-
Notifications
You must be signed in to change notification settings - Fork 835
/
pymatgen.analysis.graphs.html
1408 lines (1233 loc) · 88.1 KB
/
pymatgen.analysis.graphs.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>pymatgen.analysis.graphs module — pymatgen 2021.1.28 documentation</title>
<link rel="canonical" href="https://pymatgen.orgpymatgen.analysis.graphs.html"/>
<script type="text/javascript" src="_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/language_data.js"></script>
<script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="pymatgen.analysis.hhi module" href="pymatgen.analysis.hhi.html" />
<link rel="prev" title="pymatgen.analysis.functional_groups module" href="pymatgen.analysis.functional_groups.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33990148-1']);
_gaq.push(['_trackPageview']);
</script>
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" style="background: linear-gradient(0deg, rgba(23,63,162,1) 0%, rgba(0,70,192,1) 100%)" >
<a href="index.html" class="icon icon-home"> pymatgen
</a>
<div class="version">
2021.1.28
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="change_log.html">Change log</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage.html">Usage</a></li>
<li class="toctree-l1"><a class="reference internal" href="team.html">Development Team</a></li>
<li class="toctree-l1"><a class="reference internal" href="references.html">References</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="modules.html">API Docs</a><ul class="current">
<li class="toctree-l2 current"><a class="reference internal" href="pymatgen.html">pymatgen package</a><ul class="current">
<li class="toctree-l3 current"><a class="reference internal" href="pymatgen.html#subpackages">Subpackages</a><ul class="current">
<li class="toctree-l4"><a class="reference internal" href="pymatgen.alchemy.html">pymatgen.alchemy package</a></li>
<li class="toctree-l4 current"><a class="reference internal" href="pymatgen.analysis.html">pymatgen.analysis package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.apps.html">pymatgen.apps package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.cli.html">pymatgen.cli package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.command_line.html">pymatgen.command_line package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.core.html">pymatgen.core package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.electronic_structure.html">pymatgen.electronic_structure package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.entries.html">pymatgen.entries package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.ext.html">pymatgen.ext package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.io.html">pymatgen.io package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.optimization.html">pymatgen.optimization package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.phonon.html">pymatgen.phonon package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.plugins.html">pymatgen.plugins package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.symmetry.html">pymatgen.symmetry package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.transformations.html">pymatgen.transformations package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.util.html">pymatgen.util package</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.vis.html">pymatgen.vis package</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.html#submodules">Submodules</a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.html#module-pymatgen">Module contents</a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">pymatgen</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content style-external-links">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html">Docs</a> »</li>
<li><a href="modules.html">pymatgen</a> »</li>
<li><a href="pymatgen.html">pymatgen package</a> »</li>
<li><a href="pymatgen.analysis.html">pymatgen.analysis package</a> »</li>
<li>pymatgen.analysis.graphs module</li>
<li class="wy-breadcrumbs-aside">
<a href="https://github.com/materialsproject/pymatgen/blob/master/docs_rst/pymatgen.analysis.graphs.rst" class="fa fa-github"> Edit on GitHub</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="module-pymatgen.analysis.graphs">
<span id="pymatgen-analysis-graphs-module"></span><h1>pymatgen.analysis.graphs module<a class="headerlink" href="#module-pymatgen.analysis.graphs" title="Permalink to this headline">¶</a></h1>
<p>Module for graph representations of crystals.</p>
<dl class="py class">
<dt id="pymatgen.analysis.graphs.ConnectedSite">
<em class="property">class </em><code class="sig-name descname">ConnectedSite</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">site</span></em>, <em class="sig-param"><span class="n">jimage</span></em>, <em class="sig-param"><span class="n">index</span></em>, <em class="sig-param"><span class="n">weight</span></em>, <em class="sig-param"><span class="n">dist</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
<p>Create new instance of ConnectedSite(site, jimage, index, weight, dist)</p>
<dl class="py attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.dist">
<code class="sig-name descname">dist</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.dist" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 4</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.index">
<code class="sig-name descname">index</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.index" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.jimage">
<code class="sig-name descname">jimage</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.jimage" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.site">
<code class="sig-name descname">site</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.site" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
<dl class="py attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.weight">
<code class="sig-name descname">weight</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.weight" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 3</p>
</dd></dl>
</dd></dl>
<dl class="py exception">
<dt id="pymatgen.analysis.graphs.MolGraphSplitError">
<em class="property">exception </em><code class="sig-name descname">MolGraphSplitError</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1668-L1674"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MolGraphSplitError" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Raised when a molecule graph is failed to split into two disconnected
subgraphs</p>
</dd></dl>
<dl class="py class">
<dt id="pymatgen.analysis.graphs.MoleculeGraph">
<em class="property">class </em><code class="sig-name descname">MoleculeGraph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">molecule</span></em>, <em class="sig-param"><span class="n">graph_data</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1677-L3113"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>This is a class for annotating a Molecule with
bond information, stored in the form of a graph. A “bond” does
not necessarily have to be a chemical bond, but can store any
kind of information that connects two Sites.</p>
<p>If constructing this class manually, use the <cite>with_empty_graph</cite>
method or <cite>with_local_env_strategy</cite> method (using an algorithm
provided by the <cite>local_env</cite> module, such as O’Keeffe).</p>
<p>This class that contains connection information:
relationships between sites represented by a Graph structure,
and an associated structure object.</p>
<p>This class uses the NetworkX package to store and operate
on the graph itself, but contains a lot of helper methods
to make associating a graph with a given molecule easier.</p>
<p>Use cases for this include storing bonding information,
NMR J-couplings, Heisenberg exchange parameters, etc.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>graph_data</strong> – dict containing graph information in
dict format (not intended to be constructed manually,
see as_dict method for format)</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.add_edge">
<code class="sig-name descname">add_edge</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">from_index</span></em>, <em class="sig-param"><span class="n">to_index</span></em>, <em class="sig-param"><span class="n">weight</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">warn_duplicates</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">edge_properties</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1923-L1978"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.add_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Add edge to graph.</p>
<p>Since physically a ‘bond’ (or other connection
between sites) doesn’t have a direction, from_index,
from_jimage can be swapped with to_index, to_jimage.</p>
<p>However, images will always always be shifted so that
from_index < to_index and from_jimage becomes (0, 0, 0).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – index of site connecting from</p></li>
<li><p><strong>to_index</strong> – index of site connecting to</p></li>
<li><p><strong>(</strong><strong>float</strong><strong>)</strong> (<em>weight</em>) – e.g. bond length</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> (<em>warn_duplicates</em>) – if True, will warn if
trying to add duplicate edges (duplicate edges will not
be added in either case)</p></li>
<li><p><strong>(</strong><strong>dict</strong><strong>)</strong> (<em>edge_properties</em>) – any other information to
store on graph edges, similar to Structure’s site_properties</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.alter_edge">
<code class="sig-name descname">alter_edge</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">from_index</span></em>, <em class="sig-param"><span class="n">to_index</span></em>, <em class="sig-param"><span class="n">new_weight</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">new_edge_properties</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2060-L2097"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.alter_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Alters either the weight or the edge_properties of
an edge in the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>new_weight</strong> – alter_edge does not require
that weight be altered. As such, by default, this
is None. If weight is to be changed, it should be a
float.</p></li>
<li><p><strong>new_edge_properties</strong> – alter_edge does not require
that edge_properties be altered. As such, by default,
this is None. If any edge properties are to be changed,
it should be a dictionary of edge properties to be changed.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.as_dict">
<code class="sig-name descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2863-L2877"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>As in :Class: <cite>pymatgen.core.Molecule</cite> except
with using <cite>to_dict_of_dicts</cite> from NetworkX
to store graph information.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.break_edge">
<code class="sig-name descname">break_edge</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">from_index</span></em>, <em class="sig-param"><span class="n">to_index</span></em>, <em class="sig-param"><span class="n">allow_reverse</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2099-L2130"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.break_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove an edge from the MoleculeGraph</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will
attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.build_unique_fragments">
<code class="sig-name descname">build_unique_fragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2264-L2338"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.build_unique_fragments" title="Permalink to this definition">¶</a></dt>
<dd><p>Find all possible fragment combinations of the MoleculeGraphs (in other
words, all connected induced subgraphs)</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.diff">
<code class="sig-name descname">diff</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">other</span></em>, <em class="sig-param"><span class="n">strict</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L3034-L3113"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.diff" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares two MoleculeGraphs. Returns dict with
keys ‘self’, ‘other’, ‘both’ with edges that are
present in only one MoleculeGraph (‘self’ and
‘other’), and edges that are present in both.</p>
<p>The Jaccard distance is a simple measure of the
dissimilarity between two MoleculeGraphs (ignoring
edge weights), and is defined by 1 - (size of the
intersection / size of the union) of the sets of
edges. This is returned with key ‘dist’.</p>
<p>Important note: all node indices are in terms
of the MoleculeGraph this method is called
from, not the ‘other’ MoleculeGraph: there
is no guarantee the node indices will be the
same if the underlying Molecules are ordered
differently.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> – MoleculeGraph</p></li>
<li><p><strong>strict</strong> – if False, will compare bonds
from different Molecules, with node indices
replaced by Species strings, will not count
number of occurrences of bonds</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.draw_graph_to_file">
<code class="sig-name descname">draw_graph_to_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">filename</span><span class="o">=</span><span class="default_value">'graph'</span></em>, <em class="sig-param"><span class="n">diff</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">hide_unconnected_nodes</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">hide_image_edges</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">edge_colors</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">node_labels</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">weight_labels</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">image_labels</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">color_scheme</span><span class="o">=</span><span class="default_value">'VESTA'</span></em>, <em class="sig-param"><span class="n">keep_dot</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">algo</span><span class="o">=</span><span class="default_value">'fdp'</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2669-L2861"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.draw_graph_to_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws graph using GraphViz.</p>
<p>The networkx graph object itself can also be drawn
with networkx’s in-built graph drawing methods, but
note that this might give misleading results for
multigraphs (edges are super-imposed on each other).</p>
<p>If visualization is difficult to interpret,
<cite>hide_image_edges</cite> can help, especially in larger
graphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> – filename to output, will detect filetype
from extension (any graphviz filetype supported, such as
pdf or png)</p></li>
<li><p><strong>(</strong><strong>StructureGraph</strong><strong>)</strong> (<em>diff</em>) – an additional graph to
compare with, will color edges red that do not exist in diff
and edges green that are in diff graph but not in the
reference graph</p></li>
<li><p><strong>hide_unconnected_nodes</strong> – if True, hide unconnected
nodes</p></li>
<li><p><strong>hide_image_edges</strong> – if True, do not draw edges that
go through periodic boundaries</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> (<em>keep_dot</em>) – if True, use node colors to
color edges</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> – if True, label nodes with
species and site index</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> – if True, label edges with
weights</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> – if True, label edges with
their periodic images (usually only used for debugging,
edges to periodic images always appear as dashed lines)</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>color_scheme</em>) – “VESTA” or “JMOL”</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> – keep GraphViz .dot file for later
visualization</p></li>
<li><p><strong>algo</strong> – any graphviz algo, “neato” (for simple graphs)
or “fdp” (for more crowded graphs) usually give good outputs</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.edge_weight_name">
<em class="property">property </em><code class="sig-name descname">edge_weight_name</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of the edge weight property of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.edge_weight_unit">
<em class="property">property </em><code class="sig-name descname">edge_weight_unit</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_unit" title="Permalink to this definition">¶</a></dt>
<dd><p>Units of the edge weight property of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.find_rings">
<code class="sig-name descname">find_rings</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">including</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2563-L2611"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.find_rings" title="Permalink to this definition">¶</a></dt>
<dd><p>Find ring structures in the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>including</strong> – list of site indices. If
including is not None, then find_rings will
only return those rings including the specified
sites. By default, this parameter is None, and
all rings will be returned.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>dict {index:cycle}. Each
entry will be a ring (cycle, in graph theory terms) including the index
found in the Molecule. If there is no cycle including an index, the
value will be an empty list.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.from_dict">
<em class="property">classmethod </em><code class="sig-name descname">from_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">d</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2879-L2887"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.from_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>As in :Class: <cite>pymatgen.core.Molecule</cite> except
restoring graphs using <cite>from_dict_of_dicts</cite>
from NetworkX to restore graph information.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.get_connected_sites">
<code class="sig-name descname">get_connected_sites</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">n</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2613-L2656"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.get_connected_sites" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a named tuple of neighbors of site n:
periodic_site, jimage, index, weight.
Index is the index of the corresponding site
in the original structure, weight can be
None if not defined.
:param n: index of Site in Molecule
:param jimage: lattice vector of site
:return: list of ConnectedSite tuples,</p>
<blockquote>
<div><p>sorted by closest first</p>
</div></blockquote>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.get_coordination_of_site">
<code class="sig-name descname">get_coordination_of_site</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">n</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2658-L2667"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.get_coordination_of_site" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of neighbors of site n.
In graph terms, simply returns degree
of node corresponding to site n.
:param n: index of site
:return (int):</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.insert_node">
<code class="sig-name descname">insert_node</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">i</span></em>, <em class="sig-param"><span class="n">species</span></em>, <em class="sig-param"><span class="n">coords</span></em>, <em class="sig-param"><span class="n">validate_proximity</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">site_properties</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">edges</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1980-L2038"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.insert_node" title="Permalink to this definition">¶</a></dt>
<dd><p>A wrapper around Molecule.insert(), which also incorporates the new
site into the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>i</strong> – Index at which to insert the new site</p></li>
<li><p><strong>species</strong> – Species for the new site</p></li>
<li><p><strong>coords</strong> – 3x1 array representing coordinates of the new site</p></li>
<li><p><strong>validate_proximity</strong> – For Molecule.insert(); if True (default
False), distance will be checked to ensure that site can be safely
added.</p></li>
<li><p><strong>site_properties</strong> – Site properties for Molecule</p></li>
<li><p><strong>edges</strong> – List of dicts representing edges to be added to the
MoleculeGraph. These edges must include the index of the new site i,
and all indices used for these edges should reflect the
MoleculeGraph AFTER the insertion, NOT before. Each dict should at
least have a “to_index” and “from_index” key, and can also have a
“weight” and a “properties” key.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.isomorphic_to">
<code class="sig-name descname">isomorphic_to</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">other</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L3014-L3032"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.isomorphic_to" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks if the graphs of two MoleculeGraphs are isomorphic to one
another. In order to prevent problems with misdirected edges, both
graphs are converted into undirected nx.Graph objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>other</strong> – MoleculeGraph object to be compared.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.name">
<em class="property">property </em><code class="sig-name descname">name</code><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.remove_nodes">
<code class="sig-name descname">remove_nodes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">indices</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2132-L2149"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.remove_nodes" title="Permalink to this definition">¶</a></dt>
<dd><p>A wrapper for Molecule.remove_sites().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>indices</strong> – list of indices in the current Molecule (and graph) to
be removed.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.replace_group">
<code class="sig-name descname">replace_group</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">index</span></em>, <em class="sig-param"><span class="n">func_grp</span></em>, <em class="sig-param"><span class="n">strategy</span></em>, <em class="sig-param"><span class="n">bond_order</span><span class="o">=</span><span class="default_value">1</span></em>, <em class="sig-param"><span class="n">graph_dict</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">strategy_params</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2472-L2561"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.replace_group" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds off of Molecule.substitute and MoleculeGraph.substitute_group
to replace a functional group in self.molecule with a functional group.
This method also amends self.graph to incorporate the new functional
group.</p>
<p>TODO: Figure out how to replace into a ring structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> – Index of atom to substitute.</p></li>
<li><p><strong>func_grp</strong> – <p>Substituent molecule. There are three options:</p>
<ol class="arabic simple">
<li><p>Providing an actual molecule as the input. The first atom
must be a DummySpecies X, indicating the position of
nearest neighbor. The second atom must be the next
nearest atom. For example, for a methyl group
substitution, func_grp should be X-CH3, where X is the
first site and C is the second site. What the code will
do is to remove the index site, and connect the nearest
neighbor to the C atom in CH3. The X-C bond indicates the
directionality to connect the atoms.</p></li>
<li><p>A string name. The molecule will be obtained from the
relevant template in func_groups.json.</p></li>
<li><p>A MoleculeGraph object.</p></li>
</ol>
</p></li>
<li><p><strong>strategy</strong> – Class from pymatgen.analysis.local_env.</p></li>
<li><p><strong>bond_order</strong> – A specified bond order to calculate the bond
length between the attached functional group and the nearest
neighbor site. Defaults to 1.</p></li>
<li><p><strong>graph_dict</strong> – Dictionary representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. If None, then the algorithm
will attempt to automatically determine bonds using one of
a list of strategies defined in pymatgen.analysis.local_env.</p></li>
<li><p><strong>strategy_params</strong> – dictionary of keyword arguments for strategy.
If None, default parameters will be used.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.set_node_attributes">
<code class="sig-name descname">set_node_attributes</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2040-L2058"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.set_node_attributes" title="Permalink to this definition">¶</a></dt>
<dd><p>Replicates molecule site properties (specie, coords, etc.) in the
MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.sort">
<code class="sig-name descname">sort</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">key</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">reverse</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2946-L2979"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.sort" title="Permalink to this definition">¶</a></dt>
<dd><p>Same as Molecule.sort(), also remaps nodes in graph.
:param key:
:param reverse:
:return:</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.split_molecule_subgraphs">
<code class="sig-name descname">split_molecule_subgraphs</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">bonds</span></em>, <em class="sig-param"><span class="n">allow_reverse</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">alterations</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2151-L2262"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.split_molecule_subgraphs" title="Permalink to this definition">¶</a></dt>
<dd><p>Split MoleculeGraph into two or more MoleculeGraphs by
breaking a set of bonds. This function uses
MoleculeGraph.break_edge repeatedly to create
disjoint graphs (two or more separate molecules).
This function does not only alter the graph
information, but also changes the underlying
Moledules.
If the bonds parameter does not include sufficient
bonds to separate two molecule fragments, then this
function will fail.
Currently, this function naively assigns the charge
of the total molecule to a single submolecule. A
later effort will be to actually accurately assign
charge.
NOTE: This function does not modify the original
MoleculeGraph. It creates a copy, modifies that, and
returns two or more new MoleculeGraph objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bonds</strong> – list of tuples (from_index, to_index)
representing bonds to be broken to split the MoleculeGraph.</p></li>
<li><p><strong>alterations</strong> – a dict {(from_index, to_index): alt},
where alt is a dictionary including weight and/or edge
properties to be changed following the split.</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will
attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>list of MoleculeGraphs</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.substitute_group">
<code class="sig-name descname">substitute_group</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">index</span></em>, <em class="sig-param"><span class="n">func_grp</span></em>, <em class="sig-param"><span class="n">strategy</span></em>, <em class="sig-param"><span class="n">bond_order</span><span class="o">=</span><span class="default_value">1</span></em>, <em class="sig-param"><span class="n">graph_dict</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">strategy_params</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L2340-L2470"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.substitute_group" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds off of Molecule.substitute to replace an atom in self.molecule
with a functional group. This method also amends self.graph to
incorporate the new functional group.</p>
<p>NOTE: using a MoleculeGraph will generally produce a different graph
compared with using a Molecule or str (when not using graph_dict).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> – Index of atom to substitute.</p></li>
<li><p><strong>func_grp</strong> – <p>Substituent molecule. There are three options:</p>
<ol class="arabic simple">
<li><dl class="simple">
<dt>Providing an actual molecule as the input. The first atom</dt><dd><p>must be a DummySpecies X, indicating the position of
nearest neighbor. The second atom must be the next
nearest atom. For example, for a methyl group
substitution, func_grp should be X-CH3, where X is the
first site and C is the second site. What the code will
do is to remove the index site, and connect the nearest
neighbor to the C atom in CH3. The X-C bond indicates the
directionality to connect the atoms.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>A string name. The molecule will be obtained from the</dt><dd><p>relevant template in func_groups.json.</p>
</dd>
</dl>
</li>
<li><p>A MoleculeGraph object.</p></li>
</ol>
</p></li>
<li><p><strong>strategy</strong> – Class from pymatgen.analysis.local_env.</p></li>
<li><p><strong>bond_order</strong> – A specified bond order to calculate the bond
length between the attached functional group and the nearest
neighbor site. Defaults to 1.</p></li>
<li><p><strong>graph_dict</strong> – Dictionary representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. If None, then the algorithm
will attempt to automatically determine bonds using one of
a list of strategies defined in pymatgen.analysis.local_env.</p></li>
<li><p><strong>strategy_params</strong> – dictionary of keyword arguments for strategy.
If None, default parameters will be used.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.with_edges">
<em class="property">static </em><code class="sig-name descname">with_edges</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">molecule</span></em>, <em class="sig-param"><span class="n">edges</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1773-L1824"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_edges" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructor for MoleculeGraph, using pre-existing or pre-defined edges
with optional edge parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>edges</strong> – dict representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. Props should be None if no
additional properties are to be specified.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>mg, a MoleculeGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.with_empty_graph">
<em class="property">classmethod </em><code class="sig-name descname">with_empty_graph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">molecule</span></em>, <em class="sig-param"><span class="n">name</span><span class="o">=</span><span class="default_value">'bonds'</span></em>, <em class="sig-param"><span class="n">edge_weight_name</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">edge_weight_units</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1733-L1771"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_empty_graph" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructor for MoleculeGraph, returns a MoleculeGraph
object with an empty graph (no edges, only nodes defined
that correspond to Sites in Molecule).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>(</strong><strong>Molecule</strong><strong>)</strong> (<em>molecule</em>) – </p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>edge_weight_units</em>) – name of graph, e.g. “bonds”</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> – name of edge weights,
e.g. “bond_length” or “exchange_constant”</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> – name of edge weight units
e.g. “Å” or “eV”</p></li>
</ul>
</dd>
<dt class="field-even">Return (MoleculeGraph)</dt>
<dd class="field-even"><p></p></dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.with_local_env_strategy">
<em class="property">static </em><code class="sig-name descname">with_local_env_strategy</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">molecule</span></em>, <em class="sig-param"><span class="n">strategy</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1826-L1900"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_local_env_strategy" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructor for MoleculeGraph, using a strategy
from :Class: <cite>pymatgen.analysis.local_env</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>strategy</strong> – an instance of a
:Class: <cite>pymatgen.analysis.local_env.NearNeighbors</cite> object</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>mg, a MoleculeGraph</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt id="pymatgen.analysis.graphs.StructureGraph">
<em class="property">class </em><code class="sig-name descname">StructureGraph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">structure</span></em>, <em class="sig-param"><span class="n">graph_data</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L109-L1665"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>This is a class for annotating a Structure with
bond information, stored in the form of a graph. A “bond” does
not necessarily have to be a chemical bond, but can store any
kind of information that connects two Sites.</p>
<p>If constructing this class manually, use the <cite>with_empty_graph</cite>
method or <cite>with_local_env_strategy</cite> method (using an algorithm
provided by the <cite>local_env</cite> module, such as O’Keeffe).</p>
<p>This class that contains connection information:
relationships between sites represented by a Graph structure,
and an associated structure object.</p>
<p>This class uses the NetworkX package to store and operate
on the graph itself, but contains a lot of helper methods
to make associating a graph with a given crystallographic
structure easier.</p>
<p>Use cases for this include storing bonding information,
NMR J-couplings, Heisenberg exchange parameters, etc.</p>
<p>For periodic graphs, class stores information on the graph
edges of what lattice image the edge belongs to.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – a Structure object</p></li>
<li><p><strong>graph_data</strong> – dict containing graph information in
dict format (not intended to be constructed manually,</p></li>
</ul>
</dd>
</dl>
<p>see as_dict method for format)</p>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.StructureGraph.add_edge">
<code class="sig-name descname">add_edge</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">from_index</span></em>, <em class="sig-param"><span class="n">to_index</span></em>, <em class="sig-param"><span class="n">from_jimage</span><span class="o">=</span><span class="default_value">0, 0, 0</span></em>, <em class="sig-param"><span class="n">to_jimage</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">weight</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">warn_duplicates</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">edge_properties</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L331-L459"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.add_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Add edge to graph.</p>
<p>Since physically a ‘bond’ (or other connection
between sites) doesn’t have a direction, from_index,
from_jimage can be swapped with to_index, to_jimage.</p>
<p>However, images will always always be shifted so that
from_index < to_index and from_jimage becomes (0, 0, 0).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – index of site connecting from</p></li>
<li><p><strong>to_index</strong> – index of site connecting to</p></li>
<li><p><strong>(</strong><strong>tuple of ints</strong><strong>)</strong> (<em>to_jimage</em>) – lattice vector of periodic
image, e.g. (1, 0, 0) for periodic image in +x direction</p></li>
<li><p><strong>(</strong><strong>tuple of ints</strong><strong>)</strong> – lattice vector of image</p></li>
<li><p><strong>(</strong><strong>float</strong><strong>)</strong> (<em>weight</em>) – e.g. bond length</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> (<em>warn_duplicates</em>) – if True, will warn if
trying to add duplicate edges (duplicate edges will not
be added in either case)</p></li>
<li><p><strong>(</strong><strong>dict</strong><strong>)</strong> (<em>edge_properties</em>) – any other information to
store on graph edges, similar to Structure’s site_properties</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.StructureGraph.alter_edge">
<code class="sig-name descname">alter_edge</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">from_index</span></em>, <em class="sig-param"><span class="n">to_index</span></em>, <em class="sig-param"><span class="n">to_jimage</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">new_weight</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">new_edge_properties</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L547-L598"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.alter_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Alters either the weight or the edge_properties of
an edge in the StructureGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>to_jimage</strong> – tuple</p></li>
<li><p><strong>new_weight</strong> – alter_edge does not require
that weight be altered. As such, by default, this
is None. If weight is to be changed, it should be a
float.</p></li>
<li><p><strong>new_edge_properties</strong> – alter_edge does not require
that edge_properties be altered. As such, by default,
this is None. If any edge properties are to be changed,
it should be a dictionary of edge properties to be changed.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.StructureGraph.as_dict">
<code class="sig-name descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1123-L1137"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>As in :Class: <cite>pymatgen.core.Structure</cite> except
with using <cite>to_dict_of_dicts</cite> from NetworkX
to store graph information.</p>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.StructureGraph.break_edge">
<code class="sig-name descname">break_edge</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">from_index</span></em>, <em class="sig-param"><span class="n">to_index</span></em>, <em class="sig-param"><span class="n">to_jimage</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">allow_reverse</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L600-L643"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.break_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove an edge from the StructureGraph. If no image is given, this method will fail.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>to_jimage</strong> – tuple</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will
attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.StructureGraph.diff">
<code class="sig-name descname">diff</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">other</span></em>, <em class="sig-param"><span class="n">strict</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L1498-L1578"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.diff" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares two StructureGraphs. Returns dict with
keys ‘self’, ‘other’, ‘both’ with edges that are
present in only one StructureGraph (‘self’ and
‘other’), and edges that are present in both.</p>
<p>The Jaccard distance is a simple measure of the
dissimilarity between two StructureGraphs (ignoring
edge weights), and is defined by 1 - (size of the
intersection / size of the union) of the sets of
edges. This is returned with key ‘dist’.</p>
<p>Important note: all node indices are in terms
of the StructureGraph this method is called
from, not the ‘other’ StructureGraph: there
is no guarantee the node indices will be the
same if the underlying Structures are ordered
differently.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> – StructureGraph</p></li>
<li><p><strong>strict</strong> – if False, will compare bonds
from different Structures, with node indices
replaced by Species strings, will not count
number of occurrences of bonds</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt id="pymatgen.analysis.graphs.StructureGraph.draw_graph_to_file">
<code class="sig-name descname">draw_graph_to_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">filename</span><span class="o">=</span><span class="default_value">'graph'</span></em>, <em class="sig-param"><span class="n">diff</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">hide_unconnected_nodes</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">hide_image_edges</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">edge_colors</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">node_labels</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">weight_labels</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">image_labels</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">color_scheme</span><span class="o">=</span><span class="default_value">'VESTA'</span></em>, <em class="sig-param"><span class="n">keep_dot</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">algo</span><span class="o">=</span><span class="default_value">'fdp'</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2021.1.28/pymatgen/analysis/graphs.py#L843-L1032"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.draw_graph_to_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws graph using GraphViz.</p>
<p>The networkx graph object itself can also be drawn
with networkx’s in-built graph drawing methods, but
note that this might give misleading results for
multigraphs (edges are super-imposed on each other).</p>
<p>If visualization is difficult to interpret,
<cite>hide_image_edges</cite> can help, especially in larger
graphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> – filename to output, will detect filetype
from extension (any graphviz filetype supported, such as
pdf or png)</p></li>
<li><p><strong>(</strong><strong>StructureGraph</strong><strong>)</strong> (<em>diff</em>) – an additional graph to
compare with, will color edges red that do not exist in diff