public void IncrementAminoAcidCount(char aminoAcidCode, decimal incrementValue = 1)
{
if (!ParameterValidation.IsAminoAcidCodeValid(aminoAcidCode))
{
throw new ArgumentOutOfRangeException(nameof(aminoAcidCode));
}
IncrementAminoAcidCount(AminoAcidConversions.AminoAcidNameToNumber(aminoAcidCode), incrementValue);
}
/// <summary>
/// This method finds the PDB ID from a PDB file's filename.
/// </summary>
/// <param name="pdbFilename"></param>
/// <returns></returns>
public static string PdbIdFromPdbFilename(string pdbFilename)
{
const int proteinIdLength = 4;
if (string.IsNullOrWhiteSpace(pdbFilename))
{
throw new ArgumentOutOfRangeException(nameof(pdbFilename), pdbFilename, "parameter was " + ParameterValidation.NullEmptyOrWhiteSpaceToString(pdbFilename));
}
var proteinId = Path.GetFileNameWithoutExtension(pdbFilename).Trim();
if (proteinId.Length > proteinIdLength)
{
proteinId = proteinId.Substring(3);//.Replace("pdb", "");
}
if (proteinId.Length != proteinIdLength)
{
throw new ArgumentException("PDB ID could not be extracted from parameter pdbFilename", nameof(pdbFilename));
}
return(proteinId.ToUpperInvariant());
}
/// <summary>
/// This method loads 1 pdb file and returns the atoms contained in the different chains.
/// </summary>
/// <param name="pdbFilename"></param>
/// <param name="chainIdWhiteList"></param>
/// <param name="minimumChains"></param>
/// <param name="maximumChains"></param>
/// <returns></returns>
public static ProteinChainListContainer PdbAtomicChains(string pdbFilename, string[] chainIdWhiteList, int minimumChains = 2, int maximumChains = 2, bool onlyCarbonAlphas = false)
{
////////Console.WriteLine(pdbFilename);
// Check file exists.
if (!File.Exists(pdbFilename))
{
//return null;
throw new FileNotFoundException("File not found", pdbFilename);
}
// Check min chains not more than max chains.
if (minimumChains > maximumChains)
{
throw new ArgumentOutOfRangeException(nameof(minimumChains));
}
// Load pdb/protein file, excluding all records but ATOM, HETATM and TER.
var proteinDataBankFile = new ProteinDataBankFile(pdbFilename, new[]
{
ATOM_Record.ATOM_Field.FieldName,
HETATM_Record.HETATM_Field.FieldName,
TER_Record.TER_Field.FieldName,
MODEL_Record.MODEL_Field.FieldName,
ENDMDL_Record.ENDMDL_Field.FieldName
});
// Make new array for atom chain.
//List<ATOM_Record>[] proteinFileChains = new List<ATOM_Record>[maximumChains];
var pdbFileChains = new ProteinChainListContainer();
//var fileError = false;
//var chainCount = 0;
// Loop through all the previously loaded protein file records to make lists of atoms in each chain.
// Also make a list of residue numbers (which will be sorted later just in case it is out of order).
var atomRecordListDictionary = new Dictionary <string, List <ProteinDataBankFileRecord> >();
var hetAtomRecordListDictionary = new Dictionary <string, List <ProteinDataBankFileRecord> >();
int terCount = 0;
for (int proteinDataBankFileRecordIndex = 0; proteinDataBankFileRecordIndex < proteinDataBankFile.Count; proteinDataBankFileRecordIndex++)
{
ProteinDataBankFileRecord currentRecord = proteinDataBankFile.NextRecord();
if (currentRecord == null)
{
continue;
}
if (currentRecord.GetType() == typeof(ATOM_Record))
{
var atom = (ATOM_Record)currentRecord;
if (onlyCarbonAlphas && atom.name.FieldValue.Trim().ToUpperInvariant() != StaticValues.CarbonAlpha)
{
continue;
}
string chainIdKey = atom.chainID.FieldValue.Trim().ToUpperInvariant();
if (chainIdWhiteList != null && !chainIdWhiteList.Contains(chainIdKey))
{
continue;
}
if (!atomRecordListDictionary.ContainsKey(chainIdKey))
{
atomRecordListDictionary.Add(chainIdKey, new List <ProteinDataBankFileRecord>());
}
if (ParameterValidation.IsAminoAcidCodeValid(atom.resName.FieldValue))
{
atomRecordListDictionary[chainIdKey].Add(atom);
}
}
else if (currentRecord.GetType() == typeof(HETATM_Record))
{
var hetatm = (HETATM_Record)currentRecord;
if (onlyCarbonAlphas && hetatm.name.FieldValue.Trim().ToUpperInvariant() != StaticValues.CarbonAlpha)
{
continue;
}
string chainIdKey = hetatm.chainID.FieldValue.Trim().ToUpperInvariant();
if (chainIdWhiteList != null && !chainIdWhiteList.Contains(chainIdKey))
{
continue;
}
if (!hetAtomRecordListDictionary.ContainsKey(chainIdKey))
{
hetAtomRecordListDictionary.Add(chainIdKey, new List <ProteinDataBankFileRecord>());
}
//if (!ParameterValidation.IsAminoAcidCodeValid(hetatm.resName.FieldValue))
//{
// ////////Console.WriteLine(hetatm.columnFormatLine);
// hetatm.resName.FieldValue = UnspecifiedOrUnknownAminoAcid.Code3L;
// hetatm.columnFormatLine = hetatm.columnFormatLine.Remove(ProteinDataBankFile.HETATM_Record.resName_Field.FirstColumn - 1, (ProteinDataBankFile.HETATM_Record.resName_Field.LastColumn - ProteinDataBankFile.HETATM_Record.resName_Field.FirstColumn) + 1);
// hetatm.columnFormatLine = hetatm.columnFormatLine.Insert(ProteinDataBankFile.HETATM_Record.resName_Field.FirstColumn - 1, UnspecifiedOrUnknownAminoAcid.Code3L);
// ////////Console.WriteLine(hetatm.columnFormatLine);
//}
if (ParameterValidation.IsAminoAcidCodeValid(hetatm.resName.FieldValue))
{
hetAtomRecordListDictionary[chainIdKey].Add(hetatm);
}
}
else if (currentRecord.GetType() == typeof(TER_Record))
{
var ter = (TER_Record)currentRecord;
string chainIdKey = ter.chainID.FieldValue.Trim().ToUpperInvariant();
if (chainIdWhiteList != null && !chainIdWhiteList.Contains(chainIdKey))
{
continue;
}
terCount++;
if (terCount >= maximumChains)
{
break;
//return null;
}
}
else if (currentRecord.GetType() == typeof(ENDMDL_Record))
{
break;
}
}
// file has been parsed so clear used file data from memory as soon as possible
proteinDataBankFile.UnloadFile();
int totalChains = atomRecordListDictionary.Count > hetAtomRecordListDictionary.Count ? atomRecordListDictionary.Count : hetAtomRecordListDictionary.Count;
for (int chainIndex = 0; chainIndex < totalChains; chainIndex++)
{
pdbFileChains.ChainList.Add(new ProteinAtomListContainer());
}
atomRecordListDictionary = atomRecordListDictionary.OrderBy(a => a.Key).ToDictionary(a => a.Key, a => a.Value);
int chainIndex2 = -1;
foreach (var atomRecordListKvp in atomRecordListDictionary)
{
chainIndex2++;
string chainName = atomRecordListKvp.Key;
List <ProteinDataBankFileRecord> chainRecords = atomRecordListKvp.Value;
if (chainRecords == null || chainRecords.Count == 0)
{
continue;
}
chainRecords = chainRecords.OrderBy(a => NullableTryParseInt32(((ATOM_Record)a).serial.FieldValue)).ToList();
pdbFileChains.ChainList[chainIndex2].AtomList = chainRecords.Select(a => (ATOM_Record)a).ToList();
}
hetAtomRecordListDictionary = hetAtomRecordListDictionary.OrderBy(a => a.Key).ToDictionary(a => a.Key, a => a.Value);
int chainIndex3 = -1;
foreach (var hetAtomRecordListKvp in hetAtomRecordListDictionary)
{
chainIndex3++;
string chainName = hetAtomRecordListKvp.Key;
List <ProteinDataBankFileRecord> chainRecords = hetAtomRecordListKvp.Value;
if (chainRecords == null || chainRecords.Count == 0)
{
continue;
}
chainRecords = chainRecords.OrderBy(a => NullableTryParseInt32(((HETATM_Record)a).serial.FieldValue)).ToList();
foreach (ProteinDataBankFileRecord proteinDataBankFileRecord in chainRecords)
{
var chainRecord = (HETATM_Record)proteinDataBankFileRecord;
string residueSequenceToFind = chainRecord.resSeq.FieldValue;
string atomChainId = chainRecord.chainID.FieldValue.Trim().ToUpperInvariant();
if (!atomRecordListDictionary.ContainsKey(atomChainId) || atomRecordListDictionary[atomChainId].Count(a => ((ATOM_Record)a).resSeq.FieldValue == residueSequenceToFind) == 0)
{
ATOM_Record atom = ConvertHetatmRecordToAtomRecord(chainRecord);
pdbFileChains.ChainList[chainIndex3].AtomList.Add(atom);
}
}
}
int nonEmptyChainCount = pdbFileChains.ChainList.Count(a => a != null && a.AtomList != null && a.AtomList.Count > 0);
if (nonEmptyChainCount >= minimumChains && nonEmptyChainCount <= maximumChains)
{
return(pdbFileChains);
}
////////Console.WriteLine("Too many chains (" + nonEmptyChainCount + "): " + pdbFilename);
return(null);
}
