/// <summary>
/// Chi1v atomic valence connectivity index (order 0)
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static double Chi1v(this OBMol mol)
{
var deltas = mol.HkDeltas(false);
return(mol.Bonds().Where(b => deltas[b.GetBeginAtomIdx() - 1] * deltas[b.GetEndAtomIdx() - 1] > 0)
.Select(b => Math.Sqrt(1 / (double)(deltas[b.GetBeginAtomIdx() - 1] * deltas[b.GetEndAtomIdx() - 1]))).Sum());
}
/// <summary>
/// Calculates the approximate surface area contributions for each atom
/// </summary>
/// <param name="mol"></param>
/// <param name="includeHydrogens">Include hydrogens in calculation</param>
/// <returns></returns>
public static double[] LabuteASAContributions(this OBMol mol, bool includeHydrogens = true)
{
var numAtoms = mol.NumAtoms();
var Vi = new double[numAtoms + 1].Zero().ToArray();
var rads = new double[numAtoms + 1].Zero().ToArray();
rads[0] = AtomicConstants.GetRBO(1);
double Ri, Rj, Bij, Dij;
// OpenBabel atom numbering is 1-based
for (var i = 1; i <= numAtoms; i++)
{
rads[i] = AtomicConstants.GetRBO(mol.GetAtom(i).GetAtomicNum());
}
foreach (var bond in mol.Bonds())
{
var beginAtom = bond.GetBeginAtomIdx();
var endAtom = bond.GetEndAtomIdx();
Ri = rads[beginAtom];
Rj = rads[endAtom];
var bondOrder = bond.GetBondOrder();
Bij = !bond.IsAromatic() ? Ri + Rj - BondConstants.BondScaleFactors[bondOrder] : Ri + Rj - BondConstants.BondScaleFactors[0];
Dij = Math.Min(Math.Max(Math.Abs(Ri - Rj), Bij), Ri + Rj);
Vi[beginAtom] += Rj * Rj - Math.Pow((Ri - Dij), 2) / Dij;
Vi[endAtom] += Ri * Ri - Math.Pow((Rj - Dij), 2) / Dij;
}
if (includeHydrogens)
{
Rj = rads[0];
for (var i = 1; i <= numAtoms; i++)
{
Ri = rads[i];
Bij = Ri + Rj;
Dij = Math.Min(Math.Max(Math.Abs(Ri - Rj), Bij), Ri + Rj);
Vi[i] += Rj * Rj - Math.Pow((Ri - Dij), 2) / Dij;
Vi[0] += Ri * Ri - Math.Pow((Rj - Dij), 2) / Dij;
}
}
for (var i = 0; i <= numAtoms; i++)
{
Ri = rads[i];
Vi[i] = 4 * Math.PI * Math.Pow(Ri, 2) - Math.PI * Ri * Vi[i];
}
return(Vi);
}
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 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);
}
/// <summary>
/// Chi1n atomic valence number connectivity index (order 1)
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static double Chi1n(this OBMol mol)
{
return(mol.Bonds().Where(b => b.GetBeginAtom().ValenceNumber() * b.GetEndAtom().ValenceNumber() > 0)
.Select(b => Math.Sqrt(1 / (double)(b.GetBeginAtom().ValenceNumber() * b.GetEndAtom().ValenceNumber()))).Sum());
}
public designGraph moltoDesignGraph(OBMol mol)
{
//OBConversion obconv = new OBConversion ();
designGraph host = new designGraph();
OBConversion obconv = new OBConversion();
Dictionary <uint, int> atomid2nodeid = new Dictionary <uint, int>();
//obconv.SetInFormat("smi");
//var format =obconv.GetInFormat();
//uint d=mol.NumAtoms();
OBElementTable ptable = new OBElementTable();
//mol.FindTorsions ();
int nodecount = 0;
//loop through all atoms in the file and make them into nodes in the graph
foreach (OBAtom a in mol.Atoms())
{
node n = new node();
n.name = "n" + nodecount;
var atype = a.GetAtomType();
n.X = a.GetX() * (1 / scale);
n.Y = a.GetY() * (1 / scale);
n.Z = a.GetZ() * (1 / scale);
uint anum = a.GetAtomicNum();
string sym = ptable.GetSymbol((int)anum);
//double test =ptable.GetIonization ((int)anum);
int maxbonds = ptable.GetMaxBonds((int)anum);
uint val = a.GetImplicitValence();
n.localLabels.Add(sym);
n.localLabels.Add(atype);
n.localVariables.Add((double)maxbonds);
n.localVariables.Add((double)val);
host.addNode(n);
atomid2nodeid.Add(a.GetId(), nodecount);
//Console.WriteLine (x);
nodecount++;
}
int arccount = 0;
foreach (OBBond b in mol.Bonds())
{
arc ac = new arc();
ac.directed = false;
ac.name = "a" + arccount;
//uint bondorder = b.GetBondOrder ();
if (b.IsSingle())
{
ac.localLabels.Add("s");
}
if (b.IsTriple())
{
ac.localLabels.Add("t");
}
if (b.IsDouble())
{
ac.localLabels.Add("d");
}
uint toid = b.GetEndAtomIdx();
uint fromid = b.GetBeginAtomIdx();
ac.To = host.nodes[atomid2nodeid[toid - 1]];
ac.From = host.nodes[atomid2nodeid[fromid - 1]];
host.arcs.Add(ac);
arccount++;
}
return(host);
}
