes or no>] [--saltBridgesChainContactsColor <text>]
2796 [--saltBridgesChainCutoff <number>] [--saltBridgesChainResidues <Type, ResNames,...>]
2797 [--selectionsChain <ObjectName,SelectionSpec,...>] [--selectionsChainSurface <yes or no>]
2798 [--selectionsChainStyle <DisplayStyle>] [--selectionsPocket <ObjectName,SelectionSpec,...>]
2799 [--selectionsPocketSurface <yes or no>] [--selectionsPocketStyle <DisplayStyle>]
2800 [--surfaceChain <yes or no>] [--surfaceChainElectrostatics <yes or no>]
2801 [--surfaceChainComplex <yes or no>] [--surfaceComplex <yes or no>]
2802 [--surfaceColor <ColorName>] [--surfaceColorPalette <RedToWhite or WhiteToGreen>]
2803 [--surfaceAtomTypesColors <ColorType,ColorSpec,...>]
2804 [--surfaceTransparency <number>] [--trajectories <PDBToplogyFile,TrajFiles,...> ]
2805 [--overwrite] [-w <dir>] -i <infile1,infile2,infile3...> -o <outfile>
2806 PyMOLVisualizeMacromolecules.py -h | --help | -e | --examples
2807
2808 Description:
2809 Generate PyMOL visualization files for viewing surfaces, chains, ligands, ligand
2810 binding pockets, and interactions between ligands and binding pockets in
2811 macromolecules including proteins and nucleic acids.
2812
2813 The supported input file format are: PDB (.pdb), CIF (.cif)
2814
2815 The supported output file formats are: PyMOL script file (.pml), PyMOL session
2816 file (.pse)
2817
2818 A variety of PyMOL groups and objects may be created for visualization of
2819 macromolecules. These groups and objects correspond to complexes, surfaces,
2820 chains, ligands, inorganics, ligand binding pockets, pocket, polar interactions,
2821 and pocket hydrophobic surfaces. A complete hierarchy of all possible PyMOL
2822 groups and objects is shown below:
2823
2824 <PDBFileRoot>
2825 .Complex
2826 .Complex
2827 .Surface
2828 .Trajectories
2829 .Topology
2830 .<TrajFileID>
2831 .Trajectory
2832 .<TrajFileID>
2833 ... ... ...
2834 .<TrajFileID>
2835 ... ... ...
2836 .Chain<ID>
2837 .Complex
2838 .Complex
2839 .Surface
2840 .Chain
2841 .Chain
2842 .BFactor
2843 .Putty
2844 .Cartoon
2845 .Selections
2846 .<Name>
2847 .Selection
2848 .Surface
2849 .Surface
2850 .Hydrophobicity
2851 .Hydrophobicity_Charge
2852 .<Name>
2853 ... ... ..
2854 .Residues
2855 .Aromatic
2856 .Residues
2857 .Surface
2858 .Hydrophobic
2859 .Residues
2860 .Surface
2861 .Polar
2862 .Residues
2863 .Surface
2864 .Positively_Charged
2865 .Residues
2866 .Surface
2867 .Negatively_Charged
2868 .Residues
2869 .Surface
2870 .Other
2871 .Residues
2872 .Surface
2873 .Surface
2874 .Surface
2875 .Hydrophobicity
2876 .Hydrophobicity_Charge
2877 .Vacuum_Electrostatics
2878 .Contact_Potentials
2879 .Map
2880 .Legend
2881 .Volume
2882 .Disulfide_Bonds
2883 .Residues
2884 .Salt_Bridges
2885 .Residues
2886 .Positively_Charged
2887 .Negatively_Charged
2888 .Contacts
2889 .Solvent
2890 .Inorganic
2891 .Ligand<ID>
2892 .Ligand
2893 .Ligand
2894 .BallAndStick
2895 .Pocket
2896 .Pocket
2897 .Polar_Contacts
2898 .Hydrophobic_Contacts
2899 .Pi_Pi_Contacts
2900 .Pi_Cation_Contacts
2901 .Halogen_Contacts
2902 .Selections
2903 .<Name>
2904 .Selection
2905 .Surface
2906 .Surface
2907 .Hydrophobicity
2908 .Hydrophobicity_Charge
2909 .<Name>
2910 ... ... ..
2911 .Residues
2912 .Aromatic
2913 .Residues
2914 .Surface
2915 .Hydrophobic
2916 .Residues
2917 .Surface
2918 .Polar
2919 .Residues
2920 .Surface
2921 .Positively_Charged
2922 .Residues
2923 .Surface
2924 .Negatively_Charged
2925 .Residues
2926 .Surface
2927 .Other
2928 .Residues
2929 .Surface
2930 .Surfaces
2931 .Surface
2932 .Surface
2933 .Hydrophobicity
2934 .Hydrophobicity_Charge
2935 .Vacuum_Electrostatics
2936 .Contact_Potentials
2937 .Map
2938 .Legend
2939 .Cavity
2940 .Surface
2941 .Hydrophobicity
2942 .Hydrophobicity_Charge
2943 .Vacuum_Electrostatics
2944 .Contact_Potentials
2945 .Map
2946 .Legend
2947 .Pocket_Solvent
2948 .Pocket_Solvent
2949 .Polar_Contacts
2950 .Pocket_Inorganic
2951 .Pocket_Inorganic
2952 .Polar_Contacts
2953 .Pi_Cation_Contacts
2954 .Ligand<ID>
2955 .Ligand
2956 ... ... ...
2957 .Pocket
2958 ... ... ...
2959 .Pocket_Solvent
2960 ... ... ...
2961 .Pocket_Inorganic
2962 ... ... ...
2963 .Docked_Poses or <CustomLabel>
2964 .<InputFileID>
2965 .Poses or <CustomLabel>
2966 .Pocket
2967 .Pocket
2968 .Distance_Contacts
2969 .Contact1_At_<Distance>
2970 .Contact1_At_<Distance>
2971 ... ... ...
2972 .Polar_Contacts
2973 .Hydrophobic_Contacts
2974 .Pi_Pi_Contacts
2975 .Pi_Cation_Contacts
2976 .Halogen_Contacts
2977 .Pocket_Solvent
2978 .Pocket_Solvent
2979 .Polar_Contacts
2980 .Pocket_Inorganic
2981 .Polar_Contacts
2982 .Pi_Cation_Contacts
2983 .<InputFileID>
2984 ... ... ...
2985 .<InputFileID>
2986 ... ... ...
2987 .Chain<ID>
2988 ... ... ...
2989 .Ligand<ID>
2990 ... ... ...
2991 .Ligand<ID>
2992 ... ... ...
2993 .Chain<ID>
2994 ... ... ...
2995 <PDBFileRoot>
2996 .Complex
2997 ... ... ...
2998 .Chain<ID>
2999 ... ... ...
3000 .Ligand<ID>
3001 ... ... ...
3002 .Ligand<ID>
3003 ... ... ...
3004 .Chain<ID>
3005 ... ... ...
3006
3007 The hydrophobic and electrostatic surfaces are not created for complete complex
3008 and chain complex in input file(s) by default. A word to the wise: The creation of
3009 surface objects may slow down loading of PML file and generation of PSE file, based
3010 on the size of input complexes. The generation of PSE file may also fail.
3011
3012 Options:
3013 -a, --align <yes or no> [default: no]
3014 Align input files to a reference file before visualization. The docked poses
3015 and trajectories are not aligned.
3016 --alignMethod <align, cealign, super> [default: super]
3017 Alignment methodology to use for aligning input files to a
3018 reference file.
3019 --alignMode <FirstChain or Complex> [default: FirstChain]
3020 Portion of input and reference files to use for spatial alignment of
3021 input files against reference file. Possible values: FirstChain or
3022 Complex.
3023
3024 The FirstChain mode allows alignment of the first chain in each input
3025 file to the first chain in the reference file along with moving the rest
3026 of the complex to coordinate space of the reference file. The complete
3027 complex in each input file is aligned to the complete complex in reference
3028 file for the Complex mode.
3029 --alignRefFile <filename> [default: FirstInputFile]
3030 Reference input file name. The default is to use the first input file
3031 name specified using '-i, --infiles' option.
3032 --allowEmptyObjects <yes or no> [default: no]
3033 Allow creation of empty PyMOL objects corresponding to solvent and
3034 inorganic atom selections across chains and ligands in input file(s). By
3035 default, the empty objects are marked for deletion.
3036 -b, --BFactorChain <yes or no> [default: yes]
3037 A cartoon and putty around individual chains colored by an arbitrary set
3038 of B factor values. The minimum and maximum values for B factors are
3039 automatically detected. These values may indicate spread of electron
3040 density around atoms or correspond to any other property mapped to
3041 B factors in input file.
3042 --BFactorColorPalette <text> [default: blue_white_red]
3043 Color palette for coloring cartoon and putty around chains generated using B
3044 factor values. Any valid PyMOL color palette name is allowed. No validation is
3045 performed. The complete list of valid color palette names is a available
3046 at: pymolwiki.org/index.php/Spectrum. Examples: blue_white_red,
3047 blue_white_magenta, blue_red, green_white_red, green_red.
3048 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
3049 List of chain IDs to use for visualizing macromolecules. Possible values:
3050 First, All, or a comma delimited list of chain IDs. The default is to use the
3051 chain ID for the first chain in each input file.
3052 -d --disulfideBondsChain <yes or no> [default: auto]
3053 Disulfide bonds for chains. By default, the disulfide bonds group is
3054 automatically created for chains containing amino acids and skipped for
3055 chains only containing nucleic acids.
3056 --dockedPoses <PDBFile,ChainID,LigandID,InputFiles,...> [default: none]
3057 PDB file name, pocket chain ID, ligand specification, and input files to use
3058 for creating pockets to visualize docked poses or any arbitrary set of
3059 molecules. Any valid PyMOL input file format is allowed.
3060
3061 It's a quartet of comma limited values corresponding to PDF file name,
3062 pocket chain ID, ligand ID, and input files. Multiple input file names are
3063 delimited by spaces.
3064
3065 The supported values for docked poses are shown below:
3066
3067 PDBFile: A valid PDB file name
3068 ChainID: A valid Chain ID
3069 LigandID: A valid Ligand ID or UseInputFile
3070 InputFiles: A space delimited list of input file names
3071
3072 All docked pose values must be specified. No default values are assigned.
3073
3074 The 'ChainID' and 'LigandID' are used for creating pocket to visualize docked
3075 poses.
3076
3077 The 'LigandID' must be a valid ligand ID in 'ChainID'. Alternatively, you may use
3078 input files by specifying 'UseInputFile' to select residues in 'ChainID' for creating
3079 pockets to visualize docked poses.
3080 --dockedPosesDistanceContactsCutoffs <number1,number2...> [default: none]
3081 A comma delimited list of distances in Angstroms for identifying and displaying
3082 distance contacts between heavy atoms in pocket residues and docked poses. A
3083 PyMOL distance contact object is created for each specified distance. You may
3084 find it helpful for identifying steric clashes between docked poses and pocket
3085 residues. The maximum distance cutoff value must be less than the specified
3086 value for '--pocketDistanceCutoff' option.
3087 --dockedPosesDistanceContactsColor <text> [default: red]
3088 Color for drawing distance contacts between docked poses and pocket residues.
3089 The specified value must be valid color. No validation is performed.
3090 --dockedPosesGroupName <text> [default: Docked_Poses]
3091 PyMOL object name for docked poses group. You may use an artbitray name
3092 to reflect data in input file(s) specified in '--dockedPoses' option. It must be a valid
3093 PyMOL object name. No validation is performed.
3094 --dockedPosesName <text> [default: Poses]
3095 PyMOL object name for docked poses object. You may use an artbitray name
3096 to reflect data in input file(s) specified in '--dockedPoses' option. It must be a
3097 valid PyMOL object name. No validation is performed.
3098 -e, --examples
3099 Print examples.
3100 -h, --help
3101 Print this help message.
3102 -i, --infiles <infile1,infile2,infile3...>
3103 Input file names.
3104 --ignoreHydrogens <yes or no> [default: yes]
3105 Ignore hydrogens for ligand, pocket, selection, and residue type views.
3106 -l, --ligandIDs <Largest, All or ID1,ID2...> [default: Largest]
3107 List of ligand IDs present in chains for visualizing macromolecules to
3108 highlight ligand interactions. Possible values: Largest, All, or a comma
3109 delimited list of ligand IDs. The default is to use the largest ligand present
3110 in all or specified chains in each input file.
3111
3112 Ligands are identified using organic selection operator available in PyMOL.
3113 It'll also identify buffer molecules as ligands. The largest ligand contains
3114 the highest number of heavy atoms.
3115 --labelFontID <number> [default: 7]
3116 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
3117 The specified value must be a valid PyMOL font ID. No validation is
3118 performed. The complete lists of valid font IDs is available at:
3119 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
3120 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
3121 -o, --outfile <outfile>
3122 Output file name.
3123 -p, --PMLOut <yes or no> [default: yes]
3124 Save PML file during generation of PSE file.
3125 --pocketContactsInorganicColor <text> [default: deepsalmon]
3126 Color for drawing polar contacts between inorganic and pocket residues.
3127 The specified value must be valid color. No validation is performed.
3128 --pocketContactsInorganicPiCationColor <text> [default: limon]
3129 Color for drawing pi cation contacts between inorganic and pocket residues.
3130 The specified value must be valid color. No validation is performed. The pi
3131 cation contacts are drawn using PyMOL distance command with support for
3132 mode 7 and may require incentive version of PyMOL.
3133 --pocketContactsLigandColor <text> [default: orange]
3134 Color for drawing polar contacts between ligand and pocket residues.
3135 The specified value must be valid color. No validation is performed.
3136 --pocketContactsLigandHalogenColor <text> [default: magenta]
3137 Color for drawing halogen contacts between ligand and pocket residues.
3138 The specified value must be valid color. No validation is performed.
3139 --pocketContactsLigandHydrophobicColor <text> [default: purpleblue]
3140 Color for drawing hydrophobic contacts between ligand and pocket residues.
3141 The specified value must be valid color. No validation is performed. The
3142 hydrophobic contacts are shown between pairs of carbon atoms not
3143 connected to hydrogen bond donor or acceptors atoms as identified
3144 by PyMOL.
3145 --pocketContactsLigandPiCationColor <text> [default: yelloworange]
3146 Color for drawing pi cation contacts between ligand and pocket residues.
3147 The specified value must be valid color. No validation is performed. The pi
3148 cation contacts are drawn using PyMOL distance command with support for
3149 mode 7 and may require incentive version of PyMOL.
3150 --pocketContactsLigandPiPiColor <text> [default: cyan]
3151 Color for drawing pi pi contacts between ligand and pocket residues.
3152 The specified value must be valid color. No validation is performed. The pi
3153 pi contacts are drawn using PyMOL distance command with support for
3154 mode 6 and may require incentive version of PyMOL.
3155 --pocketContactsSolventColor <text> [default: marine]
3156 Color for drawing polar contacts between solvent and pocket residues..
3157 The specified value must be valid color. No validation is performed.
3158 --pocketContactsCutoff <number> [default: 4.0]
3159 Distance in Angstroms for identifying polar, hyrdophobic contacts, pi pi,
3160 pi cation, and halogen contacts between atoms in pocket residues and
3161 ligands.
3162 --pocketDistanceCutoff <number> [default: 5.0]
3163 Distance in Angstroms for identifying pocket residues around ligands.
3164 --pocketLabelColor <text> [default: magenta]
3165 Color for drawing residue or atom level labels for a pocket. The specified
3166 value must be valid color. No validation is performed.
3167 --pocketResidueTypes <yes or no> [default: auto]
3168 Pocket residue types. The residue groups are generated using residue types,
3169 colors, and names specified by '--residueTypes' option. It is only valid for
3170 amino acids. By default, the residue type groups are automatically created
3171 for pockets containing amino acids and skipped for chains only containing
3172 nucleic acids.
3173 --pocketSurface <yes or no> [default: auto]
3174 Surfaces around pocket residues colored by hydrophobicity alone and
3175 both hydrophobicity and charge. The hydrophobicity surface is colored
3176 at residue level using Eisenberg hydrophobicity scale for residues and color
3177 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
3178 charge surface is colored [ Ref 140 ] at atom level using colors specified for
3179 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
3180 simultaneous mapping of hyrophobicity and charge values on the surfaces.
3181
3182 The cavity surfaces around ligands are also generated. These surfaces are
3183 colored by hydrophobicity along and both hydrophobicity and charge.
3184
3185 This option is only valid for amino acids. By default, both surfaces are
3186 automatically created for pockets containing amino acids and skipped for
3187 pockets containing only nucleic acids.
3188 --pocketSurfaceElectrostatics <yes or no> [default: no]
3189 Vacuum electrostatics contact potential surface around pocket residues.
3190 A word to the wise from PyMOL documentation: The computed protein
3191 contact potentials are only qualitatively useful, due to short cutoffs,
3192 truncation, and lack of solvent "screening".
3193
3194 The cavity surface around ligands is also generated. This surface is
3195 colored by vacuum electrostatics contact potential.
3196
3197 This option is only valid for amino acids. By default, the electrostatics surface
3198 is automatically created for chains containing amino acids and skipped for chains
3199 containing only nucleic acids.
3200 -r, --residueTypes <Type,Color,ResNames,...> [default: auto]
3201 Residue types, colors, and names to generate for residue groups during
3202 '--pocketResidueTypes' and '--residueTypesChain' option. It is only
3203 valid for amino acids.
3204
3205 It is a triplet of comma delimited list of amino acid residues type, residues
3206 color, and a space delimited list three letter residue names.
3207
3208 The default values for residue type, color, and name triplets are shown
3209 below:
3210
3211 Aromatic,brightorange,HIS PHE TRP TYR,
3212 Hydrophobic,orange,ALA GLY VAL LEU ILE PRO MET,
3213 Polar,palegreen,ASN GLN SER THR CYS,
3214 Positively_Charged,marine,ARG LYS,
3215 Negatively_Charged,red,ASP GLU
3216
3217 The color name must be a valid PyMOL name. No validation is performed.
3218 An amino acid name may appear across multiple residue types. All other
3219 residues are grouped under 'Other'.
3220 --residueTypesChain <yes or no> [default: auto]
3221 Chain residue types. The residue groups are generated using residue types,
3222 colors, and names specified by '--residueTypes' option. It is only valid for
3223 amino acids. By default, the residue type groups are automatically created
3224 for chains containing amino acids and skipped for chains only containing
3225 nucleic acids.
3226 --saltBridgesChain <yes or no> [default: auto]
3227 Salt bridges for chains. By default, the salt bridges group is automatically
3228 created for chains containing amino acids and skipped for chains only
3229 containing nucleic acids. The salt bridges correspond to polar contacts
3230 between positively and negatively charges residues in a chain.
3231 --saltBridgesChainContactsColor <text> [default: brightorange]
3232 Color for drawing polar contacts between positively and negatively
3233 charged residues involved in salt bridges. The specified value must
3234 be valid color. No validation is performed.
3235 --saltBridgesChainCutoff <number> [default: 4.0]
3236 Distance in Angstroms for identifying polar contacts between positively
3237 and negatively charged residues involved in salt bridges in a chain.
3238 --saltBridgesChainResidues <Type, ResNames,...> [default: auto]
3239 Residue types and names to use for identifying positively and negatively
3240 charged residues involved in salt bridges.
3241
3242 It is a pair of comma delimited list of amino acid residue types and a space
3243 delimited list three letter residue names.
3244
3245 The default values for residue type and name pairs are shown below:
3246
3247 Positively_Charged,ARG LYS HIS HSP
3248 Negatively_Charged,ASP GLU
3249
3250 The residue names must be valid names. No validation is performed.
3251 --selectionsChain <ObjectName,SelectionSpec,...> [default: none]
3252 Custom selections for chains. It is a pairwise list of comma delimited values
3253 corresponding to PyMOL object names and selection specifications. The
3254 selection specification must be a valid PyMOL specification. No validation is
3255 performed.
3256
3257 The PyMOL objects are created for each chain corresponding to the
3258 specified selections. The display style for PyMOL objects is set using
3259 value of '--selectionsChainStyle' option.
3260
3261 The specified selection specification is automatically appended to appropriate
3262 chain specification before creating PyMOL objects.
3263
3264 For example, the following specification for '--selectionsChain' option will
3265 generate PyMOL objects for chains containing Cysteines and Serines:
3266
3267 Cysteines,resn CYS,Serines,resn SER
3268
3269 --selectionsChainSurface <yes or no> [default: auto]
3270 Surfaces around individual chain selections colored by hydrophobicity alone
3271 and both hydrophobicity and charge. This option is similar to '--surfaceChain'
3272 options for creating surfaces for chain. Additional details are available in the
3273 documentation section for '--surfaceChain' options.
3274 --selectionsChainStyle <DisplayStyle> [default: sticks]
3275 Display style for PyMOL objects created for '--selectionsChain' option. It
3276 must be a valid PyMOL display style. No validation is performed.
3277 --selectionsPocket <ObjectName,SelectionSpec,...> [default: none]
3278 Custom selections for pocket residues. It is a pairwise list of comma delimited
3279 values corresponding to PyMOL object names and selection specifications. The
3280 selection specification must be a valid PyMOL specification. No validation is
3281 performed.
3282
3283 The PyMOL objects are created for each pocket corresponding to the
3284 specified selections. The display style for PyMOL objects is set using
3285 value of '--selectionsChainStyle' option.
3286
3287 The specified selection specification is automatically appended to appropriate
3288 pocket specification before creating PyMOL objects.
3289
3290 For example, the following specification for '--selectionsPocket' option will
3291 generate PyMOL objects for pockets containing Tyrosines and Serines:
3292
3293 Tyrosines,resn TYR,Serines,resn SER
3294
3295 --selectionsPocketSurface <yes or no> [default: auto]
3296 Surfaces around individual pocket chain selections colored by hydrophobicity
3297 alone and both hydrophobicity and charge. This option is similar to '--surfaceChain'
3298 options for creating surfaces for chain. Additional details are available in the
3299 documentation section for '--surfaceChain' options.
3300 --selectionsPocketStyle <DisplayStyle> [default: sticks]
3301 Display style for PyMOL objects created for '--selectionsPocket' option. It
3302 must be a valid PyMOL display style. No validation is performed.
3303 --surfaceChain <yes or no> [default: auto]
3304 Surfaces around individual chain colored by hydrophobicity alone and
3305 both hydrophobicity and charge. The hydrophobicity surface is colored
3306 at residue level using Eisenberg hydrophobicity scale for residues and color
3307 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
3308 charge surface is colored [ Ref 140 ] at atom level using colors specified for
3309 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
3310 simultaneous mapping of hyrophobicity and charge values on the surfaces.
3311
3312 This option is only valid for amino acids. By default, both surfaces are
3313 automatically created for chains containing amino acids and skipped for
3314 chains containing only nucleic acids.
3315 --surfaceChainElectrostatics <yes or no> [default: no]
3316 Vacuum electrostatics contact potential surface and volume around individual
3317 chain. A word to the wise from PyMOL documentation: The computed protein
3318 contact potentials are only qualitatively useful, due to short cutoffs,
3319 truncation, and lack of solvent "screening".
3320
3321 This option is only valid for amino acids. By default, the electrostatics surface
3322 and volume are automatically created for chains containing amino acids and
3323 skipped for chains containing only nucleic acids.
3324 --surfaceChainComplex <yes or no> [default: no]
3325 Hydrophobic surface around chain complex. The surface is colored by
3326 hydrophobicity. It is only valid for amino acids.
3327 --surfaceComplex <yes or no> [default: no]
3328 Hydrophobic surface around complete complex. The surface is colored by
3329 hydrophobicity. It is only valid for amino acids.
3330 --surfaceAtomTypesColors <ColorType,ColorSpec,...> [default: auto]
3331 Atom colors for generating surfaces colored by hyrophobicity and charge
3332 around chains and pockets in proteins. It's a pairwise comma delimited list
3333 of atom color type and color specification for goups of atoms.
3334
3335 The default values for color types [ Ref 140 ] along wth color specifications
3336 are shown below:
3337
3338 HydrophobicAtomsColor, yellow,
3339 NegativelyChargedAtomsColor, red,
3340 PositivelyChargedAtomsColor, blue,
3341 OtherAtomsColor, gray90
3342
3343 The color names must be valid PyMOL names.
3344
3345 The color values may also be specified as space delimited RGB triplets:
3346
3347 HydrophobicAtomsColor, 0.95 0.78 0.0,
3348 NegativelyChargedAtomsColor, 1.0 0.4 0.4,
3349 PositivelyChargedAtomsColor, 0.2 0.5 0.8,
3350 OtherAtomsColor, 0.95 0.95 0.95
3351
3352 --surfaceColor <ColorName> [default: lightblue]
3353 Color name for surfaces around chains and pockets. This color is not used
3354 for surfaces colored by hydrophobicity and charge. The color name must be
3355 a valid PyMOL name.
3356 --surfaceColorPalette <RedToWhite or WhiteToGreen> [default: RedToWhite]
3357 Color palette for hydrophobic surfaces around chains and pockets in proteins.
3358 Possible values: RedToWhite or WhiteToGreen from most hydrophobic amino
3359 acid to least hydrophobic. The colors values for amino acids are taken from
3360 color_h script available as part of the Script Library at PyMOL Wiki.
3361 --surfaceTransparency <number> [default: 0.25]
3362 Surface transparency for molecular surfaces.
3363 -t, --trajectories <PDBToplogyFile,TrajFiles,...> [default: none]
3364 PDB topology file name and MD trajectories files for visualizing trajectories
3365 for PDB files.
3366
3367 It's a pair of comma limited values corresponding to a PDB file name and
3368 MD trajectory files. Multiple trajectory file names are delimited by spaces.
3369
3370 The supported values for trajectories are shown below:
3371
3372 PDBTopologyFile: A valid PDB file name
3373 TrajFiles: A space delimited list of MD trajectory file names
3374
3375 The trajectory files must correspond to the specified PDB topology file. In
3376 addition, the format of trajectory files must be a valid PyMOL format. PyMOL
3377 uses Molfile Plugin, which supports a variety of trajectory file formats. For
3378 example: HARMM, NAMD, X-PLOR (.dcd), Gromacs TRR/XTC (.trr, .xtc),
3379 XYZ (.xyz) etc.
3380 --overwrite
3381 Overwrite existing files.
3382 -w, --workingdir <dir>
3383 Location of working directory which defaults to the current directory.
3384
3385 Examples:
3386 To visualize the first chain, the largest ligand in the first chain, and ligand
3387 binding pockets to highlight ligand interaction with pocket resiudes, solvents
3388 and inorganics, in a PDB file, and generate a PML file, type:
3389
3390 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
3391
3392 To visualize the first chain along with all cysteines and serines, the largest
3393 ligand in the first chain, and ligand binding pockets to highlight ligand
3394 interaction with pocket resiudes, solvents and inorganics, in a PDB file,
3395 and generate a PML file, type:
3396
3397 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
3398 --selectionsChain "Cysteines,resn cys,Serines,resn ser"
3399
3400 To visualize the first chain along with all serines and tyrosines in binding
3401 pockets, the largest ligand in the first chain, and ligand binding pockets
3402 to highlight ligand interaction with pocket resiudes, solvents and inorganics,
3403 in a PDB file, and generate a PML file, type:
3404
3405 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
3406 --selectionsPocket "Serines,resn ser,Tyrosines,resn tyr"
3407
3408 To visualize docking poses from a SD file in a pocket corresponding to a SD file
3409 for a chain, along with visualization of other information, in a PDB file,
3410 and generate a PML file, type:
3411
3412 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3413 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
3414 SampleMproDockedPosesTop100.sdf"
3415
3416 To visualize docking poses from a SD file in a pocket corresponding to SD file
3417 for a chain, along with visualization of distance contacts at 3.0 and 3.5 Angstroms,
3418 in a PDB file, and generate a PML file, type:
3419
3420 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3421 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
3422 SampleMproDockedPosesTop100.sdf"
3423 --dockedPosesDistanceContactsCutoffs "3.0, 3.5"
3424
3425 To visualize docking poses from a SD file in a pocket corresponding to a specific
3426 ligand a chain, along with visualization of other information, in a PDB file,
3427 and generate a PML file, type:
3428
3429 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3430 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,N3,
3431 SampleMproDockedPosesTop100.sdf"
3432
3433 To visualize docking poses from multiple SDs file in a pocket corresponding SD file
3434 a for a chain, along with visualization of other information, in a PDB file, and
3435 generate a PML file, type:
3436
3437 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3438 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
3439 SampleMproDockedPosesTop100.sdf SampleMproDockedPosesDiverse100.sdf"
3440
3441 To visualize trajectory from a DCD file, along with visualization of other
3442 information, corresponding to a PDB topology file and generate a PML file,
3443 type:
3444
3445 % PyMOLVisualizeMacromolecules.py -t "Sample10.pdb, Sample10.dcd"
3446 -i Sample10.pdb -o Sample10.pml
3447
3448 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
3449 highlight ligand interaction with pocket resiudes, solvents and inorganics, in a
3450 PDB file, and generate a PML file, type:
3451
3452 % PyMOLVisualizeMacromolecules.py -c All -l All -i Sample4.pdb -o
3453 Sample4.pml
3454
3455 To visualize all chains, ligands, and ligand binding pockets along with displaying
3456 all hydrophibic surfaces and chain electrostatic surface, in a PDB file, and
3457 generate a PML file, type:
3458
3459 % PyMOLVisualizeMacromolecules.py -c All -l All
3460 --surfaceChainElectrostatics yes --surfaceChainComplex yes
3461 --surfaceComplex yes -i Sample4.pdb -o Sample4.pml
3462
3463 To visualize chain E, ligand ADP in chain E, and ligand binding pockets to
3464 highlight ligand interaction with pocket resiudes, solvents and inorganics,
3465 in a PDB file, and generate a PML file, type:
3466
3467 % PyMOLVisualizeMacromolecules.py -c E -l ADP -i Sample3.pdb
3468 -o Sample3.pml
3469
3470 To visualize chain E, ligand ADP in chain E, and ligand binding pockets to
3471 highlight ligand interaction with pocket resiudes, solvents and inorganics,
3472 in a PDB file, and generate a PSE file, type:
3473
3474 % PyMOLVisualizeMacromolecules.py -c E -l ADP -i Sample3.pdb
3475 -o Sample3.pse
3476
3477 To visualize the first chain, the largest ligand in the first chain, and ligand
3478 binding pockets to highlight ligand interaction with pocket resiudes, solvents
3479 and inorganics, in PDB files, along with aligning first chain in each input file to
3480 the first chain in first input file, and generate a PML file, type:
3481
3482 % PyMOLVisualizeMacromolecules.py --align yes -i
3483 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
3484
3485 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
3486 highlight ligand interaction with pocket resiudes, solvents and inorganics, in
3487 PDB files, along with aligning first chain in each input file to the first chain in
3488 first input file, and generate a PML file, type:
3489
3490 % PyMOLVisualizeMacromolecules.py --align yes -c All -l All -i
3491 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
3492
3493 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
3494 highlight ligand interaction with pocket resiudes, solvents and inorganics, in
3495 PDB files, along with aligning first chain in each input file to the first chain in a
3496 specified PDB file using a specified alignment method, and generate a PML
3497 file, type:
3498
3499 % PyMOLVisualizeMacromolecules.py --align yes --alignMode FirstChain
3500 --alignRefFile Sample5.pdb --alignMethod super -c All -l All -i
3501 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
3502
3503 Author:
3504 Manish Sud(msud@san.rr.com)
3505
3506 See also:
3507 DownloadPDBFiles.pl, PyMOLVisualizeCavities.py,
3508 PyMOLVisualizeCryoEMDensity.py, PyMOLVisualizeElectronDensity.py,
3509 PyMOLVisualizeInterfaces.py, PyMOLVisualizeSurfaceAndBuriedResidues.py
3510
3511 Copyright:
3512 Copyright (C) 2024 Manish Sud. All rights reserved.
3513
3514 The functionality available in this script is implemented using PyMOL, a
3515 molecular visualization system on an open source foundation originally
3516 developed by Warren DeLano.
3517
3518 This file is part of MayaChemTools.
3519
3520 MayaChemTools is free software; you can redistribute it and/or modify it under
3521 the terms of the GNU Lesser General Public License as published by the Free
3522 Software Foundation; either version 3 of the License, or (at your option) any
3523 later version.
3524
3525 """
3526
3527 if __name__ == "__main__":
3528 main()
