private void ParseLine(string line)
{
if (line.Length < 4)
{
return;
}
if (line.Substring(0, 4) == "ATOM" && line.IndexOf(" CA ") != -1)
{
string Record = line.Substring(0, 6 - 0).Trim();
string Id = line.Substring(6, 11 - 6).Trim();
string name = line.Substring(12, 16 - 12).Trim();
string residue = line.Substring(17, 20 - 17).Trim();
string chain = line.Substring(21, 23 - 21).Trim();
string residuenumber = line.Substring(22, 26 - 22).Trim();
string residueextension = line.Substring(26, 28 - 26).Trim();
string xcoord = line.Substring(30, 38 - 30).Trim();
string ycoord = line.Substring(38, 46 - 38).Trim();
string zcoord = line.Substring(46, 54 - 46).Trim();
string[] PdbComponents = Regex.Split(line, @"[ \t]+");
IResidue Residue = new IResidue(Convert.ToInt32(Id),
name,
residue,
chain,
residuenumber + residueextension,
Convert.ToDouble(xcoord),
Convert.ToDouble(ycoord),
Convert.ToDouble(zcoord));
//Add the atom to the list
Atoms.Add(Residue);
}
}
private IResidue IsLoopSolventAccessible(List <IResidue> PdbResidues, List <IResidue> LoopResidues, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
//Grad the Apex atom from the loop segment
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
IResidue ApexResidue = new IResidue();
IResidue NTermResidue = LoopResidues.First();
IResidue CTermResidue = LoopResidues.Last();
double TerminalDistance = EuclideanDistance(NTermResidue, CTermResidue);
IResidue PseudoTermResidue = new IResidue(0, "", "Virtual", "V", 0,
((NTermResidue.X + CTermResidue.X) / 2),
((NTermResidue.Y + CTermResidue.Y) / 2),
((NTermResidue.Z + CTermResidue.Z) / 2));
//Determine the Apex Residue
foreach (IResidue Residue in LoopResidues)
{
ApexDistance = EuclideanDistance(PseudoTermResidue, Residue);
if (ApexDistance > MaxApexDistance)
{
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop)
{
if (EuclideanDistance(ApexResidue, Residue) < LoopCriteria.SolventExposedThreshold)
{
//Not solvent accessible
return(null);
}
}
return(ApexResidue);
}
double EuclideanDistance(IResidue a, IResidue b)
{
return(Math.Sqrt(((a.X - b.X) * (a.X - b.X)) + ((a.Y - b.Y) * (a.Y - b.Y)) + ((a.Z - b.Z) * (a.Z - b.Z))));
}
private IResidue IsLoopVectorSolventAccessible(List <IResidue> PdbResidues, List <IResidue> LoopResidues, int VectorScale, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
IResidue[] LoopArray = LoopResidues.ToArray();
IResidue NTerm = LoopArray[0];
IResidue NTermP1 = LoopArray[1]; //Might not use this...
IResidue NTermP2 = LoopArray[2];
IResidue CTerm = LoopArray[LoopArray.Count() - 1]; //Zero base
IResidue CTermP1 = LoopArray[LoopArray.Count() - 2]; //Might not use this...
IResidue CTermP2 = LoopArray[LoopArray.Count() - 3];
//Average the positions of the N aand C sides of the loops
IResidue P0Term = new IResidue(0, "Virtual", "VP0", "N", 0,
(NTerm.X + CTerm.X) / 2,
(NTerm.Y + CTerm.Y) / 2,
(NTerm.Z + CTerm.Z) / 2);
//Might not use this...
IResidue P1Term = new IResidue(0, "Virtual", "VP1", "N", 0,
(NTermP1.X + CTermP1.X) / 2,
(NTermP1.Y + CTermP1.Y) / 2,
(NTermP1.Z + CTermP1.Z) / 2);
IResidue P2Term = new IResidue(0, "Virtual", "VP2", "N", 0,
(NTermP2.X + CTermP2.X) / 2,
(NTermP2.Y + CTermP2.Y) / 2,
(NTermP2.Z + CTermP2.Z) / 2);
//Calculate the unit vector (not using P1 for now)
double unitX = P2Term.X - P0Term.X;
double unitY = P2Term.Y - P0Term.Y;
double unitZ = P2Term.Z - P0Term.Z;
//Scaled PsuedoResidue out in the solvent
IResidue SolventResidue = new IResidue(0, "Virtual", "Solvent", "N", 0,
(unitX * VectorScale) + P0Term.X,
(unitY * VectorScale) + P0Term.Y,
(unitZ * VectorScale) + P0Term.Z);
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop)
{
if (EuclideanDistance(SolventResidue, Residue) < LoopCriteria.SolventExposedThreshold)
{
//Not solvent accessible
return(null);
}
}
//Determine the Apex Residue
IResidue ApexResidue = new IResidue();
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
foreach (IResidue Residue in LoopResidues)
{
ApexDistance = EuclideanDistance(P0Term, Residue);
if (ApexDistance > MaxApexDistance)
{
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
return(ApexResidue);
}
public ILoopsCollection Search(IPdb Pdb)
{
ILoopsCollection LoopsCollection = new ILoopsCollection();
ILoopCriteria LoopCriteria = new ILoopCriteria(true);
//Try some LINQ on this beast
var Chains = (from p in Pdb.Atoms select p.Chain).Distinct();
foreach (string ChainName in Chains)
{
//Get all the atoms in the chain
var Chain = (from p in Pdb.Atoms where p.Chain == ChainName select p);
IResidue[] AtomsInChain = Chain.ToArray();
//Set the chain length if it is not explicitly set (full length here)
if (LoopCriteria.Start == -1)
{
LoopCriteria.Start = 0;
}
if (LoopCriteria.End == -1)
{
LoopCriteria.End = AtomsInChain.Count();
}
//Search for the loops
if (LoopCriteria.Length > AtomsInChain.Count())
{
continue;
}
for (int i = LoopCriteria.Start; i < LoopCriteria.End - LoopCriteria.Length - 1; i++)
{
//Check for the terminal distances
double eDistance = EuclideanDistance(AtomsInChain[i], AtomsInChain[i + LoopCriteria.Length]);
if (eDistance < LoopCriteria.TerminiDistanceThreshold)
{
//Passes the Distance Test
//Check for the solvent accessible regions
if (LoopCriteria.SolventAccessible)
{
List <IResidue> LoopResidues = new List <IResidue>();
for (int j = i; j < i + LoopCriteria.Length; j++)
{
LoopResidues.Add(AtomsInChain[j]);
}
IResidue ApexResidue = IsLoopVectorSolventAccessible(Pdb.Atoms, LoopResidues, 4, LoopCriteria);
//IResidue ApexResidue = IsLoopSolventAccessible(Pdb.Atoms, LoopResidues, LoopCriteria);
if (ApexResidue != null)
{
//Passes the solvent test, add it to the loop collection
ILoop Loop = new ILoop();
Loop.NTermAtom = AtomsInChain[i];
Loop.NTermAtomP1 = AtomsInChain[i + 1];
Loop.NTermAtomP2 = AtomsInChain[i + 2];
Loop.CTermAtom = AtomsInChain[i + LoopCriteria.Length];
Loop.CTermAtomP1 = AtomsInChain[i + LoopCriteria.Length - 1];
Loop.CTermAtomP2 = AtomsInChain[i + LoopCriteria.Length - 2];
Loop.LoopLength = LoopCriteria.Length;
Loop.PdbCode = Pdb.PdbCode;
Loop.Chain = ChainName;
Loop.ApexAtom = ApexResidue;
Loop.UnitVector = new Vector3D(((Loop.NTermAtomP2.X + Loop.CTermAtomP2.X) / 2) - ((Loop.NTermAtom.X + Loop.CTermAtom.X) / 2),
((Loop.NTermAtomP2.Y + Loop.CTermAtomP2.Y) / 2) - ((Loop.NTermAtom.Y + Loop.CTermAtom.Y) / 2),
((Loop.NTermAtomP2.X + Loop.CTermAtomP2.X) / 2) - ((Loop.NTermAtom.X + Loop.CTermAtom.X) / 2));
//Ensure Beta-Loop-Beta
if (EuclideanDistance(Loop.NTermAtom, Loop.CTermAtom) < LoopCriteria.TerminiDistanceThreshold &&
EuclideanDistance(Loop.NTermAtomP1, Loop.CTermAtomP1) < LoopCriteria.TerminiDistanceThreshold &&
EuclideanDistance(Loop.NTermAtomP2, Loop.CTermAtomP2) < LoopCriteria.TerminiDistanceThreshold)
{
LoopsCollection.Add(Loop);
}
}
}
}
}
LoopCriteria.End = -1;
LoopCriteria.Start = -1;
}
//Cleanup
LoopCriteria = null;
//Return
return(CleanupLoops(LoopsCollection));
}
private void ParseLine(string line)
{
if (line.Length < 4) { return; }
if (line.Substring(0,4)=="ATOM" && line.IndexOf(" CA ")!=-1)
{
string Record = line.Substring(0, 6-0).Trim();
string Id = line.Substring(6, 11 - 6).Trim();
string name = line.Substring(12, 16 - 12).Trim();
string residue = line.Substring(17, 20 - 17).Trim();
string chain = line.Substring(21, 23 - 21).Trim();
string residuenumber = line.Substring(22, 26 - 22).Trim();
string residueextension = line.Substring(26, 28 - 26).Trim();
string xcoord = line.Substring(30, 38 - 30).Trim();
string ycoord = line.Substring(38, 46 - 38).Trim();
string zcoord = line.Substring(46, 54 - 46).Trim();
string[] PdbComponents = Regex.Split(line, @"[ \t]+");
IResidue Residue = new IResidue(Convert.ToInt32(Id),
name,
residue,
chain,
residuenumber + residueextension,
Convert.ToDouble(xcoord),
Convert.ToDouble(ycoord),
Convert.ToDouble(zcoord));
//Add the atom to the list
Atoms.Add(Residue);
}
}
private IResidue IsLoopVectorSolventAccessible(List<IResidue> PdbResidues, List<IResidue> LoopResidues, int VectorScale, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
IResidue[] LoopArray = LoopResidues.ToArray();
IResidue NTerm = LoopArray[0];
IResidue NTermP1 = LoopArray[1]; //Might not use this...
IResidue NTermP2 = LoopArray[2];
IResidue CTerm = LoopArray[LoopArray.Count()- 1]; //Zero base
IResidue CTermP1 = LoopArray[LoopArray.Count() - 2]; //Might not use this...
IResidue CTermP2 = LoopArray[LoopArray.Count() - 3];
//Average the positions of the N aand C sides of the loops
IResidue P0Term = new IResidue(0, "Virtual", "VP0", "N", 0,
(NTerm.X + CTerm.X) / 2,
(NTerm.Y + CTerm.Y) / 2,
(NTerm.Z + CTerm.Z) / 2);
//Might not use this...
IResidue P1Term = new IResidue(0, "Virtual", "VP1", "N", 0,
(NTermP1.X + CTermP1.X) / 2,
(NTermP1.Y + CTermP1.Y) / 2,
(NTermP1.Z + CTermP1.Z) / 2);
IResidue P2Term = new IResidue(0, "Virtual", "VP2", "N", 0,
(NTermP2.X + CTermP2.X) / 2,
(NTermP2.Y + CTermP2.Y) / 2,
(NTermP2.Z + CTermP2.Z) / 2);
//Calculate the unit vector (not using P1 for now)
double unitX = P2Term.X - P0Term.X;
double unitY = P2Term.Y - P0Term.Y;
double unitZ = P2Term.Z - P0Term.Z;
//Scaled PsuedoResidue out in the solvent
IResidue SolventResidue = new IResidue(0, "Virtual", "Solvent", "N", 0,
(unitX * VectorScale) + P0Term.X,
(unitY * VectorScale) + P0Term.Y,
(unitZ * VectorScale) + P0Term.Z);
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop)
{
if (EuclideanDistance(SolventResidue, Residue) < LoopCriteria.SolventExposedThreshold)
{
//Not solvent accessible
return null;
}
}
//Determine the Apex Residue
IResidue ApexResidue = new IResidue();
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
foreach (IResidue Residue in LoopResidues)
{
ApexDistance = EuclideanDistance(P0Term, Residue);
if (ApexDistance > MaxApexDistance)
{
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
return ApexResidue;
}
private IResidue IsLoopSolventAccessible(List<IResidue> PdbResidues, List<IResidue> LoopResidues, ILoopCriteria LoopCriteria)
{
var PdbGuids = from p in PdbResidues
select p;
var LoopGuids = from c in LoopResidues
select c;
var PdbWithoutLoop = PdbGuids.Except(LoopGuids);
//Grad the Apex atom from the loop segment
double MaxApexDistance = 0.0;
double ApexDistance = 0.0;
IResidue ApexResidue = new IResidue();
IResidue NTermResidue = LoopResidues.First();
IResidue CTermResidue = LoopResidues.Last();
double TerminalDistance = EuclideanDistance(NTermResidue, CTermResidue);
IResidue PseudoTermResidue = new IResidue(0, "", "Virtual", "V", 0,
((NTermResidue.X + CTermResidue.X) / 2),
((NTermResidue.Y+CTermResidue.Y) / 2),
((NTermResidue.Z+CTermResidue.Z) / 2));
//Determine the Apex Residue
foreach (IResidue Residue in LoopResidues) {
ApexDistance = EuclideanDistance(PseudoTermResidue, Residue);
if (ApexDistance > MaxApexDistance) {
MaxApexDistance = ApexDistance;
ApexResidue = Residue;
}
}
//Now calculate the distances between the Apex residue and all the other atoms in the PDB (minus the loop residues)
foreach (IResidue Residue in PdbWithoutLoop) {
if (EuclideanDistance(ApexResidue, Residue) < LoopCriteria.SolventExposedThreshold) {
//Not solvent accessible
return null;
}
}
return ApexResidue;
}
double EuclideanDistance(IResidue a, IResidue b)
{
return Math.Sqrt(((a.X - b.X) * (a.X - b.X)) + ((a.Y - b.Y) * (a.Y - b.Y)) + ((a.Z - b.Z) * (a.Z - b.Z)));
}