/// <summary>
///
/// </summary>
/// <param name="domainInterfaceId"></param>
/// <param name="domainInterfaceTable"></param>
/// <param name="pdbpfamTable"></param>
/// <param name="chainAtomsHash"></param>
/// <returns></returns>
private DomainInterface ReadIntraDomainInterfaceFromChain(int domainInterfaceId, DataTable domainInterfaceTable,
DataTable pdbpfamTable, Dictionary <string, ChainAtoms> chainAtomsHash)
{
DomainInterface domainInterface = new DomainInterface();
DataRow[] domainInterfaceRows = domainInterfaceTable.Select(string.Format("DomainInterfaceID = '{0}'", domainInterfaceId));
if (domainInterfaceRows.Length > 0)
{
long domainId1 = Convert.ToInt64(domainInterfaceRows[0]["DomainID1"].ToString());
long domainId2 = Convert.ToInt64(domainInterfaceRows[0]["DomainID2"].ToString());
string asymChain = domainInterfaceRows[0]["AsymChain1"].ToString().TrimEnd();
if (chainAtomsHash.ContainsKey(asymChain))
{
ChainAtoms chain = chainAtomsHash[asymChain];
Range[] domainRanges1 = GetDomainRange(pdbpfamTable, domainId1);
Range[] domainRanges2 = GetDomainRange(pdbpfamTable, domainId2);
domainInterface.domainInterfaceId = domainInterfaceId;
domainInterface.firstSymOpString = asymChain + "_1_555";
domainInterface.secondSymOpString = asymChain + "_1_555";
domainInterface.domainId1 = domainId1;
domainInterface.domainId2 = domainId2;
domainInterface.chain1 = GetDomainAtoms(chain.CartnAtoms, domainRanges1);
domainInterface.chain2 = GetDomainAtoms(chain.CartnAtoms, domainRanges2);
domainInterface.GetInterfaceResidueDist();
}
}
return(domainInterface);
}
/// <summary>
///
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="asymChain"></param>
/// <param name="threeLetterSeq"></param>
/// <returns></returns>
private AtomInfo[] ReadChainAtoms(EntryCrystal thisEntryCrystal, string asymChain, out string threeLetterSeq)
{
ChainAtoms chain = null;
threeLetterSeq = "";
for (int i = 0; i < thisEntryCrystal.atomCat.ChainAtomList.Length; i++)
{
if (thisEntryCrystal.atomCat.ChainAtomList[i].AsymChain == asymChain)
{
chain = thisEntryCrystal.atomCat.ChainAtomList[i];
break;
}
}
for (int i = 0; i < thisEntryCrystal.entityCat.EntityInfoList.Length; i++)
{
EntityInfo entityInfo = thisEntryCrystal.entityCat.EntityInfoList[i];
string[] asymChains = entityInfo.asymChains.Split(',');
if (asymChains.Contains(asymChain))
{
threeLetterSeq = entityInfo.threeLetterSeq;
}
}
if (chain == null)
{
return(null);
}
AtomInfo[] chainAtoms = chain.CartnAtoms;
return(chainAtoms);
}
/// <summary>
/// atom coordinates for domains
/// A SCOP domain may have multiple segmentations
/// </summary>
/// <param name="chain"></param>
/// <param name="ranges"></param>
/// <returns></returns>
private AtomInfo[] GetDomainAtoms(ChainAtoms chain, string rangeString)
{
AtomInfo[] domainAtoms = null;
List <AtomInfo> domainAtomList = new List <AtomInfo> ();
int startPos = -1;
int endPos = -1;
int seqId = -1;
string[] ranges = rangeString.Split(';');
foreach (string range in ranges)
{
if (range == "-")
{
domainAtoms = chain.CartnAtoms;
}
else
{
string[] posFields = range.Split('-');
startPos = ParseHelper.ConvertSeqToInt(posFields[0]);
endPos = ParseHelper.ConvertSeqToInt(posFields[1]);
foreach (AtomInfo atom in chain.CartnAtoms)
{
seqId = ParseHelper.ConvertSeqToInt(atom.seqId);
if (seqId >= startPos && seqId <= endPos)
{
domainAtomList.Add(atom);
}
}
}
}
return(domainAtomList.ToArray());
}
/// <summary>
/// atoms for each domain
/// </summary>
/// <param name="pdbId"></param>
/// <param name="chainId"></param>
/// <param name="domainRangesHash"></param>
/// <returns></returns>
public Dictionary <string, AtomInfo[]> ReadAtomsOfDomains(string pdbId, string chainId, Dictionary <string, string> domainRangesHash)
{
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string crystalXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(crystalXmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
xmlFileStream.Close();
Dictionary <string, AtomInfo[]> domainAtomsHash = new Dictionary <string, AtomInfo[]>();
ChainAtoms chain = null;
for (int i = 0; i < thisEntryCrystal.atomCat.ChainAtomList.Length; i++)
{
if (thisEntryCrystal.atomCat.ChainAtomList[i].AsymChain == chainId)
{
chain = thisEntryCrystal.atomCat.ChainAtomList[i];
}
}
foreach (string DomainID in domainRangesHash.Keys)
{
string rangeString = (string)domainRangesHash[DomainID];
domainAtomsHash.Add(DomainID, GetDomainAtoms(chain, rangeString));
}
return(domainAtomsHash);
}
// so it doesn't depend on the Appsetting
// added on Sept. 22, 2016
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="asymChain"></param>
/// <returns></returns>
public AtomInfo[] ReadChainAtomsFromFile(string coordXmlFile, string asymChain)
{
if (asymChain == "")
{
return(null);
}
// 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();
ChainAtoms chain = null;
for (int i = 0; i < thisEntryCrystal.atomCat.ChainAtomList.Length; i++)
{
if (thisEntryCrystal.atomCat.ChainAtomList[i].AsymChain == asymChain)
{
chain = thisEntryCrystal.atomCat.ChainAtomList[i];
break;
}
}
if (chain == null)
{
return(null);
}
AtomInfo[] chainAtoms = chain.CartnAtoms;
return(chainAtoms);
}
/// <summary>
///
/// </summary>
/// <param name="pdbId"></param>
/// <param name="asymChain"></param>
/// <returns></returns>
public AtomInfo[] ReadChainAtoms(string pdbId, string asymChain)
{
if (asymChain == "")
{
return(null);
}
string xmlFile = Path.Combine(ProtCidSettings.dirSettings.coordXmlPath, pdbId + ".xml.gz");
string crystalXmlFile = ParseHelper.UnZipFile(xmlFile, ProtCidSettings.tempDir);
// read data from crystal xml file
EntryCrystal thisEntryCrystal;
XmlSerializer xmlSerializer = new XmlSerializer(typeof(EntryCrystal));
FileStream xmlFileStream = new FileStream(crystalXmlFile, FileMode.Open);
thisEntryCrystal = (EntryCrystal)xmlSerializer.Deserialize(xmlFileStream);
xmlFileStream.Close();
ChainAtoms chain = null;
for (int i = 0; i < thisEntryCrystal.atomCat.ChainAtomList.Length; i++)
{
if (thisEntryCrystal.atomCat.ChainAtomList[i].AsymChain == asymChain)
{
chain = thisEntryCrystal.atomCat.ChainAtomList[i];
break;
}
}
File.Delete(crystalXmlFile);
if (chain == null)
{
return(null);
}
AtomInfo[] chainAtoms = chain.CartnAtoms;
return(chainAtoms);
}
/// <summary>
///
/// </summary>
/// <param name="chain1"></param>
/// <param name="chain2"></param>
/// <param name="modelType">local, or global</param>
/// <returns></returns>
public StructAlignOutput AlignTwoChains(ChainAtoms chain1, ChainAtoms chain2, string modelType)
{
AtomInfo[] calphaAtoms1 = chain1.CalphaAtoms();
AtomInfo[] calphaAtoms2 = chain2.CalphaAtoms();
StructAlignOutput alignOutput = AlignTwoSetsAtoms(calphaAtoms1, calphaAtoms2, modelType);
return(alignOutput);
}
/// <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="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="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="asymChain"></param>
/// <returns></returns>
public AtomInfo[] ReadChainAtomsFromFile(string coordXmlFile, string asymChain, out string threeLetterSeq)
{
threeLetterSeq = "";
if (asymChain == "")
{
return(null);
}
// 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();
ChainAtoms chain = null;
for (int i = 0; i < thisEntryCrystal.atomCat.ChainAtomList.Length; i++)
{
if (thisEntryCrystal.atomCat.ChainAtomList[i].AsymChain == asymChain)
{
chain = thisEntryCrystal.atomCat.ChainAtomList[i];
break;
}
}
for (int i = 0; i < thisEntryCrystal.entityCat.EntityInfoList.Length; i++)
{
EntityInfo entityInfo = thisEntryCrystal.entityCat.EntityInfoList[i];
string[] asymChains = entityInfo.asymChains.Split(',');
if (asymChains.Contains(asymChain))
{
threeLetterSeq = entityInfo.threeLetterSeq;
}
}
if (chain == null)
{
return(null);
}
AtomInfo[] chainAtoms = chain.CartnAtoms;
return(chainAtoms);
}
/// <summary>
///
/// </summary>
/// <param name="thisEntryCrystal"></param>
/// <param name="asymChain"></param>
/// <returns></returns>
private AtomInfo[] ReadChainAtoms(EntryCrystal thisEntryCrystal, string asymChain)
{
ChainAtoms chain = null;
for (int i = 0; i < thisEntryCrystal.atomCat.ChainAtomList.Length; i++)
{
if (thisEntryCrystal.atomCat.ChainAtomList[i].AsymChain == asymChain)
{
chain = thisEntryCrystal.atomCat.ChainAtomList[i];
break;
}
}
if (chain == null)
{
return(null);
}
AtomInfo[] chainAtoms = chain.CartnAtoms;
return(chainAtoms);
}
/// <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>
/// atoms for each domain
/// </summary>
/// <param name="pdbId"></param>
/// <param name="chainId"></param>
/// <param name="domainRangesHash"></param>
/// <returns></returns>
public Dictionary <long, AtomInfo[]> ReadAtomsOfDomains(string pdbId, string chainId, Dictionary <long, string> domainRangesHash, Dictionary <string, ChainAtoms> chainAtomsHash)
{
Dictionary <long, AtomInfo[]> domainAtomsHash = new Dictionary <long, AtomInfo[]>();
ChainAtoms chain = null;
foreach (string asymChain in chainAtomsHash.Keys)
{
if (asymChain == chainId)
{
chain = chainAtomsHash[asymChain];
}
}
foreach (long DomainID in domainRangesHash.Keys)
{
string rangeString = (string)domainRangesHash[DomainID];
AtomInfo[] domainAtoms = GetDomainAtoms(chain, rangeString);
if (domainAtoms != null && domainAtoms.Length > 0)
{
domainAtomsHash.Add(DomainID, domainAtoms);
}
}
return(domainAtomsHash);
}
/// <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);
}
//extracts atoms from pdb file
public static AtomCategory readPdbFile(string pdbfilename, ref Dictionary <Tuple <string, string>, double> partialCharges)
{
AtomCategory myAtomCategory = new AtomCategory();
ChainAtoms chainAtoms = new ChainAtoms();
ArrayList atomList = new ArrayList();
string preAsymId = "";
string asymID = "";
if (File.Exists(pdbfilename))
{
using (StreamReader sr = new StreamReader(pdbfilename))
{
String line;
// Read and display lines from the file until the end of
// the file is reached.
Int32 seqID = -1;
Int32 previousSeqID = -1;
while ((line = sr.ReadLine()) != null)
{
string[] spLine = Array.FindAll <string>(((string)line).Split(
new char[] { ' ', '\t', ',', ';' }), delegate(string s) { return(!String.IsNullOrEmpty(s)); });
List <string> splitLine = new List <string>(spLine);
if (splitLine[0] == "HETATM" && splitLine[3] == "MSE")
{
splitLine[0] = "ATOM";
splitLine[3] = "MET";
}
if (splitLine[0] == "ENDMDL")
{
break;
}
if (splitLine[0] == "ATOM")
{
AtomInfo myAtom = new AtomInfo();
asymID = line.Substring(21, 1);
myAtom.altConfID = "";
myAtom.atomId = Convert.ToInt32(line.Substring(6, 5).Trim());
myAtom.atomName = line.Substring(12, 4).Trim();
myAtom.residue = line.Substring(17, 3);
myAtom.authResidue = myAtom.residue;
myAtom.authSeqId = line.Substring(22, 4).Trim();
if (Convert.ToInt32(myAtom.authSeqId) != previousSeqID)
{
seqID = seqID + 1;
}
myAtom.seqId = seqID.ToString();
previousSeqID = Convert.ToInt32(myAtom.authSeqId);
AtomParser.Coordinate coord = new Coordinate();
coord = new Coordinate(Convert.ToDouble(line.Substring(30, 8).Trim()), Convert.ToDouble(line.Substring(38, 8).Trim()), Convert.ToDouble(line.Substring(46, 8).Trim()));
myAtom.xyz = coord;
myAtom.atomType = line.Substring(76, 2).Trim();
//This handful of conditions are occasionally different and throw off the check for hydrogen bonding, etc
if (myAtom.atomName == "HG")
{
myAtom.atomName = "HG1";
}
if (myAtom.atomName == "OG")
{
myAtom.atomName = "OG1";
}
if ((myAtom.atomName == "NH1" && myAtom.residue == "ARG") || (myAtom.atomName == "NZ" && myAtom.residue == "LYS"))
{
myAtom.atomType = "N1+";
}
if ((myAtom.atomName == "OD2" && myAtom.residue == "ASP") || (myAtom.atomName == "OE2" && myAtom.residue == "GLU"))
{
myAtom.atomType = "O1-";
}
myAtom.bFac = Convert.ToDouble(line.Substring(60, 6).Trim());
myAtom.occupancy = 1.00;
//Compare chain ID. If this is now a new chain, write existing list, and create empty new ones.
if (preAsymId != asymID && preAsymId != "" && atomList.Count > 0)
{
chainAtoms.AsymChain = preAsymId;
chainAtoms.AuthAsymChain = preAsymId;
chainAtoms.EntityID = "1"; // problem with int to string in new version
chainAtoms.PolymerType = "-";
AtomInfo[] atomArray = new AtomInfo[atomList.Count];
atomList.CopyTo(atomArray);
chainAtoms.CartnAtoms = atomArray;
myAtomCategory.AddChainAtoms(chainAtoms);
atomList = new ArrayList();
chainAtoms = new ChainAtoms();
}
//Add atom to current list of atoms if it is not a water molecule
if (myAtom.residue.ToUpper() != "HOH")
{
if (myAtom.atomType == "H")
{
Tuple <string, string> key = new Tuple <string, string> (myAtom.residue, myAtom.atomName);
if (partialCharges.ContainsKey(key) == true)
{
atomList.Add(myAtom);
}
}
else
{
atomList.Add(myAtom);
}
}
preAsymId = asymID;
}
}
//Capture final chain
if (atomList.Count > 0)
{
chainAtoms.AsymChain = preAsymId;
chainAtoms.AuthAsymChain = preAsymId;
chainAtoms.EntityID = "1";
chainAtoms.PolymerType = "-";
AtomInfo[] atomArray = new AtomInfo[atomList.Count];
atomList.CopyTo(atomArray);
chainAtoms.CartnAtoms = atomArray;
myAtomCategory.AddChainAtoms(chainAtoms);
atomList = new ArrayList();
chainAtoms = new ChainAtoms();
}
}
}
myAtomCategory.Resolution = 2.5;
return(myAtomCategory);
}
/// <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);
}
