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using System;
using GraphMolWrap;
using Xunit;
namespace RdkitTests
{
public class GeneralizedSubstructTest
{
private bool FingerprintsMatch(ExtendedQueryMol queryMol, RWMol target)
{
var queryFingerprint = queryMol.patternFingerprintQuery();
var targetFingerprint = RDKFuncs.patternFingerprintTargetMol(target);
Assert.True(queryFingerprint.getNumOnBits() > 0);
Assert.True(targetFingerprint.getNumOnBits() > 0);
var match = RDKFuncs.AllProbeBitsMatch(queryFingerprint, targetFingerprint);
return match;
}
[Fact]
public void TestControlSteps()
{
var queryMol = RWMol.MolFromSmiles("COCC1OC(N)=N1 |LN:1:1.3|");
var xqm1 = RDKFuncs.createExtendedQueryMol(queryMol);
var xqm2 = RDKFuncs.createExtendedQueryMol(queryMol, false);
var xqm3 = RDKFuncs.createExtendedQueryMol(queryMol, true, false);
var xqm4 = RDKFuncs.createExtendedQueryMol(queryMol, false, false);
var mol1 = RWMol.MolFromSmiles("COCC1OC(N)=N1");
Assert.Equal(1, xqm1.getSubstructMatches(mol1).Count);
Assert.Equal(1, xqm2.getSubstructMatches(mol1).Count);
Assert.Equal(1, xqm3.getSubstructMatches(mol1).Count);
Assert.Equal(1, xqm4.getSubstructMatches(mol1).Count);
Assert.True(FingerprintsMatch(xqm1, mol1));
Assert.True(FingerprintsMatch(xqm2, mol1));
Assert.True(FingerprintsMatch(xqm3, mol1));
Assert.True(FingerprintsMatch(xqm4, mol1));
var mol2 = RWMol.MolFromSmiles("COCC1OC(=N)N1");
Assert.Equal(1, xqm1.getSubstructMatches(mol2).Count);
Assert.Equal(1, xqm2.getSubstructMatches(mol2).Count);
Assert.Equal(0, xqm3.getSubstructMatches(mol2).Count);
Assert.Equal(0, xqm4.getSubstructMatches(mol2).Count);
Assert.True(FingerprintsMatch(xqm1, mol2));
Assert.True(FingerprintsMatch(xqm2, mol2));
Assert.False(FingerprintsMatch(xqm3, mol2));
Assert.False(FingerprintsMatch(xqm4, mol2));
var mol3 = RWMol.MolFromSmiles("COOCC1OC(N)=N1");
Assert.Equal(1, xqm1.getSubstructMatches(mol3).Count);
Assert.Equal(0, xqm2.getSubstructMatches(mol3).Count);
Assert.Equal(1, xqm3.getSubstructMatches(mol3).Count);
Assert.Equal(0, xqm4.getSubstructMatches(mol3).Count);
Assert.True(FingerprintsMatch(xqm1, mol3));
Assert.True(FingerprintsMatch(xqm3, mol3));
}
[Fact]
public void TestBundle1()
{
var block = @"
ChemDraw01052411352D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 8 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.247500 0.428587 0.000000 0
M V30 2 C -0.466950 0.016087 0.000000 0
M V30 3 C -0.466950 -0.808913 0.000000 0
M V30 4 C 0.247500 -1.221413 0.000000 0
M V30 5 N 0.961950 -0.808913 0.000000 0
M V30 6 C 0.961950 0.016087 0.000000 0
M V30 7 C -1.181400 0.428587 0.000000 0
M V30 8 * 0.604725 0.222337 0.000000 0
M V30 9 Cl 1.181400 1.221413 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 2 7
M V30 8 1 8 9 ENDPTS=(2 6 1) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
";
var query = RWMol.MolFromMolBlock(block);
var xqm = RDKFuncs.createExtendedQueryMol(query, true, true, false);
var mol = RWMol.MolFromSmiles("Cc1c(cc([nH]1)C(=O)NC2CCN(CC2)c3cc(cc(n3)Cl)C(=O)N)Br");
var matches = xqm.getSubstructMatches(mol);
Assert.True(matches.Count > 0);
}
[Fact]
public void TestKekulizeError()
{
var block = @"
ChemDraw01052410132D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 8 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.247500 0.428587 0.000000 0
M V30 2 C -0.466950 0.016087 0.000000 0
M V30 3 C -0.466950 -0.808913 0.000000 0
M V30 4 C 0.247500 -1.221413 0.000000 0
M V30 5 N 0.961950 -0.808913 0.000000 0
M V30 6 C 0.961950 0.016087 0.000000 0
M V30 7 C -1.181400 0.428587 0.000000 0
M V30 8 * 0.604725 0.222337 0.000000 0
M V30 9 Cl 1.181400 1.221413 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 2 7
M V30 8 1 8 9 ENDPTS=(2 6 1) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
";
var query = RWMol.MolFromMolBlock(block);
ExtendedQueryMol xqm = null;
var adjustQueryParameters = new AdjustQueryParameters()
{
aromatizeIfPossible = false,
adjustDegree = false,
adjustSingleBondsBetweenAromaticAtoms = true,
adjustSingleBondsToDegreeOneNeighbors = true,
makeDummiesQueries = true,
adjustConjugatedFiveRings = true
};
try
{
xqm = RDKFuncs.createExtendedQueryMol(query, true, true, true,
adjustQueryParameters);
}
catch (ApplicationException ex) when (ex.Message.Contains("MolSanitizeException: Can't kekulize mol"))
{
Assert.True(true);
}
Assert.Null(xqm);
}
}
}
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