Hi,
I see that back in 2014 there was some discussion of using CUDA inside of
RDKit and how it may be possible to produce a FastROCS-like open source
alternative. I was curious if anyone had made such a breakthrough. Since
GPU availability is now so common, and datasets are becoming so large, I
fi
] The python implementation of the subshape alignment algorithm is
> essentially just a proof-of-concept and not performant enough for real
> usage.
>
> On Mon, Nov 2, 2020 at 7:16 PM Andy Jennings
> wrote:
>
>> Hi,
>>
>> I see that back in 2014 there was some dis
Hi,
First off: great work on the RDKit - a great resource for those of us that
like to cook up our own solutions to problems.
The default behavior of certain calls (e.g. Chem.SDMolSupplier,
Chem.MolToSmiles) has default behavior that is the opposite of what I would
generally want. For instance I
#x27;)
>
> In [10]: # hydrogens have been stripped as the original function was
> invoked
>
> In [11]: suppl[0].GetNumAtoms()
> Out[11]: 34
>
> HTH, cheers
> p.
> On 10/12/17 18:09, Andy Jennings wrote:
>
> Hi,
>
> First off: great work on the RDKit - a great res
Hi,
I'm curious if anyone has figured out a way to compare two molecules based
upon their pharmacophore similarities. Specifically, I want to compare 2
molecules in their _absolute_ locations, and not simply see if they have 2
pharmacophores that match well via a translation/rotation. From what I
(there's likely a smarter way to do this).
>
> I hope this doesn't create more questions than it answers; I will try to
> do a somewhat longer writeup, but I wanted to at least get something
> minimal out there quickly.
>
> -greg
>
>
>
>
> On Fri, Oct 20, 201
s doesn't create more questions than it answers; I will try to
> do a somewhat longer writeup, but I wanted to at least get something
> minimal out there quickly.
>
> -greg
>
>
>
>
> On Fri, Oct 20, 2017 at 4:58 PM, Andy Jennings
> wrote:
>
>> Hi,
>>
rum
wrote:
>
>
> On Mon, Oct 30, 2017 at 10:14 PM, Andy Jennings > wrote:
>
>>
>> Next question on this topic, as I can't find it from digging into various
>> sources.
>>
>> The solution you pointed me to works very well. I'm now expanding it t
Hi RDKitters,
Whilst looking at generating some conformations of molecules using the
ETKDG method with EmbedMultipleConfs I've come across some strange (to me)
behavior.
When I generate conformations of some molecules with the randomSeed as -1
the result is a variable number of conformations. Tha
Hi RDKitters,
I have a question and an observation on the topic of library enumeration.
First, the question: is there a call within RDKit to trigger the exhaustive
reaction of reagents? For example, if I have two reagents - a primary amine
and an akyl chloride - can I tell RDKit to enumerate the
e in the while loop.
>
> Best,
>
> Christos
>
> Christos Kannas
>
> Chem[o]informatics Researcher & Software Developer
>
> [image: View Christos Kannas's profile on LinkedIn]
> <http://cy.linkedin.com/in/christoskannas>
>
> On 17 Januar
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