/// <summary>
/// Format any PDB xml file to my format
/// </summary>
/// <param name="pdbId"></param>
public string WritePdbXmlToMyCoordXmlFile(string pdbXmlFile)
{
FileInfo fileInfo = new FileInfo(pdbXmlFile);
string pdbCode = fileInfo.Name.Substring(0, 4);
if (!File.Exists(pdbXmlFile))
{
webClient.DownloadFile(pdbWebAddress + fileInfo.Name, pdbXmlFile);
}
if (pdbXmlFile.IndexOf(".gz") > -1)
{
ParseHelper.UnZipFile(pdbXmlFile);
pdbXmlFile = pdbXmlFile.Replace(".gz", "");
}
XmlAtomParser xmlParser = new XmlAtomParser();
EntryCrystal thisEntryCrystal = new EntryCrystal(pdbCode);
try
{
xmlParser.ParseXmlFile(pdbXmlFile, ref thisEntryCrystal, "ALL");
}
catch (Exception ex)
{
// record the error, continue to the next file
string errorMsg = string.Format("Processing {0} file errors: {1}. Skip it.",
pdbCode, ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue(errorMsg);
}
string coordXmlFile = Path.Combine(fileInfo.DirectoryName, pdbCode + "_coord.xml");
// save entry crystal data into a XML file
try
{
if (thisEntryCrystal != null)
{
XmlSerializer xmlSerializer = new XmlSerializer(thisEntryCrystal.GetType());
TextWriter crystalWriter = new StreamWriter(coordXmlFile);
xmlSerializer.Serialize(crystalWriter, thisEntryCrystal);
crystalWriter.Close();
// ParseHelper.ZipPdbFile(coordXmlFile);
}
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(ex.Message);
}
return(coordXmlFile);
}
/// <summary>
/// create crystal XML files
/// </summary>
public void CreateCrystalXmlFiles()
{
AsymUnitBuilder asuBuilder = new AsymUnitBuilder();
// bool asuChanged = false;
ProtCidSettings.LoadDirSettings();
AppSettings.LoadParameters();
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath);
ProtCidSettings.progressInfo.Reset();
SetFilePaths();
string atomType = "";
if (AppSettings.parameters.contactParams.atomType == "CA")
{
atomType = "CA";
}
else if (AppSettings.parameters.contactParams.atomType == "CB")
{
atomType = "CB";
}
else
{
atomType = "ALL";
}
// save the file list for those just created
List <string> parsedCoordXmlFiles = new List <string> ();
XmlAtomParser xmlParser = new XmlAtomParser();
if (!Directory.Exists(destFilePath.Trim('\\')))
{
Directory.CreateDirectory(destFilePath.Trim('\\'));
}
modifyType = "update";
// temporary directory
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
// get the common list of XML files, ent files and BU symmetry matrix files
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving file list. Please wait...");
string [] pdbCodes = GetFileNames();
/* string[] pdbCodes = { "4p6d"};
* string[] pdbCodes = GetMissingEntries();*/
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationLabel = "PDB Processing";
ProtCidSettings.progressInfo.totalStepNum = pdbCodes.Length;
ProtCidSettings.progressInfo.totalOperationNum = pdbCodes.Length;
ProtCidSettings.progressInfo.progressInterval = 1;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Building Coordinate XML files. Please wait...");
string crystalXmlFile = "";
foreach (string pdbCode in pdbCodes)
{
/////////////////////////////////////////
// display progress information
// get just the fileName
ProtCidSettings.progressInfo.currentFileName = pdbCode;
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
crystalXmlFile = destFilePath + pdbCode + ".xml";
FileInfo fileInfo = new FileInfo(crystalXmlFile + ".gz");
if (fileInfo.LastWriteTime.Day == DateTime.Today.Day)
{
continue;
}
string zippedXmlFile = xmlFilePath + pdbCode + xmlExtName;
if (!File.Exists(zippedXmlFile))
{
webClient.DownloadFile(pdbWebAddress + pdbCode + ".xml.gz", pdbCode + ".xml.gz");
File.Move(pdbCode + ".xml.gz", zippedXmlFile);
}
string xmlFile = ParseHelper.UnZipFile(zippedXmlFile, ProtCidSettings.tempDir);
EntryCrystal thisEntryCrystal = new EntryCrystal(pdbCode);
try
{
xmlParser.ParseXmlFile(xmlFile, ref thisEntryCrystal, atomType);
/*if (thisEntryCrystal != null)
* {
* if (thisEntryCrystal.ncsCat.NcsOperatorList.Length > 0)
* {
* asuBuilder.BuildAsymUnitFromNcs (ref thisEntryCrystal, out asuChanged);
* if (asuChanged)
* {
* UpdateAsymUnitDbTable (thisEntryCrystal);
* }
* }
* }*/
}
catch (Exception ex)
{
// record the error, continue to the next file
string errorMsg = string.Format("Processing {0} file errors: {1}. Skip it.",
pdbCode, ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue(errorMsg);
}
finally
{
// delete this processed file
File.Delete(xmlFile);
}
// save entry crystal data into a XML file
try
{
if (thisEntryCrystal != null)
{
XmlSerializer xmlSerializer = new XmlSerializer(thisEntryCrystal.GetType());
TextWriter crystalWriter = new StreamWriter(crystalXmlFile);
xmlSerializer.Serialize(crystalWriter, thisEntryCrystal);
crystalWriter.Close();
ParseHelper.ZipPdbFile(crystalXmlFile);
parsedCoordXmlFiles.Add(pdbCode + ".xml.gz");
WriteXmlFileToPdbFile(pdbCode, thisEntryCrystal);
// CopyPdbFileToLinux(pdbCode);
}
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(ex.Message);
}
}
try
{
Directory.Delete(ProtCidSettings.tempDir, true);
}
catch {}
SaveFileList(parsedCoordXmlFiles);
/* progressInfo.progStrQueue.Enqueue("Copy PDB files to Linux server.");
* CopyPdbFilesToLinux(pdbCodes);
* progressInfo.progStrQueue.Enqueue ("Done!");
*/
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Copy updated files to new directory");
string updateFilePath = pdbTextPath.Replace("regular", "updateRegular");
if (Directory.Exists(updateFilePath))
{
Directory.Delete(updateFilePath, true);
}
Directory.CreateDirectory(updateFilePath);
DateTime dtTime = DateTime.Today;
ParseHelper.CopyNewFiles(pdbTextPath, updateFilePath, dtTime);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.threadFinished = true;
}