HI Amit,

On Thu, Sep 22, 2016 at 9:23 AM, Amit singh <amitbioi...@gmail.com> wrote:

> I am a new entry in this discussion forum and also for RDKit


> I am trying to calculate shape tanimoto  and rms between two molecules
> (PDB files) from 3D functionality of RDKit.
> Code is working fine for the pdb files given in test data.
> But gives error whenever I uses other pdb files
> --------
> >>> rms = rdMolAlign.AlignMol(mol1, mol2)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
> RuntimeError: std::exception
> -----------
> It looks like there is a problem in input files, but help required

In order to be able to answer the question, we need a bit more information.
Can you please share what files you loaded mol1 and mol2 from so that we
can reproduce the problem?

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