1 #!/bin/env python
2 #
3 # File: RDKitDrawMolecules.py
4 # Author: Manish Sud <msud@san.rr.com>
5 #
6 # Copyright (C) 2024 Manish Sud. All rights reserved.
7 #
8 # The functionality available in this script is implemented using RDKit, an
9 # open source toolkit for cheminformatics developed by Greg Landrum.
10 #
11 # This file is part of MayaChemTools.
12 #
13 # MayaChemTools is free software; you can redistribute it and/or modify it under
14 # the terms of the GNU Lesser General Public License as published by the Free
15 # Software Foundation; either version 3 of the License, or (at your option) any
16 # later version.
17 #
18 # MayaChemTools is distributed in the hope that it will be useful, but without
19 # any warranty; without even the implied warranty of merchantability of fitness
20 # for a particular purpose. See the GNU Lesser General Public License for more
21 # details.
22 #
23 # You should have received a copy of the GNU Lesser General Public License
24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
26 # Boston, MA, 02111-1307, USA.
27 #
28
29 from __future__ import print_function
30
31 # Add local python path to the global path and import standard library modules...
32 import os
33 import sys; sys.path.insert(0, os.path.join(os.path.dirname(sys.argv[0]), "..", "lib", "Python"))
34 import time
35 import re
36
37 # RDKit imports...
38 try:
39 from rdkit import rdBase
40 from rdkit import Chem
41 from rdkit.Chem import AllChem
42 from rdkit.Chem import Draw
43 from rdkit.Chem.Draw.MolDrawing import DrawingOptions
44 except ImportError as ErrMsg:
45 sys.stderr.write("\nFailed to import RDKit module/package: %s\n" % ErrMsg)
46 sys.stderr.write("Check/update your RDKit environment and try again.\n\n")
47 sys.exit(1)
48
49 # MayaChemTools imports...
50 try:
51 from docopt import docopt
52 import MiscUtil
53 import RDKitUtil
54 except ImportError as ErrMsg:
55 sys.stderr.write("\nFailed to import MayaChemTools module/package: %s\n" % ErrMsg)
56 sys.stderr.write("Check/update your MayaChemTools environment and try again.\n\n")
57 sys.exit(1)
58
59 ScriptName = os.path.basename(sys.argv[0])
60 Options = {}
61 OptionsInfo = {}
62
63 def main():
64 """Start execution of the script."""
65
66 MiscUtil.PrintInfo("\n%s (RDKit v%s; MayaChemTools v%s; %s): Starting...\n" % (ScriptName, rdBase.rdkitVersion, MiscUtil.GetMayaChemToolsVersion(), time.asctime()))
67
68 (WallClockTime, ProcessorTime) = MiscUtil.GetWallClockAndProcessorTime()
69
70 # Retrieve command line arguments and options...
71 RetrieveOptions()
72
73 # Process and validate command line arguments and options...
74 ProcessOptions()
75
76 # Perform actions required by the script...
77 DrawMolecules()
78
79 MiscUtil.PrintInfo("\n%s: Done...\n" % ScriptName)
80 MiscUtil.PrintInfo("Total time: %s" % MiscUtil.GetFormattedElapsedTime(WallClockTime, ProcessorTime))
81
82 def DrawMolecules():
83 """Draw molecules."""
84
85 Infile = OptionsInfo["Infile"]
86 Outfile = OptionsInfo["Outfile"]
87
88 # Read molecules...
89 MiscUtil.PrintInfo("\nReading file %s..." % Infile)
90
91 ValidMols, MolCount, ValidMolCount = RDKitUtil.ReadAndValidateMolecules(Infile, **OptionsInfo["InfileParams"])
92
93 MiscUtil.PrintInfo("Total number of molecules: %d" % MolCount)
94 MiscUtil.PrintInfo("Number of valid molecules: %d" % ValidMolCount)
95 MiscUtil.PrintInfo("Number of ignored molecules: %d" % (MolCount - ValidMolCount))
96
97 # Compute 2D coordinates...
98 if OptionsInfo["Compute2DCoords"]:
99 MiscUtil.PrintInfo("\nComputing 2D coordinates...")
100 for Mol in ValidMols:
101 AllChem.Compute2DCoords(Mol)
102
103 MiscUtil.PrintInfo("Generating image grid...")
104
105 # Setup atoms lists for highlighting atoms and bonds...
106 AtomLists = SetupAtomListsToHighlight(ValidMols)
107 BondLists = None
108
109 # Set up legends...
110 MolNames = None
111 if OptionsInfo["ShowMolName"]:
112 MolNames = []
113 MolCount = 0
114 for Mol in ValidMols:
115 MolCount += 1
116 MolName = RDKitUtil.GetMolName(Mol, MolCount)
117 MolNames.append(MolName)
118
119 # Perform alignment to a common template...
120 PerformAlignment(ValidMols)
121
122 # Generate appropriate output files...
123 if MiscUtil.CheckFileExt(Outfile, "svg"):
124 GenerateSVGImageFile(ValidMols, MolNames, AtomLists, BondLists)
125 elif MiscUtil.CheckFileExt(Outfile, "html htm"):
126 GenerateHTMLTableFile(ValidMols, MolNames, AtomLists, BondLists)
127 else:
128 GenerateImageFile(ValidMols, MolNames, AtomLists, BondLists)
129
130 def GenerateSVGImageFile(ValidMols, MolNames, AtomLists, BondLists):
131 """Generate a SVG image file."""
132
133 MolsSVGText = RDKitUtil.GetSVGForMolecules(ValidMols, OptionsInfo["NumOfMolsPerRow"], OptionsInfo["MolImageWidth"], OptionsInfo["MolImageHeight"], Legends = MolNames, AtomListsToHighlight = AtomLists, BondListsToHighlight = BondLists, BoldText = OptionsInfo["FontBold"])
134
135 MiscUtil.PrintInfo("\nGenerating SVG image file %s..." % OptionsInfo["Outfile"])
136
137 OutFH = open(OptionsInfo["Outfile"], "w")
138 OutFH.write(MolsSVGText)
139 OutFH.close()
140
141 def GenerateImageFile(ValidMols, MolNames, AtomLists, BondLists):
142 """Generate a non SVG image file."""
143
144 Outfile = OptionsInfo["Outfile"]
145
146 NumOfMolsPerRow = OptionsInfo["NumOfMolsPerRow"]
147 Width = OptionsInfo["MolImageWidth"]
148 Height = OptionsInfo["MolImageHeight"]
149
150 # Setup drawing options...
151 UpdatedDrawingOptions = DrawingOptions()
152 UpdatedDrawingOptions.atomLabelFontSize = int(OptionsInfo["AtomLabelFontSize"])
153 UpdatedDrawingOptions.bondLineWidth = float(OptionsInfo["BondLineWidth"])
154
155 try:
156 MolsImage = Draw.MolsToGridImage(ValidMols, molsPerRow = NumOfMolsPerRow, subImgSize = (Width,Height), legends = MolNames, highlightAtomLists = AtomLists, highlightBondLists = BondLists, useSVG = False, kekulize = OptionsInfo["Kekulize"], options = UpdatedDrawingOptions)
157 except Exception as ErrMsg:
158 # MolsToGridImage doesn't appear to handle the following parameters in the latest version of RDKit:
159 # . kekulize = OptionsInfo["Kekulize"], options = UpdatedDrawingOptions
160 MolsImage = Draw.MolsToGridImage(ValidMols, molsPerRow = NumOfMolsPerRow, subImgSize = (Width,Height), legends = MolNames, highlightAtomLists = AtomLists, highlightBondLists = BondLists, useSVG = False, returnPNG = False)
161
162 MiscUtil.PrintInfo("\nGenerating image file %s..." % Outfile)
163
164 if MiscUtil.CheckFileExt(Outfile, "pdf"):
165 if MolsImage.mode == 'RGBA':
166 MolsImage = MolsImage.convert('RGB')
167
168 MolsImage.save(Outfile)
169
170 def GenerateHTMLTableFile(ValidMols, MolNames, HighlightAtomLists, HighlightBondLists):
171 """Generate a HTML table file."""
172
173 Outfile = OptionsInfo["Outfile"]
174
175 Writer = open(Outfile, "w")
176 if Writer is None:
177 MiscUtil.PrintError("Failed to setup a writer for output fie %s " % Outfile)
178
179 MiscUtil.PrintInfo("\nGenerating HTML table file %s..." % Outfile)
180
181 WriteHTMLPageHeader(Writer, len(ValidMols))
182 WriteHTMLPageTitle(Writer)
183
184 WriteHTMLTableHeader(Writer)
185 WriteHTMLTableRows(Writer, ValidMols, MolNames, HighlightAtomLists, HighlightBondLists)
186 WriteHTMLTableEnd(Writer)
187
188 WriteHTMLPageFooter(Writer)
189 WriteHTMLPageEnd(Writer)
190
191 if Writer is not None:
192 Writer.close()
193
194 def WriteHTMLTableRows(Writer, ValidMols, MolNames, HighlightAtomLists, HighlightBondLists):
195 """Write out HTML table rows."""
196
197 WriteTableHeaderRow(Writer, ValidMols)
198 WriteTableDataRows(Writer, ValidMols, MolNames, HighlightAtomLists, HighlightBondLists)
199 WriteTableFooterRow(Writer, ValidMols)
200
201 def WriteTableDataRows(Writer, ValidMols, MolNames, HighlightAtomLists, HighlightBondLists):
202 """Write out table data row."""
203
204 Writer.write(""" <tbody>\n""")
205
206 MolCount = len(ValidMols)
207 ColCount = GetColCount(MolCount)
208
209 for Index in range(0, MolCount, ColCount):
210 Writer.write(""" <tr>\n""")
211
212 if OptionsInfo["CounterCol"]:
213 Writer.write(""" <td></td>\n""")
214
215 for MolIndex in range(Index, (Index + ColCount)):
216 SetupStructureDataDrawing(Writer, MolIndex, ValidMols, MolNames, HighlightAtomLists, HighlightBondLists)
217
218 Writer.write(""" </tr>\n""")
219
220 Writer.write(""" </tbody>\n""")
221
222 def SetupStructureDataDrawing(Writer, MolIndex, Mols, MolNames, HighlightAtomLists, HighlightBondLists):
223 """Setup structure data drawing for a tabel cell."""
224
225 if MolIndex >= len(Mols):
226 Writer.write(""" <td></td>\n""")
227 return
228
229 Mol = Mols[MolIndex]
230 MolName = None if MolNames is None else MolNames[MolIndex]
231 HighlightAtomList = None if HighlightAtomLists is None else HighlightAtomLists[MolIndex]
232 HighlightBondList = None if HighlightBondLists is None else HighlightBondLists[MolIndex]
233
234 SVGText = RDKitUtil.GetInlineSVGForMolecule(Mol, OptionsInfo["MolImageWidth"], OptionsInfo["MolImageHeight"], Legend = MolName, AtomListToHighlight = HighlightAtomList, BondListToHighlight = HighlightBondList, BoldText = OptionsInfo["FontBold"], Base64Encoded = OptionsInfo["MolImageEncoded"])
235
236 PopoverTag = GetMolPopoverTag(Mol)
237 ImageTag = "img" if PopoverTag is None else "img %s" % PopoverTag
238
239 if OptionsInfo["MolImageEncoded"]:
240 SVGInlineImageTag = "%s src=\"data:image/svg+xml;base64,\n%s\"" % (ImageTag, SVGText)
241 else:
242 SVGInlineImageTag = "%s src=\"data:image/svg+xml;charset=UTF-8,\n%s\"" % (ImageTag, SVGText)
243
244 Writer.write(""" <td bgcolor="white"><%s></td>\n""" % SVGInlineImageTag)
245
246 def WriteTableHeaderRow(Writer, ValidMols):
247 """Write out table header row."""
248
249 if not OptionsInfo["TableHeader"]:
250 return
251
252 TableHeaderStyle = OptionsInfo["TableHeaderStyle"]
253 if TableHeaderStyle is None:
254 Writer.write(""" <thead>\n""")
255 Writer.write(""" <tr>\n""")
256 elif re.match("^(thead|table)", TableHeaderStyle):
257 Writer.write(""" <thead class="%s">\n""" % TableHeaderStyle)
258 Writer.write(""" <tr>\n""")
259 else:
260 Writer.write(""" <thead>\n""")
261 Writer.write(""" <tr bgcolor="%s"\n""" % TableHeaderStyle)
262
263 if OptionsInfo["CounterCol"]:
264 Writer.write(""" <th></th>\n""")
265
266 # Write out rest of the column headers...
267 MolCount = len(ValidMols)
268 ColCount = GetColCount(MolCount)
269 for ColIndex in range(0, ColCount):
270 ColLabel = MiscUtil.GetExcelStyleColumnLabel(ColIndex + 1)
271 Writer.write(""" <th>%s</th>\n""" % ColLabel)
272
273 Writer.write(""" </tr>\n""")
274 Writer.write(""" </thead>\n""")
275
276 def WriteTableFooterRow(Writer, ValidMols):
277 """Write out table footer row."""
278
279 if not OptionsInfo["TableFooter"]:
280 return
281
282 Writer.write(""" <tfoot>\n""")
283 Writer.write(""" <tr>\n""")
284
285 if OptionsInfo["CounterCol"]:
286 Writer.write(""" <td></td>\n""")
287
288 # Write out rest of the column headers...
289 MolCount = len(ValidMols)
290 ColCount = GetColCount(MolCount)
291 for ColIndex in range(0, ColCount):
292 ColLabel = MiscUtil.GetExcelStyleColumnLabel(ColIndex + 1)
293 Writer.write(""" <td>%s</td>\n""" % ColLabel)
294
295 Writer.write(""" </tr>\n""")
296 Writer.write(""" </tfoot>\n""")
297
298 def WriteHTMLPageHeader(Writer, MolCount):
299 """Write out HTML page header."""
300
301 ColCount = GetColCount(MolCount)
302
303 # Exclude counter and structure columns from sorting and searching...
304 if OptionsInfo["CounterCol"]:
305 ColIndicesList = ["0"]
306 ColVisibilityExcludeColIndicesList = ["0"]
307 ColIndexOffset = 1
308 FreezeLeftColumns = "1"
309 else:
310 ColIndicesList = []
311 ColVisibilityExcludeColIndicesList = []
312 ColIndexOffset = 0
313
314 MaxDataColVisColCount = 25
315 for Index in range(0, ColCount):
316 ColIndex = Index + ColIndexOffset
317 ColIndicesList.append("%s" % ColIndex)
318
319 if OptionsInfo["ColVisibility"]:
320 if Index >= MaxDataColVisColCount:
321 ColVisibilityExcludeColIndicesList.append("%s" %ColIndex)
322
323 ColIndices = MiscUtil.JoinWords(ColIndicesList, ", ") if len(ColIndicesList) else ""
324 ColVisibilityExcludeColIndices = MiscUtil.JoinWords(ColVisibilityExcludeColIndicesList, ", ") if len(ColVisibilityExcludeColIndicesList) else ""
325
326 DataColVisibilityExclude = False
327 if OptionsInfo["ColVisibility"]:
328 if ColCount > MaxDataColVisColCount:
329 DataColVisibilityExclude = True
330 MiscUtil.PrintWarning("The number of data columns, %d, is quite large. Only first %d data columns will be available in column visibility pulldown." % (ColCount, MaxDataColVisColCount))
331
332 DisplayButtons = False
333 if OptionsInfo["ColVisibility"]:
334 if ColCount > 0:
335 DisplayButtons = True
336
337 FreezeCols = False
338 if (OptionsInfo["CounterCol"] and OptionsInfo["ScrollX"]):
339 FreezeCols = True
340
341 Paging = "true" if OptionsInfo["Paging"] else "false"
342 PageLength = "%d" % OptionsInfo["PageLength"]
343 PagingType = "\"%s\"" % OptionsInfo["PagingType"]
344
345 ScrollX = "true" if OptionsInfo["ScrollX"] else "false"
346
347 ScrollY = ""
348 if OptionsInfo["ScrollY"]:
349 if re.search("vh$", OptionsInfo["ScrollYSize"]):
350 ScrollY = "\"%s\"" % OptionsInfo["ScrollYSize"]
351 else:
352 ScrollY = "%s" % OptionsInfo["ScrollYSize"]
353
354 # Start HTML header...
355 Title = "Molecules table" if OptionsInfo["Header"] is None else OptionsInfo["Header"]
356
357 Writer.write("""\
358 <!doctype html>
359 <html lang="en">
360 <head>
361 <title>%s</title>
362 <meta charset="utf-8">
363 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
364 <link rel="stylesheet" type="text/css" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css">
365 <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/1.10.16/css/dataTables.bootstrap4.min.css">
366
367 """ % (Title))
368
369 if (FreezeCols):
370 Writer.write("""\
371 <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/fixedcolumns/3.2.4/css/fixedColumns.bootstrap4.min.css">
372 """)
373
374 if (OptionsInfo["KeysNavigation"]):
375 Writer.write("""\
376 <link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/keytable/2.3.2/css/keyTable.bootstrap4.min.css">
377 """)
378
379 Writer.write("""\
380
381 <script type="text/javascript" language="javascript" src="https://code.jquery.com/jquery-1.12.4.js"></script>
382 <script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.16/js/jquery.dataTables.min.js"></script>
383 <script type="text/javascript" language="javascript" src="https://cdn.datatables.net/1.10.16/js/dataTables.bootstrap4.min.js"></script>
384
385 """)
386
387 if (OptionsInfo["Popover"]):
388 Writer.write("""\
389 <script type="text/javascript" language="javascript" src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js"></script>
390 <script type="text/javascript" language="javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"></script>
391
392 """)
393
394 if DisplayButtons:
395 Writer.write("""\
396 <script type="text/javascript" language="javascript" src="https://cdn.datatables.net/buttons/1.5.1/js/dataTables.buttons.min.js"></script>
397 <script type="text/javascript" language="javascript" src="https://cdn.datatables.net/buttons/1.5.1/js/buttons.bootstrap4.min.js"></script>
398 <script type="text/javascript" language="javascript" src="https://cdn.datatables.net/buttons/1.5.1/js/buttons.colVis.min.js"></script>
399
400 """)
401
402 if (FreezeCols):
403 Writer.write("""\
404 <script type="text/javascript" language="javascript" src="https://cdn.datatables.net/fixedcolumns/3.2.4/js/dataTables.fixedColumns.min.js"></script>
405 """)
406
407 if (OptionsInfo["KeysNavigation"]):
408 Writer.write("""\
409 <script type="text/javascript" language="javascript" src="https://cdn.datatables.net/keytable/2.3.2/js/dataTables.keyTable.min.js"></script>
410 """)
411
412 # Intialize table using Bootstrap, DataTables and JQuery frameworks...
413 Writer.write("""\
414
415 <script type="text/javascript" class="init">
416
417 $(document).ready(function() {
418 """)
419
420 if (OptionsInfo["Popover"]):
421 Writer.write("""\
422 $('.MolPopover').popover();
423
424 """)
425
426 Writer.write("""\
427 var MolsTable = $('#MolsTable').DataTable( {
428 "columnDefs": [
429 {
430 "orderable": false,
431 "searchable": false,
432 "targets": [%s]
433 },
434 """ % (ColIndices))
435
436 if OptionsInfo["ColVisibility"]:
437 Writer.write("""\
438 {
439 "className": "noColVisCtrl",
440 "targets": [%s]
441 }
442 """ % (ColVisibilityExcludeColIndices))
443
444 Writer.write("""\
445 ],
446 """)
447
448 # Set up dom for displaying button and other options...
449 if OptionsInfo["ColVisibility"]:
450 if OptionsInfo["Paging"]:
451 Writer.write("""\
452 "dom": "<'row'<'col-sm-6'l><'col-sm-6'<'float-right'B>>>" +
453 "<'row'<'col-sm-12'tr>>" +
454 "<'row'<'col-sm-5'i><'col-sm-7'p>>",
455 """)
456 else:
457 Writer.write("""\
458 "dom": "<'row'<'col'<'float-right'B>>>" +
459 "<'row'<'col-sm-12'tr>>" +
460 "<'row'<'col-sm-5'i><'col-sm-7'p>>",
461 """)
462 else:
463 Writer.write("""\
464 "dom": "<'row'<'col'l>>" +
465 "<'row'<'col-sm-12'tr>>" +
466 "<'row'<'col-sm-5'i><'col-sm-7'p>>",
467 """)
468
469 #
470 if OptionsInfo["ColVisibility"]:
471 # Set up buttons...
472 Writer.write("""\
473 "buttons": [
474 {
475 "extend": "colvis",
476 "text": "Column visibility",
477 "className": "btn btn-outline-light text-dark",
478 "columns": ":not(.noColVisCtrl)",
479 """)
480 if not DataColVisibilityExclude:
481 Writer.write("""\
482 "prefixButtons": [ "colvisRestore" ],
483 """)
484
485 Writer.write("""\
486 "columnText": function ( dt, colIndex, colLabel ) {
487 return "Column " + (colIndex + 1);
488 },
489 }
490 ],
491 """)
492
493 # Write out rest of the variables for DataTables...
494 if FreezeCols:
495 Writer.write("""\
496 "fixedColumns": {
497 "leftColumns": %s
498 },
499 """ % (FreezeLeftColumns))
500
501 if (OptionsInfo["KeysNavigation"]):
502 Writer.write("""\
503 "keys": true,
504 """)
505
506 Writer.write("""\
507 "pageLength": %s,
508 "lengthMenu": [ [5, 10, 15, 25, 50, 100, 500, 1000, -1], [5, 10, 15, 25, 50, 100, 500, 1000, "All"] ],
509 "paging": %s,
510 "pagingType": %s,
511 "scrollX": %s,
512 "scrollY": %s,
513 "scrollCollapse": true,
514 "order": [],
515 } );
516 """ % (PageLength, Paging, PagingType, ScrollX, ScrollY))
517
518 if OptionsInfo["CounterCol"]:
519 Writer.write("""\
520 MolsTable.on( 'order.dt search.dt', function () {
521 MolsTable.column(0, {search:'applied', order:'applied'}).nodes().each( function (cell, rowIndex) {
522 cell.innerHTML = rowIndex + 1;
523 } );
524 } ).draw();
525 """)
526
527 # End of Javacscript code...
528 Writer.write("""\
529 } );
530
531 </script>
532 """)
533
534 # Finish up HTML header...
535 Writer.write("""\
536
537 </head>
538 <body>
539 <div class="container-fluid">
540 <br/>
541 """)
542
543 def WriteHTMLPageEnd(Writer):
544 """Write out HTML page end."""
545
546 Writer.write("""\
547 </div>
548 </body>
549 </html>
550 """)
551
552 def WriteHTMLPageTitle(Writer):
553 """Write out HTML page title."""
554
555 if OptionsInfo["Header"] is None:
556 return
557
558 Writer.write(""" <%s class="text-center">%s</%s>\n""" % (OptionsInfo["HeaderStyle"], OptionsInfo["Header"], OptionsInfo["HeaderStyle"]))
559
560 def WriteHTMLPageFooter(Writer):
561 """Write out HTML page footer."""
562
563 if OptionsInfo["Footer"] is None:
564 return
565
566 Writer.write(""" <br/>\n <p class="%s">%s</p>\n""" % (OptionsInfo["FooterClass"], OptionsInfo["Footer"]))
567
568 def WriteHTMLTableHeader(Writer):
569 """Write out HTML table header."""
570
571 if OptionsInfo["TableStyle"] is None:
572 Writer.write("""\n <table id="MolsTable" cellspacing="0" width="100%">\n""")
573 else:
574 Writer.write(""" <table id="MolsTable" class="%s" cellspacing="0" width="100%s">\n""" % (OptionsInfo["TableStyle"], "%"))
575
576 def WriteHTMLTableEnd(Writer):
577 """Write out HTML table end."""
578
579 Writer.write(""" </table>\n\n""")
580
581 def GetColCount(MolCount):
582 """Get tabke column count."""
583
584 ColCount = OptionsInfo["NumOfMolsPerRow"] if OptionsInfo["NumOfMolsPerRow"] <= MolCount else MolCount
585
586 return ColCount
587
588 def SetupAtomListsToHighlight(ValidMols):
589 """Set up atom lists to highlight using specified SMARTS pattern."""
590
591 AtomListsToHighlight = None
592 if OptionsInfo["HighlightSMARTSPattern"] is None:
593 return AtomListsToHighlight
594
595 PatternMol = Chem.MolFromSmarts(OptionsInfo["HighlightSMARTSPattern"])
596 AtomListsToHighlight = []
597 for ValidMol in ValidMols:
598 # Get matched atom lists and flatten it...
599 MatchedAtomsLists = ValidMol.GetSubstructMatches(PatternMol)
600 MatchedAtoms = [ Atom for AtomsList in MatchedAtomsLists for Atom in AtomsList]
601 AtomListsToHighlight.append(MatchedAtoms)
602
603 return AtomListsToHighlight
604
605 def PerformAlignment(ValidMols):
606 """Perform alignment to a common template specified by a SMARTS pattern."""
607
608 if OptionsInfo["AlignmentSMARTSPattern"] is None:
609 return
610
611 PatternMol = Chem.MolFromSmarts(OptionsInfo["AlignmentSMARTSPattern"])
612 AllChem.Compute2DCoords(PatternMol)
613
614 MatchedValidMols = [ValidMol for ValidMol in ValidMols if ValidMol.HasSubstructMatch(PatternMol)]
615 for ValidMol in MatchedValidMols:
616 AllChem.GenerateDepictionMatching2DStructure(ValidMol, PatternMol)
617
618 def GetMolPopoverTag(Mol):
619 """Set up a popover window containing any additional information about molecule."""
620
621 if not OptionsInfo["Popover"]:
622 return None
623
624 # Set up data label and values...
625 AvailableDataLabels = Mol.GetPropNames(includePrivate = False, includeComputed = False)
626
627 DataContentLines = []
628 MaxDataCharWidth = OptionsInfo["PopoverTextWidth"]
629 MaxDataDisplayCount = OptionsInfo["PopoverDataCount"]
630
631 DataDisplayCount = 0
632 SkippedDataDisplay = False
633 for DataLabel in AvailableDataLabels:
634 DataDisplayCount += 1
635 if DataDisplayCount > MaxDataDisplayCount:
636 SkippedDataDisplay = True
637 break
638
639 DataValue = "%s" % Mol.GetProp(DataLabel)
640 DataValue = DataValue.strip()
641 if MiscUtil.IsEmpty(DataValue):
642 continue
643
644 # Change any new lines to ;
645 if re.search("(\r\n|\r|\n)", DataValue):
646 DataValue = re.sub("(\r\n|\r|\n)", "; ", DataValue)
647
648 DataValue = MiscUtil.TruncateText(DataValue, MaxDataCharWidth, "...")
649 DataValue = MiscUtil.ReplaceHTMLEntitiesInText(DataValue)
650
651 DataContent = "<b>%s</b>: %s" % (DataLabel, DataValue)
652 DataContentLines.append(DataContent)
653
654 if not len(DataContentLines):
655 return None
656
657 if SkippedDataDisplay:
658 DataContent = "<b>... ... ...</b>"
659 DataContentLines.append(DataContent)
660
661 DataContent = "Showing 1 to %s of %s" % (MaxDataDisplayCount, len(AvailableDataLabels))
662 DataContentLines.append(DataContent)
663 else:
664 DataContent = "Showing 1 to %s of %s" % (DataDisplayCount, len(AvailableDataLabels))
665 DataContentLines.append(DataContent)
666
667 DataContent = MiscUtil.JoinWords(DataContentLines, "<br/>")
668 PopoverTag = """class="MolPopover" data-toggle="popover" data-html="true" data-trigger="click" data-placement="right" title="<span class='small'><b>Additional Information</b></span>" data-content="<span class='small'>%s</span>" """ % DataContent
669
670 return PopoverTag
671
672 def ProcessOptions():
673 """Process and validate command line arguments and options."""
674
675 MiscUtil.PrintInfo("Processing options...")
676
677 # Validate options...
678 ValidateOptions()
679
680 OptionsInfo["Infile"] = Options["--infile"]
681 OptionsInfo["Outfile"] = Options["--outfile"]
682 OptionsInfo["Overwrite"] = Options["--overwrite"]
683
684 # No need for any RDKit specific --outfileParams....
685 OptionsInfo["InfileParams"] = MiscUtil.ProcessOptionInfileParameters("--infileParams", Options["--infileParams"], OptionsInfo["Infile"])
686
687 AlignmentSMARTSPattern = None
688 if not re.match("^None$", Options["--alignmentSMARTS"], re.I):
689 AlignmentSMARTSPattern = Options["--alignmentSMARTS"]
690 OptionsInfo["AlignmentSMARTSPattern"] = AlignmentSMARTSPattern
691
692 OptionsInfo["AtomLabelFontSize"] = Options["--atomLabelFontSize"]
693 OptionsInfo["BondLineWidth"] = Options["--bondLineWidth"]
694
695 Compute2DCoords = True
696 if re.match("^yes$", Options["--compute2DCoords"], re.I):
697 Compute2DCoords = True
698 elif re.match("^no$", Options["--compute2DCoords"], re.I):
699 Compute2DCoords = False
700 OptionsInfo["Compute2DCoords"] = Compute2DCoords
701
702 CounterCol = True
703 if re.match("^no$", Options["--counterCol"], re.I):
704 CounterCol = False
705 OptionsInfo["CounterCol"] = CounterCol
706
707 ColVisibility = True
708 if re.match("^no$", Options["--colVisibility"], re.I):
709 ColVisibility = False
710 OptionsInfo["ColVisibility"] = ColVisibility
711
712 OptionsInfo["FontBold"] = True
713 if re.match("^no$", Options["--fontBold"], re.I):
714 OptionsInfo["FontBold"] = False
715
716 Footer = None
717 if not re.match("^None$", Options["--footer"], re.I):
718 Footer = Options["--footer"]
719 OptionsInfo["Footer"] = Footer
720
721 FooterClass = Options["--footerClass"].strip()
722 if MiscUtil.IsEmpty(FooterClass):
723 MiscUtil.PrintError("The value specified using option \"--footerClass\" is empty.")
724 OptionsInfo["FooterClass"] = FooterClass
725
726 Header = None
727 if not re.match("^None$", Options["--header"], re.I):
728 Header = Options["--header"]
729 OptionsInfo["Header"] = Header
730
731 HeaderStyle = Options["--headerStyle"].strip()
732 if MiscUtil.IsEmpty(HeaderStyle):
733 MiscUtil.PrintError("The value specified using option \"--headerStyle\" is empty.")
734 OptionsInfo["HeaderStyle"] = HeaderStyle
735
736 HighlightSMARTSPattern = None
737 if not re.match("^None$", Options["--highlightSMARTS"], re.I):
738 HighlightSMARTSPattern = Options["--highlightSMARTS"]
739 OptionsInfo["HighlightSMARTSPattern"] = HighlightSMARTSPattern
740
741 OptionsInfo["Kekulize"] = True
742 if re.match("^no$", Options["--kekulize"], re.I):
743 OptionsInfo["Kekulize"] = False
744
745 OptionsInfo["KeysNavigation"] = True
746 if re.match("^no$", Options["--keysNavigation"], re.I):
747 OptionsInfo["KeysNavigation"] = False
748
749 SizeValues = Options["--molImageSize"].split(",")
750 OptionsInfo["MolImageWidth"] = int(SizeValues[0])
751 OptionsInfo["MolImageHeight"] = int(SizeValues[1])
752
753 OptionsInfo["MolImageEncoded"] = True
754 if re.match("^no$", Options["--molImageEncoded"], re.I):
755 OptionsInfo["MolImageEncoded"] = False
756
757 OptionsInfo["NumOfMolsPerRow"] = int(Options["--numOfMolsPerRow"])
758
759 OptionsInfo["Paging"] = True
760 if re.match("^no$", Options["--paging"], re.I):
761 OptionsInfo["Paging"] = False
762
763 PagingType = Options["--pagingType"]
764 if not re.match("^(numbers|simple|simple_numbers|full|full_numbers|simple_number)$", Options["--pagingType"], re.I):
765 MiscUtil.PrintWarning("The paging type name, %s, specified using option \"--pagingType\" appears to be a unknown type..." % (PagingType))
766 OptionsInfo["PagingType"] = PagingType.lower()
767
768 OptionsInfo["PageLength"] = int(Options["--pageLength"])
769
770 OptionsInfo["Popover"] = True
771 if re.match("^no$", Options["--popover"], re.I):
772 OptionsInfo["Popover"] = False
773 OptionsInfo["PopoverDataCount"] = int(Options["--popoverDataCount"])
774 OptionsInfo["PopoverTextWidth"] = int(Options["--popoverTextWidth"])
775
776 OptionsInfo["ShowMolName"] = True
777 if re.match("^no$", Options["--showMolName"], re.I):
778 OptionsInfo["ShowMolName"] = False
779
780 OptionsInfo["ScrollX"] = True
781 if re.match("^no$", Options["--scrollX"], re.I):
782 OptionsInfo["ScrollX"] = False
783
784 OptionsInfo["ScrollY"] = True
785 if re.match("^no$", Options["--scrollY"], re.I):
786 OptionsInfo["ScrollY"] = False
787
788 OptionsInfo["ScrollYSize"] = Options["--scrollYSize"]
789 if re.match("vh$", Options["--scrollYSize"], re.I):
790 ScrollYSize = int(re.sub("vh$", "", Options["--scrollYSize"]))
791 if ScrollYSize <= 0:
792 MiscUtil.PrintError("The value specified, %s, for option \"--scrollYSize\" is not valid. Supported value: > 0 followed by \"vh\"" % Options["--scrollYSize"])
793
794 TableStyle = None
795 if not re.match("^None$", Options["--tableStyle"], re.I):
796 if re.match("^All$", Options["--tableStyle"], re.I):
797 TableStyle = "table table-striped table-bordered table-hover table-dark"
798 else:
799 TableStyle = re.sub(" ", "", Options["--tableStyle"])
800 for Style in [Style for Style in TableStyle.split(",")]:
801 if not re.match("^(table|table-striped|table-bordered|table-hover|table-dark|table-sm)$", Style, re.I):
802 MiscUtil.PrintWarning("The table style name, %s, specified using option \"-t, --tableStyle\" appears to be a unknown style..." % (Style))
803 TableStyle = re.sub(",", " ", TableStyle.lower())
804 OptionsInfo["TableStyle"] = TableStyle
805
806 OptionsInfo["TableFooter"] = True
807 if re.match("^no$", Options["--tableFooter"], re.I):
808 OptionsInfo["TableFooter"] = False
809
810 OptionsInfo["TableHeader"] = True
811 if re.match("^no$", Options["--tableHeader"], re.I):
812 OptionsInfo["TableHeader"] = False
813
814 TableHeaderStyle = None
815 if not re.match("^None$", Options["--tableHeaderStyle"], re.I):
816 TableHeaderStyle = Options["--tableHeaderStyle"]
817 TableHeaderStyle = TableHeaderStyle.lower()
818 CheckOptionTableClassColorValues("--tableHeaderStyle", [TableHeaderStyle])
819 OptionsInfo["TableHeaderStyle"] = TableHeaderStyle
820
821 def CheckOptionTableClassColorValues(OptionName, ColorsList):
822 """Check names of table color classes and issue a warning for unknown names."""
823
824 TableClassColors = ["thead-dark", "thead-light", "table-primary", "table-success", "table-danger", "table-info", "table-warning", "table-active", "table-secondary", "table-light", "table-dark", "bg-primary", "bg-success", "bg-danger", "bg-info", "bg-warning", "bg-secondary", "bg-dark", "bg-light"]
825
826 for Color in ColorsList:
827 if not Color in TableClassColors:
828 MiscUtil.PrintWarning("The color class name, %s, specified using option \"%s\" appears to be a unknown name..." % (Color, OptionName))
829
830 def RetrieveOptions():
831 """Retrieve command line arguments and options."""
832
833 # Get options...
834 global Options
835 Options = docopt(_docoptUsage_)
836
837 # Set current working directory to the specified directory...
838 WorkingDir = Options["--workingdir"]
839 if WorkingDir:
840 os.chdir(WorkingDir)
841
842 # Handle examples option...
843 if "--examples" in Options and Options["--examples"]:
844 MiscUtil.PrintInfo(MiscUtil.GetExamplesTextFromDocOptText(_docoptUsage_))
845 sys.exit(0)
846
847 def ValidateOptions():
848 """Validate option values."""
849
850 MiscUtil.ValidateOptionFilePath("-i, --infile", Options["--infile"])
851 MiscUtil.ValidateOptionFileExt("-i, --infile", Options["--infile"], "sdf sd mol smi csv tsv txt")
852
853 MiscUtil.ValidateOptionsOutputFileOverwrite("-o, --outfile", Options["--outfile"], "--overwrite", Options["--overwrite"])
854 MiscUtil.ValidateOptionsDistinctFileNames("-i, --infile", Options["--infile"], "-o, --outfile", Options["--outfile"])
855
856 if not re.match("^None$", Options["--alignmentSMARTS"], re.I):
857 PatternMol = Chem.MolFromSmarts(Options["--alignmentSMARTS"])
858 if PatternMol is None:
859 MiscUtil.PrintError("The value specified, %s, using option \"--alignmentSMARTS\" is not a valid SMARTS: Failed to create pattern molecule" % Options["--alignmentSMARTS"])
860
861 MiscUtil.ValidateOptionIntegerValue("--atomLabelFontSize", Options["--atomLabelFontSize"], {">": 0})
862 MiscUtil.ValidateOptionFloatValue("-b, --bondLineWidth", Options["--bondLineWidth"], {">": 0.0})
863
864 MiscUtil.ValidateOptionTextValue("--compute2DCoords", Options["--compute2DCoords"], "yes no auto")
865
866 MiscUtil.ValidateOptionTextValue("--counterCol", Options["--counterCol"], "yes no")
867 MiscUtil.ValidateOptionTextValue("--colVisibility", Options["--colVisibility"], "yes no")
868
869 MiscUtil.ValidateOptionTextValue("--f, -fontBold", Options["--fontBold"], "yes no")
870
871 if not re.match("^None$", Options["--highlightSMARTS"], re.I):
872 PatternMol = Chem.MolFromSmarts(Options["--highlightSMARTS"])
873 if PatternMol is None:
874 MiscUtil.PrintError("The value specified, %s, using option \"--highlightSMARTS\" is not a valid SMARTS: Failed to create pattern molecule" % Options["--highlightSMARTS"])
875
876 MiscUtil.ValidateOptionTextValue("--kekulize", Options["--kekulize"], "yes no")
877
878 MiscUtil.ValidateOptionTextValue("-k, --keysNavigation", Options["--keysNavigation"], "yes no")
879
880 MiscUtil.ValidateOptionNumberValues("-m, --molImageSize", Options["--molImageSize"], 2, ",", "integer", {">": 0})
881 MiscUtil.ValidateOptionTextValue("--molImageEncoded", Options["--molImageEncoded"], "yes no")
882
883 MiscUtil.ValidateOptionIntegerValue("--numOfMolsPerRow", Options["--numOfMolsPerRow"], {">": 0})
884
885 MiscUtil.ValidateOptionTextValue("-p, --paging", Options["--paging"], "yes no")
886 MiscUtil.ValidateOptionIntegerValue("--pageLength", Options["--pageLength"], {">": 0})
887
888 MiscUtil.ValidateOptionTextValue("--popover", Options["--popover"], "yes no")
889 MiscUtil.ValidateOptionIntegerValue("--popoverDataCount", Options["--popoverDataCount"], {">": 0})
890 MiscUtil.ValidateOptionIntegerValue("--popoverTextWidth", Options["--popoverTextWidth"], {">": 0})
891
892 MiscUtil.ValidateOptionTextValue("--showMolName", Options["--showMolName"], "yes no")
893
894 MiscUtil.ValidateOptionTextValue("--scrollX", Options["--scrollX"], "yes no")
895 MiscUtil.ValidateOptionTextValue("--scrollY", Options["--scrollY"], "yes no")
896 if not re.search("vh$", Options["--scrollYSize"], re.I):
897 MiscUtil.ValidateOptionIntegerValue("--scrollYSize", Options["--scrollYSize"], {">": 0})
898
899 MiscUtil.ValidateOptionTextValue("--tableFooter", Options["--tableFooter"], "yes no")
900 MiscUtil.ValidateOptionTextValue("--tableHeader", Options["--tableHeader"], "yes no")
901
902 # Setup a usage string for docopt...
903 _docoptUsage_ = """
904 RDKitDrawMolecules.py - Draw molecules and generate an image or HTML file
905
906 Usage:
907 RDKitDrawMolecules.py [--alignmentSMARTS <SMARTS>] [--atomLabelFontSize <number>]
908 [--bondLineWidth <number>] [--compute2DCoords <yes | no>] [--counterCol <yes or no>]
909 [--colVisibility <yes or no>] [--fontBold <yes or no>] [--footer <text>] [--footerClass <text>]
910 [--header <text>] [--headerStyle <text>] [--highlightSMARTS <SMARTS>]
911 [--infileParams <Name,Value,...>] [--kekulize <yes or no>] [--keysNavigation <yes or no>]
912 [--molImageSize <width,height>] [--molImageEncoded <yes or no> ]
913 [--numOfMolsPerRow <number>] [--overwrite] [--paging <yes or no>]
914 [--pagingType <numbers, simple, ...>] [--pageLength <number>]
915 [--popover <yes or no>] [--popoverDataCount <number>] [--popoverTextWidth <number>]
916 [--showMolName <yes or no>] [--scrollX <yes or no>] [--scrollY <yes or no>]
917 [--scrollYSize <number>] [--tableFooter <yes or no>] [--tableHeader <yes or no>]
918 [--tableHeaderStyle <thead-dark,thead-light,...>]
919 [--tableStyle <table,table-striped,...>] [-w <dir>] -i <infile> -o <outfile>
920 RDKitDrawMolecules.py -h | --help | -e | --examples
921
922 Description:
923 Draw molecules in a grid and write them out as an image file or a HTML table file. The
924 SVG image or HTML table file appears to be the best among all the available image file
925 options, as rendered in a browser. The Python modules aggdraw/cairo are required to
926 generate high quality PNG images.
927
928 The drawing of the molecules are embedded in HTML table columns as in line SVG
929 images. The HTML table is an interactive table and requires internet access for viewing
930 in a browser. It employs he following frameworks: JQuery, Bootstrap, and DataTable.
931
932 The options '--atomLabelFontSize' and '--bondLineWidth' don't appear to work
933 during the generation of a SVG image. In addition, these may not work for other
934 image types in the latest version of RDKIT.
935
936 The supported input file formats are: Mol (.mol), SD (.sdf, .sd), SMILES (.smi,
937 .txt, .csv, .tsv)
938
939 The output image file can be saved in any format supported by the Python Image
940 Library (PIL). The image format is automatically detected from the output file extension.
941
942 Some of the most common output image file formats are: GIF (.gif), JPEG (.jpg),
943 PNG (.png), SVG (.svg), TIFF (.tif). In addition, a HTML (.html) file format
944 containing a table is supported.
945
946 Options:
947 -a, --alignmentSMARTS <SMARTS> [default: none]
948 SMARTS pattern for aligning molecules to a common template.
949 --atomLabelFontSize <number> [default: 12]
950 Font size for drawing atom labels. This option is ignored during the generation of
951 a SVG and HTML output file. This option may not work in the latest version of RDKit.
952 -b, --bondLineWidth <number> [default: 1.2]
953 Line width for drawing bonds. This option is ignored during the generation of a SVG
954 and HTML output file. This option may not work in the latest version of RDKit.
955 -c, --compute2DCoords <yes or no> [default: auto]
956 Compute 2D coordinates of molecules before drawing. Default: yes for all file
957 formats.
958 --counterCol <yes or no> [default: yes]
959 Show a counter column as the first column in the table. It contains the position
960 for each row in the HTML table. This option is only used during the generation of
961 a HTML table file.
962 --colVisibility <yes or no> [default: yes]
963 Show a dropdown button to toggle visibility of columns in the table. This option is
964 only used during the generation of a HTML table file.
965 -e, --examples
966 Print examples.
967 -f --fontBold <yes or no> [default: yes]
968 Make all text fonts bold during the generation of a SVG and HTML output file. This
969 option is ignored for all other output files. This option may not work in the latest
970 version of RDKit.
971 --footer <text> [default: none]
972 Footer text to insert at the bottom of the HTML page after the table. This option is
973 only used during the generation of a HTML table file.
974 --footerClass <text> [default: small text-center text-muted]
975 Footer class style to use with <p> tag. This option is only used during the
976 generation of a HTML table file.
977 -h, --help
978 Print this help message.
979 --header <text> [default: none]
980 Header text to insert at the top of the HTML page before the table. This option is
981 only used during the generation of a HTML table file.
982 --headerStyle <text> [default: h5]
983 Header style to use. Possible values: h1 to h6. This option is only used during the
984 generation of a HTML table file.
985 --highlightSMARTS <SMARTS> [default: none]
986 SMARTS pattern for highlighting atoms and bonds in molecules. All matched
987 substructures are highlighted.
988 -i, --infile <infile>
989 Input file name.
990 --infileParams <Name,Value,...> [default: auto]
991 A comma delimited list of parameter name and value pairs for reading
992 molecules from files. The supported parameter names for different file
993 formats, along with their default values, are shown below:
994
995 SD, MOL: removeHydrogens,yes,sanitize,yes,strictParsing,yes
996 SMILES: smilesColumn,1,smilesNameColumn,2,smilesDelimiter,space,
997 smilesTitleLine,auto,sanitize,yes
998
999 Possible values for smilesDelimiter: space, comma or tab.
1000 -k, --kekulize <yes or no> [default: yes]
1001 Perform kekulization on molecules. This option is ignored during the generation of
1002 a SVG and HTML output file.
1003 --keysNavigation <yes or no> [default: yes]
1004 Provide Excel like keyboard cell navigation for the table. This option is only used
1005 during the generation of a HTML table file.
1006 -m, --molImageSize <width,height> [default: 250,200]
1007 Image size of a molecule in pixels.
1008 --molImageEncoded <yes or no> [default: yes]
1009 Base64 encode SVG image of a molecule for inline embedding in a HTML page.
1010 The inline SVG image may fail to display in browsers without encoding.
1011 -n, --numOfMolsPerRow <number> [default: 4]
1012 Number of molecules to draw in a row.
1013 -o, --outfile <outfile>
1014 Output file name.
1015 --overwrite
1016 Overwrite existing files.
1017 -p, --paging <yes or no> [default: yes]
1018 Provide page navigation for browsing data in the table. This option is only used
1019 during the generation of a HTML table file.
1020 --pagingType <numbers, simple, ...> [default: full_numbers]
1021 Type of page navigation. Possible values: numbers, simple, simple_numbers,
1022 full, full_numbers, or first_last_numbers.
1023
1024 numbers - Page number buttons only
1025 simple - 'Previous' and 'Next' buttons only
1026 simple_numbers - 'Previous' and 'Next' buttons, plus page numbers
1027 full - 'First', 'Previous', 'Next' and 'Last' buttons
1028 full_numbers - 'First', 'Previous', 'Next' and 'Last' buttons, plus
1029 page numbers
1030 first_last_numbers - 'First' and 'Last' buttons, plus page numbers
1031
1032 This option is only used during the generation of a HTML table file.
1033 --pageLength <number> [default: 5]
1034 Number of rows to show per page. This option is only used during the
1035 generation of a HTML table file.
1036 --popover <yes or no> [default: yes]
1037 Display a popover window containing additional information about the
1038 molecule. The popover is opened after a click on the drawing of a
1039 molecule. A subsequent click on the same drawing closes the popover.
1040 This option is only used during the generation of a HTML table file.
1041 --popoverDataCount <number> [default: 25]
1042 Maximum number of data fields to show in a popover window. This option is
1043 only used during the generation of a HTML table file.
1044 --popoverTextWidth <number> [default: 50]
1045 Maximum width in characters for text display in a popover window before
1046 truncating the text. This option is only used during the generation of a HTML
1047 table file.
1048 -s, --showMolName <yes or no> [default: yes]
1049 Show molecule names under the images.This option is only used during the
1050 generation of a HTML table file.
1051 --scrollX <yes or no> [default: yes]
1052 Provide horizontal scroll bar in the table as needed.This option is only used
1053 during the generation of a HTML table file.
1054 --scrollY <yes or no> [default: yes]
1055 Provide vertical scroll bar in the table as needed.This option is only used during
1056 the generation of a HTML table file.
1057 --scrollYSize <number> [default: 75vh]
1058 Maximum height of table viewport either in pixels or percentage of the browser
1059 window height before providing a vertical scroll bar. Default: 75% of the height of
1060 browser window.This option is only used during the generation of a HTML table file.
1061 -t, --tableStyle <table,table-striped,...> [default: table,table-hover,table-sm]
1062 Style of table. Possible values: table, table-striped, table-bordered,
1063 table-hover, table-dark, table-sm, none, or All. Default: 'table,table-hover'. A
1064 comma delimited list of any valid Bootstrap table styles is also supported
1065
1066 This option is only used during the generation of a HTML table file.
1067 --tableFooter <yes or no> [default: yes]
1068 Show Excel style column headers at the end of the table. This option is only
1069 used during the generation of a HTML table file.
1070 --tableHeader <yes or no> [default: yes]
1071 Show Excel style column headers in the table. This option is only used
1072 during the generation of a HTML table file.
1073 --tableHeaderStyle <thead-dark,thead-light,...> [default: thead-dark]
1074 Style of table header. Possible values: thead-dark, thead-light, or none.
1075 The names of the following contextual color classes are also supported:
1076 table-primary (Blue), table-success (Green), table-danger (Red), table-info
1077 (Light blue), table-warning (Orange), table-active (Grey), table-light (Light
1078 grey), and table-dark (Dark grey).
1079
1080 This option is only used during the generation of a HTML table file.
1081 -w, --workingdir <dir>
1082 Location of working directory which defaults to the current directory.
1083
1084 Examples:
1085 To automatically compute 2D coordinates for molecules in a SMILES file and
1086 generate a SVG image file containing 4 molecules per row in a grid with cell
1087 size of 250 x 200 pixels, type:
1088
1089 % RDKitDrawMolecules.py -i Sample.smi -o SampleOut.svg
1090
1091 To automatically compute 2D coordinates for molecules in a SMILES file and
1092 generate a SVG image file containing 2 molecules per row in a grid with cell
1093 size of 400 x 300 pixels and without any keulization along with highlighting
1094 a specific set of atoms and bonds indicated by a SMARTS pattern, type:
1095
1096 % RDKitDrawMolecules.py -n 2 -m "400,300" -k no --fontBold no
1097 --highlightSMARTS 'c1ccccc1' -i Sample.smi -o SampleOut.svg
1098
1099 To generate a PNG image file for molecules in a SD file using existing 2D
1100 coordinates, type
1101
1102 % RDKitDrawMolecules.py --compute2DCoords no -i Sample.sdf
1103 -o SampleOut.png
1104
1105 To automatically compute 2D coordinates for molecules in a SD file and
1106 generate a HTML file containing 4 molecules per row in a table, along with
1107 all the bells and whistles to interact with the table, type:
1108
1109 % RDKitDrawMolecules.py -i Sample.sdf -o SampleOut.html
1110
1111 To automatically compute 2D coordinates for molecules in a SD file and
1112 generate a HTML file containing 4 molecules per row in a table without
1113 any bells and whistles to interact with the table, type:
1114
1115 % RDKitDrawMolecules.py --counterCol no --colVisibility no
1116 --keysNavigation no --paging no --popover no --scrollX no
1117 --scrollY no --tableFooter no --tableHeader no -i Sample.sdf
1118 -o SampleOut.html
1119
1120 To automatically compute 2D coordinates for molecules in a CSV SMILES file
1121 with column headers, SMILES strings in column 1, and name in column 2 and
1122 generate a PDF image file, type:
1123
1124 % RDKitDrawMolecules.py --infileParams "smilesDelimiter,comma,
1125 smilesTitleLine,yes,smilesColumn,1,smilesNameColumn,2"
1126 -i SampleSMILES.csv -o SampleOut.pdf
1127
1128 Author:
1129 Manish Sud(msud@san.rr.com)
1130
1131 See also:
1132 RDKitConvertFileFormat.py, RDKitDrawMoleculesAndDataTable.py, RDKitRemoveDuplicateMolecules.py,
1133 RDKitSearchFunctionalGroups.py, RDKitSearchSMARTS.py
1134
1135 Copyright:
1136 Copyright (C) 2024 Manish Sud. All rights reserved.
1137
1138 The functionality available in this script is implemented using RDKit, an
1139 open source toolkit for cheminformatics developed by Greg Landrum.
1140
1141 This file is part of MayaChemTools.
1142
1143 MayaChemTools is free software; you can redistribute it and/or modify it under
1144 the terms of the GNU Lesser General Public License as published by the Free
1145 Software Foundation; either version 3 of the License, or (at your option) any
1146 later version.
1147
1148 """
1149
1150 if __name__ == "__main__":
1151 main()
