/// <summary>
/// sort chains by atom ID
/// </summary>
public void SortByAtomId()
{
if (cartnAtoms == null)
{
return;
}
AtomInfo[] chain = this.CartnAtoms;
Hashtable seqHash = new Hashtable();
foreach (AtomInfo atom in chain)
{
// sould have unique atom id
seqHash.Add(atom.atomId, atom);
}
ArrayList atomIdList = new ArrayList(seqHash.Keys);
atomIdList.Sort();
AtomInfo[] sortedChain = new AtomInfo [chain.Length];
int count = 0;
foreach (object atomId in atomIdList)
{
sortedChain[count] = (AtomInfo)seqHash[atomId];
count++;
}
this.CartnAtoms = sortedChain;
}
/// <summary>
/// c-beta and C-alpha atoms
/// </summary>
public AtomInfo[] CalphaCbetaAtoms()
{
ArrayList calphaCbetaList = new ArrayList();
foreach (AtomInfo atom in cartnAtoms)
{
if (atom.atomName.ToUpper() == "CB" || atom.atomName.ToUpper() == "CA")
{
calphaCbetaList.Add(new AtomInfo(atom));
}
}
// for some PDB entries, there is only Calpha
/* if (calphaCbetaList.Count == 0)
* {
* foreach (AtomInfo atom in cartnAtoms)
* {
* if (atom.atomName.ToUpper () == "CA")
* {
* calphaCbetaList.Add (new AtomInfo(atom));
* }
* }
* }*/
AtomInfo[] calphaCbetaArray = new AtomInfo [calphaCbetaList.Count];
calphaCbetaList.CopyTo(calphaCbetaArray);
return(calphaCbetaArray);
}
/// <summary>
/// deep copy every fields
/// </summary>
/// <returns></returns>
public object Clone()
{
// showdow copy
AtomInfo clonedAtomInfo = (AtomInfo)this.MemberwiseClone();
// deep copy fields with reference type
clonedAtomInfo.xyz = new Coordinate(xyz.X, xyz.Y, xyz.Z);
return(clonedAtomInfo);
}
/// <summary>
/// Writes a pdbline given an atom as input (for use for those residues with insertion codes)
/// </summary>
/// <param name="_inputAtom"></param>
/// <param name="_atomCounter"></param>
/// <param name="_newResi"></param>
/// <param name="_newChain"></param>
/// <param name="_insertionCode"></param>
/// <returns></returns>
public string WriteSingleLine(AtomInfo _inputAtom, int _atomCounter, string _newResi, string _newChain, string _insertionCode)
{
string line = "";
line = "ATOM ";
string atomIdStr = _atomCounter.ToString();
line += atomIdStr.PadLeft(5, ' ');
line += " ";
string atomName = _inputAtom.atomName;
if (atomName != "" && _inputAtom.atomType != "H" && atomName.Length < 4)
{
atomName = " " + atomName;
}
line += atomName.PadRight(4, ' ');
// next line was: line += " ";
// replace by:
if (_inputAtom.altConfID == "")
{
line += " ";
}
else
{
line += _inputAtom.altConfID;
}
// end of replace block
line += _inputAtom.residue;
line += " ";
line += _newChain;
//line += _inputAtom.seqId.PadLeft(4, ' ');
line += _newResi.PadLeft(4, ' '); // replaces this line: line += _inputAtom.seqId.PadLeft(4, ' ');
line += _insertionCode;
line += " ";
line += FormatDoubleString(_inputAtom.xyz.X, 4, 3);
line += FormatDoubleString(_inputAtom.xyz.Y, 4, 3);
line += FormatDoubleString(_inputAtom.xyz.Z, 4, 3);
// next line was: line += " 1.00"; (for dummy occupancy)
// replace with:
line += _inputAtom.occupancy.ToString("##0.00").PadLeft(6);
// end of occupancy replace block
// next line was: line += " 0.00"; (for dummy bfactor)
// replace with:
//string bFacString = _inputAtom.bFac.ToString("##0.00");
line += _inputAtom.bFac.ToString("##0.00").PadLeft(6);
// end of bfactor replace block
line += " "; // old version from QiFang
//line += " "; // version consistent with pdb
line += _inputAtom.atomType;
return(line);
}
/// <summary>
/// c-beta atoms
/// </summary>
public AtomInfo[] CbetaAtoms()
{
ArrayList cbetaList = new ArrayList();
foreach (AtomInfo atom in cartnAtoms)
{
if (atom.atomName.ToUpper() == "CB")
{
cbetaList.Add(new AtomInfo(atom));
}
}
AtomInfo[] cbetaArray = new AtomInfo [cbetaList.Count];
cbetaList.CopyTo(cbetaArray);
return(cbetaArray);
}
/// <summary>
/// deep copy of external atom information
/// </summary>
/// <param name="extAtomInfo"></param>
public AtomInfo(AtomInfo extAtomInfo)
{
this.residue = extAtomInfo.residue;
this.seqId = extAtomInfo.seqId; // FASTA id
this.authSeqId = extAtomInfo.authSeqId; // residue number by author
this.atomId = extAtomInfo.atomId;
this.authResidue = extAtomInfo.authResidue;
this.xyz = new Coordinate(extAtomInfo.xyz.X, extAtomInfo.xyz.Y, extAtomInfo.xyz.Z);
this.atomName = extAtomInfo.atomName;
this.atomType = extAtomInfo.atomType;
this.bFac = extAtomInfo.bFac;
this.altConfID = extAtomInfo.altConfID;
this.occupancy = extAtomInfo.occupancy;
this.AuthAsymChain = extAtomInfo.AuthAsymChain;
this.asymChain = extAtomInfo.asymChain;
}
public string WriteSingleLine(AtomInfo _inputAtom, int _atomCounter, string _chainId)
{
string line = "";
line = "ATOM ";
string atomIdStr = _atomCounter.ToString();
line += atomIdStr.PadLeft(5, ' ');
line += " ";
string atomName = _inputAtom.atomName;
if (atomName != "" && _inputAtom.atomType != "H" && atomName.Length < 4)
{
atomName = " " + atomName;
}
line += atomName.PadRight(4, ' ');
if (_inputAtom.altConfID == "")
{
line += " ";
}
else
{
line += _inputAtom.altConfID;
}
line += _inputAtom.residue;
line += " ";
line += _chainId;
line += _inputAtom.seqId.PadLeft(4, ' ');
line += " ";
line += FormatDoubleString(_inputAtom.xyz.X, 4, 3);
line += FormatDoubleString(_inputAtom.xyz.Y, 4, 3);
line += FormatDoubleString(_inputAtom.xyz.Z, 4, 3);
// next line was: line += " 1.00"; (for dummy occupancy)
// replace with:
line += _inputAtom.occupancy.ToString("##0.00").PadLeft(6);
// end of occupancy replace block
// next line was: line += " 0.00"; (for dummy bfactor)
// replace with:
//string bFacString = _inputAtom.bFac.ToString("##0.00");
line += _inputAtom.bFac.ToString("##0.00").PadLeft(6);
// end of bfactor replace block
line += " ";
line += _inputAtom.atomType;
return(line);
}
/// <summary>
/// get backbone atoms
/// </summary>
public AtomInfo[] BackboneAtoms()
{
ArrayList backboneList = new ArrayList();
foreach (AtomInfo atom in cartnAtoms)
{
if (atom.atomName == "CA" || atom.atomName == "N" ||
atom.atomName == "C" || atom.atomName == "O" || atom.atomName == "OXT")
{
backboneList.Add(new AtomInfo(atom));
}
}
AtomInfo[] backboneArray = new AtomInfo [backboneList.Count];
backboneList.CopyTo(backboneArray);
return(backboneArray);
}
/// <summary>
/// add an atom to the list
/// </summary>
/// <param name="atom"></param>
/// <returns></returns>
public int AddAtom(AtomInfo atom)
{
return(cartnAtoms.Add(atom));
}
/// <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);
}
}
