private string GetCachedFilename(string distributionFilePath)
{
var directory = Path.GetDirectoryName(distributionFilePath);
if (directory == null)
{
return(Path.Combine("Cache", AminoAcidName.ToThreeLetterCode() + ".csv"));
}
return(Path.Combine(
directory,
"Cache",
AminoAcidName.ToThreeLetterCode() + ".csv"));
}
public RamachandranPlotGridGradientDistribution(AminoAcidName aminoAcidName, string distributionFilePath, int gridSteps = 360)
{
AminoAcidName = aminoAcidName;
this.gridSteps = gridSteps;
var distributionCacheFilename = GetCachedFilename(distributionFilePath);
try
{
GradientPlot = LoadGradientGrid(distributionCacheFilename);
}
catch (Exception)
{
var angles = RamachandranPlotFileSource.ParseRamachadranPlotFile(distributionFilePath);
GradientPlot = GenerateGradientPlot(angles);
StoreDistibutionPlot(distributionCacheFilename);
}
}
public IRamachandranPlotGradientDistribution GetDistribution(AminoAcidName aminoAcidName)
{
return(distribution);
}
public static AminoAcidReference Get(AminoAcidName aminoAcidCode, int sequenceNumber)
{
switch (aminoAcidCode)
{
case AminoAcidName.Isoleucine:
return(Isoleucine(sequenceNumber));
case AminoAcidName.Leucine:
return(Leucine(sequenceNumber));
case AminoAcidName.Valine:
return(Valine(sequenceNumber));
case AminoAcidName.Phenylalanine:
return(Phenylalanine(sequenceNumber));
case AminoAcidName.Methionine:
return(Methionine(sequenceNumber));
case AminoAcidName.Cysteine:
return(Cysteine(sequenceNumber));
case AminoAcidName.Alanine:
return(Alanine(sequenceNumber));
case AminoAcidName.Glycine:
return(Glycine(sequenceNumber));
case AminoAcidName.Proline:
return(Proline(sequenceNumber));
case AminoAcidName.Threonine:
return(Threonine(sequenceNumber));
case AminoAcidName.Serine:
return(Serine(sequenceNumber));
case AminoAcidName.Tyrosine:
return(Tyrosine(sequenceNumber));
case AminoAcidName.Tryptophan:
return(Tryptophan(sequenceNumber));
case AminoAcidName.Glutamine:
return(Glutamine(sequenceNumber));
case AminoAcidName.Asparagine:
return(Asparagine(sequenceNumber));
case AminoAcidName.Histidine:
return(Histidine(sequenceNumber));
case AminoAcidName.GlutamicAcid:
return(GlutamicAcid(sequenceNumber));
case AminoAcidName.AsparticAcid:
return(AsparticAcid(sequenceNumber));
case AminoAcidName.Lysine:
return(Lysine(sequenceNumber));
case AminoAcidName.Arginine:
return(Arginine(sequenceNumber));
default:
throw new ArgumentOutOfRangeException(nameof(aminoAcidCode), $"Unknown amino acid code '{aminoAcidCode}'");
}
}
public RamachandranPlotFixedDistribution(AminoAcidName aminoAcidName, UnitPoint2D targetPhiPsi)
{
targetPhi = targetPhiPsi.In(Unit.Degree).X.To(Unit.Degree);
targetPsi = targetPhiPsi.In(Unit.Degree).Y.To(Unit.Degree);
AminoAcidName = aminoAcidName;
}
public AminoAcidCannotBePositionedException(AminoAcidName aminoAcidName,
int sequenceNumber)
{
AminoAcidName = aminoAcidName;
SequenceNumber = sequenceNumber;
}
public static string ToThreeLetterCode(this AminoAcidName aminoAcidName)
{
return(AminoAcidThreeLetterMap[aminoAcidName]);
}
public static char ToOneLetterCode(this AminoAcidName aminoAcidName)
{
return(AminoAcidOneLetterCodeMap[aminoAcidName]);
}
public AminoAcidReference(AminoAcidName aminoAcidName, int sequenceNumber, MoleculeReference moleculeReference)
: this(aminoAcidName, sequenceNumber, moleculeReference.Molecule, moleculeReference.VertexIds, moleculeReference.FirstAtomId, moleculeReference.LastAtomId)
{
}
public AminoAcidReference(AminoAcidName name, int sequenceNumber, Molecule molecule, IEnumerable <uint> vertexIds, uint firstAtomId, uint lastAtomId)
: base(molecule, vertexIds, firstAtomId, lastAtomId)
{
Name = name;
SequenceNumber = sequenceNumber;
}
public RamachandranPlot Get(AminoAcidName aminoAcidName)
{
return(ramachandranPlots[aminoAcidName]);
}
private ApproximatedAminoAcid(long id, AminoAcidName aminoAcidName, int sequenceNumber)
{
Id = id;
Name = aminoAcidName;
SequenceNumber = sequenceNumber;
}
public ApproximatedAminoAcid(AminoAcidName aminoAcidName, int sequenceNumber)
{
Id = Interlocked.Increment(ref lastId);
Name = aminoAcidName;
SequenceNumber = sequenceNumber;
}
