/// <summary>
/// Detect all interfaces in a crystal
/// built from XML coordinates file
/// </summary>
/// <param name="xmlFile"></param>
/// <param name="paramFile"></param>
public void FindInteractChains(string xmlFile, Dictionary <int, string> interfaceDefHash)
{
asymChainTreesHash.Clear();
interfaceChainsList.Clear();
string[] symOpStrings = GetSymOpStrings(interfaceDefHash);
if (AppSettings.parameters == null)
{
AppSettings.LoadParameters();
}
pdbId = xmlFile.Substring(xmlFile.LastIndexOf("\\") + 1, 4);
CrystalBuilder crystalBuilder = new CrystalBuilder("ALL");
Dictionary <string, AtomInfo[]> interfaceChainHash = null;
try
{
interfaceChainHash = crystalBuilder.BuildCrystal(xmlFile, symOpStrings);
}
catch (Exception ex)
{
throw new Exception("Building interface chains errors: " + xmlFile + ". " + ex.Message);
}
// for each chain in a cell including original and symmetric chains
foreach (string chainAndSymOp in interfaceChainHash.Keys)
{
BVTree chainTree = new BVTree();
chainTree.BuildBVTree(interfaceChainHash[chainAndSymOp], AppSettings.parameters.kDopsParam.bvTreeMethod, true);
asymChainTreesHash.Add(chainAndSymOp, chainTree);
}
ChainContact chainContact = null;
List <int> interfaceList = new List <int> (interfaceDefHash.Keys);
interfaceList.Sort();
foreach (int interfaceId in interfaceList)
{
string[] interfaceDefStrings = interfaceDefHash[interfaceId].ToString().Split(';');
chainContact = new ChainContact(interfaceDefStrings[0], interfaceDefStrings[1]);
BVTree tree1 = (BVTree)asymChainTreesHash[interfaceDefStrings[0]];
BVTree tree2 = (BVTree)asymChainTreesHash[interfaceDefStrings[1]];
ChainContactInfo contactInfo = chainContact.GetChainContactInfo(tree1, tree2);
if (contactInfo == null)
{
continue;
}
InterfaceChains interfaceChains = null;
interfaceChains = new InterfaceChains(interfaceDefStrings[0], interfaceDefStrings[1],
tree1.Root.AtomList, tree2.Root.AtomList);
interfaceChains.pdbId = pdbId;
interfaceChains.interfaceId = interfaceId;
interfaceChains.seqDistHash = contactInfo.GetBbDistHash();
// interfaceChains.seqDistHash = contactInfo.cbetaContactHash;
interfaceChains.seqContactHash = contactInfo.GetContactsHash();
interfaceChainsList.Add(interfaceChains);
}
}
public InterfaceChains(InterfaceChains extInterChains)
{
this.interfaceId = extInterChains.interfaceId;
this.firstSymOpString = extInterChains.firstSymOpString;
this.secondSymOpString = extInterChains.secondSymOpString;
this.entityId1 = extInterChains.entityId1;
this.entityId2 = extInterChains.entityId2;
this.chain1 = (AtomInfo[])extInterChains.chain1.Clone(); // shaldow copy
this.chain2 = (AtomInfo[])extInterChains.chain2.Clone(); // shaldow copy
this.seqDistHash = new Dictionary <string, double> (extInterChains.seqDistHash);
}
/// <summary>
///
/// </summary>
/// <param name="extInterChains"></param>
/// <param name="deepCopy"></param>
public InterfaceChains(InterfaceChains extInterChains, bool deepCopy)
{
this.interfaceId = extInterChains.interfaceId;
this.firstSymOpString = extInterChains.firstSymOpString;
this.secondSymOpString = extInterChains.secondSymOpString;
this.entityId1 = extInterChains.entityId1;
this.entityId2 = extInterChains.entityId2;
if (deepCopy)
{
DeepCopyChains(extInterChains.chain1, 1); // deep copy
DeepCopyChains(extInterChains.chain2, 2);
DeepCopySeqDistHash(extInterChains.seqDistHash);
}
else
{
this.chain1 = (AtomInfo[])extInterChains.chain1.Clone(); // shaldow copy
this.chain2 = (AtomInfo[])extInterChains.chain2.Clone(); // shaldow copy
this.seqDistHash = new Dictionary <string, double> (extInterChains.seqDistHash);
}
}
/// <summary>
/// Detect all interfaces in a crystal
/// built from XML coordinates file
/// </summary>
/// <param name="xmlFile"></param>
/// <param name="paramFile"></param>
public void FindInteractChains(string xmlFile, Dictionary <int, string> interfaceDefHash, Dictionary <int, string> interfaceEntityInfoHash, out bool interfaceExist)
{
interChainId = 0;
interfaceChainsList.Clear();
asymChainTreesHash.Clear();
interfaceExist = true;
string[] symOpStrings = GetSymOpStrings(interfaceDefHash);
pdbId = xmlFile.Substring(xmlFile.LastIndexOf("\\") + 1, 4);
CrystalBuilder crystalBuilder = new CrystalBuilder(AppSettings.parameters.contactParams.atomType);
Dictionary <string, AtomInfo[]> interfaceChainHash = null;
try
{
interfaceChainHash = crystalBuilder.BuildCrystal(xmlFile, symOpStrings);
}
catch (Exception ex)
{
throw new Exception("Building interface chains errors: " + xmlFile + " " + ex.Message);
}
// for each chain in a cell including original and symmetric chains
foreach (string chainAndSymOp in interfaceChainHash.Keys)
{
BVTree chainTree = new BVTree();
chainTree.BuildBVTree(interfaceChainHash[chainAndSymOp], AppSettings.parameters.kDopsParam.bvTreeMethod, true);
asymChainTreesHash.Add(chainAndSymOp, chainTree);
}
ChainContact chainContact = null;
foreach (int interfaceId in interfaceDefHash.Keys)
{
string[] interfaceDefStrings = interfaceDefHash[interfaceId].ToString().Split(';');
chainContact = new ChainContact(interfaceDefStrings[0], interfaceDefStrings[1]);
BVTree tree1 = (BVTree)asymChainTreesHash[interfaceDefStrings[0]];
BVTree tree2 = (BVTree)asymChainTreesHash[interfaceDefStrings[1]];
if (tree1 == null || tree2 == null)
{
continue;
}
ChainContactInfo contactInfo = chainContact.GetChainContactInfo(tree1, tree2);
if (contactInfo == null)
{
interfaceExist = false;
break;
}
string[] entityStrings = interfaceEntityInfoHash[interfaceId].Split('_');
InterfaceChains interfaceChains = null;
interfaceChains = new InterfaceChains(interfaceDefStrings[0], interfaceDefStrings[1], tree1.Root.CalphaCbetaAtoms(), tree2.Root.CalphaCbetaAtoms());
// interfaceChains = new InterfaceChains (symOpStrings[0], symOpStrings[1], tree1.Root.AtomList, tree2.Root.AtomList);
interfaceChains.pdbId = pdbId;
interfaceChains.interfaceId = interfaceId;
interfaceChains.entityId1 = Convert.ToInt32(entityStrings[0]);
interfaceChains.entityId2 = Convert.ToInt32(entityStrings[1]);
interfaceChains.seqDistHash = contactInfo.GetBbDistHash();
interfaceChains.seqContactHash = contactInfo.GetContactsHash();
interfaceChainsList.Add(interfaceChains);
}
}
/// <summary>
/// add the interactive chains if it is unique
/// if it is not homomultimer, should consider the sequence alignment
/// within an entry
/// </summary>
/// <param name="interChains"></param>
private bool AddInterChainsToList(InterfaceChains interfaceChains)
{
bool hasSameInterface = false;
int interfaceIndex = 0;
foreach (InterfaceChains interfaceChainsInList in interfaceChainsList)
{
if (interfacesComp.AreInterfacesSame(interfaceChainsInList, interfaceChains))
{
hasSameInterface = true;
break;
}
interfaceIndex++;
}
if (!hasSameInterface)
{
// assign a sequential number
interChainId++;
interfaceChains.pdbId = pdbId;
interfaceChains.interfaceId = interChainId;
interfaceChainsList.Add(interfaceChains);
return(true);
}
else
{
InterfaceChains interfaceInList = (InterfaceChains)interfaceChainsList[interfaceIndex];
if ((!HasOriginalChain(interfaceInList.firstSymOpString) &&
!HasOriginalChain(interfaceInList.secondSymOpString))
&&
(HasOriginalChain(interfaceChains.firstSymOpString) ||
HasOriginalChain(interfaceChains.secondSymOpString)))
{
interfaceChains.pdbId = pdbId;
interfaceChains.interfaceId = interfaceInList.interfaceId;
interfaceChainsList[interfaceIndex] = interfaceChains;
return(true);
}
else if (((HasOriginalChain(interfaceInList.firstSymOpString) &&
interfaceInList.secondSymOpString.IndexOf("555") < 0)
||
(interfaceInList.firstSymOpString.IndexOf("555") < 0 &&
HasOriginalChain(interfaceInList.secondSymOpString)))
&&
((HasOriginalChain(interfaceChains.firstSymOpString) &&
interfaceChains.secondSymOpString.IndexOf("555") > -1)
||
(interfaceChains.firstSymOpString.IndexOf("555") > -1 &&
HasOriginalChain(interfaceChains.secondSymOpString))))
{
interfaceChains.pdbId = pdbId;
interfaceChains.interfaceId = interfaceInList.interfaceId;
interfaceChainsList[interfaceIndex] = interfaceChains;
return(true);
}
else if ((interfaceInList.firstSymOpString.IndexOf("555") < 0 &&
interfaceInList.secondSymOpString.IndexOf("555") < 0)
&&
(interfaceChains.firstSymOpString.IndexOf("555") > -1 ||
interfaceChains.secondSymOpString.IndexOf("555") > -1))
{
interfaceChains.pdbId = pdbId;
interfaceChains.interfaceId = interfaceInList.interfaceId;
interfaceChainsList[interfaceIndex] = interfaceChains;
return(true);
}
else
{
return(false);
}
}
}
/// <summary>
/// check interaction a center chain with
/// another translated chains
/// </summary>
/// <param name="chainASymOp">translated chain</param>
/// <param name="chainBSymOp">center chain</param>
/// <param name="treeA">translated tree</param>
/// <param name="treeB">center tree</param>
private bool DetectTwoChainContactWithTranslation(string translateChainSymOp, string centerChainSymOp,
BVTree translateTree, BVTree centerTree, bool skipOrig)
{
string transChainSymOp = "";
int origX = -1;
int origY = -1;
int origZ = -1;
string transVectString = translateChainSymOp.Substring(translateChainSymOp.LastIndexOf("_") + 1,
translateChainSymOp.Length - translateChainSymOp.LastIndexOf("_") - 1);
GetOrigPoint(transVectString, ref origX, ref origY, ref origZ);
bool thisNewInterfaceExist = false;
try
{
ChainContact chainContact = null;
/* total number of BVTrees: (step * 2 + 1) ^ 3
* total comparison of BVTrees: (step * 2 + 1) - 1
* e.g. steps = 1; total comparisons: 26
* compare all neighbor unit cells with the original unit cell
*/
// comare center chain B with center chain A and all its translated chains
foreach (int xA in xStepList)
{
foreach (int yA in yStepList)
{
foreach (int zA in zStepList)
{
if (xA == 0 && yA == 0 && zA == 0 && skipOrig)
{
thisNewInterfaceExist = true;
continue;
}
// chain_symmetry operator number_translation vector
// e.g. A_1_556 (chain A, symmetry operator is 1, and translation vector (0, 0, 1))
transChainSymOp = GetTransSymOpString(translateChainSymOp, origX + xA, origY + yA, origZ + zA);
if (parsedPairList.Contains(centerChainSymOp + "_" + transChainSymOp))
{
continue;
}
else
{
parsedPairList.Add(centerChainSymOp + "_" + transChainSymOp);
}
double[] fractVectorA = new double [3] {
xA, yA, zA
};
double[] translateVectorA = ComputeTransVectInCartn(fractVectorA);
// BVTree translatedTree = translateTree.UpdateBVTree (translateVectorA);
chainContact = new ChainContact(centerChainSymOp, transChainSymOp);
ChainContactInfo contactInfo = chainContact.GetChainContactInfo(centerTree, translateTree, translateVectorA);
if (contactInfo != null)
{
InterfaceChains interfaceChains = null;
Node updateRoot = new Node(translateTree.Root.CalphaCbetaAtoms());
updateRoot.UpdateLeafNode(translateVectorA);
interfaceChains = new InterfaceChains(centerChainSymOp, transChainSymOp,
centerTree.Root.CalphaCbetaAtoms(), updateRoot.AtomList);
interfaceChains.seqDistHash = contactInfo.GetBbDistHash();
interfaceChains.seqContactHash = contactInfo.GetContactsHash();
if (AddInterChainsToList(interfaceChains))
{
thisNewInterfaceExist = true;
}
}
}
}
} // end of translated chain
}
catch (Exception ex)
{
throw new Exception(string.Format("Comparisons of rotated and translated chains ({0}, {1}) errors: {2}",
translateChainSymOp, centerChainSymOp, ex.Message));
}
return(thisNewInterfaceExist);
}
/// <summary>
/// check interaction a center chain with
/// its corresponding translated chains
/// </summary>
/// <param name="chainASymOp"></param>
/// <param name="chainBSymOp"></param>
/// <param name="treeA"></param>
/// <param name="treeB"></param>
private bool DetectChainContactWithTranslation(string chainASymOp, BVTree origTreeA)
{
string transChainASymOp = "";
List <string> parsedSymOpsList = new List <string> ();
int origX = -1;
int origY = -1;
int origZ = -1;
string transVectString = chainASymOp.Substring(chainASymOp.LastIndexOf("_") + 1,
chainASymOp.Length - chainASymOp.LastIndexOf("_") - 1);
GetOrigPoint(transVectString, ref origX, ref origY, ref origZ);
bool thisNewInterfaceExist = false;
/* total number of BVTrees: (step * 2 + 1) ^ 3
* total comparison of BVTrees: (step * 2 + 1) - 1
* e.g. steps = 1; total comparisons: 26
* compare all neighbor unit cells with the original unit cell
*/
// compare a center chain with all its corresponding translated chains
foreach (int xA in xStepList)
{
foreach (int yA in yStepList)
{
foreach (int zA in zStepList)
{
// skip check contacts with itself
// probably we need to check contacts within a chain also.
if (xA == 0 && yA == 0 && zA == 0)
{
thisNewInterfaceExist = true;
continue;
}
transChainASymOp = GetTransSymOpString(chainASymOp, origX + xA, origY + yA, origZ + zA);
if (parsedPairList.Contains(chainASymOp + "_" + transChainASymOp))
{
continue;
}
else
{
parsedPairList.Add(chainASymOp + "_" + transChainASymOp);
}
double[] fractVectorA = new double [3] {
xA, yA, zA
};
double[] translateVectorA = ComputeTransVectInCartn(fractVectorA);
// get the BVtree for the translated chain
// BVTree treeA = origTreeA.UpdateBVTree (translateVectorA);
ChainContact chainContact = new ChainContact(chainASymOp, transChainASymOp);
ChainContactInfo contactInfo = chainContact.GetChainContactInfo(origTreeA, origTreeA, translateVectorA);
if (contactInfo != null)
{
InterfaceChains interfaceChains = null;
Node updateRoot = new Node(origTreeA.Root.CalphaCbetaAtoms());
updateRoot.UpdateLeafNode(translateVectorA);
interfaceChains = new InterfaceChains(chainASymOp, transChainASymOp,
origTreeA.Root.CalphaCbetaAtoms(), updateRoot.AtomList);
interfaceChains.seqDistHash = contactInfo.GetBbDistHash();
interfaceChains.seqContactHash = contactInfo.GetContactsHash();
if (AddInterChainsToList(interfaceChains))
{
thisNewInterfaceExist = true;
}
}
}
}
}
return(thisNewInterfaceExist);
}