/// <summary>
/// This method finds chemical interaction bonds between atoms on separate chains.
/// </summary>
/// <param name="cancellationToken"></param>
/// <param name="pdbFilename">The filename of the PDB file to parse for chemical interactions.</param>
/// <param name="pdbIdChainIdList"></param>
/// <param name="breakWhenFirstInteractionFound"></param>
/// <param name="totalThreads"></param>
/// <returns>Returns a list of atom pairs which are close enough in distance to have chemical interactions.</returns>
public static List <AtomPair> FindInteractions(CancellationToken cancellationToken, decimal maxAtomInterationDistance /*= 8.0m*/, string pdbFilename, Dictionary <string, List <string> > pdbIdChainIdList, bool breakWhenFirstInteractionFound = false, int totalThreads = -1, bool sort = true, int requiredChains = -1)
{
if (ParameterValidation.IsLoadFilenameInvalid(pdbFilename)) // && ParameterValidation.IsProteinChainListContainerNullOrEmpty(pdbFileChains))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilename));
}
string proteinId = ProteinDataBankFileOperations.PdbIdFromPdbFilename(pdbFilename);
bool useCache = false;
if (useCache && !string.IsNullOrWhiteSpace(proteinId))
{
var cachedInteractions = InteractionsCache.LoadPdbInteractionCache(proteinId, requiredChains);
if (cachedInteractions != null)
{
return(cachedInteractions);
}
}
var chainIdList = pdbIdChainIdList != null ? (proteinId != null && pdbIdChainIdList.ContainsKey(proteinId) ? pdbIdChainIdList[proteinId].ToArray() : null) : null;
ProteinChainListContainer proteinFileChains = ProteinDataBankFileOperations.PdbAtomicChains(pdbFilename, chainIdList, requiredChains, requiredChains, true);
List <AtomPair> atomPairList = FindInteractions(cancellationToken, maxAtomInterationDistance, proteinId, pdbIdChainIdList, proteinFileChains, breakWhenFirstInteractionFound, totalThreads, sort, requiredChains);
if (atomPairList == null)
{
// only save if null, otherwise, already saved in other method
atomPairList = new List <AtomPair>();
if (useCache)
{
InteractionsCache.SavePdbInteractionCache(proteinId, atomPairList, requiredChains);
}
}
return(atomPairList);
}
public static List <AtomPair> FindInteractions(CancellationToken cancellationToken, decimal maxAtomInterationDistance /*= 8.0m*/, string proteinId, Dictionary <string, List <string> > pdbIdChainIdList, ProteinChainListContainer proteinFileChains, bool breakWhenFirstInteractionFound = false, int totalThreads = -1, bool sort = true, int requiredChains = -1)
{
//const decimal maxInterationDistance = 8.0m;
bool useCache = false;
if (useCache && !string.IsNullOrWhiteSpace(proteinId))
{
var cachedInteractions = InteractionsCache.LoadPdbInteractionCache(proteinId, requiredChains);
if (cachedInteractions != null)
{
return(cachedInteractions);
}
}
// check required number of chains are found
if (proteinFileChains == null || proteinFileChains.ChainList == null || (requiredChains > -1 && proteinFileChains.ChainList.Count != requiredChains))
{
return(null);
}
// check that all chains have atoms
if (proteinFileChains.ChainList.Any(chain => chain.AtomList == null || chain.AtomList.Count == 0))
{
return(null);
}
// Make list of 3D positions of atoms.
var positions = new List <Point3D> [proteinFileChains.ChainList.Count];
for (int chainIndex = 0; chainIndex < proteinFileChains.ChainList.Count; chainIndex++)
{
positions[chainIndex] = Clustering.AtomRecordListToPoint3DList(proteinFileChains.ChainList[chainIndex]);
}
var tasks = new List <Task <List <AtomPair> > >();
for (int chainIndexA = 0; chainIndexA < proteinFileChains.ChainList.Count; chainIndexA++)
{
for (int chainIndexB = 0; chainIndexB < proteinFileChains.ChainList.Count; chainIndexB++)
{
if (chainIndexB == chainIndexA || chainIndexB < chainIndexA)
{
continue;
}
WorkDivision <List <AtomPair> > workDivision = new WorkDivision <List <AtomPair> >(proteinFileChains.ChainList[chainIndexA].AtomList.Count, totalThreads);
bool breakOut = false;
var lockBreakOut = new object();
for (int threadIndex = 0; threadIndex < workDivision.ThreadCount; threadIndex++)
{
int localThreadIndex = threadIndex;
int localChainIndexA = chainIndexA;
int localChainIndexB = chainIndexB;
WorkDivision <List <AtomPair> > localWorkDivision = workDivision;
Task <List <AtomPair> > task = Task.Run(() =>
{
var taskResult = new List <AtomPair>();
for (int atomIndexA = localWorkDivision.ThreadFirstIndex[localThreadIndex]; atomIndexA <= localWorkDivision.ThreadLastIndex[localThreadIndex]; atomIndexA++)
{
if (breakOut)
{
break;
}
for (int atomIndexB = 0; atomIndexB < proteinFileChains.ChainList[localChainIndexB].AtomList.Count; atomIndexB++)
{
if (breakOut || (breakWhenFirstInteractionFound && taskResult.Count > 0))
{
lock (lockBreakOut)
{
breakOut = true;
}
break;
}
if ((!positions[localChainIndexA][atomIndexA].ParseOK) || (!positions[localChainIndexB][atomIndexB].ParseOK))
{
continue;
}
decimal atomicDistanceAngstroms3D = Point3D.Distance3D(positions[localChainIndexA][atomIndexA], positions[localChainIndexB][atomIndexB], true);
// Chemical proteinInterface bonds found at 5 angstrom or less.
if (atomicDistanceAngstroms3D <= 0.0m || atomicDistanceAngstroms3D > maxAtomInterationDistance)
{
continue;
}
var atomPair = new AtomPair(
proteinId,
proteinFileChains.ChainList[localChainIndexA].AtomList[atomIndexA],
localChainIndexA,
proteinId,
localChainIndexB,
proteinFileChains.ChainList[localChainIndexB].AtomList[atomIndexB],
atomicDistanceAngstroms3D);
taskResult.Add(atomPair);
}
}
if (taskResult.Count == 0)
{
return(null);
}
return(taskResult);
}, cancellationToken);
workDivision.TaskList.Add(task);
}
tasks.AddRange(workDivision.TaskList);
}
}
try
{
Task[] tasksToWait = tasks.Where(task => task != null && !task.IsCompleted).ToArray <Task>();
if (tasksToWait.Length > 0)
{
Task.WaitAll(tasksToWait);
}
}
catch (AggregateException)
{
}
// merge all results
var atomPairList = new List <AtomPair>();
foreach (var task in tasks.Where(t => t != null && t.IsCompleted && !t.IsCanceled && !t.IsFaulted && t.Result != null && t.Result.Count > 0))
{
atomPairList.AddRange(task.Result);
}
if (sort && atomPairList != null && atomPairList.Count > 1)
{
atomPairList = atomPairList
.OrderBy(i => ProteinDataBankFileOperations.NullableTryParseInt32(i.Atom1.resSeq.FieldValue))
.ThenBy(i => ProteinDataBankFileOperations.NullableTryParseInt32(i.Atom1.serial.FieldValue))
.ThenBy(j => ProteinDataBankFileOperations.NullableTryParseInt32(j.Atom2.resSeq.FieldValue))
.ThenBy(j => ProteinDataBankFileOperations.NullableTryParseInt32(j.Atom2.serial.FieldValue))
.ToList();
}
if (useCache)
{
InteractionsCache.SavePdbInteractionCache(proteinId, atomPairList, requiredChains);
}
return(atomPairList);
}