public void TestGetAllAtomMapping()
{
var sp = new SmilesParser(ChemObjectBuilder.Instance, false);
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(target);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(queryac);
Aromaticity.CDKLegacy.Apply(target);
Aromaticity.CDKLegacy.Apply(queryac);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(queryac);
ExtAtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(target);
// Calling the main algorithm to perform MCS cearch
Aromaticity.CDKLegacy.Apply(queryac);
Aromaticity.CDKLegacy.Apply(target);
Isomorphism smsd1 = new Isomorphism(Algorithm.Default, true);
smsd1.Init(queryac, target, true, true);
smsd1.SetChemFilters(true, true, true);
Assert.IsNotNull(smsd1.GetFirstMapping());
Assert.AreEqual(2, smsd1.GetAllAtomMapping().Count);
}
/// <summary>
/// Update the template library - can be called for safety after
/// each load.
/// </summary>
public void Update()
{
var smipar = new SmilesParser();
var updated = new MultiDictionary <string, Vector2[]>();
foreach (var e in templateMap)
{
try
{
var mol = smipar.ParseSmiles(e.Key);
var order = new int[mol.Atoms.Count];
var key = CreateCanonicalSmiles(mol, order);
foreach (var coords in e.Value)
{
updated.Add(key, ReorderCoords(coords, order));
}
}
catch (CDKException ex)
{
Console.Error.WriteLine(e.Key + " could not be updated: " + ex.Message);
}
}
templateMap.Clear();
foreach (var e in updated)
{
foreach (var v in e.Value)
{
templateMap.Add(e.Key, v);
}
}
}
/// <summary>
/// Read the file content into a <see cref="IAtomContainerSet"/>.
/// </summary>
/// <param name="molSet">an <see cref="IAtomContainerSet"/> to store the structures</param>
/// <returns>the <see cref="IAtomContainerSet"/> containing the molecules read in</returns>
/// <exception cref="IOException">if there is an error during reading</exception>
private IChemObjectSet <IAtomContainer> ReadAtomContainerSet(IChemObjectSet <IAtomContainer> molSet)
{
SmilesParser parser = new SmilesParser(molSet.Builder, false);
string line = input.ReadLine();
line = input.ReadLine(); // skip the first line
while (line != null)
{
string[] cols = line.Split(',');
try
{
var mol = parser.ParseSmiles(cols[1]);
mol.SetProperty("focusSupport", cols[5]);
mol.SetProperty("complementSupport", cols[7]);
mol.SetProperty("atomCount", cols[2]);
mol.SetProperty("bondCount", cols[3]);
molSet.Add(mol);
}
catch (InvalidSmilesException exception)
{
Trace.TraceError($"Skipping invalid SMILES: {cols[1]}");
Debug.WriteLine(exception);
}
line = input.ReadLine();
}
return(molSet);
}
static void Main()
{
{
#region
SmilesParser sp = new SmilesParser();
IAtomContainer atomContainer = sp.ParseSmiles("CC(=O)OC(=O)C");
SMARTSQueryTool querytool = new SMARTSQueryTool("O=CO");
bool status = querytool.Matches(atomContainer);
if (status)
{
int nmatch = querytool.MatchesCount;
var mappings = querytool.GetMatchingAtoms();
foreach (var atomIndices in mappings)
{
// do something
}
}
#endregion
}
{
string someSmartsPattern = null;
IChemObjectSet <IAtomContainer> molecules = null;
#region SetAromaticity
SMARTSQueryTool sqt = new SMARTSQueryTool(someSmartsPattern);
sqt.SetAromaticity(new Aromaticity(ElectronDonation.CDKModel, Cycles.CDKAromaticSetFinder));
foreach (var molecule in molecules)
{
// CDK Aromatic model needs atom types
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(molecule);
sqt.Matches(molecule);
}
#endregion
}
}
/// <summary>
/// SmilesToAtomContainer
/// </summary>
/// <param name="smiles"></param>
/// <returns></returns>
public static IAtomContainer SmilesToAtomContainer(string smiles)
{
try
{
SmilesParser sp = new SmilesParser(ChemObjectBuilder.Instance);
IAtomContainer mol = sp.ParseSmiles(smiles); // may get "could not parse error" for some CorpIds, e.g.: 111, 222, 333
if (mol == null)
{
return(null);
}
ConfigureAtomContainer(mol);
return(mol);
}
catch (Exception ex)
{
ParseSmilesErrorCount++;
LastParseSmilesError = ex.Message;
throw new Exception(ex.Message, ex);
}
}
private void AssertSmiles(string smi, int expected)
{
SmilesParser smipar = CDK.SmilesParser;
var mol = smipar.ParseSmiles(smi);
Assert.AreEqual(expected.ToString(), CreateDescriptor().Calculate(mol).Value.ToString());
}
public void TestPartitionExtendedTetrahedral()
{
SmilesParser smipar = CDK.SmilesParser;
var container = smipar.ParseSmiles("CC=[C@]=CC.C");
IChemObjectSet <IAtomContainer> containerSet = ConnectivityChecker.PartitionIntoMolecules(container);
Assert.AreEqual(2, containerSet.Count);
Assert.IsTrue(containerSet[0].StereoElements.GetEnumerator().MoveNext());
}
public MoleculeSignatureTest()
{
this.parser = CDK.SmilesParser;
this.builder = ChemObjectBuilder.Instance;
mol = builder.NewAtomContainer();
mol.Atoms.Add(builder.NewAtom("C"));
mol.Atoms.Add(builder.NewAtom("C"));
mol.AddBond(mol.Atoms[0], mol.Atoms[1], BondOrder.Single);
molSig = new MoleculeSignature(mol);
}
public void TestRing()
{
sp = CDK.SmilesParser;
var mol = sp.ParseSmiles("C1CCCC1CCC2CCCNC2");
AddExplicitHydrogens(mol);
var dv = CreateDescriptor().Calculate(mol);
Assert.IsNotNull(dv);
}
public void TestCalculateOverlapsAndReduce()
{
var sp = new SmilesParser(builder);
var Molecule1 = sp.ParseSmiles("O1C=CC=C1");
var Molecule2 = sp.ParseSmiles("C1CCCC1");
CDKRMapHandler instance = new CDKRMapHandler();
instance.CalculateOverlapsAndReduce(Molecule1, Molecule2, true);
Assert.IsNotNull(FinalMappings.Instance.Count);
}
static void Main()
{
#region
SmilesParser sp = new SmilesParser();
IAtomContainer atomContainer = sp.ParseSmiles("CC(=O)OC(=O)C"); // acetic acid anhydride
IAtomContainer SMILESquery = sp.ParseSmiles("CC"); // acetic acid anhydride
IQueryAtomContainer query = QueryAtomContainerCreator.CreateBasicQueryContainer(SMILESquery);
bool isSubstructure = CDKMCS.IsSubgraph(atomContainer, query, true);
#endregion
}
public void TestCalculateOverlapsAndReduceExactMatch()
{
var sp = new SmilesParser(builder);
var Molecule1 = sp.ParseSmiles("O1C=CC=C1");
var Molecule2 = sp.ParseSmiles("O1C=CC=C1");
CDKRMapHandler instance = new CDKRMapHandler();
instance.CalculateOverlapsAndReduceExactMatch(Molecule1, Molecule2, true);
// TODO review the generated test code and remove the default call to fail.
Assert.IsNotNull(FinalMappings.Instance.Count);
}
public void Guanine_ket()
{
var smipar = new SmilesParser(builder);
var smiles = "NC1=NC2=C(N=CN2)C(=O)N1";
var mol = smipar.ParseSmiles(smiles);
var inchiFact = InChIGeneratorFactory.Instance;
var inchigen = inchiFact.GetInChIGenerator(mol, "KET");
Assert.AreEqual(InChIReturnCode.Ok, inchigen.ReturnStatus);
Assert.AreEqual("InChI=1/C5H5N5O/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,(H4,2,6,7,8,9,10,11)", inchigen.InChI);
}
public void InliningReactionsWithRadicals()
{
IChemObjectBuilder bldr = ChemObjectBuilder.Instance;
SmilesParser smipar = new SmilesParser(bldr);
IReaction reaction = smipar.ParseReactionSmiles("[CH2]CO.CC(=O)O>[H+]>CCOC(=O)C.O |^1:0| ethyl esterification");
SmilesGenerator smigen = new SmilesGenerator(SmiFlavors.CxSmiles);
// convert to molecule
IAtomContainer mol = ReactionManipulator.ToMolecule(reaction);
Assert.AreEqual("[CH2]CO.CC(=O)O.[H+].CCOC(=O)C.O |^1:0|", smigen.Create(mol));
Assert.AreEqual("[CH2]CO.CC(=O)O>[H+]>CCOC(=O)C.O |^1:0|", smigen.CreateReactionSMILES(ReactionManipulator.ToReaction(mol)));
}
static void Main()
{
UniversalIsomorphismTester universalIsomorphismTester = new UniversalIsomorphismTester();
#region
SmilesParser sp = new SmilesParser();
IAtomContainer atomContainer = sp.ParseSmiles("CC(=O)OC(=O)C"); // acetic acid anhydride
IAtomContainer SMILESquery = sp.ParseSmiles("CC"); // ethylene
IQueryAtomContainer query = QueryAtomContainerCreator.CreateBasicQueryContainer(SMILESquery);
bool isSubstructure = universalIsomorphismTester.IsSubgraph(atomContainer, query);
#endregion
}
public void TestGetMappings()
{
var sp = new SmilesParser(builder);
var Molecule1 = sp.ParseSmiles("O1C=CC=C1");
var Molecule2 = sp.ParseSmiles("O1C=CC=C1");
CDKRMapHandler instance = new CDKRMapHandler();
instance.CalculateOverlapsAndReduceExactMatch(Molecule1, Molecule2, true);
var result = instance.Mappings;
Assert.AreEqual(2, result.Count);
}
public void TestConstructorAndGetMethods()
{
SmilesParser smiles = CDK.SmilesParser;
var molecule = smiles.ParseSmiles("ClC(Br)(I)");
ILigand ligand = new ImplicitHydrogenLigand(molecule, new VisitedAtoms(), molecule.Atoms[1]);
Assert.IsNotNull(ligand);
Assert.AreEqual(molecule, ligand.AtomContainer);
Assert.AreEqual(molecule.Atoms[1], ligand.CentralAtom);
Assert.IsTrue(ligand.LigandAtom is ImmutableHydrogen);
}
public void Aminopropenol_15T()
{
var builder = CDK.Builder;
var smipar = new SmilesParser(builder);
var smiles = "N\\C=C/C=O";
var mol = smipar.ParseSmiles(smiles);
var inchiFact = InChIGeneratorFactory.Instance;
var inchigen = inchiFact.GetInChIGenerator(mol, "15T");
Assert.AreEqual(InChIReturnCode.Ok, inchigen.ReturnStatus);
Assert.AreEqual("InChI=1/C3H5NO/c4-2-1-3-5/h1-3H,(H2,4,5)", inchigen.InChI);
}
public static IAtomContainer ConvertSMILES(string smilesString)
{
if (string.IsNullOrWhiteSpace(smilesString))
{
return(null);
}
var bldr = ChemObjectBuilder.Instance;
var smipar = new SmilesParser(bldr);
var mol = smipar.ParseSmiles(smilesString);
return(mol);
}
public void Timeout()
{
var smipar = new SmilesParser(builder);
var smiles = "C(CCCNC(=N)N)(COCC(COP([O])(=O)OCCCCCCNC(NC1=CC(=C(C=C1)C2(C3=CC=C(C=C3OC=4C2=CC=C(C4)O)O)C)C(=O)[O])=S)OP(=O)([O])OCC(COCC(CCC/[NH]=C(\\[NH])/N)(CCCNC(=N)N)CCCNC(=N)N)OP(=O)([O])OCC(COCC(CCCNC(=N)N)(CCC/[NH]=C(\\[NH])/N)CCCNC(=N)N)OP(OCC(COCC(CCCNC(=N)N)(CCCNC(=N)N)CCC/[NH]=C(\\[NH])/N)OP(=O)([O])OCC(COCC(CCCNC(=N)N)(CCCNC(N)=N)CCC/[NH]=C(/N)\\[NH])OP([O])(=O)CCC(COCC(CCCNC(=N)N)(CCC/[NH]=C(\\[NH])/N)CCCNC(=N)N)OP([O])(=O)OCC(COCC(CCCNC(N)=N)(CCCNC(N)=N)CCC/[NH]=C(\\[NH])/N)OP(OCC(COCC(CCCNC(N)=N)(CCC/[NH]=C(/N)\\[NH])CCCNC(N)=N)O=P([O])(OCC(COP(=OC(COCC(CCC/[NH]=C(\\[NH])/N)(CCCNC(N)=N)CCCNC(N)=N)COP([O])(=O)OC(COP(OC(COCC(CCCNC(=N)N)(CCC/[NH]=C(\\[NH])/N)CCCNC(=N)N)COP(OC(COCC(CCCNC(=N)N)(CCC/[NH]=C(\\[NH])/N)CCCNC(=N)N)COP([O])(=O)OC(COP(OC(COP(OC(COP(=O)([O])OC(COCC(CCC/[NH]=C(/N)\\[NH])(CCCNC(N)=N)CCCNC(=N)N)COP([O])(=O)OCCCCCCNC(NC=5C=CC(=C(C5)C(=O)[O])C6(C7=CC=C(C=C7OC=8C6=CC=C(C8)O)O)C)=S)COCC(CCCNC(N)=N)(CCC/[NH]=C(\\[NH])/N)CCCNC(=N)N)([O])=O)COCC(CCCNC(=N)N)(CCC/[NH]=C(\\[NH])/N)CCCNC(=N)N)([O])=O)COCC(CCCNC(=N)N)(CCCNC(=N)N)CCC/[NH]=C(\\[NH])/N)([O])=O)([O])=O)COCC(CCC/[NH]=C(/N)\\[NH])(CCCNC(=N)N)CCCNC(=N)N)([O])[O])(C)COP(OCCCCCCO)(=O)[O])[O])(=O)[O])([O])=O)(CCC/[NH]=C(\\[NH])/[NH])CCCNC(=N)N";
var mol = smipar.ParseSmiles(smiles);
var inchiFact = InChIGeneratorFactory.Instance;
var generator = inchiFact.GetInChIGenerator(mol, "W0.01");
Assert.AreEqual(InChIReturnCode.Error, generator.ReturnStatus);
Assert.IsTrue(
generator.Log.Contains("Time limit exceeded") ||
generator.Log.Contains("Structure normalization timeout"));
}
public void HydrogenAsFirstAtomInEthane()
{
SmilesParser smipar = CDK.SmilesParser;
var ethane = smipar.ParseSmiles("[H]C([H])([H])C([H])([H])[H]");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(ethane);
ModelBuilder3D mb3d = ModelBuilder3D.GetInstance();
mb3d.Generate3DCoordinates(ethane, false);
foreach (var atom in ethane.Atoms)
{
Assert.IsNotNull(atom.Point3D);
}
}
void Main()
{
UniversalIsomorphismTester universalIsomorphismTester = null;
#region 1
SmilesParser sp = new SmilesParser();
IAtomContainer atomContainer = sp.ParseSmiles("CC(=O)OC(=O)C");
QueryAtomContainer query = SMARTSParser.Parse("C*C");
bool queryMatch = universalIsomorphismTester.IsSubgraph(atomContainer, query);
#endregion
#region 2
SMARTSParser parser = new SMARTSParser(new StringReader("C*C"));
ASTStart start = parser.Start();
#endregion
}
public void TestSMARTS()
{
var sp = new SmilesParser();
var atomContainer = sp.ParseSmiles("CC(=O)OC(=O)C"); // acetic acid anhydride
var query = new QueryAtomContainer();
var atom1 = new NCDK.Isomorphisms.Matchers.SMARTS.AnyAtom();
var atom2 = new SymbolQueryAtom()
{
Symbol = "C"
};
query.Atoms.Add(atom1);
query.Atoms.Add(atom2);
query.Bonds.Add(new NCDK.Isomorphisms.Matchers.OrderQueryBond(atom1, atom2, BondOrder.Double));
Assert.IsTrue(uiTester.IsSubgraph(atomContainer, query));
}
static void Main()
{
{
IAtomContainer container = null;
IAtom atom1 = null;
IAtom atom2 = null;
#region 1
AtomContainerManipulator.ReplaceAtomByAtom(container, atom1, atom2);
#endregion
}
#region SetSingleOrDoubleFlags
SmilesParser parser = new SmilesParser(ChemObjectBuilder.Instance, false);
IAtomContainer biphenyl = parser.ParseSmiles("c1cccc(c1)c1ccccc1");
AtomContainerManipulator.SetSingleOrDoubleFlags(biphenyl);
#endregion
}
public static void Script8_3()
{
var parser = new SmilesParser();
var hAdder = CDKHydrogenAdder.GetInstance();
var methanol = parser.ParseSmiles("CO");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(methanol);
hAdder.AddImplicitHydrogens(methanol);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(methanol);
var dimethoxymethane = parser.ParseSmiles("COC");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(dimethoxymethane);
hAdder.AddImplicitHydrogens(dimethoxymethane);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(dimethoxymethane);
var water = parser.ParseSmiles("O");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(water);
hAdder.AddImplicitHydrogens(water);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(water);
var reaction = new Reaction();
reaction.Reactants.Add(methanol, 2.0D);
reaction.Products.Add(dimethoxymethane);
reaction.Products.Add(water);
Console.WriteLine("Reactants:");
foreach (var reactant in reaction.Reactants)
{
var formula = MolecularFormulaManipulator.GetMolecularFormula(reactant);
Console.WriteLine(MolecularFormulaManipulator.GetString(formula));
}
Console.WriteLine("Products: ");
foreach (var product in reaction.Products)
{
var formula = MolecularFormulaManipulator.GetMolecularFormula(product);
Console.WriteLine(MolecularFormulaManipulator.GetString(formula));
}
}
static void Main()
{
#region
var smipar = new SmilesParser();
IAtomContainer mol = smipar.ParseSmiles("[nH]1ccc2c1cccc2");
var subsmarts = new SmartsFragmentExtractor(mol);
string smarts;
// smarts=[nH1v3X3+0][cH1v4X3+0][cH1v4X3+0][cH0v4X3+0]
// hits =1
smarts = subsmarts.Generate(new int[] { 0, 1, 3, 4 });
subsmarts.SetMode(SubstructureSelectionMode.JCompoundMapper);
// smarts=n(ccc(a)a)a
// hits = 0 - one of the 'a' atoms needs to match the nitrogen
smarts = subsmarts.Generate(new int[] { 0, 1, 3, 4 });
#endregion
}
void Main()
{
{
#region 1
SmilesParser sp = new SmilesParser();
IAtomContainer m = sp.ParseSmiles("c1[cH:5]cccc1");
var c1 = m.Atoms[1].GetProperty <int>(CDKPropertyName.AtomAtomMapping); // 5
var c2 = m.Atoms[2].GetProperty <int>(CDKPropertyName.AtomAtomMapping); // null
#endregion
}
{
#region 2
SmilesParser sp = new SmilesParser();
IAtomContainer m = sp.ParseSmiles("c1[cH:5]cccc1");
var c1 = m.Atoms[1].GetProperty <int>(CDKPropertyName.AtomAtomMapping); // 5
var c2 = m.Atoms[2].GetProperty <int>(CDKPropertyName.AtomAtomMapping); // null
#endregion
}
}
public void Ctor()
{
#region
SmilesParser sp = new SmilesParser();
IAtomContainer ac = sp.ParseSmiles("CC");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(ac);
AtomContainerManipulator.ConvertImplicitToExplicitHydrogens(ac);
MMFF94PartialCharges mmff = new MMFF94PartialCharges();
mmff.AssignMMFF94PartialCharges(ac);
#endregion
foreach (var atom in ac.Atoms)
{
Console.WriteLine(
#region result
atom.GetProperty <double>("MMFF94charge")
#endregion
);
}
}
public void TestGenerateFingerprintIsNotASubSet1()
{
string smilesT = "O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O";
string smilesQ = "OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O";
var smilesParser = new SmilesParser(builder, false);
var moleculeQ = smilesParser.ParseSmiles(smilesQ);
var moleculeT = smilesParser.ParseSmiles(smilesT);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(moleculeQ);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(moleculeT);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitArray fingerprintQ;
BitArray fingerprintT;
fingerprintQ = fingerprint.GetBitFingerprint(moleculeQ).AsBitSet();
fingerprintT = fingerprint.GetBitFingerprint(moleculeT).AsBitSet();
Assert.IsFalse(FingerprinterTool.IsSubset(fingerprintT, fingerprintQ));
}
[TestMethod(), Ignore()] // Failing but not going to be fixed
public void TestGetAllMapping()
{
var sp = new SmilesParser(ChemObjectBuilder.Instance, false);
var target = sp.ParseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
var queryac = sp.ParseSmiles("Nc1ccccc1");
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(target);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(queryac);
MCSPlusHandler smsd1 = new MCSPlusHandler();
MolHandler mol1 = new MolHandler(queryac, true, true);
MolHandler mol2 = new MolHandler(target, true, true);
smsd1.Set(mol1, mol2);
smsd1.SearchMCS(true);
Assert.IsNotNull(smsd1.GetFirstMapping());
Assert.AreEqual(4, smsd1.GetAllMapping().Count);
}