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//
// Copyright (C) 2020 Gareth Jones, Glysade LLC
//
// @@ 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.
//
using System;
using System.Collections.Generic;
using System.Linq;
using System.Reflection.PortableExecutable;
using GraphMolWrap;
using Xunit;
namespace RdkitTests
{
public class QueryAtomTest
{
[Fact]
public void TestChemdrawBlock()
{
// smiles c1[nH]ccc1
// Chemdraw will convert explicit hydrogens in aromatic compounds to query hydrogen count
var block = @"
ChemDraw05012418152D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 5 0 0 0
M V30 BEGIN ATOM
M V30 1 C -0.652854 -0.050688 0.000000 0
M V30 2 C -0.240354 0.663783 0.000000 0
M V30 3 C 0.566618 0.492256 0.000000 0
M V30 4 C 0.652854 -0.328225 0.000000 0
M V30 5 N -0.100821 -0.663783 0.000000 0 HCOUNT=1
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 4 1 2
M V30 2 4 2 3
M V30 3 4 3 4
M V30 4 4 4 5
M V30 5 4 1 5
M V30 END BOND
M V30 END CTAB
M END
";
var mol = RWMol.MolFromMolBlock(block, false);
Assert.NotNull(mol);
Assert.Equal(5U, mol.getNumAtoms());
var queryAtom = mol.getAtomWithIdx(4);
Assert.True(queryAtom.hasQuery());
var smarts = queryAtom.AtomGetSmarts();
var expected = "[#7&h{1-}]";
Assert.Equal(expected, smarts);
var description = queryAtom.describeQuery();
expected = "AtomAnd\n AtomAtomicNum 7 = val\n less_AtomImplicitHCount 1 <= \n";
Assert.Equal(expected, description);
var molSmiles = mol.MolToSmiles();
var molSmarts = RDKFuncs.MolToSmarts(mol);
var atom = new Atom(7);
atom.setNumExplicitHs(1);
mol.replaceAtom(4, atom);
mol.clearComputedProps(true);
mol.sanitizeMol();
atom = mol.getAtomWithIdx(4);
Assert.Equal(7, atom.getAtomicNum());
Assert.Equal(1U, atom.getNumExplicitHs());
molSmiles = mol.MolToSmiles();
Assert.Equal("c1cc[nH]c1", molSmiles);
}
[Fact]
public void TestReplaceQuerySimple()
{
var query = RWMol.MolFromSmiles("c1[nH]ccc1");
var nitrogen = query.getAtomWithIdx(2);
var imp = nitrogen.getNumImplicitHs();
Assert.Equal(1U, imp);
var queryAtom = RDKFuncs.replaceAtomWithQueryAtom(query, nitrogen);
queryAtom.ExpandQuery(RDKFuncs.ExplicitDegreeEqualsQueryAtom(3));
var mol1 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
Assert.True(mol1.hasSubstructMatch(query));
var mol2 = RWMol.MolFromSmiles("c1[nH]ccc1");
Assert.False(mol2.hasSubstructMatch(query));
}
[Fact]
public void TestExpandQuerySimple()
{
var query = RWMol.MolFromSmarts("c1nccc1");
var mol1 = RWMol.MolFromSmiles("c1[nH]ccc1");
Assert.True(mol1.hasSubstructMatch(query));
var atom = query.getAtomWithIdx(0);
Assert.True(atom.hasQuery());
var queryAtom = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
atom.ExpandQuery(queryAtom, CompositeQueryType.COMPOSITE_AND);
Assert.False(mol1.hasSubstructMatch(query));
var mol2 = RWMol.MolFromSmiles("Cc1[nH]ccc1");
Assert.True(mol2.hasSubstructMatch(query));
}
// adapted from Python tests
private IList<uint> GetAtomIdxsMatchingQuery(ROMol mol, QueryAtom qa)
{
return mol.getAtoms().Where(qa.MatchAtom).Select(a => a.getIdx()).ToList();
}
[Fact]
public void TestQueryAtoms()
{
var m = RWMol.MolFromSmiles("c1nc(C)n(CC)c1");
var qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
var matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 2U, 4U }, matches);
qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true));
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 4U }, matches);
qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true),
CompositeQueryType.COMPOSITE_OR);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 1U, 2U, 4U }, matches);
qa = RDKFuncs.ExplicitDegreeEqualsQueryAtom(3);
qa.ExpandQuery(RDKFuncs.AtomNumEqualsQueryAtom(6, true),
CompositeQueryType.COMPOSITE_XOR);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 1U, 2U }, matches);
qa = RDKFuncs.ExplicitDegreeGreaterQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 2U, 4U }, matches);
qa = RDKFuncs.ExplicitDegreeLessQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 3U, 6U }, matches);
m = RWMol.MolFromSmiles("N[CH][CH]");
qa = RDKFuncs.NumRadicalElectronsGreaterQueryAtom(0);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 1U, 2U }, matches);
qa = RDKFuncs.NumRadicalElectronsGreaterQueryAtom(1);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 2U }, matches);
m = RWMol.MolFromSmiles("F[C@H](Cl)C");
qa = RDKFuncs.HasChiralTagQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 1U }, matches);
qa = RDKFuncs.MissingChiralTagQueryAtom();
Assert.Equal(new List<uint> { 1U }, matches);
m = RWMol.MolFromSmiles("F[CH](Cl)C");
qa = RDKFuncs.HasChiralTagQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { }, matches);
qa = RDKFuncs.MissingChiralTagQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 1U }, matches);
m = RWMol.MolFromSmiles("CNCON");
qa = RDKFuncs.NumHeteroatomNeighborsEqualsQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 2U }, matches);
qa = RDKFuncs.NumHeteroatomNeighborsGreaterQueryAtom(0);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 0U, 2U, 3U, 4U }, matches);
m = RWMol.MolFromSmiles("CC12CCN(CC1)C2");
qa = RDKFuncs.IsBridgeheadQueryAtom();
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 1U, 4U }, matches);
m = RWMol.MolFromSmiles("OCCOC");
qa = RDKFuncs.NonHydrogenDegreeEqualsQueryAtom(2);
matches = GetAtomIdxsMatchingQuery(m, qa);
Assert.Equal(new List<uint> { 1U, 2U, 3U }, matches);
}
private IList<uint> GetBondIdxsMatchingQuery(ROMol mol, QueryBond qb)
{
return mol.getBonds().Where(qb.MatchBond).Select(a => a.getIdx()).ToList();
}
[Fact]
public void TestBondPropQueries()
{
var m = RWMol.MolFromSmiles("CCCCCCCCCCCCCC");
var bonds = m.getBonds();
bonds[0].setProp("hah", "hah");
bonds[1].setIntProp("bar", 1);
bonds[2].setIntProp("bar", 2);
bonds[3].setBoolProp("baz", true);
bonds[4].setBoolProp("baz", false);
bonds[5].setProp("boo", "hoo");
bonds[6].setProp("boo", "-urns");
bonds[7].setDoubleProp("boot", 1.0);
bonds[8].setDoubleProp("boot", 4.0);
bonds[9].setDoubleProp("number", 4.0);
bonds[10].setIntProp("number", 4);
var qb = RDKFuncs.HasIntPropWithValueQueryBond("bar",1);
var matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 1U }, matches);
qb = RDKFuncs.HasIntPropWithValueQueryBond("bar",2);
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 2U }, matches);
qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz",true);
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 3U }, matches);
qb = RDKFuncs.HasBoolPropWithValueQueryBond("baz",false);
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 4U }, matches);
qb = RDKFuncs.HasStringPropWithValueQueryBond("boo","hoo");
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 5U }, matches);
qb = RDKFuncs.HasStringPropWithValueQueryBond("boo","-urns");
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 6U }, matches);
qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot",1.0);
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 7U }, matches);
qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot",4.0);
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 8U }, matches);
qb = RDKFuncs.HasDoublePropWithValueQueryBond("boot",1.0, false, 3.0);
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 7U, 8U }, matches);
qb = RDKFuncs.HasIntPropWithValueQueryBond("number",4);
matches = GetBondIdxsMatchingQuery(m, qb);
Assert.Equal(new List<uint> { 10U }, matches);
}
}
}
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