/* * Copyright (C) 2016 Sereina Riniker, Paolo Tosco * * @@ All Rights Reserved @@ * This file is part of the RDKit. * The contents are covered by the terms of the BSD license * which is included in the file license.txt, found at the root * of the RDKit source tree. */ package org.RDKit; import static org.junit.Assert.*; import java.io.File; import java.io.FileReader; import java.io.BufferedReader; import org.junit.Test; public class TrajectoryTests extends GraphMolTest { @Test public void testBasicInstantiation_Snapshot() { Shared_Double_Array pos = new Shared_Double_Array(); Snapshot s = new Snapshot(pos); assertNotNull(s); } @Test public void testSnapshot() { Shared_Double_Array pos = new Shared_Double_Array(); Snapshot s = new Snapshot(pos); boolean e = false; try { s.getPoint2D(12); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); } @Test public void testTrajectory2D() { final int dim = 2; final int np = 10; final int ns = 5; Trajectory traj = new Trajectory(dim, np); assertEquals(traj.dimension(), dim); assertEquals(traj.numPoints(), np); final int posLen = np * dim; Double_Vect dv = new Double_Vect(posLen); for (int i = 0; i < posLen; ++i) dv.set(i, (double)i); for (int i = 0; i < ns; ++i) traj.addSnapshot(new Snapshot(dv, (double)i)); assertEquals(traj.size(), ns); boolean e = false; try { traj.getSnapshot(ns); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); e = false; try { traj.getSnapshot(0).getPoint2D(np); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); for (int i = 0; i < np; ++i) { assertEquals(traj.getSnapshot(0).getPoint2D(i).getX(), (double)(i * dim), 0.001); assertEquals(traj.getSnapshot(0).getPoint2D(i).getY(), (double)(i * dim + 1), 0.001); e = false; try { assertEquals(traj.getSnapshot(0).getPoint3D(i).getZ(), 0.0, 0.001); } catch (GenericRDKitException ex) { e = true; } assertEquals(false, e); } for (int i = 0; i < ns; ++i) assertEquals((double)(i), traj.getSnapshot(i).getEnergy(), 0.001); traj.removeSnapshot(0); assertEquals(ns - 1, traj.size()); for (int i = 0; i < (ns - 1); ++i) assertEquals((double)(i + 1), traj.getSnapshot(i).getEnergy(), 0.001); traj.insertSnapshot(0, new Snapshot(dv, 999.0)); assertEquals(ns, traj.size()); Snapshot copySnapshot = new Snapshot(traj.getSnapshot(0)); traj.addSnapshot(copySnapshot); assertEquals(ns + 1, traj.size()); assertEquals(999.0, traj.getSnapshot(0).getEnergy(), 0.001); assertEquals(1.0, traj.getSnapshot(1).getEnergy(), 0.001); assertEquals(999.0, traj.getSnapshot(traj.size() - 1).getEnergy(), 0.001); Trajectory traj2 = new Trajectory(traj); assertEquals(traj2.size(), traj.size()); } @Test public void testTrajectory3D() { final int dim = 3; final int np = 10; final int ns = 5; Trajectory traj = new Trajectory(dim, np); assertEquals(dim, traj.dimension()); assertEquals(np, traj.numPoints()); final int posLen = np * dim; Double_Vect dv = new Double_Vect(posLen); for (int i = 0; i < posLen; ++i) dv.set(i, (double)i); for (int i = 0; i < ns; ++i) traj.addSnapshot(new Snapshot(dv, (double)i)); assertEquals(ns, traj.size()); boolean e = false; try { traj.getSnapshot(ns); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); e = false; try { traj.getSnapshot(0).getPoint2D(np); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); for (int i = 0; i < np; ++i) { assertEquals((double)(i * dim), traj.getSnapshot(0).getPoint3D(i).getX(), 0.001); assertEquals((double)(i * dim + 1), traj.getSnapshot(0).getPoint3D(i).getY(), 0.001); assertEquals((double)(i * dim + 2), traj.getSnapshot(0).getPoint3D(i).getZ(), 0.001); if (i == 0) { e = false; try { traj.getSnapshot(0).getPoint2D(i); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); } } for (int i = 0; i < ns; ++i) assertEquals((double)(i), traj.getSnapshot(i).getEnergy(), 0.001); traj.removeSnapshot(0); assertEquals(ns - 1, traj.size()); for (int i = 0; i < (ns - 1); ++i) assertEquals((double)(i + 1), traj.getSnapshot(i).getEnergy(), 0.001); traj.insertSnapshot(0, new Snapshot(dv, 999.0)); assertEquals(ns, traj.size()); Snapshot copySnapshot = new Snapshot(traj.getSnapshot(0)); traj.addSnapshot(copySnapshot); assertEquals(ns + 1, traj.size()); assertEquals(999.0, traj.getSnapshot(0).getEnergy(), 0.001); assertEquals(1.0, traj.getSnapshot(1).getEnergy(), 0.001); assertEquals(999.0, traj.getSnapshot(traj.size() - 1).getEnergy(), 0.001); Trajectory traj2 = new Trajectory(traj); assertEquals(traj2.size(), traj.size()); } @Test public void testReadAmber() { String rdpath = System.getenv("RDBASE"); if (rdpath == null) org.junit.Assert.fail("No definition for RDBASE"); File base = new File(rdpath); File testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords_bad.trx"); String fName = testFile.getAbsolutePath(); Trajectory traj = new Trajectory(2, 0); boolean e = false; try { RDKFuncs.readAmberTrajectory(fName, traj); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); traj = new Trajectory(3, 3); e = false; try { RDKFuncs.readAmberTrajectory(fName, traj); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords_bad2.trx"); fName = testFile.getAbsolutePath(); e = false; traj = new Trajectory(3, 3); try { RDKFuncs.readAmberTrajectory(fName, traj); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords.trx"); fName = testFile.getAbsolutePath(); traj = new Trajectory(3, 3); RDKFuncs.readAmberTrajectory(fName, traj); assertEquals(traj.size(), 1); testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords2.trx"); fName = testFile.getAbsolutePath(); traj = new Trajectory(3, 3); RDKFuncs.readAmberTrajectory(fName, traj); assertEquals(traj.size(), 2); } @Test public void testReadAmberJava() { /* reimplemented the Amber trajectory reader in Java let's check we get the same data as the C++ reader (test for building a trajectory out of Snapshots from Java) */ String rdpath = System.getenv("RDBASE"); if (rdpath == null) org.junit.Assert.fail("No definition for RDBASE"); File base = new File(rdpath); File testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords2.trx"); String fName = testFile.getAbsolutePath(); Trajectory traj = new Trajectory(3, 3); long nCoords = traj.numPoints() * 3; int nSnapshots = 0; BufferedReader r = null; try { r = new BufferedReader(new FileReader(testFile)); } catch (Exception e) { org.junit.Assert.fail("Could not open " + fName); } int lineNum = 0; Double_Vect dv = new Double_Vect(); int i = 0; String line = null; try { line = r.readLine(); } catch (Exception e) { org.junit.Assert.fail("Could not read from " + fName); } while (line != null) { ++lineNum; if (lineNum > 1) { String[] tok = line.split(" +"); int j = 0; for (; (i < nCoords) && (j < tok.length); ++j) { if (tok[j].length() == 0) continue; dv.add(Double.parseDouble(tok[j])); ++i; } line = ""; if (i == nCoords) { ++nSnapshots; traj.addSnapshot(new Snapshot(dv)); dv.clear(); i = 0; for (; j < tok.length; ++j) { if (tok[j].length() > 0) line += tok[j] + " "; } } } else { line = ""; } try { String lineNew = r.readLine(); if (lineNew != null) line += lineNew; else if (line.length() == 0) line = null; } catch (Exception e) { org.junit.Assert.fail("Could not read from " + fName); } } try { r.close(); } catch (Exception e) { org.junit.Assert.fail("Could not close " + fName); } assertEquals(0, i); assertEquals(2, nSnapshots); Trajectory traj2 = new Trajectory(3, 3); RDKFuncs.readAmberTrajectory(fName, traj2); assertEquals(traj2.size(), traj.size()); assertEquals(traj2.numPoints(), traj.numPoints()); for (int snapshotNum = 0; snapshotNum < traj.size(); ++snapshotNum) { for (int pointNum = 0; pointNum < traj.numPoints(); ++pointNum) { assertEquals(traj2.getSnapshot(snapshotNum).getPoint3D(pointNum).getX(), traj.getSnapshot(snapshotNum).getPoint3D(pointNum).getX(), 0.001); assertEquals(traj2.getSnapshot(snapshotNum).getPoint3D(pointNum).getY(), traj.getSnapshot(snapshotNum).getPoint3D(pointNum).getY(), 0.001); assertEquals(traj2.getSnapshot(snapshotNum).getPoint3D(pointNum).getZ(), traj.getSnapshot(snapshotNum).getPoint3D(pointNum).getZ(), 0.001); } } } @Test public void testReadGromos() { String rdpath = System.getenv("RDBASE"); if (rdpath == null) org.junit.Assert.fail("No definition for RDBASE"); File base = new File(rdpath); File testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords_bad.trc"); String fName = testFile.getAbsolutePath(); Trajectory traj = new Trajectory(2, 0); boolean e = false; try { RDKFuncs.readGromosTrajectory(fName, traj); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); traj = new Trajectory(3, 3); e = false; try { RDKFuncs.readGromosTrajectory(fName, traj); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords_bad2.trc"); fName = testFile.getAbsolutePath(); e = false; traj = new Trajectory(3, 3); try { RDKFuncs.readGromosTrajectory(fName, traj); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords.trc"); fName = testFile.getAbsolutePath(); traj = new Trajectory(3, 3); RDKFuncs.readGromosTrajectory(fName, traj); assertEquals(traj.size(), 1); testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords2.trc"); fName = testFile.getAbsolutePath(); traj = new Trajectory(3, 3); RDKFuncs.readGromosTrajectory(fName, traj); assertEquals(traj.size(), 2); } @Test public void testAddConformersFromTrajectory() { String molBlock = "\n" + " RDKit 3D\n" + "\n" + " 71 74 0 0 0 0 0 0 0 0999 V2000\n" + " 8.2543 3.1901 -0.3005 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.4558 1.9712 0.0938 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.3934 1.0441 -0.9483 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 6.6660 -0.0533 -0.4641 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 5.1928 0.2346 -0.4609 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 4.3713 -0.9410 -0.5770 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 3.1852 -1.0034 -1.2291 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 2.2914 0.1276 -1.6316 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.9308 -0.4468 -1.9908 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.1417 -0.7821 -0.7545 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -0.1848 0.3695 0.0456 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -1.5661 0.7686 -0.0745 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -2.4768 -0.0640 0.8206 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -3.8874 0.1143 0.3941 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -4.6333 -0.9984 0.0264 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -6.0127 -0.9516 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -6.7062 0.1599 0.3963 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -8.0408 0.4828 -0.1977 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -7.7914 1.1180 -1.5591 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -8.7622 1.4403 0.7265 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -8.8409 -0.7397 -0.4395 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -8.9121 -1.6637 0.4258 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -9.7414 -0.7636 -1.5059 O 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -5.9736 1.2357 0.8565 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -4.5843 1.2252 0.8530 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.6263 1.4884 -0.3942 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 2.0541 1.0258 -0.4230 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 2.9225 -2.3317 -1.2963 N 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 3.6061 -2.9745 -0.3180 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 3.3554 -4.1536 0.3735 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 3.7653 -4.2712 1.6948 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 4.8254 -3.4613 2.0796 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 5.1978 -2.3436 1.3419 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 4.5694 -2.0799 0.1305 C 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 9.3138 3.1372 0.0031 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.8117 4.0754 0.1798 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 8.2358 3.3535 -1.4074 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 6.4027 2.2146 0.3634 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.9270 1.5444 1.0040 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 7.0677 -0.2415 0.5615 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 6.9530 -0.9105 -1.1025 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 4.9578 0.7259 0.5137 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 4.9985 0.9430 -1.3033 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 2.7171 0.7264 -2.4494 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.3994 0.2339 -2.6810 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 1.1342 -1.4171 -2.5076 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -0.7632 -1.3370 -1.0391 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.7845 -1.4394 -0.1311 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.0125 0.1989 1.0673 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -1.6672 1.8215 0.2925 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -1.8705 0.7271 -1.1337 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -2.3045 0.3159 1.8590 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -2.1980 -1.1367 0.7635 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -4.1513 -1.9468 -0.2114 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -6.6138 -1.7460 -0.4718 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -7.0727 0.4399 -2.0858 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -7.3144 2.1076 -1.4482 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -8.7609 1.1720 -2.1135 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -8.3137 2.4504 0.5729 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -8.6170 1.0817 1.7580 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -9.8244 1.4444 0.4200 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -6.4629 2.0541 1.3719 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " -4.0445 2.0563 1.3058 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.3329 1.8224 -1.3991 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 0.4920 2.3164 0.3160 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 2.2025 0.3766 0.4766 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 2.7945 1.8369 -0.3969 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 2.4404 -4.6964 0.1303 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 3.3157 -5.0055 2.3587 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 5.4272 -3.7654 2.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 5.5668 -1.5069 1.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n" + " 1 2 1 0\n" + " 2 3 1 0\n" + " 3 4 1 0\n" + " 4 5 1 0\n" + " 5 6 1 0\n" + " 6 7 1 0\n" + " 7 8 1 0\n" + " 8 9 1 0\n" + " 9 10 1 0\n" + " 10 11 1 0\n" + " 11 12 1 0\n" + " 12 13 1 0\n" + " 13 14 1 0\n" + " 14 15 2 0\n" + " 15 16 1 0\n" + " 16 17 2 0\n" + " 17 18 1 0\n" + " 18 19 1 0\n" + " 18 20 1 0\n" + " 18 21 1 0\n" + " 21 22 2 0\n" + " 21 23 1 0\n" + " 17 24 1 0\n" + " 24 25 2 0\n" + " 11 26 1 0\n" + " 26 27 1 0\n" + " 7 28 2 0\n" + " 28 29 1 0\n" + " 29 30 2 0\n" + " 30 31 1 0\n" + " 31 32 2 0\n" + " 32 33 1 0\n" + " 33 34 2 0\n" + " 34 6 1 0\n" + " 27 8 1 0\n" + " 34 29 1 0\n" + " 25 14 1 0\n" + " 1 35 1 0\n" + " 1 36 1 0\n" + " 1 37 1 0\n" + " 2 38 1 0\n" + " 2 39 1 0\n" + " 4 40 1 0\n" + " 4 41 1 0\n" + " 5 42 1 0\n" + " 5 43 1 0\n" + " 8 44 1 0\n" + " 9 45 1 0\n" + " 9 46 1 0\n" + " 10 47 1 0\n" + " 10 48 1 0\n" + " 11 49 1 0\n" + " 12 50 1 0\n" + " 12 51 1 0\n" + " 13 52 1 0\n" + " 13 53 1 0\n" + " 15 54 1 0\n" + " 16 55 1 0\n" + " 19 56 1 0\n" + " 19 57 1 0\n" + " 19 58 1 0\n" + " 20 59 1 0\n" + " 20 60 1 0\n" + " 20 61 1 0\n" + " 24 62 1 0\n" + " 25 63 1 0\n" + " 26 64 1 0\n" + " 26 65 1 0\n" + " 27 66 1 0\n" + " 27 67 1 0\n" + " 30 68 1 0\n" + " 31 69 1 0\n" + " 32 70 1 0\n" + " 33 71 1 0\n" + "M CHG 2 11 1 23 -1\n" + "M END\n"; ROMol mol = RWMol.MolFromMolBlock(molBlock, true, false); final int everySteps = 10; final int maxIts = 1000; final double gradTol = 0.01; String rdpath = System.getenv("RDBASE"); if (rdpath == null) org.junit.Assert.fail("No definition for RDBASE"); File base = new File(rdpath); File testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "bilastine_trajectory_java.sdf"); String fName = testFile.getAbsolutePath(); SDWriter w = new SDWriter(fName); ForceField field = ForceField.MMFFGetMoleculeForceField(mol); field.initialize(); SWIGTYPE_p_std__vectorT_RDKit__Snapshot_t sv = Snapshot.SnapshotVect(); int res = field.minimize(everySteps, sv, maxIts, gradTol); assertEquals(0, res); Trajectory traj = new Trajectory(3, mol.getNumAtoms(), sv); mol.removeConformer(0); traj.addConformersToMol(mol); for (int nConf = 0; nConf < mol.getNumConformers(); ++nConf) { String ss = String.format("%.4f", traj.getSnapshot(nConf).getEnergy()); mol.setProp("ENERGY", ss, false); w.write(mol, nConf); } w.close(); traj.clear(); long n1 = mol.getNumConformers(); traj.addConformersToMol(mol); long n2 = mol.getNumConformers(); assertEquals(n2, n1); // getSnapshot should raise exception after Clear() boolean e = false; try { traj.getSnapshot(0); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); } @Test public void testAddConformersFromAmberTrajectory() { ROMol mol = RWMol.MolFromSmiles("CCC"); String rdpath = System.getenv("RDBASE"); if (rdpath == null) org.junit.Assert.fail("No definition for RDBASE"); File base = new File(rdpath); File testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords.trx"); String fName = testFile.getAbsolutePath(); { Trajectory traj = new Trajectory(3, mol.getNumAtoms()); RDKFuncs.readAmberTrajectory(fName, traj); assertEquals(1, traj.size()); for (int i = 0; i < 2; ++i) { traj.addConformersToMol(mol); assertEquals(i + 1, mol.getNumConformers()); assertEquals(3, mol.getConformer(i).getNumAtoms()); assertEquals(0.1941767, mol.getConformer(i).getAtomPos(0).getX(), 0.001); assertEquals(-0.4088006, mol.getConformer(i).getAtomPos(2).getZ(), 0.001); } mol.clearConformers(); boolean e = false; try { traj.addConformersToMol(mol, 1); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); assertEquals(0, mol.getNumConformers()); } testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords2.trx"); fName = testFile.getAbsolutePath(); { Trajectory traj = new Trajectory(3, mol.getNumAtoms()); RDKFuncs.readAmberTrajectory(fName, traj); assertEquals(2, traj.size()); traj.addConformersToMol(mol); assertEquals(2, mol.getNumConformers()); mol.clearConformers(); traj.addConformersToMol(mol, 0, 0); assertEquals(1, mol.getNumConformers()); traj.addConformersToMol(mol, 1); assertEquals(2, mol.getNumConformers()); } } @Test public void testAddConformersFromGromosTrajectory() { ROMol mol = RWMol.MolFromSmiles("CCC"); String rdpath = System.getenv("RDBASE"); if (rdpath == null) org.junit.Assert.fail("No definition for RDBASE"); File base = new File(rdpath); File testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords.trc"); String fName = testFile.getAbsolutePath(); { Trajectory traj = new Trajectory(3, mol.getNumAtoms()); RDKFuncs.readGromosTrajectory(fName, traj); assertEquals(1, traj.size()); for (int i = 0; i < 2; ++i) { traj.addConformersToMol(mol); assertEquals(i + 1, mol.getNumConformers()); assertEquals(3, mol.getConformer(i).getNumAtoms()); assertEquals(1.941767, mol.getConformer(i).getAtomPos(0).getX(), 0.001); assertEquals(-4.088006, mol.getConformer(i).getAtomPos(2).getZ(), 0.001); } mol.clearConformers(); boolean e = false; try { traj.addConformersToMol(mol, 1); } catch (GenericRDKitException ex) { e = true; } assertEquals(true, e); assertEquals(0, mol.getNumConformers()); } testFile = new File(base, "Code" + File.separator + "GraphMol" + File.separator + "test_data" + File.separator + "water_coords2.trc"); fName = testFile.getAbsolutePath(); { Trajectory traj = new Trajectory(3, mol.getNumAtoms()); RDKFuncs.readGromosTrajectory(fName, traj); assertEquals(2, traj.size()); traj.addConformersToMol(mol); assertEquals(2, mol.getNumConformers()); mol.clearConformers(); traj.addConformersToMol(mol, 0, 0); assertEquals(1, mol.getNumConformers()); traj.addConformersToMol(mol, 1); assertEquals(2, mol.getNumConformers()); } } public static void main(String args[]) { org.junit.runner.JUnitCore.main("org.RDKit.TrajectoryTests"); } }