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);
        }