public ChainAtoms(ChainAtoms extChain)
{
this.authAsymChain = extChain.AuthAsymChain;
this.asymChain = extChain.AsymChain;
this.entityId = extChain.entityId;
this.polymerType = extChain.PolymerType;
foreach (AtomInfo atom in extChain.CartnAtoms)
{
this.cartnAtoms.Add(atom.Clone());
}
}
public void WriteProteinFragment(ref AtomParser.AtomCategory _atomCat, int _fragStart,
int _fragEnd, int _chainIndex, string _chainID, string _fileWithPath)
{
// this is complicated because the indices refer to alpha-carbon-only, while this function writes
// whole thing
AtomParser.ChainAtoms theChainAtoms = new ChainAtoms();
AtomParser.ChainAtoms onlyCAChainAtoms = new ChainAtoms();
theChainAtoms = _atomCat.ChainAtomList[_chainIndex];
onlyCAChainAtoms = _atomCat.CalphaAtomList()[_chainIndex];
string firstCAauthSeqID = onlyCAChainAtoms.CartnAtoms[_fragStart].authSeqId;
string lastCAauthSeqID = onlyCAChainAtoms.CartnAtoms[_fragEnd].authSeqId;
StreamWriter protWriter = new StreamWriter(_fileWithPath, false);
int atomCounter = new int();
atomCounter = 1;
bool writingInFragment = new bool();
bool hitLastCA = new bool();
writingInFragment = false;
hitLastCA = false;
for (int atomIndex = 0; atomIndex < theChainAtoms.CartnAtoms.Length; atomIndex++)
{
if (theChainAtoms.CartnAtoms[atomIndex].authSeqId == firstCAauthSeqID)
{
writingInFragment = true;
}
if (writingInFragment)
{
if (!hitLastCA)
{
if (theChainAtoms.CartnAtoms[atomIndex].authSeqId == lastCAauthSeqID)
{
hitLastCA = true;
}
}
else
{
if (theChainAtoms.CartnAtoms[atomIndex].authSeqId != lastCAauthSeqID) // hit the residue after the last residue in fragment
{
break;
}
}
protWriter.WriteLine(WriteSingleLine(theChainAtoms.CartnAtoms[atomIndex],
atomCounter, _chainID));
}
}
protWriter.Close();
return;
}
/// <summary>
/// chains and their Calpha and Cbeta atoms
/// </summary>
/// <returns></returns>
public ChainAtoms[] CalphaCbetaAtomList()
{
ChainAtoms[] calphaCbetaChainList = new ChainAtoms [chainAtomsList.Count];
for (int i = 0; i < chainAtomsList.Count; i++)
{
ChainAtoms chainCalphaCbetaAtoms = new ChainAtoms();
chainCalphaCbetaAtoms.CartnAtoms = ((ChainAtoms)chainAtomsList[i]).CalphaCbetaAtoms();
chainCalphaCbetaAtoms.AsymChain = ((ChainAtoms)chainAtomsList[i]).AsymChain;
chainCalphaCbetaAtoms.AuthAsymChain = ((ChainAtoms)chainAtomsList[i]).AuthAsymChain;
chainCalphaCbetaAtoms.EntityID = ((ChainAtoms)chainAtomsList[i]).EntityID;
chainCalphaCbetaAtoms.PolymerType = ((ChainAtoms)chainAtomsList[i]).PolymerType;
calphaCbetaChainList[i] = chainCalphaCbetaAtoms;
}
return(calphaCbetaChainList);
}
/// <summary>
/// chains and their backbone atoms
/// </summary>
public ChainAtoms[] BackboneAtomList()
{
ChainAtoms[] backboneChainList = new ChainAtoms [chainAtomsList.Count];
for (int i = 0; i < chainAtomsList.Count; i++)
{
ChainAtoms backboneChainAtoms = new ChainAtoms();
backboneChainAtoms.CartnAtoms = ((ChainAtoms)chainAtomsList[i]).BackboneAtoms();
backboneChainAtoms.AsymChain = ((ChainAtoms)chainAtomsList[i]).AsymChain;
backboneChainAtoms.AuthAsymChain = ((ChainAtoms)chainAtomsList[i]).AuthAsymChain;
backboneChainAtoms.EntityID = ((ChainAtoms)chainAtomsList[i]).EntityID;
backboneChainAtoms.PolymerType = ((ChainAtoms)chainAtomsList[i]).PolymerType;
backboneChainList[i] = backboneChainAtoms;
}
return(backboneChainList);
}
public void WriteCAOnlyFragment(ref AtomParser.AtomCategory _atomCat, int _fragStart,
int _fragEnd, int _chainIndex, string _chainID, string _fileWithPath)
{
AtomParser.ChainAtoms theChainAtoms = new ChainAtoms();
theChainAtoms = (_atomCat.CalphaAtomList())[_chainIndex];
StreamWriter protWriter = new StreamWriter(_fileWithPath, false);
int atomCounter = new int();
atomCounter = 1;
for (int atomIndex = _fragStart; atomIndex < _fragEnd; atomIndex++)
{
protWriter.WriteLine(WriteSingleLine(theChainAtoms.CartnAtoms[atomIndex],
atomCounter, _chainID));
}
protWriter.Close();
return;
}
/// <summary>
/// add asymmetry chain
/// </summary>
/// <param name="chainAtoms"></param>
public void AddChainAtoms(ChainAtoms chainAtoms)
{
chainAtomsList.Add(chainAtoms);
}
/// <summary>
/// parse the coordinate of C alphas
/// </summary>
/// <param name="xmlDoc"></param>
/// <param name="calphaInfoHash"></param>
/// <param name="nsManager"></param>
//private void ParseAtomsOld(ref XmlDocument xmlDoc, ref AtomCategory atomCat, ref XmlNamespaceManager nsManager,
// string retrievingAtomType)
private void ParseAtoms(ref XmlDocument xmlDoc, ref AtomCategory atomCat, ref XmlNamespaceManager nsManager,
Hashtable entityPolyTypeHash, string retrievingAtomType)
{
XmlNodeList atomNodeList = xmlDoc.DocumentElement.SelectNodes("descendant::PDBx:atom_siteCategory/PDBx:atom_site", nsManager);
int atomId = 0;
string asymId = "";
string preAsymId = "";
string preAuthAsymId = "";
string authAsymId = "";
string preEntityId = "";
string preResidue = "";
string entityId = "";
string residue = "";
string authResidue = "";
string seqId = "";
string authSeqId = "";
double cartnX = 0.0;
double cartnY = 0.0;
double cartnZ = 0.0;
string atomType = "-";
string atomName = "-";
int modelNum = 1;
int heterResidueNum = 0;
double Bfac = 0.0; // added this value here (BN)
double res = -1; // added this value here (BN)
double occ = 0.0; // added this value here (BN) for occupancy
// string polymerType = "";
// find the resolution here-- added (BN)
XmlNodeList resolutionNodes = xmlDoc.DocumentElement.SelectNodes("descendant::PDBx:refineCategory/PDBx:refine", nsManager);
foreach (XmlNode resNode in resolutionNodes) // this should only run once
{
XmlNodeList childNodes = resNode.ChildNodes;
foreach (XmlNode refineNode in childNodes)
{
if (refineNode.Name.ToLower().IndexOf("pdbx:ls_d_res_high") > -1)
{
if (refineNode.InnerText.ToString() != "")
{
string resString = refineNode.InnerText.ToString();
res = Convert.ToDouble(resString);
atomCat.Resolution = res;
}
break;
}
}
}
string altConfID = ""; // added this value
// xml tag called "B_iso_or_equiv"
ChainAtoms chainAtoms = new ChainAtoms();
ArrayList atomList = new ArrayList();
bool isAtomNeeded = false;
//Run through each atom
foreach (XmlNode atomNode in atomNodeList)
{
isAtomNeeded = false;
atomId = System.Convert.ToInt32(atomNode.Attributes[0].InnerText.ToString());
XmlNodeList atomInfoNodeList = atomNode.ChildNodes;
//Go through each "child node" and define all properties for a single atom
foreach (XmlNode atomInfoNode in atomInfoNodeList)
{
if (atomInfoNode.Name.ToLower() == "pdbx:type_symbol")
{
atomType = atomInfoNode.InnerText;
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:label_atom_id")
{
atomName = atomInfoNode.InnerText;
//I think the if/elif sections will just pull out residues depending on the input of retrieving atom type, which is currently set to null
//This means that it always returns true
if (retrievingAtomType == "CA" || retrievingAtomType == "CB")
{
if (atomInfoNode.InnerText.ToUpper() != retrievingAtomType)
{
isAtomNeeded = false;
break;
}
else
{
isAtomNeeded = true;
continue;
}
}
else if (retrievingAtomType == "CA_CB")
{
if (atomInfoNode.InnerText.ToUpper() != "CA" &&
atomInfoNode.InnerText.ToUpper() != "CB")
{
isAtomNeeded = false;
break;
}
else
{
isAtomNeeded = true;
continue;
}
}
else
{
isAtomNeeded = true;
}
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:pdbx_pdb_model_num")
{
modelNum = Convert.ToInt16(atomInfoNode.InnerText);
}
if (atomInfoNode.Name.ToLower() == "pdbx:label_comp_id")
{
residue = atomInfoNode.InnerText;
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:auth_comp_id")
{
authResidue = atomInfoNode.InnerText;
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:label_asym_id")
{
asymId = atomInfoNode.InnerText;
continue;
}
if (atomInfoNode.Name.ToLower().IndexOf("pdbx:auth_asym_id") > -1)
{
authAsymId = atomInfoNode.InnerText.ToString();
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:label_entity_id")
{
entityId = atomInfoNode.InnerText;
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:label_seq_id")
{
seqId = atomInfoNode.InnerText;
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:auth_seq_id")
{
authSeqId = atomInfoNode.InnerText;
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:cartn_x")
{
cartnX = System.Convert.ToDouble(atomInfoNode.InnerText);
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:cartn_y")
{
cartnY = System.Convert.ToDouble(atomInfoNode.InnerText);
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:cartn_z")
{
cartnZ = System.Convert.ToDouble(atomInfoNode.InnerText);
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:b_iso_or_equiv")
{
Bfac = System.Convert.ToDouble(atomInfoNode.InnerText.ToString());
continue; //added: check
}
if (atomInfoNode.Name.ToLower() == "pdbx:label_alt_id")
{
altConfID = atomInfoNode.InnerText.ToString();
continue;
}
if (atomInfoNode.Name.ToLower() == "pdbx:occupancy")
{
occ = System.Convert.ToDouble(atomInfoNode.InnerText.ToString());
continue;
}
}
//If this has crossed into the next chain, write previous residues to chain and start chain list over
if (preAsymId != asymId && preAsymId != "" && atomList.Count > 0)
{
chainAtoms.AsymChain = preAsymId;
chainAtoms.AuthAsymChain = preAuthAsymId;
chainAtoms.EntityID = preEntityId; // problem with int to string in new version
if (entityPolyTypeHash.ContainsKey(preEntityId))
{
chainAtoms.PolymerType = entityPolyTypeHash[preEntityId].ToString();
}
else
{
chainAtoms.PolymerType = "-";
}
AtomInfo[] atomArray = new AtomInfo[atomList.Count];
atomList.CopyTo(atomArray);
chainAtoms.CartnAtoms = atomArray;
atomCat.AddChainAtoms(chainAtoms);
atomList = new ArrayList();
chainAtoms = new ChainAtoms();
heterResidueNum = 0;
preResidue = "";
}
if (modelNum > 1) // only pick up the model with model number 1
{
break;
}
if (isAtomNeeded && residue.ToUpper() != "HOH")
{
if (seqId == "")
{
if (preResidue != residue)
{
heterResidueNum++;
}
seqId = heterResidueNum.ToString();
}
AtomInfo atomInfo = new AtomInfo();
atomInfo.atomId = atomId;
atomInfo.atomType = atomType;
atomInfo.atomName = atomName;
atomInfo.seqId = seqId;
atomInfo.authSeqId = authSeqId;
atomInfo.residue = residue;
atomInfo.authResidue = authResidue;
atomInfo.xyz.X = cartnX;
atomInfo.xyz.Y = cartnY;
atomInfo.xyz.Z = cartnZ;
atomInfo.bFac = Bfac;
atomInfo.altConfID = altConfID;
atomInfo.occupancy = occ;
/* if (entityPolyTypeHash.ContainsKey(entityId))
* {
* polymerType = entityPolyTypeHash[entityId].ToString();
* }
* else
* {
* polymerType = "-";
* }
* atomCat.AddAtom(entityId, asymId, polymerType, atomInfo);*/
atomList.Add(atomInfo);
}
preAsymId = asymId;
preAuthAsymId = authAsymId;
preEntityId = entityId;
preResidue = residue;
}
// add the last one
if (atomList.Count > 0)
{
chainAtoms.AsymChain = asymId;
chainAtoms.AuthAsymChain = authAsymId;
chainAtoms.EntityID = entityId;
if (entityPolyTypeHash.ContainsKey(entityId))
{
chainAtoms.PolymerType = entityPolyTypeHash[entityId].ToString();
}
else
{
chainAtoms.PolymerType = "-";
}
AtomInfo[] atomArray = new AtomInfo[atomList.Count];
atomList.CopyTo(atomArray);
chainAtoms.CartnAtoms = atomArray;
atomCat.AddChainAtoms(chainAtoms);
}
}
