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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.assertNull;
24import static org.junit.jupiter.api.Assertions.assertTrue;
25
26import java.util.ArrayList;
27import java.util.Arrays;
28import java.util.HashMap;
29import java.util.HashSet;
30import java.util.List;
31import java.util.Map;
32
33import org.junit.jupiter.api.Test;
34
35import denoptim.exception.DENOPTIMException;
36import denoptim.fragspace.FragmentSpace;
37import denoptim.fragspace.FragmentSpaceParameters;
38import denoptim.graph.APClass;
39import denoptim.graph.Candidate;
40import denoptim.graph.DGraph;
41import denoptim.graph.Edge;
42import denoptim.graph.Edge.BondType;
43import denoptim.graph.EmptyVertex;
44import denoptim.graph.Template;
45import denoptim.graph.Template.ContractLevel;
46import denoptim.graph.Vertex;
47import denoptim.graph.Vertex.BBType;
48import denoptim.programs.RunTimeParameters.ParametersType;
49import denoptim.programs.denovo.GAParameters;
50
51
58public class PopulationTest
59{
60 private static APClass APCA, APCB, APCC, APCD;
61
62//------------------------------------------------------------------------------
63
64 public static GAParameters prepare() throws DENOPTIMException
65 {
66 APCA = APClass.make("A", 0, BondType.SINGLE);
67 APCB = APClass.make("B", 0, BondType.SINGLE);
68 APCC = APClass.make("C", 0, BondType.SINGLE);
69 APCD = APClass.make("D", 99, BondType.DOUBLE);
70
71 HashMap<APClass,ArrayList<APClass>> cpMap =
72 new HashMap<APClass,ArrayList<APClass>>();
73 ArrayList<APClass> lstA = new ArrayList<APClass>();
74 lstA.add(APCA);
75 cpMap.put(APCA, lstA);
76 ArrayList<APClass> lstB = new ArrayList<APClass>();
77 lstB.add(APCB);
78 lstB.add(APCC);
79 cpMap.put(APCB, lstB);
80 ArrayList<APClass> lstC = new ArrayList<APClass>();
81 lstC.add(APCC);
82 lstC.add(APCB);
83 cpMap.put(APCC, lstC);
84 ArrayList<APClass> lstD = new ArrayList<APClass>();
85 lstD.add(APCD);
86 cpMap.put(APCD, lstD);
87
88
89 /* Compatibility matrix
90 *
91 * | A | B | C | D |
92 * -------------------------
93 * A | T | | | |
94 * -------------------------
95 * B | | T | T | |
96 * -------------------------
97 * C | | T | T | |
98 * -------------------------
99 * D | | | | T |
100 */
101
102 HashMap<APClass,APClass> capMap = new HashMap<APClass,APClass>();
103 HashSet<APClass> forbEnds = new HashSet<APClass>();
104
105 FragmentSpaceParameters fsp = new FragmentSpaceParameters();
106 FragmentSpace fs = new FragmentSpace(fsp,
107 new ArrayList<Vertex>(),
108 new ArrayList<Vertex>(),
109 new ArrayList<Vertex>(),
110 cpMap, capMap, forbEnds, cpMap);
111 fs.setAPclassBasedApproach(true);
112
113 GAParameters gaSettings = new GAParameters();
114 gaSettings.readParameterLine(ParametersType.RC_PARAMS.getKeywordRoot()
115 + "CLOSERINGS");
116 gaSettings.setParameters(fsp);
117 return gaSettings;
118 }
119
120//------------------------------------------------------------------------------
121
122 @Test
123 public void testXOverCompatibility() throws Exception
124 {
125 GAParameters gaparams = prepare();
126 FragmentSpaceParameters fsParams = (FragmentSpaceParameters) gaparams
127 .getParameters(ParametersType.FS_PARAMS);
128 FragmentSpace fs = fsParams.getFragmentSpace();
129
130 Population pop = new Population(gaparams);
131
132 DGraph g1 = makeGraphA();
133 // We give uniquefying properties to the vertexes so that they
134 // are not seen as v.sameAs(o).
135 String k = "Uniquefying";
136 int counter = 0;
137 for (int i=0; i<g1.getVertexCount(); i++)
138 {
139 Vertex v = g1.getVertexAtPosition(i);
140 v.setUniquefyingProperty(k);
141 v.setProperty(k, counter);
142 counter++;
143 }
144 Candidate c1 = new Candidate("C1",g1);
145 pop.add(c1);
146
147 DGraph g2 = makeGraphB();
148 for (int i=0; i<g2.getVertexCount(); i++)
149 {
150 Vertex v = g2.getVertexAtPosition(i);
151 v.setUniquefyingProperty(k);
152 v.setProperty(k, counter);
153 counter++;
154 }
155 Candidate c2 = new Candidate("C2",g2);
156 pop.add(c2);
157
158 DGraph g3 = makeGraphB();
159 for (int i=0; i<g3.getVertexCount(); i++)
160 {
161 Vertex v = g3.getVertexAtPosition(i);
162 v.setUniquefyingProperty(k);
163 v.setProperty(k, counter);
164 counter++;
165 }
166 Candidate c3 = new Candidate("C3",g3);
167 pop.add(c3);
168
169 DGraph g4 = makeGraphC();
170 for (int i=0; i<g4.getVertexCount(); i++)
171 {
172 Vertex v = g4.getVertexAtPosition(i);
173 v.setUniquefyingProperty(k);
174 v.setProperty(k, counter);
175 counter++;
176 }
177 Candidate c4 = new Candidate("C4",g4);
178 pop.add(c4);
179
180 DGraph g5 = makeGraphD();
181 for (int i=0; i<g5.getVertexCount(); i++)
182 {
183 Vertex v = g5.getVertexAtPosition(i);
184 v.setUniquefyingProperty(k);
185 v.setProperty(k, counter);
186 counter++;
187 }
188 Candidate c5 = new Candidate("C5",g5);
189 pop.add(c5);
190
191 List<Candidate> partnersForC1 = pop.getXoverPartners(c1,
192 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
193 List<Candidate> partnersForC2 = pop.getXoverPartners(c2,
194 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
195 List<Candidate> partnersForC3 = pop.getXoverPartners(c3,
196 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
197 List<Candidate> partnersForC4 = pop.getXoverPartners(c4,
198 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
199 List<Candidate> partnersForC5 = pop.getXoverPartners(c5,
200 new ArrayList<Candidate>(Arrays.asList(c1,c2,c3,c4,c5)), fs);
201
202 Map<Candidate,Map<Candidate,Integer>> expected =
203 new HashMap<Candidate,Map<Candidate,Integer>>();
204 Map<Candidate,Integer> expectedForC1 = new HashMap<Candidate,Integer>();
205 expectedForC1.put(c2, 9);
206 expectedForC1.put(c3, 9);
207 expectedForC1.put(c4, 5);
208 expected.put(c1, expectedForC1);
209 Map<Candidate,Integer> expectedForC2 = new HashMap<Candidate,Integer>();
210 expectedForC2.put(c1, 9);
211 //expectedForC2.put(c3, 4); NO xover between candidates with same graph!
212 expectedForC2.put(c4, 2);
213 expected.put(c2, expectedForC2);
214 Map<Candidate,Integer> expectedForC3 = new HashMap<Candidate,Integer>();
215 expectedForC3.put(c1, 9);
216 //expectedForC3.put(c2, 4); NO xover between candidates with same graph!
217 expectedForC3.put(c4, 2);
218 expected.put(c3, expectedForC3);
219 Map<Candidate,Integer> expectedForC4 = new HashMap<Candidate,Integer>();
220 expectedForC4.put(c1, 5);
221 expectedForC4.put(c2, 2);
222 expectedForC4.put(c3, 2);
223 expected.put(c4, expectedForC4);
224
225 compareSizeOfSites(c1,expectedForC1,partnersForC1,pop);
226 compareSizeOfSites(c2,expectedForC2,partnersForC2,pop);
227 compareSizeOfSites(c3,expectedForC3,partnersForC3,pop);
228 compareSizeOfSites(c4,expectedForC4,partnersForC4,pop);
229 assertEquals(partnersForC5.size(), 0, "Wrong umber of partners for C5");
230 }
231
232//------------------------------------------------------------------------------
233
234 @Test
235 public void testClone() throws Exception
236 {
237 GAParameters gaparams = prepare();
238 FragmentSpaceParameters fsParams = (FragmentSpaceParameters) gaparams
239 .getParameters(ParametersType.FS_PARAMS);
240 FragmentSpace fs = fsParams.getFragmentSpace();
241
242 Population pop = new Population(gaparams);
243
244 DGraph g1 = makeGraphA();
245 Candidate c1 = new Candidate("C1",g1);
246 pop.add(c1);
247
248 DGraph g2 = makeGraphB();
249 Candidate c2 = new Candidate("C2",g2);
250 pop.add(c2);
251
252 //Adding property to uniquefy a pair of vertexes
253 String k = "Uniquefying";
254 g1.getVertexAtPosition(1).setUniquefyingProperty(k);
255 g1.getVertexAtPosition(1).setProperty(k, 123);
256 g2.getVertexAtPosition(1).setUniquefyingProperty(k);
257 g2.getVertexAtPosition(1).setProperty(k, 456);
258
259 List<Candidate> partnersForC1 = pop.getXoverPartners(c1,
260 new ArrayList<Candidate>(Arrays.asList(c1,c2)), fs);
261 List<Candidate> partnersForC2 = pop.getXoverPartners(c2,
262 new ArrayList<Candidate>(Arrays.asList(c1,c2)), fs);
263
264 Map<Candidate,Map<Candidate,Integer>> expected =
265 new HashMap<Candidate,Map<Candidate,Integer>>();
266 Map<Candidate,Integer> expectedForC1 = new HashMap<Candidate,Integer>();
267 expectedForC1.put(c2, 9);
268 expected.put(c1, expectedForC1);
269 Map<Candidate,Integer> expectedForC2 = new HashMap<Candidate,Integer>();
270 expectedForC2.put(c1, 9);
271 expected.put(c2, expectedForC2);
272
273 Population clonedPop = pop.clone();
274
275 compareSizeOfSites(c1,expectedForC1,partnersForC1,clonedPop);
276 compareSizeOfSites(c2,expectedForC2,partnersForC2,clonedPop);
277
278 compareSitesLists(pop.getXoverSites(c1, c2),
279 clonedPop.getXoverSites(c1, c2));
280 }
281
282//------------------------------------------------------------------------------
283
287 private void compareSitesLists(List<XoverSite> listA,
288 List<XoverSite> listB)
289 {
290 for (int i=0; i<listA.size(); i++)
291 {
292 assertTrue(listA.get(i).equals(listB.get(i)));
293 }
294 }
295
296//------------------------------------------------------------------------------
297
298 private void compareSizeOfSites(Candidate parentA,
299 Map<Candidate, Integer> expectedForC1,
300 List<Candidate> partnersForC1, Population pop)
301 {
302 for (Candidate c : expectedForC1.keySet())
303 {
304 assertTrue(partnersForC1.contains(c), "Missing XOver compatibility "
305 + "between '" + parentA.getName() + "' and '" + c.getName()
306 + "'.");
307 assertEquals(expectedForC1.get(c).intValue(),
308 pop.getXoverSites(parentA, c).size(),
309 "Wrong number of sites between '" + parentA.getName()
310 + "' and '" + c.getName() + "'.");
311 }
312 }
313
314//------------------------------------------------------------------------------
315
324 static DGraph makeGraphA() throws DENOPTIMException
325 {
326 DGraph graphA = new DGraph();
327 EmptyVertex v0 = new EmptyVertex(0);
328 v0.setBuildingBlockType(BBType.SCAFFOLD);
329 v0.addAP(APCA);
330 v0.addAP(APCA);
331 graphA.addVertex(v0);
332 EmptyVertex v1 = new EmptyVertex(1);
333 v1.addAP(APCA);
334 v1.addAP(APCA);
335 graphA.addVertex(v1);
336 EmptyVertex v2 = new EmptyVertex(2);
337 v2.addAP(APCA);
338 v2.addAP(APCA);
339 graphA.addVertex(v2);
340 EmptyVertex v3 = new EmptyVertex(3);
341 v3.addAP(APCA);
342 v3.addAP(APCB);
343 graphA.addVertex(v3);
344 EmptyVertex v4 = new EmptyVertex(4);
345 v4.addAP(APCB);
346 v4.addAP(APCB);
347 graphA.addVertex(v4);
348 EmptyVertex v5 = new EmptyVertex(5);
349 v5.addAP(APCB);
350 v5.addAP(APCB);
351 graphA.addVertex(v5);
352
353 graphA.addEdge(new Edge(v0.getAP(1), v1.getAP(0)));
354 graphA.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
355 graphA.addEdge(new Edge(v2.getAP(1), v3.getAP(0)));
356 graphA.addEdge(new Edge(v3.getAP(1), v4.getAP(0)));
357 graphA.addEdge(new Edge(v4.getAP(1), v5.getAP(0)));
358
359 graphA.renumberGraphVertices();
360
361 return graphA;
362 }
363
364//------------------------------------------------------------------------------
365
373 static DGraph makeGraphB() throws DENOPTIMException
374 {
375 DGraph graphB = new DGraph();
376 EmptyVertex v0 = new EmptyVertex(0);
377 v0.setBuildingBlockType(BBType.SCAFFOLD);
378 v0.addAP(APCA);
379 graphB.addVertex(v0);
380 EmptyVertex v1 = new EmptyVertex(1);
381 v1.addAP(APCA);
382 v1.addAP(APCA);
383 graphB.addVertex(v1);
384 EmptyVertex v2 = new EmptyVertex(2);
385 v2.addAP(APCA);
386 graphB.addVertex(v2);
387
388 graphB.addEdge(new Edge(v0.getAP(0), v1.getAP(0)));
389 graphB.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
390
391 graphB.renumberGraphVertices();
392
393 return graphB;
394 }
395
396//------------------------------------------------------------------------------
397
405 static DGraph makeGraphC() throws DENOPTIMException
406 {
407 DGraph graphC = new DGraph();
408 EmptyVertex v0 = new EmptyVertex(0);
409 v0.setBuildingBlockType(BBType.SCAFFOLD);
410 v0.addAP(APCC);
411 v0.addAP(APCC);
412 graphC.addVertex(v0);
413 EmptyVertex v1 = new EmptyVertex(1);
414 v1.addAP(APCC);
415 v1.addAP(APCA);
416 graphC.addVertex(v1);
417 EmptyVertex v2 = new EmptyVertex(2);
418 v2.addAP(APCA);
419 graphC.addVertex(v2);
420
421 graphC.addEdge(new Edge(v0.getAP(1), v1.getAP(0)));
422 graphC.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
423
424 graphC.renumberGraphVertices();
425
426 return graphC;
427 }
428
429//------------------------------------------------------------------------------
430
438 static DGraph makeGraphD() throws DENOPTIMException
439 {
440 DGraph graphD = new DGraph();
441 EmptyVertex v0 = new EmptyVertex(0);
442 v0.setBuildingBlockType(BBType.SCAFFOLD);
443 v0.addAP(APCD);
444 graphD.addVertex(v0);
445 EmptyVertex v1 = new EmptyVertex(1);
446 v1.addAP(APCD);
447
448 graphD.addEdge(new Edge(v0.getAP(0), v1.getAP(0)));
449
450 graphD.renumberGraphVertices();
451
452 return graphD;
453 }
454
455//------------------------------------------------------------------------------
456
464 static DGraph makeGraphE() throws DENOPTIMException
465 {
466 DGraph graphA = new DGraph();
467 EmptyVertex v0 = new EmptyVertex(0);
468 v0.setBuildingBlockType(BBType.SCAFFOLD);
469 v0.addAP(APCB);
470 graphA.addVertex(v0);
471 EmptyVertex v1 = new EmptyVertex();
472 v1.addAP(APCB);
473 v1.addAP(APCA);
474 graphA.addVertex(v1);
475 EmptyVertex v2 = new EmptyVertex();
476 v2.addAP(APCA);
477 v2.addAP(APCB);
478 graphA.addVertex(v2);
479 EmptyVertex v3 = new EmptyVertex();
480 v3.addAP(APCB);
481 v3.addAP(APCA);
482 graphA.addVertex(v3);
483 EmptyVertex v4 = new EmptyVertex();
484 v4.addAP(APCA);
485 v4.addAP(APCB);
486 graphA.addVertex(v4);
487 EmptyVertex v5 = new EmptyVertex();
488 v5.addAP(APCB);
489 graphA.addVertex(v5);
490
491 graphA.addEdge(new Edge(v0.getAP(0), v1.getAP(0)));
492 graphA.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
493 graphA.addEdge(new Edge(v2.getAP(1), v3.getAP(0)));
494 graphA.addEdge(new Edge(v3.getAP(1), v4.getAP(0)));
495 graphA.addEdge(new Edge(v4.getAP(1), v5.getAP(0)));
496
497 return graphA;
498 }
499
500//------------------------------------------------------------------------------
501
510 static DGraph makeGraphF() throws DENOPTIMException
511 {
512 DGraph graphA = new DGraph();
513 EmptyVertex v0 = new EmptyVertex(0);
514 v0.setBuildingBlockType(BBType.SCAFFOLD);
515 v0.addAP(APCA);
516 v0.addAP(APCA);
517 graphA.addVertex(v0);
518 EmptyVertex v1 = new EmptyVertex(1);
519 v1.addAP(APCA);
520 v1.addAP(APCA);
521 graphA.addVertex(v1);
522 EmptyVertex v2 = new EmptyVertex(2);
523 v2.addAP(APCA);
524 v2.addAP(APCA);
525 graphA.addVertex(v2);
526 EmptyVertex v3 = new EmptyVertex(3);
527 v3.addAP(APCA);
528 v3.addAP(APCA);
529 graphA.addVertex(v3);
530 EmptyVertex v4 = new EmptyVertex(4);
531 v4.addAP(APCA);
532 v4.addAP(APCA);
533 graphA.addVertex(v4);
534 EmptyVertex v5 = new EmptyVertex(5);
535 v5.addAP(APCA);
536 v5.addAP(APCA);
537 graphA.addVertex(v5);
538 EmptyVertex v6 = new EmptyVertex(6);
539 v6.addAP(APCA);
540 v6.addAP(APCA);
541 graphA.addVertex(v6);
542 EmptyVertex v7 = new EmptyVertex(7);
543 v7.addAP(APCA);
544 v7.addAP(APCA);
545 graphA.addVertex(v7);
546
547 graphA.addEdge(new Edge(v0.getAP(1), v1.getAP(0)));
548 graphA.addEdge(new Edge(v1.getAP(1), v2.getAP(0)));
549 graphA.addEdge(new Edge(v2.getAP(1), v3.getAP(0)));
550 graphA.addEdge(new Edge(v3.getAP(1), v4.getAP(0)));
551 graphA.addEdge(new Edge(v4.getAP(1), v5.getAP(0)));
552 graphA.addEdge(new Edge(v5.getAP(1), v6.getAP(0)));
553 graphA.addEdge(new Edge(v6.getAP(1), v7.getAP(0)));
554
555 graphA.renumberGraphVertices();
556
557 return graphA;
558 }
559
560//------------------------------------------------------------------------------
561
562 @Test
563 public void testGetMinMax() throws Exception
564 {
565 double trsh = 0.001;
566 GAParameters gaparams = prepare();
567 Population pop = new Population(gaparams);
568
569 DGraph g1 = makeGraphA();
570 Candidate c1 = new Candidate("C1",g1);
571 c1.setFitness(-1.0);
572 pop.add(c1);
573
574 DGraph g2 = makeGraphB();
575 Candidate c2 = new Candidate("C2",g2);
576 c2.setFitness(0.02);
577 pop.add(c2);
578
579 DGraph g3 = makeGraphB();
580 Candidate c3 = new Candidate("C3",g3);
581 c3.setFitness(2.0);
582 pop.add(c3);
583
584 DGraph g4 = makeGraphC();
585 Candidate c4 = new Candidate("C4",g4);
586 c4.setFitness(0.5);
587 pop.add(c4);
588
589 DGraph g5 = makeGraphD();
590 Candidate c5 = new Candidate("C5",g5);
591 c5.setFitness(-0.5);
592 pop.add(c5);
593
594 assertTrue(Math.abs(pop.getMinFitness()-(-1.0)) < trsh,
595 "getting min fitness");
596 assertTrue(Math.abs(pop.getMaxFitness()-(2.0)) < trsh,
597 "getting max fitness");
598 }
599
600//------------------------------------------------------------------------------
601
602 @Test
603 public void testIsInPercentile() throws Exception
604 {
605 GAParameters gaparams = prepare();
606 Population pop = new Population(gaparams);
607
608 DGraph g1 = makeGraphA();
609 Candidate c1 = new Candidate("C1",g1);
610 c1.setFitness(20.0);
611 pop.add(c1);
612
613 DGraph g2 = makeGraphB();
614 Candidate c2 = new Candidate("C2",g2);
615 c2.setFitness(120);
616 pop.add(c2);
617
618 assertTrue(pop.isWithinPercentile(116, 0.05), "116 is in 5%");
619 assertTrue(pop.isWithinPercentile(70.1, 0.5), "70.1 is in 50%");
620 assertFalse(pop.isWithinPercentile(69, 0.5), "69 is not in 50%");
621 assertFalse(pop.isWithinPercentile(114, 0.05), "114 is not in 5%");
622
623 pop = new Population(gaparams);
624
625 DGraph g1b = makeGraphA();
626 Candidate c1b = new Candidate("C1",g1b);
627 c1b.setFitness(-20.0);
628 pop.add(c1b);
629
630 DGraph g2b = makeGraphB();
631 Candidate c2b = new Candidate("C2",g2b);
632 c2b.setFitness(80);
633 pop.add(c2b);
634
635 assertTrue(pop.isWithinPercentile(76, 0.05), "76 is in 5%");
636 assertTrue(pop.isWithinPercentile(30.1, 0.5), "30.1 is in 50%");
637 assertFalse(pop.isWithinPercentile(29, 0.5), "29 is not in 50%");
638 assertFalse(pop.isWithinPercentile(74, 0.05), "74 is not in 5%");
639 }
640
641//------------------------------------------------------------------------------
642
643 @Test
644 public void testPopulationVersion() throws Exception
645 {
646 GAParameters gaparams = prepare();
647 Population pop = new Population(gaparams);
648 int v0 = pop.getVersionID();
649
650 DGraph g1 = makeGraphA();
651 Candidate c1 = new Candidate("C1",g1);
652 pop.add(c1);
653 int v1 = pop.getVersionID();
654 assertTrue(v1>v0,"Version change 1");
655
656 DGraph g2 = makeGraphB();
657 Candidate c2 = new Candidate("C2",g2);
658 pop.add(c2);
659 int v2 = pop.getVersionID();
660 assertTrue(v2>v1,"Version change 2");
661
662 DGraph g3 = makeGraphB();
663 Candidate c3 = new Candidate("C3",g3);
664 pop.add(c3);
665 int v3 = pop.getVersionID();
666 assertTrue(v3>v2,"Version change 3");
667
668 pop.remove(c1);
669 int v4 = pop.getVersionID();
670 assertTrue(v4>v3,"Version change 4");
671
672 DGraph g4 = makeGraphB();
673 Candidate c4 = new Candidate("C4",g4);
674 pop.add(0,c4);
675 int v5 = pop.getVersionID();
676 assertTrue(v5>v4,"Version change 5");
677
678 DGraph g5 = makeGraphC();
679 Candidate c5 = new Candidate("C5",g5);
680 pop.set(1,c5);
681 int v6 = pop.getVersionID();
682 assertTrue(v6>v5,"Version change 6");
683 }
684
685//------------------------------------------------------------------------------
686
736 public static DGraph[] getPairOfTestGraphsB() throws Exception
737 {
738 // Prepare special building block: template T1
739 EmptyVertex v0 = new EmptyVertex(0);
740 v0.addAP(APCA);
741 v0.addAP(APCA);
742 v0.addAP(APCA);
743 v0.setProperty("Label", "tv0");
744
745 EmptyVertex v1 = new EmptyVertex(1);
746 v1.addAP(APCA);
747 v1.addAP(APCA);
748 v1.addAP(APCB);
749 v1.setProperty("Label", "tv1");
750
751 EmptyVertex v2 = new EmptyVertex(2);
752 v2.addAP(APCB);
753 v2.addAP(APCC);
754 v2.setProperty("Label", "tv2");
755
756 EmptyVertex v3 = new EmptyVertex(3);
757 v3.addAP(APCA);
758 v3.addAP(APCA);
759 v3.setProperty("Label", "tv3");
760
761 EmptyVertex v4 = new EmptyVertex(4);
762 v4.addAP(APCA);
763 v4.addAP(APCB);
764 v4.addAP(APCA);
765 v4.setProperty("Label", "tv4");
766
767 EmptyVertex v5 = new EmptyVertex(5);
768 v5.addAP(APCA);
769 v5.setProperty("Label", "tv5");
770 v5.setAsRCV(true);
771
772 EmptyVertex v6 = new EmptyVertex(6);
773 v6.addAP(APCA);
774 v6.setProperty("Label", "tv6");
775 v6.setAsRCV(true);
776
777 DGraph g = new DGraph();
778 g.addVertex(v0);
779 g.setGraphId(-1);
780 g.appendVertexOnAP(v0.getAP(1), v1.getAP(0));
781 g.appendVertexOnAP(v0.getAP(0), v3.getAP(0));
782 g.appendVertexOnAP(v3.getAP(1), v4.getAP(0));
783 g.appendVertexOnAP(v4.getAP(2), v6.getAP(0));
784 g.appendVertexOnAP(v1.getAP(2), v2.getAP(0));
785 g.appendVertexOnAP(v1.getAP(1), v5.getAP(0));
786 g.addRing(v5, v6, BondType.SINGLE);
787
788 Template t1 = new Template(BBType.NONE);
789 t1.setInnerGraph(g);
790 t1.setProperty("Label", "t1");
791 t1.setContractLevel(ContractLevel.FREE);
792
793 // Assemble the first graph: graphA
794 EmptyVertex m0 = new EmptyVertex(100);
795 m0.addAP(APCA);
796 m0.setProperty("Label", "m100");
797
798 EmptyVertex m1 = new EmptyVertex(101);
799 m1.addAP(APCC);
800 m1.setProperty("Label", "m101");
801
802 EmptyVertex m2 = new EmptyVertex(102);
803 m2.addAP(APCB);
804 m2.addAP(APCC);
805 m2.setProperty("Label", "m102");
806
807 EmptyVertex m3 = new EmptyVertex(103);
808 m3.addAP(APCC);
809 m3.setProperty("Label", "m103");
810
811 DGraph graphA = new DGraph();
812 graphA.addVertex(m0);
813 graphA.appendVertexOnAP(m0.getAP(0), t1.getAP(0)); // A on T1
814 graphA.appendVertexOnAP(t1.getAP(1), m1.getAP(0)); // C on T1
815 graphA.appendVertexOnAP(t1.getAP(2), m2.getAP(0)); // B on T1
816 graphA.appendVertexOnAP(m2.getAP(1), m3.getAP(0));
817 graphA.setGraphId(11111);
818
819 // Done with GraphA!
820
821 // Prepare special building block: template T2
822 EmptyVertex w0 = new EmptyVertex(0);
823 w0.addAP(APCA);
824 w0.addAP(APCA);
825 w0.addAP(APCA);
826 w0.setProperty("Label", "tw0");
827
828 EmptyVertex w1 = new EmptyVertex(1);
829 w1.addAP(APCA);
830 w1.addAP(APCB);
831 w1.setProperty("Label", "tw1");
832
833 EmptyVertex w2 = new EmptyVertex(2);
834 w2.addAP(APCB);
835 w2.setProperty("Label", "tw2");
836
837 EmptyVertex w3 = new EmptyVertex(3);
838 w3.addAP(APCA);
839 w3.addAP(APCA);
840 w3.setProperty("Label", "tw3");
841
842 EmptyVertex w4 = new EmptyVertex(4);
843 w4.addAP(APCA);
844 w4.addAP(APCB);
845 w4.addAP(APCA);
846 w4.setProperty("Label", "tw4");
847
848 EmptyVertex w5 = new EmptyVertex(5);
849 w5.addAP(APCA);
850 w5.setProperty("Label", "tw5");
851
852 DGraph g2 = new DGraph();
853 g2.addVertex(w0);
854 g2.setGraphId(-1);
855 g2.appendVertexOnAP(w0.getAP(1), w1.getAP(0));
856 g2.appendVertexOnAP(w1.getAP(1), w2.getAP(0));
857 g2.appendVertexOnAP(w0.getAP(0), w3.getAP(0));
858 g2.appendVertexOnAP(w3.getAP(1), w4.getAP(0));
859 g2.appendVertexOnAP(w4.getAP(2), w5.getAP(0));
860
861 Template t2 = new Template(BBType.NONE);
862 t2.setInnerGraph(g2);
863 t2.setProperty("Label", "t2");
864 t2.setContractLevel(ContractLevel.FREE);
865
866 // Assemble the first graph: graphA
867 EmptyVertex n0 = new EmptyVertex(200);
868 n0.addAP(APCA);
869 n0.setProperty("Label", "m200");
870
871 EmptyVertex n2 = new EmptyVertex(202);
872 n2.addAP(APCB);
873 n2.addAP(APCC);
874 n2.setProperty("Label", "m202");
875
876 EmptyVertex n3 = new EmptyVertex(203);
877 n3.addAP(APCC);
878 n3.setProperty("Label", "m203");
879
880 DGraph graphB = new DGraph();
881 graphB.addVertex(n0);
882 graphB.appendVertexOnAP(n0.getAP(0), t2.getAP(0)); // A on T2
883 graphB.appendVertexOnAP(t2.getAP(1), n2.getAP(0)); // B on T2
884 graphB.appendVertexOnAP(n2.getAP(1), n3.getAP(0));
885 graphB.setGraphId(22222);
886
887 // Done with GraphB!
888
889 DGraph[] pair = new DGraph[2];
890 pair[0] = graphA;
891 pair[1] = graphB;
892
893 return pair;
894 }
895
896//------------------------------------------------------------------------------
897
945 public static DGraph[] getPairOfTestGraphsBxo() throws Exception
946 {
947 // Prepare special building block: template T1
948 EmptyVertex v0 = new EmptyVertex(0);
949 v0.addAP(APCA);
950 v0.addAP(APCA);
951 v0.addAP(APCA);
952 v0.setProperty("Label", "tv0");
953
954 EmptyVertex v1 = new EmptyVertex(1);
955 v1.addAP(APCA);
956 v1.addAP(APCA);
957 v1.setProperty("Label", "tv1");
958
959 EmptyVertex v2 = new EmptyVertex(2);
960 v2.addAP(APCA);
961 v2.addAP(APCB);
962 v2.addAP(APCA);
963 v2.setProperty("Label", "tv2");
964
965 EmptyVertex v3 = new EmptyVertex(3);
966 v3.addAP(APCA);
967 v3.setProperty("Label", "tv3");
968 v3.setAsRCV(true);
969
970 EmptyVertex v4 = new EmptyVertex(4);
971 v4.addAP(APCA);
972 v4.addAP(APCB);
973 v4.addAP(APCA);
974 v4.setProperty("Label", "tv4");
975
976 EmptyVertex v5 = new EmptyVertex(5);
977 v5.addAP(APCA);
978 v5.setProperty("Label", "tv5");
979
980 DGraph g = new DGraph();
981 g.addVertex(v0);
982 g.setGraphId(-1);
983 g.appendVertexOnAP(v0.getAP(0), v1.getAP(0));
984 g.appendVertexOnAP(v1.getAP(1), v2.getAP(0));
985 g.appendVertexOnAP(v2.getAP(2), v3.getAP(0));
986 g.appendVertexOnAP(v0.getAP(1), v4.getAP(0));
987 g.appendVertexOnAP(v4.getAP(2), v5.getAP(0));
988
989 Template t1 = new Template(BBType.NONE);
990 t1.setInnerGraph(g);
991 t1.setProperty("Label", "t1");
992 t1.setContractLevel(ContractLevel.FREE);
993
994 // Assemble the first graph: graphA
995 EmptyVertex m0 = new EmptyVertex(100);
996 m0.addAP(APCA);
997 m0.setProperty("Label", "m100");
998
999 EmptyVertex m1 = new EmptyVertex(101);
1000 m1.addAP(APCC);
1001 m1.setProperty("Label", "m101");
1002
1003 EmptyVertex m2 = new EmptyVertex(102);
1004 m2.addAP(APCB);
1005 m2.addAP(APCC);
1006 m2.setProperty("Label", "m102");
1007
1008 EmptyVertex m3 = new EmptyVertex(103);
1009 m3.addAP(APCC);
1010 m3.setProperty("Label", "m103");
1011
1012 DGraph graphA = new DGraph();
1013 graphA.addVertex(m0);
1014 graphA.appendVertexOnAP(m0.getAP(0), t1.getAP(0)); // A on T1
1015 graphA.appendVertexOnAP(t1.getAP(1), m1.getAP(0)); // B on T1
1016 graphA.appendVertexOnAP(t1.getAP(2), m2.getAP(0)); // B on T1
1017 graphA.appendVertexOnAP(m2.getAP(1), m3.getAP(0));
1018 graphA.setGraphId(33333);
1019
1020 // Done with GraphA!
1021
1022 // Prepare special building block: template T2
1023 EmptyVertex w0 = new EmptyVertex(0);
1024 w0.addAP(APCA);
1025 w0.addAP(APCA);
1026 w0.addAP(APCA);
1027 w0.setProperty("Label", "tw0");
1028
1029 EmptyVertex w1 = new EmptyVertex(1);
1030 w1.addAP(APCA);
1031 w1.addAP(APCB);
1032 w1.setProperty("Label", "tw1");
1033
1034 EmptyVertex w2 = new EmptyVertex(2);
1035 w2.addAP(APCB);
1036 w2.setProperty("Label", "tw2");
1037
1038 EmptyVertex w3 = new EmptyVertex(3);
1039 w3.addAP(APCA);
1040 w3.addAP(APCA);
1041 w3.setProperty("Label", "tw3");
1042
1043 EmptyVertex w4 = new EmptyVertex(4);
1044 w4.addAP(APCA);
1045 w4.addAP(APCA);
1046 w4.addAP(APCB);
1047 w4.setProperty("Label", "tw4");
1048
1049 EmptyVertex w5 = new EmptyVertex(5);
1050 w5.addAP(APCA);
1051 w5.setProperty("Label", "tw5");
1052 w5.setAsRCV(true);
1053
1054 EmptyVertex w6 = new EmptyVertex(6);
1055 w6.addAP(APCB);
1056 w6.addAP(APCC);
1057 w6.setProperty("Label", "tw6");
1058
1059 DGraph g2 = new DGraph();
1060 g2.addVertex(w0);
1061 g2.setGraphId(-1);
1062 g2.appendVertexOnAP(w0.getAP(1), w1.getAP(0));
1063 g2.appendVertexOnAP(w1.getAP(1), w2.getAP(0));
1064 g2.appendVertexOnAP(w0.getAP(0), w3.getAP(0));
1065 g2.appendVertexOnAP(w3.getAP(1), w4.getAP(0));
1066 g2.appendVertexOnAP(w4.getAP(1), w5.getAP(0));
1067 g2.appendVertexOnAP(w4.getAP(2), w6.getAP(0));
1068
1069 Template t2 = new Template(BBType.NONE);
1070 t2.setInnerGraph(g2);
1071 t2.setProperty("Label", "tw2");
1072 t2.setContractLevel(ContractLevel.FREE);
1073
1074 // Assemble the first graph: graphA
1075 EmptyVertex n0 = new EmptyVertex(200);
1076 n0.addAP(APCA);
1077 n0.setProperty("Label", "m400");
1078
1079 EmptyVertex n2 = new EmptyVertex(202);
1080 n2.addAP(APCB);
1081 n2.addAP(APCC);
1082 n2.setProperty("Label", "m402");
1083
1084 EmptyVertex n3 = new EmptyVertex(203);
1085 n3.addAP(APCC);
1086 n3.setProperty("Label", "m403");
1087
1088 DGraph graphB = new DGraph();
1089 graphB.addVertex(n0);
1090 graphB.appendVertexOnAP(n0.getAP(0), t2.getAP(0)); // A on T2
1091 graphB.appendVertexOnAP(t2.getAP(1), n2.getAP(0)); // B on T2
1092 graphB.appendVertexOnAP(n2.getAP(1), n3.getAP(0));
1093 graphB.setGraphId(44444);
1094
1095 // Done with GraphB!
1096
1097 DGraph[] pair = new DGraph[2];
1098 pair[0] = graphA;
1099 pair[1] = graphB;
1100
1101 return pair;
1102 }
1103
1104//------------------------------------------------------------------------------
1105
1159 public static DGraph[] getPairOfTestGraphsBxoxo() throws Exception
1160 {
1161 // Prepare special building block: template T1
1162 // In the template we want APS in this order:
1163 // A(from v0), B(from v2), C(from v6)
1164
1165 EmptyVertex v0 = new EmptyVertex(0);
1166 v0.addAP(APCA);
1167 v0.addAP(APCA);
1168 v0.addAP(APCA);
1169 v0.setProperty("Label", "tv0");
1170
1171 EmptyVertex v1 = new EmptyVertex(1);
1172 v1.addAP(APCA);
1173 v1.addAP(APCA);
1174 v1.setProperty("Label", "tv1");
1175
1176 EmptyVertex v2 = new EmptyVertex(2);
1177 v2.addAP(APCA);
1178 v2.addAP(APCB);
1179 v2.addAP(APCA);
1180 v2.setProperty("Label", "tv2");
1181
1182 EmptyVertex v3 = new EmptyVertex(3);
1183 v3.addAP(APCA);
1184 v3.setProperty("Label", "tv3");
1185 v3.setAsRCV(true);
1186
1187 EmptyVertex v4 = new EmptyVertex(4);
1188 v4.addAP(APCA);
1189 v4.addAP(APCA);
1190 v4.addAP(APCB);
1191 v4.setProperty("Label", "tv4");
1192
1193 EmptyVertex v5 = new EmptyVertex(5);
1194 v5.addAP(APCA);
1195 v5.setProperty("Label", "tv5");
1196 v5.setAsRCV(true);
1197
1198 EmptyVertex v6 = new EmptyVertex(6);
1199 v6.addAP(APCB);
1200 v6.addAP(APCC);
1201 v6.setProperty("Label", "tv6");
1202
1203 DGraph g = new DGraph();
1204 g.addVertex(v0);
1205 g.setGraphId(-1);
1206 g.appendVertexOnAP(v0.getAP(0), v1.getAP(0));
1207 g.appendVertexOnAP(v1.getAP(1), v2.getAP(0));
1208 g.appendVertexOnAP(v2.getAP(2), v3.getAP(0));
1209 g.appendVertexOnAP(v0.getAP(1), v4.getAP(0));
1210 g.appendVertexOnAP(v4.getAP(2), v6.getAP(0));
1211 g.appendVertexOnAP(v4.getAP(1), v5.getAP(0));
1212 g.addRing(v5, v3, BondType.SINGLE);
1213
1214 Template t1 = new Template(BBType.NONE);
1215 t1.setInnerGraph(g);
1216 t1.setProperty("Label", "t1");
1217 t1.setContractLevel(ContractLevel.FREE);
1218
1219 // Assemble the first graph: graphA
1220 EmptyVertex m0 = new EmptyVertex(100);
1221 m0.addAP(APCA);
1222 m0.setProperty("Label", "m100");
1223
1224 EmptyVertex m1 = new EmptyVertex(101);
1225 m1.addAP(APCC);
1226 m1.setProperty("Label", "m101");
1227
1228 EmptyVertex m2 = new EmptyVertex(102);
1229 m2.addAP(APCB);
1230 m2.addAP(APCC);
1231 m2.setProperty("Label", "m102");
1232
1233 EmptyVertex m3 = new EmptyVertex(103);
1234 m3.addAP(APCC);
1235 m3.setProperty("Label", "m103");
1236
1237 DGraph graphA = new DGraph();
1238 graphA.addVertex(m0);
1239 graphA.appendVertexOnAP(m0.getAP(0), t1.getAP(0)); // A on T1
1240 graphA.appendVertexOnAP(t1.getAP(1), m1.getAP(0)); // B on T1
1241 graphA.appendVertexOnAP(t1.getAP(2), m2.getAP(0)); // C on T1
1242 graphA.appendVertexOnAP(m2.getAP(1), m3.getAP(0));
1243 graphA.setGraphId(55555);
1244
1245 // Done with GraphA!
1246
1247 // GraphB is the same as from getPairOfTestGraphsB()
1248 DGraph[] initialGraphs = getPairOfTestGraphsB();
1249 DGraph graphB = initialGraphs[1];
1250 graphB.setGraphId(66666);
1251
1252 // Done with GraphB!
1253
1254 DGraph[] pair = new DGraph[2];
1255 pair[0] = graphA;
1256 pair[1] = graphB;
1257
1258 return pair;
1259 }
1260
1261//------------------------------------------------------------------------------
1262
1263}
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:466
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:438
denoptim.ga.PopulationTest.makeGraphC
static DGraph makeGraphC()
Produced a graph like this:
Definition: PopulationTest.java:405
denoptim.ga.PopulationTest.prepare
static GAParameters prepare()
Definition: PopulationTest.java:64
denoptim.ga.PopulationTest.makeGraphB
static DGraph makeGraphB()
Produced a graph like this:
Definition: PopulationTest.java:373
denoptim.ga.PopulationTest.getPairOfTestGraphsBxoxo
static DGraph[] getPairOfTestGraphsBxoxo()
Builds a pair of graphs that contain templates with ContractLevel#FREE contract.
Definition: PopulationTest.java:1159
denoptim.ga.PopulationTest.compareSizeOfSites
void compareSizeOfSites(Candidate parentA, Map< Candidate, Integer > expectedForC1, List< Candidate > partnersForC1, Population pop)
Definition: PopulationTest.java:298
denoptim.ga.PopulationTest.compareSitesLists
void compareSitesLists(List< XoverSite > listA, List< XoverSite > listB)
Assumes the two lists have equal size.
Definition: PopulationTest.java:287
denoptim.ga.PopulationTest.makeGraphE
static DGraph makeGraphE()
Produced a graph like this:
Definition: PopulationTest.java:464
denoptim.ga.PopulationTest.makeGraphF
static DGraph makeGraphF()
Produced a graph like this:
Definition: PopulationTest.java:510
denoptim.ga.PopulationTest.getPairOfTestGraphsB
static DGraph[] getPairOfTestGraphsB()
Builds a pair of graphs that contain templates with ContractLevel#FREE contract.
Definition: PopulationTest.java:736
denoptim.ga.PopulationTest.getPairOfTestGraphsBxo
static DGraph[] getPairOfTestGraphsBxo()
Builds a pair of graphs that contain templates with ContractLevel#FREE contract.
Definition: PopulationTest.java:945
denoptim.ga.PopulationTest.makeGraphA
static DGraph makeGraphA()
Produced a graph like this:
Definition: PopulationTest.java:324
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:136
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:1097
denoptim.graph.DGraph.setGraphId
void setGraphId(int id)
Definition: DGraph.java:258
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:2514
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:5776
denoptim.graph.DGraph.renumberGraphVertices
void renumberGraphVertices()
Reassign vertex IDs to all vertices of this graph.
Definition: DGraph.java:5283
denoptim.graph.DGraph.addRing
void addRing(Ring ring)
Definition: DGraph.java:1030
denoptim.graph.DGraph.addEdge
void addEdge(Edge edge)
Adds the edge to the list of edges belonging to this graph.
Definition: DGraph.java:1021
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:254
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:1112
denoptim.graph.Vertex.setBuildingBlockType
void setBuildingBlockType(Vertex.BBType buildingBlockType)
Definition: Vertex.java:305
denoptim.graph.Vertex.setProperty
void setProperty(Object key, Object property)
Definition: Vertex.java:1148
denoptim.graph.Vertex.getAP
AttachmentPoint getAP(int i)
Get attachment point i on this vertex.
Definition: Vertex.java:920
denoptim.programs.RunTimeParameters.setParameters
void setParameters(RunTimeParameters otherParams)
Definition: RunTimeParameters.java:800
denoptim.programs.denovo.GAParameters
Parameters for genetic algorithm.
Definition: GAParameters.java:46
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:137
denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS
RC_PARAMS
Parameters pertaining to ring closures in graphs.
Definition: RunTimeParameters.java:142