public Atom(int protons, int neutrons)
{
Protons = protons;
Neutrons = neutrons;
Element = ElementMap.FromProtonCount(Protons);
Period = PeriodicTable.GetPeriod(Element);
Mass = AtomPropertyCalculator.CalculateMass(Protons, Neutrons);
Radius = PeriodicTable.GetCovalentRadius(Element);
ElectroNegativity = PeriodicTable.ElectroNegativity(Element);
FormalCharge = 0 * PhysicalConstants.ElementaryCharge;
EffectiveCharge = FormalCharge;
}
private static double[] Extents(IAtomContainer container, double[][] coords, bool withRadii)
{
double xmax = -1e30;
double ymax = -1e30;
double zmax = -1e30;
double xmin = 1e30;
double ymin = 1e30;
double zmin = 1e30;
int natom = container.Atoms.Count;
for (int i = 0; i < natom; i++)
{
var coord = new double[coords[0].Length];
Array.Copy(coords[i], 0, coord, 0, coords[0].Length);
if (withRadii)
{
var atom = container.Atoms[i];
var radius = PeriodicTable.GetCovalentRadius(atom.Symbol).Value;
xmax = Math.Max(xmax, coord[0] + radius);
ymax = Math.Max(ymax, coord[1] + radius);
zmax = Math.Max(zmax, coord[2] + radius);
xmin = Math.Min(xmin, coord[0] - radius);
ymin = Math.Min(ymin, coord[1] - radius);
zmin = Math.Min(zmin, coord[2] - radius);
}
else
{
xmax = Math.Max(xmax, coord[0]);
ymax = Math.Max(ymax, coord[1]);
zmax = Math.Max(zmax, coord[2]);
xmin = Math.Min(xmin, coord[0]);
ymin = Math.Min(ymin, coord[1]);
zmin = Math.Min(zmin, coord[2]);
}
}
var ranges = new double[3];
ranges[0] = xmax - xmin;
ranges[1] = ymax - ymin;
ranges[2] = zmax - zmin;
return(ranges);
}
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 UnitValue CalculateApproximate(ElementName element1, ElementName element2)
{
return(PeriodicTable.GetCovalentRadius(element1) + PeriodicTable.GetCovalentRadius(element2));
}
