// 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 void writeatominfotoscreen(OBAtom a)
{
Console.WriteLine("atomtype: " + a.GetAtomType() + " id " + a.GetIdx() + " index " + a.GetIndex() +
" CIdx" + a.GetCIdx() + " title" + a.GetTitle() + " hash" + a.GetHashCode());
var ddd = OpenBabel.OBBuilder.GetNewBondVector(a);
string foobar = ddd.GetX() + " " + ddd.GetY() + " " + ddd.GetZ();
Console.WriteLine(foobar);
}
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 molecule_merge(OBMol mol1, OBAtom a, OBMol mol2, OBAtom b)
{
//takes two molecules and two atoms in each molecule and
//assuming atoms are in the same place, delete one atom and copy bond to the other
//a
//foreach(OBBond bond in b.Bonds())
//{
//}
int keepid = Convert.ToInt32(a.GetIdx());
int todeleteid = Convert.ToInt32(b.GetIdx());
//var bonds = b.Bonds();
List <OBBond> bondlist = new List <OBBond>();
foreach (OBBond bon in b.Bonds())
{
bondlist.Add(bon);
}
OBBond bond = bondlist[0];
int connectid = (int)bond.GetNbrAtomIdx(b);
int prevatms = (int)mol1.NumAtoms(); //number of atoms before we combine things
//OBMol mol3 = new OBMol ();
mol1 = addmol(mol2, mol1);
mol1.BeginModify();
OBAtom keep = mol1.GetAtom(keepid);
OBAtom todelete = mol1.GetAtom(todeleteid + prevatms);
OBAtom toconnect = mol1.GetAtom(connectid + prevatms);
OBBond newbond = new OBBond();
newbond.SetBegin(keep);
newbond.SetEnd(toconnect);
newbond.SetBO(1);
mol1.AddBond(newbond);
mol1.DeleteAtom(todelete);
//OBAtom= atom1
//var a = map2[0];
//int c1 = (int)(map1[1]);
//int c2 = (int)(map2[1] + prevatms);
//int h1 = (int)(map1[0]);
///int h2 = (int)(map2[0] + prevatms);
//OBAtom carbon1 = mol1.GetAtom(c1);
//OBAtom carbon2 = mol1.GetAtom(c2);
//OBAtom hydrogen1 = mol1.GetAtom(h1);
///OBAtom hydrogen2 = mol1.GetAtom(h2);
//OBBuilder.Connect(mol1, c1, c2);//connect fragments
//mol1.DeleteAtom(hydrogen1);
//mol1.DeleteAtom(hydrogen2);
mol1.EndModify();
return(mol1);
}
public static OBMol molecule_merge(OBMol mol1, OBAtom tokeep, OBAtom todelete)
{
//takes a molecule and two atoms in the molecule and
//assuming atoms are in the same place, delete one atom and copy bond to the other
mol1.BeginModify();
uint todeleteid = todelete.GetIdx();
//var bonds = b.Bonds();
List <OBBond> bondlist = new List <OBBond>();
foreach (OBBond bon in todelete.Bonds())
{
bondlist.Add(bon);
}
foreach (OBBond bon in bondlist)
{
mol1.AddBond((int)tokeep.GetIdx(), (int)bon.GetNbrAtomIdx(todelete), (int)bon.GetBondOrder());
}
//writeatominfotoscreen(mol1);
//int connectid = (int)bond.GetNbrAtomIdx(b);
//todelete = mol1.GetAtomById(todeleteid);
///OBAtom toconnect = mol1.GetAtom(connectid);
//OBBond newbond = new OBBond();
//newbond.SetBegin(keep);
//newbond.SetEnd(toconnect);
//newbond.SetBO(1);
//mol1.AddBond(newbond);
mol1.DeleteAtom(todelete);
mol1.EndModify();
return(mol1);
}
public static OBMol addmol(OBMol source, OBMol dest)
{
//combines two OBMols into one molecule
// this is designed to do the same thing as the += operator in mol.cpp, in other words this implements functionality present in openbabel, but not in the C# api
dest.BeginModify();
uint prevatms = dest.NumAtoms();
uint nextatms = source.NumAtoms();
// First, handle atoms and bonds
foreach (OBAtom atom in source.Atoms())
{
atom.SetId(0); ////Need to remove ID which relates to source mol rather than this mol// But in the C++ it had a NoId thing I couldn't figure out
dest.AddAtom(atom);
//var foooo = dest.Atoms ();
}
//writeatominfotoscreen (dest);
foreach (OBBond bond in source.Bonds())
{
bond.SetId(0);
dest.AddBond((int)(bond.GetBeginAtomIdx() + prevatms), (int)(bond.GetEndAtomIdx() + prevatms),
(int)bond.GetBO(), (int)bond.GetFlags());
}
//don't really understand what they mean by residues
//I think it's an amino acid or nucleotide so you can build up proteins and stuff?
//don't think I'm going to use them either, but it might be useful
foreach (OBResidue residue in source.Residues())
{
OBResidue newres = new OBResidue();
dest.AddResidue(newres);
OBResidueAtomIter ai = new OBResidueAtomIter(residue);
//dammit why didn't they implement a residue.atoms sort of thing? I don't want to play with enumerators
////#define FOR_ATOMS_OF_RESIDUE(a,r) for( OBResidueAtomIter a(r); a; ++a )
while (ai.MoveNext())
{
OBAtom resatom = new OBAtom();
resatom = ai.Current;
// This is the equivalent atom in our combined molecule
OBAtom atom = dest.GetAtom((int)(resatom.GetIdx() + prevatms));
// So we add this to the last-added residue
// (i.e., what we just copied)
//[dest.NumResidues () - 1]
var res = dest.Residues().GetEnumerator();
while (!res.MoveNext())
{
} //move to the last residue
res.Current.AddAtom(atom);
//var item = dest.Cast<RMSRequestProcessor.RMSMedia> ().ElementAt (1);
}
//for(OBAtom resatom in )
}
dest.EndModify();
return(dest);
}