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DENOPTIM
ChemicalObjectModelTest.java
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1/*
2 * DENOPTIM
3 * Copyright (C) 2024 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.molecularmodeling;
20
21import static org.junit.jupiter.api.Assertions.assertEquals;
22import static org.junit.jupiter.api.Assertions.assertNotNull;
23import static org.junit.jupiter.api.Assertions.assertTrue;
24
25import java.util.ArrayList;
26import java.util.logging.Logger;
27
28import javax.vecmath.Point3d;
29
30import org.junit.jupiter.api.Test;
31import org.openscience.cdk.Atom;
32import org.openscience.cdk.interfaces.IAtom;
33import org.openscience.cdk.interfaces.IAtomContainer;
34import org.openscience.cdk.silent.SilentChemObjectBuilder;
35
36import denoptim.constants.DENOPTIMConstants;
37import denoptim.graph.DGraph;
38import denoptim.molecularmodeling.zmatrix.ZMatrix;
39import denoptim.molecularmodeling.zmatrix.ZMatrixAtom;
40
47public class ChemicalObjectModelTest
48{
49 private Logger logger = Logger.getLogger("TestLogger");
50
51//------------------------------------------------------------------------------
52
53 @Test
54 public void testUpdateXYZFromINT_FirstAtomAtOrigin() throws Exception
55 {
56 // Create a simple molecule with one atom
57 IAtomContainer fmol = SilentChemObjectBuilder.getInstance().newAtomContainer();
58 IAtom atom0 = new Atom("H");
59 fmol.addAtom(atom0);
60
61 ZMatrix zmat = new ZMatrix();
62 ZMatrixAtom zAtom0 = new ZMatrixAtom(
63 0, "H", "H.1", null, null, null,
64 null, null, null, null);
65 zmat.addAtom(zAtom0);
66
67 DGraph molGraph = new DGraph();
68 ChemicalObjectModel model = new ChemicalObjectModel(
69 molGraph, fmol, zmat, "test",
70 new ArrayList<>(), new ArrayList<>(), new ArrayList<>(),
71 logger);
72
73 model.updateXYZFromINT();
74
75 Point3d coord0 = fmol.getAtom(0).getPoint3d();
76 assertNotNull(coord0);
77 assertEquals(0.0, coord0.x, 1e-10, "First atom X coordinate");
78 assertEquals(0.0, coord0.y, 1e-10, "First atom Y coordinate");
79 assertEquals(0.0, coord0.z, 1e-10, "First atom Z coordinate");
80 }
81
82//------------------------------------------------------------------------------
83
84 @Test
85 public void testUpdateXYZFromINT_SecondAtomAlongZAxis() throws Exception
86 {
87 // Create a molecule with two atoms - second along Z axis
88 IAtomContainer fmol = SilentChemObjectBuilder.getInstance().newAtomContainer();
89 IAtom atom0 = new Atom("H");
90 IAtom atom1 = new Atom("H");
91 fmol.addAtom(atom0);
92 fmol.addAtom(atom1);
93
94 ZMatrix zmat = new ZMatrix();
95 ZMatrixAtom zAtom0 = new ZMatrixAtom(
96 0, "H", "H.1", null, null, null,
97 null, null, null, null);
98 ZMatrixAtom zAtom1 = new ZMatrixAtom(
99 1, "H", "H.1", zAtom0, null, null,
100 1.5, null, null, null);
101 zmat.addAtom(zAtom0);
102 zmat.addAtom(zAtom1);
103
104 DGraph molGraph = new DGraph();
105 ChemicalObjectModel model = new ChemicalObjectModel(
106 molGraph, fmol, zmat, "test",
107 new ArrayList<>(), new ArrayList<>(), new ArrayList<>(),
108 logger);
109
110 model.updateXYZFromINT();
111
112 Point3d coord0 = fmol.getAtom(0).getPoint3d();
113 Point3d coord1 = fmol.getAtom(1).getPoint3d();
114
115 assertEquals(0.0, coord0.x, 1e-10, "First atom X");
116 assertEquals(0.0, coord0.y, 1e-10, "First atom Y");
117 assertEquals(0.0, coord0.z, 1e-10, "First atom Z");
118
119 assertEquals(0.0, coord1.x, 1e-10, "Second atom X");
120 assertEquals(0.0, coord1.y, 1e-10, "Second atom Y");
121 assertEquals(1.5, coord1.z, 1e-10, "Second atom Z (bond length)");
122 }
123
124//------------------------------------------------------------------------------
125
126 @Test
127 public void testUpdateXYZFromINT_ThirdAtomWithAngle() throws Exception
128 {
129 // Create a molecule with three atoms - third with bond and angle
130 IAtomContainer fmol = SilentChemObjectBuilder.getInstance().newAtomContainer();
131 IAtom atom0 = new Atom("H");
132 IAtom atom1 = new Atom("O");
133 IAtom atom2 = new Atom("H");
134 fmol.addAtom(atom0);
135 fmol.addAtom(atom1);
136 fmol.addAtom(atom2);
137
138 ZMatrix zmat = new ZMatrix();
139 ZMatrixAtom zAtom0 = new ZMatrixAtom(
140 0, "H", "H.1", null, null, null,
141 null, null, null, null);
142 ZMatrixAtom zAtom1 = new ZMatrixAtom(
143 1, "O", "O.2", zAtom0, null, null,
144 1.0, null, null, null);
145 ZMatrixAtom zAtom2 = new ZMatrixAtom(
146 2, "H", "H.1", zAtom1, zAtom0, null,
147 1.0, 109.5, null, null);
148 zmat.addAtom(zAtom0);
149 zmat.addAtom(zAtom1);
150 zmat.addAtom(zAtom2);
151
152 DGraph molGraph = new DGraph();
153 ChemicalObjectModel model = new ChemicalObjectModel(
154 molGraph, fmol, zmat, "test",
155 new ArrayList<>(), new ArrayList<>(), new ArrayList<>(),
156 logger);
157
158 model.updateXYZFromINT();
159
160 Point3d coord0 = fmol.getAtom(0).getPoint3d();
161 Point3d coord1 = fmol.getAtom(1).getPoint3d();
162 Point3d coord2 = fmol.getAtom(2).getPoint3d();
163
164 // First atom at origin
165 assertEquals(0.0, coord0.x, 1e-10);
166 assertEquals(0.0, coord0.y, 1e-10);
167 assertEquals(0.0, coord0.z, 1e-10);
168
169 // Second atom along Z axis
170 assertEquals(0.0, coord1.x, 1e-10);
171 assertEquals(0.0, coord1.y, 1e-10);
172 assertEquals(1.0, coord1.z, 1e-10);
173
174 // Third atom should have non-zero X coordinate due to angle
175 assertTrue(Math.abs(coord2.x) > 1e-6, "Third atom should have X != 0");
176 assertEquals(0.0, coord2.y, 1e-10, "Third atom Y should be 0");
177 assertTrue(coord2.z > 0, "Third atom Z should be positive");
178 }
179
180//------------------------------------------------------------------------------
181
182 @Test
183 public void testUpdateXYZFromINT_FourthAtomWithDihedral() throws Exception
184 {
185 // Create a molecule with four atoms - fourth with dihedral (chirality = 0)
186 IAtomContainer fmol = SilentChemObjectBuilder.getInstance().newAtomContainer();
187 IAtom atom0 = new Atom("C");
188 IAtom atom1 = new Atom("C");
189 IAtom atom2 = new Atom("H");
190 IAtom atom3 = new Atom("H");
191 fmol.addAtom(atom0);
192 fmol.addAtom(atom1);
193 fmol.addAtom(atom2);
194 fmol.addAtom(atom3);
195
196 ZMatrix zmat = new ZMatrix();
197 ZMatrixAtom zAtom0 = new ZMatrixAtom(
198 0, "C", "C.3", null, null, null,
199 null, null, null, null);
200 ZMatrixAtom zAtom1 = new ZMatrixAtom(
201 1, "C", "C.3", zAtom0, null, null,
202 1.5, null, null, null);
203 ZMatrixAtom zAtom2 = new ZMatrixAtom(
204 2, "H", "H.1", zAtom1, zAtom0, null,
205 1.1, 109.5, null, null);
206 ZMatrixAtom zAtom3 = new ZMatrixAtom(
207 3, "H", "H.1", zAtom2, zAtom1, zAtom0,
208 1.1, 109.5, 60.0, 0);
209 zmat.addAtom(zAtom0);
210 zmat.addAtom(zAtom1);
211 zmat.addAtom(zAtom2);
212 zmat.addAtom(zAtom3);
213
214 DGraph molGraph = new DGraph();
215 ChemicalObjectModel model = new ChemicalObjectModel(
216 molGraph, fmol, zmat, "test",
217 new ArrayList<>(), new ArrayList<>(), new ArrayList<>(),
218 logger);
219
220 model.updateXYZFromINT();
221
222 // Verify all atoms have coordinates
223 for (int i = 0; i < 4; i++)
224 {
225 Point3d coord = fmol.getAtom(i).getPoint3d();
226 assertNotNull(coord, "Atom " + i + " should have coordinates");
227 }
228
229 // Fourth atom should have all three coordinates non-zero
230 Point3d coord3 = fmol.getAtom(3).getPoint3d();
231 assertTrue(Math.abs(coord3.x) > 1e-6 || Math.abs(coord3.y) > 1e-6
232 || Math.abs(coord3.z) > 1e-6,
233 "Fourth atom should have non-zero coordinates");
234 }
235
236//------------------------------------------------------------------------------
237
238 @Test
239 public void testUpdateXYZFromINT_ChiralityOne() throws Exception
240 {
241 // Test with chirality = 1
242 IAtomContainer fmol = SilentChemObjectBuilder.getInstance().newAtomContainer();
243 IAtom atom0 = new Atom("C");
244 IAtom atom1 = new Atom("C");
245 IAtom atom2 = new Atom("H");
246 IAtom atom3 = new Atom("H");
247 fmol.addAtom(atom0);
248 fmol.addAtom(atom1);
249 fmol.addAtom(atom2);
250 fmol.addAtom(atom3);
251
252 ZMatrix zmat = new ZMatrix();
253 ZMatrixAtom zAtom0 = new ZMatrixAtom(
254 0, "C", "C.3", null, null, null,
255 null, null, null, null);
256 ZMatrixAtom zAtom1 = new ZMatrixAtom(
257 1, "C", "C.3", zAtom0, null, null,
258 1.5, null, null, null);
259 ZMatrixAtom zAtom2 = new ZMatrixAtom(
260 2, "H", "H.1", zAtom1, zAtom0, null,
261 1.1, 109.5, null, null);
262 ZMatrixAtom zAtom3 = new ZMatrixAtom(
263 3, "H", "H.1", zAtom2, zAtom1, zAtom0,
264 1.1, 109.5, 60.0, 1); // chirality = 1
265 zmat.addAtom(zAtom0);
266 zmat.addAtom(zAtom1);
267 zmat.addAtom(zAtom2);
268 zmat.addAtom(zAtom3);
269
270 DGraph molGraph = new DGraph();
271 ChemicalObjectModel model = new ChemicalObjectModel(
272 molGraph, fmol, zmat, "test",
273 new ArrayList<>(), new ArrayList<>(), new ArrayList<>(),
274 logger);
275
276 model.updateXYZFromINT();
277
278 // Verify all atoms have coordinates
279 Point3d coord3 = fmol.getAtom(3).getPoint3d();
280 assertNotNull(coord3, "Atom 3 should have coordinates");
281 assertTrue(Math.abs(coord3.x) > 1e-6 || Math.abs(coord3.y) > 1e-6
282 || Math.abs(coord3.z) > 1e-6,
283 "Atom 3 should have non-zero coordinates");
284 }
285
286//------------------------------------------------------------------------------
287
288 @Test
289 public void testUpdateXYZFromINT_ChiralityMinusOne() throws Exception
290 {
291 // Test with chirality = -1
292 IAtomContainer fmol = SilentChemObjectBuilder.getInstance().newAtomContainer();
293 IAtom atom0 = new Atom("C");
294 IAtom atom1 = new Atom("C");
295 IAtom atom2 = new Atom("H");
296 IAtom atom3 = new Atom("H");
297 fmol.addAtom(atom0);
298 fmol.addAtom(atom1);
299 fmol.addAtom(atom2);
300 fmol.addAtom(atom3);
301
302 ZMatrix zmat = new ZMatrix();
303 ZMatrixAtom zAtom0 = new ZMatrixAtom(
304 0, "C", "C.3", null, null, null,
305 null, null, null, null);
306 ZMatrixAtom zAtom1 = new ZMatrixAtom(
307 1, "C", "C.3", zAtom0, null, null,
308 1.5, null, null, null);
309 ZMatrixAtom zAtom2 = new ZMatrixAtom(
310 2, "H", "H.1", zAtom1, zAtom0, null,
311 1.1, 109.5, null, null);
312 ZMatrixAtom zAtom3 = new ZMatrixAtom(
313 3, "H", "H.1", zAtom2, zAtom1, zAtom0,
314 1.1, 109.5, 60.0, -1); // chirality = -1
315 zmat.addAtom(zAtom0);
316 zmat.addAtom(zAtom1);
317 zmat.addAtom(zAtom2);
318 zmat.addAtom(zAtom3);
319
320 DGraph molGraph = new DGraph();
321 ChemicalObjectModel model = new ChemicalObjectModel(
322 molGraph, fmol, zmat, "test",
323 new ArrayList<>(), new ArrayList<>(), new ArrayList<>(),
324 logger);
325
326 model.updateXYZFromINT();
327
328 // Verify all atoms have coordinates
329 Point3d coord3 = fmol.getAtom(3).getPoint3d();
330 assertNotNull(coord3, "Atom 3 should have coordinates");
331 }
332
333//------------------------------------------------------------------------------
334
335 @Test
336 public void testUpdateXYZFromINT() throws Exception
337 {
338 IAtomContainer fmol = SilentChemObjectBuilder.getInstance().newAtomContainer();
339 IAtom atom0 = new Atom("C");
340 IAtom atom1 = new Atom("C");
341 IAtom atom2 = new Atom("H");
342 IAtom atom3 = new Atom("H");
343 IAtom atom4 = new Atom("P");
344 IAtom atom5 = new Atom("O");
345 IAtom atom6 = new Atom("Cl");
346 IAtom atom7 = new Atom("H");
347 fmol.addAtom(atom0);
348 fmol.addAtom(atom1);
349 fmol.addAtom(atom2);
350 fmol.addAtom(atom3);
351 fmol.addAtom(atom4);
352 fmol.addAtom(atom5);
353 fmol.addAtom(atom6);
354 fmol.addAtom(atom7);
355
356 ZMatrix zmat = new ZMatrix();
357 ZMatrixAtom zAtom0 = new ZMatrixAtom(
358 0, "C", "C.3", null, null, null,
359 null, null, null, null);
360 ZMatrixAtom zAtom1 = new ZMatrixAtom(
361 1, "C", "C.3", zAtom0, null, null,
362 1.0, null, null, null);
363 ZMatrixAtom zAtom2 = new ZMatrixAtom(
364 2, "H", "H.1", zAtom1, zAtom0, null,
365 1.0, 90.0, null, null);
366 ZMatrixAtom zAtom3 = new ZMatrixAtom(
367 3, "H", "H.1", zAtom2, zAtom1, zAtom0,
368 1.0, 90.0, 90.0, 0);
369 ZMatrixAtom zAtom4 = new ZMatrixAtom(
370 4, "P", "P.3", zAtom3, zAtom2, zAtom1,
371 1.0, 90.0, -90.0, 0);
372 ZMatrixAtom zAtom5 = new ZMatrixAtom(
373 5, "O", "O.3", zAtom4, zAtom3, zAtom2,
374 1.0, 90.0, 180.0, 0);
375 ZMatrixAtom zAtom6 = new ZMatrixAtom(
376 6, "Cl", "Cl.1", zAtom4, zAtom3, zAtom5,
377 1.0, 90.0, 90.0, 1);
378 ZMatrixAtom zAtom7 = new ZMatrixAtom(
379 7, "H", "H.1", zAtom4, zAtom3, zAtom5,
380 1.0, 90.0, 90.0, -1);
381
382 zmat.addAtom(zAtom0);
383 zmat.addAtom(zAtom1);
384 zmat.addAtom(zAtom2);
385 zmat.addAtom(zAtom3);
386 zmat.addAtom(zAtom4);
387 zmat.addAtom(zAtom5);
388 zmat.addAtom(zAtom6);
389 zmat.addAtom(zAtom7);
390
391 DGraph molGraph = new DGraph();
392 ChemicalObjectModel model = new ChemicalObjectModel(
393 molGraph, fmol, zmat, "test",
394 new ArrayList<>(), new ArrayList<>(), new ArrayList<>(),
395 logger);
396
397 model.updateXYZFromINT();
398
399 Point3d coord0 = fmol.getAtom(0).getPoint3d();
400 Point3d coord1 = fmol.getAtom(1).getPoint3d();
401 Point3d coord2 = fmol.getAtom(2).getPoint3d();
402 Point3d coord3 = fmol.getAtom(3).getPoint3d();
403 Point3d coord4 = fmol.getAtom(4).getPoint3d();
404 Point3d coord5 = fmol.getAtom(5).getPoint3d();
405 Point3d coord6 = fmol.getAtom(6).getPoint3d();
406 Point3d coord7 = fmol.getAtom(7).getPoint3d();
407
408 assertEquals(0.0, coord0.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
409 assertEquals(0.0, coord0.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
410 assertEquals(0.0, coord0.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
411
412 assertEquals(0.0, coord1.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
413 assertEquals(0.0, coord1.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
414 assertEquals(1.0, coord1.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
415
416 assertEquals(1.0, coord2.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
417 assertEquals(0.0, coord2.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
418 assertEquals(1.0, coord2.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
419
420 assertEquals(1.0, coord3.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
421 assertEquals(1.0, coord3.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
422 assertEquals(1.0, coord3.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
423
424 assertEquals(1.0, coord4.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
425 assertEquals(1.0, coord4.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
426 assertEquals(0.0, coord4.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
427
428 assertEquals(1.0, coord5.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
429 assertEquals(2.0, coord5.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
430 assertEquals(0.0, coord5.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
431
432 assertEquals(0.0, coord6.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
433 assertEquals(1.0, coord6.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
434 assertEquals(0.0, coord6.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
435
436 assertEquals(2.0, coord7.x, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
437 assertEquals(1.0, coord7.y, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
438 assertEquals(0.0, coord7.z, DENOPTIMConstants.FLOATCOMPARISONTOLERANCE);
439 }
440
441//------------------------------------------------------------------------------
442
443}
444
denoptim.constants.DENOPTIMConstants
General set of constants used in DENOPTIM.
Definition: DENOPTIMConstants.java:49
denoptim.constants.DENOPTIMConstants.FLOATCOMPARISONTOLERANCE
static final double FLOATCOMPARISONTOLERANCE
Smallest difference for comparison of double and float numbers.
Definition: DENOPTIMConstants.java:406
denoptim.graph.DGraph
Container for the list of vertices and the edges that connect them.
Definition: DGraph.java:102
denoptim.molecularmodeling.ChemicalObjectModel
Collector of molecular information, related to a single chemical object, that is deployed within the ...
Definition: ChemicalObjectModel.java:61
denoptim.molecularmodeling.ChemicalObjectModel.updateXYZFromINT
void updateXYZFromINT()
Converts currently loaded internal coordinates into Cartesian overwriting the current XYZ.
Definition: ChemicalObjectModel.java:316
denoptim.molecularmodeling.zmatrix.ZMatrixAtom
Representation of an atom in the ZMatrix.
Definition: ZMatrixAtom.java:9
denoptim.molecularmodeling.zmatrix.ZMatrix
Representation of an atom container's geometry with internal coordinates.
Definition: ZMatrix.java:27
denoptim.molecularmodeling.zmatrix.ZMatrix.addAtom
void addAtom(ZMatrixAtom atom)
Add an atom to the ZMatrix.
Definition: ZMatrix.java:61