erent
views).
Kangway
From: David Turnbull
Sent: Thursday, July 23, 2020 6:49 AM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] Conformer generation
Hi all,
I am trying to generate structures of calixarenes in a set shape, I am trying
to use
et the following conformer (shown in two different
views).
Kangway
From: David Turnbull
Sent: Thursday, July 23, 2020 6:49 AM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] Conformer generation
Hi all,
I am trying to generate structures of
Hi all,
I am trying to generate structures of calixarenes in a set shape, I am trying
to use constrain distances but struggling. The lowest energy conformer is not
what I want as I want it in the bowl shape. I labelled 4 oxygens with O17 (for
finding purposes) and set the distance of them as th
Dear Angelica
Here are a couple of codes that may be of interest. They don’t do exactly what
you want, but maybe they can give you some ideas.
https://github.com/jensengroup/get_conformations
https://github.com/jensengroup/TS_conf_search
Best regards, Jan
On 3 Apr 2019, at 00.58, Angelica Pare
Hi,
I’d like to generate a set of conformers with restraints on some of the
substructures. I’d like to keep one segment of the molecule frozen, allowing
the rest of the molecule to be mobile. Within the part of the molecule that is
mobile, I’d like to restrict the torsion angles for one of the
conf_id_I_want = c[0]
>
>
>
>
>
> Paul.
>
>
>
> *From:* Greg Landrum [mailto:greg.land...@gmail.com]
> *Sent:* Thursday, October 26, 2017 12:41 AM
> *To:* Paul Hawkins
> *Cc:* rdkit-discuss@lists.sourceforge.net; Sereina <
> sereina.rini...@gmai
]
Sent: Thursday, October 26, 2017 12:41 AM
To: Paul Hawkins
Cc: rdkit-discuss@lists.sourceforge.net; Sereina
Subject: Re: [Rdkit-discuss] Conformer generation
On Wed, Oct 25, 2017 at 6:52 PM, Sereina
mailto:sereina.rini...@gmail.com>> wrote:
Hi Paul,
Regarding your second question:
On
On Wed, Oct 25, 2017 at 6:52 PM, Sereina wrote:
> Hi Paul,
>
> Regarding your second question:
>
> On 25 Oct 2017, at 18:36, Paul Hawkins wrote:
>
> Also, once I generate the conformers what is best way to cluster them by
> RMSD so that each conformer has a minimum RMSD to all the others in the
Hi Paul,
Regarding your second question:
> On 25 Oct 2017, at 18:36, Paul Hawkins wrote:
>
> Also, once I generate the conformers what is best way to cluster them by RMSD
> so that each conformer has a minimum RMSD to all the others in the set?
I think the function AllChem.GetConformerRMSMatr
Hi Paul,
Your reuse of the variable num_confs inside the loop is causing that
monotonic decrease. So, if a molecule returns 190 conformers, the next
iteration has you only asking for 190 conformers. And so on.
Best,
David
On Wed, Oct 25, 2017 at 12:36 PM, Paul Hawkins
wrote:
> Hello,
>
>
> I
Hello,
I have run into a problem with using the RDKit to generate conformers of
molecules. I am using the following code:
from rdkit import Chem
from rdkit.Chem import AllChem
from timeit import default_timer as timer
def GenerateDGConfs(m,num_confs,rms):
start_time = timer()
ids =
Hi Jordan,
On Thu, Oct 5, 2017 at 6:48 AM, Jordan McCone wrote:
>
> I have a .smi file which has a number of smiles strings in it. I would
> like to generate a single 3D conformer using ETKDG for every smiles string
> in the list,
>
If you google around, you will find a number of emails, posts,
Hi all,
I have a .smi file which has a number of smiles strings in it. I would like
to generate a single 3D conformer using ETKDG for every smiles string in
the list, and then get the output as a single .mol2 file.
I am very new to rdkit and even python, and as much as i'd to do this
myself, I ne
Hi Sereina
Many thanks for investigating this.
Tim
On 29/06/2016 09:29, Sereina wrote:
Hi Tim,
I had a look at the 1DWD example and I detail in the following the
analysis I did as it may be useful to other users.
The conformer generation function has the option to print the
experimental
These papers may be relevant:
- http://pubs.acs.org/doi/full/10.1021/ci2004658
- https://jcheminf.springeropen.com/articles/10.1186/1758-2946-3-4
On Wed, Jun 29, 2016 at 1:29 AM, Sereina wrote:
> Hi Tim,
>
> I had a look at the 1DWD example and I detail in the following the
> analysis I
Hi Tim,
I had a look at the 1DWD example and I detail in the following the analysis I
did as it may be useful to other users.
The conformer generation function has the option to print the experimental
torsion preferences that were used in the generation:
printExpTorsionAngles=True
For 1DWD, it
This topic (https://sourceforge.net/p/rdkit/mailman/message/35173301/)
discussed using conformer generation as input into Open3DAlign.
One thing I noticed is that the conformer generation (using the
useExpTorsionAnglePrefs=True and
useBasicKnowledge=True options) does not generate conformers tha
Please disregard this email -- I hit the send button with too much haste...
-
Jean-Paul Ebejer
Early Stage Researcher
On 9 November 2011 15:47, JP wrote:
>
> Hi there RDKiters,
>
> Using the greatest/latest official RDKit release (2011_09_1), I am
> generating 50 conformers of a molecule, (+/
Hi,
On Fri, Oct 8, 2010 at 6:11 PM, Jean-Paul Ebejer
wrote:
>
> Is it possible to automatically generate say - 50 conformers out of a SMILES
> string ?
> Something like -
> x = generateConformers(50, 'C1CCC1OC')
There's not anything quite that simple out-of-the-box, but it wouldn't
be hard to do
Is it possible to automatically generate say - 50 conformers out of a SMILES
string ?
Something like -
x = generateConformers(50, 'C1CCC1OC')
Cheers
JP
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