/// <summary>
/// Get molecule string in correct format
/// </summary>
/// <param name="vo"></param>
/// <param name="structureExportFormat"></param>
/// <returns></returns>
string GetMoleculeString(
object vo,
ExportStructureFormat structureExportFormat)
{
string molString = "";
MoleculeMx cs = (MoleculeMx)vo;
if (structureExportFormat == ExportStructureFormat.Chime)
{
molString = cs.GetChimeString(); // save structure as Chime
}
else if (structureExportFormat == ExportStructureFormat.Smiles)
{
molString = cs.GetSmilesString(); // save structure as Smiles
}
else if (structureExportFormat == ExportStructureFormat.Molfile)
{
molString = cs.GetMolfileString(); // save structure as molfile
}
else // save structure as molfile as default
{
molString = cs.GetMolfileString();
}
return(molString);
}
/// <summary>
/// Map query against structure & return highlighted match
/// </summary>
/// <param name="cs"></param>
/// <returns></returns>
public MoleculeMx HighlightMatchingSubstructure(
MoleculeMx cs)
{
if (cs.IsBiopolymerFormat) // fix later
{
return(cs);
}
MoleculeMx cs2 = null;
PerformanceTimer pt = PT.Start("HighlightMatchingSubstructure");
string molfile = CdkMolUtil.HilightSSSMatch(cs.GetMolfileString());
cs2 = new MoleculeMx(MoleculeFormat.Molfile, molfile);
pt.Update();
return(cs2);
}
/// <summary>
/// Align supplied structure to query structure
/// </summary>
/// <param name="skid"></param>
/// <returns></returns>
public MoleculeMx AlignToMatchingSubstructure(
MoleculeMx target)
{
if (target.IsBiopolymerFormat) // fix later
{
return(target);
}
MoleculeMx cs2 = null;
PerformanceTimer pt = PT.Start("AlignToMatchingSubstructure");
Stopwatch sw = Stopwatch.StartNew();
string molfile = CdkMolUtil.OrientToMatchingSubstructure(target.GetMolfileString());
cs2 = new MoleculeMx(MoleculeFormat.Molfile, molfile);
pt.Update();
return(cs2);
}
