Hi all,
I have successfully built the RDKit on Windows against Python 3. I had
to manually compile boost though; Greg, if you wish I can send you
scripts which will do the job out-of-the-box on Windows.
Cheers,
p.
On 09/24/15 07:55, Greg Landrum wrote:
On Wed, Sep 23, 2015 at 8:55 AM, Cly
Hi John and Greg,
I now understand better what happens, thank you for your responses!
However, in this precise case, I need to not consider these atoms as
stereocenters, so I just remove them from the list returned by
FindMolChiralCenters.
When I generate conformations, I still get the differen
Hi Paolo,
That would be really great, I would be definitely interested in trying to
wrap your scripts into the conda recipe for the boost package.
Thanks,
Riccardo
--
Monitor Your Dynamic Infrastructure at Any Scale Wi
Thanks all,
The error reported on attempting to build is attached below. The colleague
in question noted that it seemed to be looking for python2.7? It may well
be that some trivial error has been made. When I get access to a windows
machine I will have a go at building rdkit from source as report
I'm trying to get to grips with using the RDKit cartridge, and so far
its going well.
One thing I'm concerned about is molecule standardization, along the
lines of the ChemAxon Standardizer that allows substructure searches to
be done is a way that is largely independent of the quirks of structu
Hi,
is it possible with RDKit to generate all stereoisomers of a given compound?
If not, is anyone working on it?
If not, how difficult would it be / what would be the best way to implement
such a function.
best regards
Soren
Hi Soren,
That functionality isn't currently there, but it's been requested a few
times and shouldn't be that tough to get into the next release.
-greg
On Thursday, September 24, 2015, Soren Wacker wrote:
> Hi,
>
> is it possible with RDKit to generate all stereoisomers of a given
> compound?
Umm... would that be all stereoisomers or all realizable stereoisomers? For
example consider two bridgeheads in a norbonane-type compound. In this
case, only a particular enantiomeric pair would be realizable, and not all
four diastereomers.
-
Dear Soren,
I have recently used the RDKit to enumerate stereocentres.
The approach I followed was to generate a 3D structure for the molecule
of interest (including hydrogens) using EmbedMolecule(), followed by
MMFF optimization; do not pay attention to stereochemistry at this
stage. Then I u
Hi Soren,
maybe this function which enumerates racemates with one stereocenter
into the corresponding enantiomers might help:
def enum_racemates(sdf_list_or_file, find_only=True, mol_id="molid"):
"""returns: result_sdf::list, racemic_molids::list
find_only==True: return new sdf as lis
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