public static Dictionary <AminoAcidReference, AminoAcidAngles> MeasureAngles(Peptide peptide)
{
var measurements = new Dictionary <AminoAcidReference, AminoAcidAngles>();
AminoAcidAngles lastAngles = null;
UnitPoint3D lastNitrogenPosition = null;
UnitPoint3D lastCarbonAlphaPosition = null;
UnitPoint3D lastCarbonPosition = null;
foreach (var aminoAcid in peptide.AminoAcids)
{
PdbAminoAcidAtomNamer.AssignNames(aminoAcid);
var nitrogen = aminoAcid.GetAtomFromName("N");
var carbonAlpha = aminoAcid.GetAtomFromName("CA");
var carbon = aminoAcid.GetAtomFromName("C");
var nitrogenPosition = nitrogen != null && nitrogen.IsPositionFixed
? nitrogen.Position
: null;
var carbonAlphaPosition = carbonAlpha != null && carbonAlpha.IsPositionFixed
? carbonAlpha.Position
: null;
var carbonPosition = carbon != null && carbon.IsPositionFixed
? carbon.Position
: null;
if (lastAngles != null &&
lastNitrogenPosition != null &&
lastCarbonAlphaPosition != null &&
lastCarbonPosition != null &&
nitrogenPosition != null)
{
var psi = DihedralAngleCalculator.Calculate(
lastNitrogenPosition,
lastCarbonAlphaPosition,
lastCarbonPosition,
nitrogenPosition);
lastAngles.Psi = psi;
}
UnitValue omega = null;
if (lastCarbonAlphaPosition != null &&
lastCarbonPosition != null &&
nitrogenPosition != null &&
carbonAlphaPosition != null)
{
omega = DihedralAngleCalculator.Calculate(
lastCarbonAlphaPosition,
lastCarbonPosition,
nitrogenPosition,
carbonAlphaPosition);
}
UnitValue phi = null;
if (lastCarbonPosition != null &&
nitrogenPosition != null &&
carbonAlphaPosition != null &&
carbonPosition != null)
{
phi = DihedralAngleCalculator.Calculate(
lastCarbonPosition,
nitrogenPosition,
carbonAlphaPosition,
carbonPosition);
}
var angles = new AminoAcidAngles
{
Omega = omega,
Phi = phi
};
measurements.Add(aminoAcid, angles);
lastNitrogenPosition = nitrogenPosition;
lastCarbonAlphaPosition = carbonAlphaPosition;
lastCarbonPosition = carbonPosition;
lastAngles = angles;
}
return(measurements);
}
public static Dictionary <ApproximatedAminoAcid, AminoAcidAngles> MeasureAngles(ApproximatePeptide peptide)
{
var measurements = new Dictionary <ApproximatedAminoAcid, AminoAcidAngles>();
AminoAcidAngles lastAngles = null;
UnitPoint3D lastNitrogenPosition = null;
UnitPoint3D lastCarbonAlphaPosition = null;
UnitPoint3D lastCarbonPosition = null;
foreach (var aminoAcid in peptide.AminoAcids)
{
var nitrogenPosition = aminoAcid.NitrogenPosition;
var carbonAlphaPosition = aminoAcid.CarbonAlphaPosition;
var carbonPosition = aminoAcid.CarbonPosition;
if (lastAngles != null &&
lastNitrogenPosition != null &&
lastCarbonAlphaPosition != null &&
lastCarbonPosition != null &&
nitrogenPosition != null)
{
var psi = DihedralAngleCalculator.Calculate(
lastNitrogenPosition,
lastCarbonAlphaPosition,
lastCarbonPosition,
nitrogenPosition);
lastAngles.Psi = psi;
}
UnitValue omega = null;
if (lastCarbonAlphaPosition != null &&
lastCarbonPosition != null &&
nitrogenPosition != null &&
carbonAlphaPosition != null)
{
omega = DihedralAngleCalculator.Calculate(
lastCarbonAlphaPosition,
lastCarbonPosition,
nitrogenPosition,
carbonAlphaPosition);
}
UnitValue phi = null;
if (lastCarbonPosition != null &&
nitrogenPosition != null &&
carbonAlphaPosition != null &&
carbonPosition != null)
{
phi = DihedralAngleCalculator.Calculate(
lastCarbonPosition,
nitrogenPosition,
carbonAlphaPosition,
carbonPosition);
}
var angles = new AminoAcidAngles
{
Omega = omega,
Phi = phi
};
measurements.Add(aminoAcid, angles);
lastNitrogenPosition = nitrogenPosition;
lastCarbonAlphaPosition = carbonAlphaPosition;
lastCarbonPosition = carbonPosition;
lastAngles = angles;
}
return(measurements);
}
