/// <summary>
/// Set substructure search query molecule
/// </summary>
/// <param name="cs"></param>
public void SetSSSQueryMolecule(
MoleculeMx cs)
{
QueryMol = cs.Clone();
SSSQueryMol = CdkMolFactory.NewCdkMol(cs);
CdkMolUtil.SetSSSQueryMolecule(SSSQueryMol);
return;
}
/// <summary>
/// Set full structure search query molecule
/// </summary>
/// <param name="cs"></param>
public void SetFSSQueryMolecule(
MoleculeMx cs)
{
if (cs.IsBiopolymerFormat) // fix later
{
QueryMol = cs;
return;
}
QueryMol = cs.Clone();
FSSQueryMol = CdkMolFactory.NewCdkMol(cs);
CdkMolUtil.SetFSSQueryMolecule(FSSQueryMol);
return;
}
/// <summary>
/// Do a similarity match
/// </summary>
/// <param name="query"></param>
/// <param name="target"></param>
/// <returns></returns>
public bool FullStructureMatch(
MoleculeMx query,
MoleculeMx target,
string switches)
{
bool newQuery = (QueryMol == null || QueryMol.PrimaryValue != query.PrimaryValue);
if (newQuery)
{
QueryMol = query.Clone();
SSSQueryMol = CdkMolFactory.NewCdkMol(query);
}
SSSTargetMol = CdkMolFactory.NewCdkMol(target);
bool b = CdkMolUtil.FullStructureMatch(SSSQueryMol, SSSTargetMol, switches);
return(b);
}
/// <summary>
/// Calculate similarity score
/// </summary>
/// <param name="query"></param>
/// <param name="target"></param>
/// <returns></returns>
public double Molsim(
MoleculeMx query,
MoleculeMx target,
SimilaritySearchType type)
{
FingerprintType fpType = FingerprintType.Undefined;
if (type == SimilaritySearchType.Normal)
{
fpType = FingerprintType.MACCS;
}
else if (type == SimilaritySearchType.ECFP4)
{
fpType = FingerprintType.Circular;
}
else
{
throw new Exception("Similarity type not supported in this context: " + type);
}
bool newQuery = (QueryMol == null || QueryMol.PrimaryValue != query.PrimaryValue);
if (newQuery) // recalc query keys if query has changed
{
QueryMol = query.Clone();
QueryFingerprint = query.BuildBitSetFingerprint(fpType);
}
object targetFingerprint = target.BuildBitSetFingerprint(fpType);
double score = MoleculeMx.CalculateBitSetFingerprintSimilarity(QueryFingerprint, targetFingerprint);
return(score);
}
