Hi
With a 2013 RDkit install we get consistent canonicalization between reaction
labelled and unlabelled atoms.
>>> mol = Chem.MolFromSmiles('C1CC([*])CCN1')
>>> Chem.MolToSmiles(mol)
'[*]C1CCNCC1'
>>> mol = Chem.MolFromSmiles('C1CC([*:1])CCN1')
>>> Chem.MolToSmiles(mol)
'[*:1]C1CCNCC1'
In 2015-
On Dec 16, 2016, at 1:55 PM, Stephen Pickett wrote:
> With a 2013 RDkit install we get consistent canonicalization between reaction
> labelled and unlabelled atoms.
> >>> mol = Chem.MolFromSmiles('C1CC([*])CCN1')
> >>> Chem.MolToSmiles(mol)
> '[*]C1CCNCC1'
> >>> mol = Chem.MolFromSmiles('C1CC([*:1
Hi Stephen,
The new canonicalization algorithm intentionally takes the atom-mapping
information into account. The logic is that the entire SMILES provided
should be canonical, so if the SMILES includes atom maps, those atom maps
should be considered while canonicalizing.
If you have a molecule wi
Thanks Greg, that’s clear.
Stephen
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 16 December 2016 14:33
To: Stephen Pickett
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Canonicalisation with reaction labels
EXTERNAL
Hi Stephen,
The new canonicalization algori
Interesting question. Not sure if it's relevant but in ECBlast we do provide
Canonicalised reaction labels. I agree with Greg that AAM is important.
https://github.com/asad/ReactionDecoder
http://www.ebi.ac.uk/thornton-srv/software/rbl/
Regards,
Asad
Sent from my iPhone
> On 16 Dec 2016, at 1
Hi all,
I try add labels to atoms in a molecule, so that lines like
A1
C12
A2
C3
are written when the molecule is written in a SD file.
Considering atom a and alias text txt,
I expected the function call SetAtomAlias(a, txt) to do the job.
I found this function in a documentation page a
Dear Jean-Marc,
here:
https://gist.github.com/ptosco/6e4468350f0fff183e4507ef24f092a1#file-pdb_atom_names-ipynb
there's an example how to use the atom aliases in RDKit.
Cheers,
p.
On 12/16/2016 10:26 PM, Jean-Marc Nuzillard wrote:
> Hi all,
>
> I try add labels to atoms in a molecule, so t
Hello,
SetMolAlias is available in Python as a function and not as an Atom method:
from rdkit import Chem
import sys
m = Chem.MolFromSmiles('CCC')
for i, atom in enumerate(m.GetAtoms()):
Chem.SetAtomAlias(atom, 'C' + str(i + 1))
w = Chem.SDWriter(sys.stdout)
w.write(m)
w.close()
Best,
Pete
Dear Users,
I was using the SDWriter in the rdkit kit to generate a SD file with
mutiple entries generated using smiles and later assign SD tag data (e.g.
pubchem_ID, IUPAC_name, etc).
However at the end of each tag header I noticed there is a number (bolded):
...
> * (1) *
N1-(2-ethylbutyl)he
Hello
In cases like this i know that Greg did the valid implementation according
to the standard. If you check the ctfile definition (
http://c4.cabrillo.edu/404/ctfile.pdf#page41) you will see that the data
header is pretty flexible. The only requirement is that it starts with a >.
Usually we fin
On Dec 17, 2016, at 1:45 AM, Milinda Samaraweera wrote:
> However at the end of each tag header I noticed there is a number (bolded):
>
> ...
> >(1)
> N1-(2-ethylbutyl)hexane-1,3,6-triamine
...
> What is this number and how you avoid printing this number when SDwriter is
> used? As this n
It's easy enough to make this an option, but given that it is part of the SDF
spec (as Andrew has pointed out) the only reason I can think of to do so would
be because it causes problems for some other piece of (likely commonly used)
software.
Are the sequence numbers causing a problem for you?
This SD file is then used as an input for another program, that program is
having problems reading the sequence numbers.
Thanks,
MAK
On Fri, Dec 16, 2016 at 10:43 PM, Greg Landrum
wrote:
> It's easy enough to make this an option, but given that it is part of the
> SDF spec (as Andrew has pointe
13 matches
Mail list logo
