On 09/10/2016 05:20 PM, Paolo Tosco wrote:
> https://gist.github.com/ptosco/ab668ad5c35875d8c47e0e6be9e37e79#file-set_chirality_from_atom_parity_flags-ipynb
Nice. I do have 3D SDFs, that is part of the reason I'm going though
this exercise, but looking at 2D SDF for PubChem's L-alanine, they do
Hi Dimitri,
glad to hear that you found a solution that works for you.
In case you were still interested, here is a way to perceive CIP
chirality based on the atom parity flags as read from the SDF atom
block, in the absence of information in the bond block:
On 09/10/2016 04:34 PM, David Cosgrove wrote:
...
> Also, the atoms in a molecule should have the property _CIPRank set, you
> might be able to do something with that.
Possibly, but since the non-typo'ed function seems to do the trick,
that's good enough for me.
Thanks
--
Dimitri Maziuk
Oops. AssignAtomChiralTagsFromStructure() does indeed work.
>> If your file has 3D coordinates, AssignAtomChrialTagsFromStructure
Good to see I'm not the only one with lysdexic fnigers. Apologies for
the noise:
;)
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison --
Hi Paul,
That's fixed in the GitHub master trunk of the RDKit, while it doesn't work
with the released version (I know because I fixed that bug myself!). Most SDF
files in the RCSB feature right-aligned elements, which is indeed allowed by
the CT file specs.
Cheers,
p.
> On 10 Sep 2016, at
On 09/09/2016 10:42 PM, Ling Chan wrote:
> If your file has 3D coordinates, AssignAtomChrialTagsFromStructure may help
> you.
Maybe, if I wasn't getting
rdkit.Chem.rdmolops.AssignAtomChrialTagsFromStructure( self._mol )
AttributeError: 'module' object has no attribute
Hi Paul,
SDF files in the RCSB database do store PDB atom names, have a look at
http://www.rcsb.org/pdb/download/downloadLigandFiles.do?ligandIdList=S58=1CX2=all=false=false
for an example.
Atom names stored in this fashion are read in by the RDKit and can be
accessed as the "molFileAlias"
Hi RDKiters,
Is it possible to store (PDB) atom names in sdf files? If so, how is this
done? (It was not
clear to me after reading CTFile.pdf.)
(I hope that this question is allowed.)
Thanks,
Paul.
--
Hi Rocco et al.,
I too found this a very clear explanation of the different classes of
hydrogen so many thanks for taking the time. Where would a chiral H fit in?
The sort of H from Cl[C@H](F)Br? That one needs to stay even if you
collapse all explicit H atoms to implicit.
On the subject of the
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