/// <summary> /// A variant which returns an OBMol based on host. /// </summary> /// <param name="host"></param> /// <returns></returns> public static OBMol designgraphtomol(designGraph host) { var mol = new OBMol(); Dictionary <string, int> nodeatomlookup = new Dictionary <string, int>(); //dictionary for looking up which nodes go to which atoms by their names int i = 0; foreach (node n in host.nodes) { OBAtom atom = new OBAtom(); double x = scale * n.X; double y = scale * n.Y; double z = scale * n.Z; //set coordinates of atom atom.SetVector(x, y, z); n.localLabels.Sort(); foreach (string label in n.localLabels) { if (label.Length < 4) { if (label != "sp2" && label != "sp3") ///so openbabel gets less crap { atom.SetAtomicNum(elementTabel[label]); //set atomic number break; } } } i++; nodeatomlookup.Add(n.name, i); //add the atom to dictionary and mol mol.AddAtom(atom); } foreach (arc a in host.arcs) { int bondorder = 0; bool hassingle = a.localLabels.Contains("s"); bool hasdouble = a.localLabels.Contains("d"); bool hastriple = a.localLabels.Contains("t"); //bonds will probably not be anything other than single, double, or triple //although we could have dative bonds if (hassingle ^ hasdouble ^ hastriple) //we do not want more than one bond type { if (hassingle) { bondorder = 1; } if (hasdouble) { bondorder = 2; } if (hastriple) { bondorder = 3; } } mol.AddBond(nodeatomlookup[a.To.name], nodeatomlookup[a.From.name], bondorder); } 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 addmol2(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 //modifies atom and bond indices in the process //dest.BeginModify(); uint prevatms = dest.NumAtoms(); uint nextatms = source.NumAtoms(); uint acount = prevatms; uint bcount = dest.NumBonds(); // First, handle atoms and bonds foreach (OBAtom atom in source.Atoms()) { atom.SetId(acount); ////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); acount++; //var foooo = dest.Atoms (); } //writeatominfotoscreen (dest); foreach (OBBond bond in source.Bonds()) { bond.SetId(bcount); OBBond b = new OBBond(); //b.SetBegin(dest.GetAtom((int)(bond.GetBeginAtomIdx() + prevatms))); //b.SetEnd(dest.GetAtom((int)(bond.GetEndAtomIdx() + prevatms))); b.Set(0, dest.GetAtom((int)(bond.GetBeginAtomIdx() + prevatms)), dest.GetAtom((int)(bond.GetEndAtomIdx() + prevatms)), (int)bond.GetBO(), (int)bond.GetFlags()); if (bond.HasData("trueBO")) { b.CloneData(bond.GetData("trueBO")); //clone true bond order so we can eventually do MOF-UFF } dest.AddBond(b); //dest.AddBond( (int)bond.GetBO(), (int)bond.GetFlags()); bcount++; } //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 //dest.EndModify(); this tends to mangle up all the atom ids, which is bad return(dest); }
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 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 bool designgraphtomol(designGraph host, ref OBMol mol) { OBElementTable periodictable = new OBElementTable(); //OBMol mol = new OBMol(); Dictionary <string, int> nodeatomlookup = new Dictionary <string, int>(); //dictionary for looking up which nodes go to which atoms by their names int i = 0; foreach (node n in host.nodes) { OBAtom atom = new OBAtom(); double x = scale * n.X; double y = scale * n.Y; double z = scale * n.Z; //set coordinates of atom atom.SetVector(x, y, z); int anum = 0; n.localLabels.Sort(); foreach (string label in n.localLabels) { if (label.Length < 4) { if (label != "sp2" && label != "sp3") ///so openbabel gets less crap { anum = periodictable.GetAtomicNum(label); if (anum > 0) { break; } } } } i++; atom.SetAtomicNum(anum); //set atomic number nodeatomlookup.Add(n.name, i); //add the atom to dictionary and mol mol.AddAtom(atom); } foreach (arc a in host.arcs) { OBBond bond = new OBBond(); int bondorder = 0; bool hassingle = a.localLabels.Contains("s"); bool hasdouble = a.localLabels.Contains("d"); bool hastriple = a.localLabels .Contains("t"); //bonds will probably not be anything other than single, double, or triple //although we could have dative bonds if (hassingle ^ hasdouble ^ hastriple) //we do not want more than one bond type { if (hassingle) { bondorder = 1; } if (hasdouble) { bondorder = 2; } if (hastriple) { bondorder = 3; } } mol.AddBond(nodeatomlookup[a.To.name], nodeatomlookup[a.From.name], bondorder); // OBAtom begin = nodeatomlookup[a.From.name]; // OBAtom end = nodeatomlookup[a.To.name]; // bond.SetBegin(begin); // bond.SetEnd(end); // bond.SetBondOrder(bondorder); // mol.AddBond(bond); // mol.Bonds(); } //mol.FindRingAtomsAndBonds(); return(true); }
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); }