1 #!/bin/env python
2 #
3 # File: PyMOLVisualizeFpockets.py
4 # Author: Manish Sud <msud@san.rr.com>
5 #
6 # Author: Manish Sud
7 #
8 # Collaborators: Joann Prescott-Roy and Pat Walters
9 #
10 # Copyright (C) 2025 Manish Sud. All rights reserved.
11 #
12 # The functionality available in this script is implemented using PyMOL, a
13 # molecular visualization system on an open source foundation originally
14 # developed by Warren DeLano.
15 #
16 # This file is part of MayaChemTools.
17 #
18 # MayaChemTools is free software; you can redistribute it and/or modify it under
19 # the terms of the GNU Lesser General Public License as published by the Free
20 # Software Foundation; either version 3 of the License, or (at your option) any
21 # later version.
22 #
23 # MayaChemTools is distributed in the hope that it will be useful, but without
24 # any warranty; without even the implied warranty of merchantability of fitness
25 # for a particular purpose. See the GNU Lesser General Public License for more
26 # details.
27 #
28 # You should have received a copy of the GNU Lesser General Public License
29 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
30 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
31 # Boston, MA, 02111-1307, USA.
32 #
33 #
34
35 from __future__ import print_function
36
37 # Add local python path to the global path and import standard library modules...
38 import os
39 import sys; sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "..", "lib", "Python"))
40 import time
41 import re
42 import glob
43 import shutil
44
45 # PyMOL imports...
46 try:
47 import pymol
48 # Finish launching PyMOL in a command line mode for batch processing (-c)
49 # along with the following options: disable loading of pymolrc and plugins (-k);
50 # suppress start up messages (-q)
51 pymol.finish_launching(['pymol', '-ckq'])
52 except ImportError as ErrMsg:
53 sys.stderr.write("\nFailed to import PyMOL module/package: %s\n" % ErrMsg)
54 sys.stderr.write("Check/update your PyMOL environment and try again.\n\n")
55 sys.exit(1)
56
57 # MayaChemTools imports...
58 try:
59 from docopt import docopt
60 import MiscUtil
61 import PyMOLUtil
62 except ImportError as ErrMsg:
63 sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg)
64 sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n")
65 sys.exit(1)
66
67 ScriptName = os.path.basename(sys.argv[0])
68 Options = {}
69 OptionsInfo = {}
70
71 def main():
72 """Start execution of the script"""
73
74 MiscUtil.PrintInfo("\n%s (PyMOL v%s; MayaChemTools v%s; %s): Starting...\n" % (ScriptName, pymol.cmd.get_version()[0], MiscUtil.GetMayaChemToolsVersion(), time.asctime()))
75
76 (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
77
78 # Retrieve command line arguments and options...
79 RetrieveOptions()
80
81 # Process and validate command line arguments and options...
82 ProcessOptions()
83
84 # Perform actions required by the script...
85 GenerateFpocketsVisualization()
86
87 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
88 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
89
90 def GenerateFpocketsVisualization():
91 """Generate fpockets visualization."""
92
93 Outfile = OptionsInfo["PMLOutfilePath"]
94 OutFH = open(Outfile, "w")
95 if OutFH is None:
96 MiscUtil.PrintError("Failed to open output fie %s " % Outfile)
97
98 MiscUtil.PrintInfo("\nGenerating file %s..." % Outfile)
99
100 # Setup header...
101 WritePMLHeader(OutFH, ScriptName)
102 WritePyMOLParameters(OutFH)
103
104 if OptionsInfo["Align"]:
105 WriteAlignReference(OutFH)
106
107 # Setup view for each input file...
108 FirstComplex = True
109 FirstComplexFirstChainName = None
110 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
111 # Setup PyMOL object names...
112 PyMOLObjectNames = SetupPyMOLObjectNames(FileIndex)
113
114 # Setup complex view...
115 WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex)
116
117 # Setup chain and pocket views...
118 SpecifiedChainsAndPocketsInfo = OptionsInfo["FpocketInfilesInfo"]["SpecifiedChainsAndPocketsInfo"][FileIndex]
119 FirstChain = True
120 for ChainID in SpecifiedChainsAndPocketsInfo["ChainIDs"]:
121 if FirstComplex and FirstChain:
122 FirstComplexFirstChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
123
124 WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID)
125
126 # Setup fpocket views...
127 FirstPocket = True
128 PocketNum = 0
129 for PocketID in SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID]:
130 PocketNum += 1
131 WriteChainPocketView(OutFH, FileIndex, PyMOLObjectNames, ChainID, PocketID, PocketNum)
132
133 # Set up pocket level group...
134 Enable, Action = [False, "close"]
135 if FirstPocket:
136 FirstPocket = False
137 Enable, Action = [True, "open"]
138 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroup"], PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroupMembers"], Enable, Action)
139
140 # Setup Chain level group...
141 Enable, Action = [False, "close"]
142 if FirstChain:
143 FirstChain = False
144 Enable, Action = [True, "open"]
145 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"], Enable, Action)
146
147 # Set up complex level group...
148 Enable, Action = [False, "close"]
149 if FirstComplex:
150 FirstComplex = False
151 Enable, Action = [True, "open"]
152 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["PDBGroup"], PyMOLObjectNames["PDBGroupMembers"], Enable, Action)
153
154 if OptionsInfo["Align"]:
155 DeleteAlignReference(OutFH)
156
157 if FirstComplexFirstChainName is not None:
158 OutFH.write("""\ncmd.orient("%s", animate = -1)\n""" % FirstComplexFirstChainName)
159 else:
160 OutFH.write("""\ncmd.orient("visible", animate = -1)\n""")
161
162 OutFH.close()
163
164 CopyPDBFilesForPML()
165
166 def WritePMLHeader(OutFH, ScriptName):
167 """Write out PML header."""
168
169 HeaderInfo = PyMOLUtil.SetupPMLHeaderInfo(ScriptName)
170 OutFH.write("%s\n" % HeaderInfo)
171
172 def WritePyMOLParameters(OutFH):
173 """Write out PyMOL global parameters. """
174
175 PMLCmds = []
176 PMLCmds.append("""cmd.set("transparency", %.2f, "", 0)""" % (OptionsInfo["SurfaceTransparency"]))
177 PMLCmds.append("""cmd.set("label_font_id", %s)""" % (OptionsInfo["LabelFontID"]))
178 PML = "\n".join(PMLCmds)
179
180 OutFH.write("""\n""\n"Setting up PyMOL gobal parameters..."\n""\n""")
181 OutFH.write("%s\n" % PML)
182
183 def WriteAlignReference(OutFH):
184 """Setup object for alignment reference """
185
186 RefFileInfo = OptionsInfo["RefFileInfo"]
187 RefFile = RefFileInfo["RefFileName"]
188 RefName = RefFileInfo["PyMOLObjectName"]
189
190 PMLCmds = []
191 PMLCmds.append("""cmd.load("%s", "%s")""" % (RefFile, RefName))
192 PMLCmds.append("""cmd.hide("everything", "%s")""" % (RefName))
193 PMLCmds.append("""cmd.disable("%s")""" % (RefName))
194 PML = "\n".join(PMLCmds)
195
196 OutFH.write("""\n""\n"Loading %s and setting up view for align reference..."\n""\n""" % RefFile)
197 OutFH.write("%s\n" % PML)
198
199 def WriteAlignComplex(OutFH, FileIndex, FpocketComplexMode, PyMOLObjectNames):
200 """Setup alignment of complex to reference"""
201
202 RefFileInfo = OptionsInfo["RefFileInfo"]
203 RefName = RefFileInfo["PyMOLObjectName"]
204
205 if FpocketComplexMode:
206 ComplexName = PyMOLObjectNames["FpocketComplex"]
207 else:
208 ComplexName = PyMOLObjectNames["InitialComplex"]
209
210 if re.match("^FirstChain$", OptionsInfo["AlignMode"], re.I):
211 RefFirstChainID = RefFileInfo["ChainsAndLigandsInfo"]["ChainIDs"][0]
212 RefAlignSelection = "%s and chain %s" % (RefName, RefFirstChainID)
213
214 ComplexFirstChainID = RetrieveFirstChainID(FileIndex, FpocketComplexMode)
215 ComplexAlignSelection = "%s and chain %s" % (ComplexName, ComplexFirstChainID)
216 else:
217 RefAlignSelection = RefName
218 ComplexAlignSelection = ComplexName
219
220 PML = PyMOLUtil.SetupPMLForAlignment(OptionsInfo["AlignMethod"], RefAlignSelection, ComplexAlignSelection)
221 OutFH.write("""\n""\n"Aligning %s against reference %s ..."\n""\n""" % (ComplexAlignSelection, RefAlignSelection))
222 OutFH.write("%s\n" % PML)
223
224 def DeleteAlignReference(OutFH):
225 """Delete alignment reference object."""
226
227 RefName = OptionsInfo["RefFileInfo"]["PyMOLObjectName"]
228 OutFH.write("""\n""\n"Deleting alignment reference object %s..."\n""\n""" % RefName)
229 OutFH.write("""cmd.delete("%s")\n""" % RefName)
230
231 def WriteComplexView(OutFH, FileIndex, PyMOLObjectNames, FirstComplex):
232 """Write out PML for viewing polymer complex."""
233
234 # Setup initial complex...
235 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
236 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["InitialComplex"], Infile, True)
237 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
238 OutFH.write("%s\n" % PML)
239
240 if OptionsInfo["Align"]:
241 # No need to align initial complex on to itself...
242 FpocketComplexMode = False
243 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
244 WriteAlignComplex(OutFH, FileIndex, FpocketComplexMode, PyMOLObjectNames)
245
246 # Setup fpocket complex...
247 Infile = OptionsInfo["FpocketInfilesInfo"]["InfilesNames"][FileIndex]
248 PML = PyMOLUtil.SetupPMLForPolymerComplexView(PyMOLObjectNames["FpocketComplex"], Infile, True)
249
250 # Modify default complex view for fpocket complex...
251 PMLModify = SetupPMLModifyDefaultPolymerComplexView(PyMOLObjectNames["FpocketComplex"])
252
253 OutFH.write("""\n""\n"Loading %s and setting up view for complex..."\n""\n""" % Infile)
254 OutFH.write("%s\n%s\n" % (PML, PMLModify))
255
256 if OptionsInfo["Align"]:
257 # No need to align initial complex on to itself...
258 FpocketComplexMode = True
259 if not (re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I) and FirstComplex):
260 WriteAlignComplex(OutFH, FileIndex, FpocketComplexMode, PyMOLObjectNames)
261
262 # Setup complex group...
263 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["ComplexGroup"], PyMOLObjectNames["ComplexGroupMembers"], False, "close")
264
265 def WriteChainView(OutFH, FileIndex, PyMOLObjectNames, ChainID):
266 """Write out PML for viewing chain."""
267
268 OutFH.write("""\n""\n"Setting up views for chain %s..."\n""\n""" % ChainID)
269
270 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
271
272 # Setup chain complex group view...
273 WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
274
275 # Setup chain view...
276 WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID)
277
278 def WriteChainComplexViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
279 """Write chain complex views. """
280
281 # Setup chain complex...
282 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
283 PML = SetupPMLForFpocketChainComplexView(FileIndex, ChainComplexName, PyMOLObjectNames["FpocketComplex"], ChainID, True)
284
285 # Modify default complex view for fpocket chain complex...
286 PMLModify = SetupPMLModifyDefaultPolymerComplexView(ChainComplexName)
287 OutFH.write("%s\n%s\n" % (PML, PMLModify))
288
289 # Setup chain complex group...
290 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"], False, "close")
291
292 def WriteChainAloneViews(OutFH, FileIndex, PyMOLObjectNames, ChainID):
293 """Write individual chain views. """
294
295 ChainComplexName = PyMOLObjectNames["Chains"][ChainID]["ChainComplex"]
296
297 # Setup chain view...
298 ChainName = PyMOLObjectNames["Chains"][ChainID]["ChainAlone"]
299 PML = PyMOLUtil.SetupPMLForPolymerChainView(ChainName, ChainComplexName, True)
300 OutFH.write("\n%s\n" % PML)
301
302 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
303 # Setup a generic color surface...
304 PML = PyMOLUtil.SetupPMLForSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"], ChainName, Enable = False, Color = OptionsInfo["SurfaceColor"])
305 OutFH.write("\n%s\n" % PML)
306
307 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
308 # Setup surface colored by hydrophobicity...
309 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"], ChainName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
310 OutFH.write("\n%s\n" % PML)
311
312 # Setup surface colored by hyrdophobicity and charge...
313 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"], ChainName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = None)
314 OutFH.write("\n%s\n" % PML)
315
316 # Setup surface group...
317 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"], True, "open")
318
319 # Setup chain group...
320 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"], PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"], True, "close")
321
322 def WriteChainPocketView(OutFH, FileIndex, PyMOLObjectNames, ChainID, PocketID, PocketNum):
323 """Write out PML for viewing pocket in a chain."""
324
325 OutFH.write("""\n""\n"Setting up views for pocket %s in chain %s..."\n""\n""" % (PocketID, ChainID))
326
327 FpocketComplexName = PyMOLObjectNames["FpocketComplex"]
328
329 # Setup pocket...
330 PML = SetupPMLForFPocketView(PyMOLObjectNames["Pockets"][ChainID][PocketID]["Pocket"], FpocketComplexName, ChainID, PocketID, PocketNum, True)
331 OutFH.write("%s\n" % PML)
332
333 # Setup pocket residues...
334 ChainsAndPocketsInfo = OptionsInfo["FpocketInfilesInfo"]["ChainsAndPocketsInfo"][FileIndex]
335 PocketResNums = ChainsAndPocketsInfo["PocketResNums"][ChainID][PocketID]
336 PocketResiduesName = PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketResidues"]
337 PML = SetupPMLForFPocketResiduesView(PocketResiduesName, FpocketComplexName, ChainID, PocketID, PocketNum, PocketResNums, True)
338 OutFH.write("%s\n" % PML)
339
340 # Setup pocket surfaces and group...
341 if GetPocketContainsSurfaceStatus(FileIndex, ChainID, PocketID):
342 # Setup a generic color surface...
343 PML = PyMOLUtil.SetupPMLForSurfaceView(PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurface"], PocketResiduesName, Enable = False, Color = OptionsInfo["SurfaceColor"])
344 OutFH.write("\n%s\n" % PML)
345
346 if GetPocketSurfaceChainStatus(FileIndex, ChainID, PocketID):
347 # Setup surface colored by hydrophobicity...
348 PML = PyMOLUtil.SetupPMLForHydrophobicSurfaceView(PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketHydrophobicitySurface"], PocketResiduesName, ColorPalette = OptionsInfo["SurfaceColorPalette"], Enable = False)
349 OutFH.write("\n%s\n" % PML)
350
351 # Setup surface colored by hyrdophobicity and charge...
352 PML = PyMOLUtil.SetupPMLForHydrophobicAndChargeSurfaceView(PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketHydrophobicityChargeSurface"], PocketResiduesName, OptionsInfo["AtomTypesColorNames"]["HydrophobicAtomsColor"], OptionsInfo["AtomTypesColorNames"]["NegativelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["PositivelyChargedAtomsColor"], OptionsInfo["AtomTypesColorNames"]["OtherAtomsColor"], Enable = False, DisplayAs = None)
353 OutFH.write("\n%s\n" % PML)
354
355 # Setup surface group...
356 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurfaceGroup"], PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurfaceGroupMembers"], True, "open")
357
358 # Setup pocket group...
359 GenerateAndWritePMLForGroup(OutFH, PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroup"], PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroupMembers"], True, "open")
360
361 def SetupPMLForFpocketChainComplexView(FileIndex, Name, Selection, ChainName, Enable = True):
362 """Setup PML commands for creating a polymer chain complex view
363 including fockets for the chain."""
364
365 PMLCmds = []
366
367 # Include fpockets as spheres for the chain complex view...
368 ChainsAndPocketsInfo = OptionsInfo["FpocketInfilesInfo"]["ChainsAndPocketsInfo"][FileIndex]
369 PocketIDs = ChainsAndPocketsInfo["PocketIDs"][ChainName]
370
371 PMLCmds.append("""cmd.create("%s", "((%s and chain %s) or (%s and (resn STP and resi %s)))")""" % (Name, Selection, ChainName, Selection, "+".join(PocketIDs)))
372 PMLCmds.append("""cmd.hide("everything", "%s")""" % (Name))
373 PMLCmds.append("""cmd.show("cartoon", "%s")""" % (Name))
374 PMLCmds.append("""util.cba(33, "%s", _self = cmd)""" % (Name))
375 PMLCmds.append("""cmd.show("sticks", "(organic and (%s))")""" % (Name))
376
377 PMLCmds.append("""cmd.show("nonbonded", "(solvent and (%s))")""" % (Name))
378 PMLCmds.append("""cmd.show("nonbonded", "(inorganic and (%s))")""" % (Name))
379
380 PMLCmds.append("""cmd.show("lines", "%s")""" % (Name))
381
382 PMLCmds.append("""cmd.set_bond("valence", "1", "%s", quiet = 1)""" % (Name))
383 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable))
384
385 PML = "\n".join(PMLCmds)
386
387 return PML
388
389 def SetupPMLModifyDefaultPolymerComplexView(Name):
390 """Setup PML to modify default polymer complex view for fpocket. """
391
392 PMLCmds = []
393 PMLCmds.append("""cmd.hide("lines", "%s")""" % (Name))
394 PMLCmds.append("""cmd.show("lines", "(polymer and (%s))")""" % (Name))
395 PMLCmds.append("""cmd.show("lines", "(solvent and (%s))")""" % (Name))
396 PMLCmds.append("""cmd.show("spheres", "(inorganic and (%s))")""" % (Name))
397 PMLCmds.append("""cmd.set("sphere_scale", "%s", "(inorganic and (%s))")""" % (OptionsInfo["SphereScale"], Name))
398 PMLCmds.append("""cmd.set("sphere_transparency", "%s", "(inorganic and (%s))")""" % (OptionsInfo["SphereTransparency"], Name))
399
400 PML = "\n".join(PMLCmds)
401
402 return PML
403
404 def SetupPMLForFPocketView(FpocketName, FpocketComplexName, ChainID, PocketID, PocketNum, Enable = True):
405 """Setup PML to visualize fpocket spheres using fpocket complex."""
406
407 PMLCmds = []
408 PMLCmds.append("""cmd.create("%s", "(%s and (resn STP and resi %s))")""" % (FpocketName, FpocketComplexName, PocketID))
409 if PocketNum == 1:
410 # Skip color index of 1: It is set to black. Use pocket one color name...
411 PMLCmds.append("""cmd.color(%s, "%s")""" % (OptionsInfo["PocketNumOneColor"], FpocketName))
412 else:
413 PMLCmds.append("""cmd.color(%s, "%s")""" % (PocketNum, FpocketName))
414 PMLCmds.append("""cmd.show("spheres", "%s")""" % (FpocketName))
415 PMLCmds.append("""cmd.set("sphere_scale", "%s", "%s")""" % (OptionsInfo["SphereScale"], FpocketName))
416 PMLCmds.append("""cmd.set("sphere_transparency", "%s", "%s")""" % (OptionsInfo["SphereTransparency"], FpocketName))
417
418 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(FpocketName, Enable))
419
420 PML = "\n".join(PMLCmds)
421 return PML
422
423 def SetupPMLForFPocketResiduesView(Name, FpocketComplexName, ChainID, PocketID, PocketNum, PocketResNums, Enable = True):
424 """Setup PML to visualize fpocket residues."""
425
426 PMLCmds = []
427
428 PMLCmds.append("""cmd.create("%s", "(%s and (chain %s) and (resi %s))")""" % (Name, FpocketComplexName, ChainID, "+".join(PocketResNums)))
429 PMLCmds.append("""cmd.hide("everything", "%s")""" % (Name))
430
431 # Setup pocket residue labels...
432 if OptionsInfo["PocketLabel"]:
433 if OptionsInfo["ThreeLetterPocketLabelType"]:
434 LabelFormat = '''"%s-%s"%(resn,resi)'''
435 PMLCmds.append("""cmd.label("(name CA+C1*+C1' and (byres(%s)))", \'\'\'%s\'\'\')""" % (Name, LabelFormat))
436 else:
437 PMLCmds.append("""cmd.label("byca(%s)", "oneletter+resi")""" % (Name))
438
439 PocketColor = OptionsInfo["PocketNumOneColor"] if PocketNum == 1 else PocketNum
440
441 if OptionsInfo["PocketColorByPocketNum"]:
442 # Setup color of pocket residues...
443 PMLCmds.append(PyMOLUtil.SetupPMLForDeepColoring(Name, PocketColor))
444
445 # Setup color of pocket residue labels...
446 PMLCmds.append("""cmd.set("label_color", %s, "%s")""" % (PocketColor, Name))
447 else:
448 PMLCmds.append("""util.cbag("%s", _self = cmd)""" % (Name))
449
450
451 PMLCmds.append("""cmd.show("lines", "%s")""" % (Name))
452
453 PMLCmds.append(PyMOLUtil.SetupPMLForEnableDisable(Name, Enable))
454
455 PML = "\n".join(PMLCmds)
456 return PML
457
458 def GenerateAndWritePMLForGroup(OutFH, GroupName, GroupMembers, Enable = False, Action = "close"):
459 """Generate and write PML for group. """
460
461 PML = PyMOLUtil.SetupPMLForGroup(GroupName, GroupMembers, Enable, Action)
462 OutFH.write("""\n""\n"Setting up group %s..."\n""\n""" % GroupName)
463 OutFH.write("%s\n" % PML)
464
465 def WritePMLToCheckAndDeleteEmptyObjects(OutFH, ObjectName, ParentObjectName = None):
466 """Write PML to check and delete empty PyMOL objects. """
467
468 if ParentObjectName is None:
469 PML = """CheckAndDeleteEmptyObjects("%s")""" % (ObjectName)
470 else:
471 PML = """CheckAndDeleteEmptyObjects("%s", "%s")""" % (ObjectName, ParentObjectName)
472
473 OutFH.write("%s\n" % PML)
474
475 def SetupPyMOLObjectNames(FileIndex):
476 """Setup hierarchy of PyMOL groups and objects for pocket centric views of
477 chains and pockets present in input file.
478 """
479
480 PyMOLObjectNames = {}
481 PyMOLObjectNames["Chains"] = {}
482 PyMOLObjectNames["Pockets"] = {}
483
484 # Setup groups and objects for complex...
485 SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames)
486
487 # Setup groups and objects for chains using fpockets info...
488 SpecifiedChainsAndPocketsInfo = OptionsInfo["FpocketInfilesInfo"]["SpecifiedChainsAndPocketsInfo"][FileIndex]
489 for ChainID in SpecifiedChainsAndPocketsInfo["ChainIDs"]:
490 SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID)
491
492 # Setup groups and objects for pocket...
493 for PocketID in SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID]:
494 SetupPyMOLObjectNamesForPocket(FileIndex, PyMOLObjectNames, ChainID, PocketID)
495
496 return PyMOLObjectNames
497
498 def SetupPyMOLObjectNamesForComplex(FileIndex, PyMOLObjectNames):
499 """Setup groups and objects for complex. """
500
501 PDBFileRoot = OptionsInfo["InfilesInfo"]["InfilesRoots"][FileIndex]
502
503 PDBGroupName = "%s" % PDBFileRoot
504 PyMOLObjectNames["PDBGroup"] = PDBGroupName
505 PyMOLObjectNames["PDBGroupMembers"] = []
506
507 ComplexGroupName = "%s.Complex" % PyMOLObjectNames["PDBGroup"]
508 PyMOLObjectNames["ComplexGroup"] = ComplexGroupName
509 PyMOLObjectNames["ComplexGroupMembers"] = []
510
511 PyMOLObjectNames["PDBGroupMembers"].append(ComplexGroupName)
512
513 PyMOLObjectNames["InitialComplex"] = "%s.Initial_Complex" % ComplexGroupName
514 PyMOLObjectNames["FpocketComplex"] = "%s.Fpocket_Complex" % ComplexGroupName
515
516 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["InitialComplex"])
517 PyMOLObjectNames["ComplexGroupMembers"].append(PyMOLObjectNames["FpocketComplex"])
518
519 def SetupPyMOLObjectNamesForChain(FileIndex, PyMOLObjectNames, ChainID):
520 """Setup groups and objects for chain."""
521
522 PDBGroupName = PyMOLObjectNames["PDBGroup"]
523
524 PyMOLObjectNames["Chains"][ChainID] = {}
525 PyMOLObjectNames["Pockets"][ChainID] = {}
526
527 # Set up chain group and chain objects...
528 ChainGroupName = "%s.Chain%s" % (PDBGroupName, ChainID)
529 PyMOLObjectNames["Chains"][ChainID]["ChainGroup"] = ChainGroupName
530 PyMOLObjectNames["PDBGroupMembers"].append(ChainGroupName)
531 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"] = []
532
533 # Setup chain complex group and objects...
534 ChainComplexGroupName = "%s.Complex" % (ChainGroupName)
535 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroup"] = ChainComplexGroupName
536 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainComplexGroupName)
537
538 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"] = []
539
540 Name = "%s.Complex" % (ChainComplexGroupName)
541 PyMOLObjectNames["Chains"][ChainID]["ChainComplex"] = Name
542 PyMOLObjectNames["Chains"][ChainID]["ChainComplexGroupMembers"].append(Name)
543
544 # Setup up a group for individual chains...
545 ChainAloneGroupName = "%s.Chain" % (ChainGroupName)
546 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroup"] = ChainAloneGroupName
547 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainAloneGroupName)
548
549 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"] = []
550
551 Name = "%s.Chain" % (ChainAloneGroupName)
552 PyMOLObjectNames["Chains"][ChainID]["ChainAlone"] = Name
553 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(Name)
554
555 if GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
556 # Setup a surface group and add it to chain alone group...
557 SurfaceGroupName = "%s.Surface" % (ChainAloneGroupName)
558 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroup"] = SurfaceGroupName
559 PyMOLObjectNames["Chains"][ChainID]["ChainAloneGroupMembers"].append(SurfaceGroupName)
560
561 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"] = []
562
563 # Setup a generic color surface...
564 Name = "%s.Surface" % (SurfaceGroupName)
565 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurface"] = Name
566 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
567
568 if GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
569 # Setup hydrophobicity surface...
570 Name = "%s.Hydrophobicity" % (SurfaceGroupName)
571 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicSurface"] = Name
572 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
573
574 # Setup hydrophobicity and charge surface...
575 Name = "%s.Hydrophobicity_Charge" % (SurfaceGroupName)
576 PyMOLObjectNames["Chains"][ChainID]["ChainAloneHydrophobicChargeSurface"] = Name
577 PyMOLObjectNames["Chains"][ChainID]["ChainAloneSurfaceGroupMembers"].append(Name)
578
579 def SetupPyMOLObjectNamesForPocket(FileIndex, PyMOLObjectNames, ChainID, PocketID):
580 """Stetup groups and objects for pocket."""
581
582 PyMOLObjectNames["Pockets"][ChainID][PocketID] = {}
583
584 ChainGroupName = PyMOLObjectNames["Chains"][ChainID]["ChainGroup"]
585
586 # Setup a chain level pocket group...
587 ChainPocketGroupName = SetupChainPocketGroupName(FileIndex, ChainGroupName, ChainID, PocketID)
588
589 PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroup"] = ChainPocketGroupName
590 PyMOLObjectNames["Chains"][ChainID]["ChainGroupMembers"].append(ChainPocketGroupName)
591
592 PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroupMembers"] = []
593
594 # Setup fpocket...
595 Name = "%s.Fpocket" % (ChainPocketGroupName)
596 PyMOLObjectNames["Pockets"][ChainID][PocketID]["Pocket"] = Name
597 PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroupMembers"].append(Name)
598
599 # Setup fpocket residues...
600 Name = "%s.Residues" % (ChainPocketGroupName)
601 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketResidues"] = Name
602 PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroupMembers"].append(Name)
603
604 if GetPocketContainsSurfaceStatus(FileIndex, ChainID, PocketID):
605 # Setup a pocket surface group and add it to chain pocket group
606 SurfaceGroupName = "%s.Surface" % (ChainPocketGroupName)
607 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurfaceGroup"] = SurfaceGroupName
608 PyMOLObjectNames["Pockets"][ChainID][PocketID]["ChainPocketGroupMembers"].append(SurfaceGroupName)
609
610 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurfaceGroupMembers"] = []
611
612 # Setup a generic color surface...
613 Name = "%s.Surface" % (SurfaceGroupName)
614 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurface"] = Name
615 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurfaceGroupMembers"].append(Name)
616
617 if GetPocketSurfaceChainStatus(FileIndex, ChainID, PocketID):
618 # Surface colored by hydrophobicity...
619 Name = "%s.Hydrophobicity" % (SurfaceGroupName)
620 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketHydrophobicitySurface"] = Name
621 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurfaceGroupMembers"].append(Name)
622
623 # Surface colored by hydrophobicity and charge...
624 Name = "%s.Hydrophobicity_Charge" % (SurfaceGroupName)
625 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketHydrophobicityChargeSurface"] = Name
626 PyMOLObjectNames["Pockets"][ChainID][PocketID]["PocketSurfaceGroupMembers"].append(Name)
627
628 def SetupChainPocketGroupName(FileIndex, ChainGroupName, ChainID, PocketID):
629 """Setup pocket group PyMOL object name. """
630
631 ChainPocketGroupName = "%s.Fpocket%s" % (ChainGroupName, PocketID)
632
633 if not OptionsInfo["FpocketPropertiesAppend"]:
634 return ChainPocketGroupName
635
636 PocketPropertiesName = SetupFpocketPropertiesForGroupName(FileIndex, ChainGroupName, ChainID, PocketID)
637
638 ChainPocketGroupName = "%s_%s" % (ChainPocketGroupName, PocketPropertiesName)
639
640 return ChainPocketGroupName
641
642 def SetupFpocketPropertiesForGroupName(FileIndex, ChainGroupName, ChainID, PocketID):
643 """Setup fpocket properties for PyMOL group name. """
644
645 ChainsAndPocketsInfo = OptionsInfo["FpocketInfilesInfo"]["ChainsAndPocketsInfo"][FileIndex]
646
647 PocketScore = FormatFpocketPropertyForGroupName(ChainsAndPocketsInfo["PocketScore"][ChainID][PocketID])
648 DrugScore = FormatFpocketPropertyForGroupName(ChainsAndPocketsInfo["DrugScore"][ChainID][PocketID])
649 HydrophobicityScore = FormatFpocketPropertyForGroupName(ChainsAndPocketsInfo["HydrophobicityScore"][ChainID][PocketID])
650 PolarityScore = FormatFpocketPropertyForGroupName(ChainsAndPocketsInfo["PolarityScore"][ChainID][PocketID])
651 PocketVolume = FormatFpocketPropertyForGroupName(ChainsAndPocketsInfo["PocketVolume"][ChainID][PocketID])
652
653 PocketProperties = "S%s_D%s_V%s_H%s_P%s" % (PocketScore, DrugScore, PocketVolume, HydrophobicityScore, PolarityScore)
654
655 return PocketProperties
656
657 def FormatFpocketPropertyForGroupName(PocketProperty):
658 """Format fpocket property for PyMOL group name. """
659
660 if PocketProperty is None:
661 PocketProperty = "NA"
662 else:
663 PocketProperty = "%.2f" % float(PocketProperty)
664 PocketProperty = re.sub("\.", "p", PocketProperty)
665 PocketProperty = re.sub("^-", "neg", PocketProperty)
666
667 return PocketProperty
668
669 def GetChainAloneContainsSurfacesStatus(FileIndex, ChainID):
670 """Get status of surfaces present in chain alone object."""
671
672 # Always set up generic color surfaces...
673 return True
674
675 def GetChainAloneSurfaceChainStatus(FileIndex, ChainID):
676 """Get status of surfaces for chain alone object."""
677
678 return OptionsInfo["SurfaceChain"]
679
680 def GetPocketContainsSurfaceStatus(FileIndex, ChainID, PocketID):
681 """Get status of surfaces present in a pocket object."""
682
683 # Always set up generic color surfaces...
684 return True
685
686 def GetPocketSurfaceChainStatus(FileIndex, ChainID, PocketID):
687 """Get status of surfaces for pocket object."""
688
689 return OptionsInfo["PocketSurface"]
690
691 def CopyPDBFilesForPML():
692 """Copy appropriate PDB files for PyMOL to OutfilesDir """
693
694 OutfilesDir = OptionsInfo["OutfilesDir"]
695
696 MiscUtil.PrintInfo("\nCopying appropriate PDB files to directory %s..." % OutfilesDir)
697
698 # Copy input PDB files...
699 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
700 Infile = OptionsInfo["InfilesInfo"]["InfilesNames"][FileIndex]
701 NewInfilePath = os.path.join(OutfilesDir, Infile)
702
703 shutil.copyfile(Infile, NewInfilePath)
704
705 # Copy fpocket output PDB files...
706 for FileIndex in range(0, len(OptionsInfo["FpocketInfilesInfo"]["InfilesNames"])):
707 Infile = OptionsInfo["FpocketInfilesInfo"]["InfilesNames"][FileIndex]
708 InfilePath = OptionsInfo["FpocketInfilesInfo"]["InfilesPaths"][FileIndex]
709 NewInfilePath = os.path.join(OutfilesDir, Infile)
710
711 shutil.copyfile(InfilePath, NewInfilePath)
712
713 def RetrieveInfilesInfo():
714 """Retrieve information for input files."""
715
716 InfilesInfo = {}
717
718 InfilesInfo["InfilesNames"] = []
719 InfilesInfo["InfilesRoots"] = []
720 InfilesInfo["ChainsAndLigandsInfo"] = []
721
722 for Infile in OptionsInfo["InfilesNames"]:
723 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
724 InfileRoot = FileName
725
726 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
727
728 InfilesInfo["InfilesNames"].append(Infile)
729 InfilesInfo["InfilesRoots"].append(InfileRoot)
730 InfilesInfo["ChainsAndLigandsInfo"].append(ChainsAndLigandInfo)
731
732 OptionsInfo["InfilesInfo"] = InfilesInfo
733
734 def RetrieveRefFileInfo():
735 """Retrieve information for ref file."""
736
737 RefFileInfo = {}
738 if not OptionsInfo["Align"]:
739 OptionsInfo["RefFileInfo"] = RefFileInfo
740 return
741
742 RefFile = OptionsInfo["RefFileName"]
743
744 FileDir, FileName, FileExt = MiscUtil.ParseFileName(RefFile)
745 RefFileRoot = FileName
746
747 if re.match("^FirstInputFile$", OptionsInfo["AlignRefFile"], re.I):
748 ChainsAndLigandInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][0]
749 else:
750 MiscUtil.PrintInfo("\nRetrieving chain and ligand information for alignment reference file %s..." % RefFile)
751 ChainsAndLigandInfo = PyMOLUtil.GetChainsAndLigandsInfo(RefFile, RefFileRoot)
752
753 RefFileInfo["RefFileName"] = RefFile
754 RefFileInfo["RefFileRoot"] = RefFileRoot
755 RefFileInfo["PyMOLObjectName"] = "AlignRef_%s" % RefFileRoot
756 RefFileInfo["ChainsAndLigandsInfo"] = ChainsAndLigandInfo
757
758 OptionsInfo["RefFileInfo"] = RefFileInfo
759
760 def RetrieveFpocketResultFilesInfo():
761 """Check and retrieve information for Fpocket result files."""
762
763 FpocketInfilesInfo = {}
764
765 FpocketInfilesInfo["InfilesNames"] = []
766 FpocketInfilesInfo["InfilesRoots"] = []
767 FpocketInfilesInfo["InfilesPaths"] = []
768 FpocketInfilesInfo["InfilesDirs"] = []
769
770 FpocketInfilesInfo["InfilesPocketsDirs"] = []
771 FpocketInfilesInfo["InfilesPocketsPDBFilesCount"] = []
772
773 FpocketInfilesInfo["ChainsAndPocketsInfo"] = []
774
775 for Infile in OptionsInfo["InfilesNames"]:
776 MiscUtil.PrintInfo("\nRetrieving Fpocket result file information for input file %s..." % Infile)
777
778 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Infile)
779 InfileRoot = FileName
780
781 FpocketInfileDir = "%s_out" % InfileRoot
782 FpocketInfileRoot = "%s_out" % InfileRoot
783 FpocketInfileName = "%s.pdb" % FpocketInfileRoot
784 FpocketInfilePath = os.path.join(FpocketInfileDir, FpocketInfileName)
785
786 FpocketInfilePocketsDir = os.path.join(FpocketInfileDir, "pockets")
787
788 if not os.path.isdir(FpocketInfileDir):
789 MiscUtil.PrintError("Fpocket result file directory, %s, is missing for input PDB file, %s." % (FpocketInfileDir, Infile))
790
791 if not os.path.isfile(FpocketInfilePath):
792 MiscUtil.PrintError("Fpocket result PDB file, %s, is missing for input PDB file, %s." % (FpocketInfilePath, Infile))
793
794 if not os.path.isdir(FpocketInfilePocketsDir):
795 MiscUtil.PrintError("Fpocket pockets result file directory, %s, is missing for input PDB file, %s." % (FpocketInfilePocketsDir, Infile))
796
797 PocketsPDBFiles = glob.glob(os.path.join(FpocketInfilePocketsDir, "pocket*_atm.pdb"))
798 PocketsPDBFilesCount = len(PocketsPDBFiles)
799 if PocketsPDBFilesCount == 0:
800 MiscUtil.PrintError("Fpocket pockets result files missing in directory, %s, for input PDB file, %s." % (FpocketInfilePocketsDir, Infile))
801
802 # Retrieve chains and pockets...
803 ChainsAndPocketsInfo = GetFpocketChainsAndPocketsInfo(FpocketInfileRoot, FpocketInfilePath, FpocketInfileDir, FpocketInfilePocketsDir)
804
805 FpocketInfilesInfo["InfilesNames"].append(FpocketInfileName)
806 FpocketInfilesInfo["InfilesRoots"].append(FpocketInfileRoot)
807 FpocketInfilesInfo["InfilesPaths"].append(FpocketInfilePath)
808 FpocketInfilesInfo["InfilesDirs"].append(FpocketInfileDir)
809
810 FpocketInfilesInfo["InfilesPocketsDirs"].append(FpocketInfilePocketsDir)
811 FpocketInfilesInfo["InfilesPocketsPDBFilesCount"].append(PocketsPDBFilesCount)
812
813 FpocketInfilesInfo["ChainsAndPocketsInfo"].append(ChainsAndPocketsInfo)
814
815 MiscUtil.PrintInfo("PDB result file: %s..." % FpocketInfileName)
816 MiscUtil.PrintInfo("Total number of pockets: %s..." % ChainsAndPocketsInfo["NumOfPockets"])
817
818 MiscUtil.PrintInfo("Pocket Chain IDs: %s" % " ".join(ChainsAndPocketsInfo["ChainIDs"]))
819 for ChainID in ChainsAndPocketsInfo["ChainIDs"]:
820 MiscUtil.PrintInfo("Pocket Chain ID: %s; NumOfPockets: %s; PocketIDs: %s" % (ChainID, len(ChainsAndPocketsInfo["PocketIDs"][ChainID]), " ".join(ChainsAndPocketsInfo["PocketIDs"][ChainID])))
821
822 OptionsInfo["FpocketInfilesInfo"] = FpocketInfilesInfo
823
824 def GetFpocketChainsAndPocketsInfo(FpocketInfileRoot, FpocketInfilePath, FpocketInfileDir, FpocketInfilePocketsDir):
825 """Get chains and pockets information for Fpocket result files. """
826
827 ChainsAndPocketsInfo = {}
828 ChainsAndPocketsInfo["ChainIDs"] = []
829 ChainsAndPocketsInfo["PocketIDs"] = {}
830 ChainsAndPocketsInfo["PocketResNums"] = {}
831
832 ChainsAndPocketsInfo["DrugScore"] = {}
833 ChainsAndPocketsInfo["PocketScore"] = {}
834 ChainsAndPocketsInfo["HydrophobicityScore"] = {}
835 ChainsAndPocketsInfo["PolarityScore"] = {}
836 ChainsAndPocketsInfo["PocketVolume"] = {}
837
838 ChainsAndPocketsInfo["NumOfPockets"] = 0
839
840 # Retrieve chain IDs corresponding to main chain atoms...
841 ChainIDs = GetPolymerChainIDs(FpocketInfilePath, FpocketInfileRoot)
842
843 # Retrieve number of pockets and pocket IDs...
844 PocketIDs = GetPocketIDs(FpocketInfilePath, FpocketInfileRoot)
845 ChainsAndPocketsInfo["NumOfPockets"] = len(PocketIDs)
846
847 # Retrieve residue numbers for fpockets across the chains...
848 for PocketID in PocketIDs:
849 PocketAtomFile = os.path.join(FpocketInfilePocketsDir, "pocket%s_atm.pdb" % PocketID)
850
851 if not os.path.isfile(PocketAtomFile):
852 MiscUtil.PrintError("Fpocket result PDB file, %s, is missing for pocket ID, %s." % (PocketAtomFile, PocketID))
853
854 # Retrieve pocket properites for a pocket across chains...
855 PocketScore, DrugScore, HydrophobicityScore, PolarityScore, PocketVolume = GetPocketProperties(PocketAtomFile)
856
857 MolName = "pocket%s_atm" % PocketID
858 pymol.cmd.load(PocketAtomFile, MolName)
859 SelectionCmd = "(%s)" % MolName
860
861 pymol.stored.FpocketInfo = []
862 pymol.cmd.iterate(SelectionCmd, "pymol.stored.FpocketInfo.append([chain, resi, resn])")
863 pymol.cmd.delete(MolName)
864
865 for ChainID, ResNum, ResName in pymol.stored.FpocketInfo:
866 if ChainID not in ChainsAndPocketsInfo["ChainIDs"]:
867 ChainsAndPocketsInfo["PocketIDs"][ChainID] = []
868 ChainsAndPocketsInfo["PocketResNums"][ChainID] = {}
869
870 ChainsAndPocketsInfo["DrugScore"][ChainID] = {}
871 ChainsAndPocketsInfo["PocketScore"][ChainID] = {}
872 ChainsAndPocketsInfo["HydrophobicityScore"][ChainID] = {}
873 ChainsAndPocketsInfo["PolarityScore"][ChainID] = {}
874 ChainsAndPocketsInfo["PocketVolume"][ChainID] = {}
875
876 ChainsAndPocketsInfo["ChainIDs"].append(ChainID)
877
878 if PocketID not in ChainsAndPocketsInfo["PocketIDs"][ChainID]:
879 ChainsAndPocketsInfo["PocketResNums"][ChainID][PocketID] = []
880 ChainsAndPocketsInfo["PocketIDs"][ChainID].append(PocketID)
881
882 # Track pocket and drug score across chains...
883 ChainsAndPocketsInfo["DrugScore"][ChainID][PocketID] = DrugScore
884 ChainsAndPocketsInfo["PocketScore"][ChainID][PocketID] = PocketScore
885 ChainsAndPocketsInfo["HydrophobicityScore"][ChainID][PocketID] = HydrophobicityScore
886 ChainsAndPocketsInfo["PolarityScore"][ChainID][PocketID] = PolarityScore
887 ChainsAndPocketsInfo["PocketVolume"][ChainID][PocketID] = PocketVolume
888
889
890 if ResNum not in ChainsAndPocketsInfo["PocketResNums"][ChainID][PocketID]:
891 ChainsAndPocketsInfo["PocketResNums"][ChainID][PocketID].append(ResNum)
892
893 ChainsAndPocketsInfo["ChainIDs"] = sorted(ChainsAndPocketsInfo["ChainIDs"])
894
895 return ChainsAndPocketsInfo
896
897 def GetPolymerChainIDs(Infile, MolName):
898 """Get chain IDs for main chain excluding hetero atoms. """
899
900 pymol.cmd.load(Infile, MolName)
901 ChainIDs = PyMOLUtil.GetChains(MolName)
902
903 # Retrieve polymer chains...
904 SelectedChainIDs = []
905 for ChainID in ChainIDs:
906 AtomsCount = pymol.cmd.count_atoms("(%s and (chain %s) and (polymer) and (not hetatm))" % (MolName, ChainID))
907 if AtomsCount > 0:
908 SelectedChainIDs.append(ChainID)
909
910 pymol.cmd.delete(MolName)
911
912 return SelectedChainIDs
913
914 def GetPocketIDs(Infile, MolName):
915 """Get pocket IDs. """
916
917 # Fpockets are annonated in PDB file as STP residue name and unique residue
918 # numbers...
919 pymol.cmd.load(Infile, MolName)
920 SelectionCmd = "(%s and (resn STP) and hetatm)" % MolName
921
922 pymol.stored.FpocketIDsInfo = []
923 pymol.cmd.iterate(SelectionCmd, "pymol.stored.FpocketIDsInfo.append(resi)")
924 pymol.cmd.delete(MolName)
925
926 PocketIDs = []
927 for PocketID in pymol.stored.FpocketIDsInfo:
928 if PocketID not in PocketIDs:
929 PocketIDs.append(PocketID)
930
931 return PocketIDs
932
933 def ProcessChainAndPocketIDs():
934 """Process specified chain and pocket IDs for infiles."""
935
936 OptionsInfo["FpocketInfilesInfo"]["SpecifiedChainsAndPocketsInfo"] = []
937
938 for FileIndex in range(0, len(OptionsInfo["InfilesInfo"]["InfilesNames"])):
939 MiscUtil.PrintInfo("\nProcessing specified chain and Pocket IDs for input file %s..." % OptionsInfo["FpocketInfilesInfo"]["InfilesNames"][FileIndex])
940
941 ChainsAndPocketsInfo = OptionsInfo["FpocketInfilesInfo"]["ChainsAndPocketsInfo"][FileIndex]
942
943 SpecifiedChainsAndPocketsInfo = ProcessChainsAndPocketsOptionsInfo(ChainsAndPocketsInfo)
944 OptionsInfo["FpocketInfilesInfo"]["SpecifiedChainsAndPocketsInfo"].append(SpecifiedChainsAndPocketsInfo)
945
946 CheckPresenceOfValidPocketIDs(ChainsAndPocketsInfo, SpecifiedChainsAndPocketsInfo)
947
948 def GetPocketProperties(PocketAtomFile):
949 """Get pocket properites from the pocket PDB file. """
950
951 PocketScore, DrugScore, HydrophobicityScore, PolarityScore, PocketVolume = [None] * 5
952
953 PocketAtomFH = open(PocketAtomFile, "r")
954 if PocketAtomFH is None:
955 return (PocketScore, DrugScore, HydrophobicityScore, PolarityScore, PocketVolume)
956
957 for Line in PocketAtomFH:
958 Line = Line.rstrip()
959 if re.search("Pocket Score", Line, re.I):
960 LineWords = Line.split()
961 PocketScore = LineWords[-1]
962 elif re.search("Drug Score", Line, re.I):
963 LineWords = Line.split()
964 DrugScore = LineWords[-1]
965 elif re.search("Hydrophobicity Score", Line, re.I):
966 LineWords = Line.split()
967 HydrophobicityScore = LineWords[-1]
968 elif re.search("Polarity Score", Line, re.I):
969 LineWords = Line.split()
970 PolarityScore = LineWords[-1]
971 elif re.search("Pocket volume \(Monte Carlo\)", Line, re.I):
972 LineWords = Line.split()
973 PocketVolume = LineWords[-1]
974
975 if not re.match("^HEADER", Line, re.I):
976 break
977
978 PocketAtomFH.close()
979
980 return (PocketScore, DrugScore, HydrophobicityScore, PolarityScore, PocketVolume)
981
982 def ProcessChainsAndPocketsOptionsInfo(ChainsAndPocketsInfo):
983 """Process specified chain and pocket IDs using command line options."""
984
985 ChainIDs = OptionsInfo["ChainIDs"]
986 FpocketMode = OptionsInfo["FpocketMode"]
987 FpocketIDs = OptionsInfo["FpocketIDs"]
988
989 SpecifiedChainsAndPocketsInfo = {}
990 SpecifiedChainsAndPocketsInfo["ChainIDs"] = []
991 SpecifiedChainsAndPocketsInfo["PocketIDs"] = {}
992
993 ProcessChainsOptionInfo(ChainsAndPocketsInfo, SpecifiedChainsAndPocketsInfo)
994 ProcessPocketsOptionInfo(ChainsAndPocketsInfo, SpecifiedChainsAndPocketsInfo)
995
996 return SpecifiedChainsAndPocketsInfo
997
998 def ProcessChainsOptionInfo(ChainsAndPocketsInfo, SpecifiedChainsAndPocketsInfo):
999 """Process chain IDs"""
1000
1001 MiscUtil.PrintInfo("Processing chain IDs...")
1002
1003 ChainsOptionName = "-c, --chainIDs"
1004 ChainsOptionValue = OptionsInfo["ChainIDs"]
1005
1006 if re.match("^All$", ChainsOptionValue, re.I):
1007 SpecifiedChainsAndPocketsInfo["ChainIDs"] = ChainsAndPocketsInfo["ChainIDs"]
1008 return
1009 elif re.match("^(First|Auto)$", ChainsOptionValue, re.I):
1010 FirstChainID = ChainsAndPocketsInfo["ChainIDs"][0] if (len(ChainsAndPocketsInfo["ChainIDs"])) else None
1011 if FirstChainID is not None:
1012 SpecifiedChainsAndPocketsInfo["ChainIDs"].append(FirstChainID)
1013 return
1014
1015 ChainIDs = re.sub(" ", "", ChainsOptionValue)
1016 if not ChainIDs:
1017 MiscUtil.PrintError("No valid value specified using \"%s\" option." % ChainsOptionName)
1018
1019 ChainIDsList = ChainsAndPocketsInfo["ChainIDs"]
1020 SpecifiedChainIDsList = []
1021
1022 ChainIDsWords = ChainIDs.split(",")
1023 for ChainID in ChainIDsWords:
1024 if not ChainID in ChainIDsList:
1025 MiscUtil.PrintWarning("The chain ID, %s, specified using \"%s\" option is not valid. It'll be ignored. Valid chain IDs: %s" % (ChainID, ChainsOptionName, ", ".join(ChainIDsList)))
1026 continue
1027 if ChainID in SpecifiedChainIDsList:
1028 MiscUtil.PrintWarning("The chain ID, %s, has already been specified using \"%s\" option. It'll be ignored." % (ChainID, ChainsOptionName))
1029 continue
1030 SpecifiedChainIDsList.append(ChainID)
1031
1032 if not len(SpecifiedChainIDsList):
1033 MiscUtil.PrintError("No valid chain IDs \"%s\" specified using \"%s\" option." % (ChainsOptionValue, ChainsOptionName))
1034
1035 SpecifiedChainsAndPocketsInfo["ChainIDs"] = SpecifiedChainIDsList
1036
1037 def ProcessPocketsOptionInfo(ChainsAndPocketsInfo, SpecifiedChainsAndPocketsInfo):
1038 """Process pocket IDs"""
1039
1040 MiscUtil.PrintInfo("Processing pocket IDs...")
1041
1042 PocketsModeOptionName = "-f, --fpocketMode"
1043 PocketsModeOptionValue = OptionsInfo["FpocketMode"]
1044
1045 PocketsIDsOptionName = "--fpocketIDs"
1046 PocketsIDsOptionValue = OptionsInfo["FpocketIDs"]
1047
1048 # Intialize pocketIDs...
1049 for ChainID in SpecifiedChainsAndPocketsInfo["ChainIDs"]:
1050 SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID] = []
1051
1052 if re.match("^All$", PocketsModeOptionValue, re.I):
1053 for ChainID in SpecifiedChainsAndPocketsInfo["ChainIDs"]:
1054 SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID] = ChainsAndPocketsInfo["PocketIDs"][ChainID]
1055 return
1056 elif re.match("^TopN$", PocketsModeOptionValue, re.I):
1057 # Setup TopN pocket IDs for each chain...
1058 TopNPocketsCount = int(PocketsIDsOptionValue[0])
1059 for ChainID in SpecifiedChainsAndPocketsInfo["ChainIDs"]:
1060 TopNPocketsIDs = []
1061 NumOfPockets = len(ChainsAndPocketsInfo["PocketIDs"][ChainID])
1062
1063 if NumOfPockets:
1064 if TopNPocketsCount > NumOfPockets:
1065 TopNPocketsIDs = ChainsAndPocketsInfo["PocketIDs"][ChainID]
1066 else:
1067 TopNPocketsIDs = ChainsAndPocketsInfo["PocketIDs"][ChainID][0 : TopNPocketsCount]
1068
1069 SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID] = TopNPocketsIDs
1070 return
1071
1072 # Process explicitly specified pocket IDs...
1073 PocketIDsWords = PocketsIDsOptionValue
1074 if not len(PocketIDsWords):
1075 MiscUtil.PrintError("No valid value specified using \"%s\" option." % PocketsIDsOptionName)
1076
1077 for ChainID in SpecifiedChainsAndPocketsInfo["ChainIDs"]:
1078 PocketIDsList = ChainsAndPocketsInfo["PocketIDs"][ChainID]
1079 SpecifiedPocketIDsList = []
1080
1081 for PocketID in PocketIDsWords:
1082 if not PocketID in PocketIDsList:
1083 MiscUtil.PrintWarning("The pocket ID, %s, specified using \"%s\" option is not valid for chain, %s. It'll be ignored. Valid pocket IDs are listed earlier." % (PocketID, PocketsIDsOptionName, ChainID))
1084 continue
1085
1086 if PocketID in SpecifiedPocketIDsList:
1087 MiscUtil.PrintWarning("The pocket ID, %s, has already been specified using \"%s\" option. It'll be ignored." % (PocketID, PocketsIDsOptionName))
1088 continue
1089
1090 SpecifiedPocketIDsList.append(PocketID)
1091
1092 if not len(SpecifiedPocketIDsList):
1093 MiscUtil.PrintWarning("No valid pocket IDs \"%s\" specified using \"%s\" option for chain ID, %s." % (PocketsIDsOptionValue, PocketsIDsOptionName, ChainID))
1094
1095 SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID] = SpecifiedPocketIDsList
1096
1097 def CheckPresenceOfValidPocketIDs(ChainsAndPocketsInfo, SpecifiedChainsAndPocketsInfo):
1098 """Check presence of valid pocket IDs."""
1099
1100 MiscUtil.PrintInfo("\nSpecified chain IDs: %s" % (", ".join(SpecifiedChainsAndPocketsInfo["ChainIDs"])))
1101
1102 for ChainID in SpecifiedChainsAndPocketsInfo["ChainIDs"]:
1103 if len (SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID]):
1104 MiscUtil.PrintInfo("Chain ID: %s; Specified PocketIDs: %s" % (ChainID, ", ".join(SpecifiedChainsAndPocketsInfo["PocketIDs"][ChainID])))
1105 else:
1106 MiscUtil.PrintInfo("Chain IDs: %s; Specified PocketIDs: None" % (ChainID))
1107 MiscUtil.PrintWarning("No valid pocket IDs found for chain ID, %s. PyMOL groups and objects related to fpockets won't be created." % (ChainID))
1108
1109 def RetrieveFirstChainID(FileIndex, FpocketComplexMode):
1110 """Get first chain ID."""
1111
1112 FirstChainID = None
1113 if FpocketComplexMode:
1114 ChainsAndPocketsInfo = OptionsInfo["FpocketInfilesInfo"]["ChainsAndPocketsInfo"][FileIndex]
1115 if len(ChainsAndPocketsInfo["ChainIDs"]):
1116 FirstChainID = ChainsAndPocketsInfo["ChainIDs"][0]
1117 else:
1118 ChainsAndLigandsInfo = OptionsInfo["InfilesInfo"]["ChainsAndLigandsInfo"][FileIndex]
1119 if len(ChainsAndLigandsInfo["ChainIDs"]):
1120 FirstChainID = ChainsAndLigandsInfo["ChainIDs"][0]
1121
1122 return FirstChainID
1123
1124 def ProcessSurfaceAtomTypesColors():
1125 """Process surface atom types colors. """
1126
1127 AtomTypesColorNamesInfo = PyMOLUtil.ProcessSurfaceAtomTypesColorsOptionsInfo("--surfaceAtomTypesColors", OptionsInfo["SurfaceAtomTypesColors"])
1128 OptionsInfo["AtomTypesColorNames"] = AtomTypesColorNamesInfo
1129
1130 def CheckAndSetupOutfilesDir():
1131 """Check and setup a directory for output files used by PyMOL."""
1132
1133 Outfile = Options["--outfile"]
1134 OutfilesDir = Options["--outfilesDir"]
1135
1136 FileDir, FileName, FileExt = MiscUtil.ParseFileName(Outfile)
1137 if re.match("^auto$", OutfilesDir, re.I):
1138 OutfilesDir = "%s_out_PyMOL" % FileName
1139
1140 if os.path.isdir(OutfilesDir):
1141 if not OptionsInfo["Overwrite"]:
1142 MiscUtil.PrintError("The output directory, %s, already exists. Use option \"--ov\" or \"--overwrite\" and try again." % OutfilesDir)
1143 MiscUtil.PrintInfo("Using existing outout dir %s..." % OutfilesDir)
1144 else:
1145 MiscUtil.PrintInfo("Creating new output dir %s..." % OutfilesDir)
1146 os.mkdir(OutfilesDir)
1147
1148 OptionsInfo["Outfile"] = Outfile
1149 OptionsInfo["OutfilesDir"] = OutfilesDir
1150
1151 OptionsInfo["PMLOutfile"] = Outfile
1152 OptionsInfo["PMLOutfilePath"] = os.path.join(OutfilesDir, Outfile)
1153
1154 def ProcessOptions():
1155 """Process and validate command line arguments and options"""
1156
1157 MiscUtil.PrintInfo("Processing options...")
1158
1159 # Validate options...
1160 ValidateOptions()
1161
1162 OptionsInfo["Align"] = True if re.match("^Yes$", Options["--align"], re.I) else False
1163 OptionsInfo["AlignMethod"] = Options["--alignMethod"].lower()
1164 OptionsInfo["AlignMode"] = Options["--alignMode"]
1165
1166 OptionsInfo["FpocketPropertiesAppend"] = True if re.match("^Yes$", Options["--fpocketPropertiesAppend"], re.I) else False
1167
1168 OptionsInfo["Infiles"] = Options["--infiles"]
1169 OptionsInfo["InfilesNames"] = Options["--infileNames"]
1170
1171 OptionsInfo["AlignRefFile"] = Options["--alignRefFile"]
1172 if re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1173 OptionsInfo["RefFileName"] = OptionsInfo["InfilesNames"][0]
1174 else:
1175 OptionsInfo["RefFileName"] = Options["--alignRefFile"]
1176
1177 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
1178
1179 OptionsInfo["FpocketMode"] = Options["--fpocketMode"]
1180 OptionsInfo["FpocketIDs"] = Options["--fpocketIDsList"]
1181
1182 OptionsInfo["Overwrite"] = Options["--overwrite"]
1183
1184 OptionsInfo["LabelFontID"] = int(Options["--labelFontID"])
1185
1186 OptionsInfo["PocketColorByPocketNum"] = True if re.match("^Yes$", Options["--pocketColorByPocketNum"], re.I) else False
1187 OptionsInfo["PocketLabel"] = True if re.match("^Yes$", Options["--pocketLabel"], re.I) else False
1188 OptionsInfo["PocketLabelType"] = Options["--pocketLabelType"]
1189 OptionsInfo["ThreeLetterPocketLabelType"] = True if re.match("^ThreeLetter$", Options["--pocketLabelType"], re.I) else False
1190
1191 OptionsInfo["PocketNumOneColor"] = "gray80"
1192
1193 OptionsInfo["PocketSurface"] = True if re.match("^Yes$", Options["--pocketSurface"], re.I) else False
1194 OptionsInfo["SurfaceChain"] = True if re.match("^Yes$", Options["--surfaceChain"], re.I) else False
1195
1196 OptionsInfo["SurfaceColor"] = Options["--surfaceColor"]
1197 OptionsInfo["SurfaceColorPalette"] = Options["--surfaceColorPalette"]
1198 OptionsInfo["SurfaceAtomTypesColors"] = Options["--surfaceAtomTypesColors"]
1199 ProcessSurfaceAtomTypesColors()
1200
1201 OptionsInfo["SphereScale"] = float(Options["--sphereScale"])
1202 OptionsInfo["SphereTransparency"] = float(Options["--sphereTransparency"])
1203
1204 OptionsInfo["SurfaceTransparency"] = float(Options["--surfaceTransparency"])
1205
1206 # Check and setup outfile dir before processing input files...
1207 CheckAndSetupOutfilesDir()
1208
1209 RetrieveInfilesInfo()
1210 RetrieveRefFileInfo()
1211 RetrieveFpocketResultFilesInfo()
1212
1213 # Process specified chain and pocket IDs..
1214 ProcessChainAndPocketIDs()
1215
1216 def RetrieveOptions():
1217 """Retrieve command line arguments and options"""
1218
1219 # Get options...
1220 global Options
1221 Options = docopt(_docoptUsage_)
1222
1223 # Set current working directory to the specified directory...
1224 WorkingDir = Options["--workingdir"]
1225 if WorkingDir:
1226 os.chdir(WorkingDir)
1227
1228 # Handle examples option...
1229 if "--examples" in Options and Options["--examples"]:
1230 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(__doc__))
1231 sys.exit(0)
1232
1233 def ValidateOptions():
1234 """Validate option values"""
1235
1236 MiscUtil.ValidateOptionTextValue("--align", Options["--align"], "yes no")
1237 MiscUtil.ValidateOptionTextValue("--alignMethod", Options["--alignMethod"], "align cealign super")
1238 MiscUtil.ValidateOptionTextValue("--alignMode", Options["--alignMode"], "FirstChain Complex")
1239
1240 MiscUtil.ValidateOptionTextValue("--fpocketPropertiesAppend", Options["--fpocketPropertiesAppend"], "yes no")
1241
1242 # Expand infiles to handle presence of multiple input files...
1243 InfileNames = MiscUtil.ExpandFileNames(Options["--infiles"], ",")
1244 if not len(InfileNames):
1245 MiscUtil.PrintError("No input files specified for \"-i, --infiles\" option")
1246
1247 # Validate file extensions...
1248 for Infile in InfileNames:
1249 MiscUtil.ValidateOptionFilePath("-i, --infiles", Infile)
1250 MiscUtil.ValidateOptionFileExt("-i, --infiles", Infile, "pdb")
1251 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infiles", Infile, "-o, --outfile", Options["--outfile"])
1252 Options["--infileNames"] = InfileNames
1253
1254 MiscUtil.ValidateOptionFileExt("-o, --outfile", Options["--outfile"], "pml")
1255
1256 if re.match("^yes$", Options["--align"], re.I):
1257 if not re.match("^FirstInputFile$", Options["--alignRefFile"], re.I):
1258 AlignRefFile = Options["--alignRefFile"]
1259 MiscUtil.ValidateOptionFilePath("--alignRefFile", AlignRefFile)
1260 MiscUtil.ValidateOptionFileExt("--alignRefFile", AlignRefFile, "pdb")
1261 MiscUtil.ValidateOptionsDistinctFileNames("--AlignRefFile", AlignRefFile, "-o, --outfile", Options["--outfile"])
1262
1263 MiscUtil.ValidateOptionTextValue("--fpocketMode", Options["--fpocketMode"], "All TopN Specify")
1264
1265 FpocketIDsList = []
1266 if re.match("^(TopN|Specify)$", Options["--fpocketMode"], re.I):
1267 if Options["--fpocketIDs"] is None:
1268 MiscUtil.PrintError("No value specified for \"--fpocketIDs\" during \"%s\" of \"-f, --fpocketMode\" option." % (Options["--fpocketMode"]))
1269
1270 FpocketIDs = re.sub(" ", "", Options["--fpocketIDs"])
1271 if not FpocketIDs:
1272 MiscUtil.PrintError("No valid value specified for \"--fpocketIDs\" during \"%s\" of \"-f, --fpocketMode\" option." % (Options["--fpocketMode"]))
1273 FpocketIDsWords = FpocketIDs.split(",")
1274 if len(FpocketIDsWords) == 0:
1275 MiscUtil.PrintError("No valid value specified for \"--fpocketIDs\" during \"%s\" of \"-f, --fpocketMode\" option." % (Options["--fpocketMode"]))
1276
1277 if re.match("^TopN$", Options["--fpocketMode"], re.I):
1278 if len(FpocketIDsWords) > 1:
1279 MiscUtil.PrintError("Number of values specified for \"--fpocketIDs\" must be 1 during \"TopN\" of \"-f, --fpocketMode\" option.")
1280
1281 for FpocketID in FpocketIDsWords:
1282 MiscUtil.ValidateOptionIntegerValue("--fpocketIDs", FpocketID, {">": 0})
1283 FpocketIDsList.append(FpocketID)
1284
1285 Options["--fpocketIDsList"] = FpocketIDsList
1286
1287 MiscUtil.ValidateOptionIntegerValue("--labelFontID", Options["--labelFontID"], {})
1288
1289 MiscUtil.ValidateOptionTextValue("--pocketColorByPocketNum", Options["--pocketColorByPocketNum"], "yes no")
1290 MiscUtil.ValidateOptionTextValue("--pocketLabel", Options["--pocketLabel"], "yes no")
1291 MiscUtil.ValidateOptionTextValue("--pocketLabelType", Options["--pocketLabelType"], "OneLetter ThreeLetter")
1292
1293 MiscUtil.ValidateOptionTextValue("--pocketSurface", Options["--pocketSurface"], "yes no")
1294 MiscUtil.ValidateOptionTextValue("--surfaceChain", Options["--surfaceChain"], "yes no")
1295
1296 MiscUtil.ValidateOptionFloatValue("--sphereScale", Options["--sphereScale"], {">": 0.0})
1297 MiscUtil.ValidateOptionFloatValue("--sphereTransparency", Options["--sphereTransparency"], {">=": 0.0, "<=": 1.0})
1298
1299 MiscUtil.ValidateOptionTextValue("--surfaceColorPalette", Options["--surfaceColorPalette"], "RedToWhite WhiteToGreen")
1300 MiscUtil.ValidateOptionFloatValue("--surfaceTransparency", Options["--surfaceTransparency"], {">=": 0.0, "<=": 1.0})
1301
1302 # Setup a usage string for docopt...
1303 _docoptUsage_ = """
1304 PyMOLVisualizeFpockets.py - Visualize fpockets for macromolecules.
1305
1306 Usage:
1307 PyMOLVisualizeFpockets.py [--align <yes or no>] [--alignMethod <align, cealign, super>]
1308 [--alignMode <FirstChain or Complex>] [--alignRefFile <filename>]
1309 [--chainIDs <First, All or ID1,ID2...>] [--fpocketMode <All, TopN, or Specify>]
1310 [--fpocketIDs <Value or Value1,Value2...>] [--fpocketPropertiesAppend <yes or no>]
1311 [--labelFontID <number>] [--outfilesDir <outfilesDir>] [--pocketColorByPocketNum <yes or no>]
1312 [--pocketLabel <yes or no>] [--pocketLabelType <OneLetter or ThreeLetter>]
1313 [--pocketSurface <yes or no>] [--sphereScale <number>] [--sphereTransparency <number>]
1314 [--surfaceChain <yes or no>] [--surfaceAtomTypesColors <ColorType,ColorSpec,...>]
1315 [--surfaceColor <ColorName>] [--surfaceColorPalette <RedToWhite or WhiteToGreen>]
1316 [--surfaceTransparency <number>] [--overwrite] [-w <dir>] -i <infile1,infile2,infile3...> -o <outfile>
1317 PyMOLVisualizeFpockets.py -h | --help | -e | --examples
1318
1319 Description:
1320 Generate a PyMOL visualization file for visualizing pockets in macromolecules
1321 detected by an open source package named Fpocket [ Ref 166 ].
1322
1323 The results of Fpocket calculations must be available in the current directory
1324 for all input files. A complete set of expected results is shown below:
1325
1326 Dir: <PDBFileRoot>_out
1327 <PDBFileRoot>_out.pdb
1328 ... .. ...
1329 Dir: pockets
1330 <PDBFileRoot><PocketID>_atm.pdb
1331 ... .. ...
1332
1333 The supported input file format is: PDB (.pdb)
1334
1335 The supported output file formats is: PyMOL script file (.pml)
1336
1337 The following directory and files are created for the visualization of pockets
1338 detected by Fpocket:
1339
1340 Dir: <OutFileRoot>_out_PyMOL or <OutfilesDir>
1341 <OutfileRoot>.pml
1342 <PDBFileRoot>.pdb
1343 <PDBFileRoot>_out.pdb
1344
1345 You may visualize pockets in PyMOL by loading <OutfileRoot>.pml from
1346 <OutfileRoot>_out_PyMOL or <OutfilesDir> directory.
1347
1348 A variety of PyMOL groups and objects may be created for visualization of
1349 fpockets in macromolecules. These groups and objects correspond to complexes,
1350 chains, fpockets, and surfaces. A complete hierarchy of all possible PyMOL
1351 groups and objects is shown below:
1352
1353 <PDBFileRoot>
1354 .Complex
1355 .Initial_PDB
1356 .Fpocket_PDB
1357 .Chain<ID>
1358 .Complex
1359 .Complex
1360 .Chain
1361 .Chain
1362 .Surface
1363 .Surface
1364 .Hydrophobicity
1365 .Hydrophobicity_Charge
1366 .FPocket<ID>
1367 .FPocket
1368 .Residues
1369 .Surface
1370 .Surface
1371 .Hydrophobicity
1372 .Hydrophobicity_Charge
1373 .Chain<ID>
1374 ... ... ...
1375 .FPocket<ID>
1376 ... ... ...
1377 .FPocket<ID>
1378 ... ... ...
1379 .Chain<ID>
1380 ... ... ...
1381 <PDBFileRoot>
1382 .Complex
1383 ... ... ...
1384 .Chain<ID>
1385 ... ... ...
1386 .FPocket<ID>
1387 ... ... ...
1388 .FPocket<ID>
1389 ... ... ...
1390 .Chain<ID>
1391 ... ... ...
1392
1393 Options:
1394 -a, --align <yes or no> [default: no]
1395 Align input files to a reference file before visualization.
1396 --alignMethod <align, cealign, super> [default: super]
1397 Alignment methodology to use for aligning input files to a
1398 reference file.
1399 --alignMode <FirstChain or Complex> [default: FirstChain]
1400 Portion of input and reference files to use for spatial alignment of
1401 input files against reference file. Possible values: FirstChain or
1402 Complex.
1403
1404 The FirstChain mode allows alignment of the first chain in each input
1405 file to the first chain in the reference file along with moving the rest
1406 of the complex to coordinate space of the reference file. The complete
1407 complex in each input file is aligned to the complete complex in reference
1408 file for the Complex mode.
1409 --alignRefFile <filename> [default: FirstInputFile]
1410 Reference input file name. The default is to use the first input file
1411 name specified using '-i, --infiles' option.
1412 -c, --chainIDs <First, All or ID1,ID2...> [default: First]
1413 List of chain IDs to use for visualizing fpockets in macromolecules. Possible
1414 values: First, All, or a comma delimited list of chain IDs. The default is to
1415 use the chain ID for the first chain in each input file.
1416 -e, --examples
1417 Print examples.
1418 -f, --fpocketMode <All, TopN, or Specify> [default: All]
1419 Fpockets specification mode for visualizing fpockets across chains in
1420 macromolecules. Possible values: All, TopN, or specify. By default, all
1421 available fpockets are visualized across specified chains.
1422
1423 The fpocket IDs must be specified using '--fpocketIDs' option for 'TopN'
1424 and 'Specifiy' value of '--fpocketMode '.
1425 --fpocketIDs <Value or Value1,Value2...>
1426 List of Fpocket IDs for visualizing fpockets across chains. This value is
1427 dependent on the value of '--fpocketMode'. The possible values are
1428 either a number or a comma delimited list of number for 'TopN' and
1429 'Specify' value '--fpocketMode' option. For example:
1430
1431 This option is ignored during 'All' value of '--fpocketMode' option.
1432 --fpocketPropertiesAppend <yes or no> [default: yes]
1433 Append fpocket properties to names of PyMOL fpocket groups and
1434 objects. The following properties are appended to the names of PyMOL
1435 groups using their abbreviations and values: PocketScore - S; DrugScore - D;
1436 PocketVolume - V; HydrophobicityScore - H; PolarityScore - P.
1437 For example:
1438
1439 Fpocket1_S0p50_D0p00_V638p81_Hneg6p67_P11p00.Fpocket
1440 -h, --help
1441 Print this help message.
1442 -i, --infiles <infile1,infile2,infile3...>
1443 Input PDB file names. The current directory must contain the results from
1444 Fpocket calculations for all the input PDB files.
1445 --labelFontID <number> [default: 7]
1446 Font ID for drawing labels. Default: 7 (Sans Bold). Valid values: 5 to 16.
1447 The specified value must be a valid PyMOL font ID. No validation is
1448 performed. The complete lists of valid font IDs is available at:
1449 pymolwiki.org/index.php/Label_font_id. Examples: 5 - Sans;
1450 7 - Sans Bold; 9 - Serif; 10 - Serif Bold.
1451 -o, --outfile <outfile>
1452 PML output file name for visualizing fpockets. The PML outfile is created
1453 in a new output directory named <OutfileRoot>_out_PyMOL. In addition, the
1454 output directory contains all appropriate PDB files generated by Fpocket for
1455 visualization of fpockets in PyMOL.
1456 --outfilesDir <outfilesDir> [default: auto]
1457 Output files directory name. Default: <OutfileRoot>_out_PyMOL.
1458 --pocketColorByPocketNum <yes or no> [default: yes]
1459 Color fpocket residues and residue labels by pocket number. Otherwise,
1460 the pocket residues are colored by element names using default PyMOL
1461 color scheme. No color is set for residue labels.
1462 --pocketLabel <yes or no> [default: yes]
1463 Display residue labels on fpocket residues. The residue number is always
1464 appended to residue label. You may specify a one or thee letter residue
1465 labels using '--pocketLabelType' option.
1466 --pocketLabelType <OneLetter or ThreeLetter> [default: OneLetter]
1467 Display one or three letter residue labels on fpocket residues
1468 --pocketSurface <yes or no> [default: yes]
1469 Surfaces around fpocket residues colored by hydrophobicity alone and
1470 both hydrophobicity and charge. The hydrophobicity surface is colored
1471 at residue level using Eisenberg hydrophobicity scale for residues and color
1472 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
1473 charge surface is colored at atom level using colors specified for
1474 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
1475 simultaneous mapping of hyrophobicity and charge values on the surfaces.
1476
1477 In addition, generic surfaces colored by '--surfaceColor' are always created
1478 for pockets.
1479 --sphereScale <number> [default: 0.4]
1480 Scaling factor for spheres used to display fpocket alpha spheres.
1481 --sphereTransparency <number> [default: 0.25]
1482 Transparency for spheres used to display fpocket alpha spheres.
1483 --surfaceChain <yes or no> [default: yes]
1484 Surfaces around individual chain colored by hydrophobicity alone and
1485 both hydrophobicity and charge. The hydrophobicity surface is colored
1486 at residue level using Eisenberg hydrophobicity scale for residues and color
1487 gradient specified by '--surfaceColorPalette' option. The hydrophobicity and
1488 charge surface is colored at atom level using colors specified for
1489 groups of atoms by '--surfaceAtomTypesColors' option. This scheme allows
1490 simultaneous mapping of hyrophobicity and charge values on the surfaces.
1491
1492 In addition, generic surfaces colored by '--surfaceColor' are always created
1493 for chains.
1494 --surfaceAtomTypesColors <ColorType,ColorSpec,...> [default: auto]
1495 Atom colors for generating surfaces colored by hyrophobicity and charge
1496 around chains and pockets in proteins. It's a pairwise comma delimited list
1497 of atom color type and color specification for groups of atoms.
1498
1499 The default values for color types along wth color specifications
1500 are shown below:
1501
1502 HydrophobicAtomsColor, yellow,
1503 NegativelyChargedAtomsColor, red,
1504 PositivelyChargedAtomsColor, blue,
1505 OtherAtomsColor, gray90
1506
1507 The color names must be valid PyMOL names.
1508
1509 The color values may also be specified as space delimited RGB triplets:
1510
1511 HydrophobicAtomsColor, 0.95 0.78 0.0,
1512 NegativelyChargedAtomsColor, 1.0 0.4 0.4,
1513 PositivelyChargedAtomsColor, 0.2 0.5 0.8,
1514 OtherAtomsColor, 0.95 0.95 0.95
1515
1516 --surfaceColor <ColorName> [default: lightblue]
1517 Color name for surfaces around chains and pockets. This color is not used
1518 for surfaces colored by hydrophobicity and charge. The color name must be
1519 a valid PyMOL name.
1520 --surfaceColorPalette <RedToWhite or WhiteToGreen> [default: RedToWhite]
1521 Color palette for hydrophobic surfaces around chains and pockets in proteins.
1522 Possible values: RedToWhite or WhiteToGreen from most hydrophobic amino
1523 acid to least hydrophobic. The colors values for amino acids are taken from
1524 color_h script available as part of the Script Library at PyMOL Wiki.
1525 --surfaceTransparency <number> [default: 0.25]
1526 Surface transparency for molecular surfaces.
1527 --overwrite
1528 Overwrite existing files.
1529 -w, --workingdir <dir>
1530 Location of working directory which defaults to the current directory.
1531
1532 Examples:
1533 To visualize all fpockets available in a directory <PDBRoot>_out for the first
1534 chain, along pocket residues and surfaces, in a PDB file, and generate a PML
1535 file in a new directory <PDBRoot>_out_pymol, type:
1536
1537 % PyMOLVisualizeFpockets.py -i Sample5.pdb -o Sample5.pml
1538
1539 To rerun the first example without displaying pocket residue labels,
1540 coloring pockets by element type, and write out a PML file, type:
1541
1542 % PyMOLVisualizeFpockets.py --pocketColorByPocketNum no
1543 --pocketLabel no -i Sample5.pdb -o Sample5.pml
1544
1545 To rerun the first example to visualize only top 5 fpockets and write out a
1546 PML file, type:
1547
1548 % PyMOLVisualizeFpockets.py -f TopN --fpocketIDs 5 -i Sample5.pdb
1549 -o Sample5.pml
1550
1551 To rerun the first example to visualize a specific set of fpockets and write
1552 out a PML file, type:
1553
1554 % PyMOLVisualizeFpockets.py -f Specify --fpocketIDs "1,2,3" -i Sample5.pdb
1555 -o Sample5.pml
1556
1557 To rerun the first example to visualize all fpockets across all chains and write
1558 out a PML file, type:
1559
1560 % PyMOLVisualizeFpockets.py -c All -f All -i Sample5.pdb -o Sample5.pml
1561
1562 To rerun the first example without displaying hydrophobic and charge surfaces
1563 around chain and pockets and and write out a PML file, type:
1564
1565 % PyMOLVisualizeFpockets.py --surfaceChain no --pocketSurface no
1566 -i Sample5.pdb -o Sample5.pml
1567
1568 To visualize top 5 fpockets available in a directories <PDBRoot>_out for the
1569 first chain, along pocket residues and surfaces, in PDB files, aligning first
1570 fchain in each input file to the first chain in first input file, and generate a
1571 PML file in a new directory <PDBRoot>_out_pymol, type:
1572
1573 % PyMOLVisualizeFpockets.py -f TopN --fpocketIDs 5 --align yes
1574 -i "Sample5.pdb,Sample6.pdb" -o Sample5Aligned.pml
1575
1576 To visualize top 5 fpockets available in a directories <PDBRoot>_out for the
1577 first chain, along pocket residues and surfaces, in PDB files, aligning first
1578 chain in each input file to the first chain in first chain in a specified PDB
1579 file using a specified alignment method,, and generate a PML file in a new
1580 directory <PDBRoot>_out_pymol, type:
1581
1582 % PyMOLVisualizeFpockets.py -f TopN --fpocketIDs 5 --align yes
1583 --alignMode FirstChain --alignRefFile Sample6.pdb --alignMethod super
1584 -i "Sample5.pdb,Sample6.pdb" -o Sample5Aligned.pml
1585
1586 Author:
1587 Manish Sud
1588
1589 Collaborators:
1590 Joann Prescott-Roy and Pat Walters
1591
1592 See also:
1593 DownloadPDBFiles.pl, PyMOLVisualizeCavities.py,
1594 PyMOLVisualizeCryoEMDensity.py, PyMOLVisualizeElectronDensity.py,
1595 PyMOLVisualizeInterfaces.py, PyMOLVisualizeMacromolecules.py,
1596 PyMOLVisualizeSurfaceAndBuriedResidues.py
1597
1598 Copyright:
1599 Copyright (C) 2025 Manish Sud. All rights reserved.
1600
1601 The functionality available in this script is implemented using PyMOL, a
1602 molecular visualization system on an open source foundation originally
1603 developed by Warren DeLano.
1604
1605 This file is part of MayaChemTools.
1606
1607 MayaChemTools is free software; you can redistribute it and/or modify it under
1608 the terms of the GNU Lesser General Public License as published by the Free
1609 Software Foundation; either version 3 of the License, or (at your option) any
1610 later version.
1611
1612 """
1613
1614 if __name__ == "__main__":
1615 main()
