Re: [Rdkit-discuss] Virtual hydrogens for metals (smiles and smarts)
For mere humans, working with SMARTS is always a pain. But, some nice people are trying to make your life easier: https://smarts.plus/ [2] K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey; From Structure Diagrams to Visual Chemical Patterns, J. Chem. Inf. Model., 2010, 50 (9), pp 1529-1535 On 19/05/2023 07:17, Jarod Younker wrote: I’ve got the following two smiles strings: [Zr]C [ZrH] The smarts string [Zr][CH3] matches [Zr]C. What’s the smarts for [ZrH]? I’ve tried [Zr][H]. It does not match. Sent from my iPhone ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Virtual hydrogens for metals (smiles and smarts)
[Zr;H1] this smarts pattern should match an Zirconium with hcount of
exactly one. see below for a demonstration:
m=Chem.MolFromSmiles("[ZrH]CC")
pat=Chem.MolFromSmarts("[Zr;H1]")
len(m.GetSubstructMatches(pat))
1
hope this helps,
wim
On Fri, May 19, 2023 at 12:33 AM Jarod Younker
wrote:
> I’ve got the following two smiles strings:
>
> [Zr]C
> [ZrH]
>
> The smarts string [Zr][CH3] matches [Zr]C. What’s the smarts for [ZrH]?
> I’ve tried [Zr][H]. It does not match.
>
> Sent from my iPhone
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] Virtual hydrogens for metals (smiles and smarts)
I’ve got the following two smiles strings: [Zr]C [ZrH] The smarts string [Zr][CH3] matches [Zr]C. What’s the smarts for [ZrH]? I’ve tried [Zr][H]. It does not match. Sent from my iPhone ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to decompose the UFF (or MMFF94) scoring of a small molecule?
But it’s not so simple. If you rotate a dihedral, all the non-bonded VdW interactions also change. Calculating a force field energy at one particular geometry is extremely fast, and the current version allows you to run multiple energies in parallel. Generate a bunch of geometries at once and then score those in parallel. Trying to “update” isn’t worth it, because there are always more non-bonded interactions (n^2) than bonds and angles. -Geoff On May 18, 2023 at 4:24 AM -0400, Francois Berenger , wrote: > Dear list, > > I asked this question in rdkit's github discussions: > > https://github.com/rdkit/rdkit/discussions/6377 > > But, apparently that's not more responsive than the ML, so here is my > question: > --- > I have a ligand, I would like to score its current conformer using > rdkit's UFF implementation. > > Later, I would like to change some rotatable bond (single bond out of > ring) and update > the conformer's energy bu just re-evaluating the part of the energy that > is supposed to have > changed (i.e. the dihedral component). > Bond lengths, bond angles and partial charges being constant. > > I suspect it should be faster than rescoring the conformer from scratch. > > How to do this with rdkit? > --- > > Thanks a lot, > Francois. > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to decompose the UFF (or MMFF94) scoring of a small molecule?
Hi Francois, I have replied on GitHub ~10’ ago. p. > On 18 May 2023, at 10:23, Francois Berenger wrote: > > Dear list, > > I asked this question in rdkit's github discussions: > > https://github.com/rdkit/rdkit/discussions/6377 > > But, apparently that's not more responsive than the ML, so here is my > question: > --- > I have a ligand, I would like to score its current conformer using rdkit's > UFF implementation. > > Later, I would like to change some rotatable bond (single bond out of ring) > and update > the conformer's energy bu just re-evaluating the part of the energy that is > supposed to have > changed (i.e. the dihedral component). > Bond lengths, bond angles and partial charges being constant. > > I suspect it should be faster than rescoring the conformer from scratch. > > How to do this with rdkit? > --- > > Thanks a lot, > Francois. > > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] How to decompose the UFF (or MMFF94) scoring of a small molecule?
Dear list, I asked this question in rdkit's github discussions: https://github.com/rdkit/rdkit/discussions/6377 But, apparently that's not more responsive than the ML, so here is my question: --- I have a ligand, I would like to score its current conformer using rdkit's UFF implementation. Later, I would like to change some rotatable bond (single bond out of ring) and update the conformer's energy bu just re-evaluating the part of the energy that is supposed to have changed (i.e. the dihedral component). Bond lengths, bond angles and partial charges being constant. I suspect it should be faster than rescoring the conformer from scratch. How to do this with rdkit? --- Thanks a lot, Francois. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
