1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeElectronDensity.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 GenerateElectronDensityVisualization()
79
80 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
81 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
82
83 def GenerateElectronDensityVisualization():
84 """Generate electron density 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 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
112 FirstChain = True
113 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
114 if FirstComplex and FirstChain:
115 FirstComplexFirstChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
116
117 WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
118
119 # Setup ligand views...
120 FirstLigand = True
121 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
122 WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID)
123
124 # Set up ligand level group...
125 Enable, Action = [False, "close"]
126 if FirstLigand:
127 FirstLigand = False
128 Enable, Action = [True, "open"]
129 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"], PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"], Enable, Action)
130
131 # Setup Chain level group...
132 Enable, Action = [False, "close"]
133 if FirstChain:
134 FirstChain = False
135 Enable, Action = [True, "open"]
136 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"], Enable, Action)
137
138 # Set up complex level group...
139 Enable, Action = [False, "close"]
140 if FirstComplex:
141 FirstComplex = False
142 Enable, Action = [True, "open"]
143 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["PDBGroup"], PyMOLObjectNames["PDBGroupMembers"], Enable, Action)
144
145 # Delete empty PyMOL objects...
146 DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames)
147
148 if OptionsInfo["Align"]:
149 DeleteAlignReference(OutFH)
150
151 if FirstComplexFirstChainName is not None:
152 OutFH.write("""\ncmd.orient("%s", animate = -1)\n""" % FirstComplexFirstChainName)
153 else:
154 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
155
156 OutFH.close()
157
158 # Generate PSE file as needed...
159 if OptionsInfo["PSEOut"]:
160 GeneratePyMOLSessionFile()
161
162 def WritePMLHeader(OutFH, ScriptName):
163 """Write out PML header for setting up complex view."""
164
165 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
166 OutFH.write("%s\n" % HeaderInfo)
167
168 def WritePyMOLParameters(OutFH):
169 """Write out PyMOL global parameters."""
170
171 PMLCmds = []
172 PMLCmds.append("""cmd.set("mesh_width", %.2f)""" % (OptionsInfo["MeshWidth"]))
173 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
174 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
175 PML = "\n".join(PMLCmds)
176
177 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
178 OutFH.write("%s\n" % PML)
179
180 def WriteAlignReference(OutFH):
181 """Setup object for alignment reference."""
182
183 RefFileInfo = OptionsInfo["RefFileInfo"]
184 RefFile = RefFileInfo["RefFileName"]
185 RefName = RefFileInfo["PyMOLObjectName"]
186
187 PMLCmds = []
188 PMLCmds.append("""cmd.load("%s", "%s")""" % (RefFile, RefName))
189 PMLCmds.append("""cmd.hide("everything", "%s")""" % (RefName))
190 PMLCmds.append("""cmd.disable("%s")""" % (RefName))
191 PML = "\n".join(PMLCmds)
192
193 OutFH.write("""\n""\n"Loading %s and setting up view for align reference..."\n""\n""" % RefFile)
194 OutFH.write("%s\n" % PML)
195
196 def WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames):
197 """Setup alignment of complex to reference."""
198
199 RefFileInfo = OptionsInfo["RefFileInfo"]
200 RefName = RefFileInfo["PyMOLObjectName"]
201
202 ComplexName = PyMOLObjectNames["Complex"]
203
204 if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
205 RefFirstChainID = RefFileInfo["ChainsAndLigandsInfo"]["ChainIDs"][0]
206 RefAlignSelection = "%s and chain %s" % (RefName, RefFirstChainID)
207
208 ComplexFirstChainID = RetrieveFirstChainID(FileIndex)
209 ComplexAlignSelection = "%s and chain %s" % (ComplexName, ComplexFirstChainID)
210 else:
211 RefAlignSelection = RefName
212 ComplexAlignSelection = ComplexName
213
214 PML = PyMOLUtil.SetupPMLForAlignment(OptionsInfo["AlignMethod"], RefAlignSelection, ComplexAlignSelection)
215 OutFH.write("""\n""\n"Aligning %s against reference %s ..."\n""\n""" % (ComplexAlignSelection, RefAlignSelection))
216 OutFH.write("%s\n" % PML)
217
218 def DeleteAlignReference(OutFH):
219 """Delete alignment reference object."""
220
221 RefName = OptionsInfo["RefFileInfo"]["PyMOLObjectName"]
222 OutFH.write("""\n""\n"Deleting alignment reference object %s..."\n""\n""" % RefName)
223 OutFH.write("""cmd.delete("%s")\n""" % RefName)
224
225 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex):
226 """Write out PML for viewing polymer complex along with electron density."""
227
228 # Setup complex...
229 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
230 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["Complex"], Infile, True)
231 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
232 OutFH.write("%s\n" % PML)
233
234 if OptionsInfo["Align"]:
235 # No need to align complex on to itself...
236 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
237 WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames)
238
239 # Setup electron density maps and meshes...
240 CompositeEDMapFile = OptionsInfo["CompositeEDMapFiles"][FileIndex]
241 WriteComplexCompositeElectronDensityMapView(OutFH, PyMOLObjectNames, CompositeEDMapFile)
242
243 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
244 DifferenceEDMapFile = OptionsInfo["DiffEDMapFiles"][FileIndex]
245 WriteComplexDifferenceElectronDensityMapView(OutFH, PyMOLObjectNames, DifferenceEDMapFile)
246
247 # Setup complex group...
248 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close")
249
250 def WriteComplexCompositeElectronDensityMapView(OutFH, PyMOLObjectNames, MapFileName):
251 """Write out PML for viewing composite maps."""
252
253 # Load composite map (2Fo - Fc) and setup mesh views...
254 Info = """\
255 ""
256 "Loading composite map (2Fo - Fc) %s and setting up mesh view for complex..."
257 "" """ % MapFileName
258 OutFH.write("\n%s\n" % Info)
259
260 MapName = PyMOLObjectNames["ComplexCompositeEDMap"]
261 ComplexName = PyMOLObjectNames["Complex"]
262
263 ContourLevel = OptionsInfo["MeshLevelCompositeMap"]
264 Color = OptionsInfo["MeshColorCompositeMap"]
265
266 VolumeColorRamp = OptionsInfo["VolumeColorRampCompositeMap"]
267
268 VolumeName = PyMOLObjectNames["ComplexCompositeEDVolume"]
269 MeshName = PyMOLObjectNames["ComplexCompositeEDMesh"]
270 SurfaceName = PyMOLObjectNames["ComplexCompositeEDSurface"]
271
272 AlignMapToObjectName = ComplexName if OptionsInfo["Align"] else None
273 EnableMap = True
274 PML = SetupPMLForElectronDensityMap(MapFileName, MapName, AlignMapToObjectName, EnableMap)
275 OutFH.write("%s\n" % PML)
276
277 EnableMesh = OptionsInfo["MeshComplex"]
278
279 EnableVolume = OptionsInfo["VolumeComplex"]
280 if EnableVolume and EnableMesh:
281 EnableVolume = False
282
283 EnableSurface = OptionsInfo["SurfaceComplex"]
284 if EnableSurface and (EnableVolume or EnableMesh):
285 EnableSurface = False
286
287 if OptionsInfo["VolumeComplex"]:
288 PML = SetupPMLForElectronDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = EnableVolume, Selection = ComplexName)
289 OutFH.write("\n%s\n" % PML)
290
291 if OptionsInfo["MeshComplex"]:
292 PML = SetupPMLForElectronDensityMesh(MapName, MeshName, ContourLevel, Color, Enable = EnableMesh, Selection = ComplexName)
293 OutFH.write("\n%s\n" % PML)
294
295 if OptionsInfo["SurfaceComplex"]:
296 PML = SetupPMLForElectronDensitySurface(MapName, SurfaceName, ContourLevel, Color, Enable = EnableSurface, Selection = ComplexName)
297 OutFH.write("\n%s\n" % PML)
298
299 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexCompositeEDGroup"], PyMOLObjectNames["ComplexCompositeEDGroupMembers"], True, "close")
300
301 def WriteComplexDifferenceElectronDensityMapView(OutFH, PyMOLObjectNames, MapFileName):
302 """Write out PML for viewing difference maps."""
303
304 # Load difference map (Fo - Fc ) and setup mesh views...
305 Info = """\
306 ""
307 "Loading difference map (Fo - Fc ) map %s and setting up mesh views..."
308 "" """ % MapFileName
309 OutFH.write("\n%s\n" % Info)
310
311 MapName = PyMOLObjectNames["ComplexDiffEDMap"]
312 ComplexName = PyMOLObjectNames["Complex"]
313
314 ContourLevel1 = OptionsInfo["Mesh1LevelDiffMap"]
315 ContourLevel2 = OptionsInfo["Mesh2LevelDiffMap"]
316 Color1 = OptionsInfo["Mesh1ColorDiffMap"]
317 Color2 = OptionsInfo["Mesh2ColorDiffMap"]
318
319 VolumeColorRamp = OptionsInfo["VolumeColorRampDiffMap"]
320
321 VolumeName = PyMOLObjectNames["ComplexDiffEDVolume"]
322 Mesh1Name = PyMOLObjectNames["ComplexDiffEDMesh1"]
323 Surface1Name = PyMOLObjectNames["ComplexDiffEDSurface1"]
324 Mesh2Name = PyMOLObjectNames["ComplexDiffEDMesh2"]
325 Surface2Name = PyMOLObjectNames["ComplexDiffEDSurface2"]
326
327 EnableMesh = OptionsInfo["MeshComplex"]
328
329 EnableVolume = OptionsInfo["VolumeComplex"]
330 if EnableVolume and EnableMesh:
331 EnableVolume = False
332
333 EnableSurface = OptionsInfo["SurfaceComplex"]
334 if EnableSurface and (EnableVolume or EnableMesh):
335 EnableSurface = False
336
337 AlignMapToObjectName = ComplexName if OptionsInfo["Align"] else None
338 EnableMap = True
339 PML = SetupPMLForElectronDensityMap(MapFileName, MapName, AlignMapToObjectName, EnableMap)
340 OutFH.write("%s\n" % PML)
341
342 if OptionsInfo["VolumeComplex"]:
343 PML = SetupPMLForElectronDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = EnableVolume, Selection = ComplexName)
344 OutFH.write("\n%s\n" % PML)
345
346 if OptionsInfo["MeshComplex"]:
347 PML = SetupPMLForElectronDensityMesh(MapName, Mesh1Name, ContourLevel1, Color1, Enable = EnableMesh, Selection = ComplexName)
348 OutFH.write("\n%s\n" % PML)
349
350 if OptionsInfo["SurfaceComplex"]:
351 PML = SetupPMLForElectronDensitySurface(MapName, Surface1Name, ContourLevel1, Color1, Enable = EnableSurface, Selection = ComplexName)
352 OutFH.write("\n%s\n" % PML)
353
354 if OptionsInfo["MeshComplex"]:
355 PML = SetupPMLForElectronDensityMesh(MapName, Mesh2Name, ContourLevel2, Color2, Enable = EnableMesh, Selection = ComplexName)
356 OutFH.write("\n%s\n" % PML)
357
358 if OptionsInfo["SurfaceComplex"]:
359 PML = SetupPMLForElectronDensitySurface(MapName, Surface2Name, ContourLevel2, Color2, Enable = EnableSurface, Selection = ComplexName)
360 OutFH.write("\n%s\n" % PML)
361
362 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexDiffEDGroup"], PyMOLObjectNames["ComplexDiffEDGroupMembers"], True, "close")
363
364 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
365 """Write out PML for viewing chain."""
366
367 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
368
369 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
370
371 # Setup chain complex group view...
372 WriteChainComplexAndMeshViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
373
374 # Setup chain view...
375 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
376
377 # Setup chain solvent view...
378 PML = PyMOLUtil.SetupPMLForSolventView(PyMOLObjectNames["Chains"][ChainID]["Solvent"], ChainComplexName, False)
379 OutFH.write("\n%s\n" % PML)
380
381 # Setup chain inorganic view...
382 PML = PyMOLUtil.SetupPMLForInorganicView(PyMOLObjectNames["Chains"][ChainID]["Inorganic"], ChainComplexName, False)
383 OutFH.write("\n%s\n" % PML)
384
385 def WriteChainComplexAndMeshViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
386 """Write chain complex and mesh views."""
387
388 # Setup chain complex...
389 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
390 PML = PyMOLUtil.SetupPMLForPolymerChainComplexView(ChainComplexName, PyMOLObjectNames["Complex"], ChainID, True)
391 OutFH.write("%s\n" % PML)
392
393 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
394
395 MeshChainComplex = SpecifiedChainsAndLigandsInfo["MeshChainComplex"][ChainID]
396 VolumeChainComplex = SpecifiedChainsAndLigandsInfo["VolumeChainComplex"][ChainID]
397 SurfaceChainComplex = SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"][ChainID]
398
399 EnableVolumeChainComplex = SpecifiedChainsAndLigandsInfo["EnableVolumeChainComplex"][ChainID]
400 EnableMeshChainComplex = SpecifiedChainsAndLigandsInfo["EnableMeshChainComplex"][ChainID]
401 EnableSurfaceChainComplex = SpecifiedChainsAndLigandsInfo["EnableSurfaceChainComplex"][ChainID]
402
403 if MeshChainComplex or VolumeChainComplex or SurfaceChainComplex:
404 # Set up composite mesh and group...
405 MapName = PyMOLObjectNames["ComplexCompositeEDMap"]
406 ContourLevel = OptionsInfo["MeshLevelCompositeMap"]
407 Color = OptionsInfo["MeshColorCompositeMap"]
408 VolumeColorRamp = OptionsInfo["VolumeColorRampCompositeMap"]
409
410 MeshName = PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDMesh"]
411 VolumeName = PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDVolume"]
412 SurfaceName = PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDSurface"]
413
414 if VolumeChainComplex:
415 PML = SetupPMLForElectronDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = EnableVolumeChainComplex, Selection = ChainComplexName)
416 OutFH.write("\n%s\n" % PML)
417
418 if MeshChainComplex:
419 PML = SetupPMLForElectronDensityMesh(MapName, MeshName, ContourLevel, Color, Enable = EnableMeshChainComplex, Selection = ChainComplexName)
420 OutFH.write("\n%s\n" % PML)
421
422 if SurfaceChainComplex:
423 PML = SetupPMLForElectronDensitySurface(MapName, SurfaceName, ContourLevel, Color, Enable = EnableSurfaceChainComplex, Selection = ChainComplexName)
424 OutFH.write("\n%s\n" % PML)
425
426 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDGroupMembers"], True, "close")
427 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
428 # Set up difference meshes and group...
429 MapName = PyMOLObjectNames["ComplexDiffEDMap"]
430
431 ContourLevel1 = OptionsInfo["Mesh1LevelDiffMap"]
432 ContourLevel2 = OptionsInfo["Mesh2LevelDiffMap"]
433 Color1 = OptionsInfo["Mesh1ColorDiffMap"]
434 Color2 = OptionsInfo["Mesh2ColorDiffMap"]
435
436 VolumeColorRamp = OptionsInfo["VolumeColorRampDiffMap"]
437 VolumeName = PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDVolume"]
438
439 Mesh1Name = PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDMesh1"]
440 Surface1Name = PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDSurface1"]
441 Mesh2Name = PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDMesh2"]
442 Surface2Name = PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDSurface2"]
443
444 if VolumeChainComplex:
445 PML = SetupPMLForElectronDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = EnableVolumeChainComplex, Selection = ChainComplexName)
446 OutFH.write("\n%s\n" % PML)
447
448 if MeshChainComplex:
449 PML = SetupPMLForElectronDensityMesh(MapName, Mesh1Name, ContourLevel1, Color1, Enable = EnableMeshChainComplex, Selection = ChainComplexName)
450 OutFH.write("\n%s\n" % PML)
451
452 if SurfaceChainComplex:
453 PML = SetupPMLForElectronDensitySurface(MapName, Surface1Name, ContourLevel1, Color1, Enable = EnableSurfaceChainComplex, Selection = ChainComplexName)
454 OutFH.write("\n%s\n" % PML)
455
456 if MeshChainComplex:
457 PML = SetupPMLForElectronDensityMesh(MapName, Mesh2Name, ContourLevel2, Color2, Enable = EnableMeshChainComplex, Selection = ChainComplexName)
458 OutFH.write("\n%s\n" % PML)
459
460 if SurfaceChainComplex:
461 PML = SetupPMLForElectronDensitySurface(MapName, Surface2Name, ContourLevel2, Color2, Enable = EnableSurfaceChainComplex, Selection = ChainComplexName)
462 OutFH.write("\n%s\n" % PML)
463
464 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroupMembers"], True, "close")
465
466 # Setup chain complex group...
467 EnableChainComplexGroup = SpecifiedChainsAndLigandsInfo["EnableChainComplexGroup"][ChainID]
468 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"], EnableChainComplexGroup, "close")
469
470 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
471 """Write individual chain views."""
472
473 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
474
475 # Setup chain view...
476 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
477 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, Enable = True)
478 OutFH.write("\n%s\n" % PML)
479
480 # Setup chain putty by B-factor view...
481 if OptionsInfo["BFactorChainCartoonPutty"]:
482 BFactorPuttyName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"]
483 PML = PyMOLUtil.SetupPMLForBFactorPuttyView(BFactorPuttyName, ChainName, ColorPalette = OptionsInfo["BFactorColorPalette"], Enable = False)
484 OutFH.write("\n%s\n" % PML)
485
486 # Setup chain selections view...
487 SetupChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
488
489 # Setup chain group...
490 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
491 EnableChainAloneGroup = SpecifiedChainsAndLigandsInfo["EnableChainAloneGroup"][ChainID]
492 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"], EnableChainAloneGroup, "close")
493
494 def SetupChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
495 """Setup chain selections view."""
496
497 if not OptionsInfo["ChainSelections"]:
498 return
499
500 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
501 SelectionsGroupIDPrefix = "ChainAloneSelections"
502
503 for Index in range(0, len(OptionsInfo["ChainSelectionsInfo"]["Names"])):
504 SelectionName = OptionsInfo["ChainSelectionsInfo"]["Names"][Index]
505 SpecifiedSelection = OptionsInfo["ChainSelectionsInfo"]["Selections"][Index]
506
507 SelectionNameGroupID = SelectionName
508
509 # Setup selection object...
510 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
511 SelectionObjectName = PyMOLObjectNames["Chains"][ChainID][SelectionObjectID]
512 SelectionCmd = "(%s and (%s))" % (ChainName, SpecifiedSelection)
513 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SelectionObjectName, SelectionCmd, OptionsInfo["SelectionsChainStyle"], Enable = True)
514 OutFH.write("\n%s\n" % PML)
515
516 # Set up composite mesh and group...
517 CompositeMeshID = "%s%sCompositeEDMesh" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
518 CompositeVolumeID = "%s%sCompositeEDVolume" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
519 CompositeSurfaceID = "%s%sCompositeEDSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
520 CompositeMeshGroupID = "%s%sCompositeEDGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
521 CompositeMeshGroupMembersID = "%s%sCompositeEDGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
522
523 CompositeMapName = PyMOLObjectNames["ComplexCompositeEDMap"]
524 CompositeMeshName = PyMOLObjectNames["Chains"][ChainID][CompositeMeshID]
525 CompositeVolumeName = PyMOLObjectNames["Chains"][ChainID][CompositeVolumeID]
526 CompositeSurfaceName = PyMOLObjectNames["Chains"][ChainID][CompositeSurfaceID]
527 CompositeMeshGroupName = PyMOLObjectNames["Chains"][ChainID][CompositeMeshGroupID]
528 CompositeMeshGroupMembers = PyMOLObjectNames["Chains"][ChainID][CompositeMeshGroupMembersID]
529
530 PML = SetupPMLForElectronDensityVolume(CompositeMapName, CompositeVolumeName, OptionsInfo["VolumeColorRampCompositeMap"], Enable = False, Selection = SelectionObjectName)
531 OutFH.write("\n%s\n" % PML)
532
533 PML = SetupPMLForElectronDensityMesh(CompositeMapName, CompositeMeshName, OptionsInfo["MeshLevelCompositeMap"], OptionsInfo["MeshColorCompositeMap"], Enable = True, Selection = SelectionObjectName)
534 OutFH.write("\n%s\n" % PML)
535
536 PML = SetupPMLForElectronDensitySurface(CompositeMapName, CompositeSurfaceName, OptionsInfo["MeshLevelCompositeMap"], OptionsInfo["MeshColorCompositeMap"], Enable = False, Selection = SelectionObjectName)
537 OutFH.write("\n%s\n" % PML)
538
539 GenerateAndWritePMLForGroup(OutFH, CompositeMeshGroupName, CompositeMeshGroupMembers, True, "close")
540
541 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
542 # Set up difference meshes and group...
543 DiffVolumeID = "%s%sDiffEDVolume" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
544 DiffMesh1ID = "%s%sDiffEDMesh1" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
545 DiffSurface1ID = "%s%sDiffEDSurface1" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
546 DiffMesh2ID = "%s%sDiffEDMesh2" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
547 DiffSurface2ID = "%s%sDiffEDSurface1" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
548 DiffMeshGroupID = "%s%sDiffEDGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
549 DiffMeshGroupMembersID = "%s%sDiffEDGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
550
551 DiffMapName = PyMOLObjectNames["ComplexDiffEDMap"]
552 DiffVolumeName = PyMOLObjectNames["Chains"][ChainID][DiffVolumeID]
553 DiffMesh1Name = PyMOLObjectNames["Chains"][ChainID][DiffMesh1ID]
554 DiffSurface1Name = PyMOLObjectNames["Chains"][ChainID][DiffSurface1ID]
555 DiffMesh2Name = PyMOLObjectNames["Chains"][ChainID][DiffMesh2ID]
556 DiffSurface2Name = PyMOLObjectNames["Chains"][ChainID][DiffSurface2ID]
557 DiffMeshGroupName = PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupID]
558 DiffMeshGroupMembers = PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID]
559
560 PML = SetupPMLForElectronDensityVolume(DiffMapName, DiffVolumeName, OptionsInfo["VolumeColorRampDiffMap"], Enable = False, Selection = SelectionObjectName)
561 OutFH.write("\n%s\n" % PML)
562
563 PML = SetupPMLForElectronDensityMesh(DiffMapName, DiffMesh1Name, OptionsInfo["Mesh1LevelDiffMap"], OptionsInfo["Mesh1ColorDiffMap"], Enable = True, Selection = SelectionObjectName)
564 OutFH.write("\n%s\n" % PML)
565
566 PML = SetupPMLForElectronDensitySurface(DiffMapName, DiffSurface1Name, OptionsInfo["Mesh1LevelDiffMap"], OptionsInfo["Mesh1ColorDiffMap"], Enable = False, Selection = SelectionObjectName)
567 OutFH.write("\n%s\n" % PML)
568
569 PML = SetupPMLForElectronDensityMesh(DiffMapName, DiffMesh2Name, OptionsInfo["Mesh2LevelDiffMap"], OptionsInfo["Mesh2ColorDiffMap"], Enable = True, Selection = SelectionObjectName)
570 OutFH.write("\n%s\n" % PML)
571
572 PML = SetupPMLForElectronDensitySurface(DiffMapName, DiffSurface2Name, OptionsInfo["Mesh2LevelDiffMap"], OptionsInfo["Mesh2ColorDiffMap"], Enable = False, Selection = SelectionObjectName)
573 OutFH.write("\n%s\n" % PML)
574
575 GenerateAndWritePMLForGroup(OutFH, DiffMeshGroupName, DiffMeshGroupMembers, True, "close")
576
577 # Setup groups for named selections...
578 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
579 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
580 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID], PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID], True, "open")
581
582 # Setup a group for selections...
583 SelectionsGroupID = "%sGroup" % (SelectionsGroupIDPrefix)
584 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupIDPrefix)
585 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID], PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID], False, "close")
586
587 def WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID):
588 """Write out PML for viewing ligand in a chain."""
589
590 for GroupID in ["Ligand", "Pocket", "PocketSolvent", "PocketInorganic"]:
591 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
592 LigandName = PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
593
594 # Setup main object...
595 GroupTypeObjectID = "%s" % (GroupID)
596 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
597
598 if re.match("^Ligand$", GroupID, re.I):
599 OutFH.write("""\n""\n"Setting up views for ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
600 PML = PyMOLUtil.SetupPMLForLigandView(GroupTypeObjectName, ComplexName, LigandID, Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
601 OutFH.write("%s\n" % PML)
602 elif re.match("^Pocket$", GroupID, re.I):
603 OutFH.write("""\n""\n"Setting up views for pocket around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
604 PML = PyMOLUtil.SetupPMLForLigandPocketView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
605 OutFH.write("%s\n" % PML)
606 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], GroupTypeObjectName))
607 elif re.match("^PocketSolvent$", GroupID, re.I):
608 OutFH.write("""\n""\n"Setting up views for solvent in pockect around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
609 PML = PyMOLUtil.SetupPMLForLigandPocketSolventView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
610 OutFH.write("%s\n" % PML)
611 elif re.match("^PocketInorganic$", GroupID, re.I):
612 OutFH.write("""\n""\n"Setting up views for inorganic in pockect around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
613 PML = PyMOLUtil.SetupPMLForLigandPocketInorganicView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
614 OutFH.write("%s\n" % PML)
615
616 # Set up composite mesh and group...
617 CompositeMeshGroupID = "%sCompositeEDMeshGroup" % (GroupID)
618 CompositeMeshGroupMembersID = "%sCompositeEDMeshGroupMembers" % (GroupID)
619 CompositeMeshID = "%sCompositeEDMesh" % (GroupID)
620 CompositeVolumeID = "%sCompositeEDVolume" % (GroupID)
621 CompositeSurfaceID = "%sCompositeEDSurface" % (GroupID)
622
623 CompositeMapName = PyMOLObjectNames["ComplexCompositeEDMap"]
624 CompositeMeshName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshID]
625 CompositeVolumeName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeVolumeID]
626 CompositeSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeSurfaceID]
627 CompositeMeshGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshGroupID]
628 CompositeMeshGroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshGroupMembersID]
629
630 PML = SetupPMLForElectronDensityVolume(CompositeMapName, CompositeVolumeName, OptionsInfo["VolumeColorRampCompositeMap"], Enable = False, Selection = GroupTypeObjectName)
631 OutFH.write("\n%s\n" % PML)
632
633 PML = SetupPMLForElectronDensityMesh(CompositeMapName, CompositeMeshName, OptionsInfo["MeshLevelCompositeMap"], OptionsInfo["MeshColorCompositeMap"], Enable = True, Selection = GroupTypeObjectName)
634 OutFH.write("\n%s\n" % PML)
635
636 PML = SetupPMLForElectronDensitySurface(CompositeMapName, CompositeSurfaceName, OptionsInfo["MeshLevelCompositeMap"], OptionsInfo["MeshColorCompositeMap"], Enable = False, Selection = GroupTypeObjectName)
637 OutFH.write("\n%s\n" % PML)
638
639 GenerateAndWritePMLForGroup(OutFH, CompositeMeshGroupName, CompositeMeshGroupMembers, True, "close")
640
641 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
642 # Set up difference meshes and group...
643 DiffMeshGroupID = "%sDiffEDMeshGroup" % (GroupID)
644 DiffMeshGroupMembersID = "%sDiffEDMeshGroupMembers" % (GroupID)
645 DiffVolumeID = "%sDiffEDVolume" % (GroupID)
646 DiffMesh1ID = "%sDiffEDMesh1" % (GroupID)
647 DiffSurface1ID = "%sDiffEDSurface1" % (GroupID)
648 DiffMesh2ID = "%sDiffEDMesh2" % (GroupID)
649 DiffSurface2ID = "%sDiffEDSurface2" % (GroupID)
650
651 DiffMapName = PyMOLObjectNames["ComplexDiffEDMap"]
652 DiffVolumeName = PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffVolumeID]
653 DiffMesh1Name = PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMesh1ID]
654 DiffSurface1Name = PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffSurface1ID]
655 DiffMesh2Name = PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMesh2ID]
656 DiffSurface2Name = PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffSurface2ID]
657 DiffMeshGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMeshGroupID]
658 DiffMeshGroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMeshGroupMembersID]
659
660 PML = SetupPMLForElectronDensityVolume(DiffMapName, DiffVolumeName, OptionsInfo["VolumeColorRampDiffMap"], Enable = False, Selection = GroupTypeObjectName)
661 OutFH.write("\n%s\n" % PML)
662
663 PML = SetupPMLForElectronDensityMesh(DiffMapName, DiffMesh1Name, OptionsInfo["Mesh1LevelDiffMap"], OptionsInfo["Mesh1ColorDiffMap"], Enable = True, Selection = GroupTypeObjectName)
664 OutFH.write("\n%s\n" % PML)
665
666 PML = SetupPMLForElectronDensitySurface(DiffMapName, DiffSurface1Name, OptionsInfo["Mesh1LevelDiffMap"], OptionsInfo["Mesh1ColorDiffMap"], Enable = False, Selection = GroupTypeObjectName)
667 OutFH.write("\n%s\n" % PML)
668
669 PML = SetupPMLForElectronDensityMesh(DiffMapName, DiffMesh2Name, OptionsInfo["Mesh2LevelDiffMap"], OptionsInfo["Mesh2ColorDiffMap"], Enable = True, Selection = GroupTypeObjectName)
670 OutFH.write("\n%s\n" % PML)
671
672 PML = SetupPMLForElectronDensitySurface(DiffMapName, DiffSurface2Name, OptionsInfo["Mesh2LevelDiffMap"], OptionsInfo["Mesh2ColorDiffMap"], Enable = False, Selection = GroupTypeObjectName)
673 OutFH.write("\n%s\n" % PML)
674
675 GenerateAndWritePMLForGroup(OutFH, DiffMeshGroupName, DiffMeshGroupMembers, True, "close")
676
677 # Set up polar contacts...
678 if re.match("^(Pocket|PocketSolvent|PocketInorganic)$", GroupID, re.I):
679 PolarContactsID = "%sPolarContacts" % (GroupID)
680 PolarContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID]
681
682 PolarContactsColor = OptionsInfo["PocketContactsLigandColor"]
683 if re.match("^PocketSolvent$", GroupID, re.I):
684 PolarContactsColor = OptionsInfo["PocketContactsSolventColor"]
685 elif re.match("^PocketInorganic$", GroupID, re.I):
686 PolarContactsColor = OptionsInfo["PocketContactsInorganicColor"]
687
688 PML = PyMOLUtil.SetupPMLForPolarContactsView(PolarContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = PolarContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
689 OutFH.write("\n%s\n" % PML)
690
691 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PolarContactsColor, PolarContactsName))
692
693 # Set up hydrophobic contacts...
694 if re.match("^Pocket$", GroupID, re.I):
695 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
696 HydrophobicContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID]
697 HydrophobicContactsColor = OptionsInfo["PocketContactsLigandHydrophobicColor"]
698
699 PML = PyMOLUtil.SetupPMLForHydrophobicContactsView(HydrophobicContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = HydrophobicContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
700 OutFH.write("\n%s\n" % PML)
701 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HydrophobicContactsColor, HydrophobicContactsName))
702
703 # Set up hydrophobic surface...
704 if re.match("^Pocket$", GroupID, re.I) and OptionsInfo["PocketSurface"]:
705 HydrophobicSurfaceID = "%sHydrophobicSurface" % (GroupID)
706 HydrophobicSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID]
707 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(HydrophobicSurfaceName, GroupTypeObjectName, ColorPalette = "RedToWhite", Enable = False)
708 OutFH.write("\n%s\n" % PML)
709
710 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], HydrophobicSurfaceName))
711
712 # Setup group....
713 GroupNameID = "%sGroup" % (GroupID)
714 GroupMembersID = "%sGroupMembers" % (GroupID)
715 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
716 GroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID]
717
718 Action = "close"
719 Enable = False
720 if re.match("^(Ligand|Pocket)$", GroupID, re.I):
721 Action = "open"
722 Enable = True
723 GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable, Action)
724
725 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable = False, Action = "close"):
726 """Generate and write PML for group."""
727
728 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
729 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
730 OutFH.write("%s\n" % PML)
731
732 def SetupPMLForElectronDensityMap(MapFileName, MapName, AlignMapToObjectName = None, Enable = True):
733 """Setup PML for loading and viewing electron density map."""
734
735 PMLCmds = []
736 PMLCmds.append("""cmd.load("%s", "%s")""" % (MapFileName, MapName))
737 if AlignMapToObjectName is not None:
738 PMLCmds.append("""cmd.matrix_copy("%s", "%s")""" % (AlignMapToObjectName, MapName))
739
740 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MapName, Enable))
741
742 PML = "\n".join(PMLCmds)
743
744 return PML
745
746 def SetupPMLForElectronDensityMesh(MapName, MeshName, SigmaLevel, Color, Enable = True, Selection = None):
747 """Setup PML for electron density mesh."""
748
749 Carve = OptionsInfo["MeshCarveRadius"]
750
751 PMLCmds = []
752 if Selection is None:
753 PMLCmds.append("""cmd.isomesh("%s", "%s", %.1f)""" % (MeshName, MapName, SigmaLevel))
754 else:
755 PMLCmds.append("""cmd.isomesh("%s", "%s", %.1f, "(%s)", carve = %.1f)""" % (MeshName, MapName, SigmaLevel, Selection, Carve))
756 PMLCmds.append(PyMOLUtil.SetupPMLForDeepColoring(MeshName, Color))
757 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MeshName, Enable))
758
759 PML = "\n".join(PMLCmds)
760
761 return PML
762
763 def SetupPMLForElectronDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = True, Selection = None):
764 """Setup PML for electron density volume."""
765
766 Carve = OptionsInfo["VolumeCarveRadius"]
767
768 PMLCmds = []
769 if Selection is None:
770 PMLCmds.append("""cmd.volume("%s", "%s", "%s")""" % (VolumeName, MapName, VolumeColorRamp))
771 else:
772 PMLCmds.append("""cmd.volume("%s", "%s", "%s", "(%s)", carve = %.1f)""" % (VolumeName, MapName, VolumeColorRamp, Selection, Carve))
773 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(VolumeName, Enable))
774
775 PML = "\n".join(PMLCmds)
776
777 return PML
778
779 def SetupPMLForElectronDensitySurface(MapName, SurfaceName, SigmaLevel, Color, Enable = True, Selection = None):
780 """Setup PML for electron density surface."""
781
782 Carve = OptionsInfo["MeshCarveRadius"]
783
784 PMLCmds = []
785 if Selection is None:
786 PMLCmds.append("""cmd.isosurface("%s", "%s", %.1f)""" % (SurfaceName, MapName, SigmaLevel))
787 else:
788 PMLCmds.append("""cmd.isosurface("%s", "%s", %.1f, "(%s)", carve = %.1f)""" % (SurfaceName, MapName, SigmaLevel, Selection, Carve))
789 PMLCmds.append(PyMOLUtil.SetupPMLForDeepColoring(SurfaceName, Color))
790 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(SurfaceName, Enable))
791
792 PML = "\n".join(PMLCmds)
793
794 return PML
795
796 def GeneratePyMOLSessionFile():
797 """Generate PME file from PML file."""
798
799 PSEOutfile = OptionsInfo["PSEOutfile"]
800 PMLOutfile = OptionsInfo["PMLOutfile"]
801
802 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
803
804 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
805
806 if not os.path.exists(PSEOutfile):
807 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
808
809 if not OptionsInfo["PMLOut"]:
810 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
811 os.remove(PMLOutfile)
812
813 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
814 """Delete empty PyMOL objects."""
815
816 if OptionsInfo["AllowEmptyObjects"]:
817 return
818
819 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
820 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
821 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
822
823 # Delete any chain level objects...
824 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
825 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
826
827 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
828 # Delete ligand level objects...
829 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
830 GroupNameID = "%sGroup" % (GroupID)
831 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
832
833 GroupTypeObjectID = "%s" % (GroupID)
834 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
835
836 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
837
838 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
839 """Write PML to check and delete empty PyMOL objects."""
840
841 if ParentObjectName is None:
842 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
843 else:
844 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
845
846 OutFH.write("%s\n" % PML)
847
848 def SetupPyMOLObjectNames(FileIndex):
849 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
850 electron density for chains and ligands present in input file.
851 """
852
853 PyMOLObjectNames = {}
854 PyMOLObjectNames["Chains"] = {}
855 PyMOLObjectNames["Ligands"] = {}
856
857 PyMOLObjectNames["SetupDiffEDMapObjects"] = False if OptionsInfo["DiffEDMapFiles"][FileIndex] is None else True
858
859 # Setup groups and objects for complex...
860 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
861
862 # Setup groups and objects for chain...
863 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
864 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
865 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
866
867 # Setup groups and objects for ligand...
868 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
869 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
870
871 return PyMOLObjectNames
872
873 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
874 """Setup groups and objects for complex."""
875
876 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
877
878 PDBGroupName = "%s" % PDBFileRoot
879 PyMOLObjectNames["PDBGroup"] = PDBGroupName
880 PyMOLObjectNames["PDBGroupMembers"] = []
881
882 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
883 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
884 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
885
886 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
887
888 CompositeMeshGroupName = "%s.2Fo-Fc" % (ComplexGroupName)
889 CompositeMapName = "%s.Map" % (CompositeMeshGroupName)
890 CompositeMeshName = "%s.Mesh" % (CompositeMeshGroupName)
891 CompositeVolumeName = "%s.Volume" % (CompositeMeshGroupName)
892 CompositeSurfaceName = "%s.Surface" % (CompositeMeshGroupName)
893
894 PyMOLObjectNames["ComplexCompositeEDGroup"] = CompositeMeshGroupName
895 PyMOLObjectNames["ComplexCompositeEDMap"] = CompositeMapName
896 PyMOLObjectNames["ComplexCompositeEDMesh"] = CompositeMeshName
897 PyMOLObjectNames["ComplexCompositeEDVolume"] = CompositeVolumeName
898 PyMOLObjectNames["ComplexCompositeEDSurface"] = CompositeSurfaceName
899
900 PyMOLObjectNames["ComplexCompositeEDGroupMembers"] = []
901 PyMOLObjectNames["ComplexCompositeEDGroupMembers"].append(CompositeMapName)
902 if OptionsInfo["VolumeComplex"]:
903 PyMOLObjectNames["ComplexCompositeEDGroupMembers"].append(CompositeVolumeName)
904 if OptionsInfo["MeshComplex"]:
905 PyMOLObjectNames["ComplexCompositeEDGroupMembers"].append(CompositeMeshName)
906 if OptionsInfo["SurfaceComplex"]:
907 PyMOLObjectNames["ComplexCompositeEDGroupMembers"].append(CompositeSurfaceName)
908 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
909 DiffMeshGroupName = "%s.Fo-Fc" % ComplexGroupName
910 DiffMapName = "%s.Map" % DiffMeshGroupName
911 DiffVolumeName = "%s.Volume" % DiffMeshGroupName
912 DiffMesh1Name = "%s.Mesh1" % DiffMeshGroupName
913 DiffSurface1Name = "%s.Surface1" % DiffMeshGroupName
914 DiffMesh2Name = "%s.Mesh2" % DiffMeshGroupName
915 DiffSurface2Name = "%s.Surface2" % DiffMeshGroupName
916
917 PyMOLObjectNames["ComplexDiffEDGroup"] = DiffMeshGroupName
918 PyMOLObjectNames["ComplexDiffEDMap"] = DiffMapName
919 PyMOLObjectNames["ComplexDiffEDVolume"] = DiffVolumeName
920 PyMOLObjectNames["ComplexDiffEDMesh1"] = DiffMesh1Name
921 PyMOLObjectNames["ComplexDiffEDSurface1"] = DiffSurface1Name
922 PyMOLObjectNames["ComplexDiffEDMesh2"] = DiffMesh2Name
923 PyMOLObjectNames["ComplexDiffEDSurface2"] = DiffSurface2Name
924
925 PyMOLObjectNames["ComplexDiffEDGroupMembers"] = []
926 PyMOLObjectNames["ComplexDiffEDGroupMembers"].append(DiffMapName)
927 if OptionsInfo["VolumeComplex"]:
928 PyMOLObjectNames["ComplexDiffEDGroupMembers"].append(DiffVolumeName)
929 if OptionsInfo["MeshComplex"]:
930 PyMOLObjectNames["ComplexDiffEDGroupMembers"].append(DiffMesh1Name)
931 if OptionsInfo["SurfaceComplex"]:
932 PyMOLObjectNames["ComplexDiffEDGroupMembers"].append(DiffSurface1Name)
933 if OptionsInfo["MeshComplex"]:
934 PyMOLObjectNames["ComplexDiffEDGroupMembers"].append(DiffMesh2Name)
935 if OptionsInfo["SurfaceComplex"]:
936 PyMOLObjectNames["ComplexDiffEDGroupMembers"].append(DiffSurface2Name)
937
938 PyMOLObjectNames["ComplexGroupMembers"] = []
939 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
940 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexCompositeEDGroup"])
941 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
942 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexDiffEDGroup"])
943
944 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
945 """Setup groups and objects for chain."""
946
947 PDBGroupName = PyMOLObjectNames["PDBGroup"]
948
949 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
950 MeshChainComplex = SpecifiedChainsAndLigandsInfo["MeshChainComplex"][ChainID]
951 VolumeChainComplex = SpecifiedChainsAndLigandsInfo["VolumeChainComplex"][ChainID]
952 SurfaceChainComplex = SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"][ChainID]
953
954 PyMOLObjectNames["Chains"][ChainID] = {}
955 PyMOLObjectNames["Ligands"][ChainID] = {}
956
957 # Set up chain group and chain objects...
958 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
959 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
960 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
961 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
962
963 # Setup chain complex group and objects...
964 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
965 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
966 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
967
968 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = "%s.Complex" % (ChainComplexGroupName)
969
970 CompositeMeshGroupName = "%s.2Fo-Fc" % (ChainComplexGroupName)
971 CompositeMeshName = "%s.Mesh" % (CompositeMeshGroupName)
972 CompositeVolumeName = "%s.Volume" % (CompositeMeshGroupName)
973 CompositeSurfaceName = "%s.Surface" % (CompositeMeshGroupName)
974
975 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDGroup"] = CompositeMeshGroupName
976 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDMesh"] = CompositeMeshName
977 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDVolume"] = CompositeVolumeName
978 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDSurface"] = CompositeSurfaceName
979
980 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDGroupMembers"] = []
981 if VolumeChainComplex:
982 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDGroupMembers"].append(CompositeVolumeName)
983 if MeshChainComplex:
984 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDGroupMembers"].append(CompositeMeshName)
985 if SurfaceChainComplex:
986 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCompositeEDGroupMembers"].append(CompositeSurfaceName)
987
988 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
989 DiffMeshGroupName = "%s.Fo-Fc" % (ChainComplexGroupName)
990 DiffVolumeName = "%s.Volume" % (DiffMeshGroupName)
991 DiffMesh1Name = "%s.Mesh1" % (DiffMeshGroupName)
992 DiffSurface1Name = "%s.Surface1" % (DiffMeshGroupName)
993 DiffMesh2Name = "%s.Mesh2" % (DiffMeshGroupName)
994 DiffSurface2Name = "%s.Surface2" % (DiffMeshGroupName)
995
996 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroup"] = DiffMeshGroupName
997 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDVolume"] = DiffVolumeName
998 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDMesh1"] = DiffMesh1Name
999 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDSurface1"] = DiffSurface1Name
1000 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDMesh2"] = DiffMesh2Name
1001 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDSurface2"] = DiffSurface2Name
1002
1003 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroupMembers"] = []
1004 if VolumeChainComplex:
1005 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroupMembers"].append(DiffVolumeName)
1006 if MeshChainComplex:
1007 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroupMembers"].append(DiffMesh1Name)
1008 if SurfaceChainComplex:
1009 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroupMembers"].append(DiffSurface1Name)
1010 if MeshChainComplex:
1011 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroupMembers"].append(DiffMesh2Name)
1012 if SurfaceChainComplex:
1013 PyMOLObjectNames["Chains"][ChainID]["ChainComplexDiffEDGroupMembers"].append(DiffSurface2Name)
1014
1015 NameIDs = ["ChainComplex"]
1016 if MeshChainComplex or VolumeChainComplex or SurfaceChainComplex :
1017 NameIDs.append("ChainComplexCompositeEDGroup")
1018 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
1019 NameIDs.append("ChainComplexDiffEDGroup")
1020
1021 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
1022 for NameID in NameIDs:
1023 Name = PyMOLObjectNames["Chains"][ChainID][NameID]
1024 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
1025
1026 # Setup up a group for individual chains...
1027 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
1028 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
1029 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
1030
1031 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
1032
1033 Name = "%s.Chain" % (ChainAloneGroupName)
1034 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
1035 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
1036
1037 if OptionsInfo["BFactorChainCartoonPutty"]:
1038 Name = "%s.BFactor" % (ChainAloneGroupName)
1039 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"] = Name
1040 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
1041
1042 if OptionsInfo["ChainSelections"]:
1043 # Setup selections group and its subgroups..
1044 SelectionsGroupName = "%s.Selections" % (ChainAloneGroupName)
1045
1046 SelectionsGroupIDPrefix = "ChainAloneSelections"
1047 SelectionsGroupID = "%sGroup" % SelectionsGroupIDPrefix
1048
1049 # Add selections group to chain alone group...
1050 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID] = SelectionsGroupName
1051 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SelectionsGroupName)
1052
1053 # Initialize selections group members...
1054 SelectionsGroupMembersID = "%sGroupMembers" % SelectionsGroupIDPrefix
1055 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID] = []
1056
1057 # Setup selections name sub group and its members...
1058 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
1059 SelectionNameGroupID = SelectionName
1060
1061 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
1062 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1063
1064 # Add selections name sub group to selections group...
1065 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID] = SelectionsNameGroupName
1066 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID].append(SelectionsNameGroupName)
1067
1068 # Initialize selections names sub group members...
1069 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1070 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID] = []
1071
1072 # Add selection object to selections name group...
1073 SelectionObjectName = "%s.Selection" % (SelectionsNameGroupName)
1074 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1075
1076 PyMOLObjectNames["Chains"][ChainID][SelectionObjectID] = SelectionObjectName
1077 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SelectionObjectName)
1078
1079 # Setup composite mesh group and add it to selections name group...
1080 CompositeMeshGroupName = "%s.2Fo-Fc" % (SelectionsNameGroupName)
1081 CompositeMeshGroupID = "%s%sCompositeEDGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1082
1083 PyMOLObjectNames["Chains"][ChainID][CompositeMeshGroupID] = CompositeMeshGroupName
1084 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(CompositeMeshGroupName)
1085
1086 # Initialize composite mesh group members...
1087 CompositeMeshGroupMembersID = "%s%sCompositeEDGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1088 PyMOLObjectNames["Chains"][ChainID][CompositeMeshGroupMembersID] = []
1089
1090 # Setup members of composite mesh group...
1091 CompositeMeshName = "%s.Mesh" % (CompositeMeshGroupName)
1092 CompositeMeshID = "%s%sCompositeEDMesh" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1093 CompositeVolumeName = "%s.Volume" % (CompositeMeshGroupName)
1094 CompositeVolumeID = "%s%sCompositeEDVolume" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1095 CompositeSurfaceName = "%s.Surface" % (CompositeMeshGroupName)
1096 CompositeSurfaceID = "%s%sCompositeEDSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1097
1098 PyMOLObjectNames["Chains"][ChainID][CompositeMeshID] = CompositeMeshName
1099 PyMOLObjectNames["Chains"][ChainID][CompositeVolumeID] = CompositeVolumeName
1100 PyMOLObjectNames["Chains"][ChainID][CompositeSurfaceID] = CompositeSurfaceName
1101
1102 PyMOLObjectNames["Chains"][ChainID][CompositeMeshGroupMembersID].append(CompositeMeshName)
1103 PyMOLObjectNames["Chains"][ChainID][CompositeMeshGroupMembersID].append(CompositeVolumeName)
1104 PyMOLObjectNames["Chains"][ChainID][CompositeMeshGroupMembersID].append(CompositeSurfaceName)
1105
1106 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
1107 # Setup diff mesh group and add it to selections name group...
1108 DiffMeshGroupName = "%s.Fo-Fc" % (SelectionsNameGroupName)
1109 DiffMeshGroupID = "%s%sDiffEDGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1110
1111 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupID] = DiffMeshGroupName
1112 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(DiffMeshGroupName)
1113
1114 # Initialize diff mesh group members...
1115 DiffMeshGroupMembersID = "%s%sDiffEDGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1116 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID] = []
1117
1118 # Setup members of diff mesh group...
1119 DiffVolumeName = "%s.Volume" % (DiffMeshGroupName)
1120 DiffVolumeID = "%s%sDiffEDVolume" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1121
1122 DiffMesh1Name = "%s.Mesh1" % (DiffMeshGroupName)
1123 DiffMesh1ID = "%s%sDiffEDMesh1" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1124 DiffSurface1Name = "%s.Surface1" % (DiffMeshGroupName)
1125 DiffSurface1ID = "%s%sDiffEDSurface1" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1126
1127 DiffMesh2Name = "%s.Mesh2" % (DiffMeshGroupName)
1128 DiffMesh2ID = "%s%sDiffEDMesh2" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1129 DiffSurface2Name = "%s.Surface2" % (DiffMeshGroupName)
1130 DiffSurface2ID = "%s%sDiffEDSurface1" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
1131
1132 PyMOLObjectNames["Chains"][ChainID][DiffVolumeID] = DiffVolumeName
1133 PyMOLObjectNames["Chains"][ChainID][DiffMesh1ID] = DiffMesh1Name
1134 PyMOLObjectNames["Chains"][ChainID][DiffSurface1ID] = DiffSurface1Name
1135 PyMOLObjectNames["Chains"][ChainID][DiffMesh2ID] = DiffMesh2Name
1136 PyMOLObjectNames["Chains"][ChainID][DiffSurface2ID] = DiffSurface2Name
1137
1138 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID] = []
1139 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID].append(DiffVolumeName)
1140 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID].append(DiffMesh1Name)
1141 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID].append(DiffSurface1Name)
1142 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID].append(DiffMesh2Name)
1143 PyMOLObjectNames["Chains"][ChainID][DiffMeshGroupMembersID].append(DiffSurface2Name)
1144
1145 # Setup solvent and inorganic objects for chain...
1146 for NameID in ["Solvent", "Inorganic"]:
1147 Name = "%s.%s" % (ChainGroupName, NameID)
1148 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
1149 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
1150
1151 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
1152 """Stetup groups and objects for ligand."""
1153
1154 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
1155
1156 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
1157
1158 # Setup a chain level ligand group...
1159 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
1160 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
1161 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
1162
1163 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
1164
1165 # Set up groups and objects for a specific ligand group...
1166 for GroupType in ["Ligand", "Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
1167 GroupID = re.sub("_", "", GroupType)
1168 GroupName = "%s.%s" % (ChainLigandGroupName, GroupType)
1169
1170 GroupNameID = "%sGroup" % (GroupID)
1171 GroupMembersID = "%sGroupMembers" % (GroupID)
1172
1173 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
1174 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
1175
1176 GroupTypeObjectName = "%s.%s" % (GroupName, GroupType)
1177 GroupTypeObjectID = "%s" % (GroupID)
1178 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID] = GroupTypeObjectName
1179
1180 CompositeMeshGroupName = "%s.2Fo-Fc" % (GroupName)
1181 CompositeMeshName = "%s.Mesh" % (CompositeMeshGroupName)
1182 CompositeVolumeName = "%s.Volume" % (CompositeMeshGroupName)
1183 CompositeSurfaceName = "%s.Surface" % (CompositeMeshGroupName)
1184
1185 CompositeMeshGroupID = "%sCompositeEDMeshGroup" % (GroupID)
1186 CompositeMeshGroupMembersID = "%sCompositeEDMeshGroupMembers" % (GroupID)
1187 CompositeMeshID = "%sCompositeEDMesh" % (GroupID)
1188 CompositeVolumeID = "%sCompositeEDVolume" % (GroupID)
1189 CompositeSurfaceID = "%sCompositeEDSurface" % (GroupID)
1190
1191 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshGroupID] = CompositeMeshGroupName
1192 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshID] = CompositeMeshName
1193 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeVolumeID] = CompositeVolumeName
1194 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeSurfaceID] = CompositeSurfaceName
1195 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshGroupMembersID] = []
1196 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshGroupMembersID].append(CompositeVolumeName)
1197 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshGroupMembersID].append(CompositeMeshName)
1198 PyMOLObjectNames["Ligands"][ChainID][LigandID][CompositeMeshGroupMembersID].append(CompositeSurfaceName)
1199
1200 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
1201 DiffMeshGroupName = "%s.Fo-Fc" % GroupName
1202 DiffVolumeName = "%s.Volume" % DiffMeshGroupName
1203 DiffMesh1Name = "%s.Mesh1" % DiffMeshGroupName
1204 DiffSurface1Name = "%s.Surface1" % DiffMeshGroupName
1205 DiffMesh2Name = "%s.Mesh2" % DiffMeshGroupName
1206 DiffSurface2Name = "%s.Surface2" % DiffMeshGroupName
1207
1208 DiffMeshGroupID = "%sDiffEDMeshGroup" % (GroupID)
1209 DiffMeshGroupMembersID = "%sDiffEDMeshGroupMembers" % (GroupID)
1210 DiffVolumeID = "%sDiffEDVolume" % (GroupID)
1211 DiffMesh1ID = "%sDiffEDMesh1" % (GroupID)
1212 DiffSurface1ID = "%sDiffEDSurface1" % (GroupID)
1213 DiffMesh2ID = "%sDiffEDMesh2" % (GroupID)
1214 DiffSurface2ID = "%sDiffEDSurface2" % (GroupID)
1215
1216 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMeshGroupID] = DiffMeshGroupName
1217 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffVolumeID] = DiffVolumeName
1218 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMesh1ID] = DiffMesh1Name
1219 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffSurface1ID] = DiffSurface1Name
1220 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMesh2ID] = DiffMesh2Name
1221 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffSurface2ID] = DiffSurface2Name
1222 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMeshGroupMembersID] = []
1223 PyMOLObjectNames["Ligands"][ChainID][LigandID][DiffMeshGroupMembersID].extend([DiffVolumeName, DiffMesh1Name, DiffSurface1Name, DiffMesh2Name, DiffSurface2Name])
1224
1225 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
1226 NameIDs = [GroupTypeObjectID, CompositeMeshGroupID]
1227 if PyMOLObjectNames["SetupDiffEDMapObjects"]:
1228 NameIDs.append(DiffMeshGroupID)
1229
1230 for NameID in NameIDs:
1231 Name = PyMOLObjectNames["Ligands"][ChainID][LigandID][NameID]
1232 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(Name)
1233
1234 if re.match("^Ligand$", GroupType, re.I):
1235 # No other object needed for Ligand group...
1236 continue
1237
1238 PolarContactsName = "%s.Polar_Contacts" % (GroupName)
1239 PolarContactsID = "%sPolarContacts" % (GroupID)
1240 PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID] = PolarContactsName
1241 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PolarContactsName)
1242
1243 if not re.match("^Pocket$", GroupType, re.I):
1244 # No other object needed for any other group besides Pocket...
1245 continue
1246
1247 if not OptionsInfo["PocketSurface"]:
1248 continue
1249
1250 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % (GroupName)
1251 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
1252 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID] = HydrophobicContactsName
1253 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HydrophobicContactsName)
1254
1255 HydrophobicSurfaceName = "%s.Surface" % (GroupName)
1256 HydrophobicSurfaceID = "%sHydrophobicSurface" % (GroupID)
1257 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID] = HydrophobicSurfaceName
1258 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HydrophobicSurfaceName)
1259
1260 def ProcessEDMapFilesAndSuffixes():
1261 """Process specified ED map files or suffixes for input files."""
1262
1263 EDMapFiles = OptionsInfo["EDMapFiles"]
1264 EDMapSuffixes = OptionsInfo["EDMapSuffixes"]
1265
1266 if (not re.match("^auto$", EDMapFiles, re.I)) and (not re.match("^auto$", EDMapSuffixes, re.I)):
1267 MiscUtil.PrintError("The values, \"%s\" and \"%s\", specified using \"--EDMapFiles\" and \"--EDMapSuffixes\" are not valid. Both of these options can't be specified simultaneously." % (EDMapFiles, EDMapSuffixes))
1268
1269 if not re.match("^auto$", EDMapFiles, re.I):
1270 ProcessEDMapFiles()
1271 else:
1272 ProcessEDMapSuffixes()
1273
1274 def ProcessEDMapFiles():
1275 """Process specified ED map files."""
1276
1277 EDMapFiles = re.sub(" ", "", OptionsInfo["EDMapFiles"])
1278 if not EDMapFiles:
1279 MiscUtil.PrintError("No valid parameter name and value pairs specified using \"--EDMapFiles\" option.")
1280
1281 EDMapFilesWords = EDMapFiles.split(",")
1282 EDMapFilesWordsCount = len(EDMapFilesWords)
1283 if EDMapFilesWordsCount % 2:
1284 MiscUtil.PrintError("The number of comma delimited ED map files, %d, specified using \"--EDMapFiles\" option must be an even number." % (EDMapFilesWordsCount))
1285
1286 InfilesNamesCount = len(OptionsInfo["InfilesNames"])
1287 if EDMapFilesWordsCount != 2*InfilesNamesCount:
1288 MiscUtil.PrintError("The number of comma delimited ED map files, %d, specified using \"--EDMapFiles\" must be twice the number of input files, %s, specified using \"-i, --infiles\" option." % (EDMapFilesWordsCount, InfilesNamesCount))
1289
1290 OptionsInfo["CompositeEDMapFiles"] = []
1291 OptionsInfo["DiffEDMapFiles"] = []
1292
1293 CompositeEDMapFiles = []
1294 DiffEDMapFiles = []
1295 for Index in range(0, EDMapFilesWordsCount, 2):
1296 CompositeEDMapFiles.append(EDMapFilesWords[Index])
1297 DiffEDMapFiles.append(EDMapFilesWords[Index + 1])
1298
1299 for Index in range(0, InfilesNamesCount):
1300 Infile = OptionsInfo["InfilesNames"][Index]
1301 CompositeEDMapFile = CompositeEDMapFiles[Index]
1302 DiffEDMapFile = DiffEDMapFiles[Index]
1303
1304 if not os.path.exists(CompositeEDMapFile):
1305 MiscUtil.PrintError("The composite ED map file, %s, specified using option \"--EDMapFiles\", corresponding to input file, %s, doesn't exist.\n" % (CompositeEDMapFile, Infile))
1306
1307 DiffEDMapFileExists = False
1308 if not re.match("^None$", DiffEDMapFile, re.I):
1309 if os.path.exists(DiffEDMapFile):
1310 DiffEDMapFileExists = True
1311 else:
1312 MiscUtil.PrintWarning("The difference ED map file, %s, specified using option \"--EDMapFiles\", corresponding to input file, %s, doesn't exist. PyMOL groups and objectes related to difference maps won't be created.\n" % (DiffEDMapFile, Infile))
1313
1314 OptionsInfo["CompositeEDMapFiles"].append(CompositeEDMapFile)
1315 if DiffEDMapFileExists:
1316 OptionsInfo["DiffEDMapFiles"].append(DiffEDMapFile)
1317 else:
1318 OptionsInfo["DiffEDMapFiles"].append(None)
1319
1320 def ProcessEDMapSuffixes():
1321 """Process suffixes for ED map files."""
1322
1323 OptionsInfo["EDMapSuffixesMap"] = {"CompositeMap" : "", "DifferenceMap" : "_diff"}
1324
1325 if re.match("^auto$", OptionsInfo["EDMapSuffixes"], re.I):
1326 SetupEDMapFileNamesUsingSuffixes()
1327 return
1328
1329 EDMapSuffixes = re.sub(" ", "", OptionsInfo["EDMapSuffixes"])
1330 if not EDMapSuffixes:
1331 MiscUtil.PrintError("No valid parameter name and value pairs specified using \"--EDMapSuffixes\" option.")
1332
1333 EDMapSuffixesWords = EDMapSuffixes.split(",")
1334 if len(EDMapSuffixesWords) % 2:
1335 MiscUtil.PrintError("The number of comma delimited ED map types names and suffixes, %d, specified using \"--EDMapSuffixes\" option must be an even number." % (len(EDMapSuffixesWords)))
1336
1337 for Index in range(0, len(EDMapSuffixesWords), 2):
1338 EDMapType = EDMapSuffixesWords[Index]
1339 EDMapSuffix = EDMapSuffixesWords[Index + 1]
1340
1341 if re.match("^CompositeMap$", EDMapType, re.I):
1342 EDMapType = "CompositeMap"
1343 elif re.match("^DifferenceMap$", EDMapType, re.I):
1344 EDMapType = "DifferenceMap"
1345 else:
1346 MiscUtil.PrintError("The ED map type, %s, specified using \"--EDMapSuffixes\" option is not a valid ED map type. Supported ED map types: CompositeMap, DifferenceMap" % (EDMapType))
1347
1348 if re.match(EDMapSuffix, "None", re.I):
1349 EDMapSuffix = ""
1350
1351 OptionsInfo["EDMapSuffixesMap"][EDMapType] = EDMapSuffix
1352
1353 SetupEDMapFileNamesUsingSuffixes()
1354
1355 def SetupEDMapFileNamesUsingSuffixes():
1356 """Set up ED map file names."""
1357
1358 OptionsInfo["CompositeEDMapFiles"] = []
1359 OptionsInfo["DiffEDMapFiles"] = []
1360
1361 CompositeMapSuffix = OptionsInfo["EDMapSuffixesMap"]["CompositeMap"]
1362 DiffMapSuffix = OptionsInfo["EDMapSuffixesMap"]["DifferenceMap"]
1363 InfilesNamesCount = len(OptionsInfo["InfilesNames"])
1364
1365 for Index in range(0, InfilesNamesCount):
1366 Infile = OptionsInfo["InfilesNames"][Index]
1367 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
1368 InfileRoot = FileName
1369
1370 CompositeEDMapFile = "%s%s.ccp4" % (InfileRoot, CompositeMapSuffix)
1371 DiffEDMapFile = "%s%s.ccp4" % (InfileRoot, DiffMapSuffix)
1372
1373 if not os.path.exists(CompositeEDMapFile):
1374 MiscUtil.PrintError("The composite ED map file, %s, for option \"--EDMapSuffixes\", corresponding to input file, %s, doesn't exist.\n" % (CompositeEDMapFile, Infile))
1375
1376 DiffEDMapFileExists = False
1377 if os.path.exists(DiffEDMapFile):
1378 DiffEDMapFileExists = True
1379 else:
1380 MiscUtil.PrintWarning("The difference ED map file, %s, for option \"--EDMapSuffixes\", corresponding to input file, %s, doesn't exist. PyMOL groups and objectes related to difference maps won't be created.\n" % (DiffEDMapFile, Infile))
1381
1382 OptionsInfo["CompositeEDMapFiles"].append(CompositeEDMapFile)
1383 if DiffEDMapFileExists:
1384 OptionsInfo["DiffEDMapFiles"].append(DiffEDMapFile)
1385 else:
1386 OptionsInfo["DiffEDMapFiles"].append(None)
1387
1388 def RetrieveInfilesInfo():
1389 """Retrieve information for input files."""
1390
1391 InfilesInfo = {}
1392
1393 InfilesInfo["InfilesNames"] = []
1394 InfilesInfo["InfilesRoots"] = []
1395 InfilesInfo["ChainsAndLigandsInfo"] = []
1396
1397 for Infile in OptionsInfo["InfilesNames"]:
1398 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
1399 InfileRoot = FileName
1400
1401 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
1402
1403 InfilesInfo["InfilesNames"].append(Infile)
1404 InfilesInfo["InfilesRoots"].append(InfileRoot)
1405 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
1406
1407 OptionsInfo["InfilesInfo"] = InfilesInfo
1408
1409 def RetrieveRefFileInfo():
1410 """Retrieve information for ref file."""
1411
1412 RefFileInfo = {}
1413 if not OptionsInfo["Align"]:
1414 OptionsInfo["RefFileInfo"] = RefFileInfo
1415 return
1416
1417 RefFile = OptionsInfo["RefFileName"]
1418
1419 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
1420 RefFileRoot = FileName
1421
1422 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
1423 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
1424 else:
1425 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
1426 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
1427
1428 RefFileInfo["RefFileName"] = RefFile
1429 RefFileInfo["RefFileRoot"] = RefFileRoot
1430 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
1431 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
1432
1433 OptionsInfo["RefFileInfo"] = RefFileInfo
1434
1435 def ProcessChainAndLigandIDs():
1436 """Process specified chain and ligand IDs for infiles."""
1437
1438 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
1439
1440 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
1441 MiscUtil.PrintInfo("\nProcessing specified chain and ligand IDs for input file %s..." % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex])
1442
1443 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
1444 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], "-l, --ligandIDs", OptionsInfo["LigandIDs"])
1445 ProcessChainMeshesVolumesAndSurfacesOptions(SpecifiedChainsAndLigandsInfo)
1446 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
1447
1448 CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo)
1449
1450 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
1451 """Check presence of valid ligand IDs."""
1452
1453 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
1454
1455 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1456 if len (SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
1457 MiscUtil.PrintInfo("Chain ID: %s; Specified LigandIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID])))
1458 else:
1459 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
1460 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))
1461
1462 def RetrieveFirstChainID(FileIndex):
1463 """Get first chain ID."""
1464
1465 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
1466
1467 FirstChainID = None
1468 if len(ChainsAndLigandsInfo["ChainIDs"]):
1469 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
1470
1471 return FirstChainID
1472
1473 def ProcessChainMeshesVolumesAndSurfacesOptions(SpecifiedChainsAndLigandsInfo):
1474 """Process options to create meshes and surfaces for chains."""
1475
1476 SpecifiedChainsAndLigandsInfo["VolumeChainComplex"] = {}
1477 SpecifiedChainsAndLigandsInfo["MeshChainComplex"] = {}
1478 SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"] = {}
1479
1480 SpecifiedChainsAndLigandsInfo["EnableVolumeChainComplex"] = {}
1481 SpecifiedChainsAndLigandsInfo["EnableMeshChainComplex"] = {}
1482 SpecifiedChainsAndLigandsInfo["EnableSurfaceChainComplex"] = {}
1483
1484 SpecifiedChainsAndLigandsInfo["EnableChainComplexGroup"] = {}
1485 SpecifiedChainsAndLigandsInfo["EnableChainAloneGroup"] = {}
1486
1487 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1488 LigandsPresent = True if len(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]) else False
1489
1490 # Create and enable mesh or volume in auto mode...
1491 if re.match("^auto$", OptionsInfo["MeshChainComplex"], re.I):
1492 MeshChainComplex = False if LigandsPresent else True
1493 EnableMeshChainComplex = False if LigandsPresent else True
1494 else:
1495 MeshChainComplex = True if re.match("^Yes$", OptionsInfo["MeshChainComplex"], re.I) else False
1496 EnableMeshChainComplex = True if re.match("^Yes$", OptionsInfo["MeshChainComplex"], re.I) else False
1497
1498 if re.match("^auto$", OptionsInfo["VolumeChainComplex"], re.I):
1499 VolumeChainComplex = False if LigandsPresent else True
1500 EnableVolumeChainComplex = False if LigandsPresent else True
1501 else:
1502 VolumeChainComplex = True if re.match("^Yes$", OptionsInfo["VolumeChainComplex"], re.I) else False
1503 EnableVolumeChainComplex = True if re.match("^Yes$", OptionsInfo["VolumeChainComplex"], re.I) else False
1504
1505 if MeshChainComplex and EnableMeshChainComplex:
1506 EnableVolumeChainComplex = False
1507
1508 # Create and enable surface in auto mode based on the status of mesh and volume...
1509 if re.match("^auto$", OptionsInfo["SurfaceChainComplex"], re.I):
1510 SurfaceChainComplex = False if LigandsPresent else True
1511 EnableSurfaceChainComplex = False if LigandsPresent else True
1512
1513 if MeshChainComplex or VolumeChainComplex:
1514 SurfaceChainComplex = False
1515 EnableSurfaceChainComplex = False
1516 else:
1517 SurfaceChainComplex = True if re.match("^Yes$", OptionsInfo["SurfaceChainComplex"], re.I) else False
1518 EnableSurfaceChainComplex = True if re.match("^Yes$", OptionsInfo["SurfaceChainComplex"], re.I) else False
1519
1520 if (MeshChainComplex and EnableMeshChainComplex) or (VolumeChainComplex or EnableVolumeChainComplex):
1521 EnableSurfaceChainComplex = False
1522
1523 if LigandsPresent:
1524 EnableChainComplexGroup = False
1525 EnableChainAloneGroup = True
1526 else:
1527 EnableChainComplexGroup = True
1528 EnableChainAloneGroup = False
1529
1530 SpecifiedChainsAndLigandsInfo["VolumeChainComplex"][ChainID] = VolumeChainComplex
1531 SpecifiedChainsAndLigandsInfo["MeshChainComplex"][ChainID] = MeshChainComplex
1532 SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"][ChainID] = SurfaceChainComplex
1533
1534 SpecifiedChainsAndLigandsInfo["EnableVolumeChainComplex"][ChainID] = EnableVolumeChainComplex
1535 SpecifiedChainsAndLigandsInfo["EnableMeshChainComplex"][ChainID] = EnableMeshChainComplex
1536 SpecifiedChainsAndLigandsInfo["EnableSurfaceChainComplex"][ChainID] = EnableSurfaceChainComplex
1537
1538 SpecifiedChainsAndLigandsInfo["EnableChainComplexGroup"][ChainID] = EnableChainComplexGroup
1539 SpecifiedChainsAndLigandsInfo["EnableChainAloneGroup"][ChainID] = EnableChainAloneGroup
1540
1541 def ProcessChainSelections():
1542 """Process custom selections for chains."""
1543
1544 ChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo("--selectionsChain", OptionsInfo["SelectionsChain"])
1545 OptionsInfo["ChainSelectionsInfo"] = ChainSelectionsInfo
1546
1547 ChainSelections = True if len(OptionsInfo["ChainSelectionsInfo"]["Names"]) else False
1548 OptionsInfo["ChainSelections"] = ChainSelections
1549
1550 def ProcessOptions():
1551 """Process and validate command line arguments and options."""
1552
1553 MiscUtil.PrintInfo("Processing options...")
1554
1555 # Validate options...
1556 ValidateOptions()
1557
1558 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
1559 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
1560 OptionsInfo["AlignMode"] = Options["--alignMode"]
1561
1562 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
1563
1564 OptionsInfo["BFactorChainCartoonPutty"] = True if re.match("^Yes$", Options["--BFactorChainCartoonPutty"], re.I) else False
1565 OptionsInfo["BFactorColorPalette"] = Options["--BFactorColorPalette"]
1566
1567 OptionsInfo["Infiles"] = Options["--infiles"]
1568 OptionsInfo["InfilesNames"] = Options["--infileNames"]
1569
1570 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
1571 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1572 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
1573 else:
1574 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
1575
1576 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
1577
1578 OptionsInfo["EDMapFiles"] = Options["--EDMapFiles"]
1579 OptionsInfo["EDMapSuffixes"] = Options["--EDMapSuffixes"]
1580 ProcessEDMapFilesAndSuffixes()
1581
1582 OptionsInfo["Overwrite"] = Options["--overwrite"]
1583 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
1584
1585 OptionsInfo["Outfile"] = Options["--outfile"]
1586 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
1587 OptionsInfo["PSEOut"] = False
1588 if re.match("^pml$", FileExt, re.I):
1589 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
1590 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
1591 elif re.match("^pse$", FileExt, re.I):
1592 OptionsInfo["PSEOut"] = True
1593 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
1594 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
1595 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
1596 MiscUtil.PrintError("The intermediate output file to be generated, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again." % OptionsInfo["PMLOutfile"] )
1597
1598 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
1599
1600 # Process mesh parameters...
1601 OptionsInfo["MeshCarveRadius"] = float(Options["--meshCarveRadius"])
1602 OptionsInfo["MeshComplex"] = True if re.match("^Yes$", Options["--meshComplex"], re.I) else False
1603 OptionsInfo["MeshChainComplex"] = Options["--meshChainComplex"]
1604 OptionsInfo["MeshWidth"] = float(Options["--meshWidth"])
1605
1606 OptionsInfo["MeshColorCompositeMap"] = Options["--meshColorCompositeMap"]
1607 OptionsInfo["MeshLevelCompositeMap"] = float(Options["--meshLevelCompositeMap"])
1608 OptionsInfo["Mesh1ColorDiffMap"] = Options["--mesh1ColorDiffMap"]
1609 OptionsInfo["Mesh1LevelDiffMap"] = float(Options["--mesh1LevelDiffMap"])
1610 OptionsInfo["Mesh2ColorDiffMap"] = Options["--mesh2ColorDiffMap"]
1611 OptionsInfo["Mesh2LevelDiffMap"] = float(Options["--mesh2LevelDiffMap"])
1612
1613 OptionsInfo["SelectionsChain"] = Options["--selectionsChain"]
1614 OptionsInfo["SelectionsChainStyle"] = Options["--selectionsChainStyle"]
1615 ProcessChainSelections()
1616
1617 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
1618 OptionsInfo["SurfaceChainComplex"] = Options["--surfaceChainComplex"]
1619 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
1620
1621 OptionsInfo["PocketContactsLigandColor"] = Options["--pocketContactsLigandColor"]
1622 OptionsInfo["PocketContactsLigandHydrophobicColor"] = Options["--pocketContactsLigandHydrophobicColor"]
1623 OptionsInfo["PocketContactsSolventColor"] = Options["--pocketContactsSolventColor"]
1624 OptionsInfo["PocketContactsInorganicColor"] = Options["--pocketContactsInorganicColor"]
1625
1626 OptionsInfo["PocketContactsCutoff"] = float(Options["--pocketContactsCutoff"])
1627 OptionsInfo["PocketDistanceCutoff"] = float(Options["--pocketDistanceCutoff"])
1628
1629 OptionsInfo["PocketLabelColor"] = Options["--pocketLabelColor"]
1630 OptionsInfo["PocketSurface"] = True if re.match("^Yes$", Options["--pocketSurface"], re.I) else False
1631
1632 OptionsInfo["VolumeCarveRadius"] = float(Options["--volumeCarveRadius"])
1633 OptionsInfo["VolumeComplex"] = True if re.match("^Yes$", Options["--volumeComplex"], re.I) else False
1634 OptionsInfo["VolumeChainComplex"] = Options["--volumeChainComplex"]
1635
1636 OptionsInfo["VolumeColorRampCompositeMap"] = Options["--volumeColorRampCompositeMap"]
1637 OptionsInfo["VolumeColorRampDiffMap"] = Options["--volumeColorRampDiffMap"]
1638
1639 RetrieveInfilesInfo()
1640 RetrieveRefFileInfo()
1641
1642 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
1643 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
1644
1645 ProcessChainAndLigandIDs()
1646
1647 def RetrieveOptions():
1648 """Retrieve command line arguments and options."""
1649
1650 # Get options...
1651 global Options
1652 Options = docopt(_docoptUsage_)
1653
1654 # Set current working directory to the specified directory...
1655 WorkingDir = Options["--workingdir"]
1656 if WorkingDir:
1657 os.chdir(WorkingDir)
1658
1659 # Handle examples option...
1660 if "--examples" in Options and Options["--examples"]:
1661 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
1662 sys.exit(0)
1663
1664 def ValidateOptions():
1665 """Validate option values."""
1666
1667 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
1668 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
1669 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
1670
1671 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
1672
1673 MiscUtil.ValidateOptionTextValue("--BFactorChainCartoonPutty", Options["--BFactorChainCartoonPutty"], "yes no")
1674
1675 # Expand infiles to handle presence of multiple input files...
1676 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
1677 if not len(InfileNames):
1678 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
1679
1680 # Validate file extensions...
1681 for Infile in InfileNames:
1682 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
1683 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
1684 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
1685 Options["--infileNames"] = InfileNames
1686
1687 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
1688 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
1689
1690 if re.match("^yes$", Options["--align"], re.I):
1691 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1692 AlignRefFile = Options["--alignRefFile"]
1693 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
1694 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
1695 MiscUtil.ValidateOptionsDistinctFileNames("--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"])
1696
1697 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
1698
1699 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
1700 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
1701
1702 MiscUtil.ValidateOptionFloatValue("--meshCarveRadius", Options["--meshCarveRadius"], {">": 0.0})
1703 MiscUtil.ValidateOptionTextValue("--meshComplex", Options["--meshComplex"], "yes no")
1704 MiscUtil.ValidateOptionTextValue("--meshChainComplex", Options["--meshChainComplex"], "yes no auto")
1705 MiscUtil.ValidateOptionFloatValue("--meshWidth", Options["--meshWidth"], {">": 0.0})
1706
1707 MiscUtil.ValidateOptionFloatValue("--meshLevelCompositeMap", Options["--meshLevelCompositeMap"], {})
1708 MiscUtil.ValidateOptionFloatValue("--mesh1LevelDiffMap", Options["--mesh1LevelDiffMap"], {})
1709 MiscUtil.ValidateOptionFloatValue("--mesh2LevelDiffMap", Options["--mesh2LevelDiffMap"], {})
1710
1711 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
1712 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no auto")
1713 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
1714
1715 MiscUtil.ValidateOptionFloatValue("--pocketContactsCutoff", Options["--pocketContactsCutoff"], {">": 0.0})
1716 MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0})
1717 if (float(Options["--pocketContactsCutoff"]) > float(Options["--pocketDistanceCutoff"])):
1718 MiscUtil.PrintError("The value, %s, specified using option \"--pocketContactsCutoff\" must be less than value, %s, specified using \"-pocketDistanceCutoff\" option." % (Options["--pocketContactsCutoff"], Options["--pocketDistanceCutoff"]))
1719
1720 MiscUtil.ValidateOptionTextValue("--pocketSurface", Options["--pocketSurface"], "yes no")
1721
1722 MiscUtil.ValidateOptionFloatValue("--volumeCarveRadius", Options["--volumeCarveRadius"], {">": 0.0})
1723 MiscUtil.ValidateOptionTextValue("--volumeComplex", Options["--volumeComplex"], "yes no")
1724 MiscUtil.ValidateOptionTextValue("--volumeChainComplex", Options["--volumeChainComplex"], "yes no auto")
1725
1726 # Setup a usage string for docopt...
1727 _docoptUsage_ = """
1728 PyMOLVisualizeElectronDensity.py - Visualize electron density
1729
1730 Usage:
1731 PyMOLVisualizeElectronDensity.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
1732 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
1733 [--allowEmptyObjects <yes or no>] [--BFactorChainCartoonPutty <yes or no>]
1734 [--BFactorColorPalette <text> ] [--chainIDs <First, All or ID1,ID2...>]
1735 [--EDMapFiles <file1,file2,...>] [--EDMapSuffixes <CompositeMap,None,...>]
1736 [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All or ID1,ID2...>] [--labelFontID <number>]
1737 [--meshCarveRadius <number>] [--meshComplex <yes or no>]
1738 [--meshChainComplex <yes or no>] [--meshColorCompositeMap <text>]
1739 [--meshLevelCompositeMap <number>] [--meshWidth <number>]
1740 [--mesh1ColorDiffMap <text>] [--mesh1LevelDiffMap <number>]
1741 [--mesh2ColorDiffMap <text>] [--mesh2LevelDiffMap <number>]
1742 [--PMLOut <yes or no>] [--pocketContactsLigandColor <text>]
1743 [--pocketContactsLigandHydrophobicColor <text>] [--pocketContactsSolventColor <text>]
1744 [--pocketContactsInorganicColor <text>] [--pocketContactsCutoff <number>]
1745 [--pocketDistanceCutoff <number>] [--pocketLabelColor <text>] [--pocketSurface <yes or no>]
1746 [--selectionsChain <ObjectName,SelectionSpec,...>] [--selectionsChainStyle <DisplayStyle>]
1747 [--surfaceComplex <yes or no> ] [--surfaceChainComplex <yes or no>] [--surfaceTransparency <number>]
1748 [--volumeCarveRadius <number>] [--volumeComplex <yes or no>]
1749 [--volumeChainComplex <yes, no, or auto>] [--volumeColorRampCompositeMap <text>]
1750 [--volumeColorRampDiffMap <text> ] [--overwrite] [-w <dir>] -i <infile1,infile2...> -o <outfile>
1751 PyMOLVisualizeElectronDensity.py -h | --help | -e | --examples
1752
1753 Description:
1754 Generate PyMOL visualization files for viewing X-ray electron density around
1755 chains, ligands, and ligand binding pockets in macromolecules including proteins
1756 and nucleic acids.
1757
1758 The supported input file formats are: Macromolecule - PDB (.pdb) or CIF(.cif),
1759 Electron Density - Collaborative Computational Project Number 4 (CCP4) ( .ccp4)
1760
1761 The supported output file formats are: PyMOL script file (.pml), PyMOL session
1762 file (.pse)
1763
1764 Two types of CCP4 electron density map files may be used for visualizing electron
1765 density. These file types along with default file names are shown below:
1766
1767 CompositeMap (2Fobs - Fcalc) - <InfileRoot>.ccp4 (required)
1768 DifferenceMap (Fobs - Fcalc) - <InfileRoot>_diff.ccp4 (optional)
1769
1770 The compsite map file must be present. The difference map file is optional.
1771 The mesh, volume, and surface PyMOL objects are not generated for missing
1772 difference map file.
1773
1774 The electron density present in a composite map file is generated by adding two
1775 difference maps to a calculated map (Fcalc) as shown below:
1776
1777 Fcalc + 2(Fobs - Fcalc) = 2Fobs - Fcalc
1778
1779 The following types of meshes and volumes may be created by default for
1780 electron density present in composite and difference map files:
1781
1782 CompositeVolume - VolumeColorRamp: 2fofc
1783 CompositeMesh - ContourLevel: 1; Color: Blue
1784 DiffVolume - VolumeColorRamp: fofc
1785 DiffMesh1 - ContourLevel: 3; Color: Green
1786 DiffMesh2 - ContourLevel: -3; Color: Red
1787
1788 The two meshes created for difference maps correspond to false negative and
1789 false positive in terms of electron density present in the model. The first mesh
1790 shown in green color corresponds to observed electron density missing in the
1791 model. The second mesh in in red color indicates model electron density not
1792 observed in the experiment.
1793
1794 A variety of PyMOL groups and objects may be created for visualization of
1795 electron density present in map files. These groups and objects correspond to
1796 maps, volumes, meshes, surfaces,chains, ligands, inorganics, ligand binding
1797 pockets, polar interactions, and pocket hydrophobic surfaces. A complete
1798 hierarchy of all possible PyMOL groups and objects is shown below:
1799
1800 <PDBFileRoot>
1801 .Complex
1802 .Complex
1803 .2Fo-Fc
1804 .Map
1805 .Volume
1806 .Mesh
1807 .Surface
1808 .Fo-Fc
1809 .Map
1810 .Volume
1811 .Mesh1
1812 .Surface1
1813 .Mesh2
1814 .Surface2
1815 .Chain<ID>
1816 .Complex
1817 .Complex
1818 .2Fo-Fc
1819 .Volume
1820 .Mesh
1821 .Surface
1822 .Fo-Fc
1823 .Volume
1824 .Mesh1
1825 .Surface1
1826 .Mesh2
1827 .Surface2
1828 .Chain
1829 .Chain
1830 .BFactor
1831 .Selections
1832 .<Name1>
1833 .Selection
1834 .2Fo-Fc
1835 .Volume
1836 .Mesh
1837 .Surface
1838 .Fo-Fc
1839 .Volume
1840 .Mesh1
1841 .Surface1
1842 .Mesh2
1843 .Surface2
1844 .<Name2>
1845 ... ... ..
1846 .Solvent
1847 .Inorganic
1848 .Ligand<ID>
1849 .Ligand
1850 .Ligand
1851 .2Fo-Fc
1852 .Volume
1853 .Mesh
1854 .Surface
1855 .Fo-Fc
1856 .Volume
1857 .Mesh1
1858 .Surface1
1859 .Mesh2
1860 .Surface2
1861 .Pocket
1862 .Pocket
1863 .2Fo-Fc
1864 .Volume
1865 .Mesh
1866 .Surface
1867 .Fo-Fc
1868 .Volume
1869 .Mesh1
1870 .Surface1
1871 .Mesh2
1872 .Surface2
1873 .Polar_Contacts
1874 .Hydrophobic_Contacts
1875 .Surface
1876 .Pocket_Solvent
1877 .Pocket_Solvent
1878 .2Fo-Fc
1879 .Volume
1880 .Mesh
1881 .Surface
1882 .Fo-Fc
1883 .Volume
1884 .Mesh1
1885 .Surface1
1886 .Mesh2
1887 .Surface2
1888 .Polar_Contacts
1889 .Pocket_Inorganic
1890 .Pocket_Inorganic
1891 .2Fo-Fc
1892 .Volume
1893 .Mesh
1894 .Surface
1895 .Fo-Fc
1896 .Volume
1897 .Mesh1
1898 .Surface1
1899 .Mesh2
1900 .Surface2
1901 .Polar_Contacts
1902 .Ligand<ID>
1903 .Ligand
1904 ... ... ...
1905 .Pocket
1906 ... ... ...
1907 .Pocket_Solvent
1908 ... ... ...
1909 .Pocket_Inorganic
1910 ... ... ...
1911 .Chain<ID>
1912 ... ... ...
1913 .Ligand<ID>
1914 ... ... ...
1915 .Ligand<ID>
1916 ... ... ...
1917 .Chain<ID>
1918 ... ... ...
1919 <PDBFileRoot>
1920 .Complex
1921 ... ... ...
1922 .Chain<ID>
1923 ... ... ...
1924 .Ligand<ID>
1925 ... ... ...
1926 .Ligand<ID>
1927 ... ... ...
1928 .Chain<ID>
1929 ... ... ...
1930
1931 The meshes, volumes, and surfaces are not created for complete complex in
1932 each input file by default. A word to the wise: The creation of these surface, volume,
1933 and mesh objects may slow down loading of PML file and generation of PSE file,
1934 based on the size of input complex and map files. The generation of PSE file
1935 may also fail.
1936
1937 Options:
1938 -a, --align <yes or no> [default: no]
1939 Align input files to a reference file before visualization along with
1940 available electron density map files.
1941 --alignMethod <align, cealign, super> [default: super]
1942 Alignment methodology to use for aligning input files to a
1943 reference file.
1944 --alignMode <FirstChain or Complex> [default: FirstChain]
1945 Portion of input and reference files to use for spatial alignment of
1946 input files against reference file. Possible values: FirstChain or
1947 Complex.
1948
1949 The FirstChain mode allows alignment of the first chain in each input
1950 file to the first chain in the reference file along with moving the rest
1951 of the complex to coordinate space of the reference file. The complete
1952 complex in each input file is aligned to the complete complex in reference
1953 file for the Complex mode.
1954 --alignRefFile <filename> [default: FirstInputFile]
1955 Reference input file name. The default is to use the first input file
1956 name specified using '-i, --infiles' option.
1957 --allowEmptyObjects <yes or no> [default: no]
1958 Allow creation of empty PyMOL objects corresponding to solvent and
1959 inorganic atom selections across chains, ligands, and ligand binding pockets
1960 in input file(s).
1961 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
1962 List of chain IDs to use for visualizing electron density. Possible values:
1963 First, All, or a comma delimited list of chain IDs. The default is to use the
1964 chain ID for the first chain in each input file.
1965 -b, --BFactorChainCartoonPutty <yes or no> [default: yes]
1966 A cartoon putty around individual chains colored by B factors. The minimum
1967 and maximum values for B factors are automatically detected. These values
1968 indicate spread of electron density around atoms. The 'blue_white_red' color
1969 palette is deployed for coloring the cartoon putty.
1970 --BFactorColorPalette <text> [default: blue_white_red]
1971 Color palette for coloring cartoon putty around chains generated using B
1972 factors. Any valid PyMOL color palette name is allowed. No validation is
1973 performed. The complete list of valid color palette names is a available
1974 at: pymolwiki.org/index.php/Spectrum. Examples: blue_white_red,
1975 blue_white_magenta, blue_red, green_white_red, green_red.
1976 -e, --examples
1977 Print examples.
1978 --EDMapFiles <file1,file1,file3...> [default: auto]
1979 Pairwise comma delimited list of composite and difference electron
1980 density map files corresponding to input files. By default, the names
1981 of electron density files are automatically generated using a combination
1982 of input file names and file suffixes '--EDMapSuffixes'.
1983
1984 The first file with in each pairs of filenames correspond to composite
1985 electron density map. A composite file must be present for each input
1986 file. The second file corresponds to difference electron density map. The
1987 difference map file is optional. A value of 'None' must be used to represent
1988 a missing difference map file.
1989
1990 The number of specified files must be twice the number of input files.
1991 --EDMapSuffixes <CompositeMap,None,...> [default: auto]
1992 Electron density map file suffixes for generating names of map files from
1993 the root of input files. It is a pairwise comma delimited list of 'EDMapType'
1994 and file suffix.
1995
1996 This option is ignored during explicit specification of electron density
1997 map files using '--EDMapFiles'.
1998
1999 Supported values for 'EDMapType': 'CompositeMap, DifferenceMap'.
2000 Supported value for file suffix: Any valid string.
2001
2002 Default value: 'CompositeMap,None,DifferenceMap,_diff'
2003
2004 This option is only used for 'Auto' value of '--EDMapFilesMode' option.
2005
2006 The default names of the map files, generated form a combination of
2007 'InfileRoot' and 'EDSMapType' are shown below:
2008
2009 CompositeMap (2Fobs - Fcalc) - <InfileRoot>.ccp4
2010 DifferenceMap (Fobs - Fcalc) - <InfileRoot>_diff.ccp4
2011
2012 The composite map files must be present. The difference map files are
2013 optional.
2014 -h, --help
2015 Print this help message.
2016 -i, --infiles <infile1,infile2,infile3...>
2017 Input file names.
2018 --ignoreHydrogens <yes or no> [default: yes]
2019 Ignore hydrogens for ligand and pocket views.
2020 -l, --ligandIDs <Largest, All or ID1,ID2...> [default: Largest]
2021 List of ligand IDs present in chains for visualizing electron density across
2022 ligands and ligand binding pockets. Possible values: Largest, All, or a comma
2023 delimited list of ligand IDs. The default is to use the largest ligand present
2024 in all or specified chains in each input file.
2025
2026 Ligands are identified using organic selection operator available in PyMOL.
2027 It'll also identify buffer molecules as ligands. The largest ligand contains
2028 the highest number of heavy atoms.
2029 --labelFontID <number> [default: 7]
2030 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
2031 The specified value must be a valid PyMOL font ID. No validation is
2032 performed. The complete lists of valid font IDs is available at:
2033 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
2034 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
2035 --meshCarveRadius <number> [default: 1.6]
2036 Radius in Angstroms around atoms for including electron density.
2037 --meshComplex <yes or no> [default: no]
2038 Create meshes for complete complex in each input file using corresponding
2039 composite and difference maps. A total of three meshes, one for composite
2040 map and two for difference map, are created for the complete complex.
2041
2042 The composite and difference maps are always loaded for the complex.
2043 --meshChainComplex <yes, no, or auto> [default: auto]
2044 Create meshes for individual chain complex in each input file using corresponding
2045 composite and difference maps. A total of three meshes, one for composite map
2046 map and two for difference map, are created for each chain complex. By default,
2047 the meshes are automatically created for chain complexes without any ligands.
2048 --meshColorCompositeMap <text> [default: blue]
2049 Line color for meshes corresponding to composite maps. The specified value
2050 must be valid color. No validation is performed.
2051 --meshLevelCompositeMap <number> [default: 1.0]
2052 Contour level in sigma units for generating meshes corresponding to composite
2053 maps.
2054 --meshWidth <number> [default: 0.5]
2055 Line width for mesh lines corresponding to composite and difference maps.
2056 --mesh1ColorDiffMap <text> [default: green]
2057 Line color for first mesh corresponding to difference maps at contour level
2058 specified by '--mesh1LevelDiffMap'. The specified value must be valid color.
2059 No validation is performed.
2060 --mesh1LevelDiffMap <number> [default: 3.0]
2061 Contour level in sigma units for generating first mesh corresponding to
2062 to difference maps.
2063 --mesh2ColorDiffMap <text> [default: red]
2064 Line color for second mesh corresponding to difference maps at contour level
2065 specified by '--mesh2LevelDiffMap'. The specified value must be valid color.
2066 No validation is performed.
2067 --mesh2LevelDiffMap <number> [default: -3.0]
2068 Contour level in sigma units for generating second mesh corresponding to
2069 difference maps.
2070 -o, --outfile <outfile>
2071 Output file name.
2072 -p, --PMLOut <yes or no> [default: yes]
2073 Save PML file during generation of PSE file.
2074 --pocketContactsLigandColor <text> [default: orange]
2075 Color for drawing polar contacts between ligand and pocket residues.
2076 The specified value must be valid color. No validation is performed.
2077 --pocketContactsLigandHydrophobicColor <text> [default: purpleblue]
2078 Color for drawing hydrophobic contacts between ligand and pocket residues.
2079 The specified value must be valid color. No validation is performed. The
2080 hydrophobic contacts are shown between pairs of carbon atoms not
2081 connected to hydrogen bond donor or acceptors atoms as identified
2082 by PyMOL.
2083 --pocketContactsSolventColor <text> [default: marine]
2084 Color for drawing polar contacts between solvent and pocket residues.
2085 The specified value must be valid color. No validation is performed.
2086 --pocketContactsInorganicColor <text> [default: deepsalmon]
2087 Color for drawing polar contacts between inorganic and pocket residues.
2088 The specified value must be valid color. No validation is performed.
2089 --pocketContactsCutoff <number> [default: 4.0]
2090 Distance in Angstroms for identifying polar and hyrdophobic contacts
2091 between atoms in pocket residues and ligands.
2092 --pocketDistanceCutoff <number> [default: 5.0]
2093 Distance in Angstroms for identifying pocket residues around ligands.
2094 --pocketLabelColor <text> [default: magenta]
2095 Color for drawing residue or atom level labels for a pocket. The specified
2096 value must be valid color. No validation is performed.
2097 --pocketSurface <yes or no> [default: yes]
2098 Hydrophobic surface around pocket. The pocket surface is colored by
2099 hydrophobicity. It is only valid for proteins. The color of amino acids is
2100 set using the Eisenberg hydrophobicity scale. The color varies from red
2101 to white, red being the most hydrophobic amino acid.
2102 --selectionsChain <ObjectName,SelectionSpec,...> [default: None]
2103 Custom selections for chains. It is a pairwise of list comma delimited values
2104 corresponding to PyMOL object names and selection specifications. The
2105 selection specification must be a valid PyMOL specification. No validation is
2106 performed.
2107
2108 The PyMOL objects are created for each chain corresponding to the
2109 specified selections. The display style for PyMOL objects is set using
2110 value of '--selectionsChainStyle' option.
2111
2112 The specified selection specification is automatically appended to appropriate
2113 chain specification before creating PyMOL objects.
2114
2115 For example, the following specification for '--selectionsChain' option will
2116 generate PyMOL objects for chains containing Cysteines and Serines:
2117
2118 Cysteines,resn CYS,Serines,resn SER
2119
2120 --selectionsChainStyle <DisplayStyle> [default: sticks]
2121 Display style for PyMOL objects created for '--selectionsChain' option. It
2122 must be a valid PyMOL display style. No validation is performed.
2123 --surfaceComplex <yes or no> [default: no]
2124 Create surfaces for complete complex in each input file using corresponding
2125 composite and difference maps. A total of three surfaces, one for composite
2126 map and two for difference map, are created for the complete complex.
2127
2128 The composite and difference maps are always loaded for the complex.
2129 --surfaceChainComplex <yes, no or auto> [default: auto]
2130 Create surfaces for individual chain complexes in each input file using corresponding
2131 composite and difference maps. A total of three surfaces, one for composite
2132 map and two for difference map, are created for each chain complex. By default,
2133 the surfaces are automatically created for chain complexes without any ligands.
2134 --surfaceTransparency <number> [default: 0.25]
2135 Surface transparency for molecular and electron density surfaces.
2136 --volumeCarveRadius <number> [default: 1.6]
2137 Radius in Angstroms around atoms for including electron density during
2138 generation of volume objects.
2139 --volumeComplex <yes or no> [default: no]
2140 Create volumes for complete complex in input file using corresponding
2141 composite and difference maps. A total of two volumes, one each for
2142 composite and difference maps, are created for the complete complex.
2143 --volumeChainComplex <yes, no, or auto> [default: auto]
2144 Create volumes for individual chain complex in each input file using corresponding
2145 composite and difference maps. A total of two volumes, one each for composite
2146 and difference maps, are created for each chain complex. By default, the
2147 volumes are automatically created for chain complexes without any ligands.
2148 --volumeColorRampCompositeMap <text> [default: 2fofc]
2149 Name of volume color ramp for composite maps. The specified value must
2150 be a valid name. No validation is performed. The following volume color ramps
2151 are currently available in PyMOL: default, 2fofc, fofc, rainbow, and rainbow2.
2152 --volumeColorRampDiffMap <text> [default: fofc]
2153 Name of volume color ramp for difference maps. The specified value must
2154 be a valid name. No validation is performed. The following volume color ramps
2155 are currently available in PyMOL: default, 2fofc, fofc, rainbow, and rainbow2.
2156 --overwrite
2157 Overwrite existing files.
2158 -w, --workingdir <dir>
2159 Location of working directory which defaults to the current directory.
2160
2161 Examples:
2162 To visualize electron density for the largest ligand in the first chain, and
2163 ligand binding pockets to highlight ligand interactions with pockect residues,
2164 solvents and inorganics, in a PDB file by using default map files, and generate a
2165 PML file, type:
2166
2167 % PyMOLVisualizeElectronDensity.py -i Sample3.pdb -o Sample3.pml
2168
2169 To visualize electron density for the largest ligand in the first chain, cysteine
2170 and serine residues in the chain, and ligand binding pockets to highlight ligand
2171 interactions with pockect residues, solvents and inorganics, in a PDB file by
2172 using default map files, and generate a PML file, type:
2173
2174 % PyMOLVisualizeElectronDensity.py -i Sample3.pdb -o Sample3.pml
2175 --selectionsChain "Cysteines,resn cys,Serines,resn ser"
2176
2177 To visualize electron density for all ligands in all chains, and ligand binding
2178 pockets to highlight ligand interactions with pockect residues, solvents
2179 and inorganics, in a PDB file by using default map files, and generate a
2180 PML file, type:
2181
2182 % PyMOLVisualizeElectronDensity.py -i Sample3.pdb -o Sample3.pml
2183 -c All -l All
2184
2185 To visualize electron density for all chains and ligands, along with displaying
2186 meshes, volumes, and surfaces for complete complex and individual chains,
2187 in a PDB file by using default map files, and generate a PML file, type:
2188
2189 % PyMOLVisualizeElectronDensity.py -i Sample3.pdb -o Sample3.pml
2190 --chainIDs All --ligandIDs All --meshComplex yes --surfaceComplex yes
2191 --volumeComplex yes --meshChainComplex yes --surfaceChainComplex yes
2192 --volumeChainComplex yes
2193
2194 To visualize electron density for ligand ADP in chain E along with ligand binding
2195 pocket, in a PDB file by using default map files, and generate a PSE file, type:
2196
2197 % PyMOLVisualizeElectronDensity.py -i Sample3.pdb -o Sample3.pse
2198 --chainIDs E --ligandIDs ADP
2199
2200 To visualize electron density for all igands in all chains along with their binding
2201 pockets in a PDB file and using explicit file name suffixes for map files, and
2202 generate a PML file, type:
2203
2204 % PyMOLVisualizeElectronDensity.py -i Sample3.pdb -o Sample3.pml
2205 --chainIDs All --ligandIDs All --EDMapSuffixes "CompositeMap,None,
2206 DifferenceMap,_diff"
2207
2208 To visualize electron density for all ligands in all chains along with their binding
2209 pockets in a PDB file by using explicit file names for map files, and generate
2210 a PML file, type:
2211
2212 % PyMOLVisualizeElectronDensity.py -i Sample3.pdb -o Sample3.pml
2213 --chainIDs All --ligandIDs All --EDMapFiles "Sample3.ccp4,
2214 Sample3_diff.ccp4"
2215
2216 To align and visualize electron density for all ligands in all chains along with their
2217 binding pockets in PDB files by using explicit file names for map files, and generate
2218 a PML file, type:
2219
2220 % PyMOLVisualizeElectronDensity.py -a yes -i "Sample3.pdb,Sample4.pdb"
2221 -o SampleOut.pml --chainIDs All --ligandIDs All --EDMapFiles
2222 "Sample3.ccp4,Sample3_diff.ccp4,Sample4.ccp4,Sample4_diff.ccp4"
2223
2224 Author:
2225 Manish Sud(msud@san.rr.com)
2226
2227 See also:
2228 DownloadPDBFiles.pl, PyMOLVisualizeCavities.py,
2229 PyMOLVisualizeCryoEMDensity.py, PyMOLVisualizeInterfaces.py,
2230 PyMOLVisualizeMacromolecules.py, PyMOLVisualizeSurfaceAndBuriedResidues.py
2231
2232 Copyright:
2233 Copyright (C) 2024 Manish Sud. All rights reserved.
2234
2235 The functionality available in this script is implemented using PyMOL, a
2236 molecular visualization system on an open source foundation originally
2237 developed by Warren DeLano.
2238
2239 This file is part of MayaChemTools.
2240
2241 MayaChemTools is free software; you can redistribute it and/or modify it under
2242 the terms of the GNU Lesser General Public License as published by the Free
2243 Software Foundation; either version 3 of the License, or (at your option) any
2244 later version.
2245
2246 """
2247
2248 if __name__ == "__main__":
2249 main()
