Hi,? ? I tryied using rdkit to match fragments with compounds only to find that
rdkit performed not well in SMARTS. The following is the notebook I worked.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FragmentMatcher
from rdkit.Chem.Draw import IPythonConsole
The RDKit has support for the TPL format, an old BioCad/MSI/Accelrys format.
It's easy to imagine something better, but this is at least already there
and there could be other software that speaks it:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/test_data/cmpd2.tpl
I'd
Dear Hongbin,
I am afraid The SMARTS you are using is not valid, as no SSSR can have
less than 3 terms, or it wouldn't be a ring. If you change[a!r0] into,
for instance, [a!r3], then you'll find the match you are looking for.
Cheers,
p.
On 27/10/2016 09:36, 杨弘宾 wrote:
Hi,
I tryied
Looking into this further, I've decided to use the Python option again, as
this seems to have more functions.
I run the current example, where rxn is the original example, and qrxn is
the 'query' for categorisation:
In [2]: import rdkit
In [3]: from rdkit import Chem
In [4]: from rdkit.Chem
Hi,
I'm trying to replicate the Schneider categorisations with a local set of
reactions that I have stored in SMILES. I currently have the categorisation
filters as Reaction SMARTS, and I was hoping to do a standard substructure
comparison between the SMARTS and the SMILES, but can't seem to do
Hello Greg,
Is the canonical SMILES string always unique for every isomer and
tautomerization state of a molecule? If yes, then I have already written a
function to load multiple molecules and their conformers, which I can share
it here.
best
Thomas
PS: thanks to David for pointing this out.
Thanks, it works! I appreciate that Rdkit is so strict in representation of
the the molecules and the substructures. I learned a lot in the mail list.
Hongbin Yang
From: Paolo ToscoDate: 2016-10-27 17:19To: 杨弘宾; rdkit-discussSubject: Re:
[Rdkit-discuss] The fragmentMatcher
It would seem that a major issue with RDKit's multiconformer file is the
inability to associate structure-level and atom-level properties with
conformations. t's not quite orthogonal to the question of how to read,
say, a multiconformer SD file into RDKit's multiconformer format, because
the
On 2016-10-26 23:39, Peter S. Shenkin wrote:
> Hey, by the way, my agenda is trying to understand all this.
(Using python syntax instead of ML)
Recommended by TFM:
from "http://www.w3.org/2000/svg; import *
All svg names should work with or without package qualifier: point(),
line(), etc., as
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