[Open Babel] Creating an OBMol by hand in C++

[Nicolas Cheron]

Dear all,

I am working with a program (in C++) which has its own way of dealing
with atoms and molecules. I would like to use the OpenBabel library to
assign types to atoms. For now, when I need to do it I write a .xyz
file and then read it in an OBMol object and assign the types.

This works, but I am not happy because it could be more efficient.
Thus, I would like to create the OBMol object by hand. I was thinking
of something such as:

struct Atom{
     float x;
     float y;
     float z;
     char Type[4];                // Element name (H, C, N, O...).
     char PotentialType[3];   // Atom type for the scoring function.
};

struct Molecule{
     Atom atom[150];
     int size;
};

/////////////

OpenBabel::OBMol obMol;
OpenBabel::OBAtom *atom;
for (int i=0; i<molecule.size ; i++ ) {
     atom->SetVector(molecule.atom[i].x, molecule.atom[i].y,
molecule.atom[i].z);
     atom->SetType(molecule.atom[i].Type);
     obMol.InsertAtom(*atom);
     }
obMol.ConnectTheDots();

When I am doing this the code compiles but crashes (Segmentation
fault) and I have not been able to find what is going wrong. I have
also tried with SetVector(const vector3 & v ) but it is the same.


Does anyone have a clue of how I can create this object atom by atom?

Thank you

Nicolas

------------------------------------------------------------------------------
Is your legacy SCM system holding you back? Join Perforce May 7 to find out:
&#149; 3 signs your SCM is hindering your productivity
&#149; Requirements for releasing software faster
&#149; Expert tips and advice for migrating your SCM now
http://p.sf.net/sfu/perforce
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss