// 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);
}
/// <summary>
/// Calculates Hall-Kier alpha value for a molecule
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static double HallKierAlpha(this OBMol mol)
{
var accum = 0.0;
foreach (var atom in mol.Atoms())
{
uint atomicNumber;
try
{
atomicNumber = atom.GetAtomicNum();
}
catch (Exception)
{
continue;
}
double alpha;
var hkAlphas = AtomicConstants.GetHallKierAlphas(atomicNumber);
if (hkAlphas != null)
{
var hyb = atom.Hybridization() - 2;
var length = hkAlphas.Length;
alpha = hyb < length ? (hkAlphas[hyb].HasValue ? hkAlphas[hyb].Value : hkAlphas[length - 1].Value) : hkAlphas[length - 1].Value;
}
else
{
alpha = AtomicConstants.GetrVdW(atomicNumber) / AtomicConstants.GetrVdW(6) - 1;
}
accum += alpha;
}
return(accum);
}
/// <summary>
/// Performs a mol copy and adds explicit hydrogens to each heavy atom to the copy
/// </summary>
/// <param name="mol"></param>
/// <returns>Copy of original mol with explicit hydrogens</returns>
public static OBMol AddExplicitHydrogens(this OBMol mol)
{
var newMol = new OBMol(mol);
foreach (var atom in newMol.Atoms())
{
newMol.AddHydrogens(atom);
}
return(newMol);
}
public static void writeatominfotoscreen(OBMol mol)
{
Console.WriteLine("new");
foreach (OBAtom a in mol.Atoms())
{
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);
}
Console.WriteLine("");
}
public static OBMol merge_atoms_at_same_location(OBMol mol)
{
double radius = 0.1;
//when we make a unit_cell by copy and pasting base cases we end up with atoms at the same location that need to be merged
//assumes only two atoms overlap at a time
Dictionary <int, int> tomerge = new Dictionary <int, int>();
foreach (OBAtom a in mol.Atoms())
{
if (!tomerge.ContainsKey((int)a.GetIdx()))
{
foreach (OBAtom b in mol.Atoms())
{
if (a.GetIdx() == b.GetIdx())
{
continue;
}
else
{
double len =
Math.Round(StarMath.norm2(obvec2dubs(OBVector3.Sub(a.GetVector(), b.GetVector()))),
7); //gets length
if (len <= radius)
{
tomerge.Add((int)b.GetIdx(), (int)a.GetIdx());
}
}
}
}
}
int atomsdeleted = 0;
foreach (int key in tomerge.Keys)
{
mol = molecule_merge(mol, mol.GetAtom(key - atomsdeleted), mol.GetAtom(tomerge[key] - atomsdeleted));
atomsdeleted++;
}
return(mol);
}
public static OBVector3 mol_com(OBMol mol)
{
//center of mass of molecule
OBVector3 sum = OBVector3.VZero;
double molw = 0;
foreach (OBAtom a in mol.Atoms())
{
double m = a.GetAtomicMass();
sum = OBVector3.Add(sum, OBVector3.Mul(m, a.GetVector()));
molw = molw + m;
}
return(OBVector3.Mul(1 / molw, sum));
}
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 double greatest_radial_distance(OBMol mol, OBAtom carbon1, OBAtom a1)
{
OBVector3 v2 = carbon1.GetVector();
OBVector3 v3 = a1.GetVector();
double maxd = 0;
foreach (OBAtom a in mol.Atoms())
{
OBVector3 v1 = a.GetVector();
double d = openbabel_csharp.Point2Line(v1, v2, v3);
if (d > maxd)
{
maxd = d;
}
}
return(maxd);
}
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 double greatest_axial_distance(OBMol mol, OBAtom carbon1, OBAtom a1)
{
//finds the distance of the most distant atom along the axis defined by the carboxyl defined by carbon 1 and a1
double[] vec = obvec2dubs(OBVector3.Sub(carbon1.GetVector(), a1.GetVector()));
vec = StarMath.normalize(vec);
double maxd = 0;
foreach (OBAtom a in mol.Atoms())
{
if (a == carbon1)
{
continue;
}
double d = StarMath.dotProduct(vec,
obvec2dubs(OBVector3.Sub(carbon1.GetVector(),
a.GetVector()))); // get pairwise axial distance by taking the scalar projection of the carbon's position to atom A
if (d > maxd)
{
maxd = d;
}
}
return(maxd);
}
public static double syntheticaccessability(OBMol mol)
{
mol.FindChiralCenters();
VectorpRing ringdata = mol.GetSSSR();
double fring = 0;
//int rings = (double)ringdata.Count;
foreach (OBRing r in ringdata)
{
var n = r.Size();
fring = fring + n * 6;
}
double ftype = 0;
double fconnect = 0;
int nchiral = 0;
foreach (OBAtom a in mol.Atoms())
{
if (a.GetAtomicNum() == 6)
{
ftype = ftype + 3;
}
else
{
ftype = ftype + 6;
}
int bcount = 0;
foreach (OBBond b in a.Bonds())
{
bcount++; //get the atom degree by counting bonds
}
switch (bcount)
{
case 4: {
fconnect = fconnect + 24;
break;
}
case 3: {
fconnect = fconnect + 12;
break;
}
case 2: {
fconnect = fconnect + 6;
break;
}
case 1: {
fconnect = fconnect + 3;
break;
}
}
if (a.IsChiral())
{
nchiral++;
}
}
//for indole() ftype= 72, fring = 66, fconnect = 129
//fring
double fchiral = nchiral * 20;
double score = fchiral + fconnect + ftype + fring;
return(score);
}
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>
/// Chi0n atomic valence number connectivity index (order 0)
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static double Chi0n(this OBMol mol)
{
return(mol.Atoms().Where(a => a.ValenceNumber() > 0).Select(a => Math.Sqrt(1 / (double)a.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);
}