public MoleCulePostion(string smiles)
{
Mol = MolImporter.importMol(smiles);
//将苯环的圈改为双线
Mol.dearomatize();
chemaxon.calculations.clean.Cleaner.clean(Mol, 2);
//重置类参数
InitPosition();
//重置原子垂直坐标
InitAtom();
}
private MemoryStream writeq()
{
//树绘图
MDocument md = new MDocument(MolImporter.importMol("O"));
MPoint p1 = new MPoint(1, 1);
MPoint p2 = new MPoint(1, 2);
MPolyline arrow = new MRectangle(p1, p2);
md.addObject(arrow);
MemoryStream stream = new MemoryStream(MolExporter.exportToBinFormat(md, "mrv"));
return(stream);
}
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 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);
}
private static bool CompareProductsAndReactantsInTables(DataTable productData, DataTable reactantData)
{
bool blStatus = true;
try
{
int productsCnt = 0;
int reactantsCnt = 0;
RxnMolecule prodRxnMolecule = null;
RxnMolecule rctRxnMolecule = null;
Molecule molReactant = null;
Molecule molProduct = null;
MolSearch srchMol = new MolSearch();
MolSearchOptions so = new MolSearchOptions();//SearchConstants.DUPLICATE
so.setQueryAbsoluteStereo(true);
so.setChargeMatching(SearchConstants.__Fields.CHARGE_MATCHING_EXACT);
so.setDoubleBondStereoMatchingMode(StereoConstants.__Fields.DBS_ALL);
so.setImplicitHMatching(SearchConstants.__Fields.IMPLICIT_H_MATCHING_ENABLED);
so.setExactBondMatching(true);
so.setStereoSearchType(SearchConstants.__Fields.STEREO_EXACT);
so.setTautomerSearch(true);
so.setAttachedDataMatch(1);
so.setOrderSensitiveSearch(true);
so.setSearchType(5);
srchMol.setSearchOptions(so);
string rctInchi = "";
string prodInchi = "";
for (int prIndx = 0; prIndx < productData.Rows.Count; prIndx++)
{
if (!string.IsNullOrEmpty(productData.Rows[prIndx]["REACTION_SCHEME"].ToString()))
{
prodRxnMolecule = RxnMolecule.getReaction(MolImporter.importMol(productData.Rows[prIndx]["REACTION_SCHEME"].ToString()));
productsCnt = prodRxnMolecule.getProductCount();
}
for (int rctIndx = 0; rctIndx < reactantData.Rows.Count; rctIndx++)
{
if (!string.IsNullOrEmpty(reactantData.Rows[rctIndx]["REACTION_SCHEME"].ToString()))
{
rctRxnMolecule = RxnMolecule.getReaction(MolImporter.importMol(reactantData.Rows[rctIndx]["REACTION_SCHEME"].ToString()));
reactantsCnt = rctRxnMolecule.getReactantCount();
}
int rctLoopCnt = productsCnt < reactantsCnt ? productsCnt : reactantsCnt;
for (int p = 0; p < productsCnt; p++)
{
molProduct = prodRxnMolecule.getProduct(p);
for (int r = 0; r < rctLoopCnt; r++)
{
molReactant = rctRxnMolecule.getReactant(r);
rctInchi = ChemistryOperations.GetStructureInchiKey(molReactant.toFormat("mol"));
prodInchi = ChemistryOperations.GetStructureInchiKey(molProduct.toFormat("mol"));
if (rctInchi == prodInchi)
{
srchMol.setQuery(molReactant);
srchMol.setTarget(molProduct);
if (!srchMol.isMatching())
{
blStatus = false;
return(blStatus);
}
}
}
}
}
}
}
catch (Exception)
{
throw;
}
return(blStatus);
}