Hi Greg,
Thanks for the answer. The graphs going in are very simple, so they will just
be a collection of C,O,S,N atoms obeying valency laws, I will have a look and
see how the sanitise function deals with my inputs when I have some of the
other functionality issues iron out.
Best,
Nick
On 21 Ma
On Mar 21, 2012, at 6:48 PM, Greg Landrum wrote:
> I don't think it's actually reading the molecule from SDF that's slow.
> The slow part is sanitizing it. More carefully: the slowest part is
> cleaning up the stereochemistry.
Without looking at the code, I can agree with that. RDKit's SD reader
u
On Wed, Mar 21, 2012 at 5:58 PM, Nicholas Firth
wrote:
> Hi All,
> I am hoping for a piece of advice, I have a graph (connectivity matrix with
> atom indexes) and I want to make a molecule from that graph. I was planning
> on creating an sdf and then reading in this way, however I've seen that
> r
Hi All,
I am hoping for a piece of advice, I have a graph (connectivity matrix with
atom indexes) and I want to make a molecule from that graph. I was planning on
creating an sdf and then reading in this way, however I've seen that rdkit
reading in sdf's is quite slow. So the question is, which
