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https://github.com/rdkit/rdkit.git
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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>
252 lines
9.8 KiB
C#
252 lines
9.8 KiB
C#
//
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// 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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using System;
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using System.Collections.Generic;
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using System.Linq;
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using System.Reflection.PortableExecutable;
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using GraphMolWrap;
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using Xunit;
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namespace RdkitTests
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{
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public class QueryAtomTest
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{
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[Fact]
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public void TestChemdrawBlock()
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{
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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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var block = @"
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ChemDraw05012418152D
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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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var mol = RWMol.MolFromMolBlock(block, false);
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Assert.NotNull(mol);
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Assert.Equal(5U, mol.getNumAtoms());
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var queryAtom = mol.getAtomWithIdx(4);
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Assert.True(queryAtom.hasQuery());
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var smarts = queryAtom.AtomGetSmarts();
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var expected = "[#7&h{1-}]";
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Assert.Equal(expected, smarts);
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var description = queryAtom.describeQuery();
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expected = "AtomAnd\n AtomAtomicNum 7 = val\n less_AtomImplicitHCount 1 <= \n";
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Assert.Equal(expected, description);
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var molSmiles = mol.MolToSmiles();
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var molSmarts = RDKFuncs.MolToSmarts(mol);
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var 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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Assert.Equal(7, atom.getAtomicNum());
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Assert.Equal(1U, atom.getNumExplicitHs());
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molSmiles = mol.MolToSmiles();
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Assert.Equal("c1cc[nH]c1", molSmiles);
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}
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[Fact]
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public void TestReplaceQuerySimple()
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{
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var query = RWMol.MolFromSmiles("c1[nH]ccc1");
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var nitrogen = query.getAtomWithIdx(2);
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var imp = nitrogen.getNumImplicitHs();
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Assert.Equal(1U, imp);
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var queryAtom = RDKFuncs.replaceAtomWithQueryAtom(query, nitrogen);
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queryAtom.ExpandQuery(RDKFuncs.ExplicitDegreeEqualsQueryAtom(3));
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var mol1 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
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Assert.True(mol1.hasSubstructMatch(query));
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var mol2 = RWMol.MolFromSmiles("c1[nH]ccc1");
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Assert.False(mol2.hasSubstructMatch(query));
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}
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[Fact]
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public void TestExpandQuerySimple()
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{
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var query = RWMol.MolFromSmarts("c1nccc1");
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var mol1 = RWMol.MolFromSmiles("c1[nH]ccc1");
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Assert.True(mol1.hasSubstructMatch(query));
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var atom = query.getAtomWithIdx(0);
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Assert.True(atom.hasQuery());
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var queryAtom = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
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atom.ExpandQuery(queryAtom, CompositeQueryType.COMPOSITE_AND);
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Assert.False(mol1.hasSubstructMatch(query));
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var mol2 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
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Assert.True(mol2.hasSubstructMatch(query));
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}
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// adapted from Python tests
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private IList<uint> GetAtomIdxsMatchingQuery(ROMol mol, QueryAtom qa)
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{
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return mol.getAtoms().Where(qa.MatchAtom).Select(a => a.getIdx()).ToList();
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}
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[Fact]
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public void TestQueryAtoms()
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{
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var m = RWMol.MolFromSmiles("c1nc(C)n(CC)c1");
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var qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
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var matches = GetAtomIdxsMatchingQuery(m, qa);
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Assert.Equal(new List<uint> { 2U, 4U }, matches);
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qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true));
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matches = GetAtomIdxsMatchingQuery(m, qa);
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Assert.Equal(new List<uint> { 4U }, 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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Assert.Equal(new List<uint> { 1U, 2U, 4U }, 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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Assert.Equal(new List<uint> { 1U, 2U }, matches);
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qa = RDKFuncs.ExplicitDegreeGreaterQueryAtom(2);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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Assert.Equal(new List<uint> { 2U, 4U }, matches);
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qa = RDKFuncs.ExplicitDegreeLessQueryAtom(2);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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Assert.Equal(new List<uint> { 3U, 6U }, 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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Assert.Equal(new List<uint> { 1U, 2U }, matches);
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qa = RDKFuncs.NumRadicalElectronsGreaterQueryAtom(1);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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Assert.Equal(new List<uint> { 2U }, 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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Assert.Equal(new List<uint> { 1U }, matches);
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qa = RDKFuncs.MissingChiralTagQueryAtom();
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Assert.Equal(new List<uint> { 1U }, 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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Assert.Equal(new List<uint> { }, matches);
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qa = RDKFuncs.MissingChiralTagQueryAtom();
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matches = GetAtomIdxsMatchingQuery(m, qa);
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Assert.Equal(new List<uint> { 1U }, 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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Assert.Equal(new List<uint> { 2U }, matches);
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qa = RDKFuncs.NumHeteroatomNeighborsGreaterQueryAtom(0);
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matches = GetAtomIdxsMatchingQuery(m, qa);
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Assert.Equal(new List<uint> { 0U, 2U, 3U, 4U }, 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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Assert.Equal(new List<uint> { 1U, 4U }, 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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Assert.Equal(new List<uint> { 1U, 2U, 3U }, matches);
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}
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private IList<uint> GetBondIdxsMatchingQuery(ROMol mol, QueryBond qb)
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{
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return mol.getBonds().Where(qb.MatchBond).Select(a => a.getIdx()).ToList();
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}
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[Fact]
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public void TestBondPropQueries()
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{
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var m = RWMol.MolFromSmiles("CCCCCCCCCCCCCC");
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var bonds = m.getBonds();
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bonds[0].setProp("hah", "hah");
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bonds[1].setIntProp("bar", 1);
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bonds[2].setIntProp("bar", 2);
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bonds[3].setBoolProp("baz", true);
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bonds[4].setBoolProp("baz", false);
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bonds[5].setProp("boo", "hoo");
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bonds[6].setProp("boo", "-urns");
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bonds[7].setDoubleProp("boot", 1.0);
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bonds[8].setDoubleProp("boot", 4.0);
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bonds[9].setDoubleProp("number", 4.0);
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bonds[10].setIntProp("number", 4);
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var qb = RDKFuncs.HasIntPropWithValueQueryBond("bar",1);
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var matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 1U }, matches);
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qb = RDKFuncs.HasIntPropWithValueQueryBond("bar",2);
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 2U }, matches);
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qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz",true);
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 3U }, matches);
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qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz",false);
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 4U }, matches);
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qb = RDKFuncs.HasStringPropWithValueQueryBond("boo","hoo");
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 5U }, matches);
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qb = RDKFuncs.HasStringPropWithValueQueryBond("boo","-urns");
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 6U }, matches);
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qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot",1.0);
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 7U }, matches);
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qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot",4.0);
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 8U }, 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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Assert.Equal(new List<uint> { 7U, 8U }, matches);
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qb = RDKFuncs.HasIntPropWithValueQueryBond("number",4);
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matches = GetBondIdxsMatchingQuery(m, qb);
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Assert.Equal(new List<uint> { 10U }, matches);
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}
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}
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} |