Hi Tim,
First the best answer: The best solution to this is to use chemfp. It's a
remarkable piece of software.
If you aren't willing to license that, the RDKit's search brute-force
fingerprint search capabilities aren't too bad for in-memory fingerprints.
There's some information in this slide
Hi Tim,
according to https://www.knime.org/files/01_greg_landrum.pdf, the
PostgreSQL cartridge can compare ~1 million compounds/sec on a single
CPU (and this talk is from 2011). ChemFP is much faster if you pre-load
all your FPs into main memory.
Hope this helps,
Nils
Am 18.05.2017 um 23:15 schr
Hi Steve,
That is indeed a bug. thanks for the detailed report!
Here's a very small reproducible that demonstrates it:
def pick2(n=1000,m=10,seed=2748):
def func(i, j):
assert(ihttps://github.com/rdkit/rdkit/issues/1421
-greg
On Thu, May 18, 2017 at 8:59 PM, Steven Wilkens wrote
I think I recall Greg mentioning that RDKit can be used for very fast
similarity search (e.g. all vs. all comparisons or searches against
multi-million sized datasets).
If so, is this part the of the standard distro, or something extra
(chemfp?).
And can it run inside the cartridge?
And any benc
I've been using MaxMinPicker() to run a series of simulations where I
select several small subsets of molecules from a larger set and I've come
across some odd behavior. In summary, this is my algorithm:
1. select a small subset using MaxMinPicker.Pick()
2. remove that subset from the input set
3.
Hi Brian, thanks a lot, this will be very useful to get my head around
smarts writing.
Best,
Alexis
On 18 May 2017 at 02:06, Brian Kelley wrote:
> Dear All,
> In case it helps, there is a wealth of functional groups already in
> RDKit available here:
>
> https://github.com/rdkit/rdkit/blob/mas
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