Never written something like this, but briefly looking at some code in
openbabel for reading molecules, you should do
atom = obMol.NewAtom();
At the beginning of each loop. Your code looks like it is just due referencing
an unset pointer, so no surprise it segfaults.
You maybe also have to do
obMol.ReserveAtoms(molecule.size);
-David
> On May 7, 2014, at 7:05 PM, Nicolas Cheron <nicolas.cheron.bou...@gmail.com>
> wrote:
>
> 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
>
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