Hi Kurt,
The Vernalis KNIME community contribution has a node "Templated Conformer
Generator (RDKit)" (see https://hub.knime.com/n/wK3RJiystQYq5M9w ) which
will do exactly this. If you don't want to do it in KNIME, then you can
see the relevant bits of the Java source at:
https://github.com/vern
It is encoded as an atom with element number 0, and unless you specify
otherwise 0 mass, 0 charge.
Steve
On Sun, 19 Sep 2021, 17:06 Gianmarco Ghiandoni,
wrote:
> I have a question for the RDKit community that regards count-based RDKit
> fingerprints. During a test, I have noticed that the compo
Hi Tim,
You mentioned the calculation is done using Java streams. Have you tried
calling #sequential() on your stream to force it to run single threaded
from the Java side?
Steve
On Wed, 3 Feb 2021, 12:58 Greg Landrum, wrote:
> Given the fun that threading is, this isn't necessarily conclusive
I recall the first time I heard the term was in a project meeting in
RiboTargets back in around 1999/2000. One of our modelling group used it
after hearing discussion of results of in vitro and in vivo studies being
discussed. My recollection is that there was a certain amount of amusement
at the
It looks like it should be deterministic, in that it always loops through
the existing non-hydrogen atoms in their internal order, adding H's to each
in turn.
https://github.com/rdkit/rdkit/blob/ffc123a6659705adae33a6f5bf3913d65aa7b54d/Code/GraphMol/AddHs.cpp
Steve
On Wed, 3 Oct 2018 at 21:23, P
You could try looping over all your atoms and calling setIntProp on each
one to set a property with the original index, then get that property value
back rather than the new atom indices.
Steve
On Mon, 2 Jul 2018, 17:43 Joshua Meyers,
wrote:
> Hey Again,
>
> Back to this problem because I did
Axel,
You need to use a SMARTS query:
q = Chem.MolFromSmarts("[CR0][CR0][CR0]")
Have a look at http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
Steve
On 29 June 2018 at 08:04, Axel Pahl wrote:
> Dear all,
>
> my google-fu is failing is me.
> Is it possible in substructure search
LES.
Steve
From: Brian Kelley [fustiga...@gmail.com]
Sent: 30 March 2017 17:59
To: Stephen Roughley
Cc: RDKit Discuss (rdkit-discuss@lists.sourceforge.net)
Subject: Re: [Rdkit-discuss] RDKit Reaction gives disconnected components
Correction here, you are not
Dear Greg/RDKitters,
This may be user error, or misunderstanding of rSMARTS, so can anyone throw
some light on the following behaviour?
First example works as expected - there are 2× Ph in m4, so we end up with
2×2×2 copies of the expected product:
rSMARTS4='([*:1]-&!@c1:[c&!H0]:[c&!H0]:[c&!H0
You can match a dummy atom (*) with the SMARTS [#0]
Steve
On 16 Mar 2017 16:43, "Chris Earnshaw" wrote:
> Hi Brian
>
> I'm by no means an expert in RDKit with Python, but until someone else
> comes along, here are a few thoughts.
>
> Your reaction SMARTS specifically defines aromatic carbons jo
Thanks Greg.
For completeness, for anyone trying this from the Java wrappers, the relevant
methods are
mol.clearConformers();
and
mol.addConformer(conf, true);
Steve
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 11 January 2017 11:01
To: Stephen Roughley
Cc: RDKit Discuss
Subject
[mailto:greg.land...@gmail.com]
Sent: 11 January 2017 07:24
To: Stephen Roughley; RDKit Discuss
Subject: Re: RDKit conformer handling possible bug?
Hi Steve,
[A general request: please send RDKit questions/comments to the rdkit-discuss
mailing list so that others can see the questions and answers. I
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