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930c7d6345
* Query atom information in swig * Atom query swig wrapping working * SWIG wrapper for queries * Add match to QueryAtom and QueryBond * CShart test * Added Java test * Replace var with type for Java test * Apply suggestions from code review Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com> * Update Code/JavaWrappers/Queries.i Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com> * Apply suggestions from code review Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com> * Get SWIG build working again * Remove trailing whitespace from Queries.i * Update Queries.i to use shared_ptr * small simplification * remove boost::make_iterator from ROMol.i * further simplification --------- Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com> Co-authored-by: ptosco <paolo.tosco@novartis.com>
269 lines
10 KiB
Java
269 lines
10 KiB
Java
// Copyright (C) 2020 Gareth Jones, Glysade LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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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.util.ArrayList;
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import java.util.List;
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import org.junit.*;
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public class QueryAtomTest extends GraphMolTest {
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@Test
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public void testChemdrawBlock() {
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// smiles c1[nH]ccc1
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// Chemdraw will convert explicit hydrogens in aromatic compounds to query hydrogen count
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String block = String.join("\n",
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"ChemDraw05012418152D",
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"",
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"0 0 0 0 0 0 V3000",
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"M V30 BEGIN CTAB",
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"M V30 COUNTS 5 5 0 0 0",
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"M V30 BEGIN ATOM",
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"M V30 1 C - 0.652854 - 0.050688 0.000000 0",
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"M V30 2 C - 0.240354 0.663783 0.000000 0",
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"M V30 3 C 0.566618 0.492256 0.000000 0",
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"M V30 4 C 0.652854 - 0.328225 0.000000 0",
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"M V30 5 N - 0.100821 - 0.663783 0.000000 0 HCOUNT = 1",
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"M V30 END ATOM",
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"M V30 BEGIN BOND",
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"M V30 1 4 1 2",
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"M V30 2 4 2 3",
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"M V30 3 4 3 4",
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"M V30 4 4 4 5",
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"M V30 5 4 1 5",
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"M V30 END BOND",
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"M V30 END CTAB",
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"M END",
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"");
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RWMol mol = RWMol.MolFromMolBlock(block, false);
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assertNotNull(mol);
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assertEquals(5, mol.getNumAtoms());
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Atom queryAtom = mol.getAtomWithIdx(4);
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assertTrue(queryAtom.hasQuery());
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String smarts = queryAtom.AtomGetSmarts();
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String expected = "[#7&h{1-}]";
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assertEquals(expected, smarts);
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String description = queryAtom.describeQuery();
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expected = "AtomAnd\n AtomAtomicNum 7 = val\n less_AtomImplicitHCount 1 <= \n";
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assertEquals(expected, description);
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String molSmiles = mol.MolToSmiles();
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Atom atom = new Atom(7);
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atom.setNumExplicitHs(1);
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mol.replaceAtom(4, atom);
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mol.clearComputedProps(true);
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mol.sanitizeMol();
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atom = mol.getAtomWithIdx(4);
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assertEquals(7, atom.getAtomicNum());
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assertEquals(1, atom.getNumExplicitHs());
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molSmiles = mol.MolToSmiles();
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assertEquals("c1cc[nH]c1", molSmiles);
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}
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@Test
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public void testReplaceQuerySimple() {
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RWMol query = RWMol.MolFromSmiles("c1[nH]ccc1");
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Atom nitrogen = query.getAtomWithIdx(2);
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long imp = nitrogen.getNumImplicitHs();
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assertEquals(1, imp);
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Atom queryAtom = RDKFuncs.replaceAtomWithQueryAtom(query, nitrogen);
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queryAtom.ExpandQuery(RDKFuncs.ExplicitDegreeEqualsQueryAtom(3));
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RWMol mol1 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
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assertTrue(mol1.hasSubstructMatch(query));
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RWMol mol2 = RWMol.MolFromSmiles("c1[nH]ccc1");
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assertFalse(mol2.hasSubstructMatch(query));
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}
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@Test
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public void testExpandQuerySimple() {
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RWMol query = RWMol.MolFromSmarts("c1nccc1");
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RWMol mol1 = RWMol.MolFromSmiles("c1[nH]ccc1");
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assertTrue(mol1.hasSubstructMatch(query));
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Atom atom = query.getAtomWithIdx(0);
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assertTrue(atom.hasQuery());
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QueryAtom queryAtom = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
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atom.ExpandQuery(queryAtom, CompositeQueryType.COMPOSITE_AND);
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assertFalse(mol1.hasSubstructMatch(query));
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RWMol mol2 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
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assertTrue(mol2.hasSubstructMatch(query));
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}
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// adapted from Python tests
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private int[] GetAtomIdxsMatchingQuery(ROMol mol, QueryAtom qa) {
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List<Integer> indices = new ArrayList<Integer>();
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for (int i =0; i< mol.getNumAtoms(); i++) {
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Atom atom = mol.getAtomWithIdx(i);
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if (qa.MatchAtom(atom)) {
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indices.add(i);
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}
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}
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int[] arr = new int[indices.size()];
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for (int i=0; i<arr.length; i++) {
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arr[i] = indices.get(i);
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}
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return arr;
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}
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@Test
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public void testQueryAtoms() {
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RWMol m = RWMol.MolFromSmiles("c1nc(C)n(CC)c1");
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QueryAtom qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
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int[] matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {2, 4}, matches);
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qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true));
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {4}, matches);
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qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
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qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true),
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CompositeQueryType.COMPOSITE_OR);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {1, 2, 4}, matches);
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qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
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qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true),
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CompositeQueryType.COMPOSITE_XOR);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {1, 2}, matches);
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qa = RDKFuncs.ExplicitDegreeGreaterQueryAtom(2);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {2, 4}, matches);
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qa = RDKFuncs.ExplicitDegreeLessQueryAtom(2);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {3, 6}, matches);
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m = RWMol.MolFromSmiles("N[CH][CH]");
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qa = RDKFuncs.NumRadicalElectronsGreaterQueryAtom(0);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {1, 2}, matches);
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qa = RDKFuncs.NumRadicalElectronsGreaterQueryAtom(1);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {2}, matches);
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m = RWMol.MolFromSmiles("F[C@H](Cl)C");
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qa = RDKFuncs.HasChiralTagQueryAtom();
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {1}, matches);
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qa = RDKFuncs.MissingChiralTagQueryAtom();
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assertArrayEquals(new int[] {1}, matches);
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m = RWMol.MolFromSmiles("F[CH](Cl)C");
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qa = RDKFuncs.HasChiralTagQueryAtom();
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {}, matches);
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qa = RDKFuncs.MissingChiralTagQueryAtom();
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {1}, matches);
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m = RWMol.MolFromSmiles("CNCON");
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qa = RDKFuncs.NumHeteroatomNeighborsEqualsQueryAtom(2);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {2}, matches);
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qa = RDKFuncs.NumHeteroatomNeighborsGreaterQueryAtom(0);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {0, 2, 3, 4}, matches);
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m = RWMol.MolFromSmiles("CC12CCN(CC1)C2");
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qa = RDKFuncs.IsBridgeheadQueryAtom();
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {1, 4}, matches);
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m = RWMol.MolFromSmiles("OCCOC");
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qa = RDKFuncs.NonHydrogenDegreeEqualsQueryAtom(2);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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assertArrayEquals(new int[] {1, 2, 3}, matches);
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}
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private int[] GetBondIdxsMatchingQuery(ROMol mol, QueryBond qa) {
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List<Integer> indices = new ArrayList<Integer>();
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for (int i =0; i< mol.getNumBonds(); i++) {
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Bond atom = mol.getBondWithIdx(i);
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if (qa.MatchBond(atom)) {
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indices.add(i);
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}
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}
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int[] arr = new int[indices.size()];
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for (int i=0; i<arr.length; i++) {
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arr[i] = indices.get(i);
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}
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return arr;
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}
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@Test
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public void TestBondPropQueries() {
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RWMol m = RWMol.MolFromSmiles("CCCCCCCCCCCCCC");
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Bond_Vect bonds = m.getBonds();
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bonds.get(0).setProp("hah", "hah");
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bonds.get(1).setIntProp("bar", 1);
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bonds.get(2).setIntProp("bar", 2);
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bonds.get(3).setBoolProp("baz", true);
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bonds.get(4).setBoolProp("baz", false);
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bonds.get(5).setProp("boo", "hoo");
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bonds.get(6).setProp("boo", "-urns");
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bonds.get(7).setDoubleProp("boot", 1.0);
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bonds.get(8).setDoubleProp("boot", 4.0);
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bonds.get(9).setDoubleProp("number", 4.0);
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bonds.get(10).setIntProp("number", 4);
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QueryBond qb = RDKFuncs.HasIntPropWithValueQueryBond("bar", 1);
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int[] matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {1}, matches);
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qb = RDKFuncs.HasIntPropWithValueQueryBond("bar", 2);
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {2}, matches);
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qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz", true);
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {3}, matches);
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qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz", false);
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {4}, matches);
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qb = RDKFuncs.HasStringPropWithValueQueryBond("boo", "hoo");
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {5}, matches);
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qb = RDKFuncs.HasStringPropWithValueQueryBond("boo", "-urns");
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {6}, matches);
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qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot", 1.0);
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {7}, matches);
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qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot", 4.0);
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {8}, matches);
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qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot", 1.0, false, 3.0);
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {7, 8}, matches);
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qb = RDKFuncs.HasIntPropWithValueQueryBond("number", 4);
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matches = GetBondIdxsMatchingQuery(m, qb);
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assertArrayEquals(new int[] {10}, matches);
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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.RascalMCESTest");
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}
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}
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