private void uniProtToolStripMenuItem_Click(object sender, EventArgs e)
{
DomainInterfaceBuilder.InitializeThread();
UnpInteractionStr unpDomainInter = new UnpInteractionStr();
unpDomainInter.BuildUnpInteractionNetTable();
}
public void BuildClanDomainInterfaces(int step)
{
ProtCidSettings.dataType = "pfam";
DomainInterfaceBuilder.InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions.");
switch (step)
{
case 1:
ClanDomainInterfaceComp domainInterfaceComp = new ClanDomainInterfaceComp();
int relSeqId1 = 11619;
int relSeqId2 = 11642;
int clanSeqId = 398;
domainInterfaceComp.CompareRepDomainInterfaces2PfamRelations(clanSeqId, relSeqId1, relSeqId2);
break;
case 2:
ClanDomainInterfaceCluster clanInterfaceCluster = new ClanDomainInterfaceCluster();
clanInterfaceCluster.ClusterSuperDomainInterfaces();
break;
case 3: // output coordinate domain interfaces for each cluster
break;
default:
break;
}
}
private void ligandsToolStripMenuItem_Click(object sender, EventArgs e)
{
DomainInterfaceBuilder domainInterfaceBuilder = new DomainInterfaceBuilder();
domainInterfaceBuilder.UpdateDomainInterfaces(3);
/* PfamLigandInteractionBuilder ligandInteractBuilder = new PfamLigandInteractionBuilder();
* ligandInteractBuilder.DebugPfamLigandInteractions();
* string[] updateEntries = ReadUpdateEntries(entryFile);
* ligandInteractBuilder.UpdatePfamLigandInteractions(updateEntries);*/
}
private void domainClusteringMenuItem_Click(object sender, EventArgs e)
{
/* DomainSeqIdentity interfaceCompIdentity = new DomainSeqIdentity();
* interfaceCompIdentity.FillDomainInterfaceCompSeqIdentities();
*/
DomainInterfaceBuilder domainInterfaceBuilder = new DomainInterfaceBuilder();
// domainInterfaceBuilder.UpdatePfamDomainInterfaceClusters();
// domainInterfaceBuilder.BuildDomainInterfaces(5);
// domainInterfaceBuilder.BuildDomainInterfaces(7);
// domainInterfaceBuilder.UpdateDomainInterfaces (1);
domainInterfaceBuilder.UpdatePfamDomainInterfaceClusters();
}
/// <summary>
///
/// </summary>
public void ClusterUserDefinedGroupDomainInterfaces()
{
ProtCidSettings.dataType = "pfam";
DomainInterfaceBuilder.InitializeThread();
DomainInterfaceTables.InitializeTables();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieving domain-domain interactions for user-defined group.");
// structure alignments between representative domains from PFAMs in a group
int groupSeqId = 100000;
/* Hashtable groupPfamHash = new Hashtable();
* string[] groupPfams = { "Integrase_Zn", "zf-H2C2" };
* groupPfamHash.Add(groupSeqId, groupPfams);
*
* PfamLib.DomainAlign.PfamDomainAlign domainAlign = new PfamLib.DomainAlign.PfamDomainAlign();
* domainAlign.AlignPfamDomainsForUserDefinedGroups(groupPfamHash);
*/
// calcuate the Q score between two different relations
groupSeqId = 100000;
Dictionary <int, int[]> groupRelationHash = new Dictionary <int, int[]> ();
List <int> relSeqIdList = new List <int> ();
relSeqIdList.Add(7956);
relSeqIdList.Add(15374);
int[] relSeqIds = new int[relSeqIdList.Count];
relSeqIdList.CopyTo(relSeqIds);
groupRelationHash.Add(groupSeqId, relSeqIds);
groupSeqId++;
relSeqIdList = new List <int> ();
relSeqIdList.Add(7954);
relSeqIdList.Add(15481);
relSeqIds = new int[relSeqIdList.Count];
relSeqIdList.CopyTo(relSeqIds);
groupRelationHash.Add(groupSeqId, relSeqIds);
Dictionary <string, string> pfamClanHash = new Dictionary <string, string> ();
pfamClanHash.Add("Integrase_Zn", "Zn_N");
pfamClanHash.Add("zf-H2C2", "Zn_N");
ClanDomainInterfaceComp domainInterfaceComp = new ClanDomainInterfaceComp();
domainInterfaceComp.CompareRepDomainInterfaces2PfamRelations(groupRelationHash, pfamClanHash);
}
/// <summary>
///
/// </summary>
/// <param name="updateEntries"></param>
public void UpdatePfamLigandInteractions(string[] updateEntries)
{
DomainInterfaceBuilder.InitializeThread();
/*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-DNA/RNA interactions info");
* ProtCidSettings.logWriter.WriteLine("Update Pfam-DNA/RNA interactions info");
* PfamDnaRnaInteractions pfamDnaInteract = new PfamDnaRnaInteractions();
* string[] updateDnaRnaEntries = null;
* updateDnaRnaEntries = pfamDnaInteract.GetUpdateEntriesWithDnaRna(updateEntries);
* pfamDnaInteract.UpdatePfamDnaRnaInteractions(updateDnaRnaEntries);
*
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-ligands interactions info");
* ProtCidSettings.logWriter.WriteLine("Update Pfam-ligands interactions info");
* PfamLigandInteractions pfamLigands = new PfamLigandInteractions();
* pfamLigands.UpdateLigandsInPdb(updateEntries);
* pfamLigands.UpdatePfamLigandInteractions(updateEntries);
* pfamLigands.UpdatePfamLigandInteractionSumInfo(updateEntries);
* pfamLigands.UpdateLigandInteractingPfamsSumInfo(updateEntries);
*
* ProtCidSettings.logWriter.WriteLine("Update Pfam-DNA/RNA interface files");
* PfamDnaRnaFileCompress dnaRnaFileCompress = new PfamDnaRnaFileCompress();
* dnaRnaFileCompress.UpdateDomainDnaRnaFiles(updateDnaRnaEntries);
*
* ProtCidSettings.logWriter.WriteLine("Update Pfam-ligands the number of common Pfam HMM positions");
* LigandComPfamHmm ligandComHmmCal = new LigandComPfamHmm();
* Dictionary<string, List<string>> updatePfamEntryListDict = ligandComHmmCal.UpdateLigandsComPfamHmmPos(updateEntries);
* // Dictionary<string, List<string>> updatePfamEntryListDict = ligandComHmmCal.GetUpdatePfams(updateEntries);
*
* ProtCidSettings.logWriter.WriteLine("Update Pfam-ligands clusters");
* PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
* ligandClusters.UpdatePfamLigandsByPfamHmm(updatePfamEntryListDict);
*/
ProtCidSettings.logWriter.WriteLine("Update compressing Pfam-ligands domain interface files. Pfam_ID.tar.gz: Pfam domain aligned (one Pfam - ligands)");
PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
domainFileCompress.UpdatePfamDomainFiles(updateEntries);
ProtCidSettings.logWriter.WriteLine("Update ligand-Pfam domain interface files. Ligand.tar.gz (one ligand - Pfams) ");
PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();
ligandFileCompress.UpdateLigandPfamDomainFilesFromPdb(updateEntries);
ProtCidSettings.logWriter.WriteLine("Pfam-ligand update is done!");
ProtCidSettings.logWriter.Flush();
}
/// <summary>
///
/// </summary>
public void BuildPfamLigandInteractions()
{
DomainInterfaceBuilder.InitializeThread();
PfamDnaRnaInteractions pfamDnaInteract = new PfamDnaRnaInteractions();
pfamDnaInteract.RetrievePfamDnaRnaInteractions();
PfamLigandInteractions pfamLigandInteract = new PfamLigandInteractions();
pfamLigandInteract.GetLigandsInPdb();
pfamLigandInteract.RetrievePfamLigandInteractions();
pfamLigandInteract.GetPfamLigandInteractionSumInfo();
pfamLigandInteract.PrintLigandInteractingPfamsSumInfo();
PfamDnaRnaFileCompress dnaRnaFileCompress = new PfamDnaRnaFileCompress();
dnaRnaFileCompress.WriteDomainDnaRnaFiles();
// LigandComAtomsPfam ligandComAtomCal = new LigandComAtomsPfam();
// ligandComAtomCal.CalculateOverlapLigandAtomsInPfam();
LigandComPfamHmm comPfamHmm = new LigandComPfamHmm();
comPfamHmm.CalculateLigandsComPfamHmmPos();
PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
ligandClusters.ClusterPfamLigandsByPfamHmm();
// need add ligand clusters to the domain tar.gz files
// move the operation here on April 28, 2017
PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
domainFileCompress.CompressPfamDomainFiles();
PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();
ligandFileCompress.CompressLigandPfamDomainFilesFromPdb();
}
public void DebugPfamLigandInteractions()
{
DomainInterfaceBuilder.InitializeThread();
/* LigandComPfamHmm comPfamHmm = new LigandComPfamHmm();
* string pfamId = "T-box";
* comPfamHmm.CalculatePfamLigandComHmmPos (pfamId);
*
* PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
* // pfamId = "1-cysPrx_C";
* ligandClusters.ClusterPfamLigandsByPfamHmm(pfamId, false);
* // ligandClusters.ClusterPfamLigandsByPfamHmm();
*
* PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
* // domainFileCompress.CompressPfamDomainFiles();
* // pfamId = "40S_S4_C"; // 40S_S4_C
* domainFileCompress.CompilePfamDomainWithLigandFiles(pfamId, null);*/
PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();
string ligandId = "DNA";
ligandFileCompress.CompressDomainDnaRnaFiles(ligandId);
ligandFileCompress.CompressLigandPfamDomainFilesFromPdb();
}
/// <summary>
///
/// </summary>
/// <param name="updateEntries"></param>
public void UpdatePfamLigandInteractions(string[] updateDnaRnaEntries, string[] updateEntries)
{
DomainInterfaceBuilder.InitializeThread();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-DNA/RNA interactions info");
PfamDnaRnaInteractions pfamDnaInteract = new PfamDnaRnaInteractions();
// pfamDnaInteract.UpdatePfamDnaRnaInteractions(updateDnaRnaEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update Pfam-ligands interactions info");
PfamLigandInteractions pfamLigands = new PfamLigandInteractions();
// pfamLigands.UpdateLigandsInPdb(updateEntries);
pfamLigands.UpdatePfamLigandInteractions(updateEntries);
pfamLigands.UpdatePfamLigandInteractionSumInfo(updateEntries);
pfamLigands.UpdateLigandInteractingPfamsSumInfo(updateEntries);
PfamDnaRnaFileCompress dnaRnaFileCompress = new PfamDnaRnaFileCompress();
dnaRnaFileCompress.UpdateDomainDnaRnaFiles(updateDnaRnaEntries);
LigandComPfamHmm ligandComHmmCal = new LigandComPfamHmm();
Dictionary <string, List <string> > updatePfamEntryListDict = ligandComHmmCal.UpdateLigandsComPfamHmmPos(updateEntries);
PfamLigandClusterHmm ligandClusters = new PfamLigandClusterHmm();
ligandClusters.UpdatePfamLigandsByPfamHmm(updatePfamEntryListDict);
PfamDomainFileCompress domainFileCompress = new PfamDomainFileCompress();
domainFileCompress.UpdatePfamDomainFiles(updateEntries);
PfamLigandFileCompress ligandFileCompress = new PfamLigandFileCompress();
ligandFileCompress.UpdateLigandPfamDomainFilesFromPdb(updateEntries);
}
private void peptideToolStripMenuItem_Click(object sender, EventArgs e)
{
DomainInterfaceBuilder domainInterfaceBuilder = new DomainInterfaceBuilder();
domainInterfaceBuilder.UpdateDomainInterfaces(2);
}