public static ATOM_Record FindAtomInsideSingularInteractionsChain(ProteinChainListContainer singularAaToAaInteractions, int chainIndex, int residueSequenceIndex)
{
if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(singularAaToAaInteractions))
{
return(null);
}
if (ParameterValidation.IsChainIndexInvalid(chainIndex))
{
throw new ArgumentOutOfRangeException(nameof(chainIndex));
}
if (ParameterValidation.IsResidueSequenceIndexInvalid(residueSequenceIndex, true))
{
throw new ArgumentOutOfRangeException(nameof(residueSequenceIndex));
}
// Loop through atoms in specified chain to find atom with given residue sequence index
for (int atomIndex = 0; atomIndex < singularAaToAaInteractions.ChainList[chainIndex].AtomList.Count; atomIndex++)
{
ATOM_Record atom = singularAaToAaInteractions.ChainList[chainIndex].AtomList[atomIndex];
if (ProteinDataBankFileOperations.NullableTryParseInt32(atom.resSeq.FieldValue) == residueSequenceIndex)
{
return(atom);
}
}
return(null);
}
public static ATOM_Record FindAtomInsidePdbFileChain(ProteinChainListContainer pdbFileChains, int chainIndex, int residueSequenceIndex)
{
if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(pdbFileChains))
{
return(null);
}
if (ParameterValidation.IsChainIndexInvalid(chainIndex))
{
throw new ArgumentOutOfRangeException(nameof(chainIndex));
}
if (ParameterValidation.IsResidueSequenceIndexInvalid(residueSequenceIndex, true))
{
throw new ArgumentOutOfRangeException(nameof(residueSequenceIndex));
}
for (int memberIndex = 0; memberIndex < pdbFileChains.ChainList[chainIndex].AtomList.Count; memberIndex++)
{
ATOM_Record atom = pdbFileChains.ChainList[chainIndex].AtomList[memberIndex];
if (ProteinDataBankFileOperations.NullableTryParseInt32(atom.resSeq.FieldValue) == residueSequenceIndex)
{
return(atom);
}
}
return(null);
}
/// <summary>
/// Get the lowest (minimum) and highest (maximum) residue sequence index (as found in the pdb file) in an interaction
/// proteinInterface.
/// </summary>
/// <param name="proteinInterface"></param>
/// <param name="singularAaToAaInteractions"></param>
/// <param name="chainIndex"></param>
/// <returns></returns>
public static MinMax MinMaxResidueSequenceIndex(ClusteringFullResultListContainer.Chain.Stage.Cluster proteinInterface, ProteinChainListContainer singularAaToAaInteractions, int chainIndex)
{
if (ParameterValidation.IsClusterNullOrEmpty(proteinInterface))
{
throw new ArgumentNullException(nameof(proteinInterface));
}
if (ParameterValidation.IsProteinChainListContainerNullOrEmpty(singularAaToAaInteractions))
{
throw new ArgumentNullException(nameof(singularAaToAaInteractions));
}
if (ParameterValidation.IsChainIndexInvalid(chainIndex))
{
throw new ArgumentOutOfRangeException(nameof(chainIndex));
}
int proteinInterfaceMin = 0;
int proteinInterfaceMax = 0;
for (int memberIndex = 0; memberIndex < proteinInterface.AtomIndexList.Count; memberIndex++)
{
int member = proteinInterface.AtomIndexList[memberIndex];
ATOM_Record atom = singularAaToAaInteractions.ChainList[chainIndex].AtomList[member];
var residueSequenceIndex = ProteinDataBankFileOperations.NullableTryParseInt32(atom.resSeq.FieldValue);
if (residueSequenceIndex == null)
{
continue;
}
if (memberIndex == 0 || residueSequenceIndex < proteinInterfaceMin)
{
proteinInterfaceMin = residueSequenceIndex.Value;
}
if (memberIndex == 0 || residueSequenceIndex > proteinInterfaceMax)
{
proteinInterfaceMax = residueSequenceIndex.Value;
}
}
return(new MinMax(proteinInterfaceMin, proteinInterfaceMax));
}