/// <summary>
///
/// </summary>
/// <param name="pdbList"></param>
/// <param name="userGroupName"></param>
public void FindCommonInterfaceInGroup(string[] pdbList, string userGroupName)
{
Initialize();
ProtCidSettings.progressInfo.Reset();
int groupId = 111111;
int[] updateGroups = new int [1];
updateGroups[0] = groupId;
ClearPreviousUserData(groupId);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("1. Classify PDB entries into homologous groups");
HomoEntryClassifier entryClassifier = new HomoEntryClassifier(groupId);
entryClassifier.ClassifyHomoEntries(pdbList, userGroupName);
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("2. Build crystal, detect common interfaces in a group");
HomoGroupInterfacesFinder interfaceFinder = new HomoGroupInterfacesFinder();
HomoGroupInterfacesFinder.modifyType = "update";
interfaceFinder.DetectHomoGroupInterfaces(updateGroups);
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("3. Generate interface files, calculate ASA in interfaces");
CrystInterfaceProcessor interfaceProcessor = new CrystInterfaceProcessor();
interfaceProcessor.GenerateEntryInterfaceFiles(pdbList);
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("4. Compare cryst interfaces with PDB/PISA BUs and ASU Interfaces");
EntryCrystBuInterfaceComp buInterfaceComp = new EntryCrystBuInterfaceComp();
buInterfaceComp.CompareEntryCrystBuInterfaces(pdbList);
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("5. Deal With Redundant Crystal Forms.");
RedundantCrystForms reduntCf = new RedundantCrystForms();
reduntCf.UpdateReduntCrystForms(updateGroups);
NonredundantCfGroups nonreduntCfGroups = new NonredundantCfGroups();
nonreduntCfGroups.UpdateCfGroupInfo(updateGroups);
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("6. Cluster cryst common interfaces");
InterfaceCluster interfaceCluster = new InterfaceCluster();
interfaceCluster.UpdateInterfaceClusters(updateGroups);
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("7. Print cryst common interfaces");
ClusterStat clusterStat = new ClusterStat();
clusterStat.PrintCrystInterfaceClusters(groupId, ProtCidSettings.dataType);
ProtCidSettings.progressInfo.threadFinished = true;
}
/// <summary>
/// build from current database by adding update/new pdb entries
/// but rebuild entry-based groups due to new PFAM version
/// regroup crystal forms
/// </summary>
public void BuildEntryInterfaceGroups(int step)
{
DbBuilderHelper.Initialize();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.totalOperationNum = 8;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Building entry-based groups, includes 8 steps: ");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("1.Calculate entry interfaces");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("2. Generate interface files, calculate ASA.");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("3. Compare cryst interfaces with PDB/PQS/PISA BU and ASU Interfaces");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("4. Classify PDB entries into homologous groups");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("5. Retrieve chain alignments in groups");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("6. Calculate similarity Q scores in an entry group.");
// ProtCidSettings.progressInfo.progStrQueue.Enqueue("7. Compare interfaces of entries in entry groups.");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("7. Deal With Redundant Crystal Forms.");
ProtCidSettings.logWriter.WriteLine(DateTime.Today.ToShortTimeString());
ProtCidSettings.logWriter.WriteLine("Build entry-based group data.");
// update entry-related data, it is not necessary to recompute entry data from scratch
string[] updateEntries = GetMissBuCompEntries();
CrystInterfaceBuilder interfaceBuilder = new CrystInterfaceBuilder();
switch (step)
{
case 1:
ProtCidSettings.logWriter.WriteLine("1. Compute interfaces from crystals");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("1. Compute interfaces from crystals");
interfaceBuilder.ComputeEntryCrystInterfaces(updateEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
goto case 2;
case 2:
ProtCidSettings.logWriter.WriteLine("2. Generate interface files, calculate ASA and contacts in interfaces");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("2. Generate interface files, calculate ASA and contacts in interfaces");
interfaceBuilder.GenerateEntryInterfaceFiles(updateEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 3:
ProtCidSettings.logWriter.WriteLine("3. Compare cryst interfaces with PDB/PISA BU and ASU Interfaces");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("3. Compare cryst interfaces with PDB/PISA BU and ASU Interfaces");
// compare cryst interfaces and BU interfaces for each entry
EntryCrystBuInterfaceComp crystBuInterfaceComp = new EntryCrystBuInterfaceComp();
crystBuInterfaceComp.UpdateEntryCrystBuInterfaces(updateEntries);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Recomputing indices.");
DbBuilderHelper.UpdateIndexes("CrystBuInterfaceComp", ProtCidSettings.protcidDbConnection);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 4:
// group entries, rebuild group tables: PfamHomoSeqInfo, PfamHomoGroupEntryAlign, PfamHomoRepEntryAlign
ProtCidSettings.logWriter.WriteLine("4. Classify PDB entries into homologous groups.");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("4. Classify PDB entries into homologous groups");
PfamEntryClassifier pfamClassifier = new PfamEntryClassifier();
pfamClassifier.ClassifyPdbPfamGroups();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Recomputing indices.");
DbBuilderHelper.UpdateIndexes("PFAMHOMO", ProtCidSettings.protcidDbConnection);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 5:
// retrieve chain alignments from HH, and fatcat alignments
ProtCidSettings.logWriter.WriteLine("5. Retrieve chain alignments in groups");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("5. Retrieve chain alignments in groups");
Alignments.GroupEntryAlignments groupAlignment = new InterfaceClusterLib.Alignments.GroupEntryAlignments();
groupAlignment.UpdateCrcHhAlignments();
groupAlignment.RetrieveChainAlignmentsInGroups();
// groupAlignment.GetRepChainPairsToBeAligned();
// groupAlignment.GetRepEntryChainAlignFilesFromMissingEntityAlign();
// groupAlignment.UpdateFatcatAlignmentsFromFile("");
// int[] updateGroups = { 10400 };
// groupAlignment.UpdateGroupEntryAlignments (updateGroups);
// groupAlignment.UpdateMissingChainAlignmentsInGroups (null);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Recomputing indices.");
DbBuilderHelper.UpdateIndexes("PFAMHOMO", ProtCidSettings.protcidDbConnection);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 6:
// compare entry interfaces in entry groups
ProtCidSettings.logWriter.WriteLine("6. Calculate similarity Q scores in a entry-grouped group");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("6. Calculate similarity Q scores in a entry-grouped group");
HomoGroupInterfacesFinder.modifyType = "build";
HomoGroupInterfacesFinder groupInterfaceFinder = new HomoGroupInterfacesFinder();
groupInterfaceFinder.DetectHomoGroupInterfaces(null);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Recomputing indices.");
DbBuilderHelper.UpdateIndexes("INTERFACE", ProtCidSettings.protcidDbConnection);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
break;
case 7:
// group crystal forms based on Q scores of entry interfaces in an entry group
ProtCidSettings.logWriter.WriteLine("7. Detecting redundant crystal forms");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("6. Detecting redundant crystal forms");
RedundantCrystForms reduntCrystForm = new RedundantCrystForms();
reduntCrystForm.CheckReduntCrystForms();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
// distinct crystal forms
ProtCidSettings.logWriter.WriteLine("8. Cluster crystal forms in entry groups");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Non-Redundant Crystal Forms");
NonredundantCfGroups nonreduntCfGroups = new NonredundantCfGroups();
nonreduntCfGroups.UpdateCfGroupInfo();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Recomputing indices.");
DbBuilderHelper.UpdateIndexes("REDUN", ProtCidSettings.protcidDbConnection);
break;
default:
break;
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Build entry-based groups Done!");
ProtCidSettings.logWriter.WriteLine("Build entry-based groups Done!");
ProtCidSettings.logWriter.Flush();
}
/// <summary>
/// update database
/// </summary>
public void UpdatePfamInterfaces()
{
DbBuilderHelper.Initialize();
ProtCidSettings.progressInfo.Reset();
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Updating PFAM Interfaces Data.");
string line = "";
string[] updateEntries = null;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Get the entries to be updated from XML file directory.");
// string lsFile = "EntriesNotInEntryLevelGroups.txt";
updateEntries = GetUpdateEntries();
// updateEntries = GetUpdateEntries(lsFile);
if (updateEntries.Length == 0)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue("No update needed.");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.threadFinished = true;
return;
}
// Update entry interfaces,
// generate interface files, calculate surface area,
// then compare crystal interfaces to interfaces in PDB/PISA BAs
// UpdateEntryInterfaceData(updateEntries);
// updateEntries = GetUpdateEntriesFromPfamUpdate();
// classify these groups
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Update classification of homologous groups");
PfamEntryClassifier pfamClassifier = new PfamEntryClassifier();
Dictionary <int, string[]> updateGroupHash = null;
updateGroupHash = pfamClassifier.UpdatePdbPfamGroups(updateEntries);
ProtCidSettings.progressInfo.currentOperationIndex++;
if (updateGroupHash == null)
{
updateGroupHash = new Dictionary <int, string[]>();
}
// divide into two groups
/* int groupIdDivide = 7000;
* ProtCidSettings.progressInfo.progStrQueue.Enqueue("This is for groupId >= 7000");
* ProtCidSettings.logWriter.WriteLine("This is for groupid >= 7000.");*/
if (updateGroupHash.Count == 0)
{
int groupId = 0;
StreamReader updateGroupReader = new StreamReader("updateGroups.txt");
// string line = "";
while ((line = updateGroupReader.ReadLine()) != null)
{
string[] fields = line.Split(' ');
groupId = Convert.ToInt32(fields[0]);
// if (groupId >= groupIdDivide)
string[] entries = new string[fields.Length - 1];
Array.Copy(fields, 1, entries, 0, entries.Length);
updateGroupHash.Add(groupId, entries);
}
updateGroupReader.Close();
}
int[] updateGroups = new int[updateGroupHash.Count];
updateGroupHash.Keys.CopyTo(updateGroups, 0);
Array.Sort(updateGroups);
// update xtal interfaces for these groups
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Retrieve alignments in a group");
Alignments.GroupEntryAlignments groupAlignment = new InterfaceClusterLib.Alignments.GroupEntryAlignments();
try
{
groupAlignment.UpdateChainAlignmentsInGroups(updateGroups);
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Stop the updating alignments and return.");
ProtCidSettings.logWriter.WriteLine(ex.Message);
ProtCidSettings.logWriter.WriteLine("Stop the updating alignments and return.");
ProtCidSettings.logWriter.Flush();
return;
}
ProtCidSettings.progressInfo.currentOperationIndex++;
// update xtal interfaces for these groups
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Build crystal, detect common interfaces in a group");
HomoGroupInterfacesFinder.modifyType = "update";
HomoGroupInterfacesFinder groupInterfaceFinder = new HomoGroupInterfacesFinder();
try
{
groupInterfaceFinder.UpdateHomoGroupInterfaces(updateGroupHash);
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Stop the updating group interfaces comparing and return.");
ProtCidSettings.logWriter.WriteLine(ex.Message);
ProtCidSettings.logWriter.WriteLine("Stop the updating group interfaces comparing and return.");
ProtCidSettings.logWriter.Flush();
return;
}
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("6. Detecting redundant crystal forms");
RedundantCrystForms reduntCrystForm = new RedundantCrystForms();
try
{
reduntCrystForm.UpdateReduntCrystForms(updateGroups);
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Stop the updating redundant cryst forms and return.");
ProtCidSettings.logWriter.WriteLine(ex.Message);
ProtCidSettings.logWriter.WriteLine("Stop the updating redundant cryst forms and return.");
ProtCidSettings.logWriter.Flush();
return;
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.currentOperationIndex++;
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Non-Redundant Crystal Forms");
NonredundantCfGroups nonreduntCfGroups = new NonredundantCfGroups();
try
{
nonreduntCfGroups.UpdateCfGroupInfo(updateGroups);
}
catch (Exception ex)
{
ProtCidSettings.progressInfo.progStrQueue.Enqueue(ex.Message);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Stop the updating CF groups and return.");
ProtCidSettings.logWriter.WriteLine(ex.Message);
ProtCidSettings.logWriter.WriteLine("Stop the updating CF groups and return.");
ProtCidSettings.logWriter.Flush();
return;
}
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Recomputing indices.");
DbBuilderHelper.UpdateIndexes("RedundantCfGroups", ProtCidSettings.protcidDbConnection);
ProtCidSettings.progressInfo.progStrQueue.Enqueue("Done!");
ProtCidSettings.logWriter.Close();
ProtCidSettings.progressInfo.threadFinished = true;
}