/// <summary>
/// Add the ligands with the same author name
/// </summary>
/// <param name="pdbId"></param>
/// <param name="interfaceInfoList"></param>
/// <param name="type"></param>
/// <param name="needAsaUpdated"></param>
/// <param name="needSameAuthorLigands"></param>
/// <returns></returns>
public ProtInterface[] GenerateInterfaceFiles(string pdbId, string coordXmlFile, ProtInterfaceInfo[] interfaceInfoList,
string type, bool needSameAuthorLigands, string interfaceFileDir, DataTable asuTable, bool isAsuInterface)
{
string[] symOpStrings = GetSymOpStringsFromInterfaces(interfaceInfoList);
// 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();
Dictionary <string, AtomInfo[]> entryChainsHash = BuildCrystalWithAllChains(thisEntryCrystal, symOpStrings);
// protein asym id and its ligands with the same author name and the atoms for the ligands
// Hashtable asymIdLigandAtomInfoHash = GetEntryLigandAtomInfoHash(asuTable, thisEntryCrystal);
Dictionary <string, string[]> asymLigandsHash = GetAsymChainLigandsHash(asuTable);
int i = 0;
string chain1 = "";
string chain2 = "";
string interfaceFile = "";
ProtInterface[] interfaces = new ProtInterface[interfaceInfoList.Length];
string[] symmetryStrings = new string[2];
foreach (ProtInterfaceInfo interfaceInfo in interfaceInfoList)
{
chain1 = interfaceInfo.Chain1 + "_" + interfaceInfo.SymmetryString1;
chain2 = interfaceInfo.Chain2 + "_" + interfaceInfo.SymmetryString2;
if (!entryChainsHash.ContainsKey(chain1) || !entryChainsHash.ContainsKey(chain2))
{
continue;
}
Dictionary <string, AtomInfo[]>[] ligandAtomInfoHashs = GetInterfaceLigandAtomInfoHashes(interfaceInfo, asymLigandsHash, entryChainsHash);
interfaceInfo.Remark += FormatInterfaceAsa(interfaceInfo.ASA);
symmetryStrings[0] = interfaceInfo.SymmetryString1;
symmetryStrings[1] = interfaceInfo.SymmetryString2;
interfaceInfo.Remark += FormatLigandsInfo(ligandAtomInfoHashs, symmetryStrings, asuTable);
if (isAsuInterface)
{
interfaceFile = Path.Combine(interfaceFileDir, pdbId + "_0" + interfaceInfo.InterfaceId.ToString() + ".cryst");
}
else
{
interfaceFile = Path.Combine(interfaceFileDir, pdbId + "_" + interfaceInfo.InterfaceId.ToString() + ".cryst");
}
interfaceWriter.WriteInterfaceToFile(interfaceFile, entryChainsHash[chain1], entryChainsHash[chain2], interfaceInfo.Remark, type, ligandAtomInfoHashs);
ParseHelper.ZipPdbFile(interfaceFile);
interfaces[i] = new ProtInterface(interfaceInfo);
interfaces[i].ResidueAtoms1 = GetSeqAtoms(entryChainsHash[chain1]);
interfaces[i].ResidueAtoms2 = GetSeqAtoms(entryChainsHash[chain2]);
i++;
}
return(interfaces);
}
/// <summary>
/// generate interface files from the input defintion
/// </summary>
/// <param name="pdbId"></param>
/// <param name="interfaceInfoList"></param>
/// <param name="type"></param>
/// <param name="needAsaUpdated"></param>
/// <returns></returns>
public ProtInterface[] GenerateInterfaceFiles(string pdbId, ProtInterfaceInfo[] interfaceInfoList, string type, out bool needAsaUpdated)
{
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string coordXmlFile = AuxFuncLib.ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
string[] symOpStrings = GetChainSymOpStringsFromInterfaces(interfaceInfoList);
Dictionary <string, AtomInfo[]> buChainsHash = base.BuildCrystal(coordXmlFile, symOpStrings);
File.Delete(coordXmlFile);
needAsaUpdated = false;
string[] asaChains = interfaceAsa.GetChainsWithoutAsa(interfaceInfoList, type);
if (asaChains.Length > 0)
{
needAsaUpdated = true;
}
Dictionary <string, double> chainSaHash = interfaceAsa.GetChainsSurfaceAreaInBu(pdbId, buChainsHash, asaChains, type);
// Hashtable chainSaHash = GetChainsSurfaceAreaInBu (pdbId, buChainsHash, type);
int i = 0;
string chain1 = "";
string chain2 = "";
ProtInterface[] interfaces = new ProtInterface [interfaceInfoList.Length];
foreach (ProtInterfaceInfo interfaceInfo in interfaceInfoList)
{
chain1 = interfaceInfo.Chain1 + "_" + interfaceInfo.SymmetryString1;
chain2 = interfaceInfo.Chain2 + "_" + interfaceInfo.SymmetryString2;
if (!buChainsHash.ContainsKey(chain1) || !buChainsHash.ContainsKey(chain2))
{
continue;
}
if (interfaceInfo.ASA < 0)
{
string interfaceComplexFile = interfaceWriter.WriteTempInterfaceToFile(pdbId, interfaceInfo.InterfaceId,
(AtomInfo[])buChainsHash[chain1], (AtomInfo[])buChainsHash[chain2], type);
double complexAsa = interfaceAsa.ComputeInterfaceSurfaceArea(interfaceComplexFile);
if (chainSaHash.ContainsKey(chain1) && chainSaHash.ContainsKey(chain2))
{
interfaceInfo.ASA = interfaceAsa.CalculateInterfaceBuriedSurfaceArea(
(double)chainSaHash[chain1], (double)chainSaHash[chain2], complexAsa);
}
}
interfaceInfo.Remark += FormatInterfaceAsa(interfaceInfo.ASA);
string interfaceFile = interfaceWriter.WriteInterfaceToFile(pdbId, interfaceInfo.InterfaceId, buChainsHash[chain1], buChainsHash[chain2], interfaceInfo.Remark, type);
ParseHelper.ZipPdbFile(interfaceFile);
interfaces[i] = new ProtInterface(interfaceInfo);
interfaces[i].ResidueAtoms1 = GetSeqAtoms(buChainsHash[chain1]);
interfaces[i].ResidueAtoms2 = GetSeqAtoms(buChainsHash[chain2]);
i++;
}
return(interfaces);
}
