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DENOPTIM
PopulationTest.java
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1/*
2 * DENOPTIM
3 * Copyright (C) 2022 Marco Foscato <marco.foscato@uib.no>
4 *
5 * This program is free software: you can redistribute it and/or modify
6 * it under the terms of the GNU Affero General Public License as published
7 * by the Free Software Foundation, either version 3 of the License, or
8 * (at your option) any later version.
9 *
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU Affero General Public License for more details.
14 *
15 * You should have received a copy of the GNU Affero General Public License
16 * along with this program. If not, see <http://www.gnu.org/licenses/>.
17 */
18
19package denoptim.ga;
20
21import static org.junit.jupiter.api.Assertions.assertEquals;
22import static org.junit.jupiter.api.Assertions.assertFalse;
23import static org.junit.jupiter.api.Assertions.assertTrue;
24
25import java.util.ArrayList;
26import java.util.Arrays;
27import java.util.HashMap;
28import java.util.HashSet;
29import java.util.List;
30import java.util.Map;
31
32import org.junit.jupiter.api.Test;
33
34import denoptim.exception.DENOPTIMException;
35import denoptim.fragspace.FragmentSpace;
36import denoptim.fragspace.FragmentSpaceParameters;
37import denoptim.graph.APClass;
38import denoptim.graph.Candidate;
39import denoptim.graph.DGraph;
40import denoptim.graph.Edge;
41import denoptim.graph.Edge.BondType;
42import denoptim.graph.EmptyVertex;
43import denoptim.graph.Template;
44import denoptim.graph.Template.ContractLevel;
45import denoptim.graph.Vertex;
46import denoptim.graph.Vertex.BBType;
47import denoptim.programs.RunTimeParameters.ParametersType;
48import denoptim.programs.denovo.GAParameters;
49
50
57public class PopulationTest
58{
59 private static APClass APCA, APCB, APCC, APCD;
60
61//------------------------------------------------------------------------------
62
63 public static GAParameters prepare() throws DENOPTIMException
64 {
65 APCA = APClass.make("A", 0, BondType.SINGLE);
66 APCB = APClass.make("B", 0, BondType.SINGLE);
67 APCC = APClass.make("C", 0, BondType.SINGLE);
68 APCD = APClass.make("D", 99, BondType.DOUBLE);
69
70 HashMap<APClass,ArrayList<APClass>> cpMap =
71 new HashMap<APClass,ArrayList<APClass>>();
72 ArrayList<APClass> lstA = new ArrayList<APClass>();
73 lstA.add(APCA);
74 cpMap.put(APCA, lstA);
75 ArrayList<APClass> lstB = new ArrayList<APClass>();
76 lstB.add(APCB);
77 lstB.add(APCC);
78 cpMap.put(APCB, lstB);
79 ArrayList<APClass> lstC = new ArrayList<APClass>();
80 lstC.add(APCC);
81 lstC.add(APCB);
82 cpMap.put(APCC, lstC);
83 ArrayList<APClass> lstD = new ArrayList<APClass>();
84 lstD.add(APCD);
85 cpMap.put(APCD, lstD);
86
87
88 /* Compatibility matrix
89 *
90 * | A | B | C | D |
91 * -------------------------
92 * A | T | | | |
93 * -------------------------
94 * B | | T | T | |
95 * -------------------------
96 * C | | T | T | |
97 * -------------------------
98 * D | | | | T |
99 */
100
101 HashMap<APClass,APClass> capMap = new HashMap<APClass,APClass>();
102 HashSet<APClass> forbEnds = new HashSet<APClass>();
103
104 FragmentSpaceParameters fsp = new FragmentSpaceParameters();
105 FragmentSpace fs = new FragmentSpace(fsp,
106 new ArrayList<Vertex>(),
107 new ArrayList<Vertex>(),
108 new ArrayList<Vertex>(),
109 cpMap, capMap, forbEnds, cpMap);
110 fs.setAPclassBasedApproach(true);
111
112 GAParameters gaSettings = new GAParameters();
113 gaSettings.readParameterLine(ParametersType.RC_PARAMS.getKeywordRoot()
114 + "CLOSERINGS");
115 gaSettings.setParameters(fsp);
116 return gaSettings;
117 }
118
119//------------------------------------------------------------------------------
120
121 @Test
122 public void testXOverCompatibility() throws Exception
123 {
124 GAParameters gaparams = prepare();
125 FragmentSpaceParameters fsParams = (FragmentSpaceParameters) gaparams
126 .getParameters(ParametersType.FS_PARAMS);
127 FragmentSpace fs = fsParams.getFragmentSpace();
128
129 Population pop = new Population(gaparams);
130
131 DGraph g1 = makeGraphA();
132 // We give uniquefying properties to the vertexes so that they
133 // are not seen as v.sameAs(o).
134 String k = "Uniquefying";
135 int counter = 0;
136 for (int i=0; i<g1.getVertexCount(); i++)
137 {
138 Vertex v = g1.getVertexAtPosition(i);
139 v.setUniquefyingProperty(k);
140 v.setProperty(k, counter);
141 counter++;
142 }
143 Candidate c1 = new Candidate("C1",g1);
144 pop.add(c1);
145
146 DGraph g2 = makeGraphB();
147 for (int i=0; i<g2.getVertexCount(); i++)
148 {
149 Vertex v = g2.getVertexAtPosition(i);
150 v.setUniquefyingProperty(k);
151 v.setProperty(k, counter);
152 counter++;
153 }
154 Candidate c2 = new Candidate("C2",g2);
155 pop.add(c2);
156
157 DGraph g3 = makeGraphB();
158 for (int i=0; i<g3.getVertexCount(); i++)
159 {
160 Vertex v = g3.getVertexAtPosition(i);
161 v.setUniquefyingProperty(k);
162 v.setProperty(k, counter);
163 counter++;
164 }
165 Candidate c3 = new Candidate("C3",g3);
166 pop.add(c3);
167
168 DGraph g4 = makeGraphC();
169 for (int i=0; i<g4.getVertexCount(); i++)
170 {
171 Vertex v = g4.getVertexAtPosition(i);
172 v.setUniquefyingProperty(k);
173 v.setProperty(k, counter);
174 counter++;
175 }
176 Candidate c4 = new Candidate("C4",g4);
177 pop.add(c4);
178
179 DGraph g5 = makeGraphD();
180 for (int i=0; i<g5.getVertexCount(); i++)
181 {
182 Vertex v = g5.getVertexAtPosition(i);
183 v.setUniquefyingProperty(k);
184 v.setProperty(k, counter);
185 counter++;
186 }
187 Candidate c5 = new Candidate("C5",g5);
188 pop.add(c5);
189
190 List<Candidate> partnersForC1 = pop.getXoverPartners(c1,
191 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
192 List<Candidate> partnersForC2 = pop.getXoverPartners(c2,
193 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
194 List<Candidate> partnersForC3 = pop.getXoverPartners(c3,
195 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
196 List<Candidate> partnersForC4 = pop.getXoverPartners(c4,
197 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
198 List<Candidate> partnersForC5 = pop.getXoverPartners(c5,
199 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
200
201 Map<Candidate,Map<Candidate,Integer>> expected =
202 new HashMap<Candidate,Map<Candidate,Integer>>();
203 Map<Candidate,Integer> expectedForC1 = new HashMap<Candidate,Integer>();
204 expectedForC1.put(c2, 9);
205 expectedForC1.put(c3, 9);
206 expectedForC1.put(c4, 5);
207 expected.put(c1, expectedForC1);
208 Map<Candidate,Integer> expectedForC2 = new HashMap<Candidate,Integer>();
209 expectedForC2.put(c1, 9);
210 //expectedForC2.put(c3, 4); NO xover between candidates with same graph!
211 expectedForC2.put(c4, 2);
212 expected.put(c2, expectedForC2);
213 Map<Candidate,Integer> expectedForC3 = new HashMap<Candidate,Integer>();
214 expectedForC3.put(c1, 9);
215 //expectedForC3.put(c2, 4); NO xover between candidates with same graph!
216 expectedForC3.put(c4, 2);
217 expected.put(c3, expectedForC3);
218 Map<Candidate,Integer> expectedForC4 = new HashMap<Candidate,Integer>();
219 expectedForC4.put(c1, 5);
220 expectedForC4.put(c2, 2);
221 expectedForC4.put(c3, 2);
222 expected.put(c4, expectedForC4);
223
224 compareSizeOfSites(c1,expectedForC1,partnersForC1,pop);
225 compareSizeOfSites(c2,expectedForC2,partnersForC2,pop);
226 compareSizeOfSites(c3,expectedForC3,partnersForC3,pop);
227 compareSizeOfSites(c4,expectedForC4,partnersForC4,pop);
228 assertEquals(partnersForC5.size(), 0, "Wrong umber of partners for C5");
229 }
230
231//------------------------------------------------------------------------------
232
233 @Test
234 public void testClone() throws Exception
235 {
236 GAParameters gaparams = prepare();
237 FragmentSpaceParameters fsParams = (FragmentSpaceParameters) gaparams
238 .getParameters(ParametersType.FS_PARAMS);
239 FragmentSpace fs = fsParams.getFragmentSpace();
240
241 Population pop = new Population(gaparams);
242
243 DGraph g1 = makeGraphA();
244 Candidate c1 = new Candidate("C1",g1);
245 pop.add(c1);
246
247 DGraph g2 = makeGraphB();
248 Candidate c2 = new Candidate("C2",g2);
249 pop.add(c2);
250
251 //Adding property to uniquefy a pair of vertexes
252 String k = "Uniquefying";
253 g1.getVertexAtPosition(1).setUniquefyingProperty(k);
254 g1.getVertexAtPosition(1).setProperty(k, 123);
255 g2.getVertexAtPosition(1).setUniquefyingProperty(k);
256 g2.getVertexAtPosition(1).setProperty(k, 456);
257
258 List<Candidate> partnersForC1 = pop.getXoverPartners(c1,
259 new ArrayList<Candidate>(Arrays.asList(c1,c2)), fs);
260 List<Candidate> partnersForC2 = pop.getXoverPartners(c2,
261 new ArrayList<Candidate>(Arrays.asList(c1,c2)), fs);
262
263 Map<Candidate,Map<Candidate,Integer>> expected =
264 new HashMap<Candidate,Map<Candidate,Integer>>();
265 Map<Candidate,Integer> expectedForC1 = new HashMap<Candidate,Integer>();
266 expectedForC1.put(c2, 9);
267 expected.put(c1, expectedForC1);
268 Map<Candidate,Integer> expectedForC2 = new HashMap<Candidate,Integer>();
269 expectedForC2.put(c1, 9);
270 expected.put(c2, expectedForC2);
271
272 Population clonedPop = pop.clone();
273
274 compareSizeOfSites(c1,expectedForC1,partnersForC1,clonedPop);
275 compareSizeOfSites(c2,expectedForC2,partnersForC2,clonedPop);
276
277 compareSitesLists(pop.getXoverSites(c1, c2),
278 clonedPop.getXoverSites(c1, c2));
279 }
280
281//------------------------------------------------------------------------------
282
286 private void compareSitesLists(List<XoverSite> listA,
287 List<XoverSite> listB)
288 {
289 for (int i=0; i<listA.size(); i++)
290 {
291 assertTrue(listA.get(i).equals(listB.get(i)));
292 }
293 }
294
295//------------------------------------------------------------------------------
296
297 private void compareSizeOfSites(Candidate parentA,
298 Map<Candidate, Integer> expectedForC1,
299 List<Candidate> partnersForC1, Population pop)
300 {
301 for (Candidate c : expectedForC1.keySet())
302 {
303 assertTrue(partnersForC1.contains(c), "Missing XOver compatibility "
304 + "between '" + parentA.getName() + "' and '" + c.getName()
305 + "'.");
306 assertEquals(expectedForC1.get(c).intValue(),
307 pop.getXoverSites(parentA, c).size(),
308 "Wrong number of sites between '" + parentA.getName()
309 + "' and '" + c.getName() + "'.");
310 }
311 }
312
313//------------------------------------------------------------------------------
314
323 static DGraph makeGraphA() throws DENOPTIMException
324 {
325 DGraph graphA = new DGraph();
326 EmptyVertex v0 = new EmptyVertex(0);
327 v0.setBuildingBlockType(BBType.SCAFFOLD);
328 v0.addAP(APCA);
329 v0.addAP(APCA);
330 graphA.addVertex(v0);
331 EmptyVertex v1 = new EmptyVertex(1);
332 v1.addAP(APCA);
333 v1.addAP(APCA);
334 graphA.addVertex(v1);
335 EmptyVertex v2 = new EmptyVertex(2);
336 v2.addAP(APCA);
337 v2.addAP(APCA);
338 graphA.addVertex(v2);
339 EmptyVertex v3 = new EmptyVertex(3);
340 v3.addAP(APCA);
341 v3.addAP(APCB);
342 graphA.addVertex(v3);
343 EmptyVertex v4 = new EmptyVertex(4);
344 v4.addAP(APCB);
345 v4.addAP(APCB);
346 graphA.addVertex(v4);
347 EmptyVertex v5 = new EmptyVertex(5);
348 v5.addAP(APCB);
349 v5.addAP(APCB);
350 graphA.addVertex(v5);
351
352 graphA.addEdge(new Edge(v0.getAP(1), v1.getAP(0)));
353 graphA.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
354 graphA.addEdge(new Edge(v2.getAP(1), v3.getAP(0)));
355 graphA.addEdge(new Edge(v3.getAP(1), v4.getAP(0)));
356 graphA.addEdge(new Edge(v4.getAP(1), v5.getAP(0)));
357
358 graphA.renumberGraphVertices();
359
360 return graphA;
361 }
362
363//------------------------------------------------------------------------------
364
372 static DGraph makeGraphB() throws DENOPTIMException
373 {
374 DGraph graphB = new DGraph();
375 EmptyVertex v0 = new EmptyVertex(0);
376 v0.setBuildingBlockType(BBType.SCAFFOLD);
377 v0.addAP(APCA);
378 graphB.addVertex(v0);
379 EmptyVertex v1 = new EmptyVertex(1);
380 v1.addAP(APCA);
381 v1.addAP(APCA);
382 graphB.addVertex(v1);
383 EmptyVertex v2 = new EmptyVertex(2);
384 v2.addAP(APCA);
385 graphB.addVertex(v2);
386
387 graphB.addEdge(new Edge(v0.getAP(0), v1.getAP(0)));
388 graphB.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
389
390 graphB.renumberGraphVertices();
391
392 return graphB;
393 }
394
395//------------------------------------------------------------------------------
396
404 static DGraph makeGraphC() throws DENOPTIMException
405 {
406 DGraph graphC = new DGraph();
407 EmptyVertex v0 = new EmptyVertex(0);
408 v0.setBuildingBlockType(BBType.SCAFFOLD);
409 v0.addAP(APCC);
410 v0.addAP(APCC);
411 graphC.addVertex(v0);
412 EmptyVertex v1 = new EmptyVertex(1);
413 v1.addAP(APCC);
414 v1.addAP(APCA);
415 graphC.addVertex(v1);
416 EmptyVertex v2 = new EmptyVertex(2);
417 v2.addAP(APCA);
418 graphC.addVertex(v2);
419
420 graphC.addEdge(new Edge(v0.getAP(1), v1.getAP(0)));
421 graphC.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
422
423 graphC.renumberGraphVertices();
424
425 return graphC;
426 }
427
428//------------------------------------------------------------------------------
429
437 static DGraph makeGraphD() throws DENOPTIMException
438 {
439 DGraph graphD = new DGraph();
440 EmptyVertex v0 = new EmptyVertex(0);
441 v0.setBuildingBlockType(BBType.SCAFFOLD);
442 v0.addAP(APCD);
443 graphD.addVertex(v0);
444 EmptyVertex v1 = new EmptyVertex(1);
445 v1.addAP(APCD);
446
447 graphD.addEdge(new Edge(v0.getAP(0), v1.getAP(0)));
448
449 graphD.renumberGraphVertices();
450
451 return graphD;
452 }
453
454//------------------------------------------------------------------------------
455
463 static DGraph makeGraphE() throws DENOPTIMException
464 {
465 DGraph graphA = new DGraph();
466 EmptyVertex v0 = new EmptyVertex(0);
467 v0.setBuildingBlockType(BBType.SCAFFOLD);
468 v0.addAP(APCB);
469 graphA.addVertex(v0);
470 EmptyVertex v1 = new EmptyVertex();
471 v1.addAP(APCB);
472 v1.addAP(APCA);
473 graphA.addVertex(v1);
474 EmptyVertex v2 = new EmptyVertex();
475 v2.addAP(APCA);
476 v2.addAP(APCB);
477 graphA.addVertex(v2);
478 EmptyVertex v3 = new EmptyVertex();
479 v3.addAP(APCB);
480 v3.addAP(APCA);
481 graphA.addVertex(v3);
482 EmptyVertex v4 = new EmptyVertex();
483 v4.addAP(APCA);
484 v4.addAP(APCB);
485 graphA.addVertex(v4);
486 EmptyVertex v5 = new EmptyVertex();
487 v5.addAP(APCB);
488 graphA.addVertex(v5);
489
490 graphA.addEdge(new Edge(v0.getAP(0), v1.getAP(0)));
491 graphA.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
492 graphA.addEdge(new Edge(v2.getAP(1), v3.getAP(0)));
493 graphA.addEdge(new Edge(v3.getAP(1), v4.getAP(0)));
494 graphA.addEdge(new Edge(v4.getAP(1), v5.getAP(0)));
495
496 return graphA;
497 }
498
499//------------------------------------------------------------------------------
500
509 static DGraph makeGraphF() throws DENOPTIMException
510 {
511 DGraph graphA = new DGraph();
512 EmptyVertex v0 = new EmptyVertex(0);
513 v0.setBuildingBlockType(BBType.SCAFFOLD);
514 v0.addAP(APCA);
515 v0.addAP(APCA);
516 graphA.addVertex(v0);
517 EmptyVertex v1 = new EmptyVertex(1);
518 v1.addAP(APCA);
519 v1.addAP(APCA);
520 graphA.addVertex(v1);
521 EmptyVertex v2 = new EmptyVertex(2);
522 v2.addAP(APCA);
523 v2.addAP(APCA);
524 graphA.addVertex(v2);
525 EmptyVertex v3 = new EmptyVertex(3);
526 v3.addAP(APCA);
527 v3.addAP(APCA);
528 graphA.addVertex(v3);
529 EmptyVertex v4 = new EmptyVertex(4);
530 v4.addAP(APCA);
531 v4.addAP(APCA);
532 graphA.addVertex(v4);
533 EmptyVertex v5 = new EmptyVertex(5);
534 v5.addAP(APCA);
535 v5.addAP(APCA);
536 graphA.addVertex(v5);
537 EmptyVertex v6 = new EmptyVertex(6);
538 v6.addAP(APCA);
539 v6.addAP(APCA);
540 graphA.addVertex(v6);
541 EmptyVertex v7 = new EmptyVertex(7);
542 v7.addAP(APCA);
543 v7.addAP(APCA);
544 graphA.addVertex(v7);
545
546 graphA.addEdge(new Edge(v0.getAP(1), v1.getAP(0)));
547 graphA.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
548 graphA.addEdge(new Edge(v2.getAP(1), v3.getAP(0)));
549 graphA.addEdge(new Edge(v3.getAP(1), v4.getAP(0)));
550 graphA.addEdge(new Edge(v4.getAP(1), v5.getAP(0)));
551 graphA.addEdge(new Edge(v5.getAP(1), v6.getAP(0)));
552 graphA.addEdge(new Edge(v6.getAP(1), v7.getAP(0)));
553
554 graphA.renumberGraphVertices();
555
556 return graphA;
557 }
558
559//------------------------------------------------------------------------------
560
561 @Test
562 public void testGetMinMax() throws Exception
563 {
564 double trsh = 0.001;
565 GAParameters gaparams = prepare();
566 Population pop = new Population(gaparams);
567
568 DGraph g1 = makeGraphA();
569 Candidate c1 = new Candidate("C1",g1);
570 c1.setFitness(-1.0);
571 pop.add(c1);
572
573 DGraph g2 = makeGraphB();
574 Candidate c2 = new Candidate("C2",g2);
575 c2.setFitness(0.02);
576 pop.add(c2);
577
578 DGraph g3 = makeGraphB();
579 Candidate c3 = new Candidate("C3",g3);
580 c3.setFitness(2.0);
581 pop.add(c3);
582
583 DGraph g4 = makeGraphC();
584 Candidate c4 = new Candidate("C4",g4);
585 c4.setFitness(0.5);
586 pop.add(c4);
587
588 DGraph g5 = makeGraphD();
589 Candidate c5 = new Candidate("C5",g5);
590 c5.setFitness(-0.5);
591 pop.add(c5);
592
593 assertTrue(Math.abs(pop.getMinFitness()-(-1.0)) < trsh,
594 "getting min fitness");
595 assertTrue(Math.abs(pop.getMaxFitness()-(2.0)) < trsh,
596 "getting max fitness");
597 }
598
599//------------------------------------------------------------------------------
600
601 @Test
602 public void testIsInPercentile() throws Exception
603 {
604 GAParameters gaparams = prepare();
605 Population pop = new Population(gaparams);
606
607 DGraph g1 = makeGraphA();
608 Candidate c1 = new Candidate("C1",g1);
609 c1.setFitness(20.0);
610 pop.add(c1);
611
612 DGraph g2 = makeGraphB();
613 Candidate c2 = new Candidate("C2",g2);
614 c2.setFitness(120);
615 pop.add(c2);
616
617 assertTrue(pop.isWithinPercentile(116, 0.05), "116 is in 5%");
618 assertTrue(pop.isWithinPercentile(70.1, 0.5), "70.1 is in 50%");
619 assertFalse(pop.isWithinPercentile(69, 0.5), "69 is not in 50%");
620 assertFalse(pop.isWithinPercentile(114, 0.05), "114 is not in 5%");
621
622 pop = new Population(gaparams);
623
624 DGraph g1b = makeGraphA();
625 Candidate c1b = new Candidate("C1",g1b);
626 c1b.setFitness(-20.0);
627 pop.add(c1b);
628
629 DGraph g2b = makeGraphB();
630 Candidate c2b = new Candidate("C2",g2b);
631 c2b.setFitness(80);
632 pop.add(c2b);
633
634 assertTrue(pop.isWithinPercentile(76, 0.05), "76 is in 5%");
635 assertTrue(pop.isWithinPercentile(30.1, 0.5), "30.1 is in 50%");
636 assertFalse(pop.isWithinPercentile(29, 0.5), "29 is not in 50%");
637 assertFalse(pop.isWithinPercentile(74, 0.05), "74 is not in 5%");
638 }
639
640//------------------------------------------------------------------------------
641
642 @Test
643 public void testPopulationVersion() throws Exception
644 {
645 GAParameters gaparams = prepare();
646 Population pop = new Population(gaparams);
647 int v0 = pop.getVersionID();
648
649 DGraph g1 = makeGraphA();
650 Candidate c1 = new Candidate("C1",g1);
651 pop.add(c1);
652 int v1 = pop.getVersionID();
653 assertTrue(v1>v0,"Version change 1");
654
655 DGraph g2 = makeGraphB();
656 Candidate c2 = new Candidate("C2",g2);
657 pop.add(c2);
658 int v2 = pop.getVersionID();
659 assertTrue(v2>v1,"Version change 2");
660
661 DGraph g3 = makeGraphB();
662 Candidate c3 = new Candidate("C3",g3);
663 pop.add(c3);
664 int v3 = pop.getVersionID();
665 assertTrue(v3>v2,"Version change 3");
666
667 pop.remove(c1);
668 int v4 = pop.getVersionID();
669 assertTrue(v4>v3,"Version change 4");
670
671 DGraph g4 = makeGraphB();
672 Candidate c4 = new Candidate("C4",g4);
673 pop.add(0,c4);
674 int v5 = pop.getVersionID();
675 assertTrue(v5>v4,"Version change 5");
676
677 DGraph g5 = makeGraphC();
678 Candidate c5 = new Candidate("C5",g5);
679 pop.set(1,c5);
680 int v6 = pop.getVersionID();
681 assertTrue(v6>v5,"Version change 6");
682 }
683
684//------------------------------------------------------------------------------
685
735 public static DGraph[] getPairOfTestGraphsB() throws Exception
736 {
737 // Prepare special building block: template T1
738 EmptyVertex v0 = new EmptyVertex(0);
739 v0.addAP(APCA);
740 v0.addAP(APCA);
741 v0.addAP(APCA);
742 v0.setProperty("Label", "tv0");
743
744 EmptyVertex v1 = new EmptyVertex(1);
745 v1.addAP(APCA);
746 v1.addAP(APCA);
747 v1.addAP(APCB);
748 v1.setProperty("Label", "tv1");
749
750 EmptyVertex v2 = new EmptyVertex(2);
751 v2.addAP(APCB);
752 v2.addAP(APCC);
753 v2.setProperty("Label", "tv2");
754
755 EmptyVertex v3 = new EmptyVertex(3);
756 v3.addAP(APCA);
757 v3.addAP(APCA);
758 v3.setProperty("Label", "tv3");
759
760 EmptyVertex v4 = new EmptyVertex(4);
761 v4.addAP(APCA);
762 v4.addAP(APCB);
763 v4.addAP(APCA);
764 v4.setProperty("Label", "tv4");
765
766 EmptyVertex v5 = new EmptyVertex(5);
767 v5.addAP(APCA);
768 v5.setProperty("Label", "tv5");
769 v5.setAsRCV(true);
770
771 EmptyVertex v6 = new EmptyVertex(6);
772 v6.addAP(APCA);
773 v6.setProperty("Label", "tv6");
774 v6.setAsRCV(true);
775
776 DGraph g = new DGraph();
777 g.addVertex(v0);
778 g.setGraphId(-1);
779 g.appendVertexOnAP(v0.getAP(1), v1.getAP(0));
780 g.appendVertexOnAP(v0.getAP(0), v3.getAP(0));
781 g.appendVertexOnAP(v3.getAP(1), v4.getAP(0));
782 g.appendVertexOnAP(v4.getAP(2), v6.getAP(0));
783 g.appendVertexOnAP(v1.getAP(2), v2.getAP(0));
784 g.appendVertexOnAP(v1.getAP(1), v5.getAP(0));
785 g.addRing(v5, v6, BondType.SINGLE);
786
787 Template t1 = new Template(BBType.NONE);
788 t1.setInnerGraph(g);
789 t1.setProperty("Label", "t1");
790 t1.setContractLevel(ContractLevel.FREE);
791
792 // Assemble the first graph: graphA
793 EmptyVertex m0 = new EmptyVertex(100);
794 m0.addAP(APCA);
795 m0.setProperty("Label", "m100");
796
797 EmptyVertex m1 = new EmptyVertex(101);
798 m1.addAP(APCC);
799 m1.setProperty("Label", "m101");
800
801 EmptyVertex m2 = new EmptyVertex(102);
802 m2.addAP(APCB);
803 m2.addAP(APCC);
804 m2.setProperty("Label", "m102");
805
806 EmptyVertex m3 = new EmptyVertex(103);
807 m3.addAP(APCC);
808 m3.setProperty("Label", "m103");
809
810 DGraph graphA = new DGraph();
811 graphA.addVertex(m0);
812 graphA.appendVertexOnAP(m0.getAP(0), t1.getAP(0)); // A on T1
813 graphA.appendVertexOnAP(t1.getAP(1), m1.getAP(0)); // C on T1
814 graphA.appendVertexOnAP(t1.getAP(2), m2.getAP(0)); // B on T1
815 graphA.appendVertexOnAP(m2.getAP(1), m3.getAP(0));
816 graphA.setGraphId(11111);
817
818 // Done with GraphA!
819
820 // Prepare special building block: template T2
821 EmptyVertex w0 = new EmptyVertex(0);
822 w0.addAP(APCA);
823 w0.addAP(APCA);
824 w0.addAP(APCA);
825 w0.setProperty("Label", "tw0");
826
827 EmptyVertex w1 = new EmptyVertex(1);
828 w1.addAP(APCA);
829 w1.addAP(APCB);
830 w1.setProperty("Label", "tw1");
831
832 EmptyVertex w2 = new EmptyVertex(2);
833 w2.addAP(APCB);
834 w2.setProperty("Label", "tw2");
835
836 EmptyVertex w3 = new EmptyVertex(3);
837 w3.addAP(APCA);
838 w3.addAP(APCA);
839 w3.setProperty("Label", "tw3");
840
841 EmptyVertex w4 = new EmptyVertex(4);
842 w4.addAP(APCA);
843 w4.addAP(APCB);
844 w4.addAP(APCA);
845 w4.setProperty("Label", "tw4");
846
847 EmptyVertex w5 = new EmptyVertex(5);
848 w5.addAP(APCA);
849 w5.setProperty("Label", "tw5");
850
851 DGraph g2 = new DGraph();
852 g2.addVertex(w0);
853 g2.setGraphId(-1);
854 g2.appendVertexOnAP(w0.getAP(1), w1.getAP(0));
855 g2.appendVertexOnAP(w1.getAP(1), w2.getAP(0));
856 g2.appendVertexOnAP(w0.getAP(0), w3.getAP(0));
857 g2.appendVertexOnAP(w3.getAP(1), w4.getAP(0));
858 g2.appendVertexOnAP(w4.getAP(2), w5.getAP(0));
859
860 Template t2 = new Template(BBType.NONE);
861 t2.setInnerGraph(g2);
862 t2.setProperty("Label", "t2");
863 t2.setContractLevel(ContractLevel.FREE);
864
865 // Assemble the first graph: graphA
866 EmptyVertex n0 = new EmptyVertex(200);
867 n0.addAP(APCA);
868 n0.setProperty("Label", "m200");
869
870 EmptyVertex n2 = new EmptyVertex(202);
871 n2.addAP(APCB);
872 n2.addAP(APCC);
873 n2.setProperty("Label", "m202");
874
875 EmptyVertex n3 = new EmptyVertex(203);
876 n3.addAP(APCC);
877 n3.setProperty("Label", "m203");
878
879 DGraph graphB = new DGraph();
880 graphB.addVertex(n0);
881 graphB.appendVertexOnAP(n0.getAP(0), t2.getAP(0)); // A on T2
882 graphB.appendVertexOnAP(t2.getAP(1), n2.getAP(0)); // B on T2
883 graphB.appendVertexOnAP(n2.getAP(1), n3.getAP(0));
884 graphB.setGraphId(22222);
885
886 // Done with GraphB!
887
888 DGraph[] pair = new DGraph[2];
889 pair[0] = graphA;
890 pair[1] = graphB;
891
892 return pair;
893 }
894
895//------------------------------------------------------------------------------
896
944 public static DGraph[] getPairOfTestGraphsBxo() throws Exception
945 {
946 // Prepare special building block: template T1
947 EmptyVertex v0 = new EmptyVertex(0);
948 v0.addAP(APCA);
949 v0.addAP(APCA);
950 v0.addAP(APCA);
951 v0.setProperty("Label", "tv0");
952
953 EmptyVertex v1 = new EmptyVertex(1);
954 v1.addAP(APCA);
955 v1.addAP(APCA);
956 v1.setProperty("Label", "tv1");
957
958 EmptyVertex v2 = new EmptyVertex(2);
959 v2.addAP(APCA);
960 v2.addAP(APCB);
961 v2.addAP(APCA);
962 v2.setProperty("Label", "tv2");
963
964 EmptyVertex v3 = new EmptyVertex(3);
965 v3.addAP(APCA);
966 v3.setProperty("Label", "tv3");
967 v3.setAsRCV(true);
968
969 EmptyVertex v4 = new EmptyVertex(4);
970 v4.addAP(APCA);
971 v4.addAP(APCB);
972 v4.addAP(APCA);
973 v4.setProperty("Label", "tv4");
974
975 EmptyVertex v5 = new EmptyVertex(5);
976 v5.addAP(APCA);
977 v5.setProperty("Label", "tv5");
978
979 DGraph g = new DGraph();
980 g.addVertex(v0);
981 g.setGraphId(-1);
982 g.appendVertexOnAP(v0.getAP(0), v1.getAP(0));
983 g.appendVertexOnAP(v1.getAP(1), v2.getAP(0));
984 g.appendVertexOnAP(v2.getAP(2), v3.getAP(0));
985 g.appendVertexOnAP(v0.getAP(1), v4.getAP(0));
986 g.appendVertexOnAP(v4.getAP(2), v5.getAP(0));
987
988 Template t1 = new Template(BBType.NONE);
989 t1.setInnerGraph(g);
990 t1.setProperty("Label", "t1");
991 t1.setContractLevel(ContractLevel.FREE);
992
993 // Assemble the first graph: graphA
994 EmptyVertex m0 = new EmptyVertex(100);
995 m0.addAP(APCA);
996 m0.setProperty("Label", "m100");
997
998 EmptyVertex m1 = new EmptyVertex(101);
999 m1.addAP(APCC);
1000 m1.setProperty("Label", "m101");
1001
1002 EmptyVertex m2 = new EmptyVertex(102);
1003 m2.addAP(APCB);
1004 m2.addAP(APCC);
1005 m2.setProperty("Label", "m102");
1006
1007 EmptyVertex m3 = new EmptyVertex(103);
1008 m3.addAP(APCC);
1009 m3.setProperty("Label", "m103");
1010
1011 DGraph graphA = new DGraph();
1012 graphA.addVertex(m0);
1013 graphA.appendVertexOnAP(m0.getAP(0), t1.getAP(0)); // A on T1
1014 graphA.appendVertexOnAP(t1.getAP(1), m1.getAP(0)); // B on T1
1015 graphA.appendVertexOnAP(t1.getAP(2), m2.getAP(0)); // B on T1
1016 graphA.appendVertexOnAP(m2.getAP(1), m3.getAP(0));
1017 graphA.setGraphId(33333);
1018
1019 // Done with GraphA!
1020
1021 // Prepare special building block: template T2
1022 EmptyVertex w0 = new EmptyVertex(0);
1023 w0.addAP(APCA);
1024 w0.addAP(APCA);
1025 w0.addAP(APCA);
1026 w0.setProperty("Label", "tw0");
1027
1028 EmptyVertex w1 = new EmptyVertex(1);
1029 w1.addAP(APCA);
1030 w1.addAP(APCB);
1031 w1.setProperty("Label", "tw1");
1032
1033 EmptyVertex w2 = new EmptyVertex(2);
1034 w2.addAP(APCB);
1035 w2.setProperty("Label", "tw2");
1036
1037 EmptyVertex w3 = new EmptyVertex(3);
1038 w3.addAP(APCA);
1039 w3.addAP(APCA);
1040 w3.setProperty("Label", "tw3");
1041
1042 EmptyVertex w4 = new EmptyVertex(4);
1043 w4.addAP(APCA);
1044 w4.addAP(APCA);
1045 w4.addAP(APCB);
1046 w4.setProperty("Label", "tw4");
1047
1048 EmptyVertex w5 = new EmptyVertex(5);
1049 w5.addAP(APCA);
1050 w5.setProperty("Label", "tw5");
1051 w5.setAsRCV(true);
1052
1053 EmptyVertex w6 = new EmptyVertex(6);
1054 w6.addAP(APCB);
1055 w6.addAP(APCC);
1056 w6.setProperty("Label", "tw6");
1057
1058 DGraph g2 = new DGraph();
1059 g2.addVertex(w0);
1060 g2.setGraphId(-1);
1061 g2.appendVertexOnAP(w0.getAP(1), w1.getAP(0));
1062 g2.appendVertexOnAP(w1.getAP(1), w2.getAP(0));
1063 g2.appendVertexOnAP(w0.getAP(0), w3.getAP(0));
1064 g2.appendVertexOnAP(w3.getAP(1), w4.getAP(0));
1065 g2.appendVertexOnAP(w4.getAP(1), w5.getAP(0));
1066 g2.appendVertexOnAP(w4.getAP(2), w6.getAP(0));
1067
1068 Template t2 = new Template(BBType.NONE);
1069 t2.setInnerGraph(g2);
1070 t2.setProperty("Label", "tw2");
1071 t2.setContractLevel(ContractLevel.FREE);
1072
1073 // Assemble the first graph: graphA
1074 EmptyVertex n0 = new EmptyVertex(200);
1075 n0.addAP(APCA);
1076 n0.setProperty("Label", "m400");
1077
1078 EmptyVertex n2 = new EmptyVertex(202);
1079 n2.addAP(APCB);
1080 n2.addAP(APCC);
1081 n2.setProperty("Label", "m402");
1082
1083 EmptyVertex n3 = new EmptyVertex(203);
1084 n3.addAP(APCC);
1085 n3.setProperty("Label", "m403");
1086
1087 DGraph graphB = new DGraph();
1088 graphB.addVertex(n0);
1089 graphB.appendVertexOnAP(n0.getAP(0), t2.getAP(0)); // A on T2
1090 graphB.appendVertexOnAP(t2.getAP(1), n2.getAP(0)); // B on T2
1091 graphB.appendVertexOnAP(n2.getAP(1), n3.getAP(0));
1092 graphB.setGraphId(44444);
1093
1094 // Done with GraphB!
1095
1096 DGraph[] pair = new DGraph[2];
1097 pair[0] = graphA;
1098 pair[1] = graphB;
1099
1100 return pair;
1101 }
1102
1103//------------------------------------------------------------------------------
1104
1158 public static DGraph[] getPairOfTestGraphsBxoxo() throws Exception
1159 {
1160 // Prepare special building block: template T1
1161 // In the template we want APS in this order:
1162 // A(from v0), B(from v2), C(from v6)
1163
1164 EmptyVertex v0 = new EmptyVertex(0);
1165 v0.addAP(APCA);
1166 v0.addAP(APCA);
1167 v0.addAP(APCA);
1168 v0.setProperty("Label", "tv0");
1169
1170 EmptyVertex v1 = new EmptyVertex(1);
1171 v1.addAP(APCA);
1172 v1.addAP(APCA);
1173 v1.setProperty("Label", "tv1");
1174
1175 EmptyVertex v2 = new EmptyVertex(2);
1176 v2.addAP(APCA);
1177 v2.addAP(APCB);
1178 v2.addAP(APCA);
1179 v2.setProperty("Label", "tv2");
1180
1181 EmptyVertex v3 = new EmptyVertex(3);
1182 v3.addAP(APCA);
1183 v3.setProperty("Label", "tv3");
1184 v3.setAsRCV(true);
1185
1186 EmptyVertex v4 = new EmptyVertex(4);
1187 v4.addAP(APCA);
1188 v4.addAP(APCA);
1189 v4.addAP(APCB);
1190 v4.setProperty("Label", "tv4");
1191
1192 EmptyVertex v5 = new EmptyVertex(5);
1193 v5.addAP(APCA);
1194 v5.setProperty("Label", "tv5");
1195 v5.setAsRCV(true);
1196
1197 EmptyVertex v6 = new EmptyVertex(6);
1198 v6.addAP(APCB);
1199 v6.addAP(APCC);
1200 v6.setProperty("Label", "tv6");
1201
1202 DGraph g = new DGraph();
1203 g.addVertex(v0);
1204 g.setGraphId(-1);
1205 g.appendVertexOnAP(v0.getAP(0), v1.getAP(0));
1206 g.appendVertexOnAP(v1.getAP(1), v2.getAP(0));
1207 g.appendVertexOnAP(v2.getAP(2), v3.getAP(0));
1208 g.appendVertexOnAP(v0.getAP(1), v4.getAP(0));
1209 g.appendVertexOnAP(v4.getAP(2), v6.getAP(0));
1210 g.appendVertexOnAP(v4.getAP(1), v5.getAP(0));
1211 g.addRing(v5, v3, BondType.SINGLE);
1212
1213 Template t1 = new Template(BBType.NONE);
1214 t1.setInnerGraph(g);
1215 t1.setProperty("Label", "t1");
1216 t1.setContractLevel(ContractLevel.FREE);
1217
1218 // Assemble the first graph: graphA
1219 EmptyVertex m0 = new EmptyVertex(100);
1220 m0.addAP(APCA);
1221 m0.setProperty("Label", "m100");
1222
1223 EmptyVertex m1 = new EmptyVertex(101);
1224 m1.addAP(APCC);
1225 m1.setProperty("Label", "m101");
1226
1227 EmptyVertex m2 = new EmptyVertex(102);
1228 m2.addAP(APCB);
1229 m2.addAP(APCC);
1230 m2.setProperty("Label", "m102");
1231
1232 EmptyVertex m3 = new EmptyVertex(103);
1233 m3.addAP(APCC);
1234 m3.setProperty("Label", "m103");
1235
1236 DGraph graphA = new DGraph();
1237 graphA.addVertex(m0);
1238 graphA.appendVertexOnAP(m0.getAP(0), t1.getAP(0)); // A on T1
1239 graphA.appendVertexOnAP(t1.getAP(1), m1.getAP(0)); // B on T1
1240 graphA.appendVertexOnAP(t1.getAP(2), m2.getAP(0)); // C on T1
1241 graphA.appendVertexOnAP(m2.getAP(1), m3.getAP(0));
1242 graphA.setGraphId(55555);
1243
1244 // Done with GraphA!
1245
1246 // GraphB is the same as from getPairOfTestGraphsB()
1247 DGraph[] initialGraphs = getPairOfTestGraphsB();
1248 DGraph graphB = initialGraphs[1];
1249 graphB.setGraphId(66666);
1250
1251 // Done with GraphB!
1252
1253 DGraph[] pair = new DGraph[2];
1254 pair[0] = graphA;
1255 pair[1] = graphB;
1256
1257 return pair;
1258 }
1259
1260//------------------------------------------------------------------------------
1261
1262}
denoptim.fragspace.FragmentSpace
Class defining a space of building blocks.
Definition: FragmentSpace.java:67
denoptim.fragspace.FragmentSpace.setAPclassBasedApproach
void setAPclassBasedApproach(boolean useAPC)
Set the fragment space to behave according to APClass-based approach.
Definition: FragmentSpace.java:472
denoptim.fragspace.FragmentSpaceParameters
Parameters defining the fragment space.
Definition: FragmentSpaceParameters.java:39
denoptim.ga.Population
A collection of candidates.
Definition: Population.java:48
denoptim.ga.Population.getMinFitness
double getMinFitness()
Gets the minimum value of the fitness in this population.
Definition: Population.java:452
denoptim.ga.Population.getXoverSites
List< XoverSite > getXoverSites(Candidate parentA, Candidate parentB)
Returns a list of crossover sites between the two given parents.
Definition: Population.java:423
denoptim.ga.Population.getXoverPartners
List< Candidate > getXoverPartners(Candidate memberA, List< Candidate > eligibleParents, FragmentSpace fragSpace)
Returns a list of population members that can do crossover with the specified member.
Definition: Population.java:370
denoptim.ga.Population.getVersionID
int getVersionID()
Returns an integer that represent the current status of the population.
Definition: Population.java:173
denoptim.ga.Population.isWithinPercentile
boolean isWithinPercentile(double value, double percentile)
Checks if a given fitness value if within the given percentile of best candidates.
Definition: Population.java:496
denoptim.ga.Population.add
boolean add(Candidate c)
Definition: Population.java:87
denoptim.ga.Population.clone
Population clone()
Does not clone the cross-over compatibility relations between each pairs of population members.
Definition: Population.java:184
denoptim.ga.Population.set
Candidate set(int index, Candidate c)
Definition: Population.java:107
denoptim.ga.Population.remove
Candidate remove(int index)
Definition: Population.java:116
denoptim.ga.Population.getMaxFitness
double getMaxFitness()
Gets the maximum value of the fitness in this population.
Definition: Population.java:477
denoptim.ga.PopulationTest.makeGraphD
static DGraph makeGraphD()
Produced a graph like this:
Definition: PopulationTest.java:437
denoptim.ga.PopulationTest.makeGraphC
static DGraph makeGraphC()
Produced a graph like this:
Definition: PopulationTest.java:404
denoptim.ga.PopulationTest.prepare
static GAParameters prepare()
Definition: PopulationTest.java:63
denoptim.ga.PopulationTest.makeGraphB
static DGraph makeGraphB()
Produced a graph like this:
Definition: PopulationTest.java:372
denoptim.ga.PopulationTest.getPairOfTestGraphsBxoxo
static DGraph[] getPairOfTestGraphsBxoxo()
Builds a pair of graphs that contain templates with ContractLevel#FREE contract.
Definition: PopulationTest.java:1158
denoptim.ga.PopulationTest.compareSizeOfSites
void compareSizeOfSites(Candidate parentA, Map< Candidate, Integer > expectedForC1, List< Candidate > partnersForC1, Population pop)
Definition: PopulationTest.java:297
denoptim.ga.PopulationTest.compareSitesLists
void compareSitesLists(List< XoverSite > listA, List< XoverSite > listB)
Assumes the two lists have equal size.
Definition: PopulationTest.java:286
denoptim.ga.PopulationTest.makeGraphE
static DGraph makeGraphE()
Produced a graph like this:
Definition: PopulationTest.java:463
denoptim.ga.PopulationTest.makeGraphF
static DGraph makeGraphF()
Produced a graph like this:
Definition: PopulationTest.java:509
denoptim.ga.PopulationTest.getPairOfTestGraphsB
static DGraph[] getPairOfTestGraphsB()
Builds a pair of graphs that contain templates with ContractLevel#FREE contract.
Definition: PopulationTest.java:735
denoptim.ga.PopulationTest.getPairOfTestGraphsBxo
static DGraph[] getPairOfTestGraphsBxo()
Builds a pair of graphs that contain templates with ContractLevel#FREE contract.
Definition: PopulationTest.java:944
denoptim.ga.PopulationTest.makeGraphA
static DGraph makeGraphA()
Produced a graph like this:
Definition: PopulationTest.java:323
denoptim.graph.APClass.make
static APClass make(String ruleAndSubclass)
Creates an APClass if it does not exist already, or returns the reference to the existing instance.
Definition: APClass.java:164
denoptim.graph.Candidate
A candidate is the combination of a denoptim graph with molecular representation and may include also...
Definition: Candidate.java:40
denoptim.graph.Candidate.setFitness
void setFitness(double fitness)
Definition: Candidate.java:480
denoptim.graph.DGraph
Container for the list of vertices and the edges that connect them.
Definition: DGraph.java:102
denoptim.graph.DGraph.addVertex
void addVertex(Vertex vertex)
Appends a vertex to this graph without creating any edge.
Definition: DGraph.java:1325
denoptim.graph.DGraph.setGraphId
void setGraphId(int id)
Definition: DGraph.java:264
denoptim.graph.DGraph.getVertexAtPosition
Vertex getVertexAtPosition(int pos)
Returns the vertex that is in the given position of the list of vertices belonging to this graph.
Definition: DGraph.java:2743
denoptim.graph.DGraph.appendVertexOnAP
void appendVertexOnAP(AttachmentPoint srcAP, AttachmentPoint trgAP)
Append a vertex to this graph: adds the new vertex to the list of vertices belonging to the graph,...
Definition: DGraph.java:6005
denoptim.graph.DGraph.renumberGraphVertices
void renumberGraphVertices()
Reassign vertex IDs to all vertices of this graph.
Definition: DGraph.java:5512
denoptim.graph.DGraph.addRing
void addRing(Ring ring)
Definition: DGraph.java:1258
denoptim.graph.DGraph.addEdge
void addEdge(Edge edge)
Adds the edge to the list of edges belonging to this graph.
Definition: DGraph.java:1249
denoptim.graph.Edge
This class represents the edge between two vertices.
Definition: Edge.java:38
denoptim.graph.EmptyVertex
An empty vertex has the behaviors of a vertex, but has no molecular structure.
Definition: EmptyVertex.java:45
denoptim.graph.EmptyVertex.addAP
void addAP()
Adds an attachment point with no APClass or other attribute.
Definition: EmptyVertex.java:298
denoptim.graph.Template.setInnerGraph
void setInnerGraph(DGraph innerGraph)
Definition: Template.java:298
denoptim.graph.Template.setContractLevel
void setContractLevel(ContractLevel contract)
Imposes the given contract to this template.
Definition: Template.java:214
denoptim.graph.Vertex
A vertex is a data structure that has an identity and holds a list of AttachmentPoints.
Definition: Vertex.java:61
denoptim.graph.Vertex.setAsRCV
void setAsRCV(boolean isRCV)
Definition: Vertex.java:274
denoptim.graph.Vertex.setUniquefyingProperty
void setUniquefyingProperty(String key)
Add the given key among the properties that are checked for equality when comparing vertices with the...
Definition: Vertex.java:1199
denoptim.graph.Vertex.setBuildingBlockType
void setBuildingBlockType(Vertex.BBType buildingBlockType)
Definition: Vertex.java:325
denoptim.graph.Vertex.setProperty
void setProperty(Object key, Object property)
Definition: Vertex.java:1235
denoptim.graph.Vertex.getAP
AttachmentPoint getAP(int i)
Get attachment point i on this vertex.
Definition: Vertex.java:1007
denoptim.programs.RunTimeParameters.setParameters
void setParameters(RunTimeParameters otherParams)
Definition: RunTimeParameters.java:814
denoptim.programs.denovo.GAParameters
Parameters for genetic algorithm.
Definition: GAParameters.java:45
denoptim.graph.Edge.BondType
Possible chemical bond types an edge can represent.
Definition: Edge.java:303
denoptim.graph.Template.ContractLevel
Enum specifying to what extent the template's inner graph can be changed.
Definition: Template.java:104
denoptim.graph.Template.ContractLevel.FREE
FREE
Inner graphs are free to change within the confines of the required AttachmentPoints.
Definition: Template.java:109
denoptim.graph.Vertex.BBType
The type of building block.
Definition: Vertex.java:86
denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS
FS_PARAMS
Parameters pertaining the definition of the fragment space.
Definition: RunTimeParameters.java:139
denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS
RC_PARAMS
Parameters pertaining to ring closures in graphs.
Definition: RunTimeParameters.java:144