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));
}
public void Add(ILoop Loop)
{
Loops.Add(Loop);
}
public void Add(ILoop Loop)
{
Loops.Add(Loop);
}
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);
}