/// <summary>
///
/// </summary>
/// <param name="domainInfo"></param>
private AtomInfo[] ChangeDomainAtomsSeqAtomIds(PfamDomainInfo domainInfo)
{
int atomSeqNo = 1;
int residueSeqNo = 1;
int atomSeqId = 0;
int preAtomSeqId = 0;
ArrayList domainAtomList = new ArrayList();
foreach (DomainSegmentInfo segInfo in domainInfo.segmentInfos)
{
atomSeqId = 0;
preAtomSeqId = 0;
segInfo.fileStart = residueSeqNo;
segInfo.fileEnd = residueSeqNo + segInfo.seqEnd - segInfo.seqStart;
for (int i = 0; i < segInfo.atoms.Length; i++)
{
segInfo.atoms[i].atomId = atomSeqNo;
atomSeqNo++;
if (atomSeqNo > 99999) // the maximum atom seq id is 5-digit
{
atomSeqNo = 1;
}
atomSeqId = Convert.ToInt32(segInfo.atoms[i].seqId);
if (preAtomSeqId == 0)
{
preAtomSeqId = atomSeqId;
}
if (preAtomSeqId == atomSeqId)
{
segInfo.atoms[i].seqId = residueSeqNo.ToString();
}
else
{
residueSeqNo = residueSeqNo + atomSeqId - preAtomSeqId;
segInfo.atoms[i].seqId = residueSeqNo.ToString();
preAtomSeqId = atomSeqId;
}
}
domainAtomList.AddRange(segInfo.atoms);
residueSeqNo = segInfo.fileEnd + 1;
}
AtomInfo[] domainAtoms = new AtomInfo[domainAtomList.Count];
domainAtomList.CopyTo(domainAtoms);
return(domainAtoms);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="domainInfo"></param>
/// <param name="chainInfo"></param>
/// <returns></returns>
private string WritePfamDomainToFile(string pdbId, PfamDomainInfo domainInfo)
{
string remarkString = "HEADER " + pdbId + "\r\n";
remarkString += "REMARK 1 PFAM " + domainInfo.domainId + "\r\n";
remarkString += ("REMARK 2 PFAM ACC: " + domainInfo.pfamAcc + ", " +
" PFAM ID: " + domainInfo.pfamId + "\r\n");
AtomInfo[] domainAtoms = ChangeDomainAtomsSeqAtomIds(domainInfo);
if (domainAtoms.Length == 0)
{
logWriter.WriteLine(pdbId + domainInfo.domainId + " no coordinates.");
logWriter.Flush();
return("");
}
string domainInfoRemark = FormatDomainSegmentInfoRemark(domainInfo.segmentInfos);
remarkString += domainInfoRemark;
string seqResRecord = FormatDomainSeqResRecord(domainInfo.segmentInfos);
remarkString += (seqResRecord + "\r\n");
string hashDir = pdbId.Substring(1, 2);
if (!Directory.Exists(Path.Combine(pfamDomainFileDir, hashDir)))
{
Directory.CreateDirectory(Path.Combine(pfamDomainFileDir, hashDir));
}
InsertDataIntoDbTable(domainInfo);
string fileName = Path.Combine(pfamDomainFileDir, hashDir + "\\" + pdbId + domainInfo.domainId + ".pfam");
WriteAtomsToFile(fileName, fileChain, remarkString, domainAtoms);
ParseHelper.ZipPdbFile(fileName);
return(fileName + ".gz");
}
/// <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>
public string[] GenerateEntryPfamDomainFiles(string pdbId)
{
DataTable entryPfamTable = GetEntryPfamDomainTable(pdbId);
if (entryPfamTable.Rows.Count == 0) // no pfam domain definition for the entry
{
return(null);
}
ArrayList entryDomainInfoList = new ArrayList();
ArrayList domainList = new ArrayList();
foreach (DataRow domainRow in entryPfamTable.Rows)
{
string domainId = domainRow["DomainID"].ToString();
if (!domainList.Contains(domainId))
{
domainList.Add(domainId);
}
}
string domainFile = "";
Hashtable entityChainInfoHash = new Hashtable();
foreach (string domainId in domainList)
{
domainFile = Path.Combine(pfamDomainFileDir, pdbId.Substring(1, 2) + "\\" +
pdbId + domainId + ".pfam.gz");
if (File.Exists(domainFile))
{
continue;
}
DataRow[] domainRows = entryPfamTable.Select(string.Format("DomainID = '{0}'", domainId), "HmmStart ASC");
PfamDomainInfo domainInfo = new PfamDomainInfo();
domainInfo.pdbId = pdbId;
domainInfo.domainId = domainId;
domainInfo.pfamAcc = domainRows[0]["Pfam_ACC"].ToString().TrimEnd();
domainInfo.pfamId = domainRows[0]["Pfam_ID"].ToString().TrimEnd();
DomainSegmentInfo[] segmentInfos = new DomainSegmentInfo[domainRows.Length];
int count = 0;
foreach (DataRow domainRow in domainRows)
{
DomainSegmentInfo segmentInfo = new DomainSegmentInfo();
segmentInfo.entityId = Convert.ToInt32(domainRow["EntityId"].ToString());
string[] chainInfos = GetAsymAuthorChainWithMaxCoord(pdbId, segmentInfo.entityId, ref entityChainInfoHash);
segmentInfo.asymChain = chainInfos[0];
segmentInfo.authChain = chainInfos[1];
segmentInfo.seqStart = Convert.ToInt32(domainRow["SeqStart"].ToString());
segmentInfo.seqEnd = Convert.ToInt32(domainRow["SeqEnd"].ToString());
segmentInfo.hmmStart = Convert.ToInt32(domainRow["HmmStart"].ToString());
segmentInfo.hmmEnd = Convert.ToInt32(domainRow["HmmEnd"].ToString());
segmentInfo.alignStart = Convert.ToInt32(domainRow["AlignStart"].ToString());
segmentInfo.alignEnd = Convert.ToInt32(domainRow["AlignEnd"].ToString());
segmentInfos[count] = segmentInfo;
count++;
}
domainInfo.segmentInfos = segmentInfos;
entryDomainInfoList.Add(domainInfo);
}
PfamDomainInfo[] entryDomainInfos = new PfamDomainInfo[entryDomainInfoList.Count];
entryDomainInfoList.CopyTo(entryDomainInfos);
string[] domainFiles = GenerateEntryPfamDomainFiles(pdbId, entryDomainInfos);
return(domainFiles);
}
