Wow, this almost makes me wanting to re-write my thesis in LaTeX. Almost!
:)
George
On 15 August 2012 16:26, Greg Landrum <[email protected]> wrote:
> On Wed, Aug 15, 2012 at 5:10 PM, Michael Palmer <[email protected]>
> wrote:
> >
> >> Now that I've at least tried to clear up what is going on, maybe I can
> >> be more helpful: was there a specific question you were trying to
> >> answer that led you to your discovery that the RDKit behaves strangely
> >> in this special case?
> >
> >
> > What I'm trying to do can be inspected here:
> >
> > http://chimpsky.uwaterloo.ca/mol2chemfig/index
> >
> > Briefly, I'm building a program for converting molecular structures from
> > smiles or molfile format to TeX code, using the syntax defined by the
> > chemfig package as the target.
>
> oooo, coool!
>
> > rdkit does all the heavy lifting. I was using
> > the GetImplicitHs method to determine how many hydrogens to attach to
> > carbons and heteroatoms and then noticed that the number of hydrogens on
> > nitrogen in rings was off.
> >
> > From your answer, it seems I should be using GetTotalNumHs. However, I
> would
> > still like to be able to distinguish between hydrogens that were
> specified
> > in a molfile, with coordinates, and those that weren't.
>
> the answer to this isn't super straightforward, so it probably won't
> come until tomorrow.
>
> >
> > Another question I ran into was accessing the coordinates of an atom,
> either
> > loaded from molfile or, with smiles, computed with
> AllChem.Compute2DCoords.
> > Does the atom object have a method to get at those? Right now, I'm using
> > some embarrassing workaround.
>
> This one I can answer quickly. You need to the molecule's conformer:
> In [7]: AllChem.Compute2DCoords(m)
> Out[7]: 0
>
> In [8]: conf = m.GetConformer()
>
> In [9]: for atom in m.GetAtoms():
> ...: aid = atom.GetIdx()
> ...: print aid,list(conf.GetAtomPosition(aid))
> ...:
> 0 [0.15858546683951269, -1.1294387542967057, 0.0]
> 1 [-1.3046720119188515, -1.4594047386916416, 0.0]
> 2 [-2.3220596761687866, -0.35716958200679838, 0.0]
> 3 [-1.8761898616603592, 1.07503155907298, 0.0]
> 4 [-0.41293238290199596, 1.4049975434679163, 0.0]
> 5 [0.60445528134793969, 0.30276238678307321, 0.0]
> 6 [2.0677127601063026, 0.63272837117800962, 0.0]
> 7 [3.0851004243562379, -0.46950678550683356, 0.0
>
> -greg
>
>
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