/// <summary>
///
/// </summary>
public void Initialize(bool isUpdate)
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
// for connecting to ProtBuD database, converting sequence numbers
if (ProtCidSettings.pdbfamDbConnection == null)
{
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.pdbfamDbPath);
}
if (alignmentDbConnection == null)
{
alignmentDbConnection = new DbConnect();
alignmentDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.alignmentDbPath;
}
alignmentDbConnection.ConnectToDatabase();
FatcatTables.InitializeTables(dbAlignTableName);
/* if (! isUpdate) // intend to comment out, to prevent drop the tables
* {
* FatcatTables.InitializeDbTable(alignmentDbConnection, dbAlignTableName); // create new fatcat alignments table in the db
* FatcatTables.InitializeDbTable(alignmentDbConnection, dbAlignTableName + "Rigid");
* }*/
if (logWriter == null)
{
logWriter = new StreamWriter("FatcatAlignmentsParsingLog.txt", true);
logWriter.WriteLine(DateTime.Today.ToShortDateString());
}
}
/// <summary>
///
/// </summary>
/// <param name="nonAlignedPairsFile"></param>
public string GetFatcatAlignmentsOnLinux(string nonAlignedPairsFile)
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (ProtCidSettings.alignmentDbConnection == null)
{
ProtCidSettings.alignmentDbConnection = new DbLib.DbConnect();
ProtCidSettings.alignmentDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;" +
"PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.alignmentDbPath;
}
string repChainPairsFileName = "NonAlignRepEntryPairs.txt";
WriteRepChainPairsToFile(nonAlignedPairsFile, repChainPairsFileName);
CmdOperations linuxOperator = new CmdOperations();
linuxOperator.CopyWindowsDataToLinux(repChainPairsFileName, exeFatcatDir + repChainPairsFileName);
string cmdLineFile = WriteFatcatCommandFile(repChainPairsFileName);
linuxOperator.RunPlink(cmdLineFile);
string alignFileInLinux = fatcatDir + repChainPairsFileName.Replace(".txt", ".aln");
string alignFileInWindows = Path.Combine(ProtCidSettings.dirSettings.fatcatPath, repChainPairsFileName.Replace(".txt", ".aln"));
linuxOperator.CopyLinuxDataToWindows(alignFileInLinux, alignFileInWindows);
return(alignFileInWindows);
}
/// <summary>
///
/// </summary>
/// <param name="updateGroups"></param>
public string ReverseClusterInterfaceFiles(int[] updateGroups)
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (AppSettings.parameters == null)
{
AppSettings.LoadParameters();
}
string updateReverseInterfaceFile = Path.Combine(ProtCidSettings.applicationStartPath, "ReverseInterfacesInCluster.txt");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Non-symmetry interface files in the clusters.");
string updateNonSymInterfaceFile = UpdateClusterNonSymmetryInterfaces(updateGroups);
// string updateNonSymInterfaceFile = "UpdateClusterNonSymInterfaces.txt";
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Compare Non symmetry interface files to the first interface in the cluster (in alphabet order)");
string updateNonSymInterfaceCompFile = interfaceComp.CompareClusterNonSymInterfaces(updateNonSymInterfaceFile);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Reverse interface files in pdb format.");
updateReverseInterfaceFile = GetInterfacesToReversed(updateNonSymInterfaceCompFile);
interfaceGenerator.ReverseInterfaceChains(updateReverseInterfaceFile);
return(updateReverseInterfaceFile);
}
public void WriteAsuToPdbFiles()
{
SetFilePaths();
ProtCidSettings.LoadDirSettings();
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath);
ProtCidSettings.pdbfamDbConnection.ConnectToDatabase();
string[] pdbCodes = GetMissingEntries();
string gzCoordXmlFile = "";
string coordXmlFile = "";
string coordXmlFileDir = @"D:\Qifang\ProjectData\DbProjectData\CoordXml";
foreach (string pdbCode in pdbCodes)
{
try
{
gzCoordXmlFile = Path.Combine(coordXmlFileDir, pdbCode + ".xml.gz");
coordXmlFile = ParseHelper.UnZipFile(gzCoordXmlFile, ProtCidSettings.tempDir);
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(coordXmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
xmlFileStream.Close();
WriteXmlFileToPdbFile(pdbCode, thisEntryCrystal);
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(pdbCode + ": " + ex.Message);
}
}
ProtCidSettings.pdbfamDbConnection.DisconnectFromDatabase();
}
/// <summary>
///
/// </summary>
public void UpdateBuAssemblies()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
bool needLigands = true;
bool authorDefined = true;
// add new/updated BU files on May 24, 2011 for Qiong's paper
string[] updateEntries = GetUpdateFileList();
// string[] updateEntries = GetEntriesWithBugs();
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.totalOperationNum = updateEntries.Length;
ProtCidSettings.progressInfo.totalStepNum = updateEntries.Length;
ProtCidSettings.progressInfo.currentOperationLabel = "Generate BU files";
string[] entryBuFiles = null;
string newLsFileName = Path.Combine(ProtCidSettings.dirSettings.pisaPath, "newls.txt");
StreamWriter lsFileWriter = new StreamWriter(newLsFileName);
foreach (string pdbId in updateEntries)
{
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
ProtCidSettings.progressInfo.currentFileName = pdbId;
entryBuFiles = GenerateEntryBuFiles(pdbId, needLigands, authorDefined);
if (entryBuFiles != null && entryBuFiles.Length > 0)
{
CopyEntryBuFilesToLinux(entryBuFiles);
foreach (string buFile in entryBuFiles)
{
FileInfo fileInfo = new FileInfo(buFile);
lsFileWriter.WriteLine(fileInfo.Name);
}
lsFileWriter.Flush();
}
}
try
{
Directory.Delete(ProtCidSettings.tempDir);
}
catch { }
logWriter.Close();
lsFileWriter.Close();
CopyLsFileToLinux(newLsFileName);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.threadFinished = true;
}
/// <summary>
///
/// </summary>
public void AddPeptideSequencesInfoToClusterFile()
{
ProtCidSettings.LoadDirSettings();
AppSettings.LoadParameters();
AppSettings.LoadSymOps();
if (ProtCidSettings.pdbfamDbConnection == null)
{
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath);
}
if (ProtCidSettings.protcidDbConnection == null)
{
ProtCidSettings.protcidDbConnection = new DbConnect();
ProtCidSettings.protcidDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath;
}
string clusterFile = @"D:\DbProjectData\pfam\PfamPeptide\Pkinase\cutoff3\PfamPepInterfaceClusters3.txt";
string clusterSequenceFile = @"D:\DbProjectData\pfam\PfamPeptide\Pkinase\cutoff3\PkinaseCluster2PeptideSeq.txt";
StreamReader dataReader = new StreamReader(clusterFile);
StreamWriter dataWriter = new StreamWriter(clusterSequenceFile);
string line = dataReader.ReadLine(); // header line
int selectedClusterId = 2;
int clusterId = 0;
string pdbId = "";
int domainInterfaceId = 0;
while ((line = dataReader.ReadLine()) != null)
{
string[] fields = line.Split('\t');
clusterId = Convert.ToInt32(fields[1]);
if (clusterId == selectedClusterId)
{
pdbId = fields[2];
domainInterfaceId = Convert.ToInt32(fields[3]);
dataWriter.WriteLine(line);
string[] pdbDbSeqInfos = GetPeptideSeqInfo(pdbId, domainInterfaceId);
if (pdbDbSeqInfos == null)
{
dataWriter.WriteLine();
}
else
{
foreach (string seq in pdbDbSeqInfos)
{
dataWriter.WriteLine(seq);
}
dataWriter.WriteLine();
}
}
}
dataReader.Close();
dataWriter.Close();
}
public void BuildPfamDatabase()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
DownloadPfamFiles();
string connectString = "Driver={MySQL ODBC 5.1 Driver}; Server=localhost;Database=pfam;UID=root;PWD=learnsql2011;";
mysqlConnect.ConnectString = connectString;
mysqlConnect.ConnectToDatabase();
// OutputPdbPfamFiles();
string tempDir = "C:\\temp";
if (!Directory.Exists(tempDir))
{
Directory.CreateDirectory(tempDir);
}
string[] sqlFiles = Directory.GetFiles(Path.Combine(ProtCidSettings.dirSettings.pfamPath, "pfam_database"), "*sql.gz");
string loadDataString = "";
string unzippedFile = "";
string unixFilePath = "";
string tableName = "";
string[] createTableStrings = null;
foreach (string sqlFile in sqlFiles)
{
unzippedFile = ParseHelper.UnZipFile(sqlFile, tempDir);
createTableStrings = ReadCreatTableString(unzippedFile);
foreach (string createTableString in createTableStrings)
{
dbQuery.Query(mysqlConnect, createTableString);
}
}
string[] pfamFiles = Directory.GetFiles(Path.Combine(ProtCidSettings.dirSettings.pfamPath, "pfam_database"), "*txt.gz");
foreach (string pfamFile in pfamFiles)
{
unzippedFile = ParseHelper.UnZipFile(pfamFile, tempDir);
tableName = GetTableName(pfamFile);
unixFilePath = unzippedFile.Replace("\\", "/");
loadDataString = "Load data local infile '" + unixFilePath + "' into table " + tableName;
// " fields enclosed by '\t';";
// int fieldIndex = loadDataString.IndexOf("fields enclosed by \'");
// loadDataString = loadDataString.Insert (fieldIndex + "fields enclosed by \'".Length, "\\");
dbQuery.Query(mysqlConnect, loadDataString);
}
Directory.Delete(tempDir, true);
OutputPdbPfamFiles();
}
/// <summary>
///
/// </summary>
/// <param name="isUpdate"></param>
private void Initialize(bool isUpdate)
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
ProtCidSettings.alignmentDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.alignmentDbPath);
}
hhAlignTable = CreateHHAlignmentTable(isUpdate, hhAlignTableName);
}
public FatcatEntryPairs()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;" +
"UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.pdbfamDbPath);
ProtCidSettings.protcidDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;" +
"UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.protcidDbPath);
}
/// <summary>
/// initialize dbconnect
/// </summary>
public static void Initialize()
{
if (IsSettingInitialized)
{
return;
}
ProtCidSettings.dataType = "pfam";
ProtCidSettings.LoadDirSettings();
AppSettings.LoadParameters();
AppSettings.LoadSymOps();
ProtCidSettings.tempDir = "C:\\xtal_temp0";
if (ProtCidSettings.pdbfamDbConnection == null)
{
ProtCidSettings.pdbfamDbConnection = new DbConnect();
ProtCidSettings.pdbfamDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath;
ProtCidSettings.pdbfamQuery = new DbQuery(ProtCidSettings.pdbfamDbConnection);
}
if (ProtCidSettings.protcidDbConnection == null)
{
ProtCidSettings.protcidDbConnection = new DbConnect();
ProtCidSettings.protcidDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath;
ProtCidSettings.protcidQuery = new DbQuery(ProtCidSettings.protcidDbConnection);
}
if (ProtCidSettings.alignmentDbConnection == null)
{
ProtCidSettings.alignmentDbConnection = new DbConnect();
ProtCidSettings.alignmentDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.alignmentDbPath;
ProtCidSettings.alignmentQuery = new DbQuery(ProtCidSettings.alignmentDbConnection);
}
if (ProtCidSettings.buCompConnection == null)
{
ProtCidSettings.buCompConnection = new DbConnect();
ProtCidSettings.buCompConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.baInterfaceDbPath;
ProtCidSettings.buCompQuery = new DbQuery(ProtCidSettings.buCompConnection);
}
ProtCidSettings.logWriter.WriteLine(DateTime.Today.ToShortDateString() + "\r\n");
DataTables.GroupDbTableNames.SetGroupDbTableNames(ProtCidSettings.dataType);
PfamLibSettings.InitializeFromProtCidSettings();
IsSettingInitialized = true;
}
/// <summary>
///
/// </summary>
public static void InitializeThread()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (AppSettings.parameters == null)
{
AppSettings.LoadParameters();
}
if (ProtCidSettings.pdbfamDbConnection == null)
{
ProtCidSettings.pdbfamDbConnection = new DbConnect();
ProtCidSettings.pdbfamDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath;
ProtCidSettings.pdbfamQuery = new DbQuery(ProtCidSettings.pdbfamDbConnection);
}
if (ProtCidSettings.protcidDbConnection == null)
{
ProtCidSettings.protcidDbConnection = new DbConnect();
ProtCidSettings.protcidDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath;
ProtCidSettings.protcidQuery = new DbQuery(ProtCidSettings.protcidDbConnection);
}
if (ProtCidSettings.alignmentDbConnection == null)
{
ProtCidSettings.alignmentDbConnection = new DbConnect();
ProtCidSettings.alignmentDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.alignmentDbPath;
ProtCidSettings.alignmentQuery = new DbQuery(ProtCidSettings.alignmentDbConnection);
}
if (ProtCidSettings.buCompConnection == null)
{
ProtCidSettings.buCompConnection = new DbConnect();
ProtCidSettings.buCompConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.baInterfaceDbPath;
ProtCidSettings.buCompQuery = new DbQuery(ProtCidSettings.buCompConnection);
}
ProtCidSettings.tempDir = "X:\\xtal_temp";
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
PfamLibSettings.pdbfamConnection = ProtCidSettings.pdbfamDbConnection;
PfamLibSettings.pdbfamDbQuery = new DbQuery(PfamLibSettings.pdbfamConnection);
PfamLibSettings.alignmentDbConnection = ProtCidSettings.alignmentDbConnection;
}
public DownloaderFileRename()
{
ProtCidSettings.LoadDirSettings();
if (ProtCidSettings.protcidDbConnection == null)
{
ProtCidSettings.protcidDbConnection = new DbConnect();
ProtCidSettings.protcidDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath;
ProtCidSettings.protcidQuery = new DbQuery(ProtCidSettings.protcidDbConnection);
}
logWriter = new StreamWriter("GroupNameRenameLog.txt", true);
logWriter.WriteLine(DateTime.Today.ToLongDateString());
}
/// <summary>
///
/// </summary>
public void SortHomoDimerInterfacesInCluster()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (AppSettings.parameters == null)
{
AppSettings.LoadParameters();
}
string queryString = "Select Distinct SuperGroupSeqID From PfamSuperClusterEntryInterfaces;";
DataTable groupTable = ProtCidSettings.protcidQuery.Query(queryString);
int superGroupId = -1;
StreamWriter logWriter = new StreamWriter("ClusterHomoDimersSortLog.txt");
string dataLine = "";
foreach (DataRow groupRow in groupTable.Rows)
{
superGroupId = Convert.ToInt32(groupRow["SuperGroupSeqID"].ToString());
if (!IsSuperGroupSamePfamArch(superGroupId))
{
continue;
}
int[] clusterIds = GetGroupClusterIds(superGroupId);
foreach (int clusterId in clusterIds)
{
string[] clusterInterfaces = GetClusterInterfaces(superGroupId, clusterId);
string firstInterface = GetRepInterfaceInAlphabetOrder(superGroupId, clusterId);
string[] nonSymmetryInterfaces = GetNonSymmetryDimers(clusterInterfaces);
if (nonSymmetryInterfaces.Length == 0)
{
logWriter.WriteLine(superGroupId.ToString() + " " + clusterId.ToString() +
" no non-symmetric h**o-dimers ");
continue;
}
dataLine = superGroupId.ToString() + " " + clusterId.ToString() + " " + firstInterface;
foreach (string nonSymmetryInterface in nonSymmetryInterfaces)
{
if (firstInterface == nonSymmetryInterface)
{
continue;
}
dataLine += ("," + nonSymmetryInterface);
}
logWriter.WriteLine(dataLine);
}
logWriter.Flush();
}
logWriter.Close();
}
/// <summary>
/// output entity sequences of groups to files
/// </summary>
/// <returns></returns>
public void WriteSequencesToFastaFiles()
{
logWriter = new StreamWriter("SeqWriteLog.txt");
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
ProtCidSettings.dirSettings.seqFastaPath = ProtCidSettings.dirSettings.seqFastaPath.Replace("\\fasta", "\\ChainFasta");
if (!Directory.Exists(ProtCidSettings.dirSettings.seqFastaPath))
{
Directory.CreateDirectory(ProtCidSettings.dirSettings.seqFastaPath);
}
webFastaFileDir = ProtCidSettings.dirSettings.seqFastaPath.Replace("\\ChainFasta", "\\webChainFasta");
if (!Directory.Exists(webFastaFileDir))
{
Directory.CreateDirectory(webFastaFileDir);
}
string queryString = "Select Distinct SuperGroupSeqID From PfamSuperInterfaceClusters Where SuperGroupSeqId > 29857";
DataTable groupTable = ProtCidSettings.protcidQuery.Query(queryString);
int superGroupId = 0;
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Update Seq Files";
ProtCidSettings.progressInfo.totalStepNum = groupTable.Rows.Count;
ProtCidSettings.progressInfo.totalOperationNum = groupTable.Rows.Count;
foreach (DataRow dRow in groupTable.Rows)
{
superGroupId = Convert.ToInt32(dRow["SuperGroupSeqID"].ToString());
ProtCidSettings.progressInfo.currentFileName = superGroupId.ToString();
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
try
{
WriteSuperGroupEntrySequences(superGroupId);
}
catch (Exception ex)
{
logWriter.WriteLine(superGroupId.ToString() + " " + ex.Message);
logWriter.Flush();
}
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Tar Sequence files for each group and its clusters");
PrintClusterFastaFiles();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Generate sequence files done!");
logWriter.Close();
}
/// <summary>
/// initialize dbconnect
/// </summary>
internal void Initialize()
{
ProtCidSettings.LoadDirSettings();
AppSettings.LoadParameters();
AppSettings.LoadSymOps();
ProtCidSettings.protcidDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath);
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath);
DataTables.GroupDbTableNames.SetGroupDbTableNames(ProtCidSettings.dataType);
ProtCidSettings.tempDir = "C:\\xtal_temp0";
}
/// <summary>
/// get data source file paths and coordinate xml file path
/// from setting xml file
/// </summary>
private void SetFilePaths()
{
ProtCidSettings.LoadDirSettings();
this.xmlFilePath = ProtCidSettings.dirSettings.xmlPath;
if (this.xmlFilePath[this.xmlFilePath.Length - 1] != '\\')
{
this.xmlFilePath += "\\";
}
this.destFilePath = ProtCidSettings.dirSettings.coordXmlPath;
if (this.destFilePath[this.destFilePath.Length - 1] != '\\')
{
this.destFilePath += "\\";
}
pdbTextPath = Regex.Replace(ProtCidSettings.dirSettings.xmlPath, "xml", "regular", RegexOptions.IgnoreCase);
}
private void Initialize()
{
ProtCidSettings.LoadDirSettings();
AppSettings.LoadParameters();
if (ProtCidSettings.protcidDbConnection == null)
{
ProtCidSettings.protcidDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath);
}
string dbv26Path = @"F:\Firebird\Xtal\Pfam\protbud.fdb";
dbConnectv26.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
dbv26Path;
}
public BuAssemblyGenerator()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (AppSettings.parameters == null)
{
AppSettings.LoadParameters();
}
if (ProtCidSettings.pdbfamDbConnection == null)
{
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath);
}
}
/// <summary>
///
/// </summary>
private void InitializeDbConnect()
{
string connectString = "Driver={MySQL ODBC 5.3 Unicode Driver}; Server=localhost;Database=" + dbName + ";UID=qifang;PWD=DunbrackR462*;";
localMysqlDbConnect.ConnectString = connectString;
localMysqlDbConnect.ConnectToDatabase();
// connectString = string.Format ("Driver={MySQL ODBC 5.3 Unicode Driver}; Server={0};Database=bioinformatics;UID={1};PWD={2};", remoteMysqlServer, uname, psw);
// always got input format error, so hard code the server, uid, psw
/* connectString = "Driver={MySQL ODBC 5.3 Unicode Driver}; Server=10.40.16.45;Database=bioinformatics;UID=qifang;PWD=mysqlqxu;";
* remotePiscesDbConnect.ConnectString = connectString;
* remotePiscesDbConnect.ConnectToDatabase();
*/
ProtCidSettings.LoadDirSettings();
protcidDbConnect.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.pdbfamDbPath;
protcidDbConnect.ConnectToDatabase();
}
public PfamData()
{
ProtCidSettings.LoadDirSettings();
if (ProtCidSettings.pdbfamDbConnection == null)
{
ProtCidSettings.pdbfamDbConnection = new DbConnect();
ProtCidSettings.pdbfamDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath;
ProtCidSettings.pdbfamQuery = new DbQuery(ProtCidSettings.pdbfamDbConnection);
}
if (ProtCidSettings.protcidDbConnection == null)
{
ProtCidSettings.protcidDbConnection = new DbConnect();
ProtCidSettings.protcidDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath;
ProtCidSettings.protcidQuery = new DbQuery(ProtCidSettings.protcidDbConnection);
}
}
public PiscesFileParser()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (ProtCidSettings.alignmentDbConnection == null)
{
ProtCidSettings.alignmentDbConnection = new DbConnect();
}
if (ProtCidSettings.alignmentDbConnection.ConnectString == "")
{
ProtCidSettings.alignmentDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;" +
"UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" + ProtCidSettings.dirSettings.alignmentDbPath;
}
asymChainFinder = new AsuInfoFinder(ProtCidSettings.dirSettings.pdbfamDbPath);
}
/// <summary>
/// Compare cryst and bu interfaces for the entries
/// </summary>
public void CompareEntryCrystBuInterfaces(string[] updatePdbList)
{
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (AppSettings.parameters == null)
{
AppSettings.LoadParameters();
}
InitializeTables();
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Comparing Cryst BU Interface";
ProtCidSettings.progressInfo.totalOperationNum = updatePdbList.Length;
ProtCidSettings.progressInfo.totalStepNum = updatePdbList.Length;
foreach (string pdbId in updatePdbList)
{
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
ProtCidSettings.progressInfo.currentFileName = pdbId;
if (IsBuCompExist(pdbId))
{
continue;
}
CompareEntryCrystBuInterfaces(pdbId);
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, crystBuInterfaceCompTables);
ClearTables();
}
try
{
Directory.Delete(ProtCidSettings.tempDir, true);
}
catch {}
}
/// <summary>
/// initialize dbconnect
/// </summary>
internal void Initialize()
{
ProtCidSettings.LoadDirSettings();
AppSettings.LoadParameters();
AppSettings.LoadSymOps();
ProtCidSettings.pdbfamDbConnection = new DbConnect();
ProtCidSettings.pdbfamDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath;
ProtCidSettings.protcidDbConnection = new DbConnect();
ProtCidSettings.protcidDbConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath;
ProtCidSettings.buCompConnection = new DbConnect();
ProtCidSettings.buCompConnection.ConnectString = "DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.baInterfaceDbPath;
DataTables.GroupDbTableNames.SetGroupDbTableNames(ProtCidSettings.dataType);
}
/// <summary>
///
/// </summary>
/// <param name="superGroupIds"></param>
public void UpdateSeqFastaFiles(int[] superGroupIds)
{
logWriter = new StreamWriter("SeqWriteLog.txt");
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.totalStepNum = superGroupIds.Length;
ProtCidSettings.progressInfo.totalOperationNum = superGroupIds.Length;
ProtCidSettings.progressInfo.currentOperationLabel = "Seq Fasta Files";
ProtCidSettings.dirSettings.seqFastaPath = ProtCidSettings.dirSettings.seqFastaPath.Replace("\\fasta", "\\ChainFasta");
// UpdateClusterFastaFiles(superGroupIds);
foreach (int superGroupId in superGroupIds)
{
try
{
ProtCidSettings.progressInfo.currentFileName = superGroupId.ToString();
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
DeleteObsoleteSeqFiles(superGroupId);
WriteSuperGroupEntrySequences(superGroupId);
}
catch (Exception ex)
{
logWriter.WriteLine(superGroupId.ToString() + " " + ex.Message);
logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(superGroupId.ToString() + " " + ex.Message);
}
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Tar the sequence files of group and clusters for the web server.");
UpdateClusterFastaFiles(superGroupIds);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update sequence files done!");
logWriter.Close();
}
/// <summary>
///
/// </summary>
public string ReverseClusterInterfaceFiles()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (AppSettings.parameters == null)
{
AppSettings.LoadParameters();
}
// string reverseInterfaceFile = "ReverseInterfacesInCluster.txt";
string querystring = "Select PdbID, InterfaceID From CrystEntryInterfaces Where IsSymmetry = '1';";
symInterfaceTable = ProtCidSettings.protcidQuery.Query(querystring);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Find Non-symmetry interface files in the clusters.");
string nonSymInterfaceFile = GetClusterNonSymmetryInterfaces();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Compare Non symmetry interface files to the first interface in the cluster (in alphabet order)");
string nonSymInterfaceCompFile = interfaceComp.CompareClusterNonSymInterfaces(nonSymInterfaceFile);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Reverse interface files in pdb format.");
string reverseInterfaceFile = GetInterfacesToReversed(nonSymInterfaceCompFile);
interfaceGenerator.ReverseInterfaceChains(reverseInterfaceFile);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("The current working directory: " + System.Environment.CurrentDirectory);
ProtCidSettings.logWriter.WriteLine("Reverse interface files in pdb format.");
ProtCidSettings.logWriter.WriteLine("The current working directory: " + System.Environment.CurrentDirectory);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Reverse hetero interface files in reversed pfam arch order");
ReverseInterfaceFilesInDifPfamOrder();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("The current working directory: " + System.Environment.CurrentDirectory);
ProtCidSettings.logWriter.WriteLine("Reverse hetero interface files in reversed pfam arch order");
ProtCidSettings.logWriter.WriteLine("The current working directory: " + System.Environment.CurrentDirectory);
return(reverseInterfaceFile);
}
/// <summary>
///
/// </summary>
public void ClusterSuperDomainInterfaces()
{
ProtCidSettings.dataType = "clan";
ProtCidSettings.LoadDirSettings();
ProtCidSettings.protcidDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.protcidDbPath);
ProtCidSettings.pdbfamDbConnection = new DbConnect("DRIVER=Firebird/InterBase(r) driver;UID=SYSDBA;PWD=fbmonkeyox;DATABASE=" +
ProtCidSettings.dirSettings.pdbfamDbPath);
InitializeTable();
InitializeDbTable();
isDomain = true;
GroupDbTableNames.SetGroupDbTableNames(ProtCidSettings.dataType);
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Cluster on Clans";
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Cluster domain interfaces in clan");
string queryString = "Select Distinct ClanSeqID From PfamDomainFamilyRelation;";
DataTable clanSeqIdTable = ProtCidSettings.protcidQuery.Query(queryString);
ProtCidSettings.progressInfo.totalOperationNum = clanSeqIdTable.Rows.Count;
ProtCidSettings.progressInfo.totalStepNum = clanSeqIdTable.Rows.Count;
int clanSeqId = 0;
foreach (DataRow clanIdRow in clanSeqIdTable.Rows)
{
clanSeqId = Convert.ToInt32(clanIdRow["ClanSeqID"].ToString());
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
ProtCidSettings.progressInfo.currentFileName = clanSeqId.ToString();
ClusterClanDomainInterfaces(clanSeqId);
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
}
/// <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;
}
/* BUs: if PISA BUs defined,
*
* if ASU heteromultimer and PISA homomultimer
* then generate BUs from PDB
* else
* then generate BUs from PISA
*
* else PISA BUs not defined
* generate BUs from PDB
*
*/
/// <summary>
///
/// </summary>
public void GenerateBuAssemblies()
{
if (ProtCidSettings.dirSettings == null)
{
ProtCidSettings.LoadDirSettings();
}
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
bool needLigands = true;
bool authorDefined = true;
logWriter.WriteLine(DateTime.Today.ToShortDateString());
string queryString = "Select Distinct PdbID From AsymUnit Where PolymerType = 'polypeptide';";
DataTable entryTable = ProtCidSettings.pdbfamQuery.Query(queryString);
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.totalOperationNum = entryTable.Rows.Count;
ProtCidSettings.progressInfo.totalStepNum = entryTable.Rows.Count;
ProtCidSettings.progressInfo.currentOperationLabel = "Generate BU files";
string lsFile = Path.Combine(ProtCidSettings.dirSettings.pisaPath, "ls.txt");
StreamWriter lsFileWriter = new StreamWriter(lsFile);
string pdbId = "";
string[] buFiles = null;
foreach (DataRow entryRow in entryTable.Rows)
{
pdbId = entryRow["PdbID"].ToString();
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
ProtCidSettings.progressInfo.currentFileName = pdbId;
if (AreFilesGenerated(pdbId))
{
continue;
}
try
{
buFiles = GenerateEntryBuFiles(pdbId, needLigands, authorDefined);
if (buFiles != null && buFiles.Length > 0)
{
CopyEntryBuFilesToLinux(buFiles);
foreach (string buFile in buFiles)
{
FileInfo fileInfo = new FileInfo(buFile);
lsFileWriter.WriteLine(fileInfo.Name);
}
lsFileWriter.Flush();
}
}
catch (Exception ex)
{
logWriter.WriteLine(pdbId + " Generate BU files error: " + ex.Message);
logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(pdbId + " Generate BU files error: " + ex.Message);
}
}
try
{
Directory.Delete(ProtCidSettings.tempDir);
}
catch { }
logWriter.Close();
lsFileWriter.Close();
CopyLsFileToLinux(lsFile);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.threadFinished = true;
}
