//functions for making openbabel easier to work with, adding functionality that isn't in the api(also adding functionality that is in the regular api, but isn't in the C# api), and functions that make debugging less of a pain
//this is in a partial class for now, but it would be pretty useful as a library
#region functions for converting double arrays to their openbabel counterparts and vice versa
public static double[] obvec2dubs(OBVector3 a)
{
//turns a horrible obvector into a very nice double array
double[] b = { a.GetX(), a.GetY(), a.GetZ() };
return(b);
}
// 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 radial_weight(OBMol mol, OBAtom carbon1, OBAtom a1)
{
OBVector3 compos = mol_com(mol);
OBVector3 v2 = carbon1.GetVector();
OBVector3 v3 = a1.GetVector();
return(openbabel_csharp.Point2Line(compos, v2, v3));
}
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 atom2linedistance(OBAtom x0, OBAtom a1, OBAtom a2)
{
//a1 and a2 are atoms that define the axis in question, x0 is the atom that we want to know the distance from the axis
OBVector3 v0 = x0.GetVector();
OBVector3 v1 = a1.GetVector();
OBVector3 v2 = a2.GetVector();
return(openbabel_csharp.Point2Line(v0, v1, v2));
}
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 OBVector3 mol_com(OBMol mol)
{
//center of mass of molecule
OBVector3 sum = OBVector3.VZero;
double molw = 0;
foreach (OBAtom a in mol.Atoms())
{
double m = a.GetAtomicMass();
sum = OBVector3.Add(sum, OBVector3.Mul(m, a.GetVector()));
molw = molw + m;
}
return(OBVector3.Mul(1 / molw, sum));
}
public static double angle_between_vectors(OBVector3 a, OBVector3 b)
{
a = a.Normalize();
b = b.Normalize();
double dot = StarMath.dotProduct(obvec2dubs(a), obvec2dubs(b));
double angle = Math.Acos(dot) * 180 / Math.PI;
if (double.IsNaN(angle))
{
angle = Math.Acos(Convert.ToInt32(dot)) * 180 / Math.PI;
}
return(angle);
}
public static double greatest_radial_distance(OBMol mol, OBAtom carbon1, OBAtom a1)
{
OBVector3 v2 = carbon1.GetVector();
OBVector3 v3 = a1.GetVector();
double maxd = 0;
foreach (OBAtom a in mol.Atoms())
{
OBVector3 v1 = a.GetVector();
double d = openbabel_csharp.Point2Line(v1, v2, v3);
if (d > maxd)
{
maxd = d;
}
}
return(maxd);
}
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);
}
public static void trajectoryFrameToCIF(string frame, string outFile, List <int> esequence,
OBConversion obconv)
{
//converts a frame from the above function into a CIF file
//lammps trajectory files have unit cell dimension data for every frame
//requires an element sequence for identifying element type from lammps atom types
OBUnitCell uc = new OBUnitCell();
OBMol mol = new OBMol();
OBMatrix3x3 mat = new OBMatrix3x3();
using (StringReader reader = new StringReader(frame)) {
string line = "";
bool foundMatrix = false;
do
{
line = reader.ReadLine();
if (line.Contains("BOX BOUNDS"))
{
//data from lammps is in this format
//ITEM: BOX BOUNDS xy xz yz
//xlo_bound xhi_bound xy
//ylo_bound yhi_bound xz
//zlo_bound zhi_bound yz
string row0 = reader.ReadLine();
double[] row0d = OBFunctions.spacedStringToDoubleArray(row0);
double xlo = row0d[0];
double xhi = row0d[1];
double xy = row0d[2];
string row1 = reader.ReadLine();
double[] row1d = OBFunctions.spacedStringToDoubleArray(row1);
double ylo = row1d[0];
double yhi = row1d[1];
double xz = row1d[2];
string row2 = reader.ReadLine();
double[] row2d = OBFunctions.spacedStringToDoubleArray(row2);
double zlo = row2d[0];
double zhi = row2d[1];
double yz = row2d[2];
//adjust box bounds, taken from VMD's source for reading lammps files
double xdelta = Math.Min(0, xy);
xdelta = Math.Min(xdelta, xz);
xdelta = Math.Min(xdelta, xy + xz);
xlo = xlo - xdelta;
xdelta = Math.Max(0, xy);
xdelta = Math.Max(xdelta, xz);
xdelta = Math.Max(xdelta, xy + xz);
xhi = xhi - xdelta;
ylo = ylo - Math.Min(0, yz);
yhi = yhi - Math.Max(0, yz);
OBVector3 A = new OBVector3(xhi - xlo, 0, 0);
OBVector3 B = new OBVector3(xy, yhi - ylo, 0);
OBVector3 C = new OBVector3(xz, yz, zhi - zlo);
//OBVector3 A = new OBVector3 (xhi-xlo, xy, xz);
//OBVector3 B = new OBVector3 (0, yhi-ylo, yz);
//OBVector3 C= new OBVector3 (0, 0, zhi-zlo);
mat = new OBMatrix3x3(A, B, C);
uc.SetData(A, B, C);
foundMatrix = true;
}
} while (!foundMatrix);
//uc.SetData (mat);
bool foundAtoms = false;
do
{
line = reader.ReadLine();
if (line.Contains("ITEM: ATOMS"))
{
foundAtoms = true;
}
} while (!foundAtoms);
while ((line = reader.ReadLine()) != null)
{
string[] splitline = line.Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
int lammpstype = Convert.ToInt32(splitline[1]) - 1;
int atype = esequence[lammpstype];
OBAtom a = new OBAtom();
a.SetAtomicNum(atype);
//position in fraction coordinates
OBVector3 fvec = new OBVector3(Convert.ToDouble(splitline[3]), Convert.ToDouble(splitline[4]),
Convert.ToDouble(splitline[5]));
//OBVector3 fvec = new OBVector3 (Convert.ToDouble (splitline [2]), Convert.ToDouble (splitline [3]), Convert.ToDouble (splitline [4]));
//convert to cartesian.
OBVector3 cvec = uc.FractionalToCartesian(fvec);
a.SetVector(cvec);
mol.AddAtom(a);
}
mol.CloneData(uc);
obconv.SetOutFormat("cif");
obconv.AddOption("b");
obconv.WriteFile(mol, outFile);
}
}
public static OBVector3 dubs2obvec(double[] a)
{
OBVector3 b = new OBVector3(a[0], a[1], a[2]);
return(b);
}