/// <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);
}
}
/// <summary>
/// get the interface between two input chains
/// </summary>
/// <param name="chain1"></param>
/// <param name="chain2"></param>
/// <returns></returns>
public ChainContactInfo GetAllChainContactInfo(AtomInfo[] chain1, AtomInfo[] chain2)
{
BVTree chain1Tree = new BVTree();
chain1Tree.BuildBVTree(chain1, AppSettings.parameters.kDopsParam.bvTreeMethod, true);
BVTree chain2Tree = new BVTree();
chain2Tree.BuildBVTree(chain2, AppSettings.parameters.kDopsParam.bvTreeMethod, true);
return(GetAnyChainContactInfo(chain1Tree, chain2Tree));
}
/// <summary>
/// build BVtrees for chains in a biological unit
/// </summary>
/// <param name="biolUnit"></param>
/// <returns></returns>
private Dictionary <string, BVTree> BuildBVtreesForAsu(Dictionary <string, AtomInfo[]> asymUnit)
{
Dictionary <string, BVTree> chainTreesHash = new Dictionary <string, BVTree> ();
// for each chain in the biological unit
// build BVtree
foreach (string chainAndSymOp in asymUnit.Keys)
{
BVTree chainTree = new BVTree();
chainTree.BuildBVTree(asymUnit[chainAndSymOp], AppSettings.parameters.kDopsParam.bvTreeMethod, true);
chainTreesHash.Add(chainAndSymOp, chainTree);
}
return(chainTreesHash);
}
/// <summary>
/// Detect all interfaces in a crystal
/// built from XML coordinates file
/// </summary>
/// <param name="xmlFile"></param>
/// <param name="paramFile"></param>
public int FindInteractChains(string xmlFile)
{
interChainId = 0;
asymChainTreesHash.Clear();
interfaceChainsList.Clear();
pdbId = xmlFile.Substring(xmlFile.LastIndexOf("\\") + 1, 4);
CrystalBuilder crystalBuilder = new CrystalBuilder(AppSettings.parameters.contactParams.atomType);
Dictionary <string, AtomInfo[]> unitCellChainsHash = null;
int[] maxSteps = null;
// build crystal based on all symmetry operations
try
{
maxSteps = crystalBuilder.BuildCrystal(xmlFile, ref unitCellChainsHash);
if (unitCellChainsHash == null)
{
throw new Exception("Cannot build unit cell.");
}
// if there are too many chains in a unit cell
// only compute the interfaces between original ASU chains
// and other chains
if (unitCellChainsHash.Count > unitCellSize)
{
// throw new Exception ("Unit cell too large. Skip processing " + pdbId + ".");
// if there are too many chains in the unit cell,
// only check the interfaces within the unit cell.
for (int i = 0; i < maxSteps.Length; i++)
{
maxSteps[i] = 0;
}
}
// if there are too many chains, only use chains in the asymmetric unit
if (unitCellChainsHash.Count >= maxUnitCellSize)
{
Dictionary <string, AtomInfo[]> asuChainHash = GetAsymUnitHash(unitCellChainsHash);
unitCellChainsHash = asuChainHash;
// if it is still too big due to Non-symmetry operators,
// only use chains in the original asu in the PDB file, may not be the real Asu
if (asuChainHash.Count >= unitCellSize)
{
Dictionary <string, AtomInfo[]> origAsuChainHash = GetOrigAsymUnitHash(asuChainHash);
unitCellChainsHash = origAsuChainHash;
}
}
}
catch (Exception ex)
{
throw new Exception("Building Crystal Errors: " + xmlFile + " " + ex.Message);
}
/*
* build BVTree for original asymmetric chains +
* their chains after applied symmetry operations
* without translations
*/
try
{
// for each chain in a cell including original and symmetric chains
foreach (string chainAndSymOp in unitCellChainsHash.Keys)
{
BVTree chainTree = new BVTree();
chainTree.BuildBVTree(unitCellChainsHash[chainAndSymOp], AppSettings.parameters.kDopsParam.bvTreeMethod, true);
asymChainTreesHash.Add(chainAndSymOp, chainTree);
}
}
catch (Exception ex)
{
throw new Exception("Building Bounding Volumn Tree Errors: " + xmlFile + ". " + ex.Message);
}
/*
* the critical step for the computation time
* check all pairs of chains including translated chains
* return a list of atompairs if exists
*/
cryst1 = crystalBuilder.Crystal1;
fract2CartnMatrix = crystalBuilder.fract2cartnMatrix;
List <string> chainAndSymOps = new List <string> (asymChainTreesHash.Keys);
List <string> orderedChainAndSymOps = SortChainsInUnitCell(chainAndSymOps);
// check interactions between 2 different chains and their translated chains
// chainAndSymOps: chainId_symmetry operator_full symmetry operations
// e.g. A_1_545
try
{
ComputeUniqueInterfacesFromCryst(orderedChainAndSymOps, maxSteps);
}
catch (Exception ex)
{
/* ProtCidSettings.progressInfo.progStrQueue.Enqueue
* ("Retrieving unique interfaces of " + pdbId + " errors: " + ex.Message);*/
throw new Exception("Retrieving unique interfaces of " + pdbId + " errors: " + ex.Message);
}
return(unitCellChainsHash.Count);
}
/// <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);
}
}