private void btnWellFormNess_Click(object sender, EventArgs e)
{
try
{
ListBox1.Items.Clear();
RichTextBox1.SaveFile(xmlFileName, RichTextBoxStreamType.PlainText);
IsWellFormedXml = true;
using (FileStream stream = File.OpenRead(AppDomain.CurrentDomain.BaseDirectory + "PatentEnhancedPrioritySubstanceIndexing-2.3.xsd"))
{
XmlReaderSettings settings = new XmlReaderSettings();
XmlSchema schema = XmlSchema.Read(stream, OnXmlSyntaxError);
settings.ValidationType = ValidationType.Schema;
settings.Schemas.Add(schema);
settings.ValidationEventHandler += OnXmlSyntaxError;
string strError = "";
using (XmlReader validator = XmlReader.Create(txtXmlFile.Text.Trim(), settings))
{
try
{
// Validate the entire xml file
while (validator.Read())
{
lineInf = (IXmlLineInfo)validator;
}
}
catch (Exception ex)
{
if (lineInf.HasLineInfo())
{
strError = lineInf.LineNumber.ToString() + ": " + lineInf.LinePosition.ToString() + " " + ex.Message;
}
ListBox1.Items.Add(strError);
}
}
}
if (IsWellFormedXml)
{
MessageBox.Show("Wellformed XML", "Wellformed", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
}
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());
}
}
private void exportToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
string strTanNumber = "";
string strSrcCntrl = "";
DataTable dtTanDetails = GetTanDetailsTableFromActiveForm(out strTanNumber, out strSrcCntrl);
if (dtTanDetails != null)
{
if (dtTanDetails.Rows.Count > 0)
{
if (strTanNumber.Trim() != "")
{
Forms.frmExportOpts objfrmExp = new Forms.frmExportOpts();
ArrayList availProplst = GetExportListOnSourceControl(strSrcCntrl);
objfrmExp.AvailProps = availProplst;
if (objfrmExp.ShowDialog() == DialogResult.OK)
{
string strFilepath = objfrmExp.FolderPath + "\\" + strTanNumber + ".sdf";
if (Export.PepsiLite_Export.EmportToSdFile(strFilepath, dtTanDetails, objfrmExp.SelectedProps))
{
MessageBox.Show("Data exported to sd file successfully", "Export", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
}
}
else
{
MessageBox.Show("Please specify TAN Number", "Export", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
}
else
{
MessageBox.Show("No data is available to export", "Export", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
}
else
{
MessageBox.Show("No data is available to export", "Export", MessageBoxButtons.OK, MessageBoxIcon.Information);
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void frmReviewer_Load(object sender, EventArgs e)
{
try
{
ucChemProps_Navigation1.FileName = FileName;
ucChemProps_Navigation1.TANNumber = TANNumber;
ucChemProps_Navigation1.LoadMolecules();
this.WindowState = FormWindowState.Maximized;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static bool SetChemaxonLicenseFilePath(string licFilePath)
{
bool blStatus = false;
try
{
LicenseManager.setLicenseFile(licFilePath);
return(blStatus = true);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blStatus);
}
private void TabControl1_SelectedIndexChanged(object sender, EventArgs e)
{
try
{
if (TabControl1.SelectedIndex == 1)
{
RichTextBox1.SaveFile(xmlFileName, RichTextBoxStreamType.PlainText);
webBrowser1.Navigate(xmlFileName);
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static bool ValidateXmlAgainstSchema(string xmlFilename, string schemaFilename, out string errmsg)
{
bool blStatus = false;
XmlValidatingReader validator = null;
try
{
XmlTextReader xmlTRdr = new XmlTextReader(xmlFilename);
validator = new XmlValidatingReader(xmlTRdr);
validator.ValidationType = ValidationType.Schema;
XmlSchemaCollection xmlSchColl = new XmlSchemaCollection();
xmlSchColl.Add(null, schemaFilename);
validator.Schemas.Add(xmlSchColl);
blValidateFail = false;
validator.ValidationEventHandler += new ValidationEventHandler(ValidationEventHandler);
while (validator.Read())
{
if (blValidateFail)
{
break;
}
}
if (blValidateFail)
{
blStatus = false;
}
else
{
blStatus = true;
}
}
catch (XmlException ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
finally
{
validator.Close();
}
errmsg = strErrMSg;
return(blStatus);
}
private void btnSubmit_Click(object sender, EventArgs e)
{
try
{
if (rbnOpenEye.Checked)
{
if (renditor_OpenEye.MolfileString != null)
{
SelectedMol = renditor_OpenEye.MolfileString;
this.Close();
}
else
{
MessageBox.Show("No Molecule in the OpenEye");
}
}
else if (rbnChemDraw.Checked)
{
if (renditor_ChemDraw.MolfileString != null)
{
SelectedMol = renditor_ChemDraw.MolfileString;
this.Close();
}
else
{
MessageBox.Show("No Molecule in the ChemDraw");
}
}
else if (rbnChemAxon.Checked)
{
if (renditor_ChemAxon.MolfileString != null)
{
SelectedMol = renditor_ChemAxon.MolfileString;
this.Close();
}
else
{
MessageBox.Show("No Molecule in the ChemAxon");
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void DisableMenuItems()
{
try
{
browsePDFToolStripMenuItem.Enabled = false;
exportToolStripMenuItem.Enabled = false;
XMLToolStripMenuItem.Enabled = false;
queryToolStripMenuItem.Enabled = false;
EnumtoolStripMenuItem.Enabled = false;
setttingsToolStripMenuItem.Enabled = false;
dictionaryToolStripMenuItem.Enabled = false;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void frmMain_PepsiLite_Load(object sender, EventArgs e)
{
try
{
CheckAndSetEnvironVariable.SetEnvironmentVariableEx(strEnvVarName, strEnvVarVal);
CheckAndSetEnvironVariable.SetChemaxonLicenseFilePath(AppDomain.CurrentDomain.BaseDirectory + "license.cxl");
//Disable menu Items
DisableMenuItems();
//Open Login form
loginToolStripMenuItem_Click(null, null);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void frmXMLViewer_Load(object sender, EventArgs e)
{
try
{
txtFileName.Text = _filename;
xmlGridView1.DataFilePath = txtFileName.Text;
xmlGridView1.DataSetTableIndex = 0;
SetBehavior();
this.WindowState = FormWindowState.Maximized;
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
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 = Validations.GetInchiKeyFromInchiString(strInchiKey);
if (!molInchiList.Contains(strInchiKey))
{
molInchiList.Add(strInchiKey);
}
else
{
intDupRecCnt++;
}
intTotalRecCnt++;
}
molImp.close();
molInStream.close();
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
totalreccnt = intTotalRecCnt;
return(intDupRecCnt);
}
private void AssignMolsToControls()
{
try
{
if (OpenEyeMol.Trim() != "")
{
txtError_OpenEye.Visible = false;
renditor_OpenEye.MolfileString = OpenEyeMol;
}
else
{
txtError_OpenEye.Visible = true;
txtError_OpenEye.Text = Error_OpenEye;
}
if (ChemDrawMol.Trim() != "")
{
txtError_ChemDraw.Visible = false;
renditor_ChemDraw.MolfileString = ChemDrawMol;
}
else
{
txtError_ChemDraw.Visible = true;
txtError_ChemDraw.Text = Error_ChemDraw;
}
if (ChemAxonMol.Trim() != "")
{
txtError_ChemAxon.Visible = false;
renditor_ChemAxon.MolfileString = ChemAxonMol;
}
else
{
txtError_ChemAxon.Visible = true;
txtError_ChemAxon.Text = Error_ChemAxon;
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void RebuildTANDetailsTable_Enum(ref DataTable _dtEnumdetails, string _pageno, string _pagelabel, string _exampleno, string _tableno)
{
try
{
if (_dtEnumdetails != null)
{
if (_dtEnumdetails.Rows.Count > 0)
{
if (!_dtEnumdetails.Columns.Contains("page_number"))
{
_dtEnumdetails.Columns.Add("page_number", typeof(int));
}
if (!_dtEnumdetails.Columns.Contains("page_label"))
{
_dtEnumdetails.Columns.Add("page_label", typeof(string));
}
if (!_dtEnumdetails.Columns.Contains("example_number"))
{
_dtEnumdetails.Columns.Add("example_number", typeof(string));
}
if (!_dtEnumdetails.Columns.Contains("table_number"))
{
_dtEnumdetails.Columns.Add("table_number", typeof(string));
}
for (int rowindx = 0; rowindx < _dtEnumdetails.Rows.Count; rowindx++)
{
_dtEnumdetails.Rows[rowindx]["page_number"] = Convert.ToInt32(_pageno);
_dtEnumdetails.Rows[rowindx]["page_label"] = _pagelabel;
_dtEnumdetails.Rows[rowindx]["example_number"] = _exampleno;
_dtEnumdetails.Rows[rowindx]["table_number"] = _tableno;
}
_dtEnumdetails.AcceptChanges();
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private void loginToolStripMenuItem_Click(object sender, EventArgs e)
{
try
{
Forms.frmLogin objLogin = new Forms.frmLogin();
if (objLogin.ShowDialog() != DialogResult.OK)
{
if (objLogin.SubmitClick)
{
EnableMenuItems(objLogin.UserRole);
statStripLbl_User.Visible = true;
statStripLbl_User.Text = Classes.Generic_PepsiLite.UserRole + ": " + Classes.Generic_PepsiLite.UserName;
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
private ArrayList GetExportListOnSourceControl(string _srcCntrl)
{
ArrayList availProplst = new ArrayList();
try
{
if (_srcCntrl.Trim() != "")
{
if (_srcCntrl.Trim().ToUpper() == "FRMCURATOR" || _srcCntrl.Trim().ToUpper() == "FRMQRYDUPLICATES")
{
availProplst.Add("Structure");
availProplst.Add("Mol Weight");
availProplst.Add("Mol Formula");
availProplst.Add("IUPAC Name");
availProplst.Add("Page Number");
availProplst.Add("Page Label");
availProplst.Add("Example Number");
availProplst.Add("En Name");
availProplst.Add("Table Number");
}
else if (_srcCntrl.Trim().ToUpper() == "FRMRGRPENUM")
{
availProplst.Add("Structure");
availProplst.Add("Mol Weight");
availProplst.Add("Mol Formula");
availProplst.Add("IUPAC Name");
availProplst.Add("Page Number");
availProplst.Add("Page Label");
availProplst.Add("Example Number");
availProplst.Add("Table Number");
}
return(availProplst);
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(availProplst);
}
public static bool CheckForV3000Format(string molfilestring)
{
bool blIsV3000 = false;
try
{
if (molfilestring != "")
{
int v3000 = molfilestring.IndexOf("V3000");
if (v3000 == -1)
{
blIsV3000 = false;
}
else
{
blIsV3000 = true;
}
#region Code Commented
//MolHandler mHandler = new MolHandler(molfilestring);
//int atomCnt = mHandler.getAtomCount();
//if (atomCnt > 999)
//{
// blIsV3000 = true;
//}
//else
//{
// blIsV3000 = false;
//}
#endregion
}
return(blIsV3000);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blIsV3000);
}
private void ListBox1_SelectedIndexChanged(object sender, EventArgs e)
{
try
{
string SelItem = null;
int linN = 0;
int colN = 0;
SelItem = ListBox1.SelectedItem.ToString();
if (!string.IsNullOrEmpty(SelItem))
{
linN = Convert.ToInt16(Regex.Replace(SelItem, "([0-9]+): ([0-9]+)(.*)", "$1"));
colN = Convert.ToInt16(Regex.Replace(SelItem, "([0-9]+): ([0-9]+)(.*)", "$2"));
MatchCollection mc = default(MatchCollection);
int i = 0;
int totc = 0;
mc = Regex.Matches(RichTextBox1.Text, "\\n", RegexOptions.Singleline);
try
{
RichTextBox1.Select(mc[linN - 2].Index + colN, 2);
RichTextBox1.SelectionColor = Color.Blue;
RichTextBox1.Focus();
}
catch (Exception ex)
{
RichTextBox1.Focus();
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static double GetStructureMolWeight_MolFormula(string _molfilestring, out string _molformula)
{
double dblMolWeight = 0.0;
string strMolFormula = "";
try
{
MolHandler mHandler = new MolHandler(_molfilestring);
dblMolWeight = mHandler.calcMolWeight();
strMolFormula = mHandler.calcMolFormula();
_molformula = strMolFormula;
return(dblMolWeight);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
_molformula = strMolFormula;
return(dblMolWeight);
}
public static string GetConvertedMolString(string MolString)
{
string strConv64 = "";
try
{
if (MolString != "")
{
byte[] byteArr = StringToByteArray(MolString);
if (byteArr != null)
{
strConv64 = Convert.ToBase64String(byteArr);
}
}
return(strConv64);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(strConv64);
}
private void btnBrowsePDFFile_Click(object sender, EventArgs e)
{
try
{
openFileDialog1.Filter = "PDF|*.pdf";
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
string strFileName = openFileDialog1.FileName;
if (strFileName.Trim() != "")
{
txtFileName.Text = strFileName;
pdfDocBrow.IsAccessible = true;
pdfDocBrow.LoadFile(strFileName);
pdfDocBrow.Visible = true;
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static bool SetEnvironmentVariableEx(string environmentVariable, string variableValue)
{
bool blStatus = false;
try
{
string strEnv = Environment.GetEnvironmentVariable(environmentVariable);
if (strEnv == null)
{
// Get the write permission to set the environment variable.
EnvironmentPermission environmentPermission = new EnvironmentPermission(EnvironmentPermissionAccess.Write, environmentVariable);
environmentPermission.Demand();
blStatus = SetEnvironmentVariable(environmentVariable, variableValue);
return(blStatus);
}
}
catch (SecurityException ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blStatus);
}
public static string GetStandardizedMolecule(string strMolFile, out bool isChiral_Out)
{
string strStandMol = "";
bool blIsChiral = false;
try
{
chemaxon.util.MolHandler molHandler = new MolHandler(strMolFile);
Molecule molObj = molHandler.getMolecule();
Molecule molObj_Stand = StandardizeMolecule(molObj, out blIsChiral);
strStandMol = molObj_Stand.toFormat("mol");
isChiral_Out = blIsChiral;
return(strStandMol);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
isChiral_Out = blIsChiral;
return(strStandMol);
}
public static string GetMoleculeWeightAndMolFormula(string molstring, out string molformula_out)
{
string strMolWeight = "";
string strMolFormula = "";
try
{
MolHandler mHandler = new MolHandler(molstring);
float fltMolWeight = mHandler.calcMolWeight();
strMolFormula = mHandler.calcMolFormula();
strMolWeight = fltMolWeight.ToString();
molformula_out = strMolFormula;
return(strMolWeight);
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
molformula_out = strMolFormula;
return(strMolWeight);
}
private void EnableMenuItems(string _userrole)
{
try
{
loginToolStripMenuItem.Enabled = false;
browsePDFToolStripMenuItem.Enabled = true;
exportToolStripMenuItem.Enabled = true;
queryToolStripMenuItem.Enabled = true;
EnumtoolStripMenuItem.Enabled = true;
setttingsToolStripMenuItem.Enabled = true;
if (_userrole.Trim().ToUpper() == "REVIEWER")
{
XMLToolStripMenuItem.Enabled = true;
userAccountsToolStripMenuItem.Enabled = false;
}
else if (_userrole.Trim().ToUpper() == "ADMINISTRATOR")
{
XMLToolStripMenuItem.Enabled = true;
userAccountsToolStripMenuItem.Enabled = true;
dictionaryToolStripMenuItem.Enabled = true;
}
else if (_userrole.Trim().ToUpper() == "CURATOR")
{
XMLToolStripMenuItem.Enabled = false;
userAccountsToolStripMenuItem.Enabled = false;
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
}
public static bool IsValidTanNumber(string tanNumString)
{
bool blStatus = false;
try
{
Regex regExp = new Regex("[0-9]{8}[A-Z]{1}$", RegexOptions.Singleline);
MatchCollection matchColl = regExp.Matches(tanNumString);
if (matchColl.Count > 0)
{
blStatus = true;
}
else
{
blStatus = false;
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blStatus);
}
public static bool WriteXmlFileUsingDataTable(DataTable _dtTandetails, string _tannumber, string outxmlfile)
{
bool blStatus = false;
try
{
if (_dtTandetails != null)
{
if (_dtTandetails.Rows.Count > 0)
{
patentInfo patentInfo_Obj = new patentInfo();
patentInfo_Obj.tan = _tannumber;
patentInfo_Obj.language = languageType.en;
int intMolCnt = _dtTandetails.Rows.Count;
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;
string strMol = "";
byte[] barr_Mol = null;
int v3000 = 0;
double nullMol = 0.0;
MolHandler objMHandler = null;
for (int i = 0; i < _dtTandetails.Rows.Count; i++)
{
objMHandler = new MolHandler(_dtTandetails.Rows[i]["structure"].ToString());
v3000 = 0;
v3000 = objMHandler.toFormat("mol").IndexOf("V3000");
nullMol = 0.0;
nullMol = objMHandler.calcMolWeight();
barr_Mol = null;
if (v3000 == -1 && nullMol != 0)
{
patLoc = new patentLocation();
patLoc.pageLabel = _dtTandetails.Rows[i]["page_label"].ToString();
patLoc.pageNumber = _dtTandetails.Rows[i]["page_number"].ToString();
patLoc.exampleLabel = _dtTandetails.Rows[i]["example_number"].ToString();
name_obj = new name();
name_obj.lang = languageType.en;
string[] strArr_EnName = new string[1];
strArr_EnName[0] = _dtTandetails.Rows[i]["en_name"].ToString();
name_obj.Text = strArr_EnName;
name_Arr = new name[1];
name_Arr[0] = name_obj;
strIUpacName = new string[1];
strIUpacName[0] = _dtTandetails.Rows[i]["iupac_name"].ToString();
namType = new nameType();
namType.Text = strIUpacName;
names_Arr = new names();
names_Arr.IUPACName = namType;
names_Arr.name = name_Arr;
strMol = _dtTandetails.Rows[i]["structure"].ToString();
barr_Mol = null;
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(outxmlfile);
xmlSer.Serialize(txtWriter, patent_Obj);
txtWriter.Close();
txtWriter.Dispose();
blStatus = true;
return(blStatus);
}
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
return(blStatus);
}
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 bool GetStructureFromCompoundName(string strCompName, out string molstring_out, out bool ischiral_out, out string errmessage_out)
{
bool blStatus = false;
string strMolString = "";
string strErrMessage = "";
bool blIsChiral = false;
try
{
string strDirPath = AppDomain.CurrentDomain.BaseDirectory.ToString();
string strExePath = strDirPath + "nam2mol.exe";
string strInputFileName = "CompName.txt";
string strOutputFileName = "CompStructure.mol";
if (System.IO.File.Exists(strDirPath + strInputFileName))
{
System.IO.File.Delete(strDirPath + strInputFileName);
}
System.IO.StreamWriter sWriter = new System.IO.StreamWriter(strDirPath + strInputFileName);
sWriter.WriteLine(strCompName.Trim());
sWriter.Close();
sWriter.Dispose();
if (System.IO.File.Exists(strDirPath + strOutputFileName))
{
System.IO.File.Delete(strDirPath + strOutputFileName);
}
//ProcessStartInfo class
ProcessStartInfo startInfo = new ProcessStartInfo();
startInfo.CreateNoWindow = true;
startInfo.UseShellExecute = false;
startInfo.RedirectStandardError = true;
startInfo.FileName = @"" + strExePath + "";
startInfo.WindowStyle = ProcessWindowStyle.Hidden;
startInfo.Arguments = @"-in """ + strDirPath + strInputFileName + @""" -out """ + strDirPath + strOutputFileName + @""" -depict true";
//startInfo.Arguments = @"-in """ + strDirPath + strInputFileName + @""" -depict true";
string strErrMsg = "";
try
{
using (Process exeProcess = Process.Start(startInfo))
{
strErrMsg = exeProcess.StandardError.ReadToEnd();
exeProcess.WaitForExit();
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
//Read Output molecule from outputfile
StreamReader sReader = new StreamReader(strDirPath + strOutputFileName);
string newMolfileString;
newMolfileString = sReader.ReadToEnd();
//Standardize the molecule
string strStandMol = GetStandardizedMolecule(newMolfileString, out blIsChiral);
sReader.Close();
sReader.Dispose();
if (newMolfileString != "")
{
strMolString = strStandMol;
molstring_out = strMolString;
errmessage_out = "";
ischiral_out = blIsChiral;
blStatus = true;
return(blStatus);
}
else
{
strErrMessage = strErrMsg;
molstring_out = "";
ischiral_out = blIsChiral;
errmessage_out = strErrMessage;
blStatus = false;
return(blStatus);
}
}
catch (Exception ex)
{
ErrorHandling_NTS.WriteErrorLog(ex.ToString());
}
molstring_out = "";
ischiral_out = blIsChiral;
errmessage_out = strErrMessage;
return(blStatus);
}
