Re: [Rdkit-discuss] Conformer generation

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 constrain distances but struggling. The lowest energy conformer is not what I

Re: [Rdkit-discuss] Conformer generation

lowing 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 calix

[Rdkit-discuss] Conformer generation

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

Re: [Rdkit-discuss] Conformer generation with torsion restraints/frozen atoms

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

[Rdkit-discuss] Conformer generation with torsion restraints/frozen atoms

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

Re: [Rdkit-discuss] Conformer generation

in cs: > > 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 <phawk...@eyesopen.com> > *Cc:* rdkit-discuss@lists.

Re: [Rdkit-discuss] Conformer generation

] Sent: Thursday, October 26, 2017 12:41 AM To: Paul Hawkins <phawk...@eyesopen.com> Cc: rdkit-discuss@lists.sourceforge.net; Sereina <sereina.rini...@gmail.com> Subject: Re: [Rdkit-discuss] Conformer generation On Wed, Oct 25, 2017 at 6:52 PM, Sereina <sereina.rini...@gmail.com<m

Re: [Rdkit-discuss] Conformer generation

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

Re: [Rdkit-discuss] Conformer generation

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

Re: [Rdkit-discuss] Conformer generation

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

Re: [Rdkit-discuss] Conformer generation using ETKDG

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

[Rdkit-discuss] Conformer generation using ETKDG

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

Re: [Rdkit-discuss] Conformer generation does not sample well?

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

Re: [Rdkit-discuss] Conformer generation does not sample well?

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,

[Rdkit-discuss] Conformer generation does not sample well?

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

Re: [Rdkit-discuss] Conformer generation problem -- stereochemistry

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 jeanpaul.ebe...@inhibox.com wrote: Hi there RDKiters, Using the greatest/latest official RDKit release (2011_09_1), I am generating 50

[Rdkit-discuss] Conformer Generation using RDKit (basic)

Is it possible to automatically generate say - 50 conformers out of a SMILES string ? Something like - x = generateConformers(50, 'C1CCC1OC') Cheers JP -- Beautiful is writing same markup. Internet Explorer 9 supports

Re: [Rdkit-discuss] Conformer Generation using RDKit (basic)

Hi, On Fri, Oct 8, 2010 at 6:11 PM, Jean-Paul Ebejer jeanpaul.ebe...@inhibox.com 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