ion wants things to be super local
> and not affected by atoms that aren't included in the radius being
> considered.
>
> -greg
>
>
>
>
> On Thu, Jan 9, 2020 at 11:06 AM Kramer, Christian via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
>&
Dear RDKit community,
Happy new year!
I am looking for a way to make the circular Morgen Fingerprints more SMILES
like. The background is that with the default definition of atom invariants
in the RDKit implementation, Morgan Fingerprints do not explicitly take
into account aromaticity, and use
Dear RDKitters,
To those of you who are interested in Matched Pairs analysis:
mmpdb, a library for doing large-scale MMP analysis, has been updated to
version 2.2. This update introduces three new features that enable reducing
the size of the database created.
These are:
Dear all,
Andrew's fix for the wildcard atom representation in RDKit 2018.3 has just
been incorporated into the main mmpdb branch. If you download the latest
version of mmpdb, it should now work with with the current version and also
with previous RDKit versions.
Note that you have to rebuild
Hi Mei,
I do not have an answer to your question about sanifix4.py, but with your
test molecule I do not get a "Can't kekulize mol" problem when
reading/writing it with RDKit. Standard RDKit seems to be doing its job:
In [1]: import rdkit
In [2]: from rdkit import Chem
In [3]: mol =
Hi Markus,
thanks for pointing this out. The reason for that error message is that
signal.SIGPIPE is not available under windows. This seems to have slipped
below our radar, since we developed the code on Linux.
There is a simple solution to this: In the mmpdb file, one needs to
import os
and
Dear RDKit users,
we would like to announce an open-source MMP package, designed to create
and query MMP databases for big-pharma sized ADMET datasets:
mmpdb 2.0 - matched molecular pair database generation and analysis
The package has been developed during the last two years by Roche and
ng to atom j, insert "*.*" before
> that token, and reparse the modified SMILES.
>
> On Jun 21, 2016, at 4:50 PM, Kramer, Christian wrote:
> > Is there a simple way of preserving chirality during splits on chiral
> atoms?
>
> To preserve chirality, I had to m
Hi RDKitters,
I am having trouble with chirality conservation during fragmentation of
molecules. Is there a simple way of preserving chirality during splits on
chiral atoms? Am I missing a simple function? Andrew has brought this topic
has come up on the mailing list before, but so far there has
9 matches
Mail list logo
