/// <summary>
/// write the interactive chains into a pdb formated text file
/// </summary>
/// <param name="pdbId"></param>
/// <param name="interChains"></param>
public string WriteBiolUnitFile(string pdbId, string buId, Dictionary <string, AtomInfo[]> buChains, string destDir, DataTable asuInfoTable, string type)
{
string fileName = Path.Combine(destDir, pdbId + "_" + buId + "." + type);
FileStream fileStream = new FileStream(Path.Combine(filePath, fileName), FileMode.Create, FileAccess.Write);
StreamWriter fileWriter = new StreamWriter(fileStream);
string header = "HEADER " + pdbId + " " + DateTime.Today;
fileWriter.WriteLine(header);
List <string> chainSymOpList = new List <string> (buChains.Keys);
chainSymOpList.Sort();
string[] chainSymOpStrs = new string[chainSymOpList.Count];
chainSymOpList.CopyTo(chainSymOpStrs);
// string[] chainSymOpStrs = SortChainSymOpList(chainSymOpList);
Dictionary <string, string> asymPolymerTypeHash = GetAsymChainPolymerTypeHash(asuInfoTable);
string chainRemarkString = GetChainComponentRemarkString(chainSymOpStrs, asuInfoTable, type);
fileWriter.WriteLine(chainRemarkString);
bool isChainLigand = false;
int atomId = 0;
int count = 0;
try
{
string preSymOpNum = "0";
foreach (string chain in chainSymOpStrs)
{
string[] fields = chain.Split('_');
string symOpNum = fields[1];
if (preSymOpNum != symOpNum)
{
atomId = 0;
}
isChainLigand = IsChainLigand(fields[0], asymPolymerTypeHash);
ChainAtoms buChain = new ChainAtoms();
buChain.CartnAtoms = (AtomInfo[])buChains[chain];
buChain.SortByAtomId();
string chainId = letters[count % letters.Length].ToString();
WriteOneChain(buChain.CartnAtoms, chainId, ref atomId, isChainLigand, fileWriter);
count++;
preSymOpNum = symOpNum;
}
fileWriter.WriteLine("END");
}
catch (Exception ex)
{
string errorMsg = ex.Message;
throw ex;
}
finally
{
fileWriter.Close();
}
return(fileName);
}
/// <summary>
/// write the interactive chains into a pdb formated text file
/// </summary>
/// <param name="pdbId"></param>
/// <param name="interChains"></param>
public string WriteBiolUnitFile(string pdbId, string buId, Dictionary <string, AtomInfo[]> buChains, string destDir, string remark, string type)
{
string fileName = Path.Combine(destDir, pdbId + "_" + buId + "." + type);
FileStream fileStream = new FileStream(Path.Combine(filePath, fileName), FileMode.Create, FileAccess.Write);
StreamWriter fileWriter = new StreamWriter(fileStream);
string header = "HEADER " + pdbId + " " + DateTime.Today;
fileWriter.WriteLine(header);
fileWriter.WriteLine(remark);
List <string> chainSymOpList = new List <string> (buChains.Keys);
string[] chainSymOpStrs = SortChainSymOpList(chainSymOpList);
int atomId = 0;
int count = 0;
try
{
string preSymOpNum = "0";
foreach (string chain in chainSymOpStrs)
{
string[] fields = chain.Split('_');
string symOpNum = fields[1];
if (preSymOpNum != symOpNum)
{
atomId = 0;
}
ChainAtoms buChain = new ChainAtoms();
buChain.CartnAtoms = (AtomInfo[])buChains[chain];
buChain.SortByAtomId();
string chainId = letters[count % letters.Length].ToString();
WriteOneChain(buChain.CartnAtoms, chainId, ref atomId, fileWriter);
count++;
preSymOpNum = symOpNum;
}
fileWriter.WriteLine("END");
}
catch (Exception ex)
{
string errorMsg = ex.Message;
throw ex;
}
finally
{
fileWriter.Close();
}
return(fileName);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="asuChains"></param>
/// <param name="destDir"></param>
/// <param name="remark"></param>
/// <returns></returns>
public string WriteAsymUnitFile(string pdbId, Dictionary <string, AtomInfo[]> asuChainsHash, string[] asymChainsInOrder,
string[] fileChainsInOrder, string[] nonpolymerAsymChains, string destDir, string remark)
{
string fileName = Path.Combine(destDir, pdbId + ".ent");
FileStream fileStream = new FileStream(Path.Combine(filePath, fileName), FileMode.Create, FileAccess.Write);
StreamWriter fileWriter = new StreamWriter(fileStream);
string header = "HEADER " + pdbId + " " + DateTime.Today;
fileWriter.WriteLine(header);
fileWriter.WriteLine(remark);
int atomId = 0;
int chainCount = 0;
string fileChain = "";
bool nonpolymerChain = false;
try
{
foreach (string asymChain in asymChainsInOrder)
{
nonpolymerChain = false;
ChainAtoms asuChain = new ChainAtoms();
asuChain.CartnAtoms = asuChainsHash[asymChain];
asuChain.SortByAtomId();
fileChain = fileChainsInOrder[chainCount];
if (Array.IndexOf(nonpolymerAsymChains, asymChain) > -1)
{
nonpolymerChain = true;
}
WriteOneChain(asuChain.CartnAtoms, fileChain, ref atomId, nonpolymerChain, fileWriter);
chainCount++;
}
fileWriter.WriteLine("END");
}
catch (Exception ex)
{
string errorMsg = ex.Message;
throw ex;
}
finally
{
fileWriter.Close();
}
return(fileName);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="asuChains"></param>
/// <param name="destDir"></param>
/// <param name="remark"></param>
/// <returns></returns>
public void WriteAsymUnitFile(string coordFileName, Dictionary <string, AtomInfo[]> asuChainsHash, string[] asymChainsInOrder, string[] fileChainsInOrder, string[] hetChains, string remark)
{
FileStream fileStream = new FileStream(coordFileName, FileMode.Create, FileAccess.Write);
StreamWriter fileWriter = new StreamWriter(fileStream);
fileWriter.WriteLine(remark);
int atomId = 0;
int chainCount = 0;
string fileChain = "";
bool isHetatmChain = false;
try
{
foreach (string asymChain in asymChainsInOrder)
{
isHetatmChain = false;
if (asuChainsHash.ContainsKey(asymChain))
{
ChainAtoms asuChain = new ChainAtoms();
asuChain.CartnAtoms = asuChainsHash[asymChain];
asuChain.SortByAtomId();
fileChain = fileChainsInOrder[chainCount];
if (Array.IndexOf(hetChains, asymChain) > -1)
{
isHetatmChain = true;
}
WriteOneChain(asuChain.CartnAtoms, fileChain, ref atomId, isHetatmChain, fileWriter);
chainCount++;
}
}
fileWriter.WriteLine("END");
}
catch (Exception ex)
{
string errorMsg = ex.Message;
throw ex;
}
finally
{
fileWriter.Close();
}
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="asuChains"></param>
/// <param name="destDir"></param>
/// <param name="remark"></param>
/// <returns></returns>
public string WriteAsymUnitFile(string pdbId, Dictionary <string, AtomInfo[]> asuChainsHash, string destDir, string remark)
{
string fileName = Path.Combine(destDir, pdbId + ".ent");
FileStream fileStream = new FileStream(Path.Combine(filePath, fileName), FileMode.Create, FileAccess.Write);
StreamWriter fileWriter = new StreamWriter(fileStream);
string header = "HEADER " + pdbId + " " + DateTime.Today;
fileWriter.WriteLine(header);
fileWriter.WriteLine(remark);
List <string> asymChainList = new List <string>(asuChainsHash.Keys);
asymChainList.Sort();
int atomId = 0;
try
{
foreach (string asymChain in asymChainList)
{
ChainAtoms asuChain = new ChainAtoms();
asuChain.CartnAtoms = asuChainsHash[asymChain];
asuChain.SortByAtomId();
WriteOneChain(asuChain.CartnAtoms, asymChain, ref atomId, fileWriter);
}
fileWriter.WriteLine("END");
}
catch (Exception ex)
{
string errorMsg = ex.Message;
throw ex;
}
finally
{
fileWriter.Close();
}
return(fileName);
}
/// <summary>
///
/// </summary>
/// <param name="fileName"></param>
/// <param name="pdbId"></param>
/// <param name="chainAtomsHash"></param>
/// <param name="remark"></param>
/// <returns></returns>
public string WriteAtoms(string fileName, string pdbId, Dictionary <string, AtomInfo[]> chainAtomsHash, string remark)
{
FileStream fileStream = new FileStream(fileName, FileMode.Create, FileAccess.Write);
StreamWriter fileWriter = new StreamWriter(fileStream);
string header = "Header " + pdbId.ToString() + " " + DateTime.Today.ToShortDateString();
fileWriter.WriteLine(header);
fileWriter.WriteLine(remark);
List <string> asymChainList = new List <string> (chainAtomsHash.Keys);
asymChainList.Sort();
int atomId = 0;
try
{
foreach (string asymChain in asymChainList)
{
ChainAtoms asuChain = new ChainAtoms();
asuChain.CartnAtoms = (AtomInfo[])chainAtomsHash[asymChain];
asuChain.SortByAtomId();
WriteOneChain(asuChain.CartnAtoms, asymChain, ref atomId, fileWriter);
}
fileWriter.WriteLine("END");
}
catch (Exception ex)
{
string errorMsg = ex.Message;
throw ex;
}
finally
{
fileWriter.Close();
}
return(fileName);
}
/// <summary>
/// write the interactive chains into a pdb formated text file
/// </summary>
/// <param name="pdbId"></param>
/// <param name="interChains"></param>
public string WriteBiolUnitFile(string pdbId, string buId, Dictionary <string, AtomInfo[]> buChains, string destDir,
CrystalInfo cryst1, Matrix fractMatrix)
{
string fileName = Path.Combine(destDir, pdbId + "_" + buId.ToString() + ".pdb");
FileStream fileStream = new FileStream(Path.Combine(filePath, fileName), FileMode.Create, FileAccess.Write);
StreamWriter fileWriter = new StreamWriter(fileStream);
string header = "HEADER " + pdbId + " " + DateTime.Today;
fileWriter.WriteLine(header);
string remark = "REMARK 290 ";
int count = 0;
List <string> chainSymOpList = new List <string> (buChains.Keys);
string[] chainSymOpStrs = SortChainSymOpList(chainSymOpList);
foreach (string chainAndSymOpStr in chainSymOpStrs)
{
string thisRemark = remark + letters[count].ToString() + ": ";
// format of chainAndSymOpStr: chain_symOpNum_fullsymString
string[] fields = chainAndSymOpStr.Split('_');
thisRemark += fields[0].PadRight(3, ' ');
thisRemark += fields[1].PadRight(3, ' ');
thisRemark += fields[2].PadRight(30, ' ');
fileWriter.WriteLine(thisRemark);
count++;
}
string crystString = FormatCrystString(cryst1);
string fractString = FormatFractString(fractMatrix);
fileWriter.WriteLine(crystString);
fileWriter.WriteLine(fractString);
int atomId = 0;
count = 0;
try
{
string preSymOpNum = "0";
foreach (string chain in chainSymOpStrs)
{
string[] fields = chain.Split('_');
string symOpNum = fields[1];
if (preSymOpNum != symOpNum)
{
atomId = 0;
}
ChainAtoms buChain = new ChainAtoms();
buChain.CartnAtoms = (AtomInfo[])buChains[chain];
buChain.SortByAtomId();
string chainId = letters[count % letters.Length].ToString();
WriteOneChain(buChain.CartnAtoms, chainId, ref atomId, fileWriter);
count++;
preSymOpNum = symOpNum;
}
fileWriter.WriteLine("END");
}
catch (Exception ex)
{
string errorMsg = ex.Message;
throw ex;
}
finally
{
fileWriter.Close();
}
return(fileName);
}