public static Molecule AddRGrpMolToCoreMolecule(RgMolecule _rgMol, Molecule _coreMol, int _rgrpNum)
{
try
{
//Get RGroup position
int rgrpPos = GetRGroupPosition(_coreMol, _rgrpNum);
//Get Radical position
int radPos = GetRadicalPosition(_rgMol);
//Add Rgroup Molecule to Core Molecule
AddRGroupToCore(ref _coreMol, _rgMol);
_coreMol.add(new MolBond(_coreMol.getAtom(rgrpPos).getBond(0).getAtom1(), _rgMol.getAtom(radPos)));
_coreMol.removeNode(_coreMol.getNode(rgrpPos), CGraph.RMCLEANUP_ALL);
_coreMol.clean(2, null, null);
rgrpPos = GetRGroupPosition(_coreMol, _rgrpNum);
_coreMol.removeNode(_coreMol.getNode(rgrpPos), CGraph.RMCLEANUP_ALL);
_coreMol.clean(2, null, null);
return(_coreMol);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(null);
}
public static RgMolecule ReturnRGroupMolecule(string _rgrpSmiles, int _rgrpNum)
{
RgMolecule rgMol = null;
try
{
if (_rgrpSmiles != "")
{
MolHandler mHandler = new MolHandler(_rgrpSmiles);
Molecule objSmileMol = mHandler.getMolecule();
rgMol = new RgMolecule();
MolAtom mAtom = new MolAtom(MolAtom.RGROUP, 1, 0, 0);
mAtom.setRgroup(_rgrpNum);
rgMol.add(mAtom);
int radNum = 0;
for (int i = 0; i < objSmileMol.getAtomCount(); i++)
{
if (objSmileMol.getAtom(i).getRadical() > 0) //objSmileMol.getRadical(i)
{
radNum = i;
break;
}
}
for (int i = 0; i < objSmileMol.getAtomCount(); i++)
{
if (i == radNum)
{
objSmileMol.getAtom(i).setRadical(MolAtom.RAD_OFF);
}
rgMol.add(objSmileMol.getAtom(i));
}
for (int j = 0; j < objSmileMol.getBondCount(); j++)
{
rgMol.add(objSmileMol.getBond(j));
}
rgMol.add(new MolBond(objSmileMol.getAtom(radNum), mAtom));
rgMol.clean(2, null, null);
return(rgMol);
}
}
catch (Exception ex)
{
PepsiLiteErrorHandling.WriteErrorLog(ex.ToString());
}
return(rgMol);
}
private static int GetRadicalPosition(RgMolecule _rgMol)
{
int radPos = 0;
try
{
for (int k = 0; k < _rgMol.getAtomCount(); k++)
{
if (_rgMol.getAtom(k).getRadical() > 0)
{
radPos = k;
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(radPos);
}
public static Molecule AddRGrpMolToCoreMolecule(RgMolecule _rgMol, Molecule _coreMol, int _rgrpNum)
{
try
{
//Get RGroup position
int rgrpPos = GetRGroupPosition(_coreMol, _rgrpNum);
//Get Radical position
int radPos = GetRadicalPosition(_rgMol);
//Add Rgroup Molecule to Core Molecule
AddRGrpMolToCoreMol(ref _coreMol, _rgMol, radPos);
_coreMol.add(new MolBond(_coreMol.getAtom(rgrpPos).getBond(0).getAtom1(), _rgMol.getAtom(radPos)));
_coreMol.removeNode(_coreMol.getNode(rgrpPos), CGraph.RMCLEANUP_ALL);
_coreMol.clean(2, null, null);
rgrpPos = GetRGroupPosition(_coreMol, _rgrpNum);
_coreMol.removeNode(_coreMol.getNode(rgrpPos), CGraph.RMCLEANUP_ALL);
_coreMol.clean(2, null, null);
//chemaxon.reaction.Standardizer stnd = new chemaxon.reaction.Standardizer("removeexplicitH:radical");
//Molecule molCore = stnd.standardize(_coreMol);
//Standardize the molecule
Standardizer objStnd = new Standardizer(new File(@"C:\Documents and Settings\sairam.punyamantula\Desktop\stand.xml"));
Molecule molCore = objStnd.standardize(_coreMol);
molCore.clean(2, null, null);
return(molCore);
}
catch (Exception ex)
{
PepsiLiteErrorHandling.WriteErrorLog(ex.ToString());
}
return(null);
}
private static void AddRGrpMolToCoreMol(ref Molecule _coreMol, RgMolecule _rgMol, int _radicalpos)
{
try
{
for (int aIndx = 0; aIndx < _rgMol.getAtomCount(); aIndx++)
{
if (aIndx == _radicalpos)
{
_rgMol.getAtom(aIndx).setRadical(MolAtom.RAD_OFF);
}
_coreMol.add(_rgMol.getAtom(aIndx));
}
for (int bIndx = 0; bIndx < _rgMol.getBondCount(); bIndx++)
{
_coreMol.add(_rgMol.getBond(bIndx));
}
}
catch (Exception ex)
{
PepsiLiteErrorHandling.WriteErrorLog(ex.ToString());
}
}
private static void AddRGroupToCore(ref Molecule _coreMol, RgMolecule _rgMol)
{
try
{
for (int aIndx = 0; aIndx < _rgMol.getAtomCount(); aIndx++)
{
if (aIndx == 0)
{
_rgMol.getAtom(0).setRadical(MolAtom.RAD_OFF);
}
_coreMol.add(_rgMol.getAtom(aIndx));
}
for (int bIndx = 0; bIndx < _rgMol.getBondCount(); bIndx++)
{
_coreMol.add(_rgMol.getBond(bIndx));
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static DataTable GetRGroupEnumerationResults(DataTable _enumDataTbl, string _qryRCore)
{
DataTable dtEnumResData = new DataTable();
try
{
dtEnumResData.Columns.Add("id", typeof(string));
dtEnumResData.Columns.Add("structure", typeof(object));
dtEnumResData.Columns.Add("mol_weight", typeof(double));
dtEnumResData.Columns.Add("mol_formula", typeof(string));
dtEnumResData.Columns.Add("iupac_name", typeof(string));
dtEnumResData.Columns.Add("inchi_key", typeof(string));
int rgrpNum = 1;
Molecule molEnum = null;
MolHandler mHandler = null;
Molecule rCoreMol = null;
RgMolecule rgMol = null;
MolHandler mHand_Result = null;
DataRow dtRow = null;
string strMolFile = "";
string strIUPACName = "";
string strErrMsg = "";
if (_enumDataTbl != null)
{
if (_enumDataTbl.Rows.Count > 0)
{
for (int rowindx = 0; rowindx < _enumDataTbl.Rows.Count; rowindx++)
{
molEnum = new Molecule();
mHandler = new MolHandler(_qryRCore);
rCoreMol = mHandler.getMolecule();
try
{
for (int colindx = 1; colindx < _enumDataTbl.Columns.Count; colindx++)
{
rgrpNum = GetRgroupNumFromRGroupName(_enumDataTbl.Columns[colindx].ColumnName);
rgMol = ReturnRGroupMolecule(_enumDataTbl.Rows[rowindx][colindx].ToString(), rgrpNum);
//molEnum = AddRGrpMolToCoreMolecule(rgMol, rCoreMol, rgrpNum);
AddRGrpMolToCoreMolecule(ref rCoreMol, rgMol, rgrpNum);
}
//Set Radical Empty to Result Mol
SetRadicalEmptyToResultMol(ref rCoreMol);
mHand_Result = new MolHandler(rCoreMol);
strMolFile = "";
strMolFile = mHand_Result.toFormat("mol");
}
catch
{
}
dtRow = dtEnumResData.NewRow();
dtRow["id"] = _enumDataTbl.Rows[rowindx][0].ToString();
dtRow["structure"] = strMolFile;
if (strMolFile != "")
{
dtRow["mol_weight"] = mHand_Result.calcMolWeight();
dtRow["mol_formula"] = mHand_Result.calcMolFormula();
dtRow["inchi_key"] = ChemistryOperations.GetStructureInchiKey(strMolFile);
strIUPACName = "";
strErrMsg = "";
if (ChemistryOperations.GetIUPACNameFromStructure(strMolFile, out strIUPACName, out strErrMsg))
{
strIUPACName = Validations.GetConvertedIUPACName(strIUPACName);
}
else
{
strIUPACName = "IUPAC name not provided";
}
dtRow["iupac_name"] = strIUPACName;
}
dtEnumResData.Rows.Add(dtRow);
}
return(dtEnumResData);
}
}
}
catch (Exception ex)
{
PepsiLiteErrorHandling.WriteErrorLog(ex.ToString());
}
return(dtEnumResData);
}