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DENOPTIM
TemplateTest.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.graph;
20
21import static org.junit.jupiter.api.Assertions.assertEquals;
22import static org.junit.jupiter.api.Assertions.assertSame;
23import static org.junit.jupiter.api.Assertions.assertThrows;
24import static org.junit.jupiter.api.Assertions.assertTrue;
25import static org.junit.jupiter.api.Assertions.fail;
26
27import java.io.File;
28import java.util.ArrayList;
29import java.util.Arrays;
30import java.util.List;
31import java.util.Random;
32
33import javax.vecmath.Point3d;
34
35import org.junit.jupiter.api.Test;
36import org.junit.jupiter.api.io.TempDir;
37import org.openscience.cdk.DefaultChemObjectBuilder;
38import org.openscience.cdk.exception.CDKException;
39import org.openscience.cdk.geometry.alignment.KabschAlignment;
40import org.openscience.cdk.interfaces.IAtom;
41import org.openscience.cdk.interfaces.IAtomContainer;
42import org.openscience.cdk.interfaces.IBond;
43import org.openscience.cdk.interfaces.IChemObjectBuilder;
44
45import denoptim.exception.DENOPTIMException;
46import denoptim.graph.Vertex.BBType;
47import denoptim.io.DenoptimIO;
48import denoptim.utils.GraphUtils;
49import denoptim.utils.MoleculeUtils;
50
55public class TemplateTest
56{
57 final long SEED = 13;
58 Random rng = new Random(SEED);
59 static IChemObjectBuilder chemBuilder = DefaultChemObjectBuilder.getInstance();
60
61 @TempDir
62 File tempDir;
63
64 private final String NL = System.getProperty("line.separator");
65 private final String SEP = System.getProperty("file.separator");
66
67//------------------------------------------------------------------------------
68
69 @Test
70 public void testClone() throws Exception
71 {
72 EmptyVertex vA = new EmptyVertex(0);
73 vA.addAP();
74 vA.addAP();
75 vA.addAP();
76 EmptyVertex vB = new EmptyVertex(1);
77 vB.addAP();
78 vB.addAP();
79 EmptyVertex vC = new EmptyVertex(2);
80 vC.addAP();
81 vC.addAP();
82 vA.addAP();
83 EmptyVertex vRcvA = new EmptyVertex(3);
84 vRcvA.addAP();
85 vRcvA.setAsRCV(true);
86 EmptyVertex vRcvC = new EmptyVertex(4);
87 vRcvC.addAP();
88 vRcvC.setAsRCV(true);
89
90 DGraph g = new DGraph();
91 g.addVertex(vA);
92 g.appendVertexOnAP(vA.getAP(0), vB.getAP(1));
93 g.appendVertexOnAP(vB.getAP(0), vC.getAP(1));
94 g.appendVertexOnAP(vA.getAP(1), vRcvA.getAP(0));
95 g.appendVertexOnAP(vC.getAP(0), vRcvC.getAP(0));
96
97 Ring r = new Ring(new ArrayList<Vertex>(
98 Arrays.asList(vRcvA, vA, vB, vC, vRcvC)));
99 g.addRing(r);
100
101 Template t = new Template(BBType.NONE);
102 //TODO-v3 add required APs and check they are cloned properly
103 t.setInnerGraph(g);
104 t.freezeTemplate();
105 t.setProperty("PROPNAME","PROVALUE");
106
107 Template c = t.clone();
108
109 assertEquals(t.getFreeAPCount(),c.getFreeAPCount(),
110 "Different #free APs");
111 assertEquals("PROVALUE",c.getProperty("PROPNAME"));
112 for (int i=0; i<t.getFreeAPCount(); i++)
113 {
114 AttachmentPoint oriAP = t.getAP(i);
115 AttachmentPoint cloAP = c.getAP(i);
116 assertTrue(oriAP.hashCode() != cloAP.hashCode(), "Hashcode of APs");
117 assertTrue(oriAP.getAPClass() == cloAP.getAPClass(), "APClass");
118 assertTrue(oriAP.getAtomPositionNumber()
119 == cloAP.getAtomPositionNumber(), "AP AtomSource");
120 }
121
122 DGraph oriIG = t.getInnerGraph();
123 DGraph cloIG = c.getInnerGraph();
124 assertTrue(oriIG.hashCode() != cloIG.hashCode(),
125 "InnerGraph graph hash");
126 assertEquals(oriIG.getVertexCount(),
127 cloIG.getVertexCount(),"InnerGraph vertex count");
128 for (int i=0; i<oriIG.getVertexCount(); i++)
129 {
130 Vertex ov = oriIG.getVertexAtPosition(i);
131 Vertex cv = cloIG.getVertexAtPosition(i);
132 assertTrue(ov.hashCode() != cv.hashCode(),"InnerGraph vertex hash");
133 }
134
135 assertEquals(oriIG.getRingCount(),
136 cloIG.getRingCount(),"InnerGraph ring count");
137 assertEquals(oriIG.getRings().get(0).getSize(),
138 cloIG.getRings().get(0).getSize(),"InnerGraph ring count");
139 }
140
141//------------------------------------------------------------------------------
142
143 @Test
144 public void testNestedTemplateCloning() {
145 try {
146 Template t = getNestedTemplate();
147 Template clone = t.clone();
148 assertTrue(t.sameAs(clone, new StringBuilder()));
149 } catch (DENOPTIMException e) {
150 fail("Unexpected exception thrown.");
151
152 }
153 }
154
155//------------------------------------------------------------------------------
156
168 private Template getNestedTemplate() throws DENOPTIMException {
169 /* Constructing innermost template */
170 Vertex ohFrag = getOHFragment();
171 DGraph g = new DGraph();
172 g.addVertex(ohFrag);
173 Template nestedTemp = new Template(BBType.FRAGMENT);
174 nestedTemp.setInnerGraph(g);
175
176 /* Constructing outermost template */
177 Vertex ch2Frag = getCH2Fragment();
178 g = new DGraph();
179 g.addVertex(ch2Frag);
180 g.appendVertexOnAP(ch2Frag.getAP(0), nestedTemp.getAP(0));
181
182 Template outerTemp = new Template(BBType.FRAGMENT);
183 outerTemp.setInnerGraph(g);
184
185 return outerTemp;
186 }
187
188//------------------------------------------------------------------------------
189
196 private static Vertex getCH2Fragment() throws DENOPTIMException
197 {
198 IAtomContainer atomContainer = chemBuilder.newAtomContainer();
199 String[] elements = new String[]{"C", "H", "H"};
200 Point3d[] atmCoords = new Point3d[]{
201 new Point3d(0.0, 0.0, 0.0),
202 new Point3d(0.0000, -0.8900, -0.6293),
203 new Point3d(0.0000, 0.8900, -0.6293),
204 };
205 for (int i=0; i<elements.length; i++) {
206 IAtom atom = chemBuilder.newAtom();
207 atom.setSymbol(elements[i]);
208 atom.setPoint3d(atmCoords[i]);
209 atomContainer.addAtom(atom);
210 }
211 atomContainer.addBond(0, 1, IBond.Order.SINGLE);
212 atomContainer.addBond(0, 2, IBond.Order.SINGLE);
213
214 Fragment v = new Fragment(
215 GraphUtils.getUniqueVertexIndex(),
216 atomContainer,
217 BBType.FRAGMENT);
218
219 Point3d[] apCoords = new Point3d[]{
220 new Point3d(-0.8900, 0.0000, 0.6293),
221 new Point3d(0.8900, 0.0000, 0.6293),
222 };
223 for (int i = 0; i < 2; i++) {
224 APClass apClass = APClass.make("c", 0);
225 v.addAP(0, apClass, apCoords[i]);
226 }
227 return v;
228 }
229
230//------------------------------------------------------------------------------
231
238 private static Vertex getAmideFragment() throws DENOPTIMException
239 {
240 IAtomContainer atomContainer = chemBuilder.newAtomContainer();
241 String[] elements = new String[]{"C", "O", "N"};
242 Point3d[] atmCoords = new Point3d[]{
243 new Point3d(0.6748, -0.1898, -0.0043),
244 new Point3d(1.0460, -1.3431, -0.0581),
245 new Point3d(-0.6427, 0.0945, -0.0002),
246 };
247 for (int i=0; i<elements.length; i++) {
248 IAtom atom = chemBuilder.newAtom();
249 atom.setSymbol(elements[i]);
250 atom.setPoint3d(atmCoords[i]);
251 atomContainer.addAtom(atom);
252 }
253 atomContainer.addBond(0, 1, IBond.Order.DOUBLE);
254 atomContainer.addBond(0, 2, IBond.Order.SINGLE);
255
256 Fragment v = new Fragment(
257 GraphUtils.getUniqueVertexIndex(),
258 atomContainer,
259 BBType.FRAGMENT);
260
261 Point3d[] apCoords = new Point3d[]{
262 new Point3d(1.6864, 0.9254, 0.0580),
263 new Point3d(-1.6259, -0.9902, 0.0560),
264 new Point3d(-1.0915, 1.4881, -0.0518),
265 };
266 int[] srcAtm = new int[] {0, 2, 2};
267 APClass[] apClass = new APClass[] {
268 APClass.make("Camide", 0),
269 APClass.make("NAmide", 0),
270 APClass.make("NAmide", 0)};
271 for (int i = 0; i < 3; i++) {
272 v.addAP(srcAtm[i], apClass[i],apCoords[i]);
273 }
274 return v;
275 }
276
277//------------------------------------------------------------------------------
278
283 private Vertex getOHFragment() throws DENOPTIMException {
284 IAtomContainer atomContainer = chemBuilder.newAtomContainer();
285 String[] elements = new String[]{"O", "H"};
286 for (String e : elements) {
287 IAtom atom = chemBuilder.newAtom();
288 atom.setSymbol(e);
289 atomContainer.addAtom(atom);
290 }
291
292 atomContainer.addBond(0, 1, IBond.Order.SINGLE);
293
294 Fragment v = new Fragment(
295 GraphUtils.getUniqueVertexIndex(),
296 atomContainer,
297 BBType.FRAGMENT);
298 double precision = 10*10*10*10;
299 APClass apClass = APClass.make("o", 0);
300 v.addAP(
301 0,
302 apClass,
303 new Point3d(
304 (double) (Math.round(rng.nextDouble() * precision)) / precision,
305 (double) (Math.round(rng.nextDouble() * precision)) / precision,
306 (double) (Math.round(rng.nextDouble() * precision)) / precision)
307 );
308 return v;
309 }
310
311//------------------------------------------------------------------------------
312
313 @Test
314 public void testGetAttachmentPoints_returnsAPsWithTemplateAsOwner()
315 throws DENOPTIMException
316 {
317 Template template = new Template(BBType.NONE);
318 EmptyVertex v = new EmptyVertex();
319 v.addAP();
320 DGraph innerGraph = new DGraph();
321 innerGraph.addVertex(v);
322 template.setInnerGraph(innerGraph);
323
324 int totalAPCount = 1;
325 for (int i = 0; i < totalAPCount; i++) {
326 Vertex actualOwner = template.getAttachmentPoints().get(i)
327 .getOwner();
328 assertSame(template, actualOwner);
329 }
330 }
331
332//------------------------------------------------------------------------------
333
334 @Test
335 public void testGetAttachmentPoints_returnsCorrectNumberOfAPs()
336 throws DENOPTIMException
337 {
338 Template template =
339 new Template(BBType.NONE);
340 int requiredAPCount = 2;
341 EmptyVertex v1 = new EmptyVertex();
342 EmptyVertex v2 = new EmptyVertex();
343 int v1APCount = 3;
344 int v2APCount = 2;
345 for (int i = 0; i < requiredAPCount; i++) {
346 template.addRequiredAP(null, null);
347 }
348 for (int i = 0; i < v1APCount; i++) {
349 v1.addAP();
350 }
351 for (int i = 0; i < v2APCount; i++) {
352 v2.addAP();
353 }
354 DGraph innerGraph = new DGraph();
355 innerGraph.addVertex(v1);
356 innerGraph.appendVertexOnAP(v1.getAP(0), v2.getAP(0));
357 template.setInnerGraph(innerGraph);
358
359// System.err.println(innerGraph.getAvailableAPs().toString());
360
361 // -2 since 2 APs are used to connect v1 and v2.
362 int expectedAPCount = v1APCount + v2APCount - 2;
363 int actualAPCount = template.getAttachmentPoints().size();
364 assertEquals(expectedAPCount, actualAPCount);
365 }
366
367//------------------------------------------------------------------------------
368
369 @Test
370 public void testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs()
371 throws DENOPTIMException {
372 int numberOfAPs = 2;
373 List<Point3d> dirVecs = Arrays.asList(
374 new Point3d(1.0, -2.1,3.2),
375 new Point3d(-2.0, 1.1, -3.2)
376 );
377 List<APClass> APClasses = Arrays.asList(
378 APClass.make("rule1", 0),
379 APClass.make("rule2", 1)
380 );
381
382 Template template =
383 new Template(BBType.NONE);
384 EmptyVertex v = new EmptyVertex();
385 for (int i = 0; i < numberOfAPs; i++) {
386 template.addRequiredAP(dirVecs.get(i),
387 APClasses.get(i));
388 v.addAP(APClasses.get(i));
389 }
390 DGraph innerGraph = new DGraph();
391 innerGraph.addVertex(v);
392
393 testAtLeastSameNumberOfAPs(template, numberOfAPs);
394 testSameAPClass(template, innerGraph);
395 }
396
397//------------------------------------------------------------------------------
398
399 private void testSameAPClass(Template t, DGraph innerGraph)
400 {
401 AttachmentPoint ap = innerGraph.getVertexAtPosition(0).getAP(1);
402 try {
403 ap.setAPClass(
404 innerGraph.getVertexAtPosition(0).getAP(0).getAPClass());
405 assertThrows(IllegalArgumentException.class,
406 () -> t.setInnerGraph(innerGraph));
407 } catch (Exception e) {
408 fail("Expected " + IllegalArgumentException.class + ", but was "
409 + e.getClass());
410 }
411 }
412
413//------------------------------------------------------------------------------
414
415 private void testAtLeastSameNumberOfAPs(Template t,
416 int expNumberOfAPs) throws DENOPTIMException
417 {
418 EmptyVertex v = new EmptyVertex();
419 for (int i = 0; i < expNumberOfAPs - 1; i++) {
420 v.addAP();
421 }
422 DGraph innerGraph = new DGraph();
423 innerGraph.addVertex(v);
424 assertThrows(IllegalArgumentException.class,
425 () -> t.setInnerGraph(innerGraph));
426 }
427
428//------------------------------------------------------------------------------
429
430 @Test
431 public void testAddAP_after_setInnerGraph_throwsException() {
432 Template t = new Template(BBType.NONE);
433 DGraph g = new DGraph();
434 t.setInnerGraph(g);
435 assertThrows(IllegalArgumentException.class, () -> t.addRequiredAP(
436 new Point3d(0,0,0), APClass.make("dummy:0")));
437 }
438
439//------------------------------------------------------------------------------
440
456 public static Template getTestAmideTemplate() throws DENOPTIMException
457 {
458 Vertex v1 = getCH2Fragment();
459 Vertex v2 = getCH2Fragment();
460 Vertex v3 = getCH2Fragment();
461 Vertex v4 = getCH2Fragment();
462 Vertex v5 = getAmideFragment();
463
464 DGraph g = new DGraph();
465 g.addVertex(v1);
466 g.appendVertexOnAP(v1.getAP(0), v5.getAP(0));
467 g.appendVertexOnAP(v1.getAP(1), v2.getAP(1));
468 g.appendVertexOnAP(v2.getAP(0), v3.getAP(1));
469 g.appendVertexOnAP(v3.getAP(0), v4.getAP(0));
470
471 Template t = new Template(BBType.UNDEFINED);
472 t.setInnerGraph(g);
473
474 return t;
475 }
476
477//------------------------------------------------------------------------------
478
479 @Test
480 public void testGetIAtomContainer() throws Exception
481 {
482 Template t = getTestAmideTemplate();
483
484 IAtomContainer mol = t.getIAtomContainer();
485
486 String[] elements = new String[]{"C", "H", "N", "O"};
487 int[] expected = new int[]{5, 8, 1, 1};
488 for (int i=0; i<elements.length; i++)
489 {
490 assertEquals(expected[i],
491 MoleculeUtils.countAtomsOfElement(mol, elements[i]),
492 "Number of '" + elements[i] + "'.");
493 }
494
495 String refGeometry = NL +
496 " CDK 04132117333D" + NL +
497 NL +
498 " 15 14 0 0 0 0 0 0 0 0999 V2000" + NL +
499 " 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
500 " 0.0000 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
501 " 0.0000 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
502 " -1.0602 0.0000 0.7497 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
503 " -1.4136 -1.0211 1.3004 O 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
504 " -1.7681 1.1349 0.9158 N 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
505 " 0.8900 0.0000 0.6293 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
506 " 0.8900 -0.8900 1.2586 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
507 " 0.8900 0.8900 1.2586 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
508 " 1.7800 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
509 " 2.3733 -0.8900 0.2098 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
510 " 2.3733 0.8900 0.2098 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
511 " 1.4834 0.0000 -1.0489 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
512 " 0.8901 -0.8900 -1.2587 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
513 " 0.8901 0.8900 -1.2587 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
514 " 1 2 1 0 0 0 0" + NL +
515 " 1 3 1 0 0 0 0" + NL +
516 " 4 5 2 0 0 0 0" + NL +
517 " 4 6 1 0 0 0 0" + NL +
518 " 1 4 1 0 0 0 0" + NL +
519 " 7 8 1 0 0 0 0" + NL +
520 " 7 9 1 0 0 0 0" + NL +
521 " 1 7 1 0 0 0 0" + NL +
522 " 10 11 1 0 0 0 0" + NL +
523 " 10 12 1 0 0 0 0" + NL +
524 " 7 10 1 0 0 0 0" + NL +
525 " 13 14 1 0 0 0 0" + NL +
526 " 13 15 1 0 0 0 0" + NL +
527 " 10 13 1 0 0 0 0" + NL +
528 "M END" + NL;
529
530 assertTrue(this.tempDir.isDirectory(),"Should be a directory ");
531 String fileName = tempDir.getAbsolutePath() + SEP + "refMol.sdf";
532 DenoptimIO.writeData(fileName, refGeometry, false);
533
534 IAtomContainer refMol = DenoptimIO.readSDFFile(fileName).get(0);
535
536 KabschAlignment sa = null;
537 try {
538 sa = new KabschAlignment(refMol,mol);
539 sa.align();
540 } catch (CDKException e){
541 e.printStackTrace();
542 fail("KabschAlignment failed: "+e.getMessage());
543 }
544 assertTrue(sa.getRMSD()<0.0001,"RMSD between generated and expected "
545 + "geometry");
546
547 // This check is done ignoring AP order
548 Point3d[] expectedAPHeads = new Point3d[] {
549 new Point3d(-2.8954,1.1648,1.8510),
550 new Point3d(-1.4101,2.3385,0.1613),
551 new Point3d(2.3734,0.0000,-1.6782)};
552 for (AttachmentPoint ap : t.getAttachmentPoints())
553 {
554 Point3d apHead = new Point3d(ap.getDirectionVector());
555 boolean found = false;
556 double[] dists = new double[3];
557 for (int i=0; i<expectedAPHeads.length; i++)
558 {
559 Point3d expectedAPHead = expectedAPHeads[i];
560 double dist = apHead.distance(expectedAPHead);
561 dists[i] = dist;
562 if (dist<0.001)
563 {
564 found = true;
565 break;
566 }
567 }
568 assertTrue(found,"Inconsistent placement of outer AP (errors: "
569 + dists[0] + ", " + dists[1] + ", " + dists[2] + "). "
570 + "AP: "+ap);
571 }
572 }
573
574//------------------------------------------------------------------------------
575
576 private Template getTemplateDeepTest() throws DENOPTIMException
577 {
578 Template v1 = null;
579 for (int i =0; i<10; i++)
580 {
581 if (v1 == null)
582 {
583 v1 = getTestAmideTemplate();
584 }
585 Vertex v2 = getCH2Fragment();
586 v2.setVertexId(100+i);
587 DGraph g = new DGraph();
588 g.addVertex(v1);
589 g.appendVertexOnAP(v1.getAP(0), v2.getAP(0));
590 Template t = new Template(BBType.UNDEFINED);
591 t.setInnerGraph(g);
592 v1 = t;
593 }
594 return v1;
595 }
596
597//------------------------------------------------------------------------------
598
599 @Test
600 public void testGetIAtomContainer_DeepVertex() throws Exception
601 {
602 Template t = getTemplateDeepTest();
603
604 IAtomContainer mol = t.getIAtomContainer();
605
606 String[] elements = new String[]{"C", "H", "N", "O"};
607 int[] expected = new int[]{15, 28, 1, 1};
608 for (int i=0; i<elements.length; i++)
609 {
610 assertEquals(expected[i],
611 MoleculeUtils.countAtomsOfElement(mol, elements[i]),
612 "Number of '" + elements[i] + "'.");
613 }
614
615 String refGeometry = NL +
616 " CDK 02222322323D" + NL +
617 NL +
618 " 45 44 0 0 0 0 0 0 0 0999 V2000" + NL +
619 " 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
620 " 0.0000 -0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
621 " 0.0000 0.8900 -0.6293 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
622 " -1.0602 0.0000 0.7497 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
623 " -1.4136 -1.0211 1.3004 O 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
624 " -1.7681 1.1349 0.9158 N 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
625 " 0.8900 0.0000 0.6293 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
626 " 0.8900 -0.8900 1.2586 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
627 " 0.8900 0.8900 1.2586 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
628 " 1.7800 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
629 " 2.3733 -0.8900 0.2098 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
630 " 2.3733 0.8900 0.2098 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
631 " 1.4834 0.0000 -1.0489 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
632 " 0.8901 -0.8900 -1.2587 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
633 " 0.8901 0.8900 -1.2587 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
634 " -2.7511 1.1609 1.7313 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
635 " -2.4728 0.6487 2.6523 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
636 " -3.0101 2.1958 1.9552 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
637 " -1.4559 2.1845 0.2578 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
638 " -1.2473 1.9156 -0.7777 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
639 " -2.2838 2.8928 0.2896 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
640 " 2.3734 0.0000 -1.6782 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
641 " 2.3734 -0.8900 -2.3075 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
642 " 2.3734 0.8900 -2.3075 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
643 " -3.6091 0.6606 1.2823 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
644 " -4.2319 0.2324 2.0677 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
645 " -4.1916 1.3822 0.7094 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
646 " -0.5703 2.6407 0.7002 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
647 " 0.3217 2.1322 0.3340 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
648 " -0.5275 3.6941 0.4234 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
649 " 3.2634 0.0000 -1.0489 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
650 " 3.8567 -0.8900 -1.2587 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
651 " 3.8567 0.8900 -1.2587 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
652 " -3.2617 -0.1330 0.6208 C 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
653 " -4.0122 -0.9222 0.5749 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
654 " -3.0987 0.2719 -0.3780 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
655 " -0.6194 2.5519 1.7855 C 0 0 0 0 0 3 0 0 0 0 0 0" + NL +
656 " -0.2733 1.5626 2.0851 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
657 " 0.0148 3.3122 2.2413 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
658 " 2.9668 0.0000 0.0000 C 0 0 0 0 0 3 0 0 0 0 0 0" + NL +
659 " 3.3624 -0.8900 0.4894 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
660 " 3.3624 0.8900 0.4894 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
661 " -2.3270 -0.5423 1.0039 C 0 0 0 0 0 3 0 0 0 0 0 0" + NL +
662 " -2.2364 -1.5857 0.7018 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
663 " -1.4891 0.0267 0.6010 H 0 0 0 0 0 0 0 0 0 0 0 0" + NL +
664 " 1 2 1 0 0 0 0" + NL +
665 " 1 3 1 0 0 0 0" + NL +
666 " 4 5 2 0 0 0 0" + NL +
667 " 4 6 1 0 0 0 0" + NL +
668 " 1 4 1 0 0 0 0" + NL +
669 " 7 8 1 0 0 0 0" + NL +
670 " 7 9 1 0 0 0 0" + NL +
671 " 1 7 1 0 0 0 0" + NL +
672 " 10 11 1 0 0 0 0" + NL +
673 " 10 12 1 0 0 0 0" + NL +
674 " 7 10 1 0 0 0 0" + NL +
675 " 13 14 1 0 0 0 0" + NL +
676 " 13 15 1 0 0 0 0" + NL +
677 " 10 13 1 0 0 0 0" + NL +
678 " 16 17 1 0 0 0 0" + NL +
679 " 16 18 1 0 0 0 0" + NL +
680 " 6 16 1 0 0 0 0" + NL +
681 " 19 20 1 0 0 0 0" + NL +
682 " 19 21 1 0 0 0 0" + NL +
683 " 6 19 1 0 0 0 0" + NL +
684 " 22 23 1 0 0 0 0" + NL +
685 " 22 24 1 0 0 0 0" + NL +
686 " 13 22 1 0 0 0 0" + NL +
687 " 25 26 1 0 0 0 0" + NL +
688 " 25 27 1 0 0 0 0" + NL +
689 " 16 25 1 0 0 0 0" + NL +
690 " 28 29 1 0 0 0 0" + NL +
691 " 28 30 1 0 0 0 0" + NL +
692 " 19 28 1 0 0 0 0" + NL +
693 " 31 32 1 0 0 0 0" + NL +
694 " 31 33 1 0 0 0 0" + NL +
695 " 22 31 1 0 0 0 0" + NL +
696 " 34 35 1 0 0 0 0" + NL +
697 " 34 36 1 0 0 0 0" + NL +
698 " 25 34 1 0 0 0 0" + NL +
699 " 37 38 1 0 0 0 0" + NL +
700 " 37 39 1 0 0 0 0" + NL +
701 " 28 37 1 0 0 0 0" + NL +
702 " 40 41 1 0 0 0 0" + NL +
703 " 40 42 1 0 0 0 0" + NL +
704 " 31 40 1 0 0 0 0" + NL +
705 " 43 44 1 0 0 0 0" + NL +
706 " 43 45 1 0 0 0 0" + NL +
707 " 34 43 1 0 0 0 0" + NL +
708 "M END";
709
710 assertTrue(this.tempDir.isDirectory(),"Should be a directory ");
711 String fileName = tempDir.getAbsolutePath() + SEP + "refMol.sdf";
712 DenoptimIO.writeData(fileName, refGeometry, false);
713
714 IAtomContainer refMol = DenoptimIO.readSDFFile(fileName).get(0);
715
716 KabschAlignment sa = null;
717 try {
718 sa = new KabschAlignment(refMol, mol);
719 sa.align();
720 } catch (CDKException e){
721 e.printStackTrace();
722 fail("KabschAlignment failed: "+e.getMessage());
723 }
724 assertTrue(sa.getRMSD()<0.0001,"RMSD between generated and expected "
725 + "geometry");
726
727 // This check is done ignoring AP order
728 Point3d[] expectedAPHeads = new Point3d[] {
729 new Point3d(-1.6488,2.6919,2.1153),
730 new Point3d(1.8790, 0.0, 0.0700),
731 new Point3d(-2.3207,-0.4772,2.0919)};
732 for (AttachmentPoint ap : t.getAttachmentPoints())
733 {
734 Point3d apHead = new Point3d(ap.getDirectionVector());
735 boolean found = false;
736 double[] dists = new double[3];
737 for (int i=0; i<expectedAPHeads.length; i++)
738 {
739 Point3d expectedAPHead = expectedAPHeads[i];
740 double dist = apHead.distance(expectedAPHead);
741 dists[i] = dist;
742 if (dist<0.001)
743 {
744 found = true;
745 break;
746 }
747 }
748 assertTrue(found,"Inconsistent placement of outer AP (errors: "
749 + dists[0] + ", " + dists[1] + ", " + dists[2] + "). "
750 + "AP: "+ap);
751 }
752 }
753}
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.AttachmentPoint
An attachment point (AP) is a possibility to attach a Vertex onto the vertex holding the AP (i....
Definition: AttachmentPoint.java:53
denoptim.graph.AttachmentPoint.setAPClass
void setAPClass(String apClass)
Set the Attachment Point class.
Definition: AttachmentPoint.java:424
denoptim.graph.AttachmentPoint.getAPClass
APClass getAPClass()
Returns the Attachment Point class.
Definition: AttachmentPoint.java:447
denoptim.graph.AttachmentPoint.getAtomPositionNumber
int getAtomPositionNumber()
The index of the source atom in the atom list of the fragment.
Definition: AttachmentPoint.java:335
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.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.getRings
List< Ring > getRings()
Definition: DGraph.java:771
denoptim.graph.DGraph.addRing
void addRing(Ring ring)
Definition: DGraph.java:1030
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.Fragment
Class representing a continuously connected portion of chemical object holding attachment points.
Definition: Fragment.java:61
denoptim.graph.Fragment.addAP
void addAP(int atomPositionNumber)
Adds an attachment point with a dummy APClass.
Definition: Fragment.java:343
denoptim.graph.Ring
This class represents the closure of a ring in a spanning tree.
Definition: Ring.java:40
denoptim.graph.Template.setInnerGraph
void setInnerGraph(DGraph innerGraph)
Definition: Template.java:298
denoptim.graph.Template.sameAs
boolean sameAs(Template other, StringBuilder reason)
Compares this and another template ignoring vertex IDs.
Definition: Template.java:956
denoptim.graph.Template.freezeTemplate
boolean freezeTemplate()
Promotes the contract level of this template to the most constrained one (i.e., ContractLevel#FIXED),...
Definition: Template.java:231
denoptim.graph.Template.getAttachmentPoints
ArrayList< AttachmentPoint > getAttachmentPoints()
Return the list of attachment points visible from outside the template, i.e., the so-called outer APs...
Definition: Template.java:458
denoptim.graph.Template.addRequiredAP
void addRequiredAP(Point3d pt, APClass apClass)
Adds attachment point (AP) to the list of required APs on this template.
Definition: Template.java:935
denoptim.graph.Template.getIAtomContainer
IAtomContainer getIAtomContainer()
The molecular representation, if any, is generated by this method and stored until further changes in...
Definition: Template.java:715
denoptim.graph.Template.clone
Template clone()
Returns a deep copy of this template.
Definition: Template.java:243
denoptim.graph.TemplateTest
Unit test for DENOPTIMTemplate.
Definition: TemplateTest.java:56
denoptim.graph.TemplateTest.testGetAttachmentPoints_returnsAPsWithTemplateAsOwner
void testGetAttachmentPoints_returnsAPsWithTemplateAsOwner()
Definition: TemplateTest.java:314
denoptim.graph.TemplateTest.getTestAmideTemplate
static Template getTestAmideTemplate()
Builds a template object meant for tests.
Definition: TemplateTest.java:456
denoptim.graph.TemplateTest.testAddAP_after_setInnerGraph_throwsException
void testAddAP_after_setInnerGraph_throwsException()
Definition: TemplateTest.java:431
denoptim.graph.TemplateTest.getAmideFragment
static Vertex getAmideFragment()
The coordinates hard coded in this method must not be changed because they are needed to reproduce re...
Definition: TemplateTest.java:238
denoptim.graph.TemplateTest.testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs
void testSetInnerGraph_throws_on_graph_incompatible_w_requiredAPs()
Definition: TemplateTest.java:370
denoptim.graph.TemplateTest.testSameAPClass
void testSameAPClass(Template t, DGraph innerGraph)
Definition: TemplateTest.java:399
denoptim.graph.TemplateTest.chemBuilder
static IChemObjectBuilder chemBuilder
Definition: TemplateTest.java:59
denoptim.graph.TemplateTest.testGetAttachmentPoints_returnsCorrectNumberOfAPs
void testGetAttachmentPoints_returnsCorrectNumberOfAPs()
Definition: TemplateTest.java:335
denoptim.graph.TemplateTest.testAtLeastSameNumberOfAPs
void testAtLeastSameNumberOfAPs(Template t, int expNumberOfAPs)
Definition: TemplateTest.java:415
denoptim.graph.TemplateTest.getNestedTemplate
Template getNestedTemplate()
Creating a template that contains another template with the following structure: |-------------------...
Definition: TemplateTest.java:168
denoptim.graph.TemplateTest.getCH2Fragment
static Vertex getCH2Fragment()
The coordinates hard coded in this method must not be changed because they are needed to reproduce re...
Definition: TemplateTest.java:196
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.setVertexId
void setVertexId(long vertexId2)
Definition: Vertex.java:261
denoptim.graph.Vertex.setAsRCV
void setAsRCV(boolean isRCV)
Definition: Vertex.java:254
denoptim.graph.Vertex.getAttachmentPoints
abstract List< AttachmentPoint > getAttachmentPoints()
denoptim.graph.Vertex.getProperty
Object getProperty(Object property)
Definition: Vertex.java:1136
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.io.DenoptimIO
Utility methods for input/output.
Definition: DenoptimIO.java:113
denoptim.io.DenoptimIO.readSDFFile
static ArrayList< IAtomContainer > readSDFFile(String fileName)
Reads a file containing multiple molecules (multiple SD format))
Definition: DenoptimIO.java:347
denoptim.io.DenoptimIO.writeData
static void writeData(String fileName, String data, boolean append)
Write text-like data file.
Definition: DenoptimIO.java:738
denoptim.utils.GraphUtils
Utilities for graphs.
Definition: GraphUtils.java:40
denoptim.utils.GraphUtils.getUniqueVertexIndex
static synchronized long getUniqueVertexIndex()
Unique counter for the number of graph vertices generated.
Definition: GraphUtils.java:97
denoptim.utils.MoleculeUtils
Utilities for molecule conversion.
Definition: MoleculeUtils.java:94
denoptim.utils.MoleculeUtils.countAtomsOfElement
static int countAtomsOfElement(IAtomContainer mol, String symbol)
Count atoms with the given elemental symbol.
Definition: MoleculeUtils.java:571
denoptim.graph.Vertex.BBType
The type of building block.
Definition: Vertex.java:86