1 #!/bin/env python
2 #
3 # File: PyMOLGenerateRamachandranPlots.py
4 # Author: Manish Sud <msud@san.rr.com>
5 #
6 # Copyright (C) 2025 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 csv
38 import matplotlib.pyplot as plt
39 import numpy as np
40
41 # PyMOL imports...
42 try:
43 import pymol
44 # Finish launching PyMOL in a command line mode for batch processing (-c)
45 # along with the following options: disable loading of pymolrc and plugins (-k);
46 # suppress start up messages (-q)
47 pymol.finish_launching(['pymol', '-ckq'])
48 except ImportError as ErrMsg:
49 sys.stderr.write("\nFailed to import PyMOL module/package: %s\n" % ErrMsg)
50 sys.stderr.write("Check/update your PyMOL environment and try again.\n\n")
51 sys.exit(1)
52
53 # MayaChemTools imports...
54 try:
55 from docopt import docopt
56 import MiscUtil
57 import PyMOLUtil
58 except ImportError as ErrMsg:
59 sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg)
60 sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n")
61 sys.exit(1)
62
63 ScriptName = os.path.basename(sys.argv[0])
64 Options = {}
65 OptionsInfo = {}
66
67 def main():
68 """Start execution of the script."""
69
70 MiscUtil.PrintInfo("\n%s (PyMOL v%s; MayaChemTools v%s; %s): Starting...\n" % (ScriptName, pymol.cmd.get_version()[0], MiscUtil.GetMayaChemToolsVersion(), time.asctime()))
71
72 (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
73
74 # Retrieve command line arguments and options...
75 RetrieveOptions()
76
77 # Process and validate command line arguments and options...
78 ProcessOptions()
79
80 # Perform actions required by the script...
81 GenerateRamachandranPlots()
82
83 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
84 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
85
86 def GenerateRamachandranPlots():
87 """Calculate phi and psi angles for macromolecules containing amino acids
88 and generate Ramachandran plots.
89 """
90
91 # Calculate phi and psi angles..
92 CalculatePhiPsiAngles()
93
94 # Read phi and psi densities...
95 ReadPhiAndPsiDensities()
96
97 # Setup contour info...
98 SetupContoursInfo()
99
100 # Generate plots...
101 if OptionsInfo["MultipleOutFiles"]:
102 GenerateMultiplePlotFiles()
103 else:
104 GenerateSinglePlotFile()
105
106 def GenerateSinglePlotFile():
107 """Generate a single plot file containg all four types of Ramachandran plots."""
108
109 Outfile = OptionsInfo["Outfile"]
110 MiscUtil.PrintInfo("\nGenerating output file %s..." % (Outfile))
111
112 SetupFontFamily()
113
114 # Setup figure...
115 PlotFigure, Axes = plt.subplots(2, 2, figsize = (OptionsInfo["FigWidth"], OptionsInfo["FigHeight"]), dpi = OptionsInfo["FigDPI"])
116 PlotAxes = [Axis for RowAxes in Axes for Axis in RowAxes]
117
118 # Adjust space between subplots...
119 plt.subplots_adjust(left = 0.1, right = 0.9, bottom = 0.1, top = 0.9, wspace = 0.3, hspace = 0.25)
120
121 for PlotIndex, PlotType in enumerate(OptionsInfo["PlotTypesInfo"]["Types"]):
122 DrawPlot(PlotAxes[PlotIndex], PlotType)
123
124 # Save figure...
125 plt.savefig(Outfile)
126
127 def GenerateMultiplePlotFiles():
128 """Generate multiple plot files corresponding to four types of Ramachandran plots."""
129
130 MiscUtil.PrintInfo("\nGenerating multiple output files...")
131
132 SetupFontFamily()
133
134 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
135 Outfile = OptionsInfo["PlotTypesInfo"]["Outfiles"][PlotType]
136 MiscUtil.PrintInfo("Generating output file %s..." % Outfile)
137
138 PlotFigure, PlotAxis = plt.subplots(1, 1, figsize = (OptionsInfo["FigWidth"], OptionsInfo["FigHeight"]), dpi = OptionsInfo["FigDPI"])
139 DrawPlot(PlotAxis, PlotType)
140
141 # Save figure...
142 plt.savefig(Outfile)
143
144 # Get ready for the next figure...
145 plt.clf()
146
147 def DrawPlot(PlotAxis, PlotType):
148 """Draw contour and scatter plot."""
149
150 PlotTypesInfo = OptionsInfo["PlotTypesInfo"]
151
152 # Draw filled contours...
153 PhiPsiContourInfo = PlotTypesInfo["PhiPsiContourInfo"][PlotType]
154 PlotAxis.contourf(PhiPsiContourInfo["X"], PhiPsiContourInfo["Y"], PhiPsiContourInfo["Z"], levels = PlotTypesInfo["Levels"][PlotType], colors = PlotTypesInfo["Colors"][PlotType])
155
156 # Draw scatter plot for phi and psi angles...
157 if PlotTypesInfo["ResCount"][PlotType]:
158 PlotAxis.scatter(PlotTypesInfo["PhiAngles"][PlotType], PlotTypesInfo["PsiAngles"][PlotType], s = OptionsInfo["ScatterMarkerSize"], c = OptionsInfo["ScatterMarkerColor"], marker = OptionsInfo["ScatterMarkerStyle"])
159
160 # Setup limits...
161 PlotAxis.set_xlim(PlotTypesInfo["Limits"][PlotType])
162 PlotAxis.set_ylim(PlotTypesInfo["Limits"][PlotType])
163
164 # Setup major tick marks...
165 PlotAxis.set_xticklabels(PlotTypesInfo["MajorTickLabels"][PlotType], fontdict = {"fontsize": OptionsInfo["FontTicksSize"], "fontweight": OptionsInfo["FontTicksWeight"]})
166 PlotAxis.set_xticks(PlotTypesInfo["MajorTickPositions"][PlotType])
167 PlotAxis.set_yticklabels(PlotTypesInfo["MajorTickLabels"][PlotType], fontdict = {"fontsize": OptionsInfo["FontTicksSize"], "fontweight": OptionsInfo["FontTicksWeight"]})
168 PlotAxis.set_yticks(PlotTypesInfo["MajorTickPositions"][PlotType])
169
170 # Set up minor ticks...
171 if OptionsInfo["TicksMinor"]:
172 PlotAxis.set_xticks(PlotTypesInfo["MinorTickPositions"][PlotType], minor = True)
173 PlotAxis.set_yticks(PlotTypesInfo["MinorTickPositions"][PlotType], minor = True)
174
175 # Setup grid...
176 if OptionsInfo["Grid"]:
177 PlotAxis.grid(True, color = OptionsInfo["GridLineColor"], linestyle = OptionsInfo["GridLineStyle"], linewidth = OptionsInfo["GridLineWidth"])
178
179 # Setup title...
180 PlotAxis.set_title(PlotTypesInfo["Titles"][PlotType], fontsize = OptionsInfo["FontTitleSize"], fontweight = OptionsInfo["FontTitleWeight"])
181
182 # Setup axes labels...
183 if PlotTypesInfo["DrawXLabel"][PlotType]:
184 XLabel = r"$\Phi$" if OptionsInfo["Greek"] else "Phi"
185 PlotAxis.set_xlabel(XLabel, fontsize = OptionsInfo["FontAxesSize"], fontweight = OptionsInfo["FontAxesWeight"])
186 if PlotTypesInfo["DrawYLabel"][PlotType]:
187 # Setup a horizontal ylabel close to the axis...
188 YLabel = r"$\Psi$" if OptionsInfo["Greek"] else "Psi"
189 YRotation = 0 if OptionsInfo["Greek"] else 90
190 PlotAxis.set_ylabel(YLabel, fontsize = OptionsInfo["FontAxesSize"], fontweight = OptionsInfo["FontAxesWeight"], rotation = YRotation, labelpad = 0)
191
192 def SetupFontFamily():
193 """Setuo global font family."""
194
195 if re.match("^auto$", OptionsInfo["FontFamily"], re.I):
196 return
197 plt.rcParams["font.family"] = OptionsInfo["FontFamily"]
198
199 def SetupContoursInfo():
200 """Setup contour info for generating contour plots."""
201
202 MiscUtil.PrintInfo("\nProcessing phi and psi densities for contour plots...")
203
204 OptionsInfo["PlotTypesInfo"]["PhiPsiContourInfo"] = {}
205 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
206 PhiPsiContourInfo = SetupPhiAndPsiContourInfo(PlotType)
207 OptionsInfo["PlotTypesInfo"]["PhiPsiContourInfo"][PlotType] = PhiPsiContourInfo
208
209 def SetupPhiAndPsiContourInfo(PlotType):
210 """Setup X, Y and Z contour arrays for generating contour plots."""
211
212 DensityInfo = OptionsInfo["PlotTypesInfo"]["PhiPsiDensityInfo"][PlotType]
213
214 X, Y = np.meshgrid(DensityInfo["PhiValues"], DensityInfo["PsiValues"])
215 Z = np.zeros((len(DensityInfo["PhiValues"]), len(DensityInfo["PsiValues"])))
216
217 # Initialize X, Y, and Z arrays for contour plots...
218 for ZRowIndex, PsiID in enumerate(DensityInfo["PhiIDs"]):
219 for ZColIndex, PhiID in enumerate(DensityInfo["PsiIDs"]):
220 Z[ZRowIndex][ZColIndex] = DensityInfo["Density"][PhiID][PsiID]
221
222 # Track contour data...
223 ContourInfo = {}
224 ContourInfo["X"] = X
225 ContourInfo["Y"] = Y
226 ContourInfo["Z"] = Z
227
228 return ContourInfo
229
230 def ReadPhiAndPsiDensities():
231 """Read phi and psi densities for generating filled contours."""
232
233 OptionsInfo["PlotTypesInfo"]["PhiPsiDensityInfo"] = {}
234 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
235 DensityFile = OptionsInfo["PlotTypesInfo"]["PhiPsiDensityFiles"][PlotType]
236 PhiPsiDensityInfo = ReadPhiAndPsiDensityFile(DensityFile)
237 OptionsInfo["PlotTypesInfo"]["PhiPsiDensityInfo"][PlotType] = PhiPsiDensityInfo
238
239 def ReadPhiAndPsiDensityFile(DensityFile):
240 """Read phi and psi desnsity file.
241
242 Format:
243 Phi,Psi,Density
244 -179.0,-179.0,0.00782923406455425
245 -179.0,-177.0,0.00641357067237856
246 ... ... ...
247 """
248
249 MiscUtil.PrintInfo("\nReading psi and psi density grid file %s..." % DensityFile)
250
251 DensityFH = open(DensityFile, "r")
252 if DensityFH is None:
253 MiscUtil.PrintError("Couldn't open phi and psi density file: %s.\n" % (DensityFile))
254
255 HeaderLine = True
256 DensityLines = []
257 for Line in DensityFH:
258 Line = Line.rstrip()
259 # Ignore comments...
260 if re.match("^#", Line, re.I):
261 continue
262 # Ignore header line...
263 if HeaderLine:
264 HeaderLine = False
265 continue
266 DensityLines.append(Line)
267
268 DensityInfo = {}
269 DensityInfo["Density"] = {}
270
271 DensityInfo["PhiIDs"] = []
272 DensityInfo["PhiValues"] = []
273
274 DensityInfo["PsiIDs"] = []
275 DensityInfo["PsiValues"] = []
276
277 PhiValuesMap = {}
278 PsiValuesMap = {}
279
280 Count = 0
281 MinDensity = 99999.0
282 MaxDensity = - MinDensity
283
284 DensityReader = csv.reader(DensityLines, delimiter=',', quotechar='"')
285 for LineWords in DensityReader:
286 Count += 1
287
288 Phi = LineWords[0]
289 Psi = LineWords[1]
290 Density = LineWords[2]
291
292 # Track unique phi and psi value...
293 if not Phi in PhiValuesMap:
294 PhiValuesMap[Phi] = float(Phi)
295 if not Psi in PsiValuesMap:
296 PsiValuesMap[Psi] = float(Psi)
297
298 # Track density data...
299 if not Phi in DensityInfo["Density"]:
300 DensityInfo["Density"][Phi] = {}
301
302 Density = float(Density)
303 DensityInfo["Density"][Phi][Psi] = Density
304 if Density < MinDensity:
305 MinDensity = Density
306 if Density > MaxDensity:
307 MaxDensity = Density
308
309 # Sort and track values for phi and psi angles...
310 DensityInfo["PhiIDs"] = sorted(PhiValuesMap.keys(), key = lambda Phi: PhiValuesMap[Phi])
311 DensityInfo["PhiValues"] = [PhiValuesMap[Phi] for Phi in DensityInfo["PhiIDs"]]
312
313 DensityInfo["PsiIDs"] = sorted(PsiValuesMap.keys(), key = lambda Psi: PsiValuesMap[Psi])
314 DensityInfo["PsiValues"] = [PsiValuesMap[Psi] for Psi in DensityInfo["PsiIDs"]]
315
316 MiscUtil.PrintInfo("Minimum density: %.4f; Maximum density: %.4f" % (MinDensity, MaxDensity))
317 MiscUtil.PrintInfo("Number of phi and psi angles: %s" % Count)
318
319 MiscUtil.PrintInfo("\nDimensions of phi and psi grid angles:")
320 MiscUtil.PrintInfo("Phi - Min: %s; Max: %s; Bin size: %s; Count: %s" % (DensityInfo["PhiValues"][0], DensityInfo["PhiValues"][-1], abs(DensityInfo["PhiValues"][1] - DensityInfo["PhiValues"][0]), len(DensityInfo["PhiValues"])))
321 MiscUtil.PrintInfo("Psi - Min: %s; Max: %s; Bin size: %s; Count: %s" % (DensityInfo["PsiValues"][0], DensityInfo["PsiValues"][-1], abs(DensityInfo["PsiValues"][1] - DensityInfo["PsiValues"][0]), len(DensityInfo["PsiValues"])))
322
323 return DensityInfo
324
325 def CalculatePhiPsiAngles():
326 """Calculate phi and psi angles for scatter plots."""
327
328 Infile = OptionsInfo["Infile"]
329 MolName = OptionsInfo["InfileRoot"]
330
331 # Load molecule...
332 pymol.cmd.reinitialize()
333 pymol.cmd.load(Infile, MolName)
334
335 MiscUtil.PrintInfo("\nCalculating phi and psi torsion angles for input file %s..." % Infile)
336
337 # Initialize...
338 OptionsInfo["PlotTypesInfo"]["PhiAngles"] = {}
339 OptionsInfo["PlotTypesInfo"]["PsiAngles"] = {}
340 OptionsInfo["PlotTypesInfo"]["ResCount"] = {}
341 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
342 OptionsInfo["PlotTypesInfo"]["PhiAngles"][PlotType] = []
343 OptionsInfo["PlotTypesInfo"]["PsiAngles"][PlotType] = []
344 OptionsInfo["PlotTypesInfo"]["ResCount"][PlotType] = 0
345
346 Precision = OptionsInfo["Precision"]
347
348 TotalResCount = 0
349 # Go over specified chain IDs..
350 for ChainID in OptionsInfo["SpecifiedChainsAndLigandsInfo"]["ChainIDs"]:
351 PhiPsiInfoList = []
352 GeneralPhiPsiInfo, GlycinePhiPsiInfo, ProlinePhiPsiInfo, PreProlinePhiPsiInfo = PyMOLUtil.GetPhiPsiCategoriesResiduesInfo(MolName, ChainID)
353 PhiPsiInfoList.extend([GeneralPhiPsiInfo, GlycinePhiPsiInfo, ProlinePhiPsiInfo, PreProlinePhiPsiInfo])
354
355 for Index, PlotType in enumerate(OptionsInfo["PlotTypesInfo"]["Types"]):
356 PhiPsiInfo = PhiPsiInfoList[Index]
357 ResCount = len(PhiPsiInfo["ResNums"])
358 if not ResCount:
359 continue
360
361 TotalResCount += ResCount
362 OptionsInfo["PlotTypesInfo"]["ResCount"][PlotType] += ResCount
363
364 PhiAngles, PsiAngles = ProcessPsiInfo(PhiPsiInfo, Precision)
365 OptionsInfo["PlotTypesInfo"]["PhiAngles"][PlotType].extend(PhiAngles)
366 OptionsInfo["PlotTypesInfo"]["PsiAngles"][PlotType].extend(PsiAngles)
367
368 # Delete MolName object
369 pymol.cmd.delete(MolName)
370
371 MiscUtil.PrintInfo("\nTotal number of phi and psi angles: %d" % TotalResCount)
372
373 MiscUtil.PrintInfo("")
374 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
375 MiscUtil.PrintInfo("Number of \"%s\" phi and psi angles: %s" % (PlotType, OptionsInfo["PlotTypesInfo"]["ResCount"][PlotType]))
376
377 if not TotalResCount:
378 MiscUtil.PrintInfo("")
379 MiscUtil.PrintWarning("No valid phi and psi angles found in input file. Ramachandran plots will be generated without phi and psi scatter plots...")
380
381 def ProcessPsiInfo(PhiPsiInfo, Precision):
382 """Process phi and psi angels for scatter plots."""
383
384 PhiAngles = []
385 PsiAngles = []
386 for ResNum in PhiPsiInfo["ResNums"]:
387 Phi = "%.*f" % (Precision, PhiPsiInfo["Phi"][ResNum])
388 Psi = "%.*f" % (Precision, PhiPsiInfo["Psi"][ResNum])
389 PhiAngles.append(float(Phi))
390 PsiAngles.append(float(Psi))
391
392 return PhiAngles, PsiAngles
393
394 def RetrieveInfileInfo():
395 """Retrieve information for input file."""
396
397 Infile = OptionsInfo["Infile"]
398 InfileRoot = OptionsInfo["InfileRoot"]
399
400 ChainsAndLigandsInfo = PyMOLUtil.GetChainsAndLigandsInfo(Infile, InfileRoot)
401 OptionsInfo["ChainsAndLigandsInfo"] = ChainsAndLigandsInfo
402
403 def ProcessChainIDs():
404 """Process specified chain IDs for infile."""
405
406 MiscUtil.PrintInfo("\nProcessing specified chain IDs for input file %s..." % OptionsInfo["Infile"])
407 ChainsAndLigandsInfo = OptionsInfo["ChainsAndLigandsInfo"]
408 SpecifiedChainsAndLigandsInfo = PyMOLUtil.ProcessChainsAndLigandsOptionsInfo(ChainsAndLigandsInfo, "-c, --chainIDs", OptionsInfo["ChainIDs"], None, None)
409
410 OptionsInfo["SpecifiedChainsAndLigandsInfo"] = SpecifiedChainsAndLigandsInfo
411
412 MiscUtil.PrintInfo("Specified chain IDs: %s" % (", ".join(SpecifiedChainsAndLigandsInfo["ChainIDs"])))
413
414 def SetupPlotsInfo():
415 """Setup information for generating plots."""
416
417 InitializePlotTypesInfo()
418 SetupPlotTypesOutfiles()
419
420 ProessContourLevelsAndColors()
421
422 def ProessContourLevelsAndColors():
423 """Process specified contour levels and colors."""
424
425 if re.match("^auto$", OptionsInfo["LevelsAndColors"], re.I):
426 return
427
428 # Setup canonical plot types for validation...
429 CanonicalPlotTypes = {}
430 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
431 CanonicalPlotTypes[PlotType.lower()] = PlotType
432
433 LevelsAndColors = re.sub(" ", "", OptionsInfo["LevelsAndColors"])
434 if not len(LevelsAndColors):
435 MiscUtil.PrintError("The levels and colors specified using \"-l, --levelsAndColors\" option are empty.")
436
437 for TypeLevelsColorsWord in LevelsAndColors.split(";"):
438 if not len(TypeLevelsColorsWord):
439 MiscUtil.PrintError("The plot types, levels, and colors, \"%s\" specified using \"-l, --levelsAndColors\" option in, \"%s\", is empty." % (TypeLevelsColorsWord, LevelsAndColors))
440
441 TypeLevelsColorsWords = TypeLevelsColorsWord.split(":")
442 if len(TypeLevelsColorsWords) !=2:
443 MiscUtil.PrintError("The format of plot type, levels, and colors specification, \"%s\", specified using \"-l, --levelsAndColors\" option, in \"%s\", is not valid: Supported format: <PlotType>: <Level>, <Color>, <Level>,..." % (TypeLevelsColorsWord, OptionsInfo["LevelsAndColors"]))
444
445 PlotType = TypeLevelsColorsWords[0]
446 if not len(PlotType):
447 MiscUtil.PrintError("The plot type, \"%s\" specified using \"-l, --levelsAndColors\" option in, \"%s\", is empty." % (PlotType, TypeLevelsColorsWord))
448 CanonicalPlotType = PlotType.lower()
449
450 if not CanonicalPlotType in CanonicalPlotTypes:
451 MiscUtil.PrintError("The plot type, \"%s\" specified using \"-l, --levelsAndColors\" option in, \"%s\", is not valid. Supported valus: %s" % (PlotType, TypeLevelsColorsWord, ", ".join(OptionsInfo["PlotTypesInfo"]["Types"])))
452 PlotType = CanonicalPlotTypes[CanonicalPlotType]
453
454 LevelsColorsWords = TypeLevelsColorsWords[1].split(",")
455 if not (len(LevelsColorsWords) % 2):
456 MiscUtil.PrintError("The format of levels and colors specifification, \"%s\", specified using \"-l, --levelsAndColors\" option in, \"%s\", is not valid. It must contain odd number of values. Supported format: <PlotType>: <Level>, <Color>, <Level>,..." % (", ".join(LevelsColorsWords), TypeLevelsColorsWord))
457
458 # Retrieve levels and colors...
459 Levels = []
460 Colors = []
461 for Index, SpecWord in enumerate(LevelsColorsWords):
462 if not len(SpecWord):
463 MiscUtil.PrintError("The level or color, \"%s\" specified using \"-l, --levelsAndColors\" option in, \"%s\", is empty." % (SpecWord, TypeLevelsColorsWord))
464
465 if Index % 2:
466 Colors.append(SpecWord)
467 continue
468
469 # Process level...
470 if not MiscUtil.IsFloat(SpecWord):
471 MiscUtil.PrintError("The level, \"%s\" specified using \"-l, --levelsAndColors\" option in, \"%s\", must be a number." % (SpecWord, TypeLevelsColorsWord))
472
473 Level = float(SpecWord)
474 if len(Levels):
475 # The current level must be greater than all previous levels..
476 for PreviousLevel in Levels:
477 if Level <= PreviousLevel:
478 MiscUtil.PrintError("The level, \"%s\" specified using \"-l, --levelsAndColors\" option in, \"%s\", must be greater than all previous levels." % (SpecWord, TypeLevelsColorsWord))
479
480 Levels.append(Level)
481
482 OptionsInfo["PlotTypesInfo"]["Levels"][PlotType] = Levels
483 OptionsInfo["PlotTypesInfo"]["Colors"][PlotType] = Colors
484
485 def InitializePlotTypesInfo():
486 """Initialize information for generating plots."""
487
488 PlotTypesInfo = {}
489 PlotTypesInfo["Types"] = []
490 PlotTypesInfo["PhiPsiDensityFiles"] = {}
491 PlotTypesInfo["PhiPsiDensityInfo"] = {}
492 PlotTypesInfo["PhiPsiContourInfo"] = {}
493
494 PlotTypesInfo["Titles"] = {}
495 PlotTypesInfo["DrawXLabel"] = {}
496 PlotTypesInfo["DrawYLabel"] = {}
497
498 PlotTypesInfo["Limits"] = {}
499 PlotTypesInfo["MajorTickPositions"] = {}
500 PlotTypesInfo["MajorTickLabels"] = {}
501 PlotTypesInfo["MinorTickPositions"] = {}
502
503 PlotTypesInfo["Levels"] = {}
504 PlotTypesInfo["Colors"] = {}
505 PlotTypesInfo["Outfiles"] = {}
506 PlotTypesInfo["PhiAngles"] = {}
507 PlotTypesInfo["PsiAngles"] = {}
508
509 MayaChemToolsDataDir = MiscUtil.GetMayaChemToolsLibDataPath()
510
511 # Setup contour colors for supported default schemes...
512 ContourColorSchemes = {}
513 ContourColorSchemes["General"] = {"MuttedColorShades1": ["#FFFFFF", "#EBF1DE", "#C3D69B"],
514 "MuttedColorShades2": ["#FFFFFF", "#EBF1DE", "#D7E4BD"],
515 "BrightColorShades": ["#FFFFFF", "#B3E8FF", "#7FD9FF"]}
516 ContourColorSchemes["Glycine"] = {"MuttedColorShades1": ["#FFFFFF", "#FDEADA", "#FAC090"],
517 "MuttedColorShades2": ["#FFFFFF", "#FDEADA", "#FCD5B5"],
518 "BrightColorShades": ["#FFFFFF", "#FFE8C5", "#FFCC7F"]}
519 ContourColorSchemes["Proline"] = {"MuttedColorShades1": ["#FFFFFF", "#E6E0EC", "#B3A2C7"],
520 "MuttedColorShades2": ["#FFFFFF", "#E6E0EC", "#CCC1DA"],
521 "BrightColorShades": ["#FFFFFF", "#D0FFC5", "#7FFF8C"]}
522 ContourColorSchemes["PreProline"] = {"MuttedColorShades1": ["#FFFFFF", "#DCE6F2", "#95B3D7"],
523 "MuttedColorShades2": ["#FFFFFF", "#DCE6F2", "#B9CDE5"],
524 "BrightColorShades": ["#FFFFFF", "#B3E8FF", "#7FD9FF"]}
525
526 if re.match("^MuttedColorShades1$", OptionsInfo["LevelsAndColorsScheme"], re.I):
527 DefaultColorScheme = "MuttedColorShades1"
528 elif re.match("^MuttedColorShades2$", OptionsInfo["LevelsAndColorsScheme"], re.I):
529 DefaultColorScheme = "MuttedColorShades2"
530 elif re.match("^BrightColorShades$", OptionsInfo["LevelsAndColorsScheme"], re.I):
531 DefaultColorScheme = "BrightColorShades"
532 else:
533 MiscUtil.PrintError("The color scheme, %s, specified using \"--levelsAndColorsScheme\" option is not supported." % (OptionsInfo["LevelsAndColorsScheme"]))
534
535 for Type in ["General", "Glycine", "Proline", "PreProline"]:
536 PlotTypesInfo["Types"].append(Type)
537
538 # Setup phi and psi density file...
539 DensityFile = os.path.join(MayaChemToolsDataDir, "PhiPsiDensity%s.csv" % (Type))
540 if not os.path.exists(DensityFile):
541 MiscUtil.PrintError("The phi and psi density file file, %s, doesn't exist. This is required for generating contour plots.\n" % (DensityFile))
542 PlotTypesInfo["PhiPsiDensityFiles"][Type] = DensityFile
543
544 # Setup plot title...
545 Title = Type
546 if re.match("^PreProline$", Type, re.I):
547 Title = "pre-Proline"
548 PlotTypesInfo["Titles"][Type] = Title
549
550 # Setup flags for drawing axis labels...
551 DrawXLabel, DrawYLabel = [True] * 2
552 if not OptionsInfo["MultipleOutFiles"]:
553 # Turn off XLabel for plots in first row...
554 DrawXLabel = False if re.match("^(General|Glycine)$", Type, re.I) else True
555
556 # Turn off YLabel for plots in second column...
557 DrawYLabel = False if re.match("^(Glycine|PreProline)$", Type, re.I) else True
558 PlotTypesInfo["DrawXLabel"][Type] = DrawXLabel
559 PlotTypesInfo["DrawYLabel"][Type] = DrawYLabel
560
561 # Setup limits...
562 (MinLimit, MaxLimit) = [-180, 180]
563 PlotTypesInfo["Limits"][Type] = [MinLimit, MaxLimit]
564
565 # Setup major tick labels and positions...
566 MajorTickPositions = list(range(MinLimit, MaxLimit, OptionsInfo["TicksMajorInterval"]))
567 MajorTickPositions.append(MaxLimit)
568 MajorTickLabels = ["%s" % Position for Position in MajorTickPositions]
569 PlotTypesInfo["MajorTickPositions"][Type] = MajorTickPositions
570 PlotTypesInfo["MajorTickLabels"][Type] = MajorTickLabels
571
572 # Setup minor tick positions without any labels...
573 MinorTickPositions = list(range(MinLimit, MaxLimit, OptionsInfo["TicksMinorInterval"]))
574 MinorTickPositions.append(MaxLimit)
575 PlotTypesInfo["MinorTickPositions"][Type] = MinorTickPositions
576
577 # Setup contour levels and colors...
578 Levels = []
579 Colors = []
580 if re.match("^General$", Type, re.I):
581 Levels = [0.0, 0.0005, 0.02, 1.0]
582 Colors = ContourColorSchemes[Type][DefaultColorScheme]
583 elif re.match("^Glycine$", Type, re.I):
584 Levels = [0.0, 0.002, 0.02, 1.0]
585 Colors = ContourColorSchemes[Type][DefaultColorScheme]
586 elif re.match("^Proline$", Type, re.I):
587 Levels = [0.0, 0.002, 0.02, 1.0]
588 Colors = ContourColorSchemes[Type][DefaultColorScheme]
589 elif re.match("^PreProline$", Type, re.I):
590 Levels = [0.0, 0.002, 0.02, 1.0]
591 Colors = ContourColorSchemes[Type][DefaultColorScheme]
592
593 PlotTypesInfo["Levels"][Type] = Levels
594 PlotTypesInfo["Colors"][Type] = Colors
595
596 OptionsInfo["PlotTypesInfo"] = PlotTypesInfo
597
598 def SetupPlotTypesOutfiles():
599 """Setup output file names for plot types."""
600
601 OptionsInfo["OutfilesList"] = []
602 OptionsInfo["OutfilesList"].append(OptionsInfo["Outfile"])
603
604 OptionsInfo["PlotTypesInfo"]["Outfiles"] = {}
605 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
606 OptionsInfo["PlotTypesInfo"]["Outfiles"][PlotType] = None
607
608 if not OptionsInfo["MultipleOutFiles"]:
609 return
610
611 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
612 OutfileRoot = FileName
613 OutfileExt = FileExt
614
615 for PlotType in OptionsInfo["PlotTypesInfo"]["Types"]:
616 PlotOutfile = "%s_%s.%s" % (OutfileRoot, PlotType, OutfileExt)
617 if os.path.exists(PlotOutfile):
618 if not OptionsInfo["Overwrite"]:
619 MiscUtil.PrintError("The plot output file, %s, already exist. Use option \"--ov\" or \"--overwrite\" and try again.\n" % (PlotOutfile))
620
621 OptionsInfo["PlotTypesInfo"]["Outfiles"][PlotType] = PlotOutfile
622 OptionsInfo["OutfilesList"].append(PlotOutfile)
623
624 def ProcessOptions():
625 """Process and validate command line arguments and options."""
626
627 MiscUtil.PrintInfo("Processing options...")
628
629 # Validate options...
630 ValidateOptions()
631
632 OptionsInfo["OutMode"] = Options["--outMode"]
633 OptionsInfo["MultipleOutFiles"] = True if re.match("^MultipleFiles$", OptionsInfo["OutMode"], re.I) else False
634 MultipleOutFiles = OptionsInfo["MultipleOutFiles"]
635
636 OptionsInfo["FigDPI"] = int(Options["--figDPI"])
637
638 FigSize = Options["--figSize"]
639 Width = 6.4
640 Height = 4.8 if MultipleOutFiles else 6.4
641
642 if not re.match("^auto$", FigSize, re.I):
643 FigSizeWords = FigSize.split(",")
644 Width = float(FigSizeWords[0])
645 Height = float(FigSizeWords[1])
646 OptionsInfo["FigSize"] = FigSize
647 OptionsInfo["FigWidth"] = Width
648 OptionsInfo["FigHeight"] = Height
649
650 OptionsInfo["FontFamily"] = Options["--fontFamily"]
651 OptionsInfo["FontAxesSize"] = Options["--fontAxesSize"]
652 OptionsInfo["FontAxesWeight"] = Options["--fontAxesWeight"]
653 OptionsInfo["FontTicksSize"] = Options["--fontTicksSize"]
654 OptionsInfo["FontTicksWeight"] = Options["--fontTicksWeight"]
655 OptionsInfo["FontTitleSize"] = Options["--fontTitleSize"]
656 OptionsInfo["FontTitleWeight"] = Options["--fontTitleWeight"]
657
658 OptionsInfo["Greek"] = True if re.match("^Yes$", Options["--greek"], re.I) else False
659
660 OptionsInfo["Grid"] = True if re.match("^Yes$", Options["--grid"], re.I) else False
661 OptionsInfo["GridLineColor"] = Options["--gridLineColor"]
662 OptionsInfo["GridLineStyle"] = Options["--gridLineStyle"]
663 OptionsInfo["GridLineWidth"] = float(Options["--gridLineWidth"])
664
665 OptionsInfo["Infile"] = Options["--infile"]
666 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Infile"])
667 OptionsInfo["InfileRoot"] = FileName
668
669 OptionsInfo["LevelsAndColorsScheme"] = Options["--levelsAndColorsScheme"]
670
671 OptionsInfo["Outfile"] = Options["--outfile"]
672 FileDir, FileName, FileExt = MiscUtil.ParseFileName(OptionsInfo["Outfile"])
673 OptionsInfo["OutfileRoot"] = FileName
674
675 OptionsInfo["Overwrite"] = Options["--overwrite"]
676 OptionsInfo["Precision"] = int(Options["--precision"])
677
678 OptionsInfo["ScatterMarkerColor"] = Options["--scatterMarkerColor"]
679 OptionsInfo["ScatterMarkerSize"] = float(Options["--scatterMarkerSize"])
680 OptionsInfo["ScatterMarkerStyle"] = Options["--scatterMarkerStyle"]
681
682 TicksMajorInterval = 90 if MultipleOutFiles else 180
683 if not re.match("^auto$", Options["--ticksMajorInterval"], re.I):
684 TicksMajorInterval = int(Options["--ticksMajorInterval"])
685 OptionsInfo["TicksMajorInterval"] = TicksMajorInterval
686
687 OptionsInfo["TicksMinor"] = True if re.match("^Yes$", Options["--ticksMinor"], re.I) else False
688 TicksMinorInterval = 10 if MultipleOutFiles else 45
689 if not re.match("^auto$", Options["--ticksMinorInterval"], re.I):
690 TicksMinorInterval = int(Options["--ticksMinorInterval"])
691 OptionsInfo["TicksMinorInterval"] = TicksMinorInterval
692
693 RetrieveInfileInfo()
694 OptionsInfo["ChainIDs"] = Options["--chainIDs"]
695
696 ProcessChainIDs()
697
698 OptionsInfo["LevelsAndColors"] = Options["--levelsAndColors"]
699 SetupPlotsInfo()
700
701 def RetrieveOptions():
702 """Retrieve command line arguments and options."""
703
704 # Get options...
705 global Options
706 Options = docopt(_docoptUsage_)
707
708 # Set current working directory to the specified directory...
709 WorkingDir = Options["--workingdir"]
710 if WorkingDir:
711 os.chdir(WorkingDir)
712
713 # Handle examples option...
714 if "--examples" in Options and Options["--examples"]:
715 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
716 sys.exit(0)
717
718 def ValidateOptions():
719 """Validate option values."""
720
721 MiscUtil.ValidateOptionIntegerValue("--figDPI", Options["--figDPI"], {">": 0})
722 if not re.match("^auto$", Options["--figSize"], re.I):
723 MiscUtil.ValidateOptionNumberValues("--figSize", Options["--figSize"], 2, ",", "float", {">": 0})
724
725 MiscUtil.ValidateOptionFilePath("-i, --infile", Options["--infile"])
726 MiscUtil.ValidateOptionFileExt("-i, --infile", Options["--infile"], "pdb cif")
727
728 MiscUtil.ValidateOptionTextValue("-g, --greek", Options["--greek"], "yes no")
729
730 MiscUtil.ValidateOptionTextValue("--grid", Options["--grid"], "yes no")
731 MiscUtil.ValidateOptionFloatValue("--gridLineWidth", Options["--gridLineWidth"], {">": 0})
732
733 MiscUtil.ValidateOptionTextValue("--levelsAndColorsScheme", Options["--levelsAndColorsScheme"], "MuttedColorShades1 MuttedColorShades2 BrightColorShades")
734
735 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
736
737 MiscUtil.ValidateOptionTextValue("--outMode", Options["--outMode"], "SingleFile MultipleFiles")
738 MiscUtil.ValidateOptionIntegerValue("-p, --precision", Options["--precision"], {">": 0})
739
740 MiscUtil.ValidateOptionFloatValue("--scatterMarkerSize", Options["--scatterMarkerSize"], {">": 0})
741
742 if not re.match("^auto$", Options["--ticksMajorInterval"], re.I):
743 MiscUtil.ValidateOptionIntegerValue("--ticksMajorInterval", Options["--ticksMajorInterval"], {">": 0, "<": 360})
744
745 MiscUtil.ValidateOptionTextValue("--ticksMinor", Options["--ticksMinor"], "yes no")
746 if not re.match("^auto$", Options["--ticksMinorInterval"], re.I):
747 MiscUtil.ValidateOptionIntegerValue("--ticksMinorInterval", Options["--ticksMinorInterval"], {">": 0, "<": 360})
748
749 # Setup a usage string for docopt...
750 _docoptUsage_ = """
751 PyMOLGenerateRamachandranPlots.py - Generate Ramachandran plots
752
753 Usage:
754 PyMOLGenerateRamachandranPlots.py [--chainIDs <First, All or ID1,ID2...>]
755 [--figDPI <number>] [--figSize <width, height>] [--fontFamily <text>]
756 [--fontAxesSize <number or text>] [--fontAxesWeight <number or text>]
757 [--fontTicksSize <number or text>] [--fontTicksWeight <number or text>]
758 [--fontTitleSize <number or text>] [--fontTitleWeight <number or text>] [--greek <yes or no>]
759 [--grid <yes or no>] [--gridLineColor <text>] [--gridLineStyle <text>] [--gridLineWidth <number>]
760 [--levelsAndColors <PlotType:Level,color,Level,...;...>] [--levelsAndColorsScheme <text>]
761 [--outMode <SingleFile or MultipleFiles>] [--overwrite] [--precision <number>]
762 [--scatterMarkerColor <text>] [--scatterMarkerSize <number>] [--scatterMarkerStyle <text>]
763 [--ticksMajorInterval <number>] [--ticksMinor <yes or no>] [--ticksMinorInterval <number>]
764 [-w <dir>] -i <infile> -o <outfile>
765 PyMOLGenerateRamachandranPlots.py -h | --help | -e | --examples
766
767 Description:
768 Generate Ramachandran plots for amino acid residues present in macromolecules.
769
770 The Ramachandran plots are generated by plotting phi and psi backbone angles
771 corresponding to the following four categories of amino acids:
772
773 General: All residues except glycine, proline, or pre-proline
774 Glycine: Only glycine residues
775 Proline: Only proline residues
776 PreProline: Only residues before proline not including glycine or
777 proline
778
779 In addition to the scatter plots for phi and psi angles, the filled contours
780 are generated for the density of phi and psi angles [ Ref 144 ] for the
781 Ramachandran plots. The contours are generated for "favored" and "allowed"
782 regions. The phi and psi density is retrieved from the following density files
783 available in MAYACHEMTOOLS/lib/data/ directory:
784
785 General: PhiPsiDensityGeneral.csv
786 Glycine: PhiPsiDensityGlycine.csv
787 Proline: PhiPsiDensityProline.csv
788 PreProline: PhiPsiDensityPreProline.csv
789
790 The supported input file format are: PDB (.pdb), mmCIF (.cif)
791
792 The output image file can be saved in any format supported by Python
793 module Matplotlib. The image format is automatically detected from the
794 output file extension.
795
796 Some of the most common output image file formats are: EPS (.eps), PDF (.pdf),
797 PNG (.png), PS (.ps), SVG (.svg).
798
799 Options:
800 -c, --chainIDs <First, All or ID1,ID2...> [default: All]
801 List of chain IDs to use for calculating phi and psi angles for residues
802 in chains. Possible values: First, All, or a comma delimited list of chain
803 IDs. The default is to use all chain IDs in input file.
804 -e, --examples
805 Print examples.
806 --figDPI <number> [default: 300]
807 Figure resolution in dots per inches. The DPI value must be supported
808 by Matplotlib during generation of an image of a specific format. No
809 validation is performed.
810 --figSize <width, height> [default: auto]
811 Figure dimensions in inches. The default values are dependent on the
812 the value of '--outMode' option as shown below:
813
814 SingleFile: 6.4, 6.4
815 MultipleFiles: 6.4, 4.8
816
817 --fontFamily <text> [default: auto]
818 Font family to use for title, axes labels, and tick marks. It must be a
819 valid Matplotlib value. The default value corresponds to the value
820 plt.rcParams["font.family"] in your environment. For example: serif,
821 sans-serif, cursive, etc.
822 --fontAxesSize <number or text> [default: 10]
823 Font size for labels on axes. It must be valid Matplotlib font size. For
824 example: size in points, xx-small, x-small, small, medium, etc.
825 --fontAxesWeight <number or text> [default: regular]
826 Font weight for labels on axes. It must be valid Matplotlib value. For
827 example: a numeric value in range 0-1000, ultralight, light, normal,
828 regular, book, medium, etc.
829 --fontTicksSize <number or text> [default: 8]
830 Font size for tick labels. It must be a valid Matplotlib font size. For
831 example: size in points, xx-small, x-small, small, medium, etc.
832 --fontTicksWeight <number or text> [default: regular]
833 Font weight for tick labels. It must be valid Matplotlib value. For
834 example: a numeric value in range 0-1000, ultralight, light,
835 normal, regular, book, medium, etc.
836 --fontTitleSize <number or text> [default: 10]
837 Font size for title. It must be a valid Matplotlib font size. For example:
838 size in points, xx-small, x-small, small, medium, etc.
839 --fontTitleWeight <number or text> [default: bold]
840 Font weight for title. It must be a valid Matplotlib value. For example: a
841 numeric value in range 0-1000, ultralight, light, normal, regular, book,
842 medium, etc.
843 -g, --greek <yes or no> [default: yes]
844 Show phi and psi labels as greek characters.
845 --grid <yes or no> [default: yes]
846 Display grid lines at major tick marks.
847 --gridLineColor <text> [default: #b0b0b0]
848 Grid line color. It must be a valid Matplotlib value. The default color
849 is light gray.
850 --gridLineStyle <text> [default: dotted]
851 Grid line style. It must be a valid Matplotlib value. For example:
852 '-' or 'solid', --' or 'dashed', '-.' or 'dashdot', ':' or 'dotted' etc.
853 --gridLineWidth <number> [default: 0.8]
854 Grid line width. It must be a valid Matplotlib value.
855 -h, --help
856 Print this help message.
857 -i, --infile <infile>
858 Input file name.
859 -l, --levelsAndColors <PlotType:Level,color,Level,...;...> [default: auto]
860 Semicolon delimited list of contour levels and colors for four types
861 of Ramachandran plots.
862
863 Three default contour level and color scheme may be specified by
864 '--levelsAndColorsScheme' option. By default, the 'MuttedColorShades1'
865 scheme is used. The default contour levels correspond to 'favored' and
866 'allowed' regions [ Ref 144 ] for phi and psi angles.
867
868 The colors are used to fill spaces between contour levels. The values
869 for contour levels must be ascending order. The number of colors
870 must be one less than the number contour levels.
871
872 The format of contour level and color specification is as follows:
873
874 PlotType:Level,Color,Level,...;PlotType:Level,Color,Level,...
875
876 The valid values for plot type are:
877
878 General, Glycine, Proline, or PreProline
879
880 The contour level must be a number. The color value must be a valid color
881 name or a hexadecimal color string supported by Matplotlib. No validation
882 is performed.
883
884 For example:
885
886 General: 0.0, #FFFFFF, 0.0005, #EBF1DE, 0.02, #C3D69B, 1.0
887
888 --levelsAndColorsScheme <text> [default: MuttedColorShades1]
889 Default contour levels and colors scheme. Possible values:
890 MuttedColorShades1, MuttedColorShades2, or BrightColorShades.
891
892 This option is only used during 'auto' value of '--levelsAndColors' option.
893 The default contour levels correspond to 'favored' and 'allowed' regions
894 [ Ref 144 ] for phi and psi angles.
895
896 The default contour and color values for different default schemes are
897 shown below:
898
899 MuttedColorShades1:
900
901 General: 0.0, #FFFFFF, 0.0005, #EBF1DE, 0.02, #C3D69B, 1.0
902 Glycine: 0.0, #FFFFFF, 0.002, #7FD9FF, 0.02, #FAC090, 1.0
903 Proline: 0.0, #FFFFFF, 0.002, #E6E0EC, 0.02, #B3A2C7, 1.0
904 PreProline: 0.0, #FFFFFF, 0.002, #DCE6F2, 0.02, #95B3D7, 1.0
905
906 MuttedColorShades2:
907
908 General: 0.0, #FFFFFF, 0.0005, #EBF1DE, 0.02, #D7E4BD, 1.0
909 Glycine: 0.0, #FFFFFF, 0.002, #FDEADA, 0.02, #FCD5B5, 1.0
910 Proline: 0.0, #FFFFFF, 0.002, #E6E0EC, 0.02, #CCC1DA, 1.0
911 PreProline: 0.0, #FFFFFF, 0.002, #DCE6F2, 0.02, #B9CDE5, 1.0
912
913 BrightColorShades: [ Ref 145 ]
914
915 General: 0.0, #FFFFFF, 0.0005, #B3E8FF, 0.02, #7FD9FF, 1.0
916 Glycine: 0.0, #FFFFFF, 0.002, #FFE8C5, 0.02, #FFCC7F, 1.0
917 Proline: 0.0, #FFFFFF, 0.002, #D0FFC5, 0.02, #7FFF8C, 1.0
918 PreProline: 0.0, #FFFFFF, 0.002, #B3E8FF, 0.02, #7FD9FF, 1.0
919
920 -o, --outfile <outfile>
921 Output image file name.
922
923 A set of output files is optionally generated for 'MultipleFiles' value of
924 '--outMode' option. The names of these output files are automatically
925 generated from the the name of the specified output file as shown
926 below:
927
928 General: <OutfileRoot>_General.<OutfileExt>
929 Glycine: <OutfileRoot>_Glycine.<OutfileExt>
930 Proline: <OutfileRoot>_Proline.<OutfileExt>
931 PreProline: <OutfileRoot>_PreProline.<OutfileExt>
932
933 --outMode <Single or Multiple> [default: SingleFile]
934 A single output file containing all four Ramachandran plots or multiple
935 output files corresponding to different types of Ramachandran plots.
936
937 The phi and psi angles are categorized into the following groups
938 corresponding to four types of Ramachandran plots:
939
940 General: All residues except glycine, proline, or pre-proline
941 Glycine: Only glycine residues
942 Proline: Only proline residues
943 PreProline: Only residues before proline not including glycine or
944 proline
945
946 --overwrite
947 Overwrite existing files.
948 -p, --precision <number> [default: 2]
949 Floating point precision for plotting the calculated phi and psi angles.
950 --scatterMarkerColor <text> [default: #1f77b4]
951 Scatter marker color for plotting to phi and psi angles. It must be a
952 valid Matplotlib value. The default color is dark blue.
953 --scatterMarkerSize <number> [default: 1.0]
954 Scatter marker size for piloting phi and psi angles. It must be a valid
955 Matplotlib value.
956 --scatterMarkerStyle <text> [default: .]
957 Scatter marker style for piloting phi and psi angles. It must be a valid
958 Matplotlib value. For example: '.' (point), ',' (pixel), 'o' (circle), etc.
959 --ticksMajorInterval <number> [default: auto]
960 Display major marks on axes at intervals specified in degrees for phi and
961 psi angles. The default value is dependent on the the value of '--outMode'
962 option: SingleFile: 180; MultipleFiles: 90
963
964 The grid lines are drawn at the locations of major tick marks.
965 --ticksMinor <yes or no> [default: yes]
966 Display minor tick marks. The major tick mark are always displayed.
967 --ticksMinorInterval <number> [default: auto]
968 Display minor marks on axes at intervals specified in degrees for phi and
969 psi angles. The default value is dependent on the the value of '--outMode'
970 option: SingleFile: 45; MultipleFiles: 10
971 -w, --workingdir <dir>
972 Location of working directory which defaults to the current directory.
973
974 Examples:
975 To generate Ramachandran plot for all residues across all chains in input
976 file and write out a single SVG file containing all four types of plots, type:
977
978 % PyMOLGenerateRamachandranPlots.py -i Sample3.pdb -o Sample3Out.svg
979
980 To generate Ramachandran plot for all residues across all chains in input
981 file and write out four SVG files corresponding to four types of plots, type:
982
983 % PyMOLGenerateRamachandranPlots.py --outMode MultipleFiles
984 -i Sample3.pdb -o Sample3Out.svg
985
986 To generate Ramachandran plot for all residues in a specific chain in input
987 file and write out a single PDF file containing all four types of plots, type:
988
989 % PyMOLGenerateRamachandranPlots.py -c E -i Sample3.pdb
990 -o Sample3Out.pdf
991
992 To generate Ramachandran plot for all residues across all chains in input
993 file using specific options and write out four PNG files containing all four
994 types of plots, type:
995
996 % PyMOLGenerateRamachandranPlots.py --outMode MultipleFiles
997 --figSize "6,4" --figDPI 600 --fontTitleSize 10 --fontTitleWeight
998 normal --greek no --grid no --levelsAndColors
999 "General: 0.0, #FFFFFF, 0.0005, #B3E8FF, 0.02, #7FD9FF, 1.0"
1000 -i Sample3.pdb -o Sample3Out.png
1001
1002 Author:
1003 Manish Sud(msud@san.rr.com)
1004
1005 See also:
1006 DownloadPDBFiles.pl, PyMOLCalculatePhiPsiAngles.py, PyMOLCalculateRMSD.py,
1007 PyMOLCalculateProperties.py
1008
1009 Copyright:
1010 Copyright (C) 2025 Manish Sud. All rights reserved.
1011
1012 The functionality available in this script is implemented using PyMOL, a
1013 molecular visualization system on an open source foundation originally
1014 developed by Warren DeLano.
1015
1016 This file is part of MayaChemTools.
1017
1018 MayaChemTools is free software; you can redistribute it and/or modify it under
1019 the terms of the GNU Lesser General Public License as published by the Free
1020 Software Foundation; either version 3 of the License, or (at your option) any
1021 later version.
1022
1023 """
1024
1025 if __name__ == "__main__":
1026 main()
