/// <summary>
/// Fragment a molecule
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static List <KeyValuePair <string, IAtomContainer> > FragmentMoleculeAndCanonicalizeSmiles(
IAtomContainer mol,
bool filterOutCommonCounterIons)
{
int aci, fi, i1;
KeyValuePair <string, IAtomContainer> kvp;
List <KeyValuePair <string, IAtomContainer> > frags = new List <KeyValuePair <string, IAtomContainer> >();
AtomContainerSet acs = (AtomContainerSet)ConnectivityChecker.partitionIntoMolecules(mol);
int acc = acs.getAtomContainerCount();
for (aci = 0; aci < acc; aci++)
{
IAtomContainer fragMol = acs.getAtomContainer(aci);
string fragSmiles = AtomContainerToSmiles(fragMol);
if (filterOutCommonCounterIons)
{
if (CommonSmallFragments.Contains(fragSmiles) ||
GetHeavyAtomCount(fragMol) <= 6)
{
continue;
}
}
kvp = new KeyValuePair <string, IAtomContainer>(fragSmiles, fragMol);
int ac = fragMol.getAtomCount();
for (fi = frags.Count - 1; fi >= 0; fi--) // insert into list so that fragments are ordered largest to smallest
{
if (frags[fi].Value.getAtomCount() >= ac)
{
break;
}
}
frags.Insert(fi + 1, kvp);
}
return(frags);
}
/// <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.getInstance();
AtomContainerSet acs = (AtomContainerSet)ConnectivityChecker.partitionIntoMolecules(mol);
PartitionIntoMoleculesTime += TimeOfDay.Delta(ref t0);
acc = acs.getAtomContainerCount();
for (aci = 0; aci < acc; aci++)
{
mol2 = acs.getAtomContainer(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;
}