I don’t think you should be getting NaNs, and that’s worth looking into,
but they are technically numeric values : that’s the double value younger
when you divide by zero.
-greg
On Fri, 30 Nov 2018 at 00:40, Jason Biggs wrote:
> I don't know enough about the GETAWAY descriptor to know if this
I don't know enough about the GETAWAY descriptor to know if this is to be
expected.
>>>m = Chem.MolFromSmiles('CC=O')
>>>m2=Chem.AddHs(m)
>>>AllChem.EmbedMolecule(m2,randomSeed = 1234)
>>>(Chem.rdMolDescriptors.CalcGETAWAY(m2))[85:90]
[0.207, 0.008, 0.027, nan, 0.0]
Is this a bug? If not, is
That seems to be it - SWIG was burying what was what into a collection of
Vect objects, so I got confused. It seems to work now.
On Thu, 29 Nov 2018 at 16:34, Paolo Tosco
wrote:
> Hi James,
>
> I think the problem here is that you are interpreting the index pairs in
> each match returned by
Hi James,
I think the problem here is that you are interpreting the index pairs in
each match returned by getSubstructMatches() as if they were the atom
indices that form a bond. Instead, each pair corresponds to a
(queryAtomIdx, molAtomIdx) pair, and has nothing to do with bonds:
I'm trying to use the Java wrapper to do a basic molecule
fragmentation, greedily matching against anything that fits the SMARTS
"[*;R]-;!@[*]" (effectively any regular bond that isn't part of a ring
system)
As a test case, I'm using a structure with a few obvious bonds that
can be broken, namely
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