/// <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);
}
