/// <summary>
/// Prepare for FSS matching of supplied query molecule
/// </summary>
/// <param name="queryMol"></param>
public void SetFSSQueryMolecule(
INativeMolMx queryMol,
string FullStructureSearchType = null)
{
FSSQueryMolecule = queryMol as CdkMol;
return;
}
/// <summary>
/// Map and hilight a substructure match
/// </summary>
/// <param name="molfile"></param>
/// <returns></returns>
public string HilightSSSMatch(string molfile)
{
// This seems to be slow for some reason when running in the VisualStudio debugger
int queryIndex;
int[] mappedAtoms, mappedBonds;
try
{
CdkMol m = new CdkMol(MoleculeFormat.Molfile, molfile);
if (GetSSSMapping(m, out queryIndex, out mappedAtoms, out mappedBonds))
{
throw new NotImplementedException();
}
else
{
return(molfile);
}
}
catch (Exception ex)
{
return(molfile); // just return the input if exception encountered
}
}
/// <summary>
/// GetMolFormulaDotDisconnect
/// </summary>
/// <param name="molfile"></param>
/// <returns></returns>
public string GetMolFormulaDotDisconnect(
string molfile)
{
ICdkMol mol = new CdkMol(MoleculeFormat.Molfile, molfile);
string mf = GetMolFormulaDotDisconnect(mol as CdkMol);
return(mf);
}
/// <summary>
/// Get mol weight for a molfile
/// </summary>
/// <param name="molfile"></param>
/// <returns></returns>
public double GetMolWeight(
string molfile)
{
CdkMol mol = new CdkMol(MoleculeFormat.Molfile, molfile);
double mw = mol.MolWeight;
return(mw);
}
/// <summary>
/// SetMoleculeAndRender
/// </summary>
/// <param name="format"></param>
/// <param name="value"></param>
public void SetMoleculeAndRender(MoleculeFormat format, string value)
{
MolFormat = format;
MolString = value;
CdkMol = new CdkMol(MolFormat, MolString);
RenderMolecule();
return;
}
/// <summary>
/// Perform a full structure search
/// </summary>
/// <param name="query"></param>
/// <param name="target"></param>
/// <param name="switches"></param>
/// <returns></returns>
public bool FullStructureMatch(
ICdkMol query,
ICdkMol target,
string FullStructureSearchType = null)
{
CdkMol q = query as CdkMol;
CdkMol t = target as CdkMol;
var fs = new UniversalIsomorphismTester();
if (fs.isIsomorph(q.NativeMol, t.NativeMol))
{
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// BuildTestFp
/// </summary>
/// <returns></returns>
public static bool[] BuildTestFp(int corpId)
{
bool[] ba = null;
string fileName = @"C:\Download\CorpId-12345.mol";
if (corpId > 0)
{
fileName = fileName.Replace("12345", corpId.ToString());
}
string molfile = FileUtil.ReadFile(fileName);
//string molfile = FileUtil.ReadFile();
IAtomContainer mol = CdkMol.MolfileToAtomContainer(molfile);
//int fpClass = CircularFingerprinterClass.ECFP6; // FP diameter
//int fpLen = 2048; // folded binary fp length
//ba = CdkFingerprint.BuildBoolArray(mol, fpClass, fpLen, true);
return(ba);
}
/// <summary>
/// Perform a full structure search
/// </summary>
/// <param name="query"></param>
/// <param name="target"></param>
/// <param name="switches"></param>
/// <returns></returns>
public bool FullStructureMatch(
INativeMolMx query,
INativeMolMx target,
string FullStructureSearchType = null)
{
if (query == null || target == null)
{
return(false);
}
CdkMol q = query as CdkMol;
q.UpdateNativeMolecule(); // be sure up to date
if (q?.NativeMol == null)
{
return(false);
}
CdkMol t = target as CdkMol;
t.UpdateNativeMolecule();
if (t?.NativeMol == null)
{
return(false);
}
var fs = new UniversalIsomorphismTester();
if (fs.IsIsomorph(q.NativeMol, t.NativeMol))
{
return(true);
}
else
{
return(false);
}
}
static INativeMolMx CdkMolUtil => StaticCdkMol.I; // static molecule shortcut for utility methods
/// <summary>
/// Build UniChem Data
/// Note that this routine takes about 14 secs the first time it's called, faster thereafter.
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static UniChemData BuildUniChemData(
IAtomContainer mol)
{
IAtomContainer mol2;
InChIGenerator ig = null;
string molSmiles, fragSmiles = "", molFile = "";
int acc, fi, ci;
//if (Lex.StartsWith(molString, "InChI="))
//{
// sourceInchi = molString;
// mol = CdkMol.InChIToAtomContainer(sourceInchi);
//}
//else // assume molfile otherwise
//{
// molfile = molString;
// mol = CdkMol.MolfileToAtomContainer(molfile);
//}
if (mol.Atoms.Count <= 1)
{
throw new Exception("Atom count <= 1");
}
int pseudoCount = CdkMol.RemovePseudoAtoms(mol);
mol = CdkMol.AtomContainerToSmilesAndBack(mol, out molSmiles);
InChIGeneratorFactory igf = InChIGeneratorFactory.Instance;
try
{
//string options = "/KET /15T"; // options to include keto-enol and 1,5-tautomerism (not recognized by CDK)
ig = igf.GetInChIGenerator(mol); //, options);
}
catch (Exception ex) // may fail for some complex mols (e.g. CorpId 12345, a MDL V3000 mol with a CF3 Sgroup/alias)
{
throw new Exception(ex.Message, ex);
}
//{
// try // try to simplify the molfile so that InChI can handle it
// {
// //if (Lex.IsUndefined(molfile)) throw ex;
// string molfile2 = SimplifyMolfileForInChIGeneration(molile);
// mol = CdkMol.MolfileToAtomContainer(molfile2);
// mol = CdkMol.AtomContainerToSmilesAndBack(mol, out molSmiles);
// ig = igf.getInChIGenerator(mol);
// }
// catch (Exception ex2)
// {
// throw new Exception(ex2.Message, ex);
// }
//}
if (!IsAcceptableInchiStatus(ig))
{
string errMsg = "InChI generation " + ig.ReturnStatus + ": " + ig.Message;
molFile = CdkMol.AtomContainerToMolfile(mol); // debug
throw new Exception(errMsg);
}
// Populate the UniChem object
UniChemData icd = new UniChemData();
//icd.Molfile = molfile;
icd.AtomContainer = mol;
icd.InChIString = ig.InChI;
icd.InChIKey = ig.GetInChIKey();
icd.CanonSmiles = molSmiles;
// Build and store fingerprint
mol = CdkMol.InChIToAtomContainer(icd.InChIString);
//int hydRemovedCnt = CdkMol.RemoveHydrogensBondedToPositiveNitrogens(mol);
mol = CdkMol.RemoveIsotopesStereoExplicitHydrogens(mol); // additional normalization for fingerprint
BitSetFingerprint fp = // generate a fingerprint
CdkFingerprint.BuildBitSetFingerprint(mol, FingerprintType.MACCS, -1, -1);
icd.Fingerprint = fp;
if (ConnectivityChecker.IsConnected(mol))
{
return(icd); // single fragment
}
//string mf = CdkMol.GetMolecularFormula(mol);
//AtomContainerSet acs = (AtomContainerSet)ConnectivityChecker.partitionIntoMolecules(mol);
List <IAtomContainer> frags = CdkMol.FragmentMolecule(mol, true); // get fragments filtering out small and common frags
for (fi = 0; fi < frags.Count; fi++)
{
mol2 = frags[fi];
int atomCnt = mol2.Atoms.Count;
if (atomCnt <= 1)
{
continue;
}
try
{
mol2 = CdkMol.AtomContainerToSmilesAndBack(mol2, out fragSmiles);
}
catch (Exception ex)
{
AtomContainerToSmilesAndBackErrorCount++; // just count error and ignore
}
ig = igf.GetInChIGenerator(mol2);
if (!IsAcceptableInchiStatus(ig))
{
continue;
}
string childInChIString = ig.InChI;
string childInChIKey = ig.GetInChIKey();
string childFIKHB = UniChemUtil.GetFIKHB(childInChIKey);
mol2 = CdkMol.InChIToAtomContainer(childInChIString); // convert from inchi
mol2 = CdkMol.RemoveIsotopesStereoExplicitHydrogens(mol2); // additional normalization for fingerprint
fp = // generate a fingerprint for the fragment
CdkFingerprint.BuildBitSetFingerprint(mol2, FingerprintType.MACCS, -1, -1);
for (ci = 0; ci < icd.Children.Count; ci++) // see if a dup child
{
if (icd.Children[ci].ChildFIKHB == childFIKHB)
{
break;
}
}
if (ci < icd.Children.Count)
{
continue; // skip if dup
}
UniChemFIKHBHierarchy icdChild = new UniChemFIKHBHierarchy();
icdChild.ParentFIKHB = icd.GetFIKHB();
icdChild.ChildFIKHB = childFIKHB;
icdChild.InChIString = childInChIString;
icdChild.CanonSmiles = fragSmiles;
icdChild.Fingerprint = fp;
icd.Children.Add(icdChild);
}
return(icd);
}
/// <summary>
/// BuildFingerprints
/// </summary>
public static void BuildFingerprints(
UniChemData icd)
{
IAtomContainer mol, mol2;
InChIGenerator ig = null;
int acc, aci, ci;
icd.Children.Clear();
string parentFIKHB = icd.GetFIKHB();
DateTime t0 = DateTime.Now;
mol = CdkMol.InChIToAtomContainer(icd.InChIString);
icd.CanonSmiles = CdkMol.AtomContainerToSmiles(mol);
InChIToAtomContainerTime += TimeOfDay.Delta(ref t0);
BitSetFingerprint fp = // generate a fingerprint
CdkFingerprint.BuildBitSetFingerprint(mol, FingerprintType.MACCS, -1, -1);
BuildFinterprintTime1 += TimeOfDay.Delta(ref t0);
icd.Fingerprint = fp;
if (ConnectivityChecker.IsConnected(mol))
{
return; // single fragment
}
InChIGeneratorFactory igf = InChIGeneratorFactory.Instance;
AtomContainerSet acs = (AtomContainerSet)ConnectivityChecker.PartitionIntoMolecules(mol);
PartitionIntoMoleculesTime += TimeOfDay.Delta(ref t0);
acc = acs.Count;
for (aci = 0; aci < acc; aci++)
{
mol2 = acs[aci];
GetAtomContainerTime += TimeOfDay.Delta(ref t0);
ig = igf.GetInChIGenerator(mol2);
if (!IsAcceptableInchiStatus(ig))
{
continue;
}
string childKey = ig.GetInChIKey();
string childFIKHB = UniChemUtil.GetFIKHB(childKey);
InChIGeneratorTime += TimeOfDay.Delta(ref t0);
fp = // generate a fingerprint for the fragment
CdkFingerprint.BuildBitSetFingerprint(mol2, FingerprintType.MACCS, -1, -1);
BuildFinterprintTime2 += TimeOfDay.Delta(ref t0);
for (ci = 0; ci < icd.Children.Count; ci++) // see if a dup child
{
if (icd.Children[ci].ChildFIKHB == childFIKHB)
{
break;
}
}
if (ci < icd.Children.Count)
{
continue; // skip if dup
}
UniChemFIKHBHierarchy fikhbHier = new UniChemFIKHBHierarchy();
fikhbHier.ParentFIKHB = parentFIKHB;
fikhbHier.ChildFIKHB = childFIKHB;
fikhbHier.CanonSmiles = CdkMol.AtomContainerToSmiles(mol2);
fikhbHier.Fingerprint = fp;
icd.Children.Add(fikhbHier);
}
return;
}
/// <summary>
/// BuildTest
/// </summary>
public static void BuildTest()
{
CircularFingerprinter cfp = null;
CircularFingerprinterClass FpClass = CircularFingerprinterClass.ECFP6; // FP diameter
int FpLen = 2048; // folded binary fp length
IAtomContainer mol, mol2;
//string molfile = FileUtil.ReadFile(@"C:\Download\CorpId-12345.mol");
//java.io.StringReader sr = new java.io.StringReader(molfile);
//if (Lex.Contains(molfile, "v2000"))
// cor = new MDLV2000Reader(sr);
//else
// cor = new MDLV3000Reader(sr);
//cor.setReaderMode(IChemObjectReader.Mode.RELAXED);
//ac = (IAtomContainer)cor.read(new AtomContainer());
//cor.close();
FpClass = CircularFingerprinterClass.ECFP4; // debug
cfp = new CircularFingerprinter(FpClass, FpLen);
StreamReader reader = new StreamReader(@"C:\Download\CorpId-12345.mol");
//FileReader FileReader = new FileReader(@"C:\Download\V3000 Mols.sdf");
EnumerableSDFReader rdr = new EnumerableSDFReader(reader.BaseStream, ChemObjectBuilder.Instance);
rdr.ReaderMode = ChemObjectReaderMode.Relaxed;
IEnumerator <IAtomContainer> cursor = rdr.GetEnumerator();
while (cursor.MoveNext())
{
mol = cursor.Current;
mol = CdkMol.GetLargestMoleculeFragment(mol);
ICountFingerprint cfp1 = cfp.GetCountFingerprint(mol); // get hash values and counts for each
cfp.Calculate(mol);
int fpCount = cfp.FPCount;
for (int fpi = 0; fpi < fpCount; fpi++) // gets
{
CircularFingerprint cfp2 = cfp.GetFP(fpi); // gets hash, iteration and lists of atoms (dups appear multiple times)
}
IBitFingerprint bfp = cfp.GetBitFingerprint(mol);
BitArray bs = bfp.AsBitSet();
int bsCard = bfp.Cardinality;
long bsSize = bfp.Length;
continue;
}
reader.Close();
return;
//java.io.StringReader sr = new java.io.StringReader(molfile);
//AtomContainer mol = new AtomContainer();
//mol.addAtom(new Atom("C"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(1)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(2)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(3)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(4)));
//FileReader FileReader = new FileReader(@"C:\Download\CorpId-12345.mol");
//MolReader mr = new MolReader(FileReader, DefaultChemObjectBuilder.getInstance());
//java.io.StringReader sr = new java.io.StringReader(molfile);
//IMol m = (IMol)mr.next();
//FileReader.close();
}