/// <summary>
/// apply cartesian symmetry operators on cartesian coordinates
/// directly to provide transformed cartesian coordinate
/// </summary>
/// <param name="symOpMatrix"></param>
/// <param name="fractTransMatrix"></param>
/// <param name="cartnInverseMatrix"></param>
/// <returns></returns>
public AtomInfo TransformAtom(SymOpMatrix symOpMatrix)
{
AtomInfo transformedAtom = (AtomInfo)this.Clone();;
transformedAtom.xyz = symOpMatrix * this.xyz;
return(transformedAtom);
}
/// <summary>
/// sort chains by atom ID
/// </summary>
public void SortByAtomId()
{
if (cartnAtoms == null)
{
return;
}
AtomInfo[] chain = this.CartnAtoms;
Dictionary <int, AtomInfo> seqHash = new Dictionary <int, AtomInfo> ();
foreach (AtomInfo atom in chain)
{
// sould have unique atom id
seqHash.Add(atom.atomId, atom);
}
List <int> atomIdList = new List <int> (seqHash.Keys);
atomIdList.Sort();
AtomInfo[] sortedChain = new AtomInfo [chain.Length];
int count = 0;
foreach (int atomId in atomIdList)
{
sortedChain[count] = seqHash[atomId];
count++;
}
this.CartnAtoms = sortedChain;
}
/// <summary>
/// transform a protein chain by applying a specific symmetry operation
/// either from PDB xml or from a user-defined
/// </summary>
/// <param name="chainCoordList"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
public AtomInfo[] TransformChainBySpecificSymOp(AtomInfo[] chainAtomList, SymOpMatrix symMatrix)
{
AtomInfo[] transformedAtomList = new AtomInfo [chainAtomList.Length];
for (int atomI = 0; atomI < chainAtomList.Length; atomI++)
{
AtomInfo thisAtomInfo = chainAtomList[atomI].TransformAtom(symMatrix, cartn2fractMatrix, fract2cartnMatrix);
transformedAtomList[atomI] = thisAtomInfo;
}
return(transformedAtomList);
}
/// <summary>
/// transform a protein chain by applying a specific symmetry operation
/// either from PDB xml or from a user-defined
/// </summary>
/// <param name="chainCoordList"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
private AtomInfo[] TransformChainByCartesianSymOp(AtomInfo[] chainAtomList, SymOpMatrix symMatrix)
{
AtomInfo[] transformedAtomList = new AtomInfo[chainAtomList.Length];
for (int atomI = 0; atomI < chainAtomList.Length; atomI++)
{
AtomInfo thisAtomInfo = chainAtomList[atomI].TransformAtom(symMatrix);
transformedAtomList[atomI] = thisAtomInfo;
}
return(transformedAtomList);
}
/// <summary>
/// a. change a cartesian coordinate to fractional coordinate
/// b. transform the fractional coordinate
/// c. compute the cartesian coordinate
/// for the transformed fractional coordinate
/// </summary>
/// <param name="symOpMatrix"></param>
/// <param name="fractTransMatrix"></param>
/// <param name="cartnInverseMatrix"></param>
/// <returns></returns>
public AtomInfo TransformAtom(SymOpMatrix symOpMatrix, Matrix fractTransMatrix, Matrix cartnInverseMatrix)
{
AtomInfo transformedAtom = (AtomInfo)this.Clone();;
if (this.fractCoord == null)
{
this.fractCoord = fractTransMatrix * this.xyz;
}
transformedAtom.fractCoord = symOpMatrix * this.fractCoord;
transformedAtom.xyz = cartnInverseMatrix * (symOpMatrix * this.fractCoord);
return(transformedAtom);
}
/// <summary>
/// transform a protein chain by applying a specific symmetry operation
/// either from PDB xml or from a user-defined
/// </summary>
/// <param name="chainCoordList"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
private AtomInfo[] TransformChainBySymOpAndTrans(AtomInfo[] chainAtomList, SymOpMatrix symMatrix, double[] transVector)
{
AtomInfo[] transformedAtomList = new AtomInfo [chainAtomList.Length];
for (int atomI = 0; atomI < chainAtomList.Length; atomI++)
{
AtomInfo thisAtomInfo = chainAtomList[atomI].TransformAtom(symMatrix, cartn2fractMatrix, fract2cartnMatrix);
thisAtomInfo.xyz.X += transVector[0];
thisAtomInfo.xyz.Y += transVector[1];
thisAtomInfo.xyz.Z += transVector[2];
transformedAtomList[atomI] = thisAtomInfo;
}
return(transformedAtomList);
}
/// <summary>
///
/// </summary>
/// <param name="atoms"></param>
/// <param name="ncsMatrix"></param>
/// <returns></returns>
private AtomInfo[] ApplyNcsMatrix(AtomInfo[] atoms, Matrix ncsMatrix)
{
AtomInfo[] newAtoms = new AtomInfo [atoms.Length];
int i = 0;
foreach (AtomInfo origAtom in atoms)
{
newAtoms[i] = (AtomInfo)origAtom.Clone();
newAtoms[i].xyz = ncsMatrix * origAtom.xyz;
i++;
}
return(newAtoms);
}
/// <summary>
/// transform one chain
/// </summary>
/// <param name="chain"></param>
/// <param name="symMatrix"></param>
/// <returns></returns>
public AtomInfo[] BuildOneChain(ChainAtoms chain, SymOpMatrix symMatrix)
{
if (symMatrix.symmetryString == "1_555")
{
return chain.CartnAtoms;
}
AtomInfo[] transformedAtoms = new AtomInfo[chain.CartnAtoms.Length];
int i = 0;
foreach (AtomInfo atom in chain.CartnAtoms)
{
AtomInfo transformedAtom = atom.TransformAtom(symMatrix);
transformedAtoms[i] = transformedAtom;
i++;
}
return transformedAtoms;
}
/// <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);
if (this.ProjectedCoord != null)
{
clonedAtomInfo.ProjectedCoord = (double[])this.ProjectedCoord.Clone();
}
if (this.fractCoord != null)
{
clonedAtomInfo.fractCoord = new Coordinate(this.fractCoord.X, this.fractCoord.Y, this.fractCoord.Z);;
}
return(clonedAtomInfo);
}
/// <summary>
/// deep copy of external atom information
/// </summary>
/// <param name="extAtomInfo"></param>
public AtomInfo(AtomInfo extAtomInfo)
{
this.residue = extAtomInfo.residue;
this.seqId = extAtomInfo.seqId;
this.authSeqId = extAtomInfo.authSeqId;
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.bfactor = extAtomInfo.bfactor;
this.occupancy = extAtomInfo.occupancy;
if (extAtomInfo.ProjectedCoord != null)
{
this.ProjectedCoord = (double[])extAtomInfo.ProjectedCoord.Clone();
}
// don't copy the fractional coordinates
this.fractCoord = null;
}
public void Add(AtomInfo atom)
{
atomList.Add(atom);
}
/// <summary>
/// add an atom to the list
/// </summary>
/// <param name="atom"></param>
/// <returns></returns>
public void AddAtom(AtomInfo atom)
{
cartnAtoms.Add(atom);
}
