public static UnitPoint3D CalculateAtomPosition(UnitPoint3D currentPosition,
Vector vector1,
Vector vector2,
UnitValue bondLength,
UnitValue bondAngle,
UnitValue bondTorsion)
{
// Spherical coordinates
var polarAngle = 180.To(Unit.Degree) - bondAngle;
var azimuthAngle = bondTorsion;
var atomCentricX = Math.Sin(polarAngle.In(Unit.Radians)) * Math.Cos(azimuthAngle.In(Unit.Radians));
var atomCentricY = Math.Sin(polarAngle.In(Unit.Radians)) * Math.Sin(azimuthAngle.In(Unit.Radians));
var atomCentricZ = Math.Cos(polarAngle.In(Unit.Radians));
var atomicBondVector = new Vector3D(atomCentricX, atomCentricY, atomCentricZ);
var zAxis = vector1.Normalize().ToVector3D();
var xAxis = -(vector2 - vector2.ProjectOnto(zAxis)).Normalize().ToVector3D();
var yAxis = zAxis.CrossProduct(xAxis);
var transformMatrix = new Matrix3X3();
transformMatrix.SetColumn(0, xAxis.Data);
transformMatrix.SetColumn(1, yAxis.Data);
transformMatrix.SetColumn(2, zAxis.Data);
var bondVector = new Vector3D(transformMatrix.Data.Multiply(atomicBondVector.Data.ConvertToMatrix()).Vectorize());
var atomPosition = currentPosition + bondLength * bondVector;
return(atomPosition);
}
public static Point3D In(this UnitPoint3D unitPoint, CompoundUnit targetUnit)
{
var multiplier = new UnitValue(unitPoint.Unit, 1).In(targetUnit);
return(new Point3D(
multiplier * unitPoint.X,
multiplier * unitPoint.Y,
multiplier * unitPoint.Z));
}
public static Point3D In(this UnitPoint3D unitPoint, SIPrefix targetSIPrefix, IUnitDefinition targetUnit)
{
var multiplier = new UnitValue(unitPoint.Unit, 1).In(targetSIPrefix, targetUnit);
return(new Point3D(
multiplier * unitPoint.X,
multiplier * unitPoint.Y,
multiplier * unitPoint.Z));
}
public static void Position(IList <ApproximatedAminoAcid> aminoAcids, UnitPoint3D startPosition)
{
ApproximatedAminoAcid lastAminoAcid = null;
foreach (var aminoAcid in aminoAcids)
{
PositionAminoAcid(aminoAcid, lastAminoAcid, startPosition);
lastAminoAcid = aminoAcid;
}
}
private UnitPoint3D CalculateCenter(List <ApproximatedAminoAcid> aminoAcids)
{
var center = new UnitPoint3D(Unit.Meter, 0, 0, 0);
foreach (var aminoAcid in aminoAcids)
{
center += aminoAcid.CarbonAlphaPosition;
}
return((1.0 / aminoAcids.Count) * center);
}
private static bool CollidesWithExistingPositions(UnitPoint3D position, List <Point3D> otherPositions, out UnitValue distanceToClosest)
{
var positionInPicoMeter = position.In(SIPrefix.Pico, Unit.Meter);
var closestOther = otherPositions
.Take(otherPositions.Count - 1)
.MinimumItem(p => p.DistanceTo(positionInPicoMeter));
var distance = closestOther.DistanceTo(positionInPicoMeter);
distanceToClosest = distance.To(SIPrefix.Pico, Unit.Meter);
return(distance < 390);
}
private UnitVector3D CalculateBondLengthForce(UnitPoint3D atom1Position, UnitPoint3D atom2Position, UnitValue equilibriumBondLength)
{
// Settings
const double BondSpringConstant = 1e4;
var atomDistance = atom1Position.DistanceTo(atom2Position);
var deviationFromEquilibrium = atomDistance - equilibriumBondLength;
var forceMagnitude = (BondSpringConstant * deviationFromEquilibrium.In(Unit.Meter)).To(Unit.Newton);
var forceDirection = atom1Position.VectorTo(atom2Position).Normalize().ToVector3D();
return(forceMagnitude * forceDirection);
}
public static UnitVector3D VectorTo(this UnitPoint3D unitPoint1, UnitPoint3D unitPoint2)
{
#if CHECK_UNITS
if (unitPoint1.Unit != unitPoint2.Unit)
{
throw new InvalidOperationException($"Cannot calculate vector between points with different units, got {unitPoint1.Unit} and {unitPoint2.Unit}");
}
#endif
var commonUnit = unitPoint1.Unit;
var vector = unitPoint1.VectorTo((Point3D)unitPoint2);
return(vector.To(commonUnit));
}
public static UnitValue DistanceTo(this UnitPoint3D unitPoint1, UnitPoint3D unitPoint2)
{
#if CHECK_UNITS
if (unitPoint1.Unit != unitPoint2.Unit)
{
throw new InvalidOperationException($"Cannot calculate distance between points with different units, got {unitPoint1.Unit} and {unitPoint2.Unit}");
}
#endif
var commonUnit = unitPoint1.Unit;
var distance = unitPoint1.DistanceTo((Point3D)unitPoint2);
return(distance.To(commonUnit));
}
public static UnitValue Calculate(UnitPoint3D point1,
UnitPoint3D point2,
UnitPoint3D point3,
UnitPoint3D point4)
{
var vector1 = point1.VectorTo(point2).Normalize().ToVector3D();
var vector2 = point2.VectorTo(point3).Normalize().ToVector3D();
var vector3 = point3.VectorTo(point4).Normalize().ToVector3D();
var plane12Normal = vector1.CrossProduct(vector2);
var plane23Normal = vector2.CrossProduct(vector3);
var angle = plane12Normal.AngleWith(plane23Normal);
var sign = vector3.DotProduct(plane12Normal) > 0 ? 1 : -1;
return(sign * angle);
}
public static void PositionAminoAcid(ApproximatedAminoAcid aminoAcid,
ApproximatedAminoAcid lastAminoAcid = null,
UnitPoint3D startPosition = null)
{
if (lastAminoAcid == null && startPosition == null)
{
throw new ArgumentNullException("Either last amino acid or start position must be non-null");
}
var nitrogenCarbonDistance = PeriodicTable.GetCovalentRadius(ElementName.Nitrogen) +
PeriodicTable.GetCovalentRadius(ElementName.Carbon);
var CaCDistance = 2 * PeriodicTable.GetCovalentRadius(ElementName.Carbon);
UnitPoint3D carbonPosition;
UnitPoint3D carbonAlphaPosition;
Vector3D carbonAlphaCarbonBondDirection;
Vector3D nitrogenCarbonAlphaBondDirection;
if (lastAminoAcid == null)
{
carbonPosition = startPosition;
carbonAlphaPosition = startPosition + new UnitPoint3D(SIPrefix.Pico, Unit.Meter, -CaCDistance.In(SIPrefix.Pico, Unit.Meter), 0, 0);
carbonAlphaCarbonBondDirection = carbonAlphaPosition.VectorTo(carbonPosition);
nitrogenCarbonAlphaBondDirection = new Vector3D(0, 1, 0);
}
else
{
carbonPosition = lastAminoAcid.CarbonPosition;
carbonAlphaPosition = lastAminoAcid.CarbonAlphaPosition;
carbonAlphaCarbonBondDirection = carbonAlphaPosition
.VectorTo(carbonPosition);
nitrogenCarbonAlphaBondDirection = lastAminoAcid.NitrogenPosition
.VectorTo(carbonAlphaPosition);
}
var omega = aminoAcid.OmegaAngle ?? Math.PI.To(Unit.Radians);
var phi = aminoAcid.PhiAngle ?? 0.To(Unit.Radians);
var psi = lastAminoAcid?.PsiAngle ?? 0.To(Unit.Radians);
var nitrogenPosition = CalculateAtomPosition(carbonPosition,
carbonAlphaCarbonBondDirection,
nitrogenCarbonAlphaBondDirection,
nitrogenCarbonDistance,
AminoAcidBondAngles.CaCNAngle,
psi);
carbonAlphaPosition = CalculateAtomPosition(nitrogenPosition,
carbonPosition.VectorTo(nitrogenPosition),
carbonAlphaCarbonBondDirection,
nitrogenCarbonDistance,
AminoAcidBondAngles.CNCaAngle,
omega);
carbonPosition = CalculateAtomPosition(carbonAlphaPosition,
nitrogenPosition.VectorTo(carbonAlphaPosition),
carbonPosition.VectorTo(nitrogenPosition),
CaCDistance,
AminoAcidBondAngles.NCaCAngle,
phi);
aminoAcid.NitrogenPosition = nitrogenPosition;
aminoAcid.CarbonAlphaPosition = carbonAlphaPosition;
aminoAcid.CarbonPosition = carbonPosition;
if (aminoAcid.OmegaAngle == null)
{
aminoAcid.OmegaAngle = omega;
}
if (aminoAcid.PhiAngle == null)
{
aminoAcid.PhiAngle = phi;
}
if (lastAminoAcid != null && lastAminoAcid.PsiAngle == null)
{
lastAminoAcid.PsiAngle = psi;
}
}
public static Point3D In(this UnitPoint3D unitPoint, IUnitDefinition targetUnit)
{
return(unitPoint.In(SIPrefix.None, targetUnit));
}
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);
}
