private void btnSchema_Click(object sender, EventArgs e)
{
try
{
#region Code Commented
//string strErr_out = "";
//string strXMLSchema = AppDomain.CurrentDomain.BaseDirectory + "PatentEnhancedPrioritySubstanceIndexing-2.3.xsd";
//if (Validations.ValidateXmlAgainstSchema(txtXmlFile.Text, strXMLSchema, out strErr_out))
//{
// MessageBox.Show("Validation success");
//}
//else
//{
// MessageBox.Show(strErr_out);
//}
#endregion
ParseXMLFile();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static DataTable CreateTANDetailsTable()
{
DataTable dtStructData = new DataTable();
try
{
dtStructData.Columns.Add("tan_dtl_id", typeof(Int32));
dtStructData.Columns.Add("structure", typeof(object));
dtStructData.Columns.Add("mol_weight", typeof(double));
dtStructData.Columns.Add("mol_formula", typeof(string));
dtStructData.Columns.Add("iupac_name", typeof(string));
dtStructData.Columns.Add("page_number", typeof(int));
dtStructData.Columns.Add("page_label", typeof(string));
dtStructData.Columns.Add("example_number", typeof(string));
dtStructData.Columns.Add("en_name", typeof(string));
dtStructData.Columns.Add("table_number", typeof(string));
dtStructData.Columns.Add("inchi_key", typeof(string));
return(dtStructData);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(dtStructData);
}
public static string GetInchiKeyFromInchiString(string inchistring)
{
string strInchikey = "";
try
{
if (inchistring.Trim() != "")
{
string[] splitter = { "InChIKey=" };
string[] strInchiArr = inchistring.Trim().Split(splitter, StringSplitOptions.RemoveEmptyEntries);
if (strInchiArr != null)
{
if (strInchiArr.Length == 2)
{
strInchikey = strInchiArr[1];
}
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(strInchikey);
}
public static ArrayList GetTANListFromTanTable(DataTable _dtTanIds)
{
try
{
if (_dtTanIds != null)
{
ArrayList lstTANIds = new ArrayList();
if (_dtTanIds.Rows.Count > 0)
{
for (int i = 0; i < _dtTanIds.Rows.Count; i++)
{
if (!lstTANIds.Contains(_dtTanIds.Rows[i][0].ToString()))
{
lstTANIds.Add(_dtTanIds.Rows[i][0].ToString());
}
}
}
return(lstTANIds);
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(null);
}
private void OpenFile()
{
try
{
openFileDialog1.Filter = "XML Files (*.xml)|*.xml|Text Files (*.txt)|*.txt|All Files (*.*)|*.*";
openFileDialog1.FilterIndex = 1;
openFileDialog1.Title = "Select a file to open";
openFileDialog1.FileName = "";
openFileDialog1.ShowDialog();
if (openFileDialog1.FileName != "")
{
xmlFileName = openFileDialog1.FileName;
txtXmlFile.Text = xmlFileName.Trim();
RichTextBox1.LoadFile(openFileDialog1.FileName, RichTextBoxStreamType.PlainText);
this.Text = "Xml Editor | " + xmlFileName.Substring(xmlFileName.LastIndexOf("\\") + 1);
}
Changed = false;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static int GetMoleculeCountFromFile(string filename)
{
try
{
string text = "";
FileStream FS = new FileStream(filename, FileMode.Open, FileAccess.Read, FileShare.Read);
StreamReader SR = new StreamReader(FS);
text = SR.ReadToEnd();
SR.Close();
SR.Dispose();
FS.Close();
FS.Dispose();
Regex RE = new Regex("^\\$\\$\\$\\$", RegexOptions.Multiline);
MatchCollection theMatches = RE.Matches(text);
return(theMatches.Count);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(0);
}
public static string RemoveSMILESFromIUPACName(string iupacname)
{
string strIUPACName = iupacname;
try
{
if (iupacname.Trim() != "")
{
string[] strSplitter = { " " };
string[] strSplitVals = iupacname.Split(strSplitter, StringSplitOptions.RemoveEmptyEntries);
if (strSplitVals != null)
{
if (strSplitVals.Length > 1)
{
//strIUPACName = strSplitVals[1].Trim();
//return strIUPACName;
strSplitVals[0] = "";
strIUPACName = String.Join(" ", strSplitVals);
return(strIUPACName.Trim());
}
else if (strSplitVals.Length == 1)
{
strIUPACName = String.Join(" ", strSplitVals);
return(strIUPACName.Trim());
}
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(strIUPACName);
}
public static string GetStructureInchiKey(string _molfilestring)
{
string strInchiKey = "Inchi Not generated";
try
{
MolHandler mHandler = new MolHandler(_molfilestring);
Molecule mol = mHandler.getMolecule();
try
{
strInchiKey = mol.toFormat("inchi:key");
}
catch //Exception is inchi not generated
{
// if inchi not generated
SetMolAbsStereo_Inchi_NotGenerated(ref mol);
strInchiKey = mol.toFormat("inchi:key");
}
if (strInchiKey != "")
{
strInchiKey = Validations.GetInchiKeyFromInchiString(strInchiKey);
}
return(strInchiKey);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(strInchiKey);
}
private static Molecule StandardizeMolecule(Molecule mol, out bool ischiral_out)
{
Molecule molChem = null;
bool blIsChiral = false;
try
{
Standardizer molSdz = new Standardizer("absolutestereo:set");
molChem = molSdz.standardize(mol);
blIsChiral = molChem.isAbsStereo();
#region Code Commented
//string strDirPath = AppDomain.CurrentDomain.BaseDirectory.ToString();
//string strXmlPath = strDirPath + "chiral.xml";
//StandardizerConfiguration sconfing = new StandardizerConfiguration();
//sconfing.read(strXmlPath);
//Standardizer sdz = sconfing.getStandardizer();
//molChem = sdz.standardize(mol);
//Standardizer sdz = new Standardizer(new File(strXmlPath));
#endregion
ischiral_out = blIsChiral;
return(molChem);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
ischiral_out = blIsChiral;
return(molChem);
}
private static void SetMolAbsStereo_Inchi_NotGenerated(ref Molecule _molobj)
{
try
{
int atno = 0;
MolAtom ma = null;
for (int i = 0; i < (_molobj.getAtomCount() - 1); i++)
{
atno = _molobj.getAtom(i).getAtno();
if (atno > 109)
{
ma = _molobj.getAtom(i);
ma.setAtno(6);
}
}
bool flag1 = _molobj.ungroupSgroups();
bool flag2 = _molobj.hydrogenize(false);
if (_molobj.isAbsStereo())
{
_molobj.setAbsStereo(true);
}
_molobj.aromatize(false);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private DataTable GetTanDetailsTableFromActiveForm(out string tan_out, out string srcCntrl_out)
{
DataTable dtTanDetails = null;
string strTanNumber = "";
string strSrcCntrl = "";
try
{
frmCurator objfrmCurator = null;
Forms.frmQryDuplicates objfrmQueryDups = null;
Enumeration.frmRGrpEnum objfrmEnum = null;
Form objActiveForm = this.ActiveMdiChild;
if (objActiveForm != null)
{
if (objActiveForm.Name.ToUpper() == "FRMCURATOR")
{
objfrmCurator = (frmCurator)objActiveForm;
dtTanDetails = objfrmCurator.TANDetailsTbl;
strTanNumber = objfrmCurator.TANNumber;
strSrcCntrl = "FRMCURATOR";
}
else if (objActiveForm.Name.ToUpper() == "FRMQRYDUPLICATES")
{
objfrmQueryDups = (Forms.frmQryDuplicates)objActiveForm;
dtTanDetails = objfrmQueryDups.ucCheckDuplicates1.SearchResults;
strTanNumber = objfrmQueryDups.ucCheckDuplicates1.TANNumber;
strSrcCntrl = "FRMQRYDUPLICATES";
}
else if (objActiveForm.Name.ToUpper() == "FRMRGRPENUM")
{
objfrmEnum = (Enumeration.frmRGrpEnum)objActiveForm;
dtTanDetails = objfrmEnum.EnumResultsTbl;
strTanNumber = objfrmEnum.TANNumber;
string strPageNo = objfrmEnum.PageNumber;
string strPageLabel = objfrmEnum.PageLabel;
string strExampleNo = objfrmEnum.ExampleNumber;
string strTableNo = objfrmEnum.TableNumber;
strSrcCntrl = "FRMRGRPENUM";
RebuildTANDetailsTable_Enum(ref dtTanDetails, strPageNo, strPageLabel, strExampleNo, strTableNo);
}
tan_out = strTanNumber;
srcCntrl_out = strSrcCntrl;
return(dtTanDetails);
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
tan_out = strTanNumber;
srcCntrl_out = strSrcCntrl;
return(dtTanDetails);
}
private void rGroupToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
FormCollection frmColl = Application.OpenForms;
Enumeration.frmRGrpEnum objRgrpEnum = null;
bool blFrmOpen = false;
foreach (Form frm in frmColl)
{
if (frm.Name.ToUpper() == "FRMRGRPENUM")
{
objRgrpEnum = (Enumeration.frmRGrpEnum)frm;
blFrmOpen = true;
objRgrpEnum.Show();
objRgrpEnum.WindowState = FormWindowState.Maximized;
}
}
if (!blFrmOpen)
{
objRgrpEnum = new Enumeration.frmRGrpEnum();
objRgrpEnum.MdiParent = this;
objRgrpEnum.Show();
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void openXMLToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
FormCollection frmColl = Application.OpenForms;
frmXMLViewer_Validation xmlView_Valid = null;
bool blFrmOpen = false;
foreach (Form frm in frmColl)
{
if (frm.Name.ToUpper() == "FRMXMLVIEWER_VALIDATION")
{
xmlView_Valid = (frmXMLViewer_Validation)frm;
blFrmOpen = true;
xmlView_Valid.Show();
xmlView_Valid.WindowState = FormWindowState.Maximized;
}
}
if (!blFrmOpen)
{
xmlView_Valid = new frmXMLViewer_Validation();
xmlView_Valid.MdiParent = this;
xmlView_Valid.Show();
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void btnBrowseXML_Click(object sender, EventArgs e)
{
try
{
OpenFile();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void frmXMLViewer_Validation_Load(object sender, EventArgs e)
{
try
{
this.WindowState = FormWindowState.Maximized;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void exitToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
this.Close();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void frmChemDraw_Load(object sender, EventArgs e)
{
try
{
AssignMolsToControls();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
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 = Validations.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_NTS.WriteErrorLog(ex.ToString());
}
totalreccnt = intTotalRecCnt;
dupreccnt = intDupRecCnt;
return(blStatus);
}
private void createToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
Forms.frmCreateUser objCreateUser = new NameToStructureApplication.Forms.frmCreateUser();
objCreateUser.Show();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void changePasswordToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
Forms.frmChangePwd objChangePwd = new NameToStructureApplication.Forms.frmChangePwd();
objChangePwd.ShowDialog();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void retrieveDictStripMenuItem1_Click(object sender, EventArgs e)
{
try
{
Forms.frmRetrieveDict objRetDict = new NameToStructureApplication.Forms.frmRetrieveDict();
objRetDict.ShowDialog();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static string GetConvertedIUPACName(string iupacname)
{
string strIUPACName = "";
try
{
if (iupacname.Trim() != "")
{
int intHashCode = 0;
foreach (Char c in iupacname.Trim())
{
intHashCode = c.GetHashCode();
switch (intHashCode)
{
case 913:
strIUPACName = strIUPACName + ".alpha.";
break;
case 914:
strIUPACName = strIUPACName + ".beta.";
break;
case 915:
strIUPACName = strIUPACName + ".gamma.";
break;
case 916:
strIUPACName = strIUPACName + ".delta.";
break;
case 917:
strIUPACName = strIUPACName + ".epsilon.";
break;
default:
strIUPACName = strIUPACName + c;
break;
}
}
return(strIUPACName);
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(strIUPACName);
}
private void deleteDictToolStripMenuItem1_Click(object sender, EventArgs e)
{
try
{
Forms.frmDeleteDict objDeleteDict = new Forms.frmDeleteDict();
objDeleteDict.ShowDialog();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private static void ValidationEventHandler(object sender, ValidationEventArgs args)
{
try
{
blValidateFail = true;
strErrMSg = "Validation error: " + args.Message;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void SetBehavior()
{
try
{
bool bFileExists = ((txtFileName.Text.Trim() != string.Empty) && File.Exists(txtFileName.Text));
xmlGridView1.ViewMode = XmlGridView.VIEW_MODE.XML;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
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 = Validations.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 = Validations.GetInchiKeyFromInchiString(strInchiKey);
intRecIndx++;
if ((strInchiKey == strqryMolInchi) && (intRecIndx != recindex))
{
blStatus = true;
mol_out = objMol;
return(blStatus);
}
}
molImp.close();
molInStream.close();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
mol_out = null;
return(blStatus);
}
private void browsePDFToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
frmCurator frmNToS = new frmCurator();
frmNToS.MdiParent = this;
frmNToS.Show();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
static void Main()
{
try
{
Application.EnableVisualStyles();
Application.SetCompatibleTextRenderingDefault(false);
Application.Run(new frmMain_PepsiLite());//Enumeration.frmRGrpEnum frmMain_PepsiLite
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void checkDuplicatesToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
Forms.frmQryDuplicates objfrmQryDups = new Forms.frmQryDuplicates();
objfrmQryDups.MdiParent = this;
objfrmQryDups.Show();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void OnXmlSyntaxError(object sender, ValidationEventArgs args)
{
try
{
IsWellFormedXml = false;
strError = lineInf.LineNumber.ToString() + ": " + lineInf.LinePosition.ToString() + " " + args.Message;
ListBox1.Items.Add(strError);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}