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
[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
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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
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,
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.
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