/// <summary>
/// generate interface files for a list representative entries
/// </summary>
/// <param name="pdbList"></param>
public void GenerateRepEntryInterfaceFiles(string[] pdbList)
{
Initialize();
CrystInterfaceProcessor interfaceFileGen = new CrystInterfaceProcessor();
interfaceFileGen.GenerateRepEntryInterfaceFiles(pdbList);
}
/// <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>
/// generate interface files for a list input entries
/// </summary>
/// <param name="pdbList"></param>
public void GenerateEntryInterfaceFiles(string[] pdbList)
{
Initialize();
if (pdbList == null)
{
DbQuery dbQuery = new DbQuery();
string queryString = "Select Distinct PdbID From CrystEntryInterfaces Where SurfaceArea < 0;";
DataTable entryTable = ProtCidSettings.protcidQuery.Query(queryString);
pdbList = new string [entryTable.Rows.Count];
int i = 0;
foreach (DataRow dRow in entryTable.Rows)
{
pdbList[i] = dRow["PdbID"].ToString();
i++;
}
}
CrystInterfaceProcessor interfaceFileGen = new CrystInterfaceProcessor();
interfaceFileGen.GenerateEntryInterfaceFiles(pdbList);
}
