Re: [Rdkit-discuss] Fast similarity search

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

Re: [Rdkit-discuss] MaxMinPicker Bug

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

[Rdkit-discuss] Fast similarity search

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

[Rdkit-discuss] MaxMinPicker Bug

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

Re: [Rdkit-discuss] How to match any halogen of a structure with any halogen of a substructure?

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: > >