/// <summary>
/// check if there are same crystal forms for all groups
/// </summary>
public void CheckReduntCrystForms()
{
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Redundant crystal forms.";
InitializeTables();
InitializeDbTables();
string queryString = string.Format("Select Distinct GroupSeqID From {0};",
GroupDbTableNames.dbTableNames[GroupDbTableNames.HomoSeqInfo]);
DataTable groupIdTable = ProtCidSettings.protcidQuery.Query(queryString);
int groupId = 0;
ProtCidSettings.progressInfo.totalStepNum = groupIdTable.Rows.Count;
ProtCidSettings.progressInfo.totalOperationNum = groupIdTable.Rows.Count;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Detecting reduntdant crystal forms.");
foreach (DataRow groupRow in groupIdTable.Rows)
{
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
groupId = Convert.ToInt32(groupRow["GroupSeqID"].ToString());
ProtCidSettings.progressInfo.currentFileName = groupId.ToString();
CheckGroupReduntCrystForms(groupId);
if (reduntCrystFormTable.Rows.Count > 0)
{
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, reduntCrystFormTable);
reduntCrystFormTable.Clear();
}
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
}
public void ClassifyHomoEntries(string[] entryList)
{
InitializeTables();
DeleteObsHomoGroupDataInDb(groupSeqNum);
AddEntryDataToTable(entryList, groupSeqNum);
RetrieveRepEntries();
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, HomoGroupTables.homoGroupTables);
HomoGroupTables.ClearTables();
}
/// <summary>
///
/// </summary>
/// <param name="crcCodes"></param>
public void ImportHHalignments(string[] crcCodes)
{
string queryString = "";
foreach (string crc in crcCodes)
{
queryString = string.Format("Select * From HHGlobal Where query = '{0}' OR hit = '{0}';", crc);
DataTable hhalignmentTable = dbQuery.Query(remotePiscesDbConnect, queryString);
hhalignmentTable.TableName = "hhglobal";
dbInsert.InsertDataIntoDBtables(localMysqlDbConnect, hhalignmentTable);
}
}
/// <summary>
///
/// </summary>
private void InsertHhAlignDataToDb(DataTable hhAlignmentTable)
{
int rowCutoff = 100;
int rowCount = 0;
DataTable subHhAlignTable = hhAlignmentTable.Clone();
subHhAlignTable.TableName = hhAlignmentTable.TableName;
for (int i = 0; i < hhAlignmentTable.Rows.Count; i++)
{
if (rowCount == rowCutoff)
{
try
{
dbInsert.BatchInsertDataIntoDBtables(ProtCidSettings.alignmentDbConnection, subHhAlignTable);
}
catch
{
dbInsert.InsertDataIntoDBtables(ProtCidSettings.alignmentDbConnection, subHhAlignTable);
}
subHhAlignTable.Clear();
rowCount = 0;
}
DataRow newDataRow = subHhAlignTable.NewRow();
newDataRow.ItemArray = hhAlignmentTable.Rows[i].ItemArray;
subHhAlignTable.Rows.Add(newDataRow);
rowCount++;
}
if (subHhAlignTable.Rows.Count > 0)
{
dbInsert.BatchInsertDataIntoDBtables(ProtCidSettings.alignmentDbConnection, subHhAlignTable);
}
}
/// <summary>
/// the domain alignments for representative domain interfaces
/// </summary>
public void GetDomainAlignments()
{
string queryString = string.Format("SELECT DISTINCT RelSeqID FROM {0}DomainInterfaces;",
ProtCidSettings.dataType);
DataTable seqIdTable = ProtCidSettings.protcidQuery.Query(queryString);
int relSeqId = -1;
string familyCode1 = "";
string familyCode2 = "";
DataTable alignInfoTable = null;
foreach (DataRow seqIdRow in seqIdTable.Rows)
{
relSeqId = Convert.ToInt32(seqIdRow["RelSeqID"].ToString());
familyCode1 = seqIdRow["Family1"].ToString().Trim();
familyCode2 = seqIdRow["Family2"].ToString().Trim();
if (familyCode1 == familyCode2)
{
alignInfoTable = GetSameFamilyDomainAlignments(relSeqId, familyCode1);
}
else
{
alignInfoTable = GetDifFamilyDomainAlignments(relSeqId, familyCode1, familyCode2);
}
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, alignInfoTable);
}
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="chainAtomsHash"></param>
public void GetIntraChainDomainInterfaces(string pdbId, Dictionary <string, AtomInfo[]> chainAtomsHash)
{
string queryString = string.Format("Select * From PdbPfam Where PdbID = '{0}';", pdbId);
DataTable domainDefTable = dbQuery.Query(ProtCidSettings.pdbfamDbConnection, queryString);
int domainInterfaceId = 1;
string asymChain = "";
int entityId = -1;
List <string> chainSymOpList = new List <string> (chainAtomsHash.Keys);
chainSymOpList.Sort();
foreach (string chainSymOpString in chainSymOpList)
{
asymChain = GetAsymChain(chainSymOpString);
entityId = asuInfoFinder.GetEntityIdForAsymChain(pdbId, asymChain);
DataRow[] domainDefRows = domainDefTable.Select(string.Format("EntityID = '{0}'", entityId));
if (domainDefRows.Length < 2)
{
continue;
}
AtomInfo[] chainAtoms = (AtomInfo[])chainAtomsHash[chainSymOpString];
Dictionary <long, AtomInfo[]> chainDomainAtomsHash = GetDomainAtoms(domainDefRows, chainAtoms);
// the interacted domain pairs intra-chain
string[] interactedDomainPairs = GetInteractedDomainPairs(chainDomainAtomsHash);
// insert domain-domain interfaces into table
InsertDataIntoTable(pdbId, asymChain, ref domainInterfaceId, interactedDomainPairs, domainDefTable);
}
dbInsert.InsertDataIntoDBtables(ProtCidSettings.buCompConnection, BuCompTables.intraChainDomainInterfaceTable);
}
public void ParsePdbSwsFiles()
{
CreateDbRefTableStructures("sws");
CreateDbRefTablesInDb("sws");
string chainFile = Path.Combine(dataDir, "pdbsws_chain.txt");
Hashtable entryEntityChainHash = new Hashtable();
string[] addedEntryChains = ParsePdbSwsChainFile(chainFile, ref entryEntityChainHash);
dbInsert.InsertDataIntoDBtables(dbRefTable);
string residueFile = Path.Combine(dataDir, "pdbsws_res.txt");
ParsePdbSwsResidueFile(residueFile, addedEntryChains, entryEntityChainHash);
dbInsert.InsertDataIntoDBtables(dbRefSeqTable);
}
/// <summary>
/// update protbudbiolassemblies table
/// </summary>
/// <param name="entries"></param>
public void UpdateProtBudBiolAssemblies(string[] entries)
{
Console.WriteLine("Retrieving biol units info");
if (entries == null)
{
string entryFile = "ProtEntries.txt";
entries = GetAsuEntries(parsedEntryFile, entryFile, true);
}
StreamWriter parsedEntryWriter = new StreamWriter(parsedEntryFile, true);
DataTable buTable = null;
foreach (string pdbId in entries)
{
if (isUpdate)
{
DeleteObsoleteBuData(pdbId);
}
buTable = new DataTable(buTableName);
buQuery.GetBiolUnitForPdbEntry(pdbId, "", "", ref buTable);
UpdateBuTableNmrEMResolution(buTable);
dbInsert.InsertDataIntoDBtables(ProtCidSettings.pdbfamDbConnection, buTable);
parsedEntryWriter.WriteLine(pdbId);
parsedEntryWriter.Flush();
}
parsedEntryWriter.Close();
Console.WriteLine("Done!");
}
/// <summary>
/// insert redundant crystal forms summary info to db table
/// </summary>
public void UpdateCfGroupInfo()
{
InitializeDbTable();
DataTable cfGroupTable = InitializeTable();
Dictionary <int, Dictionary <int, List <string> > > familyReduntCfHash = GetRedundantCFs();
/* string queryString = string.Format ("Select Distinct GroupSeqID From {0};",
* GroupDbTableNames.dbTableNames[GroupDbTableNames.SgInterfaces]);*/
string queryString = string.Format("Select Distinct GroupSeqID From {0};",
GroupDbTableNames.dbTableNames[GroupDbTableNames.HomoSeqInfo]);
DataTable groupTable = ProtCidSettings.protcidQuery.Query(queryString);
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.totalStepNum = groupTable.Rows.Count;
ProtCidSettings.progressInfo.totalOperationNum = groupTable.Rows.Count;
ProtCidSettings.progressInfo.currentOperationLabel = "Update CF Info.";
int groupId = 0;
foreach (DataRow dRow in groupTable.Rows)
{
groupId = Convert.ToInt32(dRow["GroupSeqID"].ToString());
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
ProtCidSettings.progressInfo.currentFileName = groupId.ToString();
GetNonReduntCfGroupsInFamily(groupId, familyReduntCfHash[groupId], ref cfGroupTable);
}
DbInsert dbInsert = new DbInsert();
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, cfGroupTable);
// DbBuilder.dbConnect.DisconnectFromDatabase ();
}
/// <summary>
/// Compare cryst and bu interfaces for all entries in db
/// </summary>
public void CompareEntryCrystBuInterfaces()
{
Initialize();
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
// string crystEntryQuery = "SELECT Distinct PdbID FROM CrystEntryInterfaces;";
// DataTable crystEntryTable = dbQuery.Query (crystEntryQuery);
string[] nonBuCompEntries = GetNonBuCompEntries();
// string[] nonBuCompEntries = {"1v9t"};
ProtCidSettings.progressInfo.currentOperationLabel = "Comparing Cryst BU Interface";
ProtCidSettings.progressInfo.totalOperationNum = nonBuCompEntries.Length;
ProtCidSettings.progressInfo.totalStepNum = nonBuCompEntries.Length;
#if DEBUG
StreamWriter entryWriter = new StreamWriter("notInDbEntryList.txt", true);
#endif
foreach (string pdbId in nonBuCompEntries)
{
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
ProtCidSettings.progressInfo.currentFileName = pdbId;
try
{
CompareEntryCrystBuInterfaces(pdbId);
}
catch (Exception ex)
{
ProtCidSettings.logWriter.WriteLine("Comparing " + pdbId + " cryst bu interfaces errors: " + ex.Message);
ProtCidSettings.logWriter.Flush();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Comparing " + pdbId + " cryst bu interfaces errors: " + ex.Message);
}
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, crystBuInterfaceCompTables);
ClearTables();
}
try
{
Directory.Delete(ProtCidSettings.tempDir, true);
}
catch {}
#if DEBUG
entryWriter.Close();
#endif
}
/// <summary>
///
/// </summary>
/// <param name="entryBuInterfaceHashes"></param>
public void ComapreEntryBuInterfaces(string pdbId, Dictionary <string, InterfaceChains[]>[] entryBuInterfaceHashes)
{
Dictionary <string, InterfacePairInfo[]> pdbPisaBuInterfaceCompHash = CompareEntryBuInterfaces(entryBuInterfaceHashes[(int)BuType.PDB], entryBuInterfaceHashes[(int)BuType.PISA]);
InsertDataIntoTables(pdbId, pdbPisaBuInterfaceCompHash, "pdbpisa");
dbInsert.InsertDataIntoDBtables(ProtCidSettings.buCompConnection, EntryBuCompTables.entryBuCompTables);
EntryBuCompTables.ClearTables();
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
public void GetBuDomainContents(string pdbId, ref Dictionary <string, int> familyStringGroupIdHash)
{
Dictionary <string, Dictionary <int, List <string> > > buProtChainsHash = GetProtChainComponentForEntry(pdbId);
if (buProtChainsHash.Count == 0)
{
return;
}
int groupSeqId = -1;
string buFamilyString = "";
string protFamilyString = "";
foreach (string buId in buProtChainsHash.Keys)
{
Dictionary <int, List <string> > buEntityChainsHash = buProtChainsHash[buId];
buFamilyString = "";
List <int> entityList = new List <int> (buEntityChainsHash.Keys);
entityList.Sort();
foreach (int entityId in entityList)
{
List <string> chainCountList = buEntityChainsHash[entityId];
string[] chainCountFields = chainCountList[0].ToString().Split('_');
protFamilyString = GetPfamFamiliesInChain(pdbId, chainCountFields[0]);
if (protFamilyString == "")
{
continue;
}
buFamilyString += protFamilyString + ";";
}
buFamilyString = buFamilyString.TrimEnd(';');
groupSeqId = GetGroupSeqID(buFamilyString, ref familyStringGroupIdHash);
AssignDataIntoTable(groupSeqId, pdbId, buId, buEntityChainsHash);
}
dbInsert.InsertDataIntoDBtables(ProtCidSettings.buCompConnection, groupTable);
dbInsert.InsertDataIntoDBtables(ProtCidSettings.buCompConnection, buGroupTable);
groupTable.Clear();
buGroupTable.Clear();
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="entityId"></param>
public void UpdateEntryEntityDbRefData(string pdbId, nt entityId, ref int refId, ref int alignId)
{
string srcType = "";
bool dbAccValid = true;
string[] dbAccessions = GetUnpAccessions(pdbId, entityId, out srcType, true);
try
{
dbAccValid = DoesEntityHaveValidDbAccessions(dbAccessions);
}
catch (Exception ex)
{
string stop = "";
}
if (dbAccValid && srcType != "")
{
updateLogWriter.WriteLine("Update " + pdbId + entityId.ToString () + " from " + srcType);
// delete related data to this entity
DeleteDbRefData(pdbId, entityId);
totalNumOfEntitiesUpdated++;
DataTable residueMapTable = GetEntityResidueMapTable(pdbId, entityId, srcType);
UpdatePdbDbRefInfoFromDifSrc(residueMapTable, ref refId, ref alignId, srcType);
/* if (srcType == "ssmap")
{
UpdatePdbDbRefFromSSmap(residueMapTable, ref refId, ref alignId);
}
else if (srcType == "sws")
{
UpdatePdbDbRefFromSws(residueMapTable, ref refId, ref alignId);
}
*/
dbInsert.InsertDataIntoDBtables(dbRefTable);
dbInsert.InsertDataIntoDBtables(dbRefSeqTable);
dbRefTable.Clear();
dbRefSeqTable.Clear();
}
}
/// <summary>
/// update nonredundant cf group table
/// </summary>
public void UpdateCfGroupInfo(int[] updateGroups)
{
DataTable cfGroupTable = InitializeTable();
Dictionary <int, Dictionary <int, List <string> > > familyReduntCfHash = GetRedundantCFs(updateGroups);
foreach (int groupId in updateGroups)
{
GetNonReduntCfGroupsInFamily(groupId, familyReduntCfHash[groupId], ref cfGroupTable);
}
DeleteObsData(updateGroups);
DbInsert dbInsert = new DbInsert();
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, cfGroupTable);
// DbBuilder.dbConnect.DisconnectFromDatabase ();
}
/// <summary>
///
/// </summary>
/// <param name="relSeqId"></param>
private void AddPeptideInterfaceClusterSumInfo(string pfamId, DataTable clusterStatInfoTable)
{
string queryString = string.Format("Select Distinct ClusterID From PfamPepInterfaceClusters Where PfamID = '{0}';", pfamId);
DataTable clusterTable = ProtCidSettings.protcidQuery.Query(queryString);
int[] pepRelSeqIds = GetPfamPeptideRelSeqIds(pfamId);
DataTable pepInterfaceTable = GetRelationPeptideInterfaceTable(pepRelSeqIds);
DataTable pfamDomainTable = GetPfamDomainTable(pfamId);
int clusterId = 0;
foreach (DataRow clusterRow in clusterTable.Rows)
{
clusterId = Convert.ToInt32(clusterRow["ClusterID"].ToString());
GetClusterSumInfo(pfamId, clusterId, pepInterfaceTable, pfamDomainTable, clusterStatInfoTable);
}
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, clusterStatInfoTable);
clusterStatInfoTable.Clear();
}
/// <summary>
/// add the cfgroupid for those entries are not in the pfamgroups
/// temporary added for the domain interface data, should discard later
/// </summary>
public void UpdateCfGroupInfoForDebug()
{
DbInsert dbInsert = new DbInsert();
DataTable cfGroupTable = InitializeTable();
Dictionary <int, string[]> updateGroupEntryHash = ReadUpdateEntries();
List <int> groupIdList = new List <int> (updateGroupEntryHash.Keys);
groupIdList.Sort();
foreach (int groupId in groupIdList)
{
string[] updateEntries = updateGroupEntryHash[groupId];
GetNonReduntCfGroupsInFamilyForDebug(groupId, updateEntries, ref cfGroupTable);
dbInsert.InsertDataIntoDBtables(ProtCidSettings.protcidDbConnection, cfGroupTable);
cfGroupTable.Clear();
}
// DbBuilder.dbConnect.DisconnectFromDatabase ();
}
/// <summary>
///
/// </summary>
/// <param name="domainInfo"></param>
private void InsertDataIntoDbTable(PfamDomainInfo domainInfo)
{
if (isUpdate)
{
string deleteString = string.Format("Delete From {0} Where PdbID = '{1}' AND DomainID = {2};",
domainFileInfoTable.TableName, domainInfo.pdbId, domainInfo.domainId);
dbQuery.Query(deleteString);
}
foreach (DomainSegmentInfo segInfo in domainInfo.segmentInfos)
{
DataRow fileInfoRow = domainFileInfoTable.NewRow();
fileInfoRow["PdbId"] = domainInfo.pdbId;
fileInfoRow["DomainId"] = domainInfo.domainId;
fileInfoRow["EntityID"] = segInfo.entityId;
fileInfoRow["AsymChain"] = segInfo.asymChain;
fileInfoRow["SeqStart"] = segInfo.seqStart;
fileInfoRow["SeqEnd"] = segInfo.seqEnd;
fileInfoRow["FileStart"] = segInfo.fileStart;
fileInfoRow["FileEnd"] = segInfo.fileEnd;
domainFileInfoTable.Rows.Add(fileInfoRow);
}
dbInsert.InsertDataIntoDBtables(domainFileInfoTable);
domainFileInfoTable.Clear();
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="pfamLigandTable"></param>
private void RetrieveLigandChainInteractions(string pdbId, DataTable chainLigandTable)
{
string gzCoordXmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
if (!File.Exists(gzCoordXmlFile))
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(pdbId + ".xml.gz file not exist");
return;
}
string coordXmlFile = ParseHelper.UnZipFile(gzCoordXmlFile, ProtCidSettings.tempDir);
// read data from crystal xml file
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(coordXmlFile, FileMode.Open);
EntryCrystal thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
xmlFileStream.Close();
File.Delete(coordXmlFile);
// no coordinates for waters
ChainAtoms[] chains = thisEntryCrystal.atomCat.ChainAtomList;
string[][] chainLigandNames = GetChainLigandsNames(chains);
string[] protChainNames = chainLigandNames[0]; // the list of protein chains
string[] ligandChainNames = chainLigandNames[1]; // the list of ligands, no DNA/RNA
if (ligandChainNames.Length == 0)
{
return;
}
Dictionary <string, double> seqPairDistDict = new Dictionary <string, double>();
foreach (string ligandChainName in ligandChainNames)
{
AtomInfo[] ligandAtoms = GetChainAtoms(chains, ligandChainName);
foreach (string protChainName in protChainNames)
{
AtomInfo[] protChainAtoms = GetChainAtoms(chains, protChainName);
Dictionary <string, AtomInfo[]> seqPairContactHash = CalculateAtomDistances(ligandAtoms, protChainAtoms, out seqPairDistDict);
foreach (string seqPair in seqPairDistDict.Keys)
{
string[] seqIds = seqPair.Split('_');
double distance = seqPairDistDict[seqPair];
AtomInfo[] atomPair = seqPairContactHash[seqPair];
DataRow chainLigandRow = chainLigandTable.NewRow();
chainLigandRow["PdbID"] = pdbId;
chainLigandRow["AsymID"] = ligandChainName;
// chainLigandRow["Ligand"] = ligandChainName;
chainLigandRow["ChainAsymID"] = protChainName;
chainLigandRow["SeqID"] = seqIds[0];
chainLigandRow["ChainSeqID"] = seqIds[1];
chainLigandRow["Distance"] = distance;
chainLigandRow["Atom"] = atomPair[0].atomName;
chainLigandRow["ChainAtom"] = atomPair[1].atomName;
chainLigandRow["Residue"] = atomPair[0].residue;
chainLigandRow["ChainResidue"] = atomPair[1].residue;
chainLigandTable.Rows.Add(chainLigandRow);
}
}
}
dbInsert.InsertDataIntoDBtables(ProtCidSettings.buCompConnection, chainLigandTable);
chainLigandTable.Clear();
}
/// <summary>
///
/// </summary>
/// <param name="entries"></param>
public void PrintBiolAssembliesToFile(string[] entries)
{
ProtCidSettings.logWriter.WriteLine("Retrieving biol units info");
string buFile = "";
bool headerLineExist = false;
if (entries == null)
{
string entryFile = "ProtEntries.txt";
entries = GetAsuEntries(parsedEntryFile, entryFile, true);
// entries = GetMissingEntries();
buFile = Path.Combine(ProtCidSettings.dirSettings.pfamPath, "biolAssemblies.txt");
}
else
{
buFile = Path.Combine(ProtCidSettings.dirSettings.pfamPath, "newbiolAssemblies.txt");
}
if (File.Exists(buFile))
{
headerLineExist = true;
}
StreamWriter fileWriter = new StreamWriter(buFile, true);
if (!headerLineExist)
{
string headerLine = GetHeaderLine();
fileWriter.WriteLine(headerLine);
}
StreamWriter parsedEntryWriter = new StreamWriter(parsedEntryFile, true);
DataTable buTable = null;
string line = "";
foreach (string pdbId in entries)
{
if (isUpdate)
{
DeleteObsoleteBuData(pdbId);
}
buTable = new DataTable(buTableName);
buQuery.GetBiolUnitForPdbEntry(pdbId, "", "", ref buTable);
dbInsert.InsertDataIntoDBtables(ProtCidSettings.pdbfamDbConnection, buTable);
foreach (DataRow buRow in buTable.Rows)
{
line = "";
foreach (object item in buRow.ItemArray)
{
line += item.ToString();
line += "\t";
}
fileWriter.WriteLine(line.TrimEnd('\t'));
}
fileWriter.Flush();
parsedEntryWriter.WriteLine(pdbId);
parsedEntryWriter.Flush();
}
fileWriter.Close();
parsedEntryWriter.Close();
ParseHelper.ZipPdbFile(buFile);
ProtCidSettings.logWriter.WriteLine("Done!");
}
/// <summary>
///
/// </summary>
/// <param name="dataFile"></param>
public void ParsePdbSwsFile(string dataFile)
{
CreateDataTableStructures("sws");
CreateDbTable("sws");
string line = "";
string preUnpPdbChainString = "";
string unpPdbChainString = "";
string prePdbChain = "";
string pdbChain = "";
StreamReader dataReader = new StreamReader(dataFile);
string pdbId = "";
string authorChain = "";
string dbAccession = "";
ArrayList seqNumList = new ArrayList();
ArrayList pdbSeqList = new ArrayList();
ArrayList authSeqNumList = new ArrayList();
ArrayList unpSeqList = new ArrayList();
ArrayList unpSeqNumList = new ArrayList();
int totalNumOfRowsInTable = 10000;
int numOfRowsInTable = 0;
// int numOfRowsInDb = 0;
Hashtable entryEntityHash = new Hashtable();
while ((line = dataReader.ReadLine()) != null)
{
string[] fields = ParseHelper.SplitPlus(line, ' ');
pdbChain = fields[0] + fields[1];
if (fields.Length == 8)
{
unpPdbChainString = fields[0] + fields[1] + fields[5];
}
if (preUnpPdbChainString == "")
{
preUnpPdbChainString = unpPdbChainString;
}
if (prePdbChain == "")
{
prePdbChain = pdbChain;
}
if (prePdbChain != pdbChain)
{
unpPdbChainString = "";
preUnpPdbChainString = "";
}
if (preUnpPdbChainString != unpPdbChainString || prePdbChain != pdbChain)
{
/* numOfRowsInDb++;
* if (numOfRowsInDb <= 60000)
* {
* continue;
* }*/
DataRow dataRow = pdbUnpDbTable.NewRow();
dataRow["PdbID"] = pdbId;
dataRow["AuthorChain"] = authorChain;
dataRow["EntityID"] = GetEntityIDForAuthorChain(pdbId, authorChain, ref entryEntityHash);
dataRow["DbAccession"] = dbAccession;
dataRow["PdbSequence"] = pdbSeqList.ToString();
dataRow["AuthorSeqNumbers"] = FormatArrayListToString(authSeqNumList);
dataRow["SeqNumbers"] = FormatArrayListToString(seqNumList);
dataRow["UnpSequence"] = unpSeqList.ToString();
dataRow["unpSeqNumbers"] = FormatArrayListToString(unpSeqNumList);
// dbInsert.InsertDataIntoDb(dataRow);
pdbUnpDbTable.Rows.Add(dataRow);
numOfRowsInTable++;
if (numOfRowsInTable == totalNumOfRowsInTable)
{
dbInsert.InsertDataIntoDBtables(pdbUnpDbTable);
pdbUnpDbTable.Clear();
numOfRowsInTable = 0;
}
pdbSeqList.Clear();
authSeqNumList.Clear();
seqNumList.Clear();
unpSeqList.Clear();
unpSeqNumList.Clear();
}
pdbId = fields[0];
authorChain = fields[1];
preUnpPdbChainString = unpPdbChainString;
prePdbChain = pdbChain;
seqNumList.Add(fields[2]);
pdbSeqList.Add(threeToOne(fields[3]));
authSeqNumList.Add(fields[4]);
if (fields.Length < 8)
{
unpSeqList.Add("-");
unpSeqNumList.Add("-");
}
else
{
dbAccession = fields[5];
unpSeqList.Add(fields[6]);
unpSeqNumList.Add(fields[7]);
}
}
dataReader.Close();
if (pdbUnpDbTable.Rows.Count > 0)
{
dbInsert.InsertDataIntoDBtables(pdbUnpDbTable);
pdbUnpDbTable.Clear();
}
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
public InterfaceChains[] FindUniqueInterfaces(string pdbId, bool isUpdate)
{
string spaceGroup = GetEntrySpaceGroup(pdbId);
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
if (!Directory.Exists(ProtCidSettings.tempDir))
{
Directory.CreateDirectory(ProtCidSettings.tempDir);
}
string coordXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
InterfaceChains[] entryInterfaces = null;
AsuInterfaces asuInterfacesNonCryst = new AsuInterfaces();
try
{
if (spaceGroup == "NMR")
{
entryInterfaces = asuInterfacesNonCryst.GetAsuInterfacesFromXml(coordXmlFile);
if (entryInterfaces == null)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("NMR entry " + pdbId + " is a monomer.");
#if DEBUG
ProtCidSettings.logWriter.WriteLine("NMR entry " + pdbId + " is a monomer.");
ProtCidSettings.logWriter.Flush();
#endif
}
}
else
{
ContactInCrystal contactInCrystal = new ContactInCrystal();
int numOfChainsInUnitCell = contactInCrystal.FindInteractChains(coordXmlFile);
if (numOfChainsInUnitCell > 64)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("The number of chains of " + pdbId + " in a unit cell: " + numOfChainsInUnitCell.ToString());
#if DEBUG
ProtCidSettings.logWriter.WriteLine("The number of chains of " + pdbId + " in a unit cell: " + numOfChainsInUnitCell.ToString());
ProtCidSettings.logWriter.Flush();
#endif
}
if (contactInCrystal.InterfaceChainsList == null)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("No interfaces exist in entry: " + pdbId);
}
entryInterfaces = contactInCrystal.InterfaceChainsList;
}
AssignEntryInterfacesToTable(entryInterfaces, pdbId, spaceGroup);
AssignEntryInterfaceCompToTable(pdbId, entryInterfaces);
if (isUpdate)
{
DeleteObsData(pdbId);
}
dbInsert.InsertDataIntoDBtables
(ProtCidSettings.protcidDbConnection, CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.CrystEntryInterfaces]);
dbInsert.InsertDataIntoDBtables
(ProtCidSettings.protcidDbConnection, CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.EntryInterfaceComp]);
CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.CrystEntryInterfaces].Clear();
CrystInterfaceTables.crystInterfaceTables[CrystInterfaceTables.EntryInterfaceComp].Clear();
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving interfaces from " + pdbId + " errors: " + ex.Message);
#if DEBUG
ProtCidSettings.logWriter.WriteLine("Retrieving interfaces from " + pdbId + " errors: " + ex.Message);
ProtCidSettings.logWriter.Flush();
#endif
}
finally
{
if (File.Exists(coordXmlFile))
{
File.Delete(coordXmlFile);
}
}
return(entryInterfaces);
}
/// <summary>
///
/// </summary>
/// <param name="relSeqId"></param>
public void CompareBuDomainInterfaces(int relSeqId)
{
bool isIndividualRelation = false;
#if DEBUG
if (dataWriter == null)
{
dataWriter = new StreamWriter(BuCompBuilder.BuType + "DomainInterfaceComp" + relSeqId.ToString() + ".txt");
isIndividualRelation = true;
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.currentOperationLabel = "Compare Domain Interfaces";
}
#endif
if (domainInterfaceCompTable == null)
{
InitializeTable();
}
string tableName = "";
if (BuCompBuilder.BuType == "asu")
{
tableName = BuCompBuilder.BuType + "PfamDomainInterfaces";
}
else
{
tableName = BuCompBuilder.BuType + "PfamBuDomainInterfaces";
}
string queryString = string.Format("Select Distinct PdbID From {0} Where RelSeqID = {1};",
tableName, relSeqId);
DataTable relEntryTable = dbQuery.Query(ProtCidSettings.buCompConnection, queryString);
string pdbId = "";
Dictionary <string, Dictionary <string, DomainInterface[]> > entryBuDomainInterfaceHash = new Dictionary <string, Dictionary <string, DomainInterface[]> > ();
ProtCidSettings.progressInfo.progStrQueue.Enqueue(relSeqId.ToString());
if (isIndividualRelation)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain interfaces for each entry.");
ProtCidSettings.progressInfo.totalOperationNum = relEntryTable.Rows.Count;
ProtCidSettings.progressInfo.totalStepNum = relEntryTable.Rows.Count;
}
foreach (DataRow entryRow in relEntryTable.Rows)
{
pdbId = entryRow["PdbID"].ToString();
ProtCidSettings.progressInfo.currentFileName = pdbId;
if (isIndividualRelation)
{
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
}
Dictionary <string, DomainInterface[]> buDomainInterfaceHash = domainInterfaceRetriever.RetrieveDomainInterfaces(relSeqId, pdbId, BuCompBuilder.BuType);
entryBuDomainInterfaceHash.Add(pdbId, buDomainInterfaceHash);
}
List <string> entryList = new List <string> (entryBuDomainInterfaceHash.Keys);
entryList.Sort();
if (isIndividualRelation)
{
ProtCidSettings.progressInfo.ResetCurrentProgressInfo();
ProtCidSettings.progressInfo.totalOperationNum = (int)((double)(entryList.Count * (entryList.Count - 1)) / 2.0);
ProtCidSettings.progressInfo.totalStepNum = (int)((double)(entryList.Count * (entryList.Count - 1)) / 2.0);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Compare Domain-domain interfaces in BUs.");
}
for (int i = 0; i < entryList.Count; i++)
{
Dictionary <string, DomainInterface[]> buDomainInterfacesHash1 = entryBuDomainInterfaceHash[entryList[i]];
for (int j = i + 1; j < entryList.Count; j++)
{
if (isIndividualRelation)
{
ProtCidSettings.progressInfo.currentFileName = entryList[i].ToString() + "_" + entryList[j].ToString();
ProtCidSettings.progressInfo.currentOperationNum++;
ProtCidSettings.progressInfo.currentStepNum++;
}
if (IsEntryCompExisting(entryList[i].ToString(), entryList[j].ToString()))
{
continue;
}
ProtCidSettings.progressInfo.currentFileName = entryList[i].ToString() + "_" + entryList[j].ToString();
Dictionary <string, DomainInterface[]> buDomainInterfacesHash2 = entryBuDomainInterfaceHash[entryList[j]];
foreach (string buId1 in buDomainInterfacesHash1.Keys)
{
DomainInterface[] domainInterfaces1 = (DomainInterface[])buDomainInterfacesHash1[buId1];
foreach (string buId2 in buDomainInterfacesHash2.Keys)
{
DomainInterface[] domainInterfaces2 = (DomainInterface[])buDomainInterfacesHash2[buId2];
DomainInterfacePairInfo[] compPairInfos =
domainInterfaceComp.CompareDomainInterfaces(domainInterfaces1, domainInterfaces2);
InsertDataToTable(relSeqId, entryList[i].ToString(), entryList[j].ToString(),
buId1, buId2, compPairInfos);
}
}
#if DEBUG
WriteCompDataToFile(domainInterfaceCompTable);
#endif
dbInsert.InsertDataIntoDBtables(ProtCidSettings.buCompConnection, domainInterfaceCompTable);
domainInterfaceCompTable.Clear();
}
}
if (isIndividualRelation)
{
#if DEBUG
dataWriter.Close();
#endif
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
}
}
