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.show("cartoon", "%s")""" % (Name))
1021 PMLCmds.append("""util.cba(33, "%s", _self = cmd)""" % (Name))
1022 PMLCmds.append("""cmd.show("sticks", "(organic and (%s))")""" % (Name))
1023 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable = False))
1024
1025 PML = "\n".join(PMLCmds)
1026 OutFH.write("\n%s\n" % PML)
1027
1028 # Write view for each trajectory file...
1029 for TrajFileIndex, TrajFile in enumerate(OptionsInfo["TrajectoriesInfo"]["TrajFiles"][FileIndex]):
1030 WriteTrajectoryViewTrajectoryFile(OutFH, FileIndex, PyMOLObjectNames, TrajFileIndex)
1031
1032 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"], PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"], False, "close")
1033
1034 def WriteTrajectoryViewTrajectoryFile(OutFH, PDBFileIndex, PyMOLObjectNames, TrajFileIndex):
1035 """Write out PML for viewing a trajectory file."""
1036
1037 TrajFile = OptionsInfo["TrajectoriesInfo"]["TrajFiles"][PDBFileIndex][TrajFileIndex]
1038 TrajFileID = OptionsInfo["TrajectoriesInfo"]["TrajFilesIDs"][PDBFileIndex][TrajFileIndex]
1039
1040 OutFH.write("""\n""\n"Setting up views for trajectory file ID %s..."\n""\n""" % (TrajFileID))
1041
1042 # Setup trajectory view...
1043 Name = PyMOLObjectNames["Trajectories"][TrajFileID]["Trajectory"]
1044 PDBFile = OptionsInfo["InfilesInfo"]["InfilesNames"][PDBFileIndex]
1045
1046 PMLCmds = []
1047 PMLCmds.append("""cmd.load("%s", "%s")""" % (PDBFile, Name))
1048 PMLCmds.append("""cmd.load_traj("%s", "%s", state = 1)""" % (TrajFile, Name))
1049 PMLCmds.append("""cmd.show("cartoon", "%s")""" % (Name))
1050 PMLCmds.append("""util.cba(33, "%s", _self = cmd)""" % (Name))
1051 PMLCmds.append("""cmd.show("sticks", "(organic and (%s))")""" % (Name))
1052 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable = True))
1053
1054 PML = "\n".join(PMLCmds)
1055 OutFH.write("%s\n" % PML)
1056
1057 # Setup group for a trajectory file...
1058 Action = "open" if TrajFileIndex == 0 else "close"
1059 Enable = True if TrajFileIndex == 0 else False
1060 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroup"], PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"], Enable, Action)
1061
1062 def GeneratePyMOLSessionFile():
1063 """Generate PME file from PML file."""
1064
1065 PSEOutfile = OptionsInfo["PSEOutfile"]
1066 PMLOutfile = OptionsInfo["PMLOutfile"]
1067
1068 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
1069
1070 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
1071
1072 if not os.path.exists(PSEOutfile):
1073 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
1074
1075 if not OptionsInfo["PMLOut"]:
1076 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
1077 os.remove(PMLOutfile)
1078
1079 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
1080 """Delete empty PyMOL objects."""
1081
1082 if OptionsInfo["AllowEmptyObjects"]:
1083 return
1084
1085 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1086 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1087 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
1088
1089 # Delete any chain level objects...
1090 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
1091 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
1092
1093 # Delete chain selection objects...
1094 DeleteEmptyChainSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1095
1096 # Delete residue type objects...
1097 DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1098
1099 # Delete disulfide bonds objects...
1100 DeleteEmptyChainDisulfideBondsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1101
1102 # Delete salt bridges objects...
1103 DeleteEmptyChainSaltBridgesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1104
1105 # Delete ligand objects...
1106 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
1107 # Delete ligand level objects...
1108 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
1109 GroupNameID = "%sGroup" % (GroupID)
1110 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
1111
1112 GroupTypeObjectID = "%s" % (GroupID)
1113 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
1114
1115 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
1116
1117 if re.match("^Pocket$", GroupID, re.I):
1118 DeleteEmptyPocketSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
1119 DeleteEmptyPocketResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, GroupTypeObjectID)
1120
1121 # Delete docked poses objects...
1122 DeleteEmptyChainDockedPosesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID)
1123
1124 def DeleteEmptyChainSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1125 """Delete empty chain selection objects """
1126
1127 if not GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
1128 return
1129
1130 SelectionsGroupIDPrefix = "ChainAloneSelections"
1131
1132 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
1133 SelectionNameGroupID = SelectionName
1134
1135 # Delete surface objects and surface group...
1136 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
1137 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1138 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1139 WritePMLToCheckAndDeleteEmptyObjects(OutFH, ",".join(PyMOLObjectNames["Chains"][ChainID][SurfaceGroupMembersID]), PyMOLObjectNames["Chains"][ChainID][SurfaceGroupID])
1140
1141 # Delete Selection object and selection name group...
1142 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1143 SelectionsGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1144 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionObjectID], PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID])
1145
1146 def DeleteEmptyChainResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1147 """Delete empty chain residue objects."""
1148
1149 if not GetChainAloneResidueTypesStatus(FileIndex, ChainID):
1150 return
1151
1152 ResiduesGroupIDPrefix = "ChainAloneResidues"
1153 for GroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1154 GroupID = re.sub("_", "", GroupType)
1155
1156 ResiduesGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, GroupID)
1157 GroupName = PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID]
1158
1159 GroupObjectNamesList = []
1160
1161 ResiduesObjectID = "%s%sResidues" % (ResiduesGroupIDPrefix, GroupID)
1162 ResiduesObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesObjectID]
1163 GroupObjectNamesList.append(ResiduesObjectName)
1164
1165 ResiduesSurfaceObjectID = "%s%sSurface" % (ResiduesGroupIDPrefix, GroupID)
1166 ResiduesSurfaceObjectName = PyMOLObjectNames["Chains"][ChainID][ResiduesSurfaceObjectID]
1167 GroupObjectNamesList.append(ResiduesSurfaceObjectName)
1168
1169 GroupObjectNames = ",".join(GroupObjectNamesList)
1170 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupObjectNames, GroupName)
1171
1172 def DeleteEmptyChainDisulfideBondsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1173 """Delete empty chain disulfide bonds objects."""
1174
1175 if not GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
1176 return
1177
1178 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"])
1179
1180 def DeleteEmptyChainSaltBridgesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID):
1181 """Delete empty chain salt bridges objects."""
1182
1183 if not GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
1184 return
1185
1186 Names = []
1187 Names.append(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesPositivelyCharged"])
1188 Names.append(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesNegativelyCharged"])
1189
1190 WritePMLToCheckAndDeleteEmptyObjects(OutFH, ",".join(Names), PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"])
1191
1192 def DeleteEmptyPocketSelectionsObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
1193 """Delete empty pocket selection objects."""
1194
1195 if not GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
1196 return
1197
1198 PocketObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PocketObjectID]
1199 SelectionsGroupIDPrefix = "PocketSelectionsGroup"
1200
1201 for SelectionName in OptionsInfo["PocketChainSelectionsInfo"]["Names"]:
1202 SelectionNameGroupID = SelectionName
1203
1204 # Delete surface objects and surface group...
1205 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
1206 SurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1207 SurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1208 WritePMLToCheckAndDeleteEmptyObjects(OutFH, ",".join(PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupMembersID]), PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceGroupID])
1209
1210 # Delete Selection object and selection name group...
1211 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1212 SelectionsGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1213 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionObjectID], PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID])
1214
1215 def DeleteEmptyPocketResidueTypesObjects(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID, PocketObjectID):
1216 """Delete empty chain residue objects. """
1217
1218 if not GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
1219 return
1220
1221 ResiduesGroupID = "%sResiduesGroup" % (PocketObjectID)
1222 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
1223
1224 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1225 SubGroupID = re.sub("_", "", SubGroupType)
1226
1227 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
1228 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
1229
1230 SubGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID]
1231 SubGroupObjectNames = ",".join(PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID])
1232
1233 WritePMLToCheckAndDeleteEmptyObjects(OutFH, SubGroupObjectNames, SubGroupName)
1234
1235 def DeleteEmptyChainDockedPosesObjects(OutFH, PDBFileIndex, PyMOLObjectNames, ChainID):
1236 """Delete empty chain docked poses objest."""
1237
1238 if not GetChainAloneDockedPosesStatus(PDBFileIndex, ChainID):
1239 return
1240
1241 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][PDBFileIndex]
1242 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
1243
1244 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
1245 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
1246 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
1247 GroupNameID = "%sGroup" % (GroupID)
1248 GroupName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID]
1249
1250 GroupTypeObjectID = "%sPocket" % (GroupID)
1251 GroupTypeObjectName = PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupTypeObjectID]
1252
1253 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
1254
1255 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
1256 """Write PML to check and delete empty PyMOL objects."""
1257
1258 if ParentObjectName is None:
1259 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
1260 else:
1261 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
1262
1263 OutFH.write("%s\n" % PML)
1264
1265 def SetupPyMOLObjectNames(FileIndex):
1266 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
1267 chains and ligands present in input file.
1268 """
1269
1270 PyMOLObjectNames = {}
1271 PyMOLObjectNames["Chains"] = {}
1272 PyMOLObjectNames["Ligands"] = {}
1273 PyMOLObjectNames["DockedPosesInputFile"] = {}
1274 PyMOLObjectNames["Trajectories"] = {}
1275
1276 # Setup groups and objects for complex...
1277 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
1278
1279 # Setup groups and object for trajectories...
1280 if GetTrajectoriesStatus(FileIndex):
1281 SetupPyMOLObjectNamesForTrajectories(FileIndex, PyMOLObjectNames)
1282
1283 # Setup groups and objects for chain...
1284 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1285 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1286 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
1287
1288 # Setup groups and objects for ligand...
1289 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
1290 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
1291
1292 # Setup group and objects for docked poses...
1293 if GetChainAloneDockedPosesStatus(FileIndex, ChainID):
1294 SetupPyMOLObjectNamesForDockedPoses(FileIndex, PyMOLObjectNames, ChainID)
1295
1296 return PyMOLObjectNames
1297
1298 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
1299 """Setup groups and objects for complex."""
1300
1301 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
1302
1303 PDBGroupName = "%s" % PDBFileRoot
1304 PyMOLObjectNames["PDBGroup"] = PDBGroupName
1305 PyMOLObjectNames["PDBGroupMembers"] = []
1306
1307 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
1308 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
1309 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
1310
1311 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
1312 if OptionsInfo["SurfaceComplex"]:
1313 PyMOLObjectNames["ComplexHydrophobicSurface"] = "%s.Surface" % ComplexGroupName
1314
1315 PyMOLObjectNames["ComplexGroupMembers"] = []
1316 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
1317 if OptionsInfo["SurfaceComplex"]:
1318 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexHydrophobicSurface"])
1319
1320 def SetupPyMOLObjectNamesForTrajectories(FileIndex, PyMOLObjectNames):
1321 """Setup groups and objects for a PDB file."""
1322
1323 if not GetTrajectoriesStatus(FileIndex):
1324 return
1325
1326 # Setup a group for trajectories....
1327 TrajectoriesGroupName = "%s.Trajectories" % PyMOLObjectNames["PDBGroup"]
1328 PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"] = TrajectoriesGroupName
1329 PyMOLObjectNames["PDBGroupMembers"].append(TrajectoriesGroupName)
1330
1331 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"] = []
1332
1333 # Setup a topolgy object...
1334 TopologyName = "%s.Topology" % TrajectoriesGroupName
1335 PyMOLObjectNames["Trajectories"]["Topology"] = TopologyName
1336 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"].append(TopologyName)
1337
1338 # Setup trajectory objects...
1339 for TrajFileIndex, TrajFile in enumerate(OptionsInfo["TrajectoriesInfo"]["TrajFiles"][FileIndex]):
1340 SetupPyMOLObjectNamesForTrajectoryFile(FileIndex, PyMOLObjectNames, TrajFileIndex)
1341
1342 def SetupPyMOLObjectNamesForTrajectoryFile(PDBFileIndex, PyMOLObjectNames, TrajFileIndex):
1343 """Setup groups and objest for a trajectory file for a PDB file."""
1344
1345 TrajFileID = OptionsInfo["TrajectoriesInfo"]["TrajFilesIDs"][PDBFileIndex][TrajFileIndex]
1346
1347 PyMOLObjectNames["Trajectories"][TrajFileID] = {}
1348
1349 TrajectoriesGroupName = PyMOLObjectNames["Trajectories"]["TrajectoriesGroup"]
1350
1351 # Setup a trajectories level trajectory file group...
1352 TrajectoryFileGroupName = "%s.%s" % (TrajectoriesGroupName, TrajFileID)
1353 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroup"] = TrajectoryFileGroupName
1354 PyMOLObjectNames["Trajectories"]["TrajectoriesGroupMembers"].append(TrajectoryFileGroupName)
1355
1356 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"] = []
1357
1358 # Setup object for a trajectory file...
1359 TrajectoryName = "%s.Trajectory" % (TrajectoryFileGroupName)
1360 PyMOLObjectNames["Trajectories"][TrajFileID]["Trajectory"] = TrajectoryName
1361 PyMOLObjectNames["Trajectories"][TrajFileID]["TrajectoryGroupMembers"].append(TrajectoryName)
1362
1363 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
1364 """Setup groups and objects for chain."""
1365
1366 PDBGroupName = PyMOLObjectNames["PDBGroup"]
1367
1368 PyMOLObjectNames["Chains"][ChainID] = {}
1369 PyMOLObjectNames["Ligands"][ChainID] = {}
1370
1371 # Set up chain group and chain objects...
1372 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
1373 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
1374 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
1375 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
1376
1377 # Setup chain complex group and objects...
1378 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
1379 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
1380 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
1381
1382 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
1383
1384 Name = "%s.Complex" % (ChainComplexGroupName)
1385 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = Name
1386 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1387
1388 if OptionsInfo["SurfaceChainComplex"]:
1389 Name = "%s.Surface" % (ChainComplexGroupName)
1390 PyMOLObjectNames["Chains"][ChainID]["ChainComplexHydrophobicSurface"] = Name
1391 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1392
1393 # Setup up a group for individual chains...
1394 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
1395 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
1396 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
1397
1398 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
1399
1400 Name = "%s.Chain" % (ChainAloneGroupName)
1401 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
1402 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
1403
1404 if GetChainAloneBFactorStatus(FileIndex, ChainID):
1405 # Setup B factor group and add it to chain alone group...
1406 BFactorGroupName = "%s.BFactor" % (ChainAloneGroupName)
1407 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroup"] = BFactorGroupName
1408 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(BFactorGroupName)
1409
1410 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"] = []
1411
1412 # Setup cartoon...
1413 Name = "%s.Cartoon" % (BFactorGroupName)
1414 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorCartoon"] = Name
1415 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"].append(Name)
1416
1417 # Setup putty...
1418 Name = "%s.Putty" % (BFactorGroupName)
1419 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"] = Name
1420 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorGroupMembers"].append(Name)
1421
1422 if GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
1423 # Setup selections group and its subgroups..
1424 SelectionsGroupName = "%s.Selections" % (ChainAloneGroupName)
1425
1426 SelectionsGroupIDPrefix = "ChainAloneSelections"
1427 SelectionsGroupID = "%sGroup" % SelectionsGroupIDPrefix
1428
1429 # Add selections group to chain alone group...
1430 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID] = SelectionsGroupName
1431 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SelectionsGroupName)
1432
1433 # Initialize selections group members...
1434 SelectionsGroupMembersID = "%sGroupMembers" % SelectionsGroupIDPrefix
1435 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID] = []
1436
1437 # Setup selections name sub group and its members...
1438 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
1439 SelectionNameGroupID = SelectionName
1440
1441 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
1442 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1443
1444 # Add selections name sub group to selections group...
1445 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID] = SelectionsNameGroupName
1446 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID].append(SelectionsNameGroupName)
1447
1448 # Initialize selections names sub group members...
1449 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1450 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID] = []
1451
1452 # Add selection member to selections name group...
1453 SubGroupMemberName = "%s.Selection" % (SelectionsNameGroupName)
1454 SubGroupMemberID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1455
1456 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1457 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SubGroupMemberName)
1458
1459 if GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
1460 # Setup a surface sub group and add it to selections name group...
1461
1462 SelectionsNameSurfaceGroupName = "%s.Surface" % (SelectionsNameGroupName)
1463 SelectionsNameSurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1464
1465 # Add selection surface group to selection name group...
1466 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupID] = SelectionsNameSurfaceGroupName
1467 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SelectionsNameSurfaceGroupName)
1468
1469 # Initialize surface names sub group members...
1470 SelectionsNameSurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1471 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID] = []
1472
1473 # Setup a generic color surface...
1474 SubGroupMemberName = "%s.Surface" % (SelectionsNameSurfaceGroupName)
1475 SubGroupMemberID = "%s%s%sSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface")
1476 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1477 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID].append(SubGroupMemberName)
1478
1479 if GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
1480 # Setup surfaces...
1481 for MemberType in ["Hydrophobicity", "Hydrophobicity_Charge"]:
1482 MemberID = re.sub("_", "", MemberType)
1483
1484 SubGroupMemberName = "%s.%s" % (SelectionsNameSurfaceGroupName, MemberType)
1485 SubGroupMemberID = "%s%s%s%s" % (SelectionsGroupIDPrefix, SelectionNameGroupID, "Surface", MemberID)
1486
1487 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1488 PyMOLObjectNames["Chains"][ChainID][SelectionsNameSurfaceGroupMembersID].append(SubGroupMemberName)
1489
1490 if GetChainAloneResidueTypesStatus(FileIndex, ChainID):
1491 # Setup residue type group and its subgroups...
1492 ResiduesGroupName = "%s.Residues" % (ChainAloneGroupName)
1493
1494 ResiduesGroupIDPrefix = "ChainAloneResidues"
1495 ResiduesGroupID = "%sGroup" % ResiduesGroupIDPrefix
1496
1497 # Add residue group to chain alone group...
1498 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupID] = ResiduesGroupName
1499 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(ResiduesGroupName)
1500
1501 # Initialize residue group members...
1502 ResiduesGroupMembersID = "%sGroupMembers" % ResiduesGroupIDPrefix
1503 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID] = []
1504
1505 # Setup residues sub groups and its members...
1506 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1507 SubGroupID = re.sub("_", "", SubGroupType)
1508
1509 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
1510 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupIDPrefix, SubGroupID)
1511
1512 # Add sub group to residues group...
1513 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupID] = ResiduesSubGroupName
1514 PyMOLObjectNames["Chains"][ChainID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
1515
1516 # Initialize sub group members...
1517 ResiduesSubGroupMembersID = "%s%sGroupMembers" % (ResiduesGroupIDPrefix, SubGroupID)
1518 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID] = []
1519
1520 # Add sub group members to subgroup...
1521 for MemberType in ["Residues", "Surface"]:
1522 MemberID = re.sub("_", "", MemberType)
1523
1524 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
1525 SubGroupMemberID = "%s%s%s" % (ResiduesGroupIDPrefix, SubGroupID, MemberID)
1526
1527 PyMOLObjectNames["Chains"][ChainID][SubGroupMemberID] = SubGroupMemberName
1528 PyMOLObjectNames["Chains"][ChainID][ResiduesSubGroupMembersID].append(SubGroupMemberName)
1529
1530 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
1531 # Setup a surface group and add it to chain alone group...
1532 SurfaceGroupName = "%s.Surface" % (ChainAloneGroupName)
1533 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"] = SurfaceGroupName
1534 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SurfaceGroupName)
1535
1536 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"] = []
1537
1538 # Setup a generic color surface...
1539 Name = "%s.Surface" % (SurfaceGroupName)
1540 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"] = Name
1541 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1542
1543 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
1544 # Setup hydrophobicity surface...
1545 Name = "%s.Hydrophobicity" % (SurfaceGroupName)
1546 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"] = Name
1547 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1548
1549 # Setup hydrophobicity and charge surface...
1550 Name = "%s.Hydrophobicity_Charge" % (SurfaceGroupName)
1551 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"] = Name
1552 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
1553
1554 if GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
1555 # Setup electrostatics group...
1556 GroupName = "%s.Vacuum_Electrostatics" % (SurfaceGroupName)
1557 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroup"] = GroupName
1558 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(GroupName)
1559
1560 # Setup electrostatics group members...
1561 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"] = []
1562
1563 for MemberType in ["Chain", "Contact_Potential", "Map", "Legend", "Volume"]:
1564 MemberID = re.sub("_", "", MemberType)
1565
1566 Name = "%s.%s" % (GroupName, MemberType)
1567 NameID = "ChainAloneElectrostaticsSurface%s" % MemberID
1568
1569 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
1570 PyMOLObjectNames["Chains"][ChainID]["ChainAloneElectrostaticsGroupMembers"].append(Name)
1571
1572 if GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
1573 # Setup disulfide bonds group and add it to chain alone group...
1574 DisulfideBondsGroupName = "%s.Disulfide_Bonds" % (ChainAloneGroupName)
1575 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroup"] = DisulfideBondsGroupName
1576 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(DisulfideBondsGroupName)
1577
1578 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"] = []
1579
1580 # Setup a residues object for disulfide bonds...
1581 Name = "%s.Residues" % (DisulfideBondsGroupName)
1582 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsResidues"] = Name
1583 PyMOLObjectNames["Chains"][ChainID]["ChainAloneDisulfideBondsGroupMembers"].append(Name)
1584
1585 if GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
1586 # Setup salt bridges group and add it to chain alone group...
1587 SaltBridgesGroupName = "%s.Salt_Bridges" % (ChainAloneGroupName)
1588 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroup"] = SaltBridgesGroupName
1589 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SaltBridgesGroupName)
1590
1591 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"] = []
1592
1593 # Setup residues group and add it to salt bridges group...
1594 ResiduesGroupName = "%s.Residues" % (SaltBridgesGroupName)
1595 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroup"] = ResiduesGroupName
1596 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"].append(ResiduesGroupName)
1597
1598 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"] = []
1599
1600 # Setup objects for residues group...
1601 Name = "%s.Positively_Charged" % (ResiduesGroupName)
1602 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesPositivelyCharged"] = Name
1603 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"].append(Name)
1604
1605 Name = "%s.Negatively_Charged" % (ResiduesGroupName)
1606 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesNegativelyCharged"] = Name
1607 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesResiduesGroupMembers"].append(Name)
1608
1609 # Add contacts object to salt bridges group...
1610 Name = "%s.Contacts" % (SaltBridgesGroupName)
1611 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesContacts"] = Name
1612 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSaltBridgesGroupMembers"].append(Name)
1613
1614 # Setup solvent and inorganic objects for chain...
1615 for NameID in ["Solvent", "Inorganic"]:
1616 Name = "%s.%s" % (ChainGroupName, NameID)
1617 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
1618 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
1619
1620 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
1621 """Stetup groups and objects for ligand."""
1622
1623 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
1624
1625 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
1626
1627 # Setup a chain level ligand group...
1628 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
1629 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
1630 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
1631
1632 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
1633
1634 # Set up groups and objects for a specific ligand group...
1635 for GroupType in ["Ligand", "Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
1636 GroupID = re.sub("_", "", GroupType)
1637 GroupName = "%s.%s" % (ChainLigandGroupName, GroupType)
1638
1639 GroupNameID = "%sGroup" % (GroupID)
1640 GroupMembersID = "%sGroupMembers" % (GroupID)
1641
1642 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
1643 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
1644
1645 GroupTypeObjectName = "%s.%s" % (GroupName, GroupType)
1646 GroupTypeObjectID = "%s" % (GroupID)
1647 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID] = GroupTypeObjectName
1648
1649 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
1650 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(GroupTypeObjectName)
1651
1652 if re.match("^Ligand$", GroupType, re.I):
1653 # Only need to add ball and stick...
1654 BallAndStickName = "%s.BallAndStick" % (GroupName)
1655 BallAndStickID = "%sBallAndStick" % (GroupID)
1656 PyMOLObjectNames["Ligands"][ChainID][LigandID][BallAndStickID] = BallAndStickName
1657 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(BallAndStickName)
1658
1659 if re.match("^(Pocket|Pocket_Solvent|Pocket_Inorganic)$", GroupType, re.I):
1660 PolarContactsName = "%s.Polar_Contacts" % (GroupName)
1661 PolarContactsID = "%sPolarContacts" % (GroupID)
1662 PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID] = PolarContactsName
1663 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PolarContactsName)
1664
1665 if re.match("^Pocket_Inorganic$", GroupType, re.I):
1666 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
1667 PiCationContactsID = "%sPiCationContacts" % (GroupID)
1668 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
1669 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
1670
1671 if re.match("^Pocket$", GroupType, re.I):
1672 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % (GroupName)
1673 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
1674 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID] = HydrophobicContactsName
1675 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HydrophobicContactsName)
1676
1677 PiPiContactsName = "%s.Pi_Pi_Contacts" % (GroupName)
1678 PiPiContactsID = "%sPiPiContacts" % (GroupID)
1679 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiPiContactsID] = PiPiContactsName
1680 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiPiContactsName)
1681
1682 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
1683 PiCationContactsID = "%sPiCationContacts" % (GroupID)
1684 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
1685 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
1686
1687 PiCationContactsName = "%s.Pi_Cation_Contacts" % (GroupName)
1688 PiCationContactsID = "%sPiCationContacts" % (GroupID)
1689 PyMOLObjectNames["Ligands"][ChainID][LigandID][PiCationContactsID] = PiCationContactsName
1690 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PiCationContactsName)
1691
1692 HalogenContactsName = "%s.Halogen_Contacts" % (GroupName)
1693 HalogenContactsID = "%sHalogenContacts" % (GroupID)
1694 PyMOLObjectNames["Ligands"][ChainID][LigandID][HalogenContactsID] = HalogenContactsName
1695 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HalogenContactsName)
1696
1697 if GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
1698 # Setup selections group and its subgroups..
1699 SelectionsGroupName = "%s.Selections" % (GroupName)
1700 SelectionsGroupID = "%sSelectionsGroup" % (GroupID)
1701 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupID)
1702
1703 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupID] = SelectionsGroupName
1704 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(SelectionsGroupName)
1705
1706 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID] = []
1707
1708 # Setup selections name sub group and its members...
1709 for SelectionName in OptionsInfo["PocketChainSelectionsInfo"]["Names"]:
1710 SelectionNameGroupID = SelectionName
1711
1712 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
1713 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupID, SelectionNameGroupID)
1714 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupID, SelectionNameGroupID)
1715
1716 # Add selections name sub group to selections group...
1717 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupID] = SelectionsNameGroupName
1718 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsGroupMembersID].append(SelectionsNameGroupName)
1719
1720 # Initialize selections names sub group members...
1721 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID] = []
1722
1723 # Add selection member to selections name group...
1724 SubGroupMemberName = "%s.Selection" % (SelectionsNameGroupName)
1725 SubGroupMemberID = "%s%sSelection" % (SelectionsGroupID, SelectionNameGroupID)
1726
1727 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
1728 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID].append(SubGroupMemberName)
1729
1730 if GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
1731 # Setup a surface sub group and add it to selections name group...
1732 SelectionsNameSurfaceGroupName = "%s.Surface" % (SelectionsNameGroupName)
1733 SelectionsNameSurfaceGroupID = "%s%sSurfaceGroup" % (SelectionsGroupID, SelectionNameGroupID)
1734
1735 # Add selection surface group to selection name group...
1736 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupID] = SelectionsNameSurfaceGroupName
1737 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameGroupMembersID].append(SelectionsNameSurfaceGroupName)
1738
1739 # Initialize surface names sub group members...
1740 SelectionsNameSurfaceGroupMembersID = "%s%sSurfaceGroupMembers" % (SelectionsGroupID, SelectionNameGroupID)
1741 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupMembersID] = []
1742
1743 # Setup surfaces...
1744 for MemberType in ["Surface", "Hydrophobicity", "Hydrophobicity_Charge"]:
1745 MemberID = re.sub("_", "", MemberType)
1746
1747 SubGroupMemberName = "%s.%s" % (SelectionsNameSurfaceGroupName, MemberType)
1748 SubGroupMemberID = "%s%s%s%s" % (SelectionsGroupID, SelectionNameGroupID, "Surface", MemberID)
1749
1750 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
1751 PyMOLObjectNames["Ligands"][ChainID][LigandID][SelectionsNameSurfaceGroupMembersID].append(SubGroupMemberName)
1752
1753 if GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
1754 # Setup residue type group and add to pocket group...
1755 ResiduesGroupName = "%s.Residues" % (GroupName)
1756 ResiduesGroupID = "%sResiduesGroup" % (GroupID)
1757 ResiduesGroupMembersID = "%sMembers" % (ResiduesGroupID)
1758
1759 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupID] = ResiduesGroupName
1760 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(ResiduesGroupName)
1761 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID] = []
1762
1763 # Setup residue group subgroup and its members...
1764 for SubGroupType in ["Aromatic", "Hydrophobic", "Polar", "Positively_Charged", "Negatively_Charged", "Other"]:
1765 SubGroupID = re.sub("_", "", SubGroupType)
1766 ResiduesSubGroupName = "%s.%s" % (ResiduesGroupName, SubGroupType)
1767 ResiduesSubGroupID = "%s%sGroup" % (ResiduesGroupID, SubGroupID)
1768 ResiduesSubMembersGroupID = "%sMembers" % (ResiduesSubGroupID)
1769
1770 # Add sub group to residues group...
1771 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubGroupID] = ResiduesSubGroupName
1772 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesGroupMembersID].append(ResiduesSubGroupName)
1773 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID] = []
1774
1775 # Add sub group members to subgroup...
1776 for MemberType in ["Residues", "Surface"]:
1777 MemberID = re.sub("_", "", MemberType)
1778 SubGroupMemberName = "%s.%s" % (ResiduesSubGroupName, MemberType)
1779 SubGroupMemberID = "%s%s" % (ResiduesSubGroupID, MemberID)
1780
1781 PyMOLObjectNames["Ligands"][ChainID][LigandID][SubGroupMemberID] = SubGroupMemberName
1782 PyMOLObjectNames["Ligands"][ChainID][LigandID][ResiduesSubMembersGroupID].append(SubGroupMemberName)
1783
1784 if GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
1785 # Setup a surfaces group and add it to pocket group...
1786 SurfacesGroupName = "%s.Surfaces" % (GroupName)
1787 SurfacesGroupID = "%sSurfacesGroup" % (GroupID)
1788 SurfacesGroupMembersID = "%sMembers" % (SurfacesGroupID)
1789
1790 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupID] = SurfacesGroupName
1791 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(SurfacesGroupName)
1792 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID] = []
1793
1794 # Setup surfaces subgroup and its members...
1795 for SubGroupType in ["Surface", "Cavity"]:
1796 SubGroupID = re.sub("_", "", SubGroupType)
1797 SurfacesSubGroupName = "%s.%s" % (SurfacesGroupName, SubGroupType)
1798 SurfacesSubGroupID = "%s%sGroup" % (SurfacesGroupID, SubGroupID)
1799 SurfacesSubGroupMembersID = "%sMembers" % (SurfacesSubGroupID)
1800
1801 # Add sub group to surfaces group...
1802 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupID] = SurfacesSubGroupName
1803 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesGroupMembersID].append(SurfacesSubGroupName)
1804 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID] = []
1805
1806 # Setup a generic color surface...
1807 SurfaceName = "%s.Surface" % (SurfacesSubGroupName)
1808 SurfaceID = "%sSurface" % (SurfacesSubGroupID)
1809 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfaceID] = SurfaceName
1810 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(SurfaceName)
1811
1812 if GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
1813 # Surface colored by hydrophobicity...
1814 HydrophobicSurfaceName = "%s.Hydrophobicity" % (SurfacesSubGroupName)
1815 HydrophobicSurfaceID = "%sHydrophobicSurface" % (SurfacesSubGroupID)
1816 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID] = HydrophobicSurfaceName
1817 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(HydrophobicSurfaceName)
1818
1819 # Surface colored by hydrophobicity and charge...
1820 HydrophobicChargeSurfaceName = "%s.Hydrophobicity_Charge" % (SurfacesSubGroupName)
1821 HydrophobicChargeSurfaceID = "%sHydrophobicChargeSurface" % (SurfacesSubGroupID)
1822 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicChargeSurfaceID] = HydrophobicChargeSurfaceName
1823 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(HydrophobicChargeSurfaceName)
1824
1825 if GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
1826 ElectrostaticsGroupName = "%s.Vacuum_Electrostatics" % (SurfacesSubGroupName)
1827 ElectrostaticsGroupID = "%sElectrostaticsGroup" % (SurfacesSubGroupID)
1828 ElectrostaticsGroupMembersID = "%sElectrostaticsGroupMembers" % (SurfacesSubGroupID)
1829
1830 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupID] = ElectrostaticsGroupName
1831 PyMOLObjectNames["Ligands"][ChainID][LigandID][SurfacesSubGroupMembersID].append(ElectrostaticsGroupName)
1832
1833 # Setup electrostatics group members without the volume object...
1834 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupMembersID] = []
1835
1836 for MemberType in ["Pocket", "Contact_Potential", "Map", "Legend"]:
1837 MemberID = re.sub("_", "", MemberType)
1838
1839 Name = "%s.%s" % (ElectrostaticsGroupName, MemberType)
1840 NameID = "%s%s" % (ElectrostaticsGroupID, MemberID)
1841
1842 PyMOLObjectNames["Ligands"][ChainID][LigandID][NameID] = Name
1843 PyMOLObjectNames["Ligands"][ChainID][LigandID][ElectrostaticsGroupMembersID].append(Name)
1844
1845 def SetupPyMOLObjectNamesForDockedPoses(FileIndex, PyMOLObjectNames, ChainID):
1846 """Stetup groups and objects for docked poses in input files for a chain."""
1847
1848 PyMOLObjectNames["DockedPosesInputFile"][ChainID] = {}
1849
1850 if not GetChainAloneDockedPosesStatus(FileIndex, ChainID):
1851 return
1852
1853 # Setup group for docked poses...
1854 if "DockedPosesGroup" not in PyMOLObjectNames["Chains"][ChainID]:
1855 # Setup docked poses group at a chain level...
1856 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
1857 DockedPosesGroupName = "%s.%s" % (ChainGroupName, OptionsInfo["DockedPosesGroupName"])
1858
1859 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"] = DockedPosesGroupName
1860 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(DockedPosesGroupName)
1861 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"] = []
1862
1863 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
1864 for InputFileIndex, InputFile in enumerate(SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID]):
1865 SetupPyMOLObjectNamesForDockedPosesInputFile(FileIndex, PyMOLObjectNames, ChainID, InputFileIndex)
1866
1867 def SetupPyMOLObjectNamesForDockedPosesInputFile(PDBFileIndex, PyMOLObjectNames, ChainID, InputFileIndex):
1868 """Stetup groups and objects for docked poses in an input file for a chain."""
1869
1870 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
1871 DockedPosesDistanceContactsInfo = OptionsInfo["DockedPosesDistanceContactsInfo"]
1872
1873 InputFileID = DockedPosesInfo["InputFilesIDs"][PDBFileIndex][InputFileIndex]
1874
1875 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID] = {}
1876
1877 DockedPosesGroupName = PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroup"]
1878
1879 # Setup a docked poses level InputFile group...
1880 DockedPosesInputFileGroupName = "%s.%s" % (DockedPosesGroupName, InputFileID)
1881 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupName"] = DockedPosesInputFileGroupName
1882 PyMOLObjectNames["Chains"][ChainID]["DockedPosesGroupMembers"].append(DockedPosesInputFileGroupName)
1883
1884 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"] = []
1885
1886 # Setup objects for docked poses...
1887 PosesName = "%s.%s" % (DockedPosesInputFileGroupName, OptionsInfo["DockedPosesName"])
1888 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["Poses"] = PosesName
1889 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"].append(PosesName)
1890
1891 for GroupType in ["Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
1892 GroupID = re.sub("_", "", GroupType)
1893 GroupName = "%s.%s" % (DockedPosesInputFileGroupName, GroupType)
1894
1895 GroupNameID = "%sGroup" % (GroupID)
1896 GroupMembersID = "%sGroupMembers" % (GroupID)
1897
1898 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupNameID] = GroupName
1899 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID]["DockedPosesGroupMembers"].append(GroupName)
1900
1901 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID] = []
1902
1903 PocketID = "%sPocket" % GroupID
1904 PocketName = "%s.Pocket" % GroupName
1905 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PocketID] = PocketName
1906 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PocketName)
1907
1908 if DockedPosesInfo["DistanceContacts"] and re.match("^Pocket$", GroupType, re.I):
1909 # Setup distance contacts group and add it to pocket group...
1910 DistanceContactGroupName = "%s.Distance_Contacts" % GroupName
1911
1912 DistanceContactGroupNameID = "%sDistanceContactsGroup" % GroupID
1913 DistanceContactGroupMembersID = "%sDistanceContactsGroupMembers" % GroupID
1914
1915 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupNameID] = DistanceContactGroupName
1916 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(DistanceContactGroupName)
1917
1918 # Setup distance contacts group members...
1919 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID] = []
1920
1921 for ContactID in DockedPosesDistanceContactsInfo["ContactIDs"]:
1922 DistanceContactID = "%sPocketDistanceContacts%s" % (GroupID, ContactID)
1923 DistanceContactName = "%s.Distance_Contacts.%s" % (GroupName, ContactID)
1924
1925 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactID] = DistanceContactName
1926 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][DistanceContactGroupMembersID].append(DistanceContactName)
1927
1928 PolarContactsID = "%sPolarContacts" % GroupID
1929 PolarContactsName = "%s.Polar_Contacts" % GroupName
1930 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PolarContactsID] = PolarContactsName
1931 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PolarContactsName)
1932
1933 if re.match("^Pocket_Inorganic$", GroupType, re.I):
1934 PiCationContactsID = "%sPiCationContacts" % GroupID
1935 PiCationContactsName = "%s.Pi_Cation_Contacts" % GroupName
1936 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID] = PiCationContactsName
1937 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiCationContactsName)
1938
1939 if re.match("^Pocket$", GroupType, re.I):
1940 HydrophobicContactsID = "%sHydrophobicContacts" % GroupID
1941 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % GroupName
1942 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HydrophobicContactsID] = HydrophobicContactsName
1943 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(HydrophobicContactsName)
1944
1945 PiPiContactsID = "%sPiPiContacts" % GroupID
1946 PiPiContactsName = "%s.Pi_Pi_Contacts" % GroupName
1947 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiPiContactsID] = PiPiContactsName
1948 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiPiContactsName)
1949
1950 PiCationContactsID = "%sPiCationContacts" % GroupID
1951 PiCationContactsName = "%s.Pi_Cation_Contacts" % GroupName
1952 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][PiCationContactsID] = PiCationContactsName
1953 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(PiCationContactsName)
1954
1955 HalogenContactsID = "%sHalogenContacts" % GroupID
1956 HalogenContactsName = "%s.Halogen_Contacts" % GroupName
1957 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][HalogenContactsID] = HalogenContactsName
1958 PyMOLObjectNames["DockedPosesInputFile"][ChainID][InputFileID][GroupMembersID].append(HalogenContactsName)
1959
1960 def RetrieveInfilesInfo():
1961 """Retrieve information for input files."""
1962
1963 InfilesInfo = {}
1964
1965 InfilesInfo["InfilesNames"] = []
1966 InfilesInfo["InfilesRoots"] = []
1967 InfilesInfo["ChainsAndLigandsInfo"] = []
1968
1969 for Infile in OptionsInfo["InfilesNames"]:
1970 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
1971 InfileRoot = FileName
1972
1973 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
1974
1975 InfilesInfo["InfilesNames"].append(Infile)
1976 InfilesInfo["InfilesRoots"].append(InfileRoot)
1977 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
1978
1979 OptionsInfo["InfilesInfo"] = InfilesInfo
1980
1981 def RetrieveRefFileInfo():
1982 """Retrieve information for ref file."""
1983
1984 RefFileInfo = {}
1985 if not OptionsInfo["Align"]:
1986 OptionsInfo["RefFileInfo"] = RefFileInfo
1987 return
1988
1989 RefFile = OptionsInfo["RefFileName"]
1990
1991 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
1992 RefFileRoot = FileName
1993
1994 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
1995 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
1996 else:
1997 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
1998 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
1999
2000 RefFileInfo["RefFileName"] = RefFile
2001 RefFileInfo["RefFileRoot"] = RefFileRoot
2002 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
2003 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
2004
2005 OptionsInfo["RefFileInfo"] = RefFileInfo
2006
2007 def ProcessChainAndLigandIDs():
2008 """Process specified chain and ligand IDs for infiles."""
2009
2010 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
2011
2012 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2013 MiscUtil.PrintInfo("\nProcessing specified chain and ligand IDs for input file %s..." % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex])
2014
2015 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
2016 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], "-l, --ligandIDs", OptionsInfo["LigandIDs"])
2017 ProcessResidueTypesAndSurfaceAndChainSelectionsOptions(FileIndex, SpecifiedChainsAndLigandsInfo)
2018
2019 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
2020
2021 CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo)
2022
2023 def ProcessResidueTypesAndSurfaceAndChainSelectionsOptions(FileIndex, SpecifiedChainsAndLigandsInfo):
2024 """Process residue types, surface, and chian selections options for chains and pockets."""
2025
2026 SpecifiedChainsAndLigandsInfo["ChainSurfaces"] = {}
2027 SpecifiedChainsAndLigandsInfo["SurfaceChain"] = {}
2028 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"] = {}
2029
2030 SpecifiedChainsAndLigandsInfo["PocketChainSelections"] = {}
2031 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"] = {}
2032 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"] = {}
2033
2034 SpecifiedChainsAndLigandsInfo["PocketSurfaces"] = {}
2035 SpecifiedChainsAndLigandsInfo["SurfacePocket"] = {}
2036 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"] = {}
2037
2038 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"] = {}
2039 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"] = {}
2040
2041 SpecifiedChainsAndLigandsInfo["ChainSelections"] = {}
2042 SpecifiedChainsAndLigandsInfo["ChainSelectionsSurfaces"] = {}
2043 SpecifiedChainsAndLigandsInfo["SurfaceChainSelections"] = {}
2044
2045 SpecifiedChainsAndLigandsInfo["DisulfideBondsChain"] = {}
2046 SpecifiedChainsAndLigandsInfo["SaltBridgesChain"] = {}
2047
2048 SpecifiedChainsAndLigandsInfo["BFactorChain"] = {}
2049
2050 # Load infile...
2051 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2052 MolName = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
2053 pymol.cmd.load(Infile, MolName)
2054
2055 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2056 AminoAcidsPresent = PyMOLUtil.AreAminoAcidResiduesPresent(MolName, ChainID)
2057
2058 # Process BFactors for chains...
2059 BFactorChain = True if re.match("^yes$", OptionsInfo["BFactorChain"], re.I) else False
2060 SpecifiedChainsAndLigandsInfo["BFactorChain"][ChainID] = BFactorChain
2061
2062 # Process surfaces for chains...
2063 if re.match("^auto$", OptionsInfo["SurfaceChain"], re.I):
2064 SurfaceChain = True if AminoAcidsPresent else False
2065 else:
2066 SurfaceChain = True if re.match("^yes$", OptionsInfo["SurfaceChain"], re.I) else False
2067 SpecifiedChainsAndLigandsInfo["SurfaceChain"][ChainID] = SurfaceChain
2068
2069 if re.match("^auto$", OptionsInfo["SurfaceChainElectrostatics"], re.I):
2070 SurfaceChainElectrostatics = True if AminoAcidsPresent else False
2071 else:
2072 SurfaceChainElectrostatics = True if re.match("^yes$", OptionsInfo["SurfaceChainElectrostatics"], re.I) else False
2073 SpecifiedChainsAndLigandsInfo["SurfaceChainElectrostatics"][ChainID] = SurfaceChainElectrostatics
2074
2075 SpecifiedChainsAndLigandsInfo["ChainSurfaces"][ChainID] = SurfaceChain
2076
2077 # Process disulfide bonds for chains...
2078 if re.match("^auto$", OptionsInfo["DisulfideBondsChain"], re.I):
2079 DisulfideBondsChain = True if AminoAcidsPresent else False
2080 else:
2081 DisulfideBondsChain = True if re.match("^yes$", OptionsInfo["DisulfideBondsChain"], re.I) else False
2082 SpecifiedChainsAndLigandsInfo["DisulfideBondsChain"][ChainID] = DisulfideBondsChain
2083
2084 # Process salt bridges bonds for chains...
2085 if re.match("^auto$", OptionsInfo["SaltBridgesChain"], re.I):
2086 SaltBridgesChain = True if AminoAcidsPresent else False
2087 else:
2088 SaltBridgesChain = True if re.match("^yes$", OptionsInfo["SaltBridgesChain"], re.I) else False
2089 SpecifiedChainsAndLigandsInfo["SaltBridgesChain"][ChainID] = SaltBridgesChain
2090
2091 # Process residue types for chains...
2092 if re.match("^auto$", OptionsInfo["ResidueTypesChain"], re.I):
2093 ResidueTypesChain = True if AminoAcidsPresent else False
2094 else:
2095 ResidueTypesChain = True if re.match("^yes$", OptionsInfo["ResidueTypesChain"], re.I) else False
2096 SpecifiedChainsAndLigandsInfo["ResidueTypesChain"][ChainID] = ResidueTypesChain
2097
2098 # Process chain selections...
2099 ChainSelections = True if len(OptionsInfo["ChainSelectionsInfo"]["Names"]) else False
2100 SpecifiedChainsAndLigandsInfo["ChainSelections"][ChainID] = ChainSelections
2101
2102 # Process surfaces for chain selections...
2103 if re.match("^auto$", OptionsInfo["SelectionsChainSurface"], re.I):
2104 SurfaceChainSelections = True if AminoAcidsPresent else False
2105 else:
2106 SurfaceChainSelections = True if re.match("^yes$", OptionsInfo["SelectionsChainSurface"], re.I) else False
2107 SpecifiedChainsAndLigandsInfo["SurfaceChainSelections"][ChainID] = SurfaceChainSelections
2108
2109 SpecifiedChainsAndLigandsInfo["ChainSelectionsSurfaces"][ChainID] = SurfaceChainSelections
2110
2111 # Process selections, residue types and surfaces for pockets...
2112 SpecifiedChainsAndLigandsInfo["PocketChainSelections"][ChainID] = {}
2113 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"][ChainID] = {}
2114 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"][ChainID] = {}
2115
2116 SpecifiedChainsAndLigandsInfo["PocketSurfaces"][ChainID] = {}
2117 SpecifiedChainsAndLigandsInfo["SurfacePocket"][ChainID] = {}
2118 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"][ChainID] = {}
2119
2120 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"][ChainID] = {}
2121
2122 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
2123 #Process pocket chain selections and surfaces...
2124 PocketChainSelections = True if len(OptionsInfo["PocketChainSelectionsInfo"]["Names"]) else False
2125 SpecifiedChainsAndLigandsInfo["PocketChainSelections"][ChainID][LigandID] = PocketChainSelections
2126
2127 # Process surfaces for chain selections...
2128 if re.match("^auto$", OptionsInfo["SelectionsPocketSurface"], re.I):
2129 PocketChainSelectionsSurface = True if AminoAcidsPresent else False
2130 else:
2131 PocketChainSelectionsSurface = True if re.match("^yes$", OptionsInfo["SelectionsPocketSurface"], re.I) else False
2132
2133 SpecifiedChainsAndLigandsInfo["PocketChainSelectionsSurfaces"][ChainID][LigandID] = PocketChainSelectionsSurface
2134
2135 SpecifiedChainsAndLigandsInfo["SurfacePocketChainSelections"][ChainID][LigandID] = PocketChainSelectionsSurface
2136
2137 #Process pocket surfaces...
2138 if re.match("^auto$", OptionsInfo["PocketSurface"], re.I):
2139 PocketSurface = True if AminoAcidsPresent else False
2140 else:
2141 PocketSurface = True if re.match("^yes$", OptionsInfo["PocketSurface"], re.I) else False
2142 SpecifiedChainsAndLigandsInfo["SurfacePocket"][ChainID][LigandID] = PocketSurface
2143
2144 if re.match("^auto$", OptionsInfo["PocketSurfaceElectrostatics"], re.I):
2145 PocketSurfaceElectrostatics = True if AminoAcidsPresent else False
2146 else:
2147 PocketSurfaceElectrostatics = True if re.match("^yes$", OptionsInfo["PocketSurfaceElectrostatics"], re.I) else False
2148 SpecifiedChainsAndLigandsInfo["SurfacePocketElectrostatics"][ChainID][LigandID] = PocketSurfaceElectrostatics
2149
2150 #Process pocket residue types...
2151 SpecifiedChainsAndLigandsInfo["PocketSurfaces"][ChainID][LigandID] = PocketSurface
2152
2153 if re.match("^auto$", OptionsInfo["PocketResidueTypes"], re.I):
2154 PocketResidueTypes = True if AminoAcidsPresent else False
2155 else:
2156 PocketResidueTypes = True if re.match("^yes$", OptionsInfo["PocketResidueTypes"], re.I) else False
2157 SpecifiedChainsAndLigandsInfo["ResidueTypesPocket"][ChainID][LigandID] = PocketResidueTypes
2158
2159 # Delete loaded object...
2160 pymol.cmd.delete(MolName)
2161
2162 def GetChainAloneResidueTypesStatus(FileIndex, ChainID):
2163 """Get status of residue types for chain alone object."""
2164
2165 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesChain"][ChainID]
2166
2167 return Status
2168
2169 def GetChainAloneBFactorStatus(FileIndex, ChainID):
2170 """Get status of B factors for chain alone object."""
2171
2172 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["BFactorChain"][ChainID]
2173
2174 return Status
2175
2176 def GetChainAloneDisulfideBondsStatus(FileIndex, ChainID):
2177 """Get status of disulfide bonds for chain alone object."""
2178
2179 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["DisulfideBondsChain"][ChainID]
2180
2181 return Status
2182
2183 def GetChainAloneSaltBridgesStatus(FileIndex, ChainID):
2184 """Get status of salt bridges for chain alone object."""
2185
2186 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SaltBridgesChain"][ChainID]
2187
2188 return Status
2189
2190 def GetChainAloneDockedPosesStatus(FileIndex, ChainID):
2191 """Get status of docked for chain alone object."""
2192
2193 Status = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["DockedPoses"][ChainID]
2194
2195 return Status
2196
2197 def GetTrajectoriesStatus(FileIndex):
2198 """Get status of trajectories for a PDB object."""
2199
2200 if OptionsInfo["TrajectoriesInfo"] is None:
2201 return False
2202
2203 Status = True if FileIndex in OptionsInfo["TrajectoriesInfo"]["PDBFileIndices"] else False
2204
2205 return Status
2206
2207 def GetPocketResidueTypesStatus(FileIndex, ChainID, LigandID):
2208 """Get status of residue types for a pocket."""
2209
2210 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ResidueTypesPocket"][ChainID][LigandID]
2211
2212 def GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
2213 """Get status of surfaces present in chain alone object."""
2214
2215 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSurfaces"][ChainID]
2216
2217 def GetPocketContainsSelectionsStatus(FileIndex, ChainID, LigandID):
2218 """Get status of selections present in a pocket."""
2219
2220 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["PocketChainSelections"][ChainID][LigandID]
2221
2222 def GetPocketContainsSurfaceStatus(FileIndex, ChainID, LigandID):
2223 """Get status of surfaces present in a pocket."""
2224
2225 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["PocketSurfaces"][ChainID][LigandID]
2226
2227 def GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
2228 """Get status of hydrophobic surfaces for chain alone object."""
2229
2230 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChain"][ChainID]
2231
2232 def GetChainAloneSurfaceChainElectrostaticsStatus(FileIndex, ChainID):
2233 """Get status of electrostatics surfaces for chain alone object."""
2234
2235 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainElectrostatics"][ChainID]
2236
2237 def GetPocketSelectionSurfaceChainStatus(FileIndex, ChainID, LigandID):
2238 """Get status of surfaces for a pocket selection in a chain."""
2239
2240 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocketChainSelections"][ChainID][LigandID]
2241
2242 def GetPocketSurfaceChainStatus(FileIndex, ChainID, LigandID):
2243 """Get status of hydrophobic surfaces for a pocket."""
2244
2245 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocket"][ChainID][LigandID]
2246
2247 def GetPocketSurfaceChainElectrostaticsStatus(FileIndex, ChainID, LigandID):
2248 """Get status of hydrophobic surfaces for a pocket."""
2249
2250 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfacePocketElectrostatics"][ChainID][LigandID]
2251
2252 def GetChainAloneContainsSelectionsStatus(FileIndex, ChainID):
2253 """Get status of selections present in chain alone object."""
2254 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSelections"][ChainID]
2255
2256 def GetChainAloneContainsChainSelectionSurfacesStatus(FileIndex, ChainID):
2257 """Get status of chain selections surfaces present in chain alone object."""
2258 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["ChainSelectionsSurfaces"][ChainID]
2259
2260 def GetChainAloneSurfaceChainSelectionStatus(FileIndex, ChainID):
2261 """Get status of hydrophobic surfaces for chain alone object."""
2262 return OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]["SurfaceChainSelections"][ChainID]
2263
2264 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
2265 """Check presence of valid ligand IDs."""
2266
2267 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
2268
2269 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2270 if len (SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
2271 MiscUtil.PrintInfo("Chain ID: %s; Specified LigandIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID])))
2272 else:
2273 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
2274 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))
2275
2276 def RetrieveFirstChainID(FileIndex):
2277 """Get first chain ID."""
2278
2279 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
2280
2281 FirstChainID = None
2282 if len(ChainsAndLigandsInfo["ChainIDs"]):
2283 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
2284
2285 return FirstChainID
2286
2287 def ProcessDockedPoses():
2288 """Process docked poses."""
2289
2290 OptionsInfo["DockedPosesGroupName"] = Options["--dockedPosesGroupName"]
2291 OptionsInfo["DockedPosesName"] = Options["--dockedPosesName"]
2292
2293 DockedPosesInfo = ProcessDockedPosesOptionsInfo("--dockedPoses", OptionsInfo["DockedPoses"])
2294 OptionsInfo["DockedPosesInfo"] = DockedPosesInfo
2295
2296 ProcessDockedPosesInfoForInfiles()
2297
2298 OptionsInfo["DockedPosesDistanceContactsCutoffs"] = Options["--dockedPosesDistanceContactsCutoffs"]
2299 OptionsInfo["DockedPosesDistanceContactsColor"] = Options["--dockedPosesDistanceContactsColor"]
2300
2301 DockedPosesDistanceContactsInfo = ProcessDockedPosesDistanceContactsOptionsInfo()
2302 OptionsInfo["DockedPosesDistanceContactsInfo"] = DockedPosesDistanceContactsInfo
2303
2304 # Setup distance conatcts status for dockes poses...
2305 if DockedPosesInfo is not None:
2306 DockedPosesInfo["DistanceContacts"] = False
2307 if DockedPosesDistanceContactsInfo is not None:
2308 if len(DockedPosesDistanceContactsInfo["ContactIDs"]):
2309 DockedPosesInfo["DistanceContacts"] = True
2310
2311 def ProcessDockedPosesInfoForInfiles():
2312 """Process docked poses info for infiles."""
2313
2314 DockedPosesInfo = OptionsInfo["DockedPosesInfo"]
2315 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2316 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
2317 ProcessDockedPosesInfoForInfileAndChains(FileIndex, SpecifiedChainsAndLigandsInfo, DockedPosesInfo)
2318
2319 def ProcessDockedPosesInfoForInfileAndChains(FileIndex, SpecifiedChainsAndLigandsInfo, DockedPosesInfo):
2320 """Process docked poses info for a specific infile."""
2321
2322 SpecifiedChainsAndLigandsInfo["DockedPoses"] = {}
2323 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"] = {}
2324
2325 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2326 DockedPoses = False
2327 if DockedPosesInfo is not None:
2328 if FileIndex in DockedPosesInfo["PDBFileIndices"]:
2329 if ChainID == DockedPosesInfo['ChainID'][FileIndex]:
2330 DockedPoses = True
2331
2332 SpecifiedChainsAndLigandsInfo["DockedPoses"][ChainID] = DockedPoses
2333
2334 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID] = []
2335 if DockedPoses:
2336 SpecifiedChainsAndLigandsInfo["DockedPosesInputFiles"][ChainID].extend(DockedPosesInfo['InputFiles'][FileIndex])
2337
2338 def ProcessDockedPosesOptionsInfo(DockedPosesOptionName, DockedPosesOptionValue):
2339 """Process docked poses options info."""
2340
2341 DockedPoses = DockedPosesOptionValue
2342 if re.match("^none$", DockedPoses, re.I):
2343 return None
2344
2345 MiscUtil.PrintInfo("\nProcessing docked poses...")
2346
2347 # Initialize docked poses info...
2348 DockedPosesInfo = {}
2349 DockedPosesInfo["PDBFileIndices"] = []
2350
2351 DockedPosesInfo["PDBFile"] = {}
2352 DockedPosesInfo["ChainID"] = {}
2353 DockedPosesInfo["LigandID"] = {}
2354 DockedPosesInfo["UseInputFileAsLigandID"] = {}
2355 DockedPosesInfo["InputFiles"] = {}
2356 DockedPosesInfo["InputFilesRoots"] = {}
2357 DockedPosesInfo["InputFilesIDs"] = {}
2358
2359 # Parse docked poses values...
2360 DockedPosesWords = DockedPoses.split(",")
2361 if len(DockedPosesWords) % 4:
2362 MiscUtil.PrintError("The number of comma delimited docked poses values, %d, specified using \"%s\" option must be a multple of 4." % (len(DockedPosesWords), DockedPosesOptionName))
2363
2364 # Validate and process specified values...
2365 for Index in range(0, len(DockedPosesWords), 4):
2366 PDBFile = DockedPosesWords[Index].strip()
2367 ChainID = DockedPosesWords[Index + 1].strip()
2368 LigandID = DockedPosesWords[Index + 2].strip()
2369 InputFiles = DockedPosesWords[Index + 3].strip()
2370
2371 InputFiles = re.sub("[ ]+", " ", InputFiles)
2372 InputFiles = InputFiles.split(" ")
2373
2374 # Process PDB file...
2375 MiscUtil.ValidateOptionFilePath("--dockedPoses", PDBFile)
2376
2377 PDBFileIndex = None
2378 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2379 PDBInfile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2380 if PDBFile == PDBInfile:
2381 PDBFileIndex = FileIndex
2382 break
2383 if PDBFileIndex is None:
2384 MiscUtil.PrintError("The PDB file specified, %s, using option \"--dockedPoses\" is not valid. It must be specified as an input file." % (PDBFile))
2385
2386 if PDBFileIndex in DockedPosesInfo['PDBFileIndices']:
2387 MiscUtil.PrintError("The PDB file specified, %s, using option \"--dockedPoses\" is not valid. It is a duplicate and has already been specified." % (PDBFile))
2388
2389 # Process chain ID...
2390 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][PDBFileIndex]
2391 if ChainID not in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
2392 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))
2393
2394 # Process ligand ID...
2395 UseInputFileAsLigandID = True if re.match("^UseInputFile$", LigandID, re.I) else False
2396 if not UseInputFileAsLigandID:
2397 if LigandID not in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
2398 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))
2399
2400 # Process input files...
2401 InputFilesRoots = []
2402 InputFilesIDs = []
2403 for InputFile in InputFiles:
2404 MiscUtil.ValidateOptionFilePath("--dockedPoses", InputFile)
2405 MiscUtil.ValidateOptionFileExt("--dockedPoses", InputFile, "sdf sd")
2406
2407 FileDir, FileName, FileExt = MiscUtil.ParseFileName(InputFile)
2408 InputFileRoot = FileName
2409
2410 # Clean up input file names for generating PyMOL object names...
2411 InputFileID = re.sub("[^a-zA-Z0-9]", "_", FileName)
2412
2413 if InputFileRoot in InputFilesRoots:
2414 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))
2415
2416 InputFilesRoots.append(InputFileRoot)
2417 InputFilesIDs.append(InputFileID)
2418
2419 # Track values...
2420 DockedPosesInfo['PDBFileIndices'].append(PDBFileIndex)
2421
2422 DockedPosesInfo["PDBFile"][PDBFileIndex] = PDBFile
2423 DockedPosesInfo["ChainID"][PDBFileIndex] = ChainID
2424
2425 DockedPosesInfo["LigandID"][PDBFileIndex] = LigandID
2426 DockedPosesInfo["UseInputFileAsLigandID"][PDBFileIndex] = UseInputFileAsLigandID
2427
2428 DockedPosesInfo["InputFiles"][PDBFileIndex] = InputFiles
2429 DockedPosesInfo["InputFilesRoots"][PDBFileIndex] = InputFilesRoots
2430 DockedPosesInfo["InputFilesIDs"][PDBFileIndex] = InputFilesIDs
2431
2432 return DockedPosesInfo
2433
2434 def ProcessDockedPosesDistanceContactsOptionsInfo():
2435 """Process dockes poses distance contacts info. """
2436
2437 DistanceContactsCutoffs = OptionsInfo["DockedPosesDistanceContactsCutoffs"]
2438 if re.match("^none$", DistanceContactsCutoffs):
2439 return None
2440
2441 DistanceContactsInfo = {}
2442 DistanceContactsInfo["ContactIDs"] = []
2443 DistanceContactsInfo["ContactCutoff"] = {}
2444
2445 DistanceContactsCutoffs = re.sub(" ", "", DistanceContactsCutoffs)
2446 if not DistanceContactsCutoffs:
2447 MiscUtil.PrintError("No value specified using \"--dockedPosesDistanceContactsCutoffs\" option.")
2448
2449 ContactCutoffValues = DistanceContactsCutoffs.split(",")
2450 for Index, ContactCutoff in enumerate(ContactCutoffValues):
2451 MiscUtil.ValidateOptionFloatValue("--dockedPosesDistanceContactsCutoffs", ContactCutoff, {">" : 0.0, "<=": OptionsInfo["PocketDistanceCutoff"]})
2452 ContactCutoff = float(ContactCutoff.strip())
2453
2454 ContactID = "Contact%s_At_%s" % ((Index + 1),ContactCutoff)
2455 ContactID = re.sub("\.", "pt", ContactID)
2456
2457 DistanceContactsInfo["ContactIDs"].append(ContactID)
2458 DistanceContactsInfo["ContactCutoff"][ContactID] = ContactCutoff
2459
2460 return DistanceContactsInfo
2461
2462 def ProcessTrajectories():
2463 """Process trajectories."""
2464
2465 TrajectoriesInfo = ProcessTrajectoriesOptionsInfo("--Trajectories", OptionsInfo["Trajectories"])
2466 OptionsInfo["TrajectoriesInfo"] = TrajectoriesInfo
2467
2468 def ProcessTrajectoriesOptionsInfo(TrajectoriesOptionName, TrajectoriesOptionValue):
2469 """Process trajectories options info."""
2470
2471 Trajectories = TrajectoriesOptionValue
2472 if re.match("^none$", Trajectories, re.I):
2473 return None
2474
2475 MiscUtil.PrintInfo("\nProcessing trajectories...")
2476
2477 # Initialize trajectories info...
2478 TrajectoriesInfo = {}
2479 TrajectoriesInfo["PDBFileIndices"] = []
2480
2481 TrajectoriesInfo["PDBFile"] = {}
2482 TrajectoriesInfo["TrajFiles"] = {}
2483 TrajectoriesInfo["TrajFilesRoots"] = {}
2484 TrajectoriesInfo["TrajFilesIDs"] = {}
2485
2486 # Parse trajectories values...
2487 TrajectoriesWords = Trajectories.split(",")
2488 if len(TrajectoriesWords) % 2:
2489 MiscUtil.PrintError("The number of comma delimited trajectories values, %d, specified using \"%s\" option must be a multple of 2." % (len(TrajectoriesWords), TrajectoriesOptionName))
2490
2491 # Validate and process specified values...
2492 for Index in range(0, len(TrajectoriesWords), 2):
2493 PDBFile = TrajectoriesWords[Index].strip()
2494 TrajFiles = TrajectoriesWords[Index + 1].strip()
2495
2496 TrajFiles = re.sub("[ ]+", " ", TrajFiles)
2497 TrajFiles = TrajFiles.split(" ")
2498
2499 # Process PDB file...
2500 MiscUtil.ValidateOptionFilePath(TrajectoriesOptionName, PDBFile)
2501
2502 PDBFileIndex = None
2503 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
2504 PDBInfile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
2505 if PDBFile == PDBInfile:
2506 PDBFileIndex = FileIndex
2507 break
2508 if PDBFileIndex is None:
2509 MiscUtil.PrintError("The topology PDB file specified, %s, using option \"%s\" is not valid. It must be specified as an input file." % (PDBFile, TrajectoriesOptionName))
2510
2511 if PDBFileIndex in TrajectoriesInfo['PDBFileIndices']:
2512 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))
2513
2514 # Process trajectory files...
2515 TrajFilesRoots = []
2516 TrajFilesIDs = []
2517 for TrajFile in TrajFiles:
2518 MiscUtil.ValidateOptionFilePath(TrajectoriesOptionName, TrajFile)
2519
2520 FileDir, FileName, FileExt = MiscUtil.ParseFileName(TrajFile)
2521 TrajFileRoot = FileName
2522
2523 # Clean up trajectory file names for generating PyMOL object names...
2524 TrajFileID = re.sub("[^a-zA-Z0-9]", "_", FileName)
2525
2526 if TrajFileRoot in TrajFilesRoots:
2527 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))
2528
2529 TrajFilesRoots.append(TrajFileRoot)
2530 TrajFilesIDs.append(TrajFileID)
2531
2532 # Track values...
2533 TrajectoriesInfo['PDBFileIndices'].append(PDBFileIndex)
2534
2535 TrajectoriesInfo["PDBFile"][PDBFileIndex] = PDBFile
2536
2537 TrajectoriesInfo["TrajFiles"][PDBFileIndex] = TrajFiles
2538 TrajectoriesInfo["TrajFilesRoots"][PDBFileIndex] = TrajFilesRoots
2539 TrajectoriesInfo["TrajFilesIDs"][PDBFileIndex] = TrajFilesIDs
2540
2541 return TrajectoriesInfo
2542
2543 def ProcessResidueTypes():
2544 """Process residue types."""
2545
2546 ResidueTypesNamesInfo, ResidueTypesParamsInfo = PyMOLUtil.ProcessResidueTypesOptionsInfo("-r, --residueTypes", OptionsInfo["ResidueTypes"])
2547 OptionsInfo["ResidueTypesNames"] = ResidueTypesNamesInfo
2548 OptionsInfo["ResidueTypesParams"] = ResidueTypesParamsInfo
2549
2550 def ProcessSaltBridgesChainResidues():
2551 """Process salt bridges chain residues."""
2552
2553 SaltBridgesChainResiduesInfo = PyMOLUtil.ProcessSaltBridgesChainResiduesOptionsInfo("--saltBridgesChainResidues", OptionsInfo["SaltBridgesChainResidues"])
2554 OptionsInfo["SaltBridgesChainResiduesInfo"] = SaltBridgesChainResiduesInfo
2555
2556 def ProcessSurfaceAtomTypesColors():
2557 """Process surface atom types colors."""
2558
2559 AtomTypesColorNamesInfo = PyMOLUtil.ProcessSurfaceAtomTypesColorsOptionsInfo("--surfaceAtomTypesColors", OptionsInfo["SurfaceAtomTypesColors"])
2560 OptionsInfo["AtomTypesColorNames"] = AtomTypesColorNamesInfo
2561
2562 def ProcessPockectChainSelections():
2563 """Process custom selections for pocket chains."""
2564
2565 PocketChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo("--selectionsPocket", OptionsInfo["SelectionsPocket"])
2566 OptionsInfo["PocketChainSelectionsInfo"] = PocketChainSelectionsInfo
2567
2568 def ProcessChainSelections():
2569 """Process custom selections for chains."""
2570
2571 ChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo("--selectionsChain", OptionsInfo["SelectionsChain"])
2572 OptionsInfo["ChainSelectionsInfo"] = ChainSelectionsInfo
2573
2574 def ProcessOptions():
2575 """Process and validate command line arguments and options."""
2576
2577 MiscUtil.PrintInfo("Processing options...")
2578
2579 # Validate options...
2580 ValidateOptions()
2581
2582 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
2583 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
2584 OptionsInfo["AlignMode"] = Options["--alignMode"]
2585
2586 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
2587
2588 OptionsInfo["BFactorChain"] = Options["--BFactorChain"]
2589 OptionsInfo["BFactorColorPalette"] = Options["--BFactorColorPalette"]
2590
2591 OptionsInfo["Infiles"] = Options["--infiles"]
2592 OptionsInfo["InfilesNames"] = Options["--infileNames"]
2593
2594 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
2595 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
2596 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
2597 else:
2598 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
2599
2600 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
2601
2602 OptionsInfo["Overwrite"] = Options["--overwrite"]
2603 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
2604
2605 OptionsInfo["Outfile"] = Options["--outfile"]
2606 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
2607 OptionsInfo["PSEOut"] = False
2608 if re.match("^pml$", FileExt, re.I):
2609 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
2610 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
2611 elif re.match("^pse$", FileExt, re.I):
2612 OptionsInfo["PSEOut"] = True
2613 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
2614 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
2615 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
2616 MiscUtil.PrintError("The intermediate output file to be generated, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again." % OptionsInfo["PMLOutfile"] )
2617
2618 OptionsInfo["DisulfideBondsChain"] = Options["--disulfideBondsChain"]
2619
2620 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
2621
2622 OptionsInfo["PocketContactsLigandColor"] = Options["--pocketContactsLigandColor"]
2623 OptionsInfo["PocketContactsLigandHydrophobicColor"] = Options["--pocketContactsLigandHydrophobicColor"]
2624 OptionsInfo["PocketContactsLigandPiPiColor"] = Options["--pocketContactsLigandPiPiColor"]
2625 OptionsInfo["PocketContactsLigandPiCationColor"] = Options["--pocketContactsLigandPiCationColor"]
2626 OptionsInfo["PocketContactsLigandHalogenColor"] = Options["--pocketContactsLigandHalogenColor"]
2627
2628 OptionsInfo["PocketContactsSolventColor"] = Options["--pocketContactsSolventColor"]
2629
2630 OptionsInfo["PocketContactsInorganicColor"] = Options["--pocketContactsInorganicColor"]
2631 OptionsInfo["PocketContactsInorganicPiCationColor"] = Options["--pocketContactsInorganicPiCationColor"]
2632
2633 OptionsInfo["PocketContactsCutoff"] = float(Options["--pocketContactsCutoff"])
2634 OptionsInfo["PocketDistanceCutoff"] = float(Options["--pocketDistanceCutoff"])
2635
2636 OptionsInfo["PocketLabelColor"] = Options["--pocketLabelColor"]
2637
2638 OptionsInfo["PocketResidueTypes"] = Options["--pocketResidueTypes"]
2639 OptionsInfo["PocketSurface"] = Options["--pocketSurface"]
2640 OptionsInfo["PocketSurfaceElectrostatics"] = Options["--pocketSurfaceElectrostatics"]
2641
2642 OptionsInfo["ResidueTypesChain"] = Options["--residueTypesChain"]
2643 OptionsInfo["ResidueTypes"] = Options["--residueTypes"]
2644 ProcessResidueTypes()
2645
2646 OptionsInfo["SaltBridgesChain"] = Options["--saltBridgesChain"]
2647 OptionsInfo["SaltBridgesChainContactsColor"] = Options["--saltBridgesChainContactsColor"]
2648 OptionsInfo["SaltBridgesChainCutoff"] = float(Options["--saltBridgesChainCutoff"])
2649 OptionsInfo["SaltBridgesChainResidues"] = Options["--saltBridgesChainResidues"]
2650 ProcessSaltBridgesChainResidues()
2651
2652 OptionsInfo["SelectionsChain"] = Options["--selectionsChain"]
2653 OptionsInfo["SelectionsChainSurface"] = Options["--selectionsChainSurface"]
2654 OptionsInfo["SelectionsChainStyle"] = Options["--selectionsChainStyle"]
2655 ProcessChainSelections()
2656
2657 OptionsInfo["SelectionsPocket"] = Options["--selectionsPocket"]
2658 OptionsInfo["SelectionsPocketSurface"] = Options["--selectionsPocketSurface"]
2659 OptionsInfo["SelectionsPocketStyle"] = Options["--selectionsPocketStyle"]
2660 ProcessPockectChainSelections()
2661
2662 OptionsInfo["SurfaceChain"] = Options["--surfaceChain"]
2663 OptionsInfo["SurfaceChainElectrostatics"] = Options["--surfaceChainElectrostatics"]
2664
2665 OptionsInfo["SurfaceChainComplex"] = True if re.match("^Yes$", Options["--surfaceChainComplex"], re.I) else False
2666 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
2667
2668 OptionsInfo["SurfaceColor"] = Options["--surfaceColor"]
2669 OptionsInfo["SurfaceColorPalette"] = Options["--surfaceColorPalette"]
2670 OptionsInfo["SurfaceAtomTypesColors"] = Options["--surfaceAtomTypesColors"]
2671 ProcessSurfaceAtomTypesColors()
2672
2673 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
2674
2675 RetrieveInfilesInfo()
2676 RetrieveRefFileInfo()
2677
2678 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
2679 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
2680
2681 ProcessChainAndLigandIDs()
2682
2683 OptionsInfo["DockedPoses"] = Options["--dockedPoses"]
2684 ProcessDockedPoses()
2685
2686 OptionsInfo["Trajectories"] = Options["--trajectories"]
2687 ProcessTrajectories()
2688
2689 def RetrieveOptions():
2690 """Retrieve command line arguments and options."""
2691
2692 # Get options...
2693 global Options
2694 Options = docopt(_docoptUsage_)
2695
2696 # Set current working directory to the specified directory...
2697 WorkingDir = Options["--workingdir"]
2698 if WorkingDir:
2699 os.chdir(WorkingDir)
2700
2701 # Handle examples option...
2702 if "--examples" in Options and Options["--examples"]:
2703 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
2704 sys.exit(0)
2705
2706 def ValidateOptions():
2707 """Validate option values."""
2708
2709 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
2710 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
2711 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
2712
2713 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
2714
2715 MiscUtil.ValidateOptionTextValue("--BFactorChain", Options["--BFactorChain"], "yes no")
2716
2717 # Expand infiles to handle presence of multiple input files...
2718 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
2719 if not len(InfileNames):
2720 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
2721
2722 # Validate file extensions...
2723 for Infile in InfileNames:
2724 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
2725 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
2726 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
2727 Options["--infileNames"] = InfileNames
2728
2729 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
2730 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
2731
2732 if re.match("^yes$", Options["--align"], re.I):
2733 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
2734 AlignRefFile = Options["--alignRefFile"]
2735 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
2736 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
2737 MiscUtil.ValidateOptionsDistinctFileNames("--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"])
2738
2739 MiscUtil.ValidateOptionTextValue("--disulfideBondsChain", Options["--disulfideBondsChain"], "yes no auto")
2740
2741 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
2742
2743 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
2744 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
2745
2746 MiscUtil.ValidateOptionFloatValue("--pocketContactsCutoff", Options["--pocketContactsCutoff"], {">": 0.0})
2747 MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0})
2748 if (float(Options["--pocketContactsCutoff"]) > float(Options["--pocketDistanceCutoff"])):
2749 MiscUtil.PrintError("The value, %s, specified using option \"--pocketContactsCutoff\" must be less than value, %s, specified using \"-pocketDistanceCutoff\" option." % (Options["--pocketContactsCutoff"], Options["--pocketDistanceCutoff"]))
2750
2751 MiscUtil.ValidateOptionTextValue("--pocketResidueTypes", Options["--pocketResidueTypes"], "yes no auto")
2752 MiscUtil.ValidateOptionTextValue("--pocketSurface", Options["--pocketSurface"], "yes no auto")
2753 MiscUtil.ValidateOptionTextValue("--pocketSurfaceElectrostatics", Options["--pocketSurfaceElectrostatics"], "yes no auto")
2754
2755 MiscUtil.ValidateOptionTextValue("--residueTypesChain", Options["--residueTypesChain"], "yes no auto")
2756
2757 MiscUtil.ValidateOptionTextValue("--saltBridgesChain", Options["--saltBridgesChain"], "yes no auto")
2758 MiscUtil.ValidateOptionFloatValue("--saltBridgesChainCutoff", Options["--saltBridgesChainCutoff"], {">": 0.0})
2759
2760 MiscUtil.ValidateOptionTextValue("--selectionsChainSurface", Options["--selectionsChainSurface"], "yes no auto")
2761 MiscUtil.ValidateOptionTextValue("--selectionsPocketSurface", Options["--selectionsPocketSurface"], "yes no auto")
2762
2763 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
2764 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no")
2765 MiscUtil.ValidateOptionTextValue("--surfaceChain", Options["--surfaceChain"], "yes no auto")
2766 MiscUtil.ValidateOptionTextValue("--surfaceChainElectrostatics", Options["--surfaceChainElectrostatics"], "yes no auto")
2767
2768 MiscUtil.ValidateOptionTextValue("--surfaceColorPalette", Options["--surfaceColorPalette"], "RedToWhite WhiteToGreen")
2769 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
2770
2771 # Setup a usage string for docopt...
2772 _docoptUsage_ = """
2773 PyMOLVisualizeMacromolecules.py - Visualize macromolecules
2774
2775 Usage:
2776 PyMOLVisualizeMacromolecules.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
2777 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
2778 [--allowEmptyObjects <yes or no>] [--BFactorChain <yes or no>] [--BFactorColorPalette <text>]
2779 [--chainIDs <First, All or ID1,ID2...>] [--disulfideBondsChain <yes or no>]
2780 [--dockedPoses <PDBFile,ChainID,LigandID,InputFiles,...>] [--dockedPosesDistanceContactsCutoffs <number1,number2...>]
2781 [--dockedPosesDistanceContactsColor <text>] [--dockedPosesGroupName <text>]
2782 [--dockedPosesName <text>] [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All or ID1,ID2...>]
2783 [--labelFontID <number>] [--PMLOut <yes or no>] [--pocketContactsInorganicColor <text>]
2784 [--pocketContactsInorganicPiCationColor <text>] [--pocketContactsLigandColor <text>]
2785 [--pocketContactsLigandHydrophobicColor <text>] [--pocketContactsLigandHalogenColor <text>]
2786 [--pocketContactsLigandPiCationColor <text>] [--pocketContactsLigandPiPiColor <text>]
2787 [--pocketContactsSolventColor <text>] [--pocketContactsCutoff <number>]
2788 [--pocketDistanceCutoff <number>] [--pocketLabelColor <text>] [--pocketResidueTypes <yes or no>]
2789 [--pocketSurface <yes or no>] [--pocketSurfaceElectrostatics <yes or no>]
2790 [--residueTypes <Type,Color,ResNames,...>] [--residueTypesChain <yes or no>]
2791 [--saltBridgesChain <yes or no>] [--saltBridgesChainContactsColor <text>]
2792 [--saltBridgesChainCutoff <number>] [--saltBridgesChainResidues <Type, ResNames,...>]
2793 [--selectionsChain <ObjectName,SelectionSpec,...>] [--selectionsChainSurface <yes or no>]
2794 [--selectionsChainStyle <DisplayStyle>] [--selectionsPocket <ObjectName,SelectionSpec,...>]
2795 [--selectionsPocketSurface <yes or no>] [--selectionsPocketStyle <DisplayStyle>]
2796 [--surfaceChain <yes or no>] [--surfaceChainElectrostatics <yes or no>]
2797 [--surfaceChainComplex <yes or no>] [--surfaceComplex <yes or no>]
2798 [--surfaceColor <ColorName>] [--surfaceColorPalette <RedToWhite or WhiteToGreen>]
2799 [--surfaceAtomTypesColors <ColorType,ColorSpec,...>]
2800 [--surfaceTransparency <number>] [--trajectories <PDBToplogyFile,TrajFiles,...> ]
2801 [--overwrite] [-w <dir>] -i <infile1,infile2,infile3...> -o <outfile>
2802 PyMOLVisualizeMacromolecules.py -h | --help | -e | --examples
2803
2804 Description:
2805 Generate PyMOL visualization files for viewing surfaces, chains, ligands, ligand
2806 binding pockets, and interactions between ligands and binding pockets in
2807 macromolecules including proteins and nucleic acids.
2808
2809 The supported input file format are: PDB (.pdb), CIF (.cif)
2810
2811 The supported output file formats are: PyMOL script file (.pml), PyMOL session
2812 file (.pse)
2813
2814 A variety of PyMOL groups and objects may be created for visualization of
2815 macromolecules. These groups and objects correspond to complexes, surfaces,
2816 chains, ligands, inorganics, ligand binding pockets, pocket, polar interactions,
2817 and pocket hydrophobic surfaces. A complete hierarchy of all possible PyMOL
2818 groups and objects is shown below:
2819
2820 <PDBFileRoot>
2821 .Complex
2822 .Complex
2823 .Surface
2824 .Trajectories
2825 .Topology
2826 .<TrajFileID>
2827 .Trajectory
2828 .<TrajFileID>
2829 ... ... ...
2830 .<TrajFileID>
2831 ... ... ...
2832 .Chain<ID>
2833 .Complex
2834 .Complex
2835 .Surface
2836 .Chain
2837 .Chain
2838 .BFactor
2839 .Putty
2840 .Cartoon
2841 .Selections
2842 .<Name>
2843 .Selection
2844 .Surface
2845 .Surface
2846 .Hydrophobicity
2847 .Hydrophobicity_Charge
2848 .<Name>
2849 ... ... ..
2850 .Residues
2851 .Aromatic
2852 .Residues
2853 .Surface
2854 .Hydrophobic
2855 .Residues
2856 .Surface
2857 .Polar
2858 .Residues
2859 .Surface
2860 .Positively_Charged
2861 .Residues
2862 .Surface
2863 .Negatively_Charged
2864 .Residues
2865 .Surface
2866 .Other
2867 .Residues
2868 .Surface
2869 .Surface
2870 .Surface
2871 .Hydrophobicity
2872 .Hydrophobicity_Charge
2873 .Vacuum_Electrostatics
2874 .Contact_Potentials
2875 .Map
2876 .Legend
2877 .Volume
2878 .Disulfide_Bonds
2879 .Residues
2880 .Salt_Bridges
2881 .Residues
2882 .Positively_Charged
2883 .Negatively_Charged
2884 .Contacts
2885 .Solvent
2886 .Inorganic
2887 .Ligand<ID>
2888 .Ligand
2889 .Ligand
2890 .BallAndStick
2891 .Pocket
2892 .Pocket
2893 .Polar_Contacts
2894 .Hydrophobic_Contacts
2895 .Pi_Pi_Contacts
2896 .Pi_Cation_Contacts
2897 .Halogen_Contacts
2898 .Selections
2899 .<Name>
2900 .Selection
2901 .Surface
2902 .Surface
2903 .Hydrophobicity
2904 .Hydrophobicity_Charge
2905 .<Name>
2906 ... ... ..
2907 .Residues
2908 .Aromatic
2909 .Residues
2910 .Surface
2911 .Hydrophobic
2912 .Residues
2913 .Surface
2914 .Polar
2915 .Residues
2916 .Surface
2917 .Positively_Charged
2918 .Residues
2919 .Surface
2920 .Negatively_Charged
2921 .Residues
2922 .Surface
2923 .Other
2924 .Residues
2925 .Surface
2926 .Surfaces
2927 .Surface
2928 .Surface
2929 .Hydrophobicity
2930 .Hydrophobicity_Charge
2931 .Vacuum_Electrostatics
2932 .Contact_Potentials
2933 .Map
2934 .Legend
2935 .Cavity
2936 .Surface
2937 .Hydrophobicity
2938 .Hydrophobicity_Charge
2939 .Vacuum_Electrostatics
2940 .Contact_Potentials
2941 .Map
2942 .Legend
2943 .Pocket_Solvent
2944 .Pocket_Solvent
2945 .Polar_Contacts
2946 .Pocket_Inorganic
2947 .Pocket_Inorganic
2948 .Polar_Contacts
2949 .Pi_Cation_Contacts
2950 .Ligand<ID>
2951 .Ligand
2952 ... ... ...
2953 .Pocket
2954 ... ... ...
2955 .Pocket_Solvent
2956 ... ... ...
2957 .Pocket_Inorganic
2958 ... ... ...
2959 .Docked_Poses or <CustomLabel>
2960 .<InputFileID>
2961 .Poses or <CustomLabel>
2962 .Pocket
2963 .Pocket
2964 .Distance_Contacts
2965 .Contact1_At_<Distance>
2966 .Contact1_At_<Distance>
2967 ... ... ...
2968 .Polar_Contacts
2969 .Hydrophobic_Contacts
2970 .Pi_Pi_Contacts
2971 .Pi_Cation_Contacts
2972 .Halogen_Contacts
2973 .Pocket_Solvent
2974 .Pocket_Solvent
2975 .Polar_Contacts
2976 .Pocket_Inorganic
2977 .Polar_Contacts
2978 .Pi_Cation_Contacts
2979 .<InputFileID>
2980 ... ... ...
2981 .<InputFileID>
2982 ... ... ...
2983 .Chain<ID>
2984 ... ... ...
2985 .Ligand<ID>
2986 ... ... ...
2987 .Ligand<ID>
2988 ... ... ...
2989 .Chain<ID>
2990 ... ... ...
2991 <PDBFileRoot>
2992 .Complex
2993 ... ... ...
2994 .Chain<ID>
2995 ... ... ...
2996 .Ligand<ID>
2997 ... ... ...
2998 .Ligand<ID>
2999 ... ... ...
3000 .Chain<ID>
3001 ... ... ...
3002
3003 The hydrophobic and electrostatic surfaces are not created for complete complex
3004 and chain complex in input file(s) by default. A word to the wise: The creation of
3005 surface objects may slow down loading of PML file and generation of PSE file, based
3006 on the size of input complexes. The generation of PSE file may also fail.
3007
3008 Options:
3009 -a, --align <yes or no> [default: no]
3010 Align input files to a reference file before visualization. The docked poses
3011 and trajectories are not aligned.
3012 --alignMethod <align, cealign, super> [default: super]
3013 Alignment methodology to use for aligning input files to a
3014 reference file.
3015 --alignMode <FirstChain or Complex> [default: FirstChain]
3016 Portion of input and reference files to use for spatial alignment of
3017 input files against reference file. Possible values: FirstChain or
3018 Complex.
3019
3020 The FirstChain mode allows alignment of the first chain in each input
3021 file to the first chain in the reference file along with moving the rest
3022 of the complex to coordinate space of the reference file. The complete
3023 complex in each input file is aligned to the complete complex in reference
3024 file for the Complex mode.
3025 --alignRefFile <filename> [default: FirstInputFile]
3026 Reference input file name. The default is to use the first input file
3027 name specified using '-i, --infiles' option.
3028 --allowEmptyObjects <yes or no> [default: no]
3029 Allow creation of empty PyMOL objects corresponding to solvent and
3030 inorganic atom selections across chains and ligands in input file(s). By
3031 default, the empty objects are marked for deletion.
3032 -b, --BFactorChain <yes or no> [default: yes]
3033 A cartoon and putty around individual chains colored by an arbitrary set
3034 of B factor values. The minimum and maximum values for B factors are
3035 automatically detected. These values may indicate spread of electron
3036 density around atoms or correspond to any other property mapped to
3037 B factors in input file.
3038 --BFactorColorPalette <text> [default: blue_white_red]
3039 Color palette for coloring cartoon and putty around chains generated using B
3040 factor values. Any valid PyMOL color palette name is allowed. No validation is
3041 performed. The complete list of valid color palette names is a available
3042 at: pymolwiki.org/index.php/Spectrum. Examples: blue_white_red,
3043 blue_white_magenta, blue_red, green_white_red, green_red.
3044 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
3045 List of chain IDs to use for visualizing macromolecules. Possible values:
3046 First, All, or a comma delimited list of chain IDs. The default is to use the
3047 chain ID for the first chain in each input file.
3048 -d --disulfideBondsChain <yes or no> [default: auto]
3049 Disulfide bonds for chains. By default, the disulfide bonds group is
3050 automatically created for chains containing amino acids and skipped for
3051 chains only containing nucleic acids.
3052 --dockedPoses <PDBFile,ChainID,LigandID,InputFiles,...> [default: none]
3053 PDB file name, pocket chain ID, ligand specification, and input files to use
3054 for creating pockets to visualize docked poses or any arbitrary set of
3055 molecules. Any valid PyMOL input file format is allowed.
3056
3057 It's a quartet of comma limited values corresponding to PDF file name,
3058 pocket chain ID, ligand ID, and input files. Multiple input file names are
3059 delimited by spaces.
3060
3061 The supported values for docked poses are shown below:
3062
3063 PDBFile: A valid PDB file name
3064 ChainID: A valid Chain ID
3065 LigandID: A valid Ligand ID or UseInputFile
3066 InputFiles: A space delimited list of input file names
3067
3068 All docked pose values must be specified. No default values are assigned.
3069
3070 The 'ChainID' and 'LigandID' are used for creating pocket to visualize docked
3071 poses.
3072
3073 The 'LigandID' must be a valid ligand ID in 'ChainID'. Alternatively, you may use
3074 input files by specifying 'UseInputFile' to select residues in 'ChainID' for creating
3075 pockets to visualize docked poses.
3076 --dockedPosesDistanceContactsCutoffs <number1,number2...> [default: none]
3077 A comma delimited list of distances in Angstroms for identifying and displaying
3078 distance contacts between heavy atoms in pocket residues and docked poses. A
3079 PyMOL distance contact object is created for each specified distance. You may
3080 find it helpful for identifying steric clashes between docked poses and pocket
3081 residues. The maximum distance cutoff value must be less than the specified
3082 value for '--pocketDistanceCutoff' option.
3083 --dockedPosesDistanceContactsColor <text> [default: red]
3084 Color for drawing distance contacts between docked poses and pocket residues.
3085 The specified value must be valid color. No validation is performed.
3086 --dockedPosesGroupName <text> [default: Docked_Poses]
3087 PyMOL object name for docked poses group. You may use an artbitray name
3088 to reflect data in input file(s) specified in '--dockedPoses' option. It must be a valid
3089 PyMOL object name. No validation is performed.
3090 --dockedPosesName <text> [default: Poses]
3091 PyMOL object name for docked poses object. You may use an artbitray name
3092 to reflect data in input file(s) specified in '--dockedPoses' option. It must be a
3093 valid PyMOL object name. No validation is performed.
3094 -e, --examples
3095 Print examples.
3096 -h, --help
3097 Print this help message.
3098 -i, --infiles <infile1,infile2,infile3...>
3099 Input file names.
3100 --ignoreHydrogens <yes or no> [default: yes]
3101 Ignore hydrogens for ligand, pocket, selection, and residue type views.
3102 -l, --ligandIDs <Largest, All or ID1,ID2...> [default: Largest]
3103 List of ligand IDs present in chains for visualizing macromolecules to
3104 highlight ligand interactions. Possible values: Largest, All, or a comma
3105 delimited list of ligand IDs. The default is to use the largest ligand present
3106 in all or specified chains in each input file.
3107
3108 Ligands are identified using organic selection operator available in PyMOL.
3109 It'll also identify buffer molecules as ligands. The largest ligand contains
3110 the highest number of heavy atoms.
3111 --labelFontID <number> [default: 7]
3112 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
3113 The specified value must be a valid PyMOL font ID. No validation is
3114 performed. The complete lists of valid font IDs is available at:
3115 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
3116 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
3117 -o, --outfile <outfile>
3118 Output file name.
3119 -p, --PMLOut <yes or no> [default: yes]
3120 Save PML file during generation of PSE file.
3121 --pocketContactsInorganicColor <text> [default: deepsalmon]
3122 Color for drawing polar contacts between inorganic and pocket residues.
3123 The specified value must be valid color. No validation is performed.
3124 --pocketContactsInorganicPiCationColor <text> [default: limon]
3125 Color for drawing pi cation contacts between inorganic and pocket residues.
3126 The specified value must be valid color. No validation is performed. The pi
3127 cation contacts are drawn using PyMOL distance command with support for
3128 mode 7 and may require incentive version of PyMOL.
3129 --pocketContactsLigandColor <text> [default: orange]
3130 Color for drawing polar contacts between ligand and pocket residues.
3131 The specified value must be valid color. No validation is performed.
3132 --pocketContactsLigandHalogenColor <text> [default: magenta]
3133 Color for drawing halogen contacts between ligand and pocket residues.
3134 The specified value must be valid color. No validation is performed.
3135 --pocketContactsLigandHydrophobicColor <text> [default: purpleblue]
3136 Color for drawing hydrophobic contacts between ligand and pocket residues.
3137 The specified value must be valid color. No validation is performed. The
3138 hydrophobic contacts are shown between pairs of carbon atoms not
3139 connected to hydrogen bond donor or acceptors atoms as identified
3140 by PyMOL.
3141 --pocketContactsLigandPiCationColor <text> [default: yelloworange]
3142 Color for drawing pi cation contacts between ligand and pocket residues.
3143 The specified value must be valid color. No validation is performed. The pi
3144 cation contacts are drawn using PyMOL distance command with support for
3145 mode 7 and may require incentive version of PyMOL.
3146 --pocketContactsLigandPiPiColor <text> [default: cyan]
3147 Color for drawing pi pi contacts between ligand and pocket residues.
3148 The specified value must be valid color. No validation is performed. The pi
3149 pi contacts are drawn using PyMOL distance command with support for
3150 mode 6 and may require incentive version of PyMOL.
3151 --pocketContactsSolventColor <text> [default: marine]
3152 Color for drawing polar contacts between solvent and pocket residues..
3153 The specified value must be valid color. No validation is performed.
3154 --pocketContactsCutoff <number> [default: 4.0]
3155 Distance in Angstroms for identifying polar, hyrdophobic contacts, pi pi,
3156 pi cation, and halogen contacts between atoms in pocket residues and
3157 ligands.
3158 --pocketDistanceCutoff <number> [default: 5.0]
3159 Distance in Angstroms for identifying pocket residues around ligands.
3160 --pocketLabelColor <text> [default: magenta]
3161 Color for drawing residue or atom level labels for a pocket. The specified
3162 value must be valid color. No validation is performed.
3163 --pocketResidueTypes <yes or no> [default: auto]
3164 Pocket residue types. The residue groups are generated using residue types,
3165 colors, and names specified by '--residueTypes' option. It is only valid for
3166 amino acids. By default, the residue type groups are automatically created
3167 for pockets containing amino acids and skipped for chains only containing
3168 nucleic acids.
3169 --pocketSurface <yes or no> [default: auto]
3170 Surfaces around pocket residues colored by hydrophobicity alone and
3171 both hydrophobicity and charge. The hydrophobicity surface is colored
3172 at residue level using Eisenberg hydrophobicity scale for residues and color
3173 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
3174 charge surface is colored [ Ref 140 ] at atom level using colors specified for
3175 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
3176 simultaneous mapping of hyrophobicity and charge values on the surfaces.
3177
3178 The cavity surfaces around ligands are also generated. These surfaces are
3179 colored by hydrophobicity along and both hydrophobicity and charge.
3180
3181 This option is only valid for amino acids. By default, both surfaces are
3182 automatically created for pockets containing amino acids and skipped for
3183 pockets containing only nucleic acids.
3184 --pocketSurfaceElectrostatics <yes or no> [default: no]
3185 Vacuum electrostatics contact potential surface around pocket residues.
3186 A word to the wise from PyMOL documentation: The computed protein
3187 contact potentials are only qualitatively useful, due to short cutoffs,
3188 truncation, and lack of solvent "screening".
3189
3190 The cavity surface around ligands is also generated. This surface is
3191 colored by vacuum electrostatics contact potential.
3192
3193 This option is only valid for amino acids. By default, the electrostatics surface
3194 is automatically created for chains containing amino acids and skipped for chains
3195 containing only nucleic acids.
3196 -r, --residueTypes <Type,Color,ResNames,...> [default: auto]
3197 Residue types, colors, and names to generate for residue groups during
3198 '--pocketResidueTypes' and '--residueTypesChain' option. It is only
3199 valid for amino acids.
3200
3201 It is a triplet of comma delimited list of amino acid residues type, residues
3202 color, and a space delimited list three letter residue names.
3203
3204 The default values for residue type, color, and name triplets are shown
3205 below:
3206
3207 Aromatic,brightorange,HIS PHE TRP TYR,
3208 Hydrophobic,orange,ALA GLY VAL LEU ILE PRO MET,
3209 Polar,palegreen,ASN GLN SER THR CYS,
3210 Positively_Charged,marine,ARG LYS,
3211 Negatively_Charged,red,ASP GLU
3212
3213 The color name must be a valid PyMOL name. No validation is performed.
3214 An amino acid name may appear across multiple residue types. All other
3215 residues are grouped under 'Other'.
3216 --residueTypesChain <yes or no> [default: auto]
3217 Chain residue types. The residue groups are generated using residue types,
3218 colors, and names specified by '--residueTypes' option. It is only valid for
3219 amino acids. By default, the residue type groups are automatically created
3220 for chains containing amino acids and skipped for chains only containing
3221 nucleic acids.
3222 --saltBridgesChain <yes or no> [default: auto]
3223 Salt bridges for chains. By default, the salt bridges group is automatically
3224 created for chains containing amino acids and skipped for chains only
3225 containing nucleic acids. The salt bridges correspond to polar contacts
3226 between positively and negatively charges residues in a chain.
3227 --saltBridgesChainContactsColor <text> [default: brightorange]
3228 Color for drawing polar contacts between positively and negatively
3229 charged residues involved in salt bridges. The specified value must
3230 be valid color. No validation is performed.
3231 --saltBridgesChainCutoff <number> [default: 4.0]
3232 Distance in Angstroms for identifying polar contacts between positively
3233 and negatively charged residues involved in salt bridges in a chain.
3234 --saltBridgesChainResidues <Type, ResNames,...> [default: auto]
3235 Residue types and names to use for identifying positively and negatively
3236 charged residues involved in salt bridges.
3237
3238 It is a pair of comma delimited list of amino acid residue types and a space
3239 delimited list three letter residue names.
3240
3241 The default values for residue type and name pairs are shown below:
3242
3243 Positively_Charged,ARG LYS HIS HSP
3244 Negatively_Charged,ASP GLU
3245
3246 The residue names must be valid names. No validation is performed.
3247 --selectionsChain <ObjectName,SelectionSpec,...> [default: none]
3248 Custom selections for chains. It is a pairwise list of comma delimited values
3249 corresponding to PyMOL object names and selection specifications. The
3250 selection specification must be a valid PyMOL specification. No validation is
3251 performed.
3252
3253 The PyMOL objects are created for each chain corresponding to the
3254 specified selections. The display style for PyMOL objects is set using
3255 value of '--selectionsChainStyle' option.
3256
3257 The specified selection specification is automatically appended to appropriate
3258 chain specification before creating PyMOL objects.
3259
3260 For example, the following specification for '--selectionsChain' option will
3261 generate PyMOL objects for chains containing Cysteines and Serines:
3262
3263 Cysteines,resn CYS,Serines,resn SER
3264
3265 --selectionsChainSurface <yes or no> [default: auto]
3266 Surfaces around individual chain selections colored by hydrophobicity alone
3267 and both hydrophobicity and charge. This option is similar to '--surfaceChain'
3268 options for creating surfaces for chain. Additional details are available in the
3269 documentation section for '--surfaceChain' options.
3270 --selectionsChainStyle <DisplayStyle> [default: sticks]
3271 Display style for PyMOL objects created for '--selectionsChain' option. It
3272 must be a valid PyMOL display style. No validation is performed.
3273 --selectionsPocket <ObjectName,SelectionSpec,...> [default: none]
3274 Custom selections for pocket residues. It is a pairwise list of comma delimited
3275 values corresponding to PyMOL object names and selection specifications. The
3276 selection specification must be a valid PyMOL specification. No validation is
3277 performed.
3278
3279 The PyMOL objects are created for each pocket corresponding to the
3280 specified selections. The display style for PyMOL objects is set using
3281 value of '--selectionsChainStyle' option.
3282
3283 The specified selection specification is automatically appended to appropriate
3284 pocket specification before creating PyMOL objects.
3285
3286 For example, the following specification for '--selectionsPocket' option will
3287 generate PyMOL objects for pockets containing Tyrosines and Serines:
3288
3289 Tyrosines,resn TYR,Serines,resn SER
3290
3291 --selectionsPocketSurface <yes or no> [default: auto]
3292 Surfaces around individual pocket chain selections colored by hydrophobicity
3293 alone and both hydrophobicity and charge. This option is similar to '--surfaceChain'
3294 options for creating surfaces for chain. Additional details are available in the
3295 documentation section for '--surfaceChain' options.
3296 --selectionsPocketStyle <DisplayStyle> [default: sticks]
3297 Display style for PyMOL objects created for '--selectionsPocket' option. It
3298 must be a valid PyMOL display style. No validation is performed.
3299 --surfaceChain <yes or no> [default: auto]
3300 Surfaces around individual chain colored by hydrophobicity alone and
3301 both hydrophobicity and charge. The hydrophobicity surface is colored
3302 at residue level using Eisenberg hydrophobicity scale for residues and color
3303 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
3304 charge surface is colored [ Ref 140 ] at atom level using colors specified for
3305 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
3306 simultaneous mapping of hyrophobicity and charge values on the surfaces.
3307
3308 This option is only valid for amino acids. By default, both surfaces are
3309 automatically created for chains containing amino acids and skipped for
3310 chains containing only nucleic acids.
3311 --surfaceChainElectrostatics <yes or no> [default: no]
3312 Vacuum electrostatics contact potential surface and volume around individual
3313 chain. A word to the wise from PyMOL documentation: The computed protein
3314 contact potentials are only qualitatively useful, due to short cutoffs,
3315 truncation, and lack of solvent "screening".
3316
3317 This option is only valid for amino acids. By default, the electrostatics surface
3318 and volume are automatically created for chains containing amino acids and
3319 skipped for chains containing only nucleic acids.
3320 --surfaceChainComplex <yes or no> [default: no]
3321 Hydrophobic surface around chain complex. The surface is colored by
3322 hydrophobicity. It is only valid for amino acids.
3323 --surfaceComplex <yes or no> [default: no]
3324 Hydrophobic surface around complete complex. The surface is colored by
3325 hydrophobicity. It is only valid for amino acids.
3326 --surfaceAtomTypesColors <ColorType,ColorSpec,...> [default: auto]
3327 Atom colors for generating surfaces colored by hyrophobicity and charge
3328 around chains and pockets in proteins. It's a pairwise comma delimited list
3329 of atom color type and color specification for goups of atoms.
3330
3331 The default values for color types [ Ref 140 ] along wth color specifications
3332 are shown below:
3333
3334 HydrophobicAtomsColor, yellow,
3335 NegativelyChargedAtomsColor, red,
3336 PositivelyChargedAtomsColor, blue,
3337 OtherAtomsColor, gray90
3338
3339 The color names must be valid PyMOL names.
3340
3341 The color values may also be specified as space delimited RGB triplets:
3342
3343 HydrophobicAtomsColor, 0.95 0.78 0.0,
3344 NegativelyChargedAtomsColor, 1.0 0.4 0.4,
3345 PositivelyChargedAtomsColor, 0.2 0.5 0.8,
3346 OtherAtomsColor, 0.95 0.95 0.95
3347
3348 --surfaceColor <ColorName> [default: lightblue]
3349 Color name for surfaces around chains and pockets. This color is not used
3350 for surfaces colored by hydrophobicity and charge. The color name must be
3351 a valid PyMOL name.
3352 --surfaceColorPalette <RedToWhite or WhiteToGreen> [default: RedToWhite]
3353 Color palette for hydrophobic surfaces around chains and pockets in proteins.
3354 Possible values: RedToWhite or WhiteToGreen from most hydrophobic amino
3355 acid to least hydrophobic. The colors values for amino acids are taken from
3356 color_h script available as part of the Script Library at PyMOL Wiki.
3357 --surfaceTransparency <number> [default: 0.25]
3358 Surface transparency for molecular surfaces.
3359 -t, --trajectories <PDBToplogyFile,TrajFiles,...> [default: none]
3360 PDB topology file name and MD trajectories files for visualizing trajectories
3361 for PDB files.
3362
3363 It's a pair of comma limited values corresponding to a PDB file name and
3364 MD trajectory files. Multiple trajectory file names are delimited by spaces.
3365
3366 The supported values for trajectories are shown below:
3367
3368 PDBTopologyFile: A valid PDB file name
3369 TrajFiles: A space delimited list of MD trajectory file names
3370
3371 The trajectory files must correspond to the specified PDB topology file. In
3372 addition, the format of trajectory files must be a valid PyMOL format. PyMOL
3373 uses Molfile Plugin, which supports a variety of trajectory file formats. For
3374 example: HARMM, NAMD, X-PLOR (.dcd), Gromacs TRR/XTC (.trr, .xtc),
3375 XYZ (.xyz) etc.
3376 --overwrite
3377 Overwrite existing files.
3378 -w, --workingdir <dir>
3379 Location of working directory which defaults to the current directory.
3380
3381 Examples:
3382 To visualize the first chain, the largest ligand in the first chain, and ligand
3383 binding pockets to highlight ligand interaction with pocket resiudes, solvents
3384 and inorganics, in a PDB file, and generate a PML file, type:
3385
3386 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
3387
3388 To visualize the first chain along with all cysteines and serines, the largest
3389 ligand in the first chain, and ligand binding pockets to highlight ligand
3390 interaction with pocket resiudes, solvents and inorganics, in a PDB file,
3391 and generate a PML file, type:
3392
3393 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
3394 --selectionsChain "Cysteines,resn cys,Serines,resn ser"
3395
3396 To visualize the first chain along with all serines and tyrosines in binding
3397 pockets, the largest ligand in the first chain, and ligand binding pockets
3398 to highlight ligand interaction with pocket resiudes, solvents and inorganics,
3399 in a PDB file, and generate a PML file, type:
3400
3401 % PyMOLVisualizeMacromolecules.py -i Sample4.pdb -o Sample4.pml
3402 --selectionsPocket "Serines,resn ser,Tyrosines,resn tyr"
3403
3404 To visualize docking poses from a SD file in a pocket corresponding to a SD file
3405 for a chain, along with visualization of other information, in a PDB file,
3406 and generate a PML file, type:
3407
3408 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3409 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
3410 SampleMproDockedPosesTop100.sdf"
3411
3412 To visualize docking poses from a SD file in a pocket corresponding to SD file
3413 for a chain, along with visualization of distance contacts at 3.0 and 3.5 Angstroms,
3414 in a PDB file, and generate a PML file, type:
3415
3416 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3417 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
3418 SampleMproDockedPosesTop100.sdf"
3419 --dockedPosesDistanceContactsCutoffs "3.0, 3.5"
3420
3421 To visualize docking poses from a SD file in a pocket corresponding to a specific
3422 ligand a chain, along with visualization of other information, in a PDB file,
3423 and generate a PML file, type:
3424
3425 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3426 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,N3,
3427 SampleMproDockedPosesTop100.sdf"
3428
3429 To visualize docking poses from multiple SDs file in a pocket corresponding SD file
3430 a for a chain, along with visualization of other information, in a PDB file, and
3431 generate a PML file, type:
3432
3433 % PyMOLVisualizeMacromolecules.py -c All -l "N3" -i SampleMpro6LU7.pdb
3434 -o SampleMpro6LU7.pml --dockedPoses "SampleMpro6LU7.pdb,A,UseInputFile,
3435 SampleMproDockedPosesTop100.sdf SampleMproDockedPosesDiverse100.sdf"
3436
3437 To visualize trajectory from a DCD file, along with visualization of other
3438 information, corresponding to a PDB topology file and generate a PML file,
3439 type:
3440
3441 % PyMOLVisualizeMacromolecules.py -t "Sample10.pdb, Sample10.dcd"
3442 -i Sample10.pdb -o Sample10.pml
3443
3444 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
3445 highlight ligand interaction with pocket resiudes, solvents and inorganics, in a
3446 PDB file, and generate a PML file, type:
3447
3448 % PyMOLVisualizeMacromolecules.py -c All -l All -i Sample4.pdb -o
3449 Sample4.pml
3450
3451 To visualize all chains, ligands, and ligand binding pockets along with displaying
3452 all hydrophibic surfaces and chain electrostatic surface, in a PDB file, and
3453 generate a PML file, type:
3454
3455 % PyMOLVisualizeMacromolecules.py -c All -l All
3456 --surfaceChainElectrostatics yes --surfaceChainComplex yes
3457 --surfaceComplex yes -i Sample4.pdb -o Sample4.pml
3458
3459 To visualize chain E, ligand ADP in chain E, and ligand binding pockets to
3460 highlight ligand interaction with pocket resiudes, solvents and inorganics,
3461 in a PDB file, and generate a PML file, type:
3462
3463 % PyMOLVisualizeMacromolecules.py -c E -l ADP -i Sample3.pdb
3464 -o Sample3.pml
3465
3466 To visualize chain E, ligand ADP in chain E, and ligand binding pockets to
3467 highlight ligand interaction with pocket resiudes, solvents and inorganics,
3468 in a PDB file, and generate a PSE file, type:
3469
3470 % PyMOLVisualizeMacromolecules.py -c E -l ADP -i Sample3.pdb
3471 -o Sample3.pse
3472
3473 To visualize the first chain, the largest ligand in the first chain, and ligand
3474 binding pockets to highlight ligand interaction with pocket resiudes, solvents
3475 and inorganics, in PDB files, along with aligning first chain in each input file to
3476 the first chain in first input file, and generate a PML file, type:
3477
3478 % PyMOLVisualizeMacromolecules.py --align yes -i
3479 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
3480
3481 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
3482 highlight ligand interaction with pocket resiudes, solvents and inorganics, in
3483 PDB files, along with aligning first chain in each input file to the first chain in
3484 first input file, and generate a PML file, type:
3485
3486 % PyMOLVisualizeMacromolecules.py --align yes -c All -l All -i
3487 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
3488
3489 To visualize all chains, all ligands in all chains, and all ligand binding pockets to
3490 highlight ligand interaction with pocket resiudes, solvents and inorganics, in
3491 PDB files, along with aligning first chain in each input file to the first chain in a
3492 specified PDB file using a specified alignment method, and generate a PML
3493 file, type:
3494
3495 % PyMOLVisualizeMacromolecules.py --align yes --alignMode FirstChain
3496 --alignRefFile Sample5.pdb --alignMethod super -c All -l All -i
3497 "Sample5.pdb,Sample6.pdb,Sample7.pdb" -o SampleOut.pml
3498
3499 Author:
3500 Manish Sud(msud@san.rr.com)
3501
3502 See also:
3503 DownloadPDBFiles.pl, PyMOLVisualizeCavities.py,
3504 PyMOLVisualizeCryoEMDensity.py, PyMOLVisualizeElectronDensity.py,
3505 PyMOLVisualizeInterfaces.py, PyMOLVisualizeSurfaceAndBuriedResidues.py
3506
3507 Copyright:
3508 Copyright (C) 2024 Manish Sud. All rights reserved.
3509
3510 The functionality available in this script is implemented using PyMOL, a
3511 molecular visualization system on an open source foundation originally
3512 developed by Warren DeLano.
3513
3514 This file is part of MayaChemTools.
3515
3516 MayaChemTools is free software; you can redistribute it and/or modify it under
3517 the terms of the GNU Lesser General Public License as published by the Free
3518 Software Foundation; either version 3 of the License, or (at your option) any
3519 later version.
3520
3521 """
3522
3523 if __name__ == "__main__":
3524 main()
