1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeCryoEMDensity.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 import xml.etree.ElementTree as ElementTree
38
39 # PyMOL imports...
40 try:
41 import pymol
42 # Finish launching PyMOL in a command line mode for batch processing (-c)
43 # along with the following options: disable loading of pymolrc and plugins (-k);
44 # suppress start up messages (-q)
45 pymol.finish_launching(['pymol', '-ckq'])
46 except ImportError as ErrMsg:
47 sys.stderr.write("\nFailed to import PyMOL module/package: %s\n" % ErrMsg)
48 sys.stderr.write("Check/update your PyMOL environment and try again.\n\n")
49 sys.exit(1)
50
51 # MayaChemTools imports...
52 try:
53 from docopt import docopt
54 import MiscUtil
55 import PyMOLUtil
56 except ImportError as ErrMsg:
57 sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg)
58 sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n")
59 sys.exit(1)
60
61 ScriptName = os.path.basename(sys.argv[0])
62 Options = {}
63 OptionsInfo = {}
64
65 def main():
66 """Start execution of the script."""
67
68 MiscUtil.PrintInfo("\n%s (PyMOL v%s; MayaChemTools v%s; %s): Starting...\n" % (ScriptName, pymol.cmd.get_version()[0], MiscUtil.GetMayaChemToolsVersion(), time.asctime()))
69
70 (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
71
72 # Retrieve command line arguments and options...
73 RetrieveOptions()
74
75 # Process and validate command line arguments and options...
76 ProcessOptions()
77
78 # Perform actions required by the script...
79 GenerateCryoEMDensityVisualization()
80
81 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
82 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
83
84 def GenerateCryoEMDensityVisualization():
85 """Generate cryo-EM density visualization."""
86
87 Outfile = OptionsInfo["PMLOutfile"]
88 OutFH = open(Outfile, "w")
89 if OutFH is None:
90 MiscUtil.PrintError("Failed to open output fie %s " % Outfile)
91
92 MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
93
94 # Setup header...
95 WritePMLHeader(OutFH, ScriptName)
96 WritePyMOLParameters(OutFH)
97
98 # Load reffile for alignment..
99 if OptionsInfo["Align"]:
100 WriteAlignReference(OutFH)
101
102 # Setup view for each input file...
103 FirstComplex = True
104 FirstComplexFirstChainName = None
105 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
106 # Setup PyMOL object names...
107 PyMOLObjectNames = SetupPyMOLObjectNames(FileIndex)
108
109 # Setup complex view...
110 WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex)
111
112 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
113 FirstChain = True
114 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
115 if FirstComplex and FirstChain:
116 FirstComplexFirstChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
117
118 WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
119
120 # Setup ligand views...
121 FirstLigand = True
122 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
123 WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID)
124
125 # Set up ligand level group...
126 Enable, Action = [False, "close"]
127 if FirstLigand:
128 FirstLigand = False
129 Enable, Action = [True, "open"]
130 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"], PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"], Enable, Action)
131
132 # Setup Chain level group...
133 Enable, Action = [False, "close"]
134 if FirstChain:
135 FirstChain = False
136 Enable, Action = [True, "open"]
137 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"], Enable, Action)
138
139 # Set up complex level group...
140 Enable, Action = [False, "close"]
141 if FirstComplex:
142 FirstComplex = False
143 Enable, Action = [True, "open"]
144 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["PDBGroup"], PyMOLObjectNames["PDBGroupMembers"], Enable, Action)
145
146 # Delete empty PyMOL objects...
147 DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames)
148
149 if OptionsInfo["Align"]:
150 DeleteAlignReference(OutFH)
151
152 if FirstComplexFirstChainName is not None:
153 OutFH.write("""\ncmd.orient("%s", animate = -1)\n""" % FirstComplexFirstChainName)
154 else:
155 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
156
157 OutFH.close()
158
159 # Generate PSE file as needed...
160 if OptionsInfo["PSEOut"]:
161 GeneratePyMOLSessionFile()
162
163 def WritePMLHeader(OutFH, ScriptName):
164 """Write out PML setting up complex view."""
165
166 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
167 OutFH.write("%s\n" % HeaderInfo)
168
169 def WritePyMOLParameters(OutFH):
170 """Write out PyMOL global parameters."""
171
172 PMLCmds = []
173 PMLCmds.append("""cmd.set("mesh_width", %.2f)""" % (OptionsInfo["MeshWidth"]))
174 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
175 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
176
177 if OptionsInfo["VolumeColorRampCreate"]:
178 ColorRampName = OptionsInfo["VolumeColorRampName"]
179 ContourLevel = OptionsInfo["VolumeColorRampContourLevel"]
180 LowerContourLevel = ContourLevel - 0.3
181 UpperContourLevel = ContourLevel + 0.3
182 PMLCmds.append("""cmd.volume_ramp_new("%s", "%.2f blue 0.00 %.2f cyan 0.20 %.2f blue 0.00")""" % (ColorRampName, LowerContourLevel, ContourLevel, UpperContourLevel))
183
184 PML = "\n".join(PMLCmds)
185
186 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
187 OutFH.write("%s\n" % PML)
188
189 def WriteAlignReference(OutFH):
190 """Setup object for alignment reference."""
191
192 RefFileInfo = OptionsInfo["RefFileInfo"]
193 RefFile = RefFileInfo["RefFileName"]
194 RefName = RefFileInfo["PyMOLObjectName"]
195
196 PMLCmds = []
197 PMLCmds.append("""cmd.load("%s", "%s")""" % (RefFile, RefName))
198 PMLCmds.append("""cmd.hide("everything", "%s")""" % (RefName))
199 PMLCmds.append("""cmd.disable("%s")""" % (RefName))
200 PML = "\n".join(PMLCmds)
201
202 OutFH.write("""\n""\n"Loading %s and setting up view for align reference..."\n""\n""" % RefFile)
203 OutFH.write("%s\n" % PML)
204
205 def WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames):
206 """Setup alignment of complex to reference."""
207
208 RefFileInfo = OptionsInfo["RefFileInfo"]
209 RefName = RefFileInfo["PyMOLObjectName"]
210
211 ComplexName = PyMOLObjectNames["Complex"]
212
213 if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
214 RefFirstChainID = RefFileInfo["ChainsAndLigandsInfo"]["ChainIDs"][0]
215 RefAlignSelection = "%s and chain %s" % (RefName, RefFirstChainID)
216
217 ComplexFirstChainID = RetrieveFirstChainID(FileIndex)
218 ComplexAlignSelection = "%s and chain %s" % (ComplexName, ComplexFirstChainID)
219 else:
220 RefAlignSelection = RefName
221 ComplexAlignSelection = ComplexName
222
223 PML = PyMOLUtil.SetupPMLForAlignment(OptionsInfo["AlignMethod"], RefAlignSelection, ComplexAlignSelection)
224 OutFH.write("""\n""\n"Aligning %s against reference %s ..."\n""\n""" % (ComplexAlignSelection, RefAlignSelection))
225 OutFH.write("%s\n" % PML)
226
227 def DeleteAlignReference(OutFH):
228 """Delete alignment reference object."""
229
230 RefName = OptionsInfo["RefFileInfo"]["PyMOLObjectName"]
231 OutFH.write("""\n""\n"Deleting alignment reference object %s..."\n""\n""" % RefName)
232 OutFH.write("""cmd.delete("%s")\n""" % RefName)
233
234 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex):
235 """Write out PML for viewing polymer complex along with cryo-EM density."""
236
237 # Setup complex...
238 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
239 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["Complex"], Infile, True)
240 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
241 OutFH.write("%s\n" % PML)
242
243 if OptionsInfo["Align"]:
244 # No need to align complex on to itself...
245 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
246 WriteAlignComplex(OutFH, FileIndex, PyMOLObjectNames)
247
248 # Setup cryo-EM density maps and meshes...
249 DensityMapFile = OptionsInfo["DensityMapFilesNames"][FileIndex]
250 ContourLevel = OptionsInfo["MeshLevels"][FileIndex]
251 WriteComplexCryoEMDensityMapView(OutFH, PyMOLObjectNames, DensityMapFile, ContourLevel)
252
253 # Setup complex group...
254 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close")
255
256 def WriteComplexCryoEMDensityMapView(OutFH, PyMOLObjectNames, MapFileName, ContourLevel):
257 """Write out PML for viewing cryoEM density map."""
258
259 # Load cryo-EM density map and setup mesh views...
260 Info = """\
261 ""
262 "Loading cryo-EM density map %s and setting up mesh view for complex..."
263 "" """ % MapFileName
264 OutFH.write("\n%s\n" % Info)
265
266 MapName = PyMOLObjectNames["ComplexCryoEMMap"]
267 ComplexName = PyMOLObjectNames["Complex"]
268
269 Color = OptionsInfo["MeshColor"]
270 VolumeColorRamp = OptionsInfo["VolumeColorRampName"]
271
272 VolumeName = PyMOLObjectNames["ComplexCryoEMVolume"]
273 MeshName = PyMOLObjectNames["ComplexCryoEMMesh"]
274 SurfaceName = PyMOLObjectNames["ComplexCryoEMSurface"]
275
276 AlignMapToObjectName = ComplexName if OptionsInfo["Align"] else None
277 EnableMap = True
278 PML = SetupPMLForCryoEMDensityMap(MapFileName, MapName, AlignMapToObjectName, EnableMap)
279 OutFH.write("%s\n" % PML)
280
281 EnableMesh = OptionsInfo["MeshComplex"]
282
283 EnableVolume = OptionsInfo["VolumeComplex"]
284 if EnableVolume and EnableMesh:
285 EnableVolume = False
286
287 EnableSurface = OptionsInfo["SurfaceComplex"]
288 if EnableSurface and (EnableVolume or EnableMesh):
289 EnableSurface = False
290
291 if OptionsInfo["VolumeComplex"]:
292 PML = SetupPMLForCryoEMDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = EnableVolume, Selection = ComplexName)
293 OutFH.write("\n%s\n" % PML)
294
295 if OptionsInfo["MeshComplex"]:
296 PML = SetupPMLForCryoEMDensityMesh(MapName, MeshName, ContourLevel, Color, Enable = EnableMesh, Selection = ComplexName)
297 OutFH.write("\n%s\n" % PML)
298
299 if OptionsInfo["SurfaceComplex"]:
300 PML = SetupPMLForCryoEMDensitySurface(MapName, SurfaceName, ContourLevel, Color, Enable = EnableSurface, Selection = ComplexName)
301 OutFH.write("\n%s\n" % PML)
302
303 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexCryoEMGroup"], PyMOLObjectNames["ComplexCryoEMGroupMembers"], True, "close")
304
305 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
306 """Write out PML for viewing chain."""
307
308 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
309
310 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
311
312 # Setup chain complex group view...
313 WriteChainComplexAndMeshViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
314
315 # Setup chain view...
316 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
317
318 # Setup chain solvent view...
319 PML = PyMOLUtil.SetupPMLForSolventView(PyMOLObjectNames["Chains"][ChainID]["Solvent"], ChainComplexName, False)
320 OutFH.write("\n%s\n" % PML)
321
322 # Setup chain inorganic view...
323 PML = PyMOLUtil.SetupPMLForInorganicView(PyMOLObjectNames["Chains"][ChainID]["Inorganic"], ChainComplexName, False)
324 OutFH.write("\n%s\n" % PML)
325
326 def WriteChainComplexAndMeshViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
327 """Write chain complex and mesh views."""
328
329 # Setup chain complex...
330 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
331 PML = PyMOLUtil.SetupPMLForPolymerChainComplexView(ChainComplexName, PyMOLObjectNames["Complex"], ChainID, True)
332 OutFH.write("%s\n" % PML)
333
334 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
335
336 MeshChainComplex = SpecifiedChainsAndLigandsInfo["MeshChainComplex"][ChainID]
337 VolumeChainComplex = SpecifiedChainsAndLigandsInfo["VolumeChainComplex"][ChainID]
338 SurfaceChainComplex = SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"][ChainID]
339
340 EnableVolumeChainComplex = SpecifiedChainsAndLigandsInfo["EnableVolumeChainComplex"][ChainID]
341 EnableMeshChainComplex = SpecifiedChainsAndLigandsInfo["EnableMeshChainComplex"][ChainID]
342 EnableSurfaceChainComplex = SpecifiedChainsAndLigandsInfo["EnableSurfaceChainComplex"][ChainID]
343
344 if MeshChainComplex or VolumeChainComplex or SurfaceChainComplex:
345 # Set up cryoEM mesh and group...
346 MapName = PyMOLObjectNames["ComplexCryoEMMap"]
347 ContourLevel = OptionsInfo["MeshLevels"][FileIndex]
348 Color = OptionsInfo["MeshColor"]
349
350 VolumeColorRamp = OptionsInfo["VolumeColorRampName"]
351
352 VolumeName = PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMVolume"]
353 MeshName = PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMMesh"]
354 SurfaceName = PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMSurface"]
355
356 if VolumeChainComplex:
357 PML = SetupPMLForCryoEMDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = EnableVolumeChainComplex, Selection = ChainComplexName)
358 OutFH.write("\n%s\n" % PML)
359
360 if MeshChainComplex:
361 PML = SetupPMLForCryoEMDensityMesh(MapName, MeshName, ContourLevel, Color, Enable = EnableMeshChainComplex, Selection = ChainComplexName)
362 OutFH.write("\n%s\n" % PML)
363
364 if SurfaceChainComplex:
365 PML = SetupPMLForCryoEMDensitySurface(MapName, SurfaceName, ContourLevel, Color, Enable = EnableSurfaceChainComplex, Selection = ChainComplexName)
366 OutFH.write("\n%s\n" % PML)
367
368 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMGroupMembers"], True, "close")
369
370 # Setup chain complex group...
371 EnableChainComplexGroup = SpecifiedChainsAndLigandsInfo["EnableChainComplexGroup"][ChainID]
372 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"], EnableChainComplexGroup, "close")
373
374 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
375 """Write individual chain views."""
376
377 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
378
379 # Setup chain view...
380 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
381 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, Enable = True)
382 OutFH.write("\n%s\n" % PML)
383
384 # Setup chain putty by B-factor view...
385 if OptionsInfo["BFactorChainCartoonPutty"]:
386 BFactorPuttyName = PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"]
387 PML = PyMOLUtil.SetupPMLForBFactorPuttyView(BFactorPuttyName, ChainName, ColorPalette = OptionsInfo["BFactorColorPalette"], Enable = False)
388 OutFH.write("\n%s\n" % PML)
389
390 # Setup chain selections view...
391 SetupChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
392
393 # Setup chain group...
394 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
395 EnableChainAloneGroup = SpecifiedChainsAndLigandsInfo["EnableChainAloneGroup"][ChainID]
396 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"], EnableChainAloneGroup, "close")
397
398 def SetupChainSelectionsView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
399 """Setup chain selectons view."""
400
401 if not OptionsInfo["ChainSelections"]:
402 return
403
404 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
405 SelectionsGroupIDPrefix = "ChainAloneSelections"
406
407 for Index in range(0, len(OptionsInfo["ChainSelectionsInfo"]["Names"])):
408 SelectionName = OptionsInfo["ChainSelectionsInfo"]["Names"][Index]
409 SpecifiedSelection = OptionsInfo["ChainSelectionsInfo"]["Selections"][Index]
410
411 SelectionNameGroupID = SelectionName
412
413 # Setup selection object...
414 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
415 SelectionObjectName = PyMOLObjectNames["Chains"][ChainID][SelectionObjectID]
416 SelectionCmd = "(%s and (%s))" % (ChainName, SpecifiedSelection)
417 PML = PyMOLUtil.SetupPMLForSelectionDisplayView(SelectionObjectName, SelectionCmd, OptionsInfo["SelectionsChainStyle"], Enable = True)
418 OutFH.write("\n%s\n" % PML)
419
420 # Set up cryo-EM mesh and group...
421 CryoEMVolumeID = "%s%sCryoEMVolume" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
422 CryoEMMeshID = "%s%sCryoEMMesh" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
423 CryoEMSurfaceID = "%s%sCryoEMSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
424 CryoEMMeshGroupID = "%s%sCryoEMGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
425 CryoEMMeshGroupMembersID = "%s%sCryoEMGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
426
427 CryoEMVolumeName = PyMOLObjectNames["Chains"][ChainID][CryoEMVolumeID]
428 CryoEMMeshName = PyMOLObjectNames["Chains"][ChainID][CryoEMMeshID]
429 CryoEMSurfaceName = PyMOLObjectNames["Chains"][ChainID][CryoEMSurfaceID]
430 CryoEMMeshGroupName = PyMOLObjectNames["Chains"][ChainID][CryoEMMeshGroupID]
431 CryoEMMeshGroupMembers = PyMOLObjectNames["Chains"][ChainID][CryoEMMeshGroupMembersID]
432
433 MapName = PyMOLObjectNames["ComplexCryoEMMap"]
434 ContourLevel = OptionsInfo["MeshLevels"][FileIndex]
435 Color = OptionsInfo["MeshColor"]
436
437 PML = SetupPMLForCryoEMDensityVolume(MapName, CryoEMVolumeName, OptionsInfo["VolumeColorRampName"], Enable = False, Selection = SelectionObjectName)
438 OutFH.write("\n%s\n" % PML)
439
440 PML = SetupPMLForCryoEMDensityMesh(MapName, CryoEMMeshName, ContourLevel, Color, Enable = True, Selection = SelectionObjectName)
441 OutFH.write("\n%s\n" % PML)
442
443 PML = SetupPMLForCryoEMDensitySurface(MapName, CryoEMSurfaceName, ContourLevel, Color, Enable = False, Selection = SelectionObjectName)
444 OutFH.write("\n%s\n" % PML)
445
446 GenerateAndWritePMLForGroup(OutFH, CryoEMMeshGroupName, CryoEMMeshGroupMembers, True, "close")
447
448 # Setup groups for named selections...
449 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
450 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
451 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID], PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID], True, "open")
452
453 # Setup a group for selections...
454 SelectionsGroupID = "%sGroup" % (SelectionsGroupIDPrefix)
455 SelectionsGroupMembersID = "%sGroupMembers" % (SelectionsGroupIDPrefix)
456 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID], PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID], False, "close")
457
458 def WriteChainLigandView(OutFH, FileIndex, PyMOLObjectNames, ChainID, LigandID):
459 """Write out PML for viewing ligand in a chain."""
460
461 for GroupID in ["Ligand", "Pocket", "PocketSolvent", "PocketInorganic"]:
462 ComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
463 LigandName = PyMOLObjectNames["Ligands"][ChainID][LigandID]["Ligand"]
464
465 # Setup main object...
466 GroupTypeObjectID = "%s" % (GroupID)
467 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
468
469 if re.match("^Ligand$", GroupID, re.I):
470 OutFH.write("""\n""\n"Setting up views for ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
471 PML = PyMOLUtil.SetupPMLForLigandView(GroupTypeObjectName, ComplexName, LigandID, Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
472 OutFH.write("%s\n" % PML)
473 elif re.match("^Pocket$", GroupID, re.I):
474 OutFH.write("""\n""\n"Setting up views for pocket around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
475 PML = PyMOLUtil.SetupPMLForLigandPocketView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True, IgnoreHydrogens = OptionsInfo["IgnoreHydrogens"])
476 OutFH.write("%s\n" % PML)
477 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], GroupTypeObjectName))
478 elif re.match("^PocketSolvent$", GroupID, re.I):
479 OutFH.write("""\n""\n"Setting up views for solvent in pockect around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
480 PML = PyMOLUtil.SetupPMLForLigandPocketSolventView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
481 OutFH.write("%s\n" % PML)
482 elif re.match("^PocketInorganic$", GroupID, re.I):
483 OutFH.write("""\n""\n"Setting up views for inorganic in pockect around ligand %s in chain %s..."\n""\n""" % (LigandID, ChainID))
484 PML = PyMOLUtil.SetupPMLForLigandPocketInorganicView(GroupTypeObjectName, ComplexName, LigandName, OptionsInfo["PocketDistanceCutoff"], Enable = True)
485 OutFH.write("%s\n" % PML)
486
487 # Set up cryoEM mesh and group...
488 CryoEMMeshGroupID = "%sCryoEMMeshGroup" % (GroupID)
489 CryoEMMeshGroupMembersID = "%sCryoEMMeshGroupMembers" % (GroupID)
490 CryoEMVolumeID = "%sCryoEMVolume" % (GroupID)
491 CryoEMMeshID = "%sCryoEMMesh" % (GroupID)
492 CryoEMSurfaceID = "%sCryoEMSurface" % (GroupID)
493
494 CryoEMMapName = PyMOLObjectNames["ComplexCryoEMMap"]
495 CryoEMVolumeName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMVolumeID]
496 CryoEMMeshName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshID]
497 CryoEMSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMSurfaceID]
498 CryoEMMeshGroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshGroupID]
499 CryoEMMeshGroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshGroupMembersID]
500
501 PML = SetupPMLForCryoEMDensityVolume(CryoEMMapName, CryoEMVolumeName, OptionsInfo["VolumeColorRampName"], Enable = False, Selection = GroupTypeObjectName)
502 OutFH.write("\n%s\n" % PML)
503
504 ContourLevel = OptionsInfo["MeshLevels"][FileIndex]
505 PML = SetupPMLForCryoEMDensityMesh(CryoEMMapName, CryoEMMeshName, ContourLevel, OptionsInfo["MeshColor"], Enable = True, Selection = GroupTypeObjectName)
506 OutFH.write("\n%s\n" % PML)
507
508 PML = SetupPMLForCryoEMDensitySurface(CryoEMMapName, CryoEMSurfaceName, ContourLevel, OptionsInfo["MeshColor"], Enable = False, Selection = GroupTypeObjectName)
509 OutFH.write("\n%s\n" % PML)
510
511 GenerateAndWritePMLForGroup(OutFH, CryoEMMeshGroupName, CryoEMMeshGroupMembers, True, "close")
512
513 # Set up polar contacts...
514 if re.match("^(Pocket|PocketSolvent|PocketInorganic)$", GroupID, re.I):
515 PolarContactsID = "%sPolarContacts" % (GroupID)
516 PolarContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID]
517
518 PolarContactsColor = OptionsInfo["PocketContactsLigandColor"]
519 if re.match("^PocketSolvent$", GroupID, re.I):
520 PolarContactsColor = OptionsInfo["PocketContactsSolventColor"]
521 elif re.match("^PocketInorganic$", GroupID, re.I):
522 PolarContactsColor = OptionsInfo["PocketContactsInorganicColor"]
523
524 PML = PyMOLUtil.SetupPMLForPolarContactsView(PolarContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = PolarContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
525 OutFH.write("\n%s\n" % PML)
526
527 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (PolarContactsColor, PolarContactsName))
528
529 # Set up hydrophobic contacts...
530 if re.match("^Pocket$", GroupID, re.I):
531 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
532 HydrophobicContactsName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID]
533 HydrophobicContactsColor = OptionsInfo["PocketContactsLigandHydrophobicColor"]
534
535 PML = PyMOLUtil.SetupPMLForHydrophobicContactsView(HydrophobicContactsName, LigandName, GroupTypeObjectName, Enable = False, Color = HydrophobicContactsColor, Cutoff = OptionsInfo["PocketContactsCutoff"])
536 OutFH.write("\n%s\n" % PML)
537 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (HydrophobicContactsColor, HydrophobicContactsName))
538
539 # Set up hydrophobic surface...
540 if re.match("^Pocket$", GroupID, re.I) and OptionsInfo["PocketSurface"]:
541 HydrophobicSurfaceID = "%sHydrophobicSurface" % (GroupID)
542 HydrophobicSurfaceName = PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID]
543 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(HydrophobicSurfaceName, GroupTypeObjectName, ColorPalette = "RedToWhite", Enable = False)
544 OutFH.write("\n%s\n" % PML)
545
546 OutFH.write("""cmd.set("label_color", "%s", "%s")\n""" % (OptionsInfo["PocketLabelColor"], HydrophobicSurfaceName))
547
548 # Setup group....
549 GroupNameID = "%sGroup" % (GroupID)
550 GroupMembersID = "%sGroupMembers" % (GroupID)
551 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
552 GroupMembers = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID]
553
554 Action = "close"
555 Enable = False
556 if re.match("^(Ligand|Pocket)$", GroupID, re.I):
557 Action = "open"
558 Enable = True
559 GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable, Action)
560
561 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable = False, Action = "close"):
562 """Generate and write PML for group."""
563
564 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
565 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
566 OutFH.write("%s\n" % PML)
567
568 def SetupPMLForCryoEMDensityMap(MapFileName, MapName, AlignMapToObjectName = None, Enable = True):
569 """Setup PML for loading and viewing cryo-EM density map."""
570
571 PMLCmds = []
572 PMLCmds.append("""cmd.load("%s", "%s")""" % (MapFileName, MapName))
573 if AlignMapToObjectName is not None:
574 PMLCmds.append("""cmd.matrix_copy("%s", "%s")""" % (AlignMapToObjectName, MapName))
575
576 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MapName, Enable))
577
578 PML = "\n".join(PMLCmds)
579
580 return PML
581
582 def SetupPMLForCryoEMDensityMesh(MapName, MeshName, SigmaLevel, Color, Enable = True, Selection = None):
583 """Setup PML for cryo-EM density mesh."""
584
585 Carve = OptionsInfo["MeshCarveRadius"]
586
587 PMLCmds = []
588 if Selection is None:
589 PMLCmds.append("""cmd.isomesh("%s", "%s", %.1f)""" % (MeshName, MapName, SigmaLevel))
590 else:
591 PMLCmds.append("""cmd.isomesh("%s", "%s", %.1f, "(%s)", carve = %.1f)""" % (MeshName, MapName, SigmaLevel, Selection, Carve))
592 PMLCmds.append(PyMOLUtil.SetupPMLForDeepColoring(MeshName, Color))
593 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(MeshName, Enable))
594
595 PML = "\n".join(PMLCmds)
596
597 return PML
598
599 def SetupPMLForCryoEMDensityVolume(MapName, VolumeName, VolumeColorRamp, Enable = True, Selection = None):
600 """Setup PML for cryo-EM density volume."""
601
602 Carve = OptionsInfo["VolumeCarveRadius"]
603
604 PMLCmds = []
605 if Selection is None:
606 PMLCmds.append("""cmd.volume("%s", "%s", "%s")""" % (VolumeName, MapName, VolumeColorRamp))
607 else:
608 PMLCmds.append("""cmd.volume("%s", "%s", "%s", "(%s)", carve = %.1f)""" % (VolumeName, MapName, VolumeColorRamp, Selection, Carve))
609 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(VolumeName, Enable))
610
611 PML = "\n".join(PMLCmds)
612
613 return PML
614
615 def SetupPMLForCryoEMDensitySurface(MapName, SurfaceName, SigmaLevel, Color, Enable = True, Selection = None):
616 """Setup PML for cryo-EM density surface."""
617
618 Carve = OptionsInfo["MeshCarveRadius"]
619
620 PMLCmds = []
621 if Selection is None:
622 PMLCmds.append("""cmd.isosurface("%s", "%s", %.1f)""" % (SurfaceName, MapName, SigmaLevel))
623 else:
624 PMLCmds.append("""cmd.isosurface("%s", "%s", %.1f, "(%s)", carve = %.1f)""" % (SurfaceName, MapName, SigmaLevel, Selection, Carve))
625 PMLCmds.append(PyMOLUtil.SetupPMLForDeepColoring(SurfaceName, Color))
626 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(SurfaceName, Enable))
627
628 PML = "\n".join(PMLCmds)
629
630 return PML
631
632 def GeneratePyMOLSessionFile():
633 """Generate PME file from PML file."""
634
635 PSEOutfile = OptionsInfo["PSEOutfile"]
636 PMLOutfile = OptionsInfo["PMLOutfile"]
637
638 MiscUtil.PrintInfo("\nGenerating file %s..." % PSEOutfile)
639
640 PyMOLUtil.ConvertPMLFileToPSEFile(PMLOutfile, PSEOutfile)
641
642 if not os.path.exists(PSEOutfile):
643 MiscUtil.PrintWarning("Failed to generate PSE file, %s..." % (PSEOutfile))
644
645 if not OptionsInfo["PMLOut"]:
646 MiscUtil.PrintInfo("Deleting file %s..." % PMLOutfile)
647 os.remove(PMLOutfile)
648
649 def DeleteEmptyPyMOLObjects(OutFH, FileIndex, PyMOLObjectNames):
650 """Delete empty PyMOL objects."""
651
652 if OptionsInfo["AllowEmptyObjects"]:
653 return
654
655 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
656 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
657 OutFH.write("""\n""\n"Checking and deleting empty objects for chain %s..."\n""\n""" % (ChainID))
658
659 # Delete any chain level objects...
660 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Solvent"])
661 WritePMLToCheckAndDeleteEmptyObjects(OutFH, PyMOLObjectNames["Chains"][ChainID]["Inorganic"])
662
663 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
664 # Delete ligand level objects...
665 for GroupID in ["Pocket", "PocketSolvent", "PocketInorganic"]:
666 GroupNameID = "%sGroup" % (GroupID)
667 GroupName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID]
668
669 GroupTypeObjectID = "%s" % (GroupID)
670 GroupTypeObjectName = PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID]
671
672 WritePMLToCheckAndDeleteEmptyObjects(OutFH, GroupTypeObjectName, GroupName)
673
674 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
675 """Write PML to check and delete empty PyMOL objects."""
676
677 if ParentObjectName is None:
678 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
679 else:
680 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
681
682 OutFH.write("%s\n" % PML)
683
684 def SetupPyMOLObjectNames(FileIndex):
685 """Setup hierarchy of PyMOL groups and objects for ligand centric views of
686 cryo-EM density for chains and ligands present in input file.
687 """
688
689 PyMOLObjectNames = {}
690 PyMOLObjectNames["Chains"] = {}
691 PyMOLObjectNames["Ligands"] = {}
692
693 # Setup groups and objects for complex...
694 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
695
696 # Setup groups and objects for chain...
697 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
698 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
699 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
700
701 # Setup groups and objects for ligand...
702 for LigandID in SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]:
703 SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID)
704
705 return PyMOLObjectNames
706
707 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
708 """Stetup groups and objects for complex."""
709
710 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
711
712 PDBGroupName = "%s" % PDBFileRoot
713 PyMOLObjectNames["PDBGroup"] = PDBGroupName
714 PyMOLObjectNames["PDBGroupMembers"] = []
715
716 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
717 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
718 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
719
720 PyMOLObjectNames["Complex"] = "%s.Complex" % ComplexGroupName
721
722 CryoEMMeshGroupName = "%s.CryoEM" % (ComplexGroupName)
723 CryoEMMapName = "%s.Map" % (CryoEMMeshGroupName)
724 CryoEMVolumeName = "%s.Volume" % (CryoEMMeshGroupName)
725 CryoEMMeshName = "%s.Mesh" % (CryoEMMeshGroupName)
726 CryoEMSurfaceName = "%s.Surface" % (CryoEMMeshGroupName)
727
728 PyMOLObjectNames["ComplexCryoEMGroup"] = CryoEMMeshGroupName
729 PyMOLObjectNames["ComplexCryoEMMap"] = CryoEMMapName
730 PyMOLObjectNames["ComplexCryoEMVolume"] = CryoEMVolumeName
731 PyMOLObjectNames["ComplexCryoEMMesh"] = CryoEMMeshName
732 PyMOLObjectNames["ComplexCryoEMSurface"] = CryoEMSurfaceName
733
734 PyMOLObjectNames["ComplexCryoEMGroupMembers"] = []
735 PyMOLObjectNames["ComplexCryoEMGroupMembers"].append(CryoEMMapName)
736 if OptionsInfo["VolumeComplex"]:
737 PyMOLObjectNames["ComplexCryoEMGroupMembers"].append(CryoEMVolumeName)
738 if OptionsInfo["MeshComplex"]:
739 PyMOLObjectNames["ComplexCryoEMGroupMembers"].append(CryoEMMeshName)
740 if OptionsInfo["SurfaceComplex"]:
741 PyMOLObjectNames["ComplexCryoEMGroupMembers"].append(CryoEMSurfaceName)
742
743 PyMOLObjectNames["ComplexGroupMembers"] = []
744 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["Complex"])
745 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["ComplexCryoEMGroup"])
746
747 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
748 """Setup groups and objects for chain."""
749
750 PDBGroupName = PyMOLObjectNames["PDBGroup"]
751
752 SpecifiedChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"][FileIndex]
753 MeshChainComplex = SpecifiedChainsAndLigandsInfo["MeshChainComplex"][ChainID]
754 VolumeChainComplex = SpecifiedChainsAndLigandsInfo["VolumeChainComplex"][ChainID]
755 SurfaceChainComplex = SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"][ChainID]
756
757 PyMOLObjectNames["Chains"][ChainID] = {}
758 PyMOLObjectNames["Ligands"][ChainID] = {}
759
760 # Set up chain group and chain objects...
761 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
762 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
763 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
764 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
765
766 # Setup chain complex group and objects...
767 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
768 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
769 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
770
771 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = "%s.Complex" % (ChainComplexGroupName)
772
773 CryoEMMeshGroupName = "%s.CryoEM" % (ChainComplexGroupName)
774 CryoEMVolumeName = "%s.Volume" % (CryoEMMeshGroupName)
775 CryoEMMeshName = "%s.Mesh" % (CryoEMMeshGroupName)
776 CryoEMSurfaceName = "%s.Surface" % (CryoEMMeshGroupName)
777
778 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMGroup"] = CryoEMMeshGroupName
779 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMVolume"] = CryoEMVolumeName
780 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMMesh"] = CryoEMMeshName
781 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMSurface"] = CryoEMSurfaceName
782
783 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMGroupMembers"] = []
784 if VolumeChainComplex:
785 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMGroupMembers"].append(CryoEMVolumeName)
786 if MeshChainComplex:
787 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMGroupMembers"].append(CryoEMMeshName)
788 if SurfaceChainComplex:
789 PyMOLObjectNames["Chains"][ChainID]["ChainComplexCryoEMGroupMembers"].append(CryoEMSurfaceName)
790
791 NameIDs = ["ChainComplex"]
792 if MeshChainComplex or VolumeChainComplex or SurfaceChainComplex :
793 NameIDs.append("ChainComplexCryoEMGroup")
794
795 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
796 for NameID in NameIDs:
797 Name = PyMOLObjectNames["Chains"][ChainID][NameID]
798 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
799
800 # Setup up a group for individual chains...
801 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
802 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
803 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
804
805 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
806
807 Name = "%s.Chain" % (ChainAloneGroupName)
808 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
809 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
810
811 if OptionsInfo["BFactorChainCartoonPutty"]:
812 Name = "%s.BFactor" % (ChainAloneGroupName)
813 PyMOLObjectNames["Chains"][ChainID]["ChainAloneBFactorPutty"] = Name
814 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
815
816 if OptionsInfo["ChainSelections"]:
817 # Setup selections group and its subgroups..
818 SelectionsGroupName = "%s.Selections" % (ChainAloneGroupName)
819
820 SelectionsGroupIDPrefix = "ChainAloneSelections"
821 SelectionsGroupID = "%sGroup" % SelectionsGroupIDPrefix
822
823 # Add selections group to chain alone group...
824 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupID] = SelectionsGroupName
825 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SelectionsGroupName)
826
827 # Initialize selections group members...
828 SelectionsGroupMembersID = "%sGroupMembers" % SelectionsGroupIDPrefix
829 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID] = []
830
831 # Setup selections name sub group and its members...
832 for SelectionName in OptionsInfo["ChainSelectionsInfo"]["Names"]:
833 SelectionNameGroupID = SelectionName
834
835 SelectionsNameGroupName = "%s.%s" % (SelectionsGroupName, SelectionName)
836 SelectionsNameGroupID = "%s%sGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
837
838 # Add selections name sub group to selections group...
839 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupID] = SelectionsNameGroupName
840 PyMOLObjectNames["Chains"][ChainID][SelectionsGroupMembersID].append(SelectionsNameGroupName)
841
842 # Initialize selections names sub group members...
843 SelectionsNameGroupMembersID = "%s%sGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
844 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID] = []
845
846 # Add selection object to selections name group...
847 SelectionObjectName = "%s.Selection" % (SelectionsNameGroupName)
848 SelectionObjectID = "%s%sSelection" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
849
850 PyMOLObjectNames["Chains"][ChainID][SelectionObjectID] = SelectionObjectName
851 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(SelectionObjectName)
852
853 # Setup cryo-EM mesh group and add it to selections name group...
854 CryoEMMeshGroupName = "%s.CryoEM" % (SelectionsNameGroupName)
855 CryoEMMeshGroupID = "%s%sCryoEMGroup" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
856
857 PyMOLObjectNames["Chains"][ChainID][CryoEMMeshGroupID] = CryoEMMeshGroupName
858 PyMOLObjectNames["Chains"][ChainID][SelectionsNameGroupMembersID].append(CryoEMMeshGroupName)
859
860 # Initialize cryo-EM mesh group members...
861 CryoEMMeshGroupMembersID = "%s%sCryoEMGroupMembers" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
862 PyMOLObjectNames["Chains"][ChainID][CryoEMMeshGroupMembersID] = []
863
864 # Setup members of cryo-EM mesh group...
865 CryoEMVolumeName = "%s.Volume" % (CryoEMMeshGroupName)
866 CryoEMVolumeID = "%s%sCryoEMVolume" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
867 CryoEMMeshName = "%s.Mesh" % (CryoEMMeshGroupName)
868 CryoEMMeshID = "%s%sCryoEMMesh" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
869 CryoEMSurfaceName = "%s.Surface" % (CryoEMMeshGroupName)
870 CryoEMSurfaceID = "%s%sCryoEMSurface" % (SelectionsGroupIDPrefix, SelectionNameGroupID)
871
872 PyMOLObjectNames["Chains"][ChainID][CryoEMVolumeID] = CryoEMVolumeName
873 PyMOLObjectNames["Chains"][ChainID][CryoEMMeshID] = CryoEMMeshName
874 PyMOLObjectNames["Chains"][ChainID][CryoEMSurfaceID] = CryoEMSurfaceName
875
876 PyMOLObjectNames["Chains"][ChainID][CryoEMMeshGroupMembersID].append(CryoEMVolumeName)
877 PyMOLObjectNames["Chains"][ChainID][CryoEMMeshGroupMembersID].append(CryoEMMeshName)
878 PyMOLObjectNames["Chains"][ChainID][CryoEMMeshGroupMembersID].append(CryoEMSurfaceName)
879
880 # Setup solvent and inorganic objects for chain...
881 for NameID in ["Solvent", "Inorganic"]:
882 Name = "%s.%s" % (ChainGroupName, NameID)
883 PyMOLObjectNames["Chains"][ChainID][NameID] = Name
884 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(Name)
885
886 def SetupPyMOLObjectNamesForLigand(FileIndex, PyMOLObjectNames, ChainID, LigandID):
887 """Stetup groups and objects for ligand."""
888
889 PyMOLObjectNames["Ligands"][ChainID][LigandID] = {}
890
891 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
892
893 # Setup a chain level ligand group...
894 ChainLigandGroupName = "%s.Ligand%s" % (ChainGroupName, LigandID)
895 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroup"] = ChainLigandGroupName
896 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainLigandGroupName)
897
898 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"] = []
899
900 # Set up groups and objects for a specific ligand group...
901 for GroupType in ["Ligand", "Pocket", "Pocket_Solvent", "Pocket_Inorganic"]:
902 GroupID = re.sub("_", "", GroupType)
903 GroupName = "%s.%s" % (ChainLigandGroupName, GroupType)
904
905 GroupNameID = "%sGroup" % (GroupID)
906 GroupMembersID = "%sGroupMembers" % (GroupID)
907
908 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupNameID] = GroupName
909 PyMOLObjectNames["Ligands"][ChainID][LigandID]["ChainLigandGroupMembers"].append(GroupName)
910
911 GroupTypeObjectName = "%s.%s" % (GroupName, GroupType)
912 GroupTypeObjectID = "%s" % (GroupID)
913 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupTypeObjectID] = GroupTypeObjectName
914
915 CryoEMMeshGroupName = "%s.CryoEM" % (GroupName)
916 CryoEMVolumeName = "%s.Volume" % (CryoEMMeshGroupName)
917 CryoEMMeshName = "%s.Mesh" % (CryoEMMeshGroupName)
918 CryoEMSurfaceName = "%s.Surface" % (CryoEMMeshGroupName)
919
920 CryoEMMeshGroupID = "%sCryoEMMeshGroup" % (GroupID)
921 CryoEMMeshGroupMembersID = "%sCryoEMMeshGroupMembers" % (GroupID)
922 CryoEMVolumeID = "%sCryoEMVolume" % (GroupID)
923 CryoEMMeshID = "%sCryoEMMesh" % (GroupID)
924 CryoEMSurfaceID = "%sCryoEMSurface" % (GroupID)
925
926 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshGroupID] = CryoEMMeshGroupName
927 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMVolumeID] = CryoEMVolumeName
928 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshID] = CryoEMMeshName
929 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMSurfaceID] = CryoEMSurfaceName
930 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshGroupMembersID] = []
931 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshGroupMembersID].append(CryoEMVolumeName)
932 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshGroupMembersID].append(CryoEMMeshName)
933 PyMOLObjectNames["Ligands"][ChainID][LigandID][CryoEMMeshGroupMembersID].append(CryoEMSurfaceName)
934
935 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID] = []
936 NameIDs = [GroupTypeObjectID, CryoEMMeshGroupID]
937
938 for NameID in NameIDs:
939 Name = PyMOLObjectNames["Ligands"][ChainID][LigandID][NameID]
940 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(Name)
941
942 if re.match("^Ligand$", GroupType, re.I):
943 # No other object needed for Ligand group...
944 continue
945
946 PolarContactsName = "%s.Polar_Contacts" % (GroupName)
947 PolarContactsID = "%sPolarContacts" % (GroupID)
948 PyMOLObjectNames["Ligands"][ChainID][LigandID][PolarContactsID] = PolarContactsName
949 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(PolarContactsName)
950
951 if not re.match("^Pocket$", GroupType, re.I):
952 # No other object needed for any other group besides Pocket...
953 continue
954
955 if not OptionsInfo["PocketSurface"]:
956 continue
957
958 HydrophobicContactsName = "%s.Hydrophobic_Contacts" % (GroupName)
959 HydrophobicContactsID = "%sHydrophobicContacts" % (GroupID)
960 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicContactsID] = HydrophobicContactsName
961 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HydrophobicContactsName)
962
963 HydrophobicSurfaceName = "%s.Surface" % (GroupName)
964 HydrophobicSurfaceID = "%sHydrophobicSurface" % (GroupID)
965 PyMOLObjectNames["Ligands"][ChainID][LigandID][HydrophobicSurfaceID] = HydrophobicSurfaceName
966 PyMOLObjectNames["Ligands"][ChainID][LigandID][GroupMembersID].append(HydrophobicSurfaceName)
967
968 def ProcessDensityMapFiles():
969 """Process density map files."""
970
971 DensityMapFiles = OptionsInfo["DensityMapFiles"]
972 if re.match("^auto$", DensityMapFiles, re.I):
973 ProcessAutoDensityMapFiles()
974 else:
975 ProcessSpecifiedDensityMapFiles()
976
977 def ProcessSpecifiedDensityMapFiles():
978 """Process specified density map files."""
979
980 OptionsInfo["DensityMapFilesNames"] = []
981
982 MiscUtil.PrintInfo("\nProcessing cryo-EM density file names...")
983
984 DensityMapFiles = re.sub(" ", "", OptionsInfo["DensityMapFiles"])
985 if not DensityMapFiles:
986 MiscUtil.PrintError("No valid value specified using \"--densityMapFiles\" option.")
987
988 DensityMapFilesWords = DensityMapFiles.split(",")
989 DensityMapFilesWordsCount = len(DensityMapFilesWords)
990
991 InfilesNamesCount = len(OptionsInfo["InfilesNames"])
992
993 if DensityMapFilesWordsCount != InfilesNamesCount:
994 MiscUtil.PrintError("The number of comma delimited cryo-EM density map files, %d, specified using \"--DensityMapFiles\" must be equal to the number of input files, %s, specified using \"-i, --infiles\" option." % (DensityMapFilesWordsCount, InfilesNamesCount))
995
996 for Index in range(0, InfilesNamesCount):
997 Infile = OptionsInfo["InfilesNames"][Index]
998 DensityMapFile = DensityMapFilesWords[Index]
999
1000 if not os.path.exists(DensityMapFile):
1001 MiscUtil.PrintError("The cryo-EM density ED map file, %s, specified using option \"--DensityMapFiles\", corresponding to input file, %s, doesn't exist.\n" % (DensityMapFile, Infile))
1002
1003 OptionsInfo["DensityMapFilesNames"].append(DensityMapFile)
1004
1005 def ProcessAutoDensityMapFiles():
1006 """Set up and process name of density map files."""
1007
1008 OptionsInfo["DensityMapFilesNames"] = []
1009 InfilesNamesCount = len(OptionsInfo["InfilesNames"])
1010
1011 MiscUtil.PrintInfo("\nSetting cryo-EM density file names...")
1012
1013 for Index in range(0, InfilesNamesCount):
1014 Infile = OptionsInfo["InfilesNames"][Index]
1015
1016 EMDBID = RetrieveEMDBID(Infile)
1017 if EMDBID is None:
1018 MiscUtil.PrintError("Failed to retrieve EMDB ID from input file %s to automatically set density map file name. Use option \"-d, --densityMapFiles \" to specify density map file name and try again." % Infile)
1019
1020 DensityMapFile = None
1021 MapFileRoot = "emd_%s" % EMDBID
1022 MapFile1 = "%s.map.gz" % MapFileRoot
1023 MapFile2 = "%s.map" % MapFileRoot
1024 if os.path.exists(MapFile1):
1025 DensityMapFile = MapFile1
1026 elif os.path.exists(MapFile2):
1027 DensityMapFile = MapFile2
1028 else:
1029 MiscUtil.PrintError("Density map files %s or %s don't exist. Use option \"-d, --densityMapFiles \" to specify density map file name and try again" % (MapFile1, MapFile2))
1030
1031 MiscUtil.PrintInfo("Setting density map file name as %s for input file %s..." % (DensityMapFile, Infile))
1032 OptionsInfo["DensityMapFilesNames"].append(DensityMapFile)
1033
1034 def RetrieveRecommededContourLevel(Infile):
1035 """Retrieve recommened contour level."""
1036
1037 if Infile in OptionsInfo["InfilesRecommededContourLevels"]:
1038 RecommendedContourLevel = OptionsInfo["InfilesRecommededContourLevels"][Infile]
1039 return RecommendedContourLevel
1040
1041 RecommendedContourLevel = None
1042 EMDBID = RetrieveEMDBID(Infile)
1043 if EMDBID is None:
1044 MiscUtil.PrintWarning("Failed to retrieve EMDB ID from input file %s to detect local header file already downloaded from EMDB server..." % Infile)
1045 OptionsInfo["InfilesRecommededContourLevels"][Infile] = RecommendedContourLevel
1046 return RecommendedContourLevel
1047
1048 MetadataHeaderFile = "emd-%s.xml" % (EMDBID)
1049 if not os.path.exists(MetadataHeaderFile):
1050 MiscUtil.PrintWarning("Failed to find a local header file, %s, for EMDB ID %s..." % (MetadataHeaderFile, EMDBID))
1051 OptionsInfo["InfilesRecommededContourLevels"][Infile] = RecommendedContourLevel
1052 return RecommendedContourLevel
1053
1054 MiscUtil.PrintInfo("\nRetrieving recommeded contour level from header file, %s, for input file, %s..." % (MetadataHeaderFile, Infile))
1055
1056 ContourLevel = None
1057 Source = None
1058 XMLTree = ElementTree.parse(MetadataHeaderFile)
1059 XMLRoot = XMLTree.getroot()
1060
1061 MapElement = XMLTree.find("map")
1062 if MapElement is not None:
1063 ContourLevelElement = MapElement.find("contourLevel")
1064 if ContourLevelElement is not None:
1065 ContourLevel = ContourLevelElement.text
1066 Source = ContourLevelElement.get("source")
1067
1068 if ContourLevel is not None:
1069 if Source is None:
1070 Source = "NA"
1071 MiscUtil.PrintInfo("Retrieved recommended (Source: %s) contour level %s..." % (Source, ContourLevel))
1072 RecommendedContourLevel = ContourLevel
1073
1074 OptionsInfo["InfilesRecommededContourLevels"][Infile] = RecommendedContourLevel
1075
1076 return RecommendedContourLevel
1077
1078 def RetrieveEMDBID(Infile):
1079 """Retrieve EMDB ID from input file."""
1080
1081 if Infile in OptionsInfo["InfilesEMDBIDs"]:
1082 EMDBID = OptionsInfo["InfilesEMDBIDs"][Infile]
1083 return EMDBID
1084
1085 EMDBID = None
1086 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
1087
1088 if re.match("^pdb$", FileExt, re.I):
1089 EMDBID = RetriveEMDBIDFromPDBFile(Infile)
1090 elif re.match("^cif$", FileExt, re.I):
1091 EMDBID = RetriveEMDBIDFromCIFFile(Infile)
1092 else:
1093 EMDBID = None
1094
1095 OptionsInfo["InfilesEMDBIDs"][Infile] = EMDBID
1096
1097 return EMDBID
1098
1099 def RetriveEMDBIDFromPDBFile(Infile):
1100 """Retrieve EMDB ID from PDB file."""
1101
1102 EMDBID = None
1103 InfileFH = open(Infile, "r")
1104 if InfileFH is None:
1105 MiscUtil.PrintError("Couldn't open input file: %s.\n" % (Infile))
1106
1107 MiscUtil.PrintInfo("\nRetrieving EMDB ID from input file %s..." % Infile)
1108
1109 EMDBID = None
1110 for Line in InfileFH:
1111 Line = Line.rstrip()
1112 if re.match("^REMARK", Line, re.I):
1113 if re.search("DB: EMDB", Line, re.I):
1114 for Word in Line.split(" "):
1115 # Retrieve string with EMD-
1116 if re.search("EMD-", Word, re.I):
1117 Word = Word.strip()
1118 EMDBID = re.sub("EMD-", "", Word)
1119 break
1120 break
1121 InfileFH.close()
1122
1123 return EMDBID
1124
1125 def RetriveEMDBIDFromCIFFile(Infile):
1126 """Retrieve EMDB ID from CIF file."""
1127
1128 InfileFH = open(Infile, "r")
1129 if InfileFH is None:
1130 MiscUtil.PrintError("Couldn't open input file: %s.\n" % (Infile))
1131
1132 MiscUtil.PrintInfo("\nRetrieving EMDB ID from input file %s..." % Infile)
1133
1134 EMDBID = None
1135 for Line in InfileFH:
1136 Line = Line.rstrip()
1137 if re.match("^EMDB EMD", Line, re.I):
1138 for Word in Line.split(" "):
1139 # Retrieve string with EMD-
1140 if re.search("EMD-", Word, re.I):
1141 Word = Word.strip()
1142 EMDBID = re.sub("EMD-", "", Word)
1143 break
1144 break
1145 InfileFH.close()
1146
1147 return EMDBID
1148
1149 def RetrieveInfilesInfo():
1150 """Retrieve information for input files."""
1151
1152 InfilesInfo = {}
1153
1154 InfilesInfo["InfilesNames"] = []
1155 InfilesInfo["InfilesRoots"] = []
1156 InfilesInfo["ChainsAndLigandsInfo"] = []
1157
1158 for Infile in OptionsInfo["InfilesNames"]:
1159 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
1160 InfileRoot = FileName
1161
1162 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
1163
1164 InfilesInfo["InfilesNames"].append(Infile)
1165 InfilesInfo["InfilesRoots"].append(InfileRoot)
1166 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
1167
1168 OptionsInfo["InfilesInfo"] = InfilesInfo
1169
1170 def RetrieveRefFileInfo():
1171 """Retrieve information for ref file."""
1172
1173 RefFileInfo = {}
1174 if not OptionsInfo["Align"]:
1175 OptionsInfo["RefFileInfo"] = RefFileInfo
1176 return
1177
1178 RefFile = OptionsInfo["RefFileName"]
1179
1180 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
1181 RefFileRoot = FileName
1182
1183 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
1184 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
1185 else:
1186 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
1187 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
1188
1189 RefFileInfo["RefFileName"] = RefFile
1190 RefFileInfo["RefFileRoot"] = RefFileRoot
1191 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
1192 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
1193
1194 OptionsInfo["RefFileInfo"] = RefFileInfo
1195
1196 def ProcessChainAndLigandIDs():
1197 """Process specified chain and ligand IDs for infiles."""
1198
1199 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"] = []
1200
1201 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
1202 MiscUtil.PrintInfo("\nProcessing specified chain and ligand IDs for input file %s..." % OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex])
1203
1204 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
1205 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], "-l, --ligandIDs", OptionsInfo["LigandIDs"])
1206 ProcessChainMeshesVolumesAndSurfacesOptions(SpecifiedChainsAndLigandsInfo)
1207 OptionsInfo["InfilesInfo"]["SpecifiedChainsAndLigandsInfo"].append(SpecifiedChainsAndLigandsInfo)
1208
1209 CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo)
1210
1211 def CheckPresenceOfValidLigandIDs(ChainsAndLigandsInfo, SpecifiedChainsAndLigandsInfo):
1212 """Check presence of valid ligand IDs."""
1213
1214 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
1215
1216 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1217 if len (SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]):
1218 MiscUtil.PrintInfo("Chain ID: %s; Specified LigandIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID])))
1219 else:
1220 MiscUtil.PrintInfo("Chain IDs: %s; Specified LigandIDs: None" % (ChainID))
1221 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))
1222
1223 def RetrieveFirstChainID(FileIndex):
1224 """Get first chain ID."""
1225
1226 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
1227
1228 FirstChainID = None
1229 if len(ChainsAndLigandsInfo["ChainIDs"]):
1230 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
1231
1232 return FirstChainID
1233
1234 def ProcessChainMeshesVolumesAndSurfacesOptions(SpecifiedChainsAndLigandsInfo):
1235 """Process options to create meshes and surfaces for chains."""
1236
1237 SpecifiedChainsAndLigandsInfo["VolumeChainComplex"] = {}
1238 SpecifiedChainsAndLigandsInfo["MeshChainComplex"] = {}
1239 SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"] = {}
1240
1241 SpecifiedChainsAndLigandsInfo["EnableVolumeChainComplex"] = {}
1242 SpecifiedChainsAndLigandsInfo["EnableMeshChainComplex"] = {}
1243 SpecifiedChainsAndLigandsInfo["EnableSurfaceChainComplex"] = {}
1244
1245 SpecifiedChainsAndLigandsInfo["EnableChainComplexGroup"] = {}
1246 SpecifiedChainsAndLigandsInfo["EnableChainAloneGroup"] = {}
1247
1248 for ChainID in SpecifiedChainsAndLigandsInfo["ChainIDs"]:
1249 LigandsPresent = True if len(SpecifiedChainsAndLigandsInfo["LigandIDs"][ChainID]) else False
1250
1251 # Create and enable mesh or volume in auto mode...
1252 if re.match("^auto$", OptionsInfo["MeshChainComplex"], re.I):
1253 MeshChainComplex = False if LigandsPresent else True
1254 EnableMeshChainComplex = False if LigandsPresent else True
1255 else:
1256 MeshChainComplex = True if re.match("^Yes$", OptionsInfo["MeshChainComplex"], re.I) else False
1257 EnableMeshChainComplex = True if re.match("^Yes$", OptionsInfo["MeshChainComplex"], re.I) else False
1258
1259 if re.match("^auto$", OptionsInfo["VolumeChainComplex"], re.I):
1260 VolumeChainComplex = False if LigandsPresent else True
1261 EnableVolumeChainComplex = False if LigandsPresent else True
1262 else:
1263 VolumeChainComplex = True if re.match("^Yes$", OptionsInfo["VolumeChainComplex"], re.I) else False
1264 EnableVolumeChainComplex = True if re.match("^Yes$", OptionsInfo["VolumeChainComplex"], re.I) else False
1265
1266 if MeshChainComplex and EnableMeshChainComplex:
1267 EnableVolumeChainComplex = False
1268
1269 # Create and enable surface in auto mode based on the status of mesh and volume...
1270 if re.match("^auto$", OptionsInfo["SurfaceChainComplex"], re.I):
1271 SurfaceChainComplex = False if LigandsPresent else True
1272 EnableSurfaceChainComplex = False if LigandsPresent else True
1273
1274 if MeshChainComplex or VolumeChainComplex:
1275 SurfaceChainComplex = False
1276 EnableSurfaceChainComplex = False
1277 else:
1278 SurfaceChainComplex = True if re.match("^Yes$", OptionsInfo["SurfaceChainComplex"], re.I) else False
1279 EnableSurfaceChainComplex = True if re.match("^Yes$", OptionsInfo["SurfaceChainComplex"], re.I) else False
1280
1281 if (MeshChainComplex and EnableMeshChainComplex) or (VolumeChainComplex or EnableVolumeChainComplex):
1282 EnableSurfaceChainComplex = False
1283
1284 if LigandsPresent:
1285 EnableChainComplexGroup = False
1286 EnableChainAloneGroup = True
1287 else:
1288 EnableChainComplexGroup = True
1289 EnableChainAloneGroup = False
1290
1291 SpecifiedChainsAndLigandsInfo["VolumeChainComplex"][ChainID] = VolumeChainComplex
1292 SpecifiedChainsAndLigandsInfo["MeshChainComplex"][ChainID] = MeshChainComplex
1293 SpecifiedChainsAndLigandsInfo["SurfaceChainComplex"][ChainID] = SurfaceChainComplex
1294
1295 SpecifiedChainsAndLigandsInfo["EnableVolumeChainComplex"][ChainID] = EnableVolumeChainComplex
1296 SpecifiedChainsAndLigandsInfo["EnableMeshChainComplex"][ChainID] = EnableMeshChainComplex
1297 SpecifiedChainsAndLigandsInfo["EnableSurfaceChainComplex"][ChainID] = EnableSurfaceChainComplex
1298
1299 SpecifiedChainsAndLigandsInfo["EnableChainComplexGroup"][ChainID] = EnableChainComplexGroup
1300 SpecifiedChainsAndLigandsInfo["EnableChainAloneGroup"][ChainID] = EnableChainAloneGroup
1301
1302 def ProcessChainSelections():
1303 """Process custom selections for chains."""
1304
1305 ChainSelectionsInfo = PyMOLUtil.ProcessChainSelectionsOptionsInfo("--selectionsChain", OptionsInfo["SelectionsChain"])
1306 OptionsInfo["ChainSelectionsInfo"] = ChainSelectionsInfo
1307
1308 ChainSelections = True if len(OptionsInfo["ChainSelectionsInfo"]["Names"]) else False
1309 OptionsInfo["ChainSelections"] = ChainSelections
1310
1311 def ProcessMeshLevel():
1312 """Process mesh level."""
1313
1314 MeshLevel = OptionsInfo["MeshLevel"]
1315
1316 if re.match("^auto$", MeshLevel, re.I):
1317 ProcessAutoMeshLevel()
1318 else:
1319 ProcessSpecifiedMeshLevel()
1320
1321 def ProcessAutoMeshLevel():
1322 """Process auto mesh level."""
1323
1324 OptionsInfo["MeshLevels"] = []
1325 InfilesNamesCount = len(OptionsInfo["InfilesNames"])
1326
1327 MiscUtil.PrintInfo("\nSetting mesh levels...")
1328
1329 for Index in range(0, InfilesNamesCount):
1330 Infile = OptionsInfo["InfilesNames"][Index]
1331
1332 RecommededContourLevel = RetrieveRecommededContourLevel(Infile)
1333 if RecommededContourLevel is None:
1334 MiscUtil.PrintWarning("Failed to retrieve recommended mesh contour level from header. It's being set to 1.0. Use \"--meshLevel\" option to specify a different contour mesh level.")
1335 MeshLevel = 1.0
1336 else:
1337 MeshLevel = float(RecommededContourLevel)
1338 OptionsInfo["MeshLevels"].append(MeshLevel)
1339
1340 def ProcessSpecifiedMeshLevel():
1341 """Process specified mesh level."""
1342
1343 MiscUtil.PrintInfo("\nProcessing mesh levels...")
1344
1345 OptionsInfo["MeshLevels"] = []
1346 InfilesNamesCount = len(OptionsInfo["InfilesNames"])
1347
1348 MeshLevels = re.sub(" ", "", OptionsInfo["MeshLevel"])
1349 if not MeshLevels:
1350 MiscUtil.PrintError("No valid value specified using \"--meshLevel\" option.")
1351
1352 MeshLevelWords = MeshLevels.split(",")
1353 MeshLevelWordsCount = len(MeshLevelWords)
1354
1355 if MeshLevelWordsCount != InfilesNamesCount:
1356 MiscUtil.PrintError("The number of comma delimited mesh levels, %d, specified using \"--meshLevel\" must be equal to the number of input files, %s, specified using \"-i, --infiles\" option." % (MeshLevelWordsCount, InfilesNamesCount))
1357
1358 for Index in range(0, InfilesNamesCount):
1359 Infile = OptionsInfo["InfilesNames"][Index]
1360 MeshLevel = MeshLevelWords[Index]
1361 if not MiscUtil.IsFloat(MeshLevel):
1362 MiscUtil.PrintError("The mesh level, %s, specified using \"--meshLevel\" for input file, %s, must be a float." % (MeshLevel, Infile))
1363
1364 MeshLevel = float(MeshLevel)
1365 OptionsInfo["MeshLevels"].append(MeshLevel)
1366
1367 def ProcessVolumeColorRamp():
1368 """Process volume color ramp."""
1369
1370 MiscUtil.PrintInfo("\nProcessing volume color ramp...")
1371
1372 ColorRamp = Options["--volumeColorRamp"]
1373 ColorRampName = None
1374 CreateColorRamp = False
1375 ColorRampContourLevel = None
1376 if re.match("^auto$", ColorRamp, re.I):
1377 FirstInfile = OptionsInfo["InfilesNames"][0]
1378 RecommededContourLevel = RetrieveRecommededContourLevel(FirstInfile)
1379 if RecommededContourLevel is None:
1380 ColorRampName = "default"
1381 MiscUtil.PrintWarning("Failed to retrieve recommended contour level from header file corresponding to input file, %s, to create a new ramp. Using PyMOL default volume color ramp." % (FirstInfile))
1382 else:
1383 ColorRampName = "CryoEMAuto"
1384 CreateColorRamp = True
1385 ColorRampContourLevel = float(RecommededContourLevel)
1386 MiscUtil.PrintInfo("\nSetting up a new volume color ramp, %s, at recommended contour level, %.2f, from input file, %s..." % (ColorRampName, ColorRampContourLevel, FirstInfile))
1387 else:
1388 ColorRampName = ColorRamp
1389
1390 OptionsInfo["VolumeColorRamp"] = ColorRamp
1391 OptionsInfo["VolumeColorRampName"] = ColorRampName
1392 OptionsInfo["VolumeColorRampCreate"] = CreateColorRamp
1393 OptionsInfo["VolumeColorRampContourLevel"] = ColorRampContourLevel
1394
1395 def ProcessOptions():
1396 """Process and validate command line arguments and options."""
1397
1398 MiscUtil.PrintInfo("Processing options...")
1399
1400 # Validate options...
1401 ValidateOptions()
1402
1403 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
1404 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
1405 OptionsInfo["AlignMode"] = Options["--alignMode"]
1406
1407 OptionsInfo["AllowEmptyObjects"] = True if re.match("^Yes$", Options["--allowEmptyObjects"], re.I) else False
1408
1409 OptionsInfo["BFactorChainCartoonPutty"] = True if re.match("^Yes$", Options["--BFactorChainCartoonPutty"], re.I) else False
1410 OptionsInfo["BFactorColorPalette"] = Options["--BFactorColorPalette"]
1411
1412 OptionsInfo["Infiles"] = Options["--infiles"]
1413 OptionsInfo["InfilesNames"] = Options["--infileNames"]
1414
1415 OptionsInfo["InfilesEMDBIDs"] = {}
1416 OptionsInfo["InfilesRecommededContourLevels"] = {}
1417
1418 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
1419 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1420 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
1421 else:
1422 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
1423
1424 OptionsInfo["IgnoreHydrogens"] = True if re.match("^Yes$", Options["--ignoreHydrogens"], re.I) else False
1425
1426 OptionsInfo["DensityMapFiles"] = Options["--densityMapFiles"]
1427 ProcessDensityMapFiles()
1428
1429 OptionsInfo["Overwrite"] = Options["--overwrite"]
1430 OptionsInfo["PMLOut"] = True if re.match("^Yes$", Options["--PMLOut"], re.I) else False
1431
1432 OptionsInfo["Outfile"] = Options["--outfile"]
1433 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
1434 OptionsInfo["PSEOut"] = False
1435 if re.match("^pml$", FileExt, re.I):
1436 OptionsInfo["PMLOutfile"] = OptionsInfo["Outfile"]
1437 OptionsInfo["PMEOutfile"] = re.sub(".pml$", ".pme", OptionsInfo["Outfile"])
1438 elif re.match("^pse$", FileExt, re.I):
1439 OptionsInfo["PSEOut"] = True
1440 OptionsInfo["PSEOutfile"] = OptionsInfo["Outfile"]
1441 OptionsInfo["PMLOutfile"] = re.sub(".pse$", ".pml", OptionsInfo["Outfile"])
1442 if os.path.exists(OptionsInfo["PMLOutfile"]) and (not OptionsInfo["Overwrite"]):
1443 MiscUtil.PrintError("The intermediate output file to be generated, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again." % OptionsInfo["PMLOutfile"] )
1444
1445 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
1446
1447 # Process mesh parameters...
1448 OptionsInfo["MeshCarveRadius"] = float(Options["--meshCarveRadius"])
1449 OptionsInfo["MeshComplex"] = True if re.match("^Yes$", Options["--meshComplex"], re.I) else False
1450 OptionsInfo["MeshChainComplex"] = Options["--meshChainComplex"]
1451
1452 OptionsInfo["MeshWidth"] = float(Options["--meshWidth"])
1453 OptionsInfo["MeshColor"] = Options["--meshColor"]
1454
1455 OptionsInfo["MeshLevel"] = Options["--meshLevel"]
1456 ProcessMeshLevel()
1457
1458 OptionsInfo["SurfaceComplex"] = True if re.match("^Yes$", Options["--surfaceComplex"], re.I) else False
1459 OptionsInfo["SurfaceChainComplex"] = Options["--surfaceChainComplex"]
1460 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
1461
1462 OptionsInfo["PocketContactsLigandColor"] = Options["--pocketContactsLigandColor"]
1463 OptionsInfo["PocketContactsLigandHydrophobicColor"] = Options["--pocketContactsLigandHydrophobicColor"]
1464 OptionsInfo["PocketContactsSolventColor"] = Options["--pocketContactsSolventColor"]
1465 OptionsInfo["PocketContactsInorganicColor"] = Options["--pocketContactsInorganicColor"]
1466
1467 OptionsInfo["PocketContactsCutoff"] = float(Options["--pocketContactsCutoff"])
1468 OptionsInfo["PocketDistanceCutoff"] = float(Options["--pocketDistanceCutoff"])
1469
1470 OptionsInfo["PocketLabelColor"] = Options["--pocketLabelColor"]
1471 OptionsInfo["PocketSurface"] = True if re.match("^Yes$", Options["--pocketSurface"], re.I) else False
1472
1473 OptionsInfo["SelectionsChain"] = Options["--selectionsChain"]
1474 OptionsInfo["SelectionsChainStyle"] = Options["--selectionsChainStyle"]
1475 ProcessChainSelections()
1476
1477 OptionsInfo["VolumeCarveRadius"] = float(Options["--volumeCarveRadius"])
1478 OptionsInfo["VolumeComplex"] = True if re.match("^Yes$", Options["--volumeComplex"], re.I) else False
1479 OptionsInfo["VolumeChainComplex"] = Options["--volumeChainComplex"]
1480
1481 ProcessVolumeColorRamp()
1482
1483 RetrieveInfilesInfo()
1484 RetrieveRefFileInfo()
1485
1486 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
1487 OptionsInfo["LigandIDs"] = Options["--ligandIDs"]
1488
1489 ProcessChainAndLigandIDs()
1490
1491 def RetrieveOptions():
1492 """Retrieve command line arguments and options."""
1493
1494 # Get options...
1495 global Options
1496 Options = docopt(_docoptUsage_)
1497
1498 # Set current working directory to the specified directory...
1499 WorkingDir = Options["--workingdir"]
1500 if WorkingDir:
1501 os.chdir(WorkingDir)
1502
1503 # Handle examples option...
1504 if "--examples" in Options and Options["--examples"]:
1505 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
1506 sys.exit(0)
1507
1508 def ValidateOptions():
1509 """Validate option values."""
1510
1511 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
1512 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
1513 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
1514
1515 MiscUtil.ValidateOptionTextValue("--allowEmptyObjects", Options["--allowEmptyObjects"], "yes no")
1516
1517 MiscUtil.ValidateOptionTextValue("--BFactorChainCartoonPutty", Options["--BFactorChainCartoonPutty"], "yes no")
1518
1519 # Expand infiles to handle presence of multiple input files...
1520 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
1521 if not len(InfileNames):
1522 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
1523
1524 # Validate file extensions...
1525 for Infile in InfileNames:
1526 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
1527 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb cif")
1528 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
1529 Options["--infileNames"] = InfileNames
1530
1531 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml pse")
1532 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
1533
1534 if re.match("^yes$", Options["--align"], re.I):
1535 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1536 AlignRefFile = Options["--alignRefFile"]
1537 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
1538 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb cif")
1539 MiscUtil.ValidateOptionsDistinctFileNames("--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"])
1540
1541 MiscUtil.ValidateOptionTextValue("--ignoreHydrogens", Options["--ignoreHydrogens"], "yes no")
1542
1543 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
1544 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
1545
1546 MiscUtil.ValidateOptionFloatValue("--meshCarveRadius", Options["--meshCarveRadius"], {">": 0.0})
1547 MiscUtil.ValidateOptionTextValue("--meshComplex", Options["--meshComplex"], "yes no")
1548 MiscUtil.ValidateOptionTextValue("--meshChainComplex", Options["--meshChainComplex"], "yes no auto")
1549 MiscUtil.ValidateOptionFloatValue("--meshWidth", Options["--meshWidth"], {">": 0.0})
1550
1551 MiscUtil.ValidateOptionTextValue("--PMLOut", Options["--PMLOut"], "yes no")
1552
1553 MiscUtil.ValidateOptionFloatValue("--pocketContactsCutoff", Options["--pocketContactsCutoff"], {">": 0.0})
1554 MiscUtil.ValidateOptionFloatValue("--pocketDistanceCutoff", Options["--pocketDistanceCutoff"], {">": 0.0})
1555 if (float(Options["--pocketContactsCutoff"]) > float(Options["--pocketDistanceCutoff"])):
1556 MiscUtil.PrintError("The value, %s, specified using option \"--pocketContactsCutoff\" must be less than value, %s, specified using \"-pocketDistanceCutoff\" option." % (Options["--pocketContactsCutoff"], Options["--pocketDistanceCutoff"]))
1557
1558 MiscUtil.ValidateOptionTextValue("--pocketSurface", Options["--pocketSurface"], "yes no")
1559
1560 MiscUtil.ValidateOptionTextValue("--surfaceComplex", Options["--surfaceComplex"], "yes no")
1561 MiscUtil.ValidateOptionTextValue("--surfaceChainComplex", Options["--surfaceChainComplex"], "yes no auto")
1562 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
1563
1564 MiscUtil.ValidateOptionFloatValue("--volumeCarveRadius", Options["--volumeCarveRadius"], {">": 0.0})
1565 MiscUtil.ValidateOptionTextValue("--volumeComplex", Options["--volumeComplex"], "yes no")
1566 MiscUtil.ValidateOptionTextValue("--volumeChainComplex", Options["--volumeChainComplex"], "yes no auto")
1567
1568 # Setup a usage string for docopt...
1569 _docoptUsage_ = """
1570 PyMOLVisualizeCryoEMDensity.py - Visualize cryo-EM density
1571
1572 Usage:
1573 PyMOLVisualizeCryoEMDensity.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
1574 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
1575 [--allowEmptyObjects <yes or no>] [--BFactorChainCartoonPutty <yes or no>]
1576 [--BFactorColorPalette <text> ] [--chainIDs <First, All or ID1,ID2...>]
1577 [--densityMapFiles <file1,file2,file3,...>]
1578 [--ignoreHydrogens <yes or no>] [--ligandIDs <Largest, All or ID1,ID2...>] [--labelFontID <number>]
1579 [--meshCarveRadius <number>] [--meshComplex <yes or no>]
1580 [--meshChainComplex <yes, no, or auto>] [--meshColor <text>]
1581 [--meshLevel <number>] [--meshWidth <number>] [--PMLOut <yes or no>]
1582 [--pocketContactsLigandColor <text>] [--pocketContactsLigandHydrophobicColor <text>]
1583 [--pocketContactsSolventColor <text>] [--pocketContactsCutoff <number>]
1584 [--pocketContactsInorganicColor <text>] [--pocketDistanceCutoff <number>]
1585 [--pocketLabelColor <text>] [--pocketSurface <yes or no>]
1586 [--selectionsChain <ObjectName,SelectionSpec,...>] [--selectionsChainStyle <DisplayStyle>]
1587 [--surfaceComplex <yes or no>] [--surfaceChainComplex <yes, no or auto>]
1588 [--surfaceTransparency <number>] [--volumeCarveRadius <number>]
1589 [--volumeComplex <yes or no>] [--volumeChainComplex <yes, no, or auto>]
1590 [--volumeColorRamp <text>] [--overwrite] [-w <dir>] -i <infile1,infile2,...> -o <outfile>
1591 PyMOLVisualizeCryoEMDensity.py -h | --help | -e | --examples
1592
1593 Description:
1594 Generate PyMOL visualization files for viewing electron microscopy (EM) or
1595 cryo-EM density around chains, ligands, and ligand binding pockets in
1596 macromolecules including proteins and nucleic acids.
1597
1598 The supported input file formats are: Macromolecule - PDB (.pdb) or CIF(.cif),
1599 Cryo-EM Density - Collaborative Computational Project Number 4 (CCP4) ( .map)
1600
1601 The supported output file formats are: PyMOL script file (.pml), PyMOL session
1602 file (.pse)
1603
1604 The cryo-EM density and header files along with PDB files may be downloaded
1605 from appropriate servers using DownloadPDBFiles.pl script.
1606
1607 A variety of PyMOL groups and objects may be created for visualization of
1608 cryo-EM density present in map files. These groups and objects correspond to
1609 maps, volumes, meshes, surfaces,chains, ligands, inorganics, ligand binding
1610 pockets, polar interactions, and pocket hydrophobic surfaces. A complete
1611 hierarchy of all possible PyMOL groups and objects is shown below:
1612
1613 <PDBFileRoot>
1614 .Complex
1615 .Complex
1616 .CryoEM
1617 .Map
1618 .Volume
1619 .Mesh
1620 .Surface
1621 .Chain<ID>
1622 .Complex
1623 .Complex
1624 .CryoEM
1625 .Volume
1626 .Mesh
1627 .Surface
1628 .Chain
1629 .Chain
1630 .BFactor
1631 .Selections
1632 .<Name1>
1633 .Selection
1634 .CryoEM
1635 .Volume
1636 .Mesh
1637 .Surface
1638 .<Name2>
1639 ... ... ..
1640 .Solvent
1641 .Inorganic
1642 .Ligand<ID>
1643 .Ligand
1644 .Ligand
1645 .CryoEM
1646 .Volume
1647 .Mesh
1648 .Surface
1649 .Pocket
1650 .Pocket
1651 .CryoEM
1652 .Volume
1653 .Mesh
1654 .Surface
1655 .Polar_Contacts
1656 .Hydrophobic_Contacts
1657 .Surface
1658 .Pocket_Solvent
1659 .Pocket_Solvent
1660 .CryoEM
1661 .Volume
1662 .Mesh
1663 .Surface
1664 .Polar_Contacts
1665 .Pocket_Inorganic
1666 .Pocket_Inorganic
1667 .CryoEM
1668 .Volume
1669 .Mesh
1670 .Surface
1671 .Polar_Contacts
1672 .Ligand<ID>
1673 .Ligand
1674 ... ... ...
1675 .Pocket
1676 ... ... ...
1677 .Pocket_Solvent
1678 ... ... ...
1679 .Pocket_Inorganic
1680 ... ... ...
1681 .Chain<ID>
1682 ... ... ...
1683 .Ligand<ID>
1684 ... ... ...
1685 .Ligand<ID>
1686 ... ... ...
1687 .Chain<ID>
1688 ... ... ...
1689 <PDBFileRoot>
1690 .Complex
1691 ... ... ...
1692 .Chain<ID>
1693 ... ... ...
1694 .Ligand<ID>
1695 ... ... ...
1696 .Ligand<ID>
1697 ... ... ...
1698 .Chain<ID>
1699 ... ... ...
1700
1701 The meshes, volumes, and surfaces are not created for complete complex in input
1702 files by default. A word to the wise: The creation of these mesh, volume, and surface
1703 objects may slow down loading of PML file and generation of PSE file, based on the
1704 size of input complex and map files. The generation of PSE file may also fail. In
1705 addition, you may want to interactively manipulate the contour level for meshes,
1706 volumes, and surfaces. The recommended value for contour level is automatically
1707 retrieved from header files available from EM density server. The recommended
1708 value may not always work.
1709
1710 Options:
1711 -a, --align <yes or no> [default: no]
1712 Align input files to a reference file before visualization along with
1713 available cryo-EM density map files.
1714 --alignMethod <align, cealign, super> [default: super]
1715 Alignment methodology to use for aligning input files to a reference
1716 file.
1717 --alignMode <FirstChain or Complex> [default: FirstChain]
1718 Portion of input and reference files to use for spatial alignment of
1719 input files against reference file. Possible values: FirstChain or
1720 Complex.
1721
1722 The FirstChain mode allows alignment of the first chain in each input
1723 file to the first chain in the reference file along with moving the rest
1724 of the complex to coordinate space of the reference file. The complete
1725 complex in each input file is aligned to the complete complex in reference
1726 file for the Complex mode.
1727 --alignRefFile <filename> [default: FirstInputFile]
1728 Reference input file name. The default is to use the first input file
1729 name specified using '-i, --infiles' option.
1730 --allowEmptyObjects <yes or no> [default: no]
1731 Allow creation of empty PyMOL objects corresponding to solvent and
1732 inorganic atom selections across chains, ligands, and ligand binding pockets
1733 in input file(s).
1734 -b, --BFactorChainCartoonPutty <yes or no> [default: yes]
1735 A cartoon putty around individual chains colored by B factors. The minimum
1736 and maximum values for B factors are automatically detected. These values
1737 indicate spread of cryo-EM density around atoms. The 'blue_white_red' color
1738 palette is deployed for coloring the cartoon putty.
1739 --BFactorColorPalette <text> [default: blue_white_red]
1740 Color palette for coloring cartoon putty around chains generated using B
1741 factors. Any valid PyMOL color palette name is allowed. No validation is
1742 performed. The complete list of valid color palette names is a available
1743 at: pymolwiki.org/index.php/Spectrum. Examples: blue_white_red,
1744 blue_white_magenta, blue_red, green_white_red, green_red.
1745 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
1746 List of chain IDs to use for visualizing cryo-EM density. Possible values:
1747 First, All, or a comma delimited list of chain IDs. The default is to use the
1748 chain ID for the first chain in each input file.
1749 -d, --densityMapFiles <file1,file2,file3,...> [default: auto]
1750 CryoEM density map file names. The EMDB ID is retrieved from PDB and CIF
1751 file to set the cryo-EM density file name during automatic detection of
1752 density files. The format of the file name is as follows:
1753
1754 emd_<EMDBID>.map.gz or emd_<EMDBID>.map
1755
1756 The density files must be present in the working directory.
1757 -e, --examples
1758 Print examples.
1759 -h, --help
1760 Print this help message.
1761 -i, --infiles <infile1,infile2,infile3...>
1762 Input file names.
1763 --ignoreHydrogens <yes or no> [default: yes]
1764 Ignore hydrogens for ligand and pocket views.
1765 -l, --ligandIDs <Largest, All or ID1,ID2...> [default: Largest]
1766 List of ligand IDs present in chains for visualizing cryo-EM density across
1767 ligands and ligand binding pockets. Possible values: Largest, All, or a comma
1768 delimited list of ligand IDs. The default is to use the largest ligand present
1769 in all or specified chains in each input file.
1770
1771 Ligands are identified using organic selection operator available in PyMOL.
1772 It'll also identify buffer molecules as ligands. The largest ligand contains
1773 the highest number of heavy atoms.
1774 --labelFontID <number> [default: 7]
1775 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
1776 The specified value must be a valid PyMOL font ID. No validation is
1777 performed. The complete lists of valid font IDs is available at:
1778 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
1779 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
1780 --meshCarveRadius <number> [default: 1.6]
1781 Radius in Angstroms around atoms for including cryo-EM density.
1782 --meshComplex <yes or no> [default: no]
1783 Create meshes for complete complex in each input file using corresponding
1784 density map file.
1785 --meshChainComplex <yes, no, or auto> [default: auto]
1786 Create meshes for individual chain complex in each input file using
1787 corresponding density map file. By default, the meshes are automatically
1788 created for chain complexes without any ligands.
1789 --meshColor <text> [default: blue]
1790 Line color for meshes corresponding to density maps.. The specified value
1791 must be valid color. No validation is performed.
1792 --meshLevel <number1,number2,...> [default: auto]
1793 Comma delimited list of contour levels in sigma units for generating meshes
1794 for each input file using corresponding density map file. The default is to
1795 automatically retrieve the recommended contour levels for each input
1796 file. The header file emd-<EMDBID>.xml corresponding to an input file
1797 must be present in the working directory to automatically retrieve
1798 recommended value for mesh contour level. Otherwise, the default contour
1799 level is set to 1.
1800
1801 You may want to interactively manipulate the contour level for meshes and
1802 surfaces. The default recommended value may not always work.
1803 --meshWidth <number> [default: 0.5]
1804 Line width for mesh lines corresponding to density maps.
1805 -o, --outfile <outfile>
1806 Output file name.
1807 -p, --PMLOut <yes or no> [default: yes]
1808 Save PML file during generation of PSE file.
1809 --pocketContactsLigandColor <text> [default: orange]
1810 Color for drawing polar contacts between ligand and pocket residues.
1811 The specified value must be valid color. No validation is performed.
1812 --pocketContactsLigandHydrophobicColor <text> [default: purpleblue]
1813 Color for drawing hydrophobic contacts between ligand and pocket residues.
1814 The specified value must be valid color. No validation is performed. The
1815 hydrophobic contacts are shown between pairs of carbon atoms not
1816 connected to hydrogen bond donor or acceptors atoms as identified
1817 by PyMOL.
1818 --pocketContactsSolventColor <text> [default: marine]
1819 Color for drawing polar contacts between solvent and pocket residues.
1820 The specified value must be valid color. No validation is performed.
1821 --pocketContactsInorganicColor <text> [default: deepsalmon]
1822 Color for drawing polar contacts between inorganic and pocket residues.
1823 The specified value must be valid color. No validation is performed.
1824 --pocketContactsCutoff <number> [default: 4.0]
1825 Distance in Angstroms for identifying polar and hyrdophobic contacts
1826 between atoms in pocket residues and ligands.
1827 --pocketDistanceCutoff <number> [default: 5.0]
1828 Distance in Angstroms for identifying pocket residues around ligands.
1829 --pocketLabelColor <text> [default: magenta]
1830 Color for drawing residue or atom level labels for a pocket. The specified
1831 value must be valid color. No validation is performed.
1832 --pocketSurface <yes or no> [default: yes]
1833 Hydrophobic surface around pocket. The pocket surface is colored by
1834 hydrophobicity. It is only valid for proteins. The color of amino acids is
1835 set using the Eisenberg hydrophobicity scale. The color varies from red
1836 to white, red being the most hydrophobic amino acid.
1837 --selectionsChain <ObjectName,SelectionSpec,...> [default: None]
1838 Custom selections for chains. It is a pairwise list of comma delimited values
1839 corresponding to PyMOL object names and selection specifications. The
1840 selection specification must be a valid PyMOL specification. No validation is
1841 performed.
1842
1843 The PyMOL objects are created for each chain corresponding to the
1844 specified selections. The display style for PyMOL objects is set using
1845 value of '--selectionsChainStyle' option.
1846
1847 The specified selection specification is automatically appended to appropriate
1848 chain specification before creating PyMOL objects.
1849
1850 For example, the following specification for '--selectionsChain' option will
1851 generate PyMOL objects for chains containing Cysteines and Serines:
1852
1853 Cysteines,resn CYS,Serines,resn SER
1854
1855 --selectionsChainStyle <DisplayStyle> [default: sticks]
1856 Display style for PyMOL objects created for '--selectionsChain' option. It
1857 must be a valid PyMOL display style. No validation is performed.
1858 --surfaceComplex <yes or no> [default: no]
1859 Create surfaces for complete complex in input file(s) corresponding to density
1860 map.
1861 --surfaceChainComplex <yes, no or auto> [default: auto]
1862 Create surfaces for individual chain complexes in each input file using corresponding
1863 density map file. By default, the surfaces are automatically created for chain complexes
1864 without any ligands.
1865 --surfaceTransparency <number> [default: 0.25]
1866 Surface transparency for molecular and cryo-EM density surfaces.
1867 --overwrite
1868 Overwrite existing files.
1869 --volumeCarveRadius <number> [default: 1.6]
1870 Radius in Angstroms around atoms for including cryo-EM density.
1871 --volumeComplex <yes or no> [default: no]
1872 Create volumes for complete complex in each input file using corresponding density
1873 map file.
1874 --volumeChainComplex <yes, no, or auto> [default: auto]
1875 Create volumes for individual chain complex in each input file using corresponding
1876 density map file. By default, the volumes are automatically created for chain
1877 complexes without any ligands.
1878 --volumeColorRamp <text> [default: auto]
1879 Name of a volume color ramp for density map files. The specified value must
1880 be a valid name. No validation is performed. The following volume color ramps
1881 are currently available in PyMOL: default, 2fofc, fofc, rainbow, and rainbow2.
1882
1883 The default is to automatically create a new volume color ramp for the first
1884 input file using recommended contour level with an offset of 0.3 around this value.
1885 The header file emd-<EMDBID>.xml must be present in the working directory to
1886 automatically retrieve recommended contour level and generate a volume color ramp.
1887 Otherwise, PyMOL default volume color ramp is employed to color volumes.
1888
1889 The volume color ramp automatically created for the first input file is used for all
1890 other input files.
1891 -w, --workingdir <dir>
1892 Location of working directory which defaults to the current directory.
1893
1894 Examples:
1895 To download structure and cryo-EM data for 5K12, 5UMD, 5W81, and 5UAK
1896 before running the following examples, type:
1897
1898 % DownloadPDBFiles.pl --DensityMap yes 5K12,5UMD,5W81,5UAK
1899
1900 To visualize cryo-EM density at recommended contour level for the first
1901 chain complex in a PDB file using corresponding density map and header
1902 file, and generate a PML file type:
1903
1904 % PyMOLVisualizeCryoEMDensity.py -i 5K12.pdb -o 5K12.pml
1905
1906 To visualize cryo-EM density at recommended contour level for the first
1907 chain complex in a PDB file and highlighting densities for all cysteines and
1908 serines using corresponding density map and header file, and generate
1909 a PML file type:
1910
1911 % PyMOLVisualizeCryoEMDensity.py -i 5K12.pdb -o 5K12.pml
1912 --selectionsChain "Csysteines,resn cys,Serines,resn ser"
1913
1914 To visualize electron density for the largest ligand in chain K, and ligand
1915 binding pocket to highlight ligand interactions with pockect residues,
1916 solvents and inorganics, in a PDB and using corresponding map files, and
1917 generate a PML file, type:
1918
1919 % PyMOLVisualizeCryoEMDensity.py -c K -i 5UMD.cif -o 5UMD.pml
1920
1921 To visualize cryo-EM density for all chains along with any solvents in a
1922 PDB file and using corresponding map files, and generate a PML file, type:
1923
1924 % PyMOLVisualizeCryoEMDensity.py -c all -i 5K12.pdb -o 5K12.pml
1925
1926 To visualize cryo-EM density at a specific contour level for the first chain
1927 complex along with volume and surface in a PDB file using corresponding
1928 to a specific density map file, and generate a PML file, type:
1929
1930 % PyMOLVisualizeCryoEMDensity.py -d emd_8194.map.gz --meshLevel 1.0
1931 --surfaceChainComplex yes --volumeChainComplex yes -i 5K12.pdb
1932 -o 5K12.pml
1933
1934 To align and visualize cryo-EM density at recommended contour levels for the
1935 largest ligand in the first chain along with pockets or the first chain complex
1936 in input files using corresponding maps and header files, type:
1937
1938 % PyMOLVisualizeCryoEMDensity.py -a yes -i "5W81.pdb,5UAK.pdb"
1939 -o SampleOut.pml
1940
1941 To align and visualize cryo-EM density at recommended contour levels for all
1942 chains and ligands in input files using specified density files, type:
1943 in input files using corresponding maps and header files, type:
1944
1945 % PyMOLVisualizeCryoEMDensity.py -a yes -i "5W81.pdb,5UAK.pdb"
1946 -o SampleOut.pml -c all -l all -d "emd_8782.map.gz,emd_8516.map.gz"
1947
1948 Author:
1949 Manish Sud(msud@san.rr.com)
1950
1951 See also:
1952 DownloadPDBFiles.pl, PyMOLVisualizeCavities.py,
1953 PyMOLVisualizeElectronDensity.py, PyMOLVisualizeInterfaces.py,
1954 PyMOLVisualizeMacromolecules.py, PyMOLVisualizeSurfaceAndBuriedResidues.py
1955
1956 Copyright:
1957 Copyright (C) 2024 Manish Sud. All rights reserved.
1958
1959 The functionality available in this script is implemented using PyMOL, a
1960 molecular visualization system on an open source foundation originally
1961 developed by Warren DeLano.
1962
1963 This file is part of MayaChemTools.
1964
1965 MayaChemTools is free software; you can redistribute it and/or modify it under
1966 the terms of the GNU Lesser General Public License as published by the Free
1967 Software Foundation; either version 3 of the License, or (at your option) any
1968 later version.
1969
1970 """
1971
1972 if __name__ == "__main__":
1973 main()
