public static bool DeleteAllDuplicateStructures(string filename, out int totalreccnt, out int dupreccnt)
{
bool blStatus = false;
int intDupRecCnt = 0;
int intTotalRecCnt = 0;
try
{
MolInputStream molInStream = new MolInputStream(new FileInputStream(filename));
MolImporter molImp = new MolImporter(molInStream);
Molecule objMol = new Molecule();
DataOutputStream dOutStream = new DataOutputStream(new FileOutputStream(filename));
MolExporter molExpt = new MolExporter(dOutStream, "sdf");
bool blIsChiral = false;
string strInchiKey = "";
ArrayList molInchiList = new ArrayList();
while (molImp.read(objMol))
{
objMol = StandardizeMolecule(objMol, out blIsChiral);
strInchiKey = objMol.toFormat("inchi:key");
strInchiKey = GetInchiKeyFromInchiString(strInchiKey);
if (!molInchiList.Contains(strInchiKey))
{
molInchiList.Add(strInchiKey);
molExpt.write(objMol);
}
else
{
intDupRecCnt++;
}
intTotalRecCnt++;
}
//Close all the import & export objects
molImp.close();
molInStream.close();
dOutStream.close();
molExpt.close();
blStatus = true;
}
catch (Exception ex)
{
ErrorHandling.WriteErrorLog(ex.ToString());
}
totalreccnt = intTotalRecCnt;
dupreccnt = intDupRecCnt;
return(blStatus);
}
public static bool CheckForDuplicateStructure(string filename, string qrymolfile, int recindex, out Molecule mol_out)
{
bool blStatus = false;
try
{
bool blIsChiral = false;
MolHandler mHandler = new MolHandler(qrymolfile);
Molecule qryMol = mHandler.getMolecule();
qryMol = StandardizeMolecule(qryMol, out blIsChiral);
string strqryMolInchi = qryMol.toFormat("inchi:key");
strqryMolInchi = GetInchiKeyFromInchiString(strqryMolInchi);
//Specify input file to MolInputStream object
MolInputStream molInStream = new MolInputStream(new FileInputStream(filename));
MolImporter molImp = new MolImporter(molInStream);
Molecule objMol = new Molecule();
blIsChiral = false;
string strInchiKey = "";
int intRecIndx = 0;
Molecule molObj_Stand = null;
while (molImp.read(objMol))
{
molObj_Stand = StandardizeMolecule(objMol, out blIsChiral);
strInchiKey = objMol.toFormat("inchi:key");
strInchiKey = GetInchiKeyFromInchiString(strInchiKey);
intRecIndx++;
if ((strInchiKey == strqryMolInchi) && (intRecIndx != recindex))
{
blStatus = true;
mol_out = objMol;
return(blStatus);
}
}
molImp.close();
// molInStream.close();
}
catch (Exception ex)
{
ErrorHandling.WriteErrorLog(ex.ToString());
}
mol_out = null;
return(blStatus);
}
public static bool DeleteRecordFromSDFile(string _infilename, int _recindex)
{
bool blStatus = false;
try
{
int intRecIndex = 0;
MolInputStream molInStream = new MolInputStream(new FileInputStream(_infilename));
MolImporter molImp = new MolImporter(molInStream);
string strInputFilePath = System.IO.Path.GetDirectoryName(_infilename);
string strExecPath = Application.StartupPath;
string strFileName = System.IO.Path.GetFileName(_infilename);
string strOutFile = strExecPath + "\\" + strFileName;
DataOutputStream dOutStream = new DataOutputStream(new FileOutputStream(strOutFile));
MolExporter mExpt = new MolExporter(dOutStream, "sdf");
Molecule objMol = new Molecule();
while (molImp.read(objMol))
{
intRecIndex++;
if (intRecIndex != _recindex)
{
mExpt.write(objMol);
}
}
molImp.close();
molInStream.close();
mExpt.close();
dOutStream.close();
System.IO.File.Copy(strOutFile, _infilename, true);
System.IO.File.Delete(strOutFile);
blStatus = true;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blStatus);
}
public static void ImportAgentsMaster(string filePath)
{
DataTable dtSolvAgents = null;
try
{
if (GlobalVariables.SolvCatalystMaster == null)
{
FileInputStream fInStream = new FileInputStream(filePath);
MolImporter molImp = new MolImporter(fInStream, "sdf");
Molecule objMol = new Molecule();
GlobalVariables.SolvCatalystMaster = new DataTable();
GlobalVariables.SolvCatalystMaster.Columns.Add("MOL_FILE");
GlobalVariables.SolvCatalystMaster.Columns.Add("IUPAC_NAME");
GlobalVariables.SolvCatalystMaster.Columns.Add("INCHI_KEY");
GlobalVariables.SolvCatalystMaster.Columns.Add("OTHER_NAMES");
while (molImp.read(objMol))
{
DataRow dRow = GlobalVariables.SolvCatalystMaster.NewRow();
dRow["MOL_FILE"] = objMol.toFormat("mol");
dRow["IUPAC_NAME"] = objMol.getProperty("MOL:SYMBOL(1)");
dRow["INCHI_KEY"] = objMol.getProperty("MOL:INCHIKEY");
int propCnt = objMol.getPropertyCount();
string strOtherName = "";
for (int i = 0; i < propCnt; i++)
{
string propName = objMol.getPropertyKey(i);
if (propName.ToUpper() != "MOL:SYMBOL(1)" && propName.ToUpper().StartsWith("MOL:SYMBOL("))
{
strOtherName = string.IsNullOrEmpty(strOtherName) ? objMol.getPropertyObject(propName).ToString() : strOtherName.Trim() + "," + objMol.getPropertyObject(propName).ToString();
}
}
dRow["OTHER_NAMES"] = strOtherName;
GlobalVariables.SolvCatalystMaster.Rows.Add(dRow);
}
}
}
catch (Exception)
{
throw;
}
// return dtSolvAgents;
}
public static int GetDuplicateRecordsCount(string filename, out int totalreccnt)
{
int intDupRecCnt = 0;
int intTotalRecCnt = 0;
try
{
MolInputStream molInStream = new MolInputStream(new FileInputStream(filename));
MolImporter molImp = new MolImporter(molInStream);
Molecule objMol = new Molecule();
bool blIsChiral = false;
string strInchiKey = "";
ArrayList molInchiList = new ArrayList();
while (molImp.read(objMol))
{
objMol = StandardizeMolecule(objMol, out blIsChiral);
strInchiKey = objMol.toFormat("inchi:key");
strInchiKey = GetInchiKeyFromInchiString(strInchiKey);
if (!molInchiList.Contains(strInchiKey))
{
molInchiList.Add(strInchiKey);
}
else
{
intDupRecCnt++;
}
intTotalRecCnt++;
}
molImp.close();
//molInStream.close();
}
catch (Exception ex)
{
ErrorHandling.WriteErrorLog(ex.ToString());
}
totalreccnt = intTotalRecCnt;
return(intDupRecCnt);
}
private DataTable ReadAllMoleculesIntoTable(MolImporter _molImporter)
{
DataTable dtMolData = null;
try
{
dtMolData = ChemistryOperations.CreateTANDetailsTable();
#region Code Commented
//dtMolData.Columns.Add("Structure", typeof(object));
//dtMolData.Columns.Add("MolWeight", typeof(string));
//dtMolData.Columns.Add("MolFormula", typeof(string));
//dtMolData.Columns.Add("IupacName", typeof(string));
//dtMolData.Columns.Add("PageNumber", typeof(string));
//dtMolData.Columns.Add("PageLabel", typeof(string));
//dtMolData.Columns.Add("ExampleNumber", typeof(string));
//dtMolData.Columns.Add("EnName", typeof(string));
//dtMolData.Columns.Add("IsChiral", typeof(string));
#endregion
DataRow dtRow = null;
while (_molImporter.read(mol))
{
dtRow = dtMolData.NewRow();
//Mol Structure
dtRow["Structure"] = mol.toFormat("mol");
//Mol Weight
dtRow["MolWeight"] = mol.getMass().ToString();
//Mol Formula
dtRow["MolFormula"] = mol.getFormula();
//Page No
dtRow["PageNumber"] = mol.getProperty("Page Number").Trim();
//Page Label
dtRow["PageLabel"] = mol.getProperty("Page Label").Trim();
//Example Number
dtRow["ExampleNumber"] = mol.getProperty("Example Number").Trim();
//IUPAC Name
dtRow["IupacName"] = mol.getProperty("IUPAC Name").Trim();
//en name
dtRow["EnName"] = mol.getProperty("en name").Trim();
//Is Chiral
if (mol.isAbsStereo())
{
dtRow["IsChiral"] = "True";
}
else
{
dtRow["IsChiral"] = "False";
}
dtMolData.Rows.Add(dtRow);
}
return(dtMolData);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(dtMolData);
}
public static bool WriteXmlFile(string infilename, string tannumber, string outputfilepath)
{
System.IO.StreamWriter sWriter = null;
try
{
sWriter = new System.IO.StreamWriter(outputfilepath);
//xml file header information
sWriter.WriteLine("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>");
sWriter.WriteLine("<patent xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"PatentEnhancedPrioritySubstanceIndexing-2.3.xsd\">");
sWriter.WriteLine("<patentInfo>");
sWriter.WriteLine("<tan>" + tannumber + "</tan>");
sWriter.WriteLine("<language>en</language>");
sWriter.WriteLine("</patentInfo>");
sWriter.WriteLine("<propheticSubstances>");
//Specify input file to MolInputStream object
MolInputStream molInStream = new MolInputStream(new FileInputStream(infilename));
MolImporter molImp = new MolImporter(molInStream);
Molecule mol = new Molecule();
//Declare mol property variables
string strPage_No = "";
string strPage_Lbl = "";
string strExample_Lbl = "";
string strEn_name = "";
string strIUPAC_Name = "";
string strStandMol = "";
string strMolBase64 = "";
//Read molecules from molImporter
while (molImp.read(mol))
{
sWriter.WriteLine("<propheticSubstance>");
sWriter.WriteLine("<patentLocation>");
//Page No
strPage_No = "";
strPage_No = mol.getProperty("Page Number").Trim();
sWriter.WriteLine("<pageNumber>" + strPage_No + "</pageNumber>");
//Page Label
strPage_Lbl = "";
strPage_Lbl = mol.getProperty("Page Label").Trim();
sWriter.WriteLine("<pageLabel>" + strPage_Lbl + "</pageLabel>");
//Example label
strExample_Lbl = "";
strExample_Lbl = mol.getProperty("Example Number").Trim();
sWriter.WriteLine("<exampleLabel>" + strExample_Lbl + "</exampleLabel>");
sWriter.WriteLine("</patentLocation>");
sWriter.WriteLine("<names>");
//en Name
strEn_name = "";
strEn_name = mol.getProperty("en name").Trim();//En Name
sWriter.WriteLine("<name lang=\"en\">" + strEn_name + "</name>");
//IUPAC Name
strIUPAC_Name = "";
strIUPAC_Name = mol.getProperty("IUPAC Name").Trim();
sWriter.WriteLine("<IUPACName>" + strIUPAC_Name + "</IUPACName>");
sWriter.WriteLine("</names>");
//Check here for V2000 format, if not write in error log
string mol2d = mol.toFormat("mol");
int v3000 = mol2d.IndexOf("V3000");
if (v3000 != -1)
{
//System.out.println("V3000 Error has occured! at Molecule Number: " + molCount + " in SDF file " + fileName);
//System.exit(0);
}
double nullMol = mol.getExactMass();
if (nullMol == 0)
{
//System.out.println("NULL Mol Error has occured! at Molecule Number: " + molCount + " in SDF file " + fileName);
//System.exit(0);
}
strStandMol = "";
strStandMol = mol.toFormat("mol");//MoleculeStandardizer.GetStandardizedMolecule(mol.toFormat("mol"));
strMolBase64 = "";
strMolBase64 = ConvertToBase64.GetConvertedMolString(strStandMol);
sWriter.WriteLine("<structureData encoding=\"Base64\" type=\"MDL Molfile V2000\">" + strMolBase64 + "</structureData>");//Base64 Molstring
sWriter.WriteLine("</propheticSubstance>");
}
sWriter.WriteLine("</propheticSubstances>");
sWriter.WriteLine("</patent>");
sWriter.Close();
sWriter.Dispose();
return(true);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
finally
{
sWriter.Close();
sWriter.Dispose();
}
return(true);
}
public static bool WriteXmlFileUsingXSD(string infilename, string tannumber, string outputfilepath)
{
bool blStatus = false;
try
{
patentInfo patentInfo_Obj = new patentInfo();
patentInfo_Obj.tan = tannumber;
patentInfo_Obj.language = languageType.en;
//Specify input file to MolInputStream object
MolInputStream molInStream = new MolInputStream(new FileInputStream(infilename));
MolImporter molImp = new MolImporter(molInStream);
Molecule mol = new Molecule();
//int intMolCnt = molImp.getRecordCount();
int intMolCnt = ChemistryOperations.GetMoleculeCountFromFile(infilename);
patentLocation patLoc = null;
name[] name_Arr = null;
name name_obj = null;
names names_Arr = null;
nameType namType = null;
structureDataType structDtype = null;
string[] strIUpacName = null;
propheticSubstance propSubstance_Obj = null;
propheticSubstance[] propSubstance_Arr = new propheticSubstance[intMolCnt];
propheticSubstances propSubstances_Obj = null;
patent patent_Obj = new patent();
int intCntr = 0;
//Read molecules from molImporter
while (molImp.read(mol))
{
patLoc = new patentLocation();
patLoc.pageLabel = mol.getProperty("Page Label");
patLoc.pageNumber = mol.getProperty("Page Number");
patLoc.exampleLabel = mol.getProperty("Example Number");
name_Arr = new name[1];
name_obj = new name();
name_obj.lang = languageType.en;
string[] strArr_EnName = new string[1];
strArr_EnName[0] = mol.getProperty("en name").Trim();
name_obj.Text = strArr_EnName;
name_Arr[0] = name_obj;
strIUpacName = new string[1];
strIUpacName[0] = mol.getProperty("IUPAC Name").Trim();
namType = new nameType();
namType.Text = strIUpacName;
names_Arr = new names();
names_Arr.IUPACName = namType;
names_Arr.name = name_Arr;
string strMol = mol.toFormat("mol");
int v3000 = strMol.IndexOf("V3000");
double nullMol = mol.getExactMass();
byte[] barr_Mol = null;
if (v3000 == -1 && nullMol != 0)
{
barr_Mol = System.Text.ASCIIEncoding.ASCII.GetBytes(strMol);
}
structDtype = new structureDataType();
structDtype.Value = barr_Mol;
propSubstance_Obj = new propheticSubstance();
propSubstance_Obj.structureData = structDtype;
propSubstance_Obj.patentLocation = patLoc;
propSubstance_Obj.names = names_Arr;
propSubstance_Arr[intCntr] = propSubstance_Obj;
intCntr++;
}
propSubstances_Obj = new propheticSubstances();
propSubstances_Obj.propheticSubstance = propSubstance_Arr;
patent_Obj.patentInfo = patentInfo_Obj;
patent_Obj.propheticSubstances = propSubstances_Obj;
// Serialization
XmlSerializer xmlSer = new XmlSerializer(typeof(patent));
TextWriter txtWriter = new StreamWriter(outputfilepath);
xmlSer.Serialize(txtWriter, patent_Obj);
txtWriter.Close();
txtWriter.Dispose();
molInStream.close();
molImp.close();
blStatus = true;
return(blStatus);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blStatus);
}
public static DataTable GetDuplicateRecords(string filename, string qrymolstring, out int totalrecs_out)
{
DataTable dtDupRecs = null;
int totalRecCnt = 0;
try
{
dtDupRecs = CreateTANDetailsTable();
dtDupRecs.Columns.Add("OrigRecIndex", typeof(Int32));
bool blIsChiral = false;
string InchiKey_Qry = "";
string InchiKey_Trgt = "";
MolHandler mHandler = new MolHandler(qrymolstring);
Molecule qryMol = mHandler.getMolecule();
StandardizeMolecule(qryMol, out blIsChiral);
InchiKey_Qry = qryMol.toFormat("inchi:key");
InchiKey_Qry = Validations.GetInchiKeyFromInchiString(InchiKey_Qry);
MolInputStream molInStream = new MolInputStream(new FileInputStream(filename));
MolImporter molImp = new MolImporter(molInStream);
Molecule objMol = new Molecule();
DataRow dtRow = null;
while (molImp.read(objMol))
{
objMol = StandardizeMolecule(objMol, out blIsChiral);
InchiKey_Trgt = objMol.toFormat("inchi:key");
InchiKey_Trgt = Validations.GetInchiKeyFromInchiString(InchiKey_Trgt);
if (InchiKey_Qry == InchiKey_Trgt)
{
dtRow = dtDupRecs.NewRow();
//Mol Structure
dtRow["Structure"] = objMol.toFormat("mol");
//Mol Weight
dtRow["MolWeight"] = objMol.getMass().ToString();
//Mol Formula
dtRow["MolFormula"] = objMol.getFormula();
//Page No
dtRow["PageNumber"] = objMol.getProperty("Page Number").Trim();
//Page Label
dtRow["PageLabel"] = objMol.getProperty("Page Label").Trim();
//Example Number
dtRow["ExampleNumber"] = objMol.getProperty("Example Number").Trim();
//IUPAC Name
dtRow["IupacName"] = objMol.getProperty("IUPAC Name").Trim();
//en name
dtRow["EnName"] = objMol.getProperty("en name").Trim();
//Is Chiral
if (objMol.isAbsStereo())
{
dtRow["IsChiral"] = "True";
}
else
{
dtRow["IsChiral"] = "False";
}
dtRow["OrigRecIndex"] = totalRecCnt;
dtDupRecs.Rows.Add(dtRow);
}
totalRecCnt++;
}
molImp.close();
molInStream.close();
totalrecs_out = totalRecCnt;
return(dtDupRecs);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
totalrecs_out = totalRecCnt;
return(dtDupRecs);
}
public static bool UpdateRecordInSdFile(string filename, int recindex, string molstring, string pagenum, string pagelabel, string examplenum, string iupacname, string enname)
{
bool blStatus = false;
try
{
int intRecIndex = 0;
MolInputStream molInStream = new MolInputStream(new FileInputStream(filename));
MolImporter molImp = new MolImporter(molInStream);
string strInputFilePath = System.IO.Path.GetDirectoryName(filename);
string strExecPath = Application.StartupPath;
string strFileName = System.IO.Path.GetFileName(filename);
string strOutFile = strExecPath + "\\" + strFileName;
DataOutputStream dOutStream = new DataOutputStream(new FileOutputStream(strOutFile));
MolExporter mExpt = new MolExporter(dOutStream, "sdf");
Molecule objMolecule = new Molecule();
try
{
while (molImp.read(objMolecule))
{
intRecIndex++;
if (intRecIndex == recindex)
{
MolHandler molHandler = new MolHandler(molstring);
Molecule molObj = molHandler.getMolecule();
objMolecule = molObj;
objMolecule.setProperty("Page Number", pagenum);
objMolecule.setProperty("Page Label", pagelabel);
objMolecule.setProperty("Example Number", examplenum);
objMolecule.setProperty("IUPAC Name", iupacname);
objMolecule.setProperty("en name", enname);
blStatus = true;
}
mExpt.write(objMolecule);
}
molImp.close();
molInStream.close();
mExpt.close();
dOutStream.close();
System.IO.File.Copy(strOutFile, filename, true);
System.IO.File.Delete(strOutFile);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
finally
{
molImp.close();
molInStream.close();
mExpt.close();
dOutStream.close();
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blStatus);
}