public VectorProteinInterfacePart(VectorProteinInterfacePart vectorProteinInterfacePart)
: this(
vectorProteinInterfacePart.FullProteinInterfaceId,
vectorProteinInterfacePart.InteractionAminoAcids1L,
vectorProteinInterfacePart.InteractionFlagBools,
vectorProteinInterfacePart.InteractionNonProteinInterfaceAminoAcids1L,
vectorProteinInterfacePart.InteractionToNonProteinInterface,
vectorProteinInterfacePart.ResidueId,
vectorProteinInterfacePart.SourceAminoAcid1L,
vectorProteinInterfacePart.SourceAminoAcid3L
)
{
if (vectorProteinInterfacePart == null)
{
throw new ArgumentNullException(nameof(vectorProteinInterfacePart));
}
}
/*
* private static int[] LastPdbChainResidueIndexes(string pdbFilename)
* {
* //var result = new Dictionary<string,int>();
* var pdbFile = new ProteinDataBankFile(pdbFilename, new []{ ATOM_Record.ATOM_Field.FieldName });
*
* //var x = ProteinDataBankFileOperations.PdbAtomAcidList();
*
* var atomList = pdbFile.ProteinDataBankFileRecordList.Where(a => a.GetType() == typeof (ATOM_Record)).Select(a=>(ATOM_Record)a).ToList();
*
* var chainIdList = atomList.Select(a=>a.chainID.FieldValue.ToUpperInvariant()).Distinct().ToList();
*
* var result = new int[chainIdList.Count];
*
* for (int index = 0; index < chainIdList.Count; index++)
* {
* var chainId = chainIdList[index];
* var maxResidueIndex = atomList.Where(a => a.chainID.FieldValue.ToUpperInvariant() == chainId).Select(a => int.Parse(a.resSeq.FieldValue)).Max();
*
* result[index] = maxResidueIndex;
* }
*
* return result;
* }
*/
private static VectorProteinInterfaceWhole MakeVectorProteinInterfaceWhole(string pdbFilename, ProteinInterfaceSequenceAndPositionData proteinInterfaceSequenceAndPositionData, bool reversedSequence, bool reversedInteractions)
{
if (pdbFilename == null)
{
throw new ArgumentNullException(nameof(pdbFilename));
}
if (proteinInterfaceSequenceAndPositionData == null)
{
throw new ArgumentNullException(nameof(proteinInterfaceSequenceAndPositionData));
}
ProteinInterfaceAminoAcidMetaData[] proteinInterfaceAminoAcidMetaDataArray = proteinInterfaceSequenceAndPositionData.AminoAcidSequenceAllResidueSequenceIndexes;
var vectorProteinInterfaceWhole = new VectorProteinInterfaceWhole
{
FullProteinInterfaceId = new FullProteinInterfaceId(proteinInterfaceSequenceAndPositionData.FullProteinInterfaceId),
ProteinInterfaceLength = proteinInterfaceSequenceAndPositionData.ProteinInterfaceLength,
FirstResidueSequenceIndex = proteinInterfaceSequenceAndPositionData.StartPosition,
LastResidueSequenceIndex = proteinInterfaceSequenceAndPositionData.EndPosition,
ReversedInteractions = reversedInteractions,
ReversedSequence = reversedSequence,
};
//vectorProteinInterfaceWhole.FullSequenceLength = LastPdbChainResidueIndexes(pdbFilename)[vectorProteinInterfaceWhole.FullProteinInterfaceId.ChainId];
vectorProteinInterfaceWhole.SecondaryStructure = ProteinInterfaceSecondaryStructureLoader.ProteinInterfaceSecondaryStructure(pdbFilename, SpreadsheetFileHandler.AlphabetLetterRollOver(vectorProteinInterfaceWhole.FullProteinInterfaceId.ChainId), vectorProteinInterfaceWhole.FirstResidueSequenceIndex, vectorProteinInterfaceWhole.LastResidueSequenceIndex, vectorProteinInterfaceWhole.ReversedSequence);
for (int proteinInterfaceAminoAcidMetaDataArrayIndex = 0; proteinInterfaceAminoAcidMetaDataArrayIndex < proteinInterfaceAminoAcidMetaDataArray.Length; proteinInterfaceAminoAcidMetaDataArrayIndex++)
{
ProteinInterfaceAminoAcidMetaData proteinInterfaceAminoAcidMetaData = proteinInterfaceAminoAcidMetaDataArray[proteinInterfaceAminoAcidMetaDataArrayIndex];
var vectorProteinInterfacePart = new VectorProteinInterfacePart(proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions.Length)
{
FullProteinInterfaceId = new FullProteinInterfaceId(proteinInterfaceSequenceAndPositionData.FullProteinInterfaceId),
ResidueId = proteinInterfaceAminoAcidMetaDataArrayIndex,
SourceAminoAcid1L = proteinInterfaceAminoAcidMetaData.ResidueName1L,
SourceAminoAcid3L = proteinInterfaceAminoAcidMetaData.ResidueName3L,
InteractionAminoAcids1L = proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionResidueNames1L,
InteractionNonProteinInterfaceAminoAcids1L = proteinInterfaceAminoAcidMetaData.NonProteinInterfaceInteractionResidueNames1L,
InteractionFlagBools = new bool[proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions.Length]
};
vectorProteinInterfaceWhole.VectorProteinInterfacePartList.Add(vectorProteinInterfacePart);
Array.Copy(proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions, vectorProteinInterfacePart.InteractionFlagBools, proteinInterfaceAminoAcidMetaData.OppoproteinInterfaceInteractions.Length);
if (reversedInteractions)
{
Array.Reverse(vectorProteinInterfacePart.InteractionFlagBools);
}
vectorProteinInterfacePart.InteractionToNonProteinInterface = proteinInterfaceAminoAcidMetaData.ProteinInterfaceInteractionType.HasFlag(ProteinInterfaceInteractionType.InteractionWithNonProteinInterface);
}
if (vectorProteinInterfaceWhole.ReversedSequence)
{
vectorProteinInterfaceWhole.VectorProteinInterfacePartList.Reverse();
}
return(vectorProteinInterfaceWhole);
}
