/// <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 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 void trajectoryFrameToCIF(string frame, string outFile, List <int> esequence,
OBConversion obconv)
{
//converts a frame from the above function into a CIF file
//lammps trajectory files have unit cell dimension data for every frame
//requires an element sequence for identifying element type from lammps atom types
OBUnitCell uc = new OBUnitCell();
OBMol mol = new OBMol();
OBMatrix3x3 mat = new OBMatrix3x3();
using (StringReader reader = new StringReader(frame)) {
string line = "";
bool foundMatrix = false;
do
{
line = reader.ReadLine();
if (line.Contains("BOX BOUNDS"))
{
//data from lammps is in this format
//ITEM: BOX BOUNDS xy xz yz
//xlo_bound xhi_bound xy
//ylo_bound yhi_bound xz
//zlo_bound zhi_bound yz
string row0 = reader.ReadLine();
double[] row0d = OBFunctions.spacedStringToDoubleArray(row0);
double xlo = row0d[0];
double xhi = row0d[1];
double xy = row0d[2];
string row1 = reader.ReadLine();
double[] row1d = OBFunctions.spacedStringToDoubleArray(row1);
double ylo = row1d[0];
double yhi = row1d[1];
double xz = row1d[2];
string row2 = reader.ReadLine();
double[] row2d = OBFunctions.spacedStringToDoubleArray(row2);
double zlo = row2d[0];
double zhi = row2d[1];
double yz = row2d[2];
//adjust box bounds, taken from VMD's source for reading lammps files
double xdelta = Math.Min(0, xy);
xdelta = Math.Min(xdelta, xz);
xdelta = Math.Min(xdelta, xy + xz);
xlo = xlo - xdelta;
xdelta = Math.Max(0, xy);
xdelta = Math.Max(xdelta, xz);
xdelta = Math.Max(xdelta, xy + xz);
xhi = xhi - xdelta;
ylo = ylo - Math.Min(0, yz);
yhi = yhi - Math.Max(0, yz);
OBVector3 A = new OBVector3(xhi - xlo, 0, 0);
OBVector3 B = new OBVector3(xy, yhi - ylo, 0);
OBVector3 C = new OBVector3(xz, yz, zhi - zlo);
//OBVector3 A = new OBVector3 (xhi-xlo, xy, xz);
//OBVector3 B = new OBVector3 (0, yhi-ylo, yz);
//OBVector3 C= new OBVector3 (0, 0, zhi-zlo);
mat = new OBMatrix3x3(A, B, C);
uc.SetData(A, B, C);
foundMatrix = true;
}
} while (!foundMatrix);
//uc.SetData (mat);
bool foundAtoms = false;
do
{
line = reader.ReadLine();
if (line.Contains("ITEM: ATOMS"))
{
foundAtoms = true;
}
} while (!foundAtoms);
while ((line = reader.ReadLine()) != null)
{
string[] splitline = line.Split((char[])null, StringSplitOptions.RemoveEmptyEntries);
int lammpstype = Convert.ToInt32(splitline[1]) - 1;
int atype = esequence[lammpstype];
OBAtom a = new OBAtom();
a.SetAtomicNum(atype);
//position in fraction coordinates
OBVector3 fvec = new OBVector3(Convert.ToDouble(splitline[3]), Convert.ToDouble(splitline[4]),
Convert.ToDouble(splitline[5]));
//OBVector3 fvec = new OBVector3 (Convert.ToDouble (splitline [2]), Convert.ToDouble (splitline [3]), Convert.ToDouble (splitline [4]));
//convert to cartesian.
OBVector3 cvec = uc.FractionalToCartesian(fvec);
a.SetVector(cvec);
mol.AddAtom(a);
}
mol.CloneData(uc);
obconv.SetOutFormat("cif");
obconv.AddOption("b");
obconv.WriteFile(mol, outFile);
}
}
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);
}