/// <summary>
/// return the overlapped leaf nodes
/// </summary>
/// <param name="extTree"></param>
/// <returns></returns>
public void Intersect(BVTree treeA, BVTree treeB)
{
if (treeA == null || treeB == null)
{
return;
}
if (!treeA.Root.BoundBox.MayOverlap
(treeB.Root.BoundBox, AppSettings.parameters.contactParams.cutoffAtomDist))
{
return;
}
// if it is a leaf node of tree A
if (treeA.Root.AtomList.Length <= BVTree.leafAtomNumber)
{
// it is a leaf node of tree B
if (treeB.Root.AtomList.Length <= BVTree.leafAtomNumber)
{
foreach (AtomInfo atomA in treeA.Root.AtomList)
{
foreach (AtomInfo atomB in treeB.Root.AtomList)
{
float atomDist = (float)(atomA - atomB);
// if distance is less than the threshold
// possible atomic contact
if (atomDist < AppSettings.parameters.contactParams.cutoffAtomDist)
{
AtomPair atomPair = new AtomPair();
atomPair.firstAtom = atomA;
atomPair.secondAtom = atomB;
atomPair.distance = atomDist;
string seqIdString = atomA.seqId + "_" + atomB.seqId;
if (!chainContactInfo.atomContactHash.ContainsKey(seqIdString))
{
chainContactInfo.atomContactHash.Add(seqIdString, atomPair);
}
else
{
// give priority to Cbeta then Calpha
if (atomPair.firstAtom.atomName == "CB" && atomPair.secondAtom.atomName == "CB")
{
chainContactInfo.atomContactHash[seqIdString] = atomPair;
}
}
}
}
}
}
else
{
Intersect(treeA, treeB.LeftBranch);
Intersect(treeA, treeB.RightBranch);
}
}
else
{
Intersect(treeA.LeftBranch, treeB);
Intersect(treeA.RightBranch, treeB);
}
}
/// <summary>
/// contacts
/// </summary>
/// <returns></returns>
public Dictionary <string, Contact> GetContactsHash()
{
Dictionary <string, Contact> contactsHash = new Dictionary <string, Contact>();
foreach (string seqString in atomContactHash.Keys)
{
AtomPair atomPair = (AtomPair)atomContactHash[seqString];
Contact contact = new Contact();
contact.Atom1 = atomPair.firstAtom.atomName;
contact.Atom2 = atomPair.secondAtom.atomName;
contact.Residue1 = atomPair.firstAtom.residue;
contact.Residue2 = atomPair.secondAtom.residue;
contact.SeqID1 = atomPair.firstAtom.seqId;
contact.SeqID2 = atomPair.secondAtom.seqId;
contact.Distance = atomPair.distance;
contactsHash.Add(seqString, contact);
}
return(contactsHash);
}
/// <summary>
///
/// </summary>
/// <param name="extAtomPair"></param>
public void DeepCopy(AtomPair extAtomPair)
{
this.firstAtom = (AtomInfo)extAtomPair.firstAtom.Clone(); // deep copy the atom info
this.secondAtom = (AtomInfo)extAtomPair.secondAtom.Clone();
this.distance = extAtomPair.distance;
}
/// <summary>
/// get contacts between two chains
/// </summary>
/// <param name="chain1"></param>
/// <param name="chain2"></param>
/// <returns></returns>
public void ComputeChainsContact(AtomInfo[] chain1, AtomInfo[] chain2)
{
chainContactInfo = new ChainContactInfo();
Dictionary <string, AtomInfo[]> residueAtomsHash1 = null;
Dictionary <string, BoundingBox> residueBbHash1 = null;
Dictionary <string, AtomInfo[]> residueAtomsHash2 = null;
Dictionary <string, BoundingBox> residueBbHash2 = null;
GetResidueBb(chain1, ref residueAtomsHash1, ref residueBbHash1);
GetResidueBb(chain2, ref residueAtomsHash2, ref residueBbHash2);
double contactCutoffSquare = Math.Pow(AppSettings.parameters.contactParams.cutoffAtomDist, 2);
foreach (string seqId1 in residueBbHash1.Keys)
{
foreach (string seqId2 in residueBbHash2.Keys)
{
// bounding box overlap
if (((BoundingBox)residueBbHash1[seqId1]).MayOverlap
((BoundingBox)residueBbHash2[seqId2], AppSettings.parameters.contactParams.cutoffAtomDist))
{
double dX2 = 0.0;
// inter-atomic contacts between 2 residues
bool contactCompDone = false;
foreach (AtomInfo atom1 in residueAtomsHash1[seqId1])
{
if (contactCompDone)
{
break;
}
foreach (AtomInfo atom2 in residueAtomsHash2[seqId2])
{
// inter-atomic distance
dX2 = Math.Pow(atom1.xyz.X - atom2.xyz.X, 2);
if (dX2 > contactCutoffSquare)
{
continue;
}
else
{
double dXY2 = Math.Pow(atom1.xyz.Y - atom2.xyz.Y, 2) + dX2;
if (dXY2 > contactCutoffSquare)
{
continue;
} // X
else
{
double dXYZ2 = Math.Pow(atom1.xyz.Z - atom2.xyz.Z, 2) + dXY2;
if (dXYZ2 > contactCutoffSquare)
{
continue;
} // Y
else
{
AtomPair atomPair = new AtomPair();
atomPair.firstAtom = atom1;
atomPair.secondAtom = atom2;
atomPair.distance = Math.Sqrt(dXYZ2);
string seqIdString = atom1.seqId + "_" + atom2.seqId;
chainContactInfo.atomContactHash.Add(seqIdString, atomPair);
contactCompDone = true;
break;
} //Z
} // X, Y, Z
} // inter-atomic distance
}
} // inter-atomic contacts
} // bounding box overlap
}
} // loop chains
}
/// <summary>
/// Contacts between two chains
/// update the treeB when it is necessary
/// </summary>
/// <param name="treeA">center tree</param>
/// <param name="treeB">the tree need to be translated by translateVectorA</param>
/// <param name="translateVectorA"></param>
private void IntersectResidues(BVTree treeA, BVTree treeB)
{
if (!treeA.Root.BoundBox.MayOverlap
(treeB.Root.BoundBox, AppSettings.parameters.contactParams.cutoffResidueDist))
{
return;
}
// if it is a leaf node of tree A
if (treeA.LeftBranch == null && treeA.RightBranch == null)
{
// it is a leaf node of tree B
if (treeB.LeftBranch == null && treeB.RightBranch == null)
{
foreach (AtomInfo atomA in treeA.Root.AtomList)
{
foreach (AtomInfo atomB in treeB.Root.AtomList)
{
float atomDist = (float)(atomA - atomB);
if ((atomA.atomName == "CB" || atomA.atomName == "CA") &&
(atomB.atomName == "CB" || atomB.atomName == "CA") &&
atomDist < AppSettings.parameters.contactParams.cutoffResidueDist)
{
AtomPair atomPair = new AtomPair();
atomPair.firstAtom = atomA;
atomPair.secondAtom = atomB;
atomPair.distance = atomDist;
string seqIdString = atomA.seqId + "_" + atomB.seqId;
if (!chainContactInfo.cbetaContactHash.ContainsKey(seqIdString))
{
chainContactInfo.cbetaContactHash.Add(seqIdString, atomPair);
}
else
{
// give priority to Cbeta then Calpha
/* if (atomPair.firstAtom.atomName == "CB" && atomPair.secondAtom.atomName == "CB")
* {
* chainContactInfo.cbetaContactHash[seqIdString] = atomPair;
* }*/
// minimum distance between bb atoms
double dist = ((AtomPair)chainContactInfo.cbetaContactHash[seqIdString]).distance;
if (dist > atomDist)
{
chainContactInfo.cbetaContactHash[seqIdString] = atomPair;
}
}
}
// if distance is less than the threshold
// atomic contact
if (atomDist < AppSettings.parameters.contactParams.cutoffAtomDist)
{
string seqIdString = atomA.seqId + "_" + atomB.seqId;
if (!chainContactInfo.atomContactHash.ContainsKey(seqIdString))
{
AtomPair atomPair = new AtomPair();
atomPair.firstAtom = atomA;
atomPair.secondAtom = atomB;
atomPair.distance = atomDist;
chainContactInfo.atomContactHash.Add(seqIdString, atomPair);
}
else
{
// find the atom pair with minimum distance
AtomPair atomPair = (AtomPair)chainContactInfo.atomContactHash[seqIdString];
if (atomDist < atomPair.distance)
{
atomPair.firstAtom = atomA;
atomPair.secondAtom = atomB;
atomPair.distance = atomDist;
chainContactInfo.atomContactHash[seqIdString] = atomPair;
}
}
}
}
}
}
else
{
IntersectResidues(treeA, treeB.LeftBranch);
IntersectResidues(treeA, treeB.RightBranch);
}
}
else
{
IntersectResidues(treeA.LeftBranch, treeB);
IntersectResidues(treeA.RightBranch, treeB);
}
}
/// <summary>
/// Contacts between two chains
/// update the treeB when it is necessary
/// </summary>
/// <param name="treeA">center tree</param>
/// <param name="treeB">the tree need to be translated by translateVectorA</param>
/// <param name="translateVectorA"></param>
public void Intersect(BVTree treeA, BVTree treeB, double[] translateVectorA)
{
if (treeA == null || treeB == null)
{
return;
}
BoundingBox bb = treeB.Root.BoundBox.UpdateBoundingBox(translateVectorA);
if (!treeA.Root.BoundBox.MayOverlap(bb, AppSettings.parameters.contactParams.cutoffAtomDist))
{
return;
}
// if it is a leaf node of tree A
if (treeA.LeftBranch == null && treeA.RightBranch == null)
{
// it is a leaf node of tree B
if (treeB.LeftBranch == null && treeB.RightBranch == null)
{
Node leafNode = new Node(treeB.Root);
leafNode.UpdateLeafNode(translateVectorA);
foreach (AtomInfo atomA in treeA.Root.AtomList)
{
foreach (AtomInfo atomB in leafNode.AtomList)
{
float atomDist = (float)(atomA - atomB);
// if distance is less than the threshold
// possible atomic contact
if (atomDist < AppSettings.parameters.contactParams.cutoffAtomDist)
{
AtomPair atomPair = new AtomPair();
atomPair.firstAtom = atomA;
atomPair.secondAtom = atomB;
atomPair.distance = atomDist;
string seqIdString = atomA.seqId + "_" + atomB.seqId;
if (!chainContactInfo.atomContactHash.ContainsKey(seqIdString))
{
chainContactInfo.atomContactHash.Add(seqIdString, atomPair);
}
else
{
// give priority to Cbeta
if (atomPair.firstAtom.atomName == "CB" && atomPair.secondAtom.atomName == "CB")
{
chainContactInfo.atomContactHash[seqIdString] = atomPair;
}
}
}
}
}
}
else
{
Intersect(treeA, treeB.LeftBranch, translateVectorA);
Intersect(treeA, treeB.RightBranch, translateVectorA);
}
}
else
{
Intersect(treeA.LeftBranch, treeB, translateVectorA);
Intersect(treeA.RightBranch, treeB, translateVectorA);
}
}
