Hi Jan,
On Friday, August 29, 2014, Jan Domanski <[email protected]> wrote:
> Hi there,
>
> I'm trying to wrap the very handy method getPositions from
> rdkit/Code/GraphMol/Wrap/Conformer.cpp to return coordinates of a conformer
> as a numpy array.
>
> So far I was able to return a tuple of tuples, as below
>
> PyObject *convertPoint(RDGeom::Point3D &point){
> PyObject *res = PyTuple_New(3);
> PyTuple_SetItem(res,0,PyFloat_FromDouble(point.x));
> PyTuple_SetItem(res,1,PyFloat_FromDouble(point.y));
> PyTuple_SetItem(res,2,PyFloat_FromDouble(point.z));
> return res;
> }
>
> PyObject* GetPos(const Conformer *conf) {
> RDGeom::POINT3D_VECT pos=conf->getPositions();
> PyObject *res = PyTuple_New(pos.size());
> for(int idx=0;idx<pos.size();idx++){
> PyTuple_SetItem(res,idx,convertPoint(pos[idx]));
> }
> return res;
> }
>
> Getting the PyArray_SimpleNew was a little tricky in my hands, but I
> assume that's what I need to use somehow. Does anybody have any pointers?
>
There are some examples in the RDKit source that may be helpful. Here's one
of them:
https://github.com/rdkit/rdkit/blob/master/Code/Numerics/Alignment/Wrap/rdAlignment.cpp#L134
-greg
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