/// <summary>
///
/// </summary>
/// <param name="domainEntityInfo"></param>
/// <param name="chainInfo"></param>
/// <returns></returns>
private AtomInfo[] GetDomainSegmentAtoms(DomainSegmentInfo domainEntityInfo, ChainAtoms chainInfo)
{
ArrayList domainAtomList = new ArrayList();
int seqId = -1;
foreach (AtomInfo atom in chainInfo.CartnAtoms)
{
seqId = Convert.ToInt16(atom.seqId);
if (seqId >= domainEntityInfo.seqStart && seqId <= domainEntityInfo.seqEnd)
{
// AddAtomToList(atom, domainAtomList);
domainAtomList.Add(atom);
}
}
AtomInfo[] domainAtoms = new AtomInfo[domainAtomList.Count];
domainAtomList.CopyTo(domainAtoms);
return(domainAtoms);
}
/// <summary>
///
/// </summary>
/// <param name="domainSegInfo"></param>
/// <param name="entryEntityInfos"></param>
/// <returns></returns>
private string[] GetDomainSegmentThreeLetterResidues(DomainSegmentInfo domainSegInfo, EntityInfo[] entryEntityInfos)
{
foreach (EntityInfo entityInfo in entryEntityInfos)
{
if (entityInfo.entityId == domainSegInfo.entityId)
{
string[] residues = entityInfo.threeLetterSeq.TrimEnd(' ').Split(' ');
string[] segmentResidues = new string[domainSegInfo.seqEnd - domainSegInfo.seqStart + 1];
try
{
Array.Copy(residues, domainSegInfo.seqStart - 1, segmentResidues, 0,
domainSegInfo.seqEnd - domainSegInfo.seqStart + 1);
return(segmentResidues);
}
catch (Exception ex)
{
throw new Exception("Get Segment three letter sequences error: " + ex.Message);
}
}
}
return(null);
}
/// <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);
}
