-
Notifications
You must be signed in to change notification settings - Fork 5
/
Copy pathtutorial03.html
1177 lines (1143 loc) · 112 KB
/
tutorial03.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>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>3. How to Setup the Initial Condition — E-Cell4 latest documentation</title>
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700">
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto+Mono"><link rel="stylesheet" href="../_static/typlog.css?v=0.7.3" type="text/css" />
<link rel="stylesheet" href="../_static/theme.css?v=0.7.3" type="text/css" />
<link rel="index" title="Index" href="../genindex.html"/>
<link rel="search" title="Search" href="../search.html"/>
<link rel="top" title="E-Cell4 latest documentation" href="../index.html"/>
<link rel="up" title="<no title>" href="index.html"/>
<link rel="next" title="4. How to Run a Simulation" href="tutorial04.html"/>
<link rel="prev" title="2. How to Build a Model" href="tutorial02.html"/>
<script>(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');ga('create', '');ga('send', 'pageview');</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 crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
<script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
<meta property="og:type" content="website">
<meta property="og:site_name" content="E-Cell4">
<meta property="og:title" content="3. How to Setup the Initial Condition">
<meta property="og:description" content="A software platform for modeling, simulation and analysis of a cell">
<meta name="twitter:card" content="summary">
</head>
<body role="document" data-page="tutorials/tutorial03">
<header class="t-head">
<div class="t-head_menu"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path d="M64 384h384v-42.666H64V384zm0-106.666h384v-42.667H64v42.667zM64 128v42.665h384V128H64z"/></svg></div>
<a class="t-head_logo" href="../index.html">E-Cell4
</a>
</header>
<aside class="t-sidebar">
<div class="t-sidebar_close">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path d="M405 136.798L375.202 107 256 226.202 136.798 107 107 136.798 226.202 256 107 375.202 136.798 405 256 285.798 375.202 405 405 375.202 285.798 256z"/></svg>
</div>
<div class="inner">
<a class="logo" href="../index.html">
ecell4
</a><div class="logo_desc">A software platform for modeling, simulation and analysis of a cell</div><div class="globaltoc">
<ul>
<li><a class="reference internal" href="#">3. How to Setup the Initial Condition</a><ul>
<li><a class="reference internal" href="#3.1.-Common-APIs-of-World">3.1. Common APIs of World</a></li>
<li><a class="reference internal" href="#3.2.-How-to-Get-Molecule-Positions">3.2. How to Get Molecule Positions</a></li>
<li><a class="reference internal" href="#3.3.-Lattice-based-Coordinate">3.3. Lattice-based Coordinate</a></li>
<li><a class="reference internal" href="#3.4-Structure">3.4 Structure</a></li>
<li><a class="reference internal" href="#3.5.-Random-Number-Generator">3.5. Random Number Generator</a></li>
</ul>
</li>
</ul>
</div>
<div id="searchbox">
<form class="search" action="../search.html" method="get">
<div class="input-group">
<input type="text" name="q" placeholder="Search" />
<button type="submit">Go</button>
</div>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
</aside>
<div class="t-content">
<div class="t-body yue">
<style>
/* CSS for nbsphinx extension */
/* remove conflicting styling from Sphinx themes */
div.nbinput.container,
div.nbinput.container div.prompt,
div.nbinput.container div.input_area,
div.nbinput.container div[class*=highlight],
div.nbinput.container div[class*=highlight] pre,
div.nboutput.container,
div.nboutput.container div.prompt,
div.nboutput.container div.output_area,
div.nboutput.container div[class*=highlight],
div.nboutput.container div[class*=highlight] pre {
background: none;
border: none;
padding: 0 0;
margin: 0;
box-shadow: none;
}
/* avoid gaps between output lines */
div.nboutput.container div[class*=highlight] pre {
line-height: normal;
}
/* input/output containers */
div.nbinput.container,
div.nboutput.container {
display: -webkit-flex;
display: flex;
align-items: flex-start;
margin: 0;
width: 100%;
}
@media (max-width: 540px) {
div.nbinput.container,
div.nboutput.container {
flex-direction: column;
}
}
/* input container */
div.nbinput.container {
padding-top: 5px;
}
/* last container */
div.nblast.container {
padding-bottom: 5px;
}
/* input prompt */
div.nbinput.container div.prompt pre {
color: #307FC1;
}
/* output prompt */
div.nboutput.container div.prompt pre {
color: #BF5B3D;
}
/* all prompts */
div.nbinput.container div.prompt,
div.nboutput.container div.prompt {
width: 4.5ex;
padding-top: 5px;
position: relative;
user-select: none;
}
div.nbinput.container div.prompt > div,
div.nboutput.container div.prompt > div {
position: absolute;
right: 0;
margin-right: 0.3ex;
}
@media (max-width: 540px) {
div.nbinput.container div.prompt,
div.nboutput.container div.prompt {
width: unset;
text-align: left;
padding: 0.4em;
}
div.nboutput.container div.prompt.empty {
padding: 0;
}
div.nbinput.container div.prompt > div,
div.nboutput.container div.prompt > div {
position: unset;
}
}
/* disable scrollbars on prompts */
div.nbinput.container div.prompt pre,
div.nboutput.container div.prompt pre {
overflow: hidden;
}
/* input/output area */
div.nbinput.container div.input_area,
div.nboutput.container div.output_area {
-webkit-flex: 1;
flex: 1;
overflow: auto;
}
@media (max-width: 540px) {
div.nbinput.container div.input_area,
div.nboutput.container div.output_area {
width: 100%;
}
}
/* input area */
div.nbinput.container div.input_area {
border: 1px solid #e0e0e0;
border-radius: 2px;
background: #f5f5f5;
}
/* override MathJax center alignment in output cells */
div.nboutput.container div[class*=MathJax] {
text-align: left !important;
}
/* override sphinx.ext.imgmath center alignment in output cells */
div.nboutput.container div.math p {
text-align: left;
}
/* standard error */
div.nboutput.container div.output_area.stderr {
background: #fdd;
}
/* ANSI colors */
.ansi-black-fg { color: #3E424D; }
.ansi-black-bg { background-color: #3E424D; }
.ansi-black-intense-fg { color: #282C36; }
.ansi-black-intense-bg { background-color: #282C36; }
.ansi-red-fg { color: #E75C58; }
.ansi-red-bg { background-color: #E75C58; }
.ansi-red-intense-fg { color: #B22B31; }
.ansi-red-intense-bg { background-color: #B22B31; }
.ansi-green-fg { color: #00A250; }
.ansi-green-bg { background-color: #00A250; }
.ansi-green-intense-fg { color: #007427; }
.ansi-green-intense-bg { background-color: #007427; }
.ansi-yellow-fg { color: #DDB62B; }
.ansi-yellow-bg { background-color: #DDB62B; }
.ansi-yellow-intense-fg { color: #B27D12; }
.ansi-yellow-intense-bg { background-color: #B27D12; }
.ansi-blue-fg { color: #208FFB; }
.ansi-blue-bg { background-color: #208FFB; }
.ansi-blue-intense-fg { color: #0065CA; }
.ansi-blue-intense-bg { background-color: #0065CA; }
.ansi-magenta-fg { color: #D160C4; }
.ansi-magenta-bg { background-color: #D160C4; }
.ansi-magenta-intense-fg { color: #A03196; }
.ansi-magenta-intense-bg { background-color: #A03196; }
.ansi-cyan-fg { color: #60C6C8; }
.ansi-cyan-bg { background-color: #60C6C8; }
.ansi-cyan-intense-fg { color: #258F8F; }
.ansi-cyan-intense-bg { background-color: #258F8F; }
.ansi-white-fg { color: #C5C1B4; }
.ansi-white-bg { background-color: #C5C1B4; }
.ansi-white-intense-fg { color: #A1A6B2; }
.ansi-white-intense-bg { background-color: #A1A6B2; }
.ansi-default-inverse-fg { color: #FFFFFF; }
.ansi-default-inverse-bg { background-color: #000000; }
.ansi-bold { font-weight: bold; }
.ansi-underline { text-decoration: underline; }
div.nbinput.container div.input_area div[class*=highlight] > pre,
div.nboutput.container div.output_area div[class*=highlight] > pre,
div.nboutput.container div.output_area div[class*=highlight].math,
div.nboutput.container div.output_area.rendered_html,
div.nboutput.container div.output_area > div.output_javascript,
div.nboutput.container div.output_area:not(.rendered_html) > img{
padding: 5px;
}
/* fix copybtn overflow problem in chromium (needed for 'sphinx_copybutton') */
div.nbinput.container div.input_area > div[class^='highlight'],
div.nboutput.container div.output_area > div[class^='highlight']{
overflow-y: hidden;
}
/* hide copybtn icon on prompts (needed for 'sphinx_copybutton') */
.prompt a.copybtn {
display: none;
}
/* Some additional styling taken form the Jupyter notebook CSS */
div.rendered_html table {
border: none;
border-collapse: collapse;
border-spacing: 0;
color: black;
font-size: 12px;
table-layout: fixed;
}
div.rendered_html thead {
border-bottom: 1px solid black;
vertical-align: bottom;
}
div.rendered_html tr,
div.rendered_html th,
div.rendered_html td {
text-align: right;
vertical-align: middle;
padding: 0.5em 0.5em;
line-height: normal;
white-space: normal;
max-width: none;
border: none;
}
div.rendered_html th {
font-weight: bold;
}
div.rendered_html tbody tr:nth-child(odd) {
background: #f5f5f5;
}
div.rendered_html tbody tr:hover {
background: rgba(66, 165, 245, 0.2);
}
</style>
<script src='http://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js'></script>
<script>require=requirejs;</script><div class="admonition seealso">
<p class="admonition-title">See also</p>
<p>This page was generated from <a class="reference external" href="https://github.com/kaizu/ecell4_docs/blob/latest/en/tutorials/tutorial03.ipynb">tutorials/tutorial03.ipynb</a>.</p>
<p>Download the <a class="reference external" href="https://jupyter.org/">Jupyter Notebook</a> for this section: <a class="reference download internal" download="" href="../_downloads/50fa624193721faeb84d68b519c8451d/tutorial03.ipynb"><code class="xref download docutils literal notranslate"><span class="pre">tutorial03.ipynb</span></code></a>. <a class="reference external" href="https://nbviewer.jupyter.org/github/kaizu/ecell4_docs/blob/latest/en/tutorials/tutorial03.ipynb">View in nbviewer</a>.</p>
<a class="reference external image-reference" href="https://colab.research.google.com/github/kaizu/ecell4_docs/blob/latest/en/tutorials/tutorial03.ipynb"><img alt="https://colab.research.google.com/assets/colab-badge.svg" src="https://colab.research.google.com/assets/colab-badge.svg" /></a>
<a class="reference external image-reference" href="https://mybinder.org/v2/gh/kaizu/ecell4_docs/latest?filepath=en/tutorials/tutorial03.ipynb"><img alt="https://mybinder.org/badge_logo.svg" src="https://mybinder.org/badge_logo.svg" /></a>
</div>
<div class="section" id="3.-How-to-Setup-the-Initial-Condition">
<h1>3. How to Setup the Initial Condition<a class="headerlink" href="#3.-How-to-Setup-the-Initial-Condition" title="Permalink to this headline">¶</a></h1>
<p>Here, we explain the basics of <code class="docutils literal notranslate"><span class="pre">World</span></code> classes. In E-Cell4, six types of World classes are supported now: <code class="docutils literal notranslate"><span class="pre">spatiocyte.SpatiocyteWorld</span></code>, <code class="docutils literal notranslate"><span class="pre">egfrd.EGFRDWorld</span></code>, <code class="docutils literal notranslate"><span class="pre">bd.BDWorld</span></code>, <code class="docutils literal notranslate"><span class="pre">meso.MesoscopicWorld</span></code>, <code class="docutils literal notranslate"><span class="pre">gillespie.GillespieWorld</span></code>, and <code class="docutils literal notranslate"><span class="pre">ode.ODEWorld</span></code>.</p>
<p>In the most of softwares, the initial condition is supposed to be a part of <code class="docutils literal notranslate"><span class="pre">Model</span></code>. But, in E-Cell4, the initial condition must be set up as <code class="docutils literal notranslate"><span class="pre">World</span></code> separately from <code class="docutils literal notranslate"><span class="pre">Model</span></code>. <code class="docutils literal notranslate"><span class="pre">World</span></code> stores an information about the state, such as a current time, the number of molecules, coordinate of molecules, structures, and random number generator, at a time point. Meanwhile, <code class="docutils literal notranslate"><span class="pre">Model</span></code> contains the type of interactions between molecules and the common properties of molecules. <code class="docutils literal notranslate"><span class="pre">Model</span></code> is reusable
among algorithms.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[1]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="kn">from</span> <span class="nn">ecell4_base.core</span> <span class="kn">import</span> <span class="o">*</span>
</pre></div>
</div>
</div>
<div class="section" id="3.1.-Common-APIs-of-World">
<h2>3.1. Common APIs of World<a class="headerlink" href="#3.1.-Common-APIs-of-World" title="Permalink to this headline">¶</a></h2>
<p>Even though <code class="docutils literal notranslate"><span class="pre">World</span></code> describes the spatial representation specific to the corresponding algorithm, it has compatible APIs. In this section, we introduce the common interfaces of the six <code class="docutils literal notranslate"><span class="pre">World</span></code> classes.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[2]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="kn">from</span> <span class="nn">ecell4_base</span> <span class="kn">import</span> <span class="o">*</span>
</pre></div>
</div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">World</span></code> classes accept different sets of arguments in the constructor, which determine the parameters specific to the algorithm. However, at least, all <code class="docutils literal notranslate"><span class="pre">World</span></code> classes can be instantiated only with their size, named <code class="docutils literal notranslate"><span class="pre">edge_lengths</span></code>. The type of <code class="docutils literal notranslate"><span class="pre">edge_lengths</span></code> is <code class="docutils literal notranslate"><span class="pre">Real3</span></code>, which represents a triplet of <code class="docutils literal notranslate"><span class="pre">Real</span></code>s. In E-Cell4, all 3-dimensional positions are treated as a <code class="docutils literal notranslate"><span class="pre">Real3</span></code>. See also <a class="reference external" href="tutorial8.html">8. More about 1. Brief Tour of E-Cell4 Simulations</a>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[3]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">edge_lengths</span> <span class="o">=</span> <span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="n">w1</span> <span class="o">=</span> <span class="n">gillespie</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">edge_lengths</span><span class="p">)</span>
<span class="n">w2</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">edge_lengths</span><span class="p">)</span>
<span class="n">w3</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">edge_lengths</span><span class="p">)</span>
<span class="n">w4</span> <span class="o">=</span> <span class="n">bd</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">edge_lengths</span><span class="p">)</span>
<span class="n">w5</span> <span class="o">=</span> <span class="n">meso</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">edge_lengths</span><span class="p">)</span>
<span class="n">w6</span> <span class="o">=</span> <span class="n">egfrd</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">edge_lengths</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">World</span></code> has getter methods for the size and volume.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[4]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w1</span><span class="o">.</span><span class="n">volume</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">w2</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w2</span><span class="o">.</span><span class="n">volume</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w3</span><span class="o">.</span><span class="n">volume</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w4</span><span class="o">.</span><span class="n">volume</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">w5</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w5</span><span class="o">.</span><span class="n">volume</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w6</span><span class="o">.</span><span class="n">volume</span><span class="p">())</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
(1.0, 2.0, 3.0) 6.0
(1.0, 2.0, 3.0) 6.0
(1.0124557603503803, 2.0091789367798976, 3.0) 6.102614364352381
(1.0, 2.0, 3.0) 6.0
(1.0, 2.0, 3.0) 6.0
(1.0, 2.0, 3.0) 6.0
</pre></div></div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">spatiocyte.World</span></code> (<code class="docutils literal notranslate"><span class="pre">w3</span></code>) would have a bit larger volume to fit regular hexagonal close-packed (HCP) lattice.</p>
<p>Next, let’s add molecules into the World. Here, you must give <code class="docutils literal notranslate"><span class="pre">Species</span></code> attributed with <strong>radius</strong> and <strong>D</strong> to tell the shape of molecules. In the example below <strong>0.0025</strong> corresponds to <strong>radius</strong> and <strong>1</strong> to <strong>D</strong>. Positions of the molecules are randomly determined in the <code class="docutils literal notranslate"><span class="pre">World</span></code> if needed. <strong>10</strong> in <strong>add_molecules</strong> function represents the number of molecules to be added.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[5]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">sp1</span> <span class="o">=</span> <span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">,</span> <span class="mf">0.0025</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">w1</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p>After a model is bound to the world, you do not need to rewrite the <strong>radius</strong> and <strong>D</strong> once set in <code class="docutils literal notranslate"><span class="pre">Species</span></code> (unless you want to change it).</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[6]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">m</span> <span class="o">=</span> <span class="n">NetworkModel</span><span class="p">()</span>
<span class="n">m</span><span class="o">.</span><span class="n">add_species_attribute</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">,</span> <span class="mf">0.0025</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
<span class="n">m</span><span class="o">.</span><span class="n">add_species_attribute</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">,</span> <span class="mf">0.0025</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
<span class="n">w1</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">w1</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">20</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">20</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">20</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">20</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">20</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">20</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p>Similarly, <code class="docutils literal notranslate"><span class="pre">remove_molecules</span></code> and <code class="docutils literal notranslate"><span class="pre">num_molecules_exact</span></code> are also available.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[7]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">w1</span><span class="o">.</span><span class="n">remove_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">5</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">remove_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">5</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">remove_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">5</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">remove_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">5</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">remove_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">5</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">remove_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">),</span> <span class="mi">5</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules_exact</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
10 10 10 10 10 10
15 15 15 15 15 15
</pre></div></div>
</div>
<p>Unlike <code class="docutils literal notranslate"><span class="pre">num_molecules_exact</span></code>, <code class="docutils literal notranslate"><span class="pre">num_molecules</span></code> returns the numbers that match a given <code class="docutils literal notranslate"><span class="pre">Species</span></code> in rule-based fashion. When all <code class="docutils literal notranslate"><span class="pre">Species</span></code> in the <code class="docutils literal notranslate"><span class="pre">World</span></code> has a single <code class="docutils literal notranslate"><span class="pre">UnitSpecies</span></code> with no sites, <code class="docutils literal notranslate"><span class="pre">num_molecules</span></code> is same with <code class="docutils literal notranslate"><span class="pre">num_molecules_exact</span></code>.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[9]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
10 10 10 10 10 10
15 15 15 15 15 15
</pre></div></div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">World</span></code> holds its simulation time.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[10]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w2</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w3</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w4</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w5</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w6</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="n">w1</span><span class="o">.</span><span class="n">set_t</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">set_t</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">set_t</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">set_t</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">set_t</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">set_t</span><span class="p">(</span><span class="mf">1.0</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w2</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w3</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w4</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w5</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="n">w6</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
0.0 0.0 0.0 0.0 0.0 0.0
1.0 1.0 1.0 1.0 1.0 1.0
</pre></div></div>
</div>
<p>Finally, you can <code class="docutils literal notranslate"><span class="pre">save</span></code> and <code class="docutils literal notranslate"><span class="pre">load</span></code> the state of a <code class="docutils literal notranslate"><span class="pre">World</span></code> into/from a HDF5 file.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[11]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">w1</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s2">"gillespie.h5"</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s2">"ode.h5"</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s2">"spatiocyte.h5"</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s2">"bd.h5"</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s2">"meso.h5"</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s2">"egfrd.h5"</span><span class="p">)</span>
<span class="k">del</span> <span class="n">w1</span><span class="p">,</span> <span class="n">w2</span><span class="p">,</span> <span class="n">w3</span><span class="p">,</span> <span class="n">w4</span><span class="p">,</span> <span class="n">w5</span><span class="p">,</span> <span class="n">w6</span>
</pre></div>
</div>
</div>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[12]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">w1</span> <span class="o">=</span> <span class="n">gillespie</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w2</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w3</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w4</span> <span class="o">=</span> <span class="n">bd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w5</span> <span class="o">=</span> <span class="n">meso</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w6</span> <span class="o">=</span> <span class="n">egfrd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w1</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w1</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w1</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w2</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w2</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w2</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w3</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w4</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w5</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w5</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w5</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w6</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
0.0 (1.0, 1.0, 1.0) 1.0 0 0
0.0 (1.0, 1.0, 1.0) 1.0 0 0
0.0 (1.0124557603503803, 1.0045894683899488, 1.0) 1.0171023940587303 0 0
0.0 (1.0, 1.0, 1.0) 1.0 0 0
0.0 (1.0, 1.0, 1.0) 1.0 0 0
0.0 (1.0, 1.0, 1.0) 1.0 0 0
</pre></div></div>
</div>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[13]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">w1</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"gillespie.h5"</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"ode.h5"</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"spatiocyte.h5"</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"bd.h5"</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"meso.h5"</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s2">"egfrd.h5"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w1</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w1</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w1</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w2</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w2</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w2</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w2</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w3</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w3</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w4</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w4</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w5</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w5</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w5</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w5</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">t</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">edge_lengths</span><span class="p">()),</span> <span class="n">w6</span><span class="o">.</span><span class="n">volume</span><span class="p">(),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">)),</span> <span class="n">w6</span><span class="o">.</span><span class="n">num_molecules</span><span class="p">(</span><span class="n">Species</span><span class="p">(</span><span class="s2">"B"</span><span class="p">)))</span>
<span class="k">del</span> <span class="n">w1</span><span class="p">,</span> <span class="n">w2</span><span class="p">,</span> <span class="n">w3</span><span class="p">,</span> <span class="n">w4</span><span class="p">,</span> <span class="n">w5</span><span class="p">,</span> <span class="n">w6</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
1.0 (1.0, 2.0, 3.0) 6.0 10 15
1.0 (1.0, 2.0, 3.0) 6.0 10 15
1.0 (1.0124557603503803, 2.0091789367798976, 3.0) 6.102614364352381 10 15
1.0 (1.0, 2.0, 3.0) 6.0 10 15
1.0 (1.0, 2.0, 3.0) 6.0 10 15
1.0 (1.0, 2.0, 3.0) 6.0 10 15
</pre></div></div>
</div>
<p>All the <code class="docutils literal notranslate"><span class="pre">World</span></code> classes also accept a HDF5 file path as an unique argument of the constructor.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[14]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="n">gillespie</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="s2">"gillespie.h5"</span><span class="p">)</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="s2">"ode.h5"</span><span class="p">)</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">spatiocyte</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="s2">"spatiocyte.h5"</span><span class="p">)</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">bd</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="s2">"bd.h5"</span><span class="p">)</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">meso</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="s2">"meso.h5"</span><span class="p">)</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">egfrd</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="s2">"egfrd.h5"</span><span class="p">)</span><span class="o">.</span><span class="n">t</span><span class="p">())</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
1.0
1.0
1.0
1.0
1.0
1.0
</pre></div></div>
</div>
</div>
<div class="section" id="3.2.-How-to-Get-Molecule-Positions">
<h2>3.2. How to Get Molecule Positions<a class="headerlink" href="#3.2.-How-to-Get-Molecule-Positions" title="Permalink to this headline">¶</a></h2>
<p><code class="docutils literal notranslate"><span class="pre">World</span></code> also has the common functions to access the coordinates of the molecules.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[15]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">w1</span> <span class="o">=</span> <span class="n">gillespie</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w2</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w3</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w4</span> <span class="o">=</span> <span class="n">bd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w5</span> <span class="o">=</span> <span class="n">meso</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w6</span> <span class="o">=</span> <span class="n">egfrd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
</pre></div>
</div>
</div>
<p>First, you can place a molecule at the certain position with <code class="docutils literal notranslate"><span class="pre">new_particle</span></code>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[16]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">sp1</span> <span class="o">=</span> <span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">,</span> <span class="mf">0.0025</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">pos</span> <span class="o">=</span> <span class="n">Real3</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
<span class="p">(</span><span class="n">pid1</span><span class="p">,</span> <span class="n">p1</span><span class="p">),</span> <span class="n">suc1</span> <span class="o">=</span> <span class="n">w1</span><span class="o">.</span><span class="n">new_particle</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="n">pos</span><span class="p">)</span>
<span class="p">(</span><span class="n">pid2</span><span class="p">,</span> <span class="n">p2</span><span class="p">),</span> <span class="n">suc2</span> <span class="o">=</span> <span class="n">w2</span><span class="o">.</span><span class="n">new_particle</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="n">pos</span><span class="p">)</span>
<span class="n">pid3</span> <span class="o">=</span> <span class="n">w3</span><span class="o">.</span><span class="n">new_particle</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="n">pos</span><span class="p">)</span>
<span class="p">(</span><span class="n">pid4</span><span class="p">,</span> <span class="n">p4</span><span class="p">),</span> <span class="n">suc4</span> <span class="o">=</span> <span class="n">w4</span><span class="o">.</span><span class="n">new_particle</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="n">pos</span><span class="p">)</span>
<span class="p">(</span><span class="n">pid5</span><span class="p">,</span> <span class="n">p5</span><span class="p">),</span> <span class="n">suc5</span> <span class="o">=</span> <span class="n">w5</span><span class="o">.</span><span class="n">new_particle</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="n">pos</span><span class="p">)</span>
<span class="p">(</span><span class="n">pid6</span><span class="p">,</span> <span class="n">p6</span><span class="p">),</span> <span class="n">suc6</span> <span class="o">=</span> <span class="n">w6</span><span class="o">.</span><span class="n">new_particle</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="n">pos</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">new_particle</span></code> returns a particle created and whether it’s succeeded or not. The resolution in representation of molecules differs. For example, <code class="docutils literal notranslate"><span class="pre">GillespieWorld</span></code> has almost no information about the coordinate of molecules. Thus, it simply ignores the given position, and just counts up the number of molecules here.</p>
<p><code class="docutils literal notranslate"><span class="pre">ParticleID</span></code> is a pair of <code class="docutils literal notranslate"><span class="pre">Integer</span></code>s named <code class="docutils literal notranslate"><span class="pre">lot</span></code> and <code class="docutils literal notranslate"><span class="pre">serial</span></code>.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[17]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="n">pid6</span><span class="o">.</span><span class="n">lot</span><span class="p">(),</span> <span class="n">pid6</span><span class="o">.</span><span class="n">serial</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">pid6</span> <span class="o">==</span> <span class="n">ParticleID</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">)))</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
0 1
False
</pre></div></div>
</div>
<p>Particle simulators, i.e. <code class="docutils literal notranslate"><span class="pre">spatiocyte</span></code>, <code class="docutils literal notranslate"><span class="pre">bd</span></code> and <code class="docutils literal notranslate"><span class="pre">egfrd</span></code>, provide an interface to access a particle by its id. <code class="docutils literal notranslate"><span class="pre">has_particle</span></code> returns if a particles exists or not for the given <code class="docutils literal notranslate"><span class="pre">ParticleID</span></code>.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[18]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># print(w1.has_particle(pid1))</span>
<span class="c1"># print(w2.has_particle(pid2))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">has_particle</span><span class="p">(</span><span class="n">pid3</span><span class="p">))</span> <span class="c1"># => True</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">has_particle</span><span class="p">(</span><span class="n">pid4</span><span class="p">))</span> <span class="c1"># => True</span>
<span class="c1"># print(w5.has_particle(pid5))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">has_particle</span><span class="p">(</span><span class="n">pid6</span><span class="p">))</span> <span class="c1"># => True</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
True
True
True
</pre></div></div>
</div>
<p>After checking the existence, you can get the partcle by <code class="docutils literal notranslate"><span class="pre">get_particle</span></code> as follows.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[19]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># pid1, p1 = w1.get_particle(pid1)</span>
<span class="c1"># pid2, p2 = w2.get_particle(pid2)</span>
<span class="n">pid3</span><span class="p">,</span> <span class="n">p3</span> <span class="o">=</span> <span class="n">w3</span><span class="o">.</span><span class="n">get_particle</span><span class="p">(</span><span class="n">pid3</span><span class="p">)</span>
<span class="n">pid4</span><span class="p">,</span> <span class="n">p4</span> <span class="o">=</span> <span class="n">w4</span><span class="o">.</span><span class="n">get_particle</span><span class="p">(</span><span class="n">pid4</span><span class="p">)</span>
<span class="c1"># pid5, p5 = w5.get_particle(pid5)</span>
<span class="n">pid6</span><span class="p">,</span> <span class="n">p6</span> <span class="o">=</span> <span class="n">w6</span><span class="o">.</span><span class="n">get_particle</span><span class="p">(</span><span class="n">pid6</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">Particle</span></code> consists of <code class="docutils literal notranslate"><span class="pre">species</span></code>, <code class="docutils literal notranslate"><span class="pre">position</span></code>, <code class="docutils literal notranslate"><span class="pre">radius</span></code> and <code class="docutils literal notranslate"><span class="pre">D</span></code>.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[20]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># print(p1.species().serial(), tuple(p1.position()), p1.radius(), p1.D())</span>
<span class="c1"># print(p2.species().serial(), tuple(p2.position()), p2.radius(), p2.D())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">p3</span><span class="o">.</span><span class="n">species</span><span class="p">()</span><span class="o">.</span><span class="n">serial</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">p3</span><span class="o">.</span><span class="n">position</span><span class="p">()),</span> <span class="n">p3</span><span class="o">.</span><span class="n">radius</span><span class="p">(),</span> <span class="n">p3</span><span class="o">.</span><span class="n">D</span><span class="p">())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">p4</span><span class="o">.</span><span class="n">species</span><span class="p">()</span><span class="o">.</span><span class="n">serial</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">p4</span><span class="o">.</span><span class="n">position</span><span class="p">()),</span> <span class="n">p4</span><span class="o">.</span><span class="n">radius</span><span class="p">(),</span> <span class="n">p4</span><span class="o">.</span><span class="n">D</span><span class="p">())</span>
<span class="c1"># print(p5.species().serial(), tuple(p5.position()), p5.radius(), p5.D())</span>
<span class="nb">print</span><span class="p">(</span><span class="n">p6</span><span class="o">.</span><span class="n">species</span><span class="p">()</span><span class="o">.</span><span class="n">serial</span><span class="p">(),</span> <span class="nb">tuple</span><span class="p">(</span><span class="n">p6</span><span class="o">.</span><span class="n">position</span><span class="p">()),</span> <span class="n">p6</span><span class="o">.</span><span class="n">radius</span><span class="p">(),</span> <span class="n">p6</span><span class="o">.</span><span class="n">D</span><span class="p">())</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
A (0.5062278801751902, 0.5080682368868706, 0.5) 0.0025 1.0
A (0.5, 0.5, 0.5) 0.0025 1.0
A (0.5, 0.5, 0.5) 0.0025 1.0
</pre></div></div>
</div>
<p>In the case of <code class="docutils literal notranslate"><span class="pre">spatiocyte</span></code>, a particle position is automatically round to the center of the voxel nearest to the given position.</p>
<p>You can even move the position of the particle. <code class="docutils literal notranslate"><span class="pre">update_particle</span></code> replace the particle specified with the given <code class="docutils literal notranslate"><span class="pre">ParticleID</span></code> with the given <code class="docutils literal notranslate"><span class="pre">Particle</span></code> and return <code class="docutils literal notranslate"><span class="pre">False</span></code>. If no corresponding particle is found, create new particle and return <code class="docutils literal notranslate"><span class="pre">True</span></code>. If you give a <code class="docutils literal notranslate"><span class="pre">Particle</span></code> with the different type of <code class="docutils literal notranslate"><span class="pre">Species</span></code>, the <code class="docutils literal notranslate"><span class="pre">Species</span></code> of the <code class="docutils literal notranslate"><span class="pre">Particle</span></code> will be also changed.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[21]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">newp</span> <span class="o">=</span> <span class="n">Particle</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="n">Real3</span><span class="p">(</span><span class="mf">0.3</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">),</span> <span class="mf">0.0025</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="c1"># print(w1.update_particle(pid1, newp))</span>
<span class="c1"># print(w2.update_particle(pid2, newp))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">update_particle</span><span class="p">(</span><span class="n">pid3</span><span class="p">,</span> <span class="n">newp</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">update_particle</span><span class="p">(</span><span class="n">pid4</span><span class="p">,</span> <span class="n">newp</span><span class="p">))</span>
<span class="c1"># print(w5.update_particle(pid5, newp))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">update_particle</span><span class="p">(</span><span class="n">pid6</span><span class="p">,</span> <span class="n">newp</span><span class="p">))</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
False
False
False
</pre></div></div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">list_particles</span></code> and <code class="docutils literal notranslate"><span class="pre">list_particles_exact</span></code> return a list of pairs of <code class="docutils literal notranslate"><span class="pre">ParticleID</span></code> and <code class="docutils literal notranslate"><span class="pre">Particle</span></code> in the <code class="docutils literal notranslate"><span class="pre">World</span></code>. <code class="docutils literal notranslate"><span class="pre">World</span></code> automatically makes up for the gap with random numbers. For example, <code class="docutils literal notranslate"><span class="pre">GillespieWorld</span></code> returns a list of positions randomly distributed in the <code class="docutils literal notranslate"><span class="pre">World</span></code> size.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[22]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="n">w1</span><span class="o">.</span><span class="n">list_particles_exact</span><span class="p">(</span><span class="n">sp1</span><span class="p">))</span>
<span class="c1"># print(w2.list_particles_exact(sp1)) # ODEWorld has no member named list_particles</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">list_particles_exact</span><span class="p">(</span><span class="n">sp1</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">list_particles_exact</span><span class="p">(</span><span class="n">sp1</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w5</span><span class="o">.</span><span class="n">list_particles_exact</span><span class="p">(</span><span class="n">sp1</span><span class="p">))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">list_particles_exact</span><span class="p">(</span><span class="n">sp1</span><span class="p">))</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
[(<ecell4_base.core.ParticleID object at 0x15330c38d1f0>, <ecell4_base.core.Particle object at 0x15330c38d228>)]
[(<ecell4_base.core.ParticleID object at 0x15330c38d1b8>, <ecell4_base.core.Particle object at 0x15330c38d260>)]
[(<ecell4_base.core.ParticleID object at 0x15330c38d1f0>, <ecell4_base.core.Particle object at 0x15330c38d308>)]
[(<ecell4_base.core.ParticleID object at 0x15330c38d1b8>, <ecell4_base.core.Particle object at 0x15330c38d228>)]
[(<ecell4_base.core.ParticleID object at 0x15330c38d1f0>, <ecell4_base.core.Particle object at 0x15330c38d260>)]
</pre></div></div>
</div>
<p>You can remove a specific particle with <code class="docutils literal notranslate"><span class="pre">remove_particle</span></code>.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[23]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># w1.remove_particle(pid1)</span>
<span class="c1"># w2.remove_particle(pid2)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">remove_particle</span><span class="p">(</span><span class="n">pid3</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">remove_particle</span><span class="p">(</span><span class="n">pid4</span><span class="p">)</span>
<span class="c1"># w5.remove_particle(pid5)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">remove_particle</span><span class="p">(</span><span class="n">pid6</span><span class="p">)</span>
<span class="c1"># print(w1.has_particle(pid1))</span>
<span class="c1"># print(w2.has_particle(pid2))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w3</span><span class="o">.</span><span class="n">has_particle</span><span class="p">(</span><span class="n">pid3</span><span class="p">))</span> <span class="c1"># => False</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w4</span><span class="o">.</span><span class="n">has_particle</span><span class="p">(</span><span class="n">pid4</span><span class="p">))</span> <span class="c1"># => False</span>
<span class="c1"># print(w5.has_particle(pid5))</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w6</span><span class="o">.</span><span class="n">has_particle</span><span class="p">(</span><span class="n">pid6</span><span class="p">))</span> <span class="c1"># => False</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
False
False
False
</pre></div></div>
</div>
</div>
<div class="section" id="3.3.-Lattice-based-Coordinate">
<h2>3.3. Lattice-based Coordinate<a class="headerlink" href="#3.3.-Lattice-based-Coordinate" title="Permalink to this headline">¶</a></h2>
<p>In addition to the common interface, each <code class="docutils literal notranslate"><span class="pre">World</span></code> can have their own interfaces. As an example, we explain methods to handle lattice-based coordinate here. <code class="docutils literal notranslate"><span class="pre">SpatiocyteWorld</span></code> is based on a space discretized to hexiagonal close packing lattices, <code class="docutils literal notranslate"><span class="pre">LatticeSpace</span></code>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[24]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">w</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">World</span><span class="p">(</span><span class="n">Real3</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">voxel_radius</span><span class="o">=</span><span class="mf">0.01</span><span class="p">)</span>
<span class="n">w</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p>The size of a single lattice, called <code class="docutils literal notranslate"><span class="pre">Voxel</span></code>, can be obtained by <code class="docutils literal notranslate"><span class="pre">voxel_radius()</span></code>. <code class="docutils literal notranslate"><span class="pre">SpatiocyteWorld</span></code> has methods to get the numbers of rows, columns, and layers. These sizes are automatically calculated based on the given <code class="docutils literal notranslate"><span class="pre">edge_lengths</span></code> at the construction.</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[25]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="nb">print</span><span class="p">(</span><span class="n">w</span><span class="o">.</span><span class="n">voxel_radius</span><span class="p">())</span> <span class="c1"># => 0.01</span>
<span class="nb">print</span><span class="p">(</span><span class="nb">tuple</span><span class="p">(</span><span class="n">w</span><span class="o">.</span><span class="n">shape</span><span class="p">()))</span> <span class="c1"># => (64, 152, 118)</span>
<span class="c1"># print(w.col_size(), w.row_size(), w.layer_size()) # => (64, 152, 118)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">w</span><span class="o">.</span><span class="n">size</span><span class="p">())</span> <span class="c1"># => 1147904 = 64 * 152 * 118</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt empty docutils container">
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
0.01
(64, 152, 118)
1147904
</pre></div></div>
</div>
<p>A position in the lattice-based space is treated as an <code class="docutils literal notranslate"><span class="pre">Integer3</span></code>, column, row and layer, called a global coordinate. Thus, <code class="docutils literal notranslate"><span class="pre">SpatiocyteWorld</span></code> provides the function to convert the <code class="docutils literal notranslate"><span class="pre">Real3</span></code> into a lattice-based coordinate.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[26]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># p1 = Real3(0.5, 0.5, 0.5)</span>
<span class="c1"># g1 = w.position2global(p1)</span>
<span class="c1"># p2 = w.global2position(g1)</span>
<span class="c1"># print(tuple(g1)) # => (31, 25, 29)</span>
<span class="c1"># print(tuple(p2)) # => (0.5062278801751902, 0.5080682368868706, 0.5)</span>
</pre></div>
</div>
</div>
<p>In <code class="docutils literal notranslate"><span class="pre">SpatiocyteWorld</span></code>, the global coordinate is translated to a single integer. It is just called a coordinate. You can also treat the coordinate as in the same way with a global coordinate.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[27]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># p1 = Real3(0.5, 0.5, 0.5)</span>
<span class="c1"># c1 = w.position2coordinate(p1)</span>
<span class="c1"># p2 = w.coordinate2position(c1)</span>
<span class="c1"># g1 = w.coord2global(c1)</span>
<span class="c1"># print(c1) # => 278033</span>
<span class="c1"># print(tuple(p2)) # => (0.5062278801751902, 0.5080682368868706, 0.5)</span>
<span class="c1"># print(tuple(g1)) # => (31, 25, 29)</span>
</pre></div>
</div>
</div>
<p>With these coordinates, you can handle a <code class="docutils literal notranslate"><span class="pre">Voxel</span></code>, which represents a <code class="docutils literal notranslate"><span class="pre">Particle</span></code> object. Instead of <code class="docutils literal notranslate"><span class="pre">new_particle</span></code>, <code class="docutils literal notranslate"><span class="pre">new_voxel</span></code> provides the way to create a new <code class="docutils literal notranslate"><span class="pre">Voxel</span></code> with a coordinate.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[28]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># c1 = w.position2coordinate(Real3(0.5, 0.5, 0.5))</span>
<span class="c1"># ((pid, v), is_succeeded) = w.new_voxel(Species("A"), c1)</span>
<span class="c1"># print(pid, v, is_succeeded)</span>
</pre></div>
</div>
</div>
<p>A <code class="docutils literal notranslate"><span class="pre">Voxel</span></code> consists of <code class="docutils literal notranslate"><span class="pre">species</span></code>, <code class="docutils literal notranslate"><span class="pre">coordinate</span></code>, <code class="docutils literal notranslate"><span class="pre">radius</span></code> and <code class="docutils literal notranslate"><span class="pre">D</span></code>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[29]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># print(v.species().serial(), v.coordinate(), v.radius(), v.D()) # => (u'A', 278033, 0.0025, 1.0)</span>
</pre></div>
</div>
</div>
<p>Of course, you can get a voxel and list voxels with <code class="docutils literal notranslate"><span class="pre">get_voxel</span></code> and <code class="docutils literal notranslate"><span class="pre">list_voxels_exact</span></code> similar to <code class="docutils literal notranslate"><span class="pre">get_particle</span></code> and <code class="docutils literal notranslate"><span class="pre">list_particles_exact</span></code>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[30]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># print(w.num_voxels_exact(Species("A")))</span>
<span class="c1"># print(w.list_voxels_exact(Species("A")))</span>
<span class="c1"># print(w.get_voxel(pid))</span>
</pre></div>
</div>
</div>
<p>You can move and update the voxel with <code class="docutils literal notranslate"><span class="pre">update_voxel</span></code> corresponding to <code class="docutils literal notranslate"><span class="pre">update_particle</span></code>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[31]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># c2 = w.position2coordinate(Real3(0.5, 0.5, 1.0))</span>
<span class="c1"># w.update_voxel(pid, Voxel(v.species(), c2, v.radius(), v.D()))</span>
<span class="c1"># pid, newv = w.get_voxel(pid)</span>
<span class="c1"># print(c2) # => 278058</span>
<span class="c1"># print(newv.species().serial(), newv.coordinate(), newv.radius(), newv.D()) # => (u'A', 278058, 0.0025, 1.0)</span>
<span class="c1"># print(w.num_voxels_exact(Species("A"))) # => 1</span>
</pre></div>
</div>
</div>
<p>Finally, <code class="docutils literal notranslate"><span class="pre">remove_voxel</span></code> remove a voxel as <code class="docutils literal notranslate"><span class="pre">remove_particle</span></code> does.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[32]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># print(w.has_voxel(pid)) # => True</span>
<span class="c1"># w.remove_voxel(pid)</span>
<span class="c1"># print(w.has_voxel(pid)) # => False</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="3.4-Structure">
<h2>3.4 Structure<a class="headerlink" href="#3.4-Structure" title="Permalink to this headline">¶</a></h2>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[33]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">w1</span> <span class="o">=</span> <span class="n">gillespie</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w2</span> <span class="o">=</span> <span class="n">ode</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w3</span> <span class="o">=</span> <span class="n">spatiocyte</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w4</span> <span class="o">=</span> <span class="n">bd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w5</span> <span class="o">=</span> <span class="n">meso</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
<span class="n">w6</span> <span class="o">=</span> <span class="n">egfrd</span><span class="o">.</span><span class="n">World</span><span class="p">()</span>
</pre></div>
</div>
</div>
<p>By using a <code class="docutils literal notranslate"><span class="pre">Shape</span></code> object, you can confine initial positions of molecules to a part of <code class="docutils literal notranslate"><span class="pre">World</span></code>. In the case below, 60 molecules are positioned inside the given <code class="docutils literal notranslate"><span class="pre">Sphere</span></code>. Diffusion of the molecules placed here is <strong>NOT</strong> restricted in the <code class="docutils literal notranslate"><span class="pre">Shape</span></code>. This <code class="docutils literal notranslate"><span class="pre">Shape</span></code> is only for the initialization.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[34]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">sp1</span> <span class="o">=</span> <span class="n">Species</span><span class="p">(</span><span class="s2">"A"</span><span class="p">,</span> <span class="mf">0.0025</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">sphere</span> <span class="o">=</span> <span class="n">Sphere</span><span class="p">(</span><span class="n">Real3</span><span class="p">(</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">),</span> <span class="mf">0.3</span><span class="p">)</span>
<span class="n">w1</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">60</span><span class="p">,</span> <span class="n">sphere</span><span class="p">)</span>
<span class="n">w2</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">60</span><span class="p">,</span> <span class="n">sphere</span><span class="p">)</span>
<span class="n">w3</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">60</span><span class="p">,</span> <span class="n">sphere</span><span class="p">)</span>
<span class="n">w4</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">60</span><span class="p">,</span> <span class="n">sphere</span><span class="p">)</span>
<span class="n">w5</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">60</span><span class="p">,</span> <span class="n">sphere</span><span class="p">)</span>
<span class="n">w6</span><span class="o">.</span><span class="n">add_molecules</span><span class="p">(</span><span class="n">sp1</span><span class="p">,</span> <span class="mi">60</span><span class="p">,</span> <span class="n">sphere</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p>A property of <code class="docutils literal notranslate"><span class="pre">Species</span></code>, <code class="docutils literal notranslate"><span class="pre">'location'</span></code>, is available to restrict diffusion of molecules. <code class="docutils literal notranslate"><span class="pre">'location'</span></code> is not fully supported yet, but only supported in <code class="docutils literal notranslate"><span class="pre">spatiocyte</span></code> and <code class="docutils literal notranslate"><span class="pre">meso</span></code>. <code class="docutils literal notranslate"><span class="pre">add_structure</span></code> defines a new structure given as a pair of <code class="docutils literal notranslate"><span class="pre">Species</span></code> and <code class="docutils literal notranslate"><span class="pre">Shape</span></code>.</p>
<p>NOTICE: To use <code class="docutils literal notranslate"><span class="pre">add_structure</span></code> with <code class="docutils literal notranslate"><span class="pre">spatiocyte</span></code>, you should define a model to describe the attributes of your <code class="docutils literal notranslate"><span class="pre">Species</span></code> and bind it to an instance of <code class="docutils literal notranslate"><span class="pre">spatiocyte.World</span></code>.</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[35]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="c1"># The below codes defines a model and bind it to w3(spatiocyte world).</span>
<span class="c1"># Here, the model contains a species 'B' for the following context.</span>
<span class="kn">from</span> <span class="nn">ecell4</span> <span class="kn">import</span> <span class="n">species_attributes</span><span class="p">,</span> <span class="n">get_model</span>
<span class="k">with</span> <span class="n">species_attributes</span><span class="p">():</span>
<span class="n">M</span> <span class="o">|</span> <span class="p">{</span><span class="s1">'dimension'</span><span class="p">:</span> <span class="mi">2</span><span class="p">}</span>
<span class="n">B</span> <span class="o">|</span> <span class="p">{</span><span class="s1">'radius'</span><span class="p">:</span> <span class="mf">0.0025</span><span class="p">,</span> <span class="s1">'D'</span><span class="p">:</span> <span class="mf">0.1</span><span class="p">,</span> <span class="s1">'location'</span><span class="p">:</span> <span class="s1">'M'</span><span class="p">}</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">get_model</span><span class="p">()</span>
<span class="n">w3</span><span class="o">.</span><span class="n">bind_to</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>