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);
}
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);
}
/// <summary>
/// 返回整个路线列表
/// </summary>
/// <param name="result"></param>
/// <returns></returns>
public string WriteToMrvWithAllRouteWithStr(string result)
{
//取根路线
List <TreeNodes> treeNodes = JsonConvert.DeserializeObject <List <TreeNodes> >(result);
TreeNodes rootTree = new TreeNodes();
foreach (var item in treeNodes)
{
if (item.PID == 0)
{
rootTree = item;
}
}
//树绘图
MDocument md = WriteTree(rootTree);
return(MolExporter.exportToFormat(md, "mrv"));
}
/// <summary>
/// 返回文件流的mrv
/// </summary>
/// <param name="result"></param>
/// <returns></returns>
public MemoryStream WriteToMrvWithBranch(string result)
{
//取根路线
List <TreeNodes> treeNodes = JsonConvert.DeserializeObject <List <TreeNodes> >(result);
TreeNodes rootTree = new TreeNodes();
foreach (var item in treeNodes)
{
if (item.PID == 0)
{
rootTree = item;
}
}
//树绘图
MDocument md = WriteBrachTree(rootTree);
MemoryStream stream = new MemoryStream(MolExporter.exportToBinFormat(md, "cdx"));
return(stream);
}
public static bool EmportToSdFile(string _filename, DataTable _dtTanDetails, ArrayList _selproplist)
{
bool blWriteStatus = false;
try
{
if (_filename.Trim() != "" && _dtTanDetails != null)
{
if (_dtTanDetails.Rows.Count > 0)
{
FileOutputStream fOutStream = new FileOutputStream(_filename, true);
MolExporter objmExporter = new MolExporter(fOutStream, "sdf");
MolHandler objmHandler = null;
Molecule objMol = null;
for (int rIndx = 0; rIndx < _dtTanDetails.Rows.Count; rIndx++)
{
objmHandler = new MolHandler(_dtTanDetails.Rows[rIndx]["structure"].ToString());
objMol = objmHandler.getMolecule();
if (_selproplist.Contains("Mol Weight"))
{
objMol.setProperty("Mol Weight", _dtTanDetails.Rows[rIndx]["mol_weight"].ToString());
}
if (_selproplist.Contains("Mol Formula"))
{
objMol.setProperty("Mol Formula", _dtTanDetails.Rows[rIndx]["mol_formula"].ToString());
}
if (_selproplist.Contains("Page Number"))
{
objMol.setProperty("Page Number", _dtTanDetails.Rows[rIndx]["page_number"].ToString());
}
if (_selproplist.Contains("Page Label"))
{
objMol.setProperty("Page Label", _dtTanDetails.Rows[rIndx]["page_label"].ToString());
}
if (_selproplist.Contains("Example Number"))
{
objMol.setProperty("Example Number", _dtTanDetails.Rows[rIndx]["example_number"].ToString());
}
if (_selproplist.Contains("Table Number"))
{
objMol.setProperty("Table Number", _dtTanDetails.Rows[rIndx]["table_number"].ToString());
}
if (_selproplist.Contains("en name"))
{
objMol.setProperty("en name", _dtTanDetails.Rows[rIndx]["en_name"].ToString());
}
if (_selproplist.Contains("IUPAC Name"))
{
objMol.setProperty("IUPAC Name", _dtTanDetails.Rows[rIndx]["iupac_name"].ToString());
}
objmExporter.write(objMol);
}
fOutStream.close();
objmExporter.close();
blWriteStatus = true;
return(blWriteStatus);
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blWriteStatus);
}
public static bool ExportToSDF(SpectralInfo compSpectralData, string outputFolderPath)
{
bool blStatus = false;
try
{
if (compSpectralData != null && !string.IsNullOrEmpty(outputFolderPath))
{
MolHandler objMolHandler = null;
Molecule objMol = null;
int intMolRegNo = 0;
string strOutFileName = "";
//NMR Spectral
for (int i = 0; i < compSpectralData.NMRSpectralList.Count; i++)
{
intMolRegNo = intMolRegNo + 1;
strOutFileName = strOutFileName + "_" + compSpectralData.NMRSpectralList[i].Nucleus + ".sdf";
FileOutputStream fOutStream = new FileOutputStream(strOutFileName, true);
MolExporter objmExporter = new MolExporter(fOutStream, "sdf");
//Compound Molecule
objMolHandler = new MolHandler(compSpectralData.CompoundInformation.Compound.ToString());
objMol = objMolHandler.getMolecule();
//Article Information
objMol.setProperty("journal name", compSpectralData.ArticleInformation.JournalName);
objMol.setProperty("article doi", compSpectralData.ArticleInformation.DOI);
objMol.setProperty("authors", compSpectralData.ArticleInformation.Authors);
//Compound Information
objMol.setProperty("MOLREGNO", intMolRegNo.ToString());
objMol.setProperty("chemical name", compSpectralData.CompoundInformation.IUPACName);
objMol.setProperty("mol comments", compSpectralData.CompoundInformation.Comments);
objMol.setProperty("pagenumber", compSpectralData.CompoundInformation.PageNo);
//NMR information
objMol.setProperty("nmr spectrometer", compSpectralData.NMRSpectralList[i].SpectroMeter);
objMol.setProperty("nucleus", compSpectralData.NMRSpectralList[i].Nucleus);
objMol.setProperty("solvent", compSpectralData.NMRSpectralList[i].Solvent);
objMol.setProperty("nmr frequency", compSpectralData.NMRSpectralList[i].Frequency);
objMol.setProperty("nmr shift values", compSpectralData.NMRSpectralList[i].ShiftValues);
objMol.setProperty("nmr standard", compSpectralData.NMRSpectralList[i].StdSolvent);
objmExporter.write(objMol);
fOutStream.close();
objmExporter.close();
}
//Other Spectral
for (int i = 0; i < compSpectralData.OtherSpectralList.Count; i++)
{
intMolRegNo = intMolRegNo + 1;
strOutFileName = strOutFileName + "_" + compSpectralData.OtherSpectralList[i].ValueType + ".sdf";
FileOutputStream fOutStream = new FileOutputStream(strOutFileName, true);
MolExporter objmExporter = new MolExporter(fOutStream, "sdf");
//Compound Molecule
objMolHandler = new MolHandler(compSpectralData.CompoundInformation.Compound.ToString());
objMol = objMolHandler.getMolecule();
//Article Information
objMol.setProperty("journal name", compSpectralData.ArticleInformation.JournalName);
objMol.setProperty("article doi", compSpectralData.ArticleInformation.DOI);
objMol.setProperty("authors", compSpectralData.ArticleInformation.Authors);
//Compound Information
objMol.setProperty("MOLREGNO", intMolRegNo.ToString());
objMol.setProperty("chemical name", compSpectralData.CompoundInformation.IUPACName);
objMol.setProperty("mol comments", compSpectralData.CompoundInformation.Comments);
objMol.setProperty("pagenumber", compSpectralData.CompoundInformation.PageNo);
//IR information
if (compSpectralData.OtherSpectralList[i].ValueType.ToUpper() == "IR")
{
objMol.setProperty("ir spectrometer", compSpectralData.OtherSpectralList[i].SpectroMeter);
objMol.setProperty("ir spectral peaks", compSpectralData.OtherSpectralList[i].PeakValues);
objMol.setProperty("sample prep", compSpectralData.OtherSpectralList[i].SamplePreparation);
}
//Mass information
if (compSpectralData.OtherSpectralList[i].ValueType.ToUpper() == "MASS")
{
objMol.setProperty("mass spectrometer", compSpectralData.OtherSpectralList[i].SpectroMeter);
objMol.setProperty("mass spectral peaks", compSpectralData.OtherSpectralList[i].PeakValues);
objMol.setProperty("mass.method", compSpectralData.OtherSpectralList[i].Method);
objMol.setProperty("eV", compSpectralData.OtherSpectralList[i].ElectronVolts);
}
//UV information
if (compSpectralData.OtherSpectralList[i].ValueType.ToUpper() == "UV")
{
objMol.setProperty("mass spectrometer", compSpectralData.OtherSpectralList[i].SpectroMeter);
objMol.setProperty("mass spectral peaks", compSpectralData.OtherSpectralList[i].PeakValues);
objMol.setProperty("comments", compSpectralData.OtherSpectralList[i].Comments);
}
objmExporter.write(objMol);
fOutStream.close();
objmExporter.close();
}
blStatus = true;
}
}
catch (Exception ex)
{
ErrorHandling.WriteErrorLog(ex.ToString());
}
return(blStatus);
}
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);
}
