// public static bool isInCone(OBVector3 x, OBVector3 apex, OBVector3 axis, double aperture )
// {
// //got it from here:http://stackoverflow.com/questions/10768142/verify-if-point-is-inside-a-cone-in-3d-space
// //test if point x is inside an infinite cone defined by apex point with normal vector axis and aperture angle(in radians)
// double halfAperture=aperture/2;
// OBVector3 apexToXVect = OBVector3(apex,x);
// OBVector3.
// bool insideCone = StarMath.dotProduct(apex,axis)/StarMath.norm2(apexToXVect)/StarMath.norm2(axis) > Math.Cos(aperture);
// return insideCone;
// }
public static bool atomsInCarboxylateCone(OBAtom a, OBAtom carba, OBMol mol)
{
//angle should probably not be hardcoded
double aperture = 120 * Math.PI / 180;
double[] axis = obvec2dubs(OBVector3.Sub(carba.GetVector(), a.GetVector()));
//axis = StarMath.divide (axis, StarMath.norm2 (axis));
double[] apex = obvec2dubs(carba.GetVector());
List <uint> exclude = new List <uint>();
exclude.Add(carba.GetIdx());
foreach (OBBond b in carba.Bonds())
{
OBAtom other = b.GetNbrAtom(carba);
if (other != a)
{
exclude.Add(other.GetIdx());
}
}
foreach (OBAtom n in mol.Atoms())
{
if (!exclude.Contains(n.GetIdx()))
{
double[] x = obvec2dubs(n.GetVector());
//if any point is found to be in the carboxylate's cone, return true
if (isInCone(x, apex, axis, aperture))
{
return(true);
}
}
}
return(false);
}
public static double atomdist(OBAtom a0, OBAtom a1)
{
OBVector3 disp = OBVector3.Sub(a0.GetVector(), a1.GetVector());
double x = disp.GetX();
double y = disp.GetY();
double z = disp.GetZ();
double dist = Math.Sqrt(x * x + y * y + z * z);
return(dist);
}
public static double pairwiseangle(OBAtom carbon1, OBAtom a1, OBAtom carbon2, OBAtom a2)
{
//carbon1 and carbon2 are carbon atoms connected to oxygen
//a1 and a2 connect to carbon1 and carbon2 respectively
OBVector3 vec1 = OBVector3.Sub(carbon1.GetVector(), a1.GetVector());
OBVector3 vec2 = OBVector3.Sub(carbon2.GetVector(), a2.GetVector());
double angle = angle_between_vectors(vec1, vec2);
return(angle);
}
public static OBMol connect_within_radius(OBMol mol, OBAtom n, double radius)
{
foreach (OBAtom a in mol.Atoms())
{
if (a.GetIdx() == n.GetIdx())
{
continue;
}
else
{
double len = Math.Round(StarMath.norm2(obvec2dubs(OBVector3.Sub(a.GetVector(), n.GetVector()))),
7); //gets length
if (len <= radius)
{
mol.AddBond((int)a.GetIdx(), (int)n.GetIdx(), 1);
}
}
}
return(mol);
}
public static OBMol merge_atoms_at_same_location(OBMol mol)
{
double radius = 0.1;
//when we make a unit_cell by copy and pasting base cases we end up with atoms at the same location that need to be merged
//assumes only two atoms overlap at a time
Dictionary <int, int> tomerge = new Dictionary <int, int>();
foreach (OBAtom a in mol.Atoms())
{
if (!tomerge.ContainsKey((int)a.GetIdx()))
{
foreach (OBAtom b in mol.Atoms())
{
if (a.GetIdx() == b.GetIdx())
{
continue;
}
else
{
double len =
Math.Round(StarMath.norm2(obvec2dubs(OBVector3.Sub(a.GetVector(), b.GetVector()))),
7); //gets length
if (len <= radius)
{
tomerge.Add((int)b.GetIdx(), (int)a.GetIdx());
}
}
}
}
}
int atomsdeleted = 0;
foreach (int key in tomerge.Keys)
{
mol = molecule_merge(mol, mol.GetAtom(key - atomsdeleted), mol.GetAtom(tomerge[key] - atomsdeleted));
atomsdeleted++;
}
return(mol);
}
public static double greatest_axial_distance(OBMol mol, OBAtom carbon1, OBAtom a1)
{
//finds the distance of the most distant atom along the axis defined by the carboxyl defined by carbon 1 and a1
double[] vec = obvec2dubs(OBVector3.Sub(carbon1.GetVector(), a1.GetVector()));
vec = StarMath.normalize(vec);
double maxd = 0;
foreach (OBAtom a in mol.Atoms())
{
if (a == carbon1)
{
continue;
}
double d = StarMath.dotProduct(vec,
obvec2dubs(OBVector3.Sub(carbon1.GetVector(),
a.GetVector()))); // get pairwise axial distance by taking the scalar projection of the carbon's position to atom A
if (d > maxd)
{
maxd = d;
}
}
return(maxd);
}