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353 lines
12 KiB
Java
353 lines
12 KiB
Java
/*
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* $Id: DistanceGeometryTests.java 131 2011-01-20 22:01:29Z ebakke $
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*
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* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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* All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are
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* met:
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*
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* * Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* * Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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* * Neither the name of Novartis Institutes for BioMedical Research Inc.
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* nor the names of its contributors may be used to endorse or promote
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* products derived from this software without specific prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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package org.RDKit;
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import static org.junit.Assert.*;
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import java.io.File;
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import org.junit.*;
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public class DistanceGeometryTests extends GraphMolTest {
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@Before
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public void setUp() {
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}
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@Test
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public void testBasicEmbedding() {
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String[] smiString = new String[] {
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"CC1=C(C(C)=CC=C2)C2=CC=C1", "c1ccccc1C", "C/C=C/CC",
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"C/12=C(\\CSC2)Nc3cc(n[n]3C1=O)c4ccccc4", "C1CCCCS1(=O)(=O)", "c1ccccc1",
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"C1CCCC1", "C1CCCCC1",
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"C1CC1(C)C", "C12(C)CC1CC2"};
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String fname = new File(getRdBase(),
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"Code/GraphMol/DistGeomHelpers/test_data/initCoords.sdf").getPath();
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SDMolSupplier sdsup = new SDMolSupplier(fname);
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for (String smi : smiString) {
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RWMol m = RWMol.MolFromSmiles(smi, 0, true);
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DistanceGeom.EmbedMolecule(m, 10, 1,true,false,2,true,1,null,1e-2);
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ROMol m2 = sdsup.next();
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if(m2 != null){
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int nat = (int) m.getNumAtoms();
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Conformer conf1 = m.getConformer(0);
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Conformer conf2 = m2.getConformer(0);
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for (int i = 0; i < nat; i++) {
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Point3D pt1i = conf1.getAtomPos(i);
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Point3D pt2i = conf2.getAtomPos(i);
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for(int j=i+1;j<nat;j++){
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Point3D pt1j = conf1.getAtomPos(j);
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Point3D pt2j = conf2.getAtomPos(j);
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double d1 = pt1j.minus(pt1i).length();
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double d2 = pt2j.minus(pt2i).length();
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if(m.getBondBetweenAtoms(i,j) != null)
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assertEquals(d1, d2, 0.06);
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else
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assertEquals(d1, d2, 0.12);
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}
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}
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}
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}
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}
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private void computeDistMat(Point3D_Vect origCoords, DoubleSymmMatrix distMat) {
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int N = (int) origCoords.size();
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assertEquals(N, distMat.numRows());
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int i, j;
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Point3D pti, ptj;
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double d;
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for (i = 1; i < N; i++) {
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pti = origCoords.get(i);
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for (j = 0; j < i; j++) {
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ptj = origCoords.get(j);
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ptj = ptj.minus(pti);
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d = ptj.length();
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distMat.setVal(i,j, d);
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}
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}
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}
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private void computeMolDmat(ROMol mol, DoubleSymmMatrix distMat) {
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Point3D_Vect origCoords = new Point3D_Vect();
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int nat = (int) mol.getNumAtoms();
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Conformer conf = mol.getConformer(0);
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for (int i = 0; i < nat; i++) {
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origCoords.add(conf.getAtomPos(i));
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}
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computeDistMat(origCoords, distMat);
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}
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@Test
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public void testInRingDistances() {
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String smi = "Cc1c(C=CC(C)N2)c2[nH]n1";
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ROMol mol = RWMol.MolFromSmiles(smi, 0, true);
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int cid;
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long nat = mol.getNumAtoms();
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BoundsMatrix bm = new BoundsMatrix(nat);
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RDKFuncs.initBoundsMat(bm, 0.0, 1000.0);
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DistanceGeom.SetTopolBounds(mol, bm);
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cid = DistanceGeom.EmbedMolecule(mol, 10, 1);
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assertTrue(cid>-1);
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DoubleSymmMatrix dmat = new DoubleSymmMatrix(nat, 0.0);
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computeMolDmat(mol, dmat);
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assertTrue((bm.getUpperBound(0,9) - bm.getLowerBound(0,9)) < 0.13);
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assertTrue((bm.getUpperBound(0,9) - dmat.getVal(0,9) > -0.1 )
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&& (bm.getLowerBound(0,9) - dmat.getVal(0,9) < 0.10));
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assertTrue((bm.getUpperBound(10,7) - bm.getLowerBound(10,7)) < 0.13);
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assertTrue((bm.getUpperBound(10,7) - dmat.getVal(10,7) > -0.1 )
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&& (bm.getLowerBound(10,7) - dmat.getVal(10,7) < 0.10 ));
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assertTrue((bm.getUpperBound(2,5) - bm.getLowerBound(2,5)) < 0.20);
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assertTrue((bm.getUpperBound(2,5) - dmat.getVal(2,5) > -0.1 )
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&& (bm.getLowerBound(2,5) - dmat.getVal(2,5) < 0.10 ));
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assertTrue((bm.getUpperBound(8,4) - bm.getLowerBound(8,4)) > 1.);
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assertTrue((bm.getUpperBound(8,4) - bm.getLowerBound(8,4)) < 1.2);
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assertTrue((bm.getUpperBound(8,4) - dmat.getVal(8,4) > -0.1 )
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&& (bm.getLowerBound(8,4) - dmat.getVal(8,4) < 0.10));
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assertTrue((bm.getUpperBound(8,6) - bm.getLowerBound(8,6)) > 1.0);
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assertTrue((bm.getUpperBound(8,6) - bm.getLowerBound(8,6)) < 1.2);
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assertTrue((bm.getUpperBound(8,6) - dmat.getVal(8,6) > -0.1)
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&& (bm.getLowerBound(8,6) - dmat.getVal(8,6) < 0.10 ));
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}
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@Test
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public void testChainOfSingles_1() {
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// chain of singles
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String smi = "CCCC";
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ROMol mol = RWMol.MolFromSmiles(smi, 0, true);
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long nat = mol.getNumAtoms();
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BoundsMatrix bm = new BoundsMatrix(nat);
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RDKFuncs.initBoundsMat(bm, 0.0, 1000.0);
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DistanceGeom.SetTopolBounds(mol, bm);
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int cid = DistanceGeom.EmbedMolecule(mol, 10, 1);
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assertTrue(cid>-1);
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DoubleSymmMatrix dmat = new DoubleSymmMatrix(nat, 0.0);
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computeMolDmat(mol, dmat);
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assertTrue( (bm.getUpperBound(0,3) - bm.getLowerBound(0,3)) > 1.0);
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assertTrue( (bm.getUpperBound(0,3) - bm.getLowerBound(0,3)) < 1.3);
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assertTrue( (bm.getUpperBound(0,3) - dmat.getVal(0,3) > -0.1)
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&& (bm.getLowerBound(0,3) - dmat.getVal(0,3) < 0.10 ));
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}
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@Test
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public void testCompareEmbeddingToCombiCoords () {
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String fname = new File(getRdBase(),
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"Code/GraphMol/DistGeomHelpers/test_data/combi_coords.sdf").getPath();
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SDMolSupplier sdsup = new SDMolSupplier(fname);
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while (!sdsup.atEnd()) {
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ROMol mol = sdsup.next();
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Point3D_Vect origCoords = new Point3D_Vect();
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long nat = mol.getNumAtoms();
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Conformer conf = mol.getConformer(0);
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for (int i = 0; i < nat; i++) {
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origCoords.add(conf.getAtomPos(i));
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}
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DoubleSymmMatrix distMat = new DoubleSymmMatrix(nat, 0.0);
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computeDistMat(origCoords, distMat);
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assertTrue(DistanceGeom.ComputeInitialCoords(distMat, origCoords));
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DoubleSymmMatrix distMatNew = new DoubleSymmMatrix(nat, 0.0);
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computeDistMat(origCoords, distMatNew);
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for (int i = 1; i < nat; i++) {
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for (int j = 0; j < i; j++) {
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assertEquals(distMat.getVal(i,j), distMatNew.getVal(i,j), 0.01);
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}
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}
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}
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}
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@Test
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public void testIssue215 () {
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ROMol m = RWMol.MolFromSmiles("C=C1C2CC1C2");
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assertNotNull(m);
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BoundsMatrix bm = new BoundsMatrix(m.getNumAtoms());
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assertNotNull(bm);
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RDKFuncs.initBoundsMat(bm,0.0,1000.0);
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DistanceGeom.SetTopolBounds(m, bm);
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// this was the specific problem:
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assertTrue(bm.getUpperBound(0,4)<100.0);
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assertTrue(RDKFuncs.triangleSmoothBounds(bm));
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}
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@Test
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public void test15Dists() {
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ROMol m = RWMol.MolFromSmiles("c1ccccc1C");
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int nat = (int) m.getNumAtoms();
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BoundsMatrix mat = new BoundsMatrix(nat);
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RDKFuncs.initBoundsMat(mat);
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DistanceGeom.SetTopolBounds(m, mat);
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assertEquals(mat.getUpperBound(2,6), 4.32, 0.01);
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assertEquals(mat.getLowerBound(2,6), 4.16, 0.01);
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m = RWMol.MolFromSmiles("CC1=C(C(C)=CC=C2)C2=CC=C1");
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nat = (int) m.getNumAtoms();
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mat = new BoundsMatrix(nat);
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RDKFuncs.initBoundsMat(mat);
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DistanceGeom.SetTopolBounds(m, mat);
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assertEquals(mat.getLowerBound(0,4), 2.31, 0.01);
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assertEquals(mat.getUpperBound(0,4), 2.47, 0.01);
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assertEquals(mat.getLowerBound(4,11), 4.11, 0.01);
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assertEquals(mat.getUpperBound(4,11), 4.27, 0.01) ;
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m = RWMol.MolFromSmiles("C/C=C/C=C/C", 0, true);
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nat = (int) m.getNumAtoms();
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mat = new BoundsMatrix(nat);
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RDKFuncs.initBoundsMat(mat);
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DistanceGeom.SetTopolBounds(m, mat);
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assertEquals(mat.getLowerBound(0,4), 4.1874, 0.01);
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assertEquals(mat.getUpperBound(0,4), 4.924, 0.01);
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assertEquals(mat.getLowerBound(1,5), 4.1874, 0.01);
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assertEquals(mat.getUpperBound(1,5), 4.924, 0.01) ;
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}
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@Test
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public void testMultipleConfs() {
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String smi = "CC(C)(C)c(cc1)ccc1c(cc23)n[n]3C(=O)/C(=C\\N2)C(=O)OCC";
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ROMol m = RWMol.MolFromSmiles(smi, 0, true);
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Int_Vect cids = DistanceGeom.EmbedMultipleConfs(m, 10, 30, 100, true, false,-1);
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SDWriter writer = new SDWriter("junk.sdf");
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double energy;
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for (int i = 0; i < cids.size(); i++ ) {
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writer.write(m, cids.get(i));
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ForceField ff = RDKFuncs.constructForceField(m, 10, cids.get(i));
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ff.initialize();
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energy = ff.calcEnergy();
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assertTrue(energy>100.0);
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assertTrue(energy<300.0);
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}
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}
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@Test
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public void testConstrainedEmbedding() {
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String fname = new File(getRdBase(),
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"Code/GraphMol/DistGeomHelpers/test_data/constrain1.sdf").getPath();
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SDMolSupplier sdsup = new SDMolSupplier(fname);
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ROMol ref=sdsup.next();
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ROMol test = new ROMol(ref);
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Int_Point3D_Map coords = new Int_Point3D_Map();
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coords.set(0, ref.getConformer().getAtomPos(0));
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coords.set(1, ref.getConformer().getAtomPos(1));
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coords.set(2, ref.getConformer().getAtomPos(2));
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coords.set(3, ref.getConformer().getAtomPos(3));
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coords.set(4, ref.getConformer().getAtomPos(4));
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int cid = DistanceGeom.EmbedMolecule(test, 30,23,true,false,2.,true,1, coords);
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assertTrue(cid>-1);
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Match_Vect alignMap = new Match_Vect();
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alignMap.add(new Int_Pair(0, 0));
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alignMap.add(new Int_Pair(1, 1));
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alignMap.add(new Int_Pair(2, 2));
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alignMap.add(new Int_Pair(3, 3));
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alignMap.add(new Int_Pair(4, 4));
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double ssd = test.alignMol(ref,-1,-1,alignMap);
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assertTrue(ssd<0.1);
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test = sdsup.next();
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coords.clear();
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coords.set(4, ref.getConformer().getAtomPos(0));
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coords.set(5, ref.getConformer().getAtomPos(1));
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coords.set(6, ref.getConformer().getAtomPos(2));
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coords.set(7, ref.getConformer().getAtomPos(3));
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coords.set(8, ref.getConformer().getAtomPos(4));
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cid = DistanceGeom.EmbedMolecule(test, 30,23,true,false,2.,true,1,coords);
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assertTrue(cid>-1);
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alignMap.clear();
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alignMap.add(new Int_Pair(4,0));
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alignMap.add(new Int_Pair(5,1));
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alignMap.add(new Int_Pair(6,2));
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alignMap.add(new Int_Pair(7,3));
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alignMap.add(new Int_Pair(8,4));
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ssd = test.alignMol(ref,-1,-1,alignMap);
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assertTrue(ssd < 0.1);
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}
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@Test
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public void testIssue2835784() {
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String smi="C1C=C1";
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RWMol m = RWMol.MolFromSmiles(smi);
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int cid = DistanceGeom.EmbedMolecule(m);
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assertTrue(cid >= 0);
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Int_Vect cids=DistanceGeom.EmbedMultipleConfs(m, 10);
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assertEquals(cids.size(), 10);
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// Make sure there are no id values of -1
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for (int i = 0; i < cids.size(); i++)
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assertFalse("No id of -1 expected", -1 == cids.get(i));
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}
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// from testDistGeom.py
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@Test
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public void test7ConstrainedEmbedding() {
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File ofile = new File(getRdBase(),
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"Code/GraphMol/DistGeomHelpers/test_data/constrain1.sdf");
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SDMolSupplier suppl = new SDMolSupplier(ofile.getPath());
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ROMol ref = suppl.next();
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ROMol probe = new ROMol(ref);
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Int_Point3D_Map cmap = new Int_Point3D_Map();
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for (int i = 0; i < 5; i++)
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cmap.set(i, ref.getConformer().getAtomPos(i));
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int ci = DistanceGeom.EmbedMolecule(probe,
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0, 23, true, false, 2.0, false, 1, cmap);
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assertTrue(ci>-1);
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Match_Vect algMap = new Match_Vect();
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for (int i = 0; i < 5; i++)
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algMap.add(new Int_Pair(i, i));
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double ssd = probe.alignMol(ref, -1, -1, algMap);
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assertTrue(ssd<0.1);
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}
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public static void main(String args[]) {
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org.junit.runner.JUnitCore.main("org.RDKit.DistanceGeometryTests");
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}
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}
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