private AminoAcidAngles GetAnglesFromGridPosition(Point2D gridPosition)
{
var angles = new AminoAcidAngles
{
Omega = 180.To(Unit.Degree),
Phi = (360 * (gridPosition.X + 0.5) / gridSteps - 180).To(Unit.Degree),
Psi = (180 - 360 * (gridPosition.Y + 0.5) / gridSteps).To(Unit.Degree)
};
return(angles);
}
private static void ApplyOmegaDeviationForce(ApproximatedAminoAcid lastAminoAcid,
ApproximatedAminoAcid aminoAcid,
AminoAcidAngles aminoAcidAngles,
Dictionary <ApproximatedAminoAcid, ApproximateAminoAcidForces> forceDictionary)
{
if (lastAminoAcid == null)
{
return;
}
var omegaDeviation = aminoAcidAngles.Omega.In(Unit.Degree) < 0
? -180 - aminoAcidAngles.Omega.In(Unit.Degree)
: 180 - aminoAcidAngles.Omega.In(Unit.Degree);
if (!forceDictionary.ContainsKey(aminoAcid))
{
forceDictionary.Add(aminoAcid, new ApproximateAminoAcidForces());
}
var aminoAcidForces = forceDictionary[aminoAcid];
if (!forceDictionary.ContainsKey(lastAminoAcid))
{
forceDictionary.Add(lastAminoAcid, new ApproximateAminoAcidForces());
}
var lastAminoAcidForces = forceDictionary[lastAminoAcid];
var carbonNitrogenVector = lastAminoAcid.CarbonPosition
.VectorTo(aminoAcid.NitrogenPosition)
.In(SIPrefix.Pico, Unit.Meter);
var previousCarbonCarbonAlphaVector = lastAminoAcid.CarbonPosition
.VectorTo(lastAminoAcid.CarbonAlphaPosition)
.In(SIPrefix.Pico, Unit.Meter);
var forceMagnitude1 = forceScaling * omegaDeviation * 1.0.To(Unit.Newton);
var forceDirection1 = previousCarbonCarbonAlphaVector
.CrossProduct(carbonNitrogenVector)
.Normalize()
.ToVector3D();
lastAminoAcidForces.CarbonAlphaForce += forceMagnitude1 * forceDirection1;
var nitrogenCarbonAlphaVector = aminoAcid.NitrogenPosition
.VectorTo(aminoAcid.CarbonAlphaPosition)
.In(SIPrefix.Pico, Unit.Meter);
var forceMagnitude2 = forceScaling * omegaDeviation * 1.0.To(Unit.Newton);
var forceDirection2 = -nitrogenCarbonAlphaVector
.CrossProduct(carbonNitrogenVector)
.Normalize()
.ToVector3D();
aminoAcidForces.CarbonAlphaForce += forceMagnitude2 * forceDirection2;
}
