[Rdkit-discuss] Avogadro2 scripts for RDKit
Dear all, For years, people have asked about running RDKit inside Avogadro (e.g., generating conformers with ETKDG instead of Open Babel). The new Avogadro 1.94 release makes it much easier to download and install Python scripts - Avogadro hands off a SDF file, something happens and RDKit hands back a new SDF. i started a few quick scripts: https://github.com/ghutchis/avogadro-rdkit - ETKDG v3 conformer (soon this will generate a specified number of conformers and rank with UFF or MMFF94 .. also will add all conformer coordinates) - Generate canonical tautomer - Optimize with UFF or MMFF94 The scripts are tiny but useful - and most is boilerplate to pop up dialogs or set the menu item. I don't know how many people use Avogadro here, but I'm curious for suggestions on common "molecule building" tasks: - Full standardize(?) - Canonical conformer frame of reference? Thanks, -Geoff ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] DeleteSubstructs issue
Hi
There appears to be an issue with the DeleteSubstructs method when deleting
groups from an aromatic N. The H-count is not reset properly leading to a
kekulise error.
The workaround is to Kekulise the molecule first. Of course, this would require
more extensive SMARTS based substructures to use the Kekule form.
Here is an example
import rdkit
from rdkit import Chem
print(rdkit.__version__)
smiles = 'c1cccn1C'
mol = Chem.MolFromSmiles(smiles)
Chem.Kekulize(mol,clearAromaticFlags=True)
sub = Chem.MolFromSmarts('[CH3]')
newmol = Chem.rdmolops.DeleteSubstructs(mol,sub)
Chem.SanitizeMol(newmol)
print("1: {}".format(Chem.MolToSmiles(newmol)))
mol = Chem.MolFromSmiles(smiles)
sub = Chem.MolFromSmarts('[CH3]')
newmol = Chem.rdmolops.DeleteSubstructs(mol,sub)
print("2: {}".format(Chem.MolToSmiles(newmol)))
Chem.SanitizeMol(newmol)
print("3: {}".format(Chem.MolToSmiles(newmol)))
With output
2021.03.2
1: c1cc[nH]c1
2: c1ccnc1
[09:50:41] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
Traceback (most recent call last):
File "test.py", line 21, in
Chem.SanitizeMol(newmol)
rdkit.Chem.rdchem.KekulizeException: Can't kekulize mol. Unkekulized atoms: 0
1 2 3 4
Thanks
Stephen
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Re: [Rdkit-discuss] RDKfingerprint function
Sorry I missed this thread earlier.
I think the documentation answers this question:
https://www.rdkit.org/docs/RDKit_Book.html#rdkit-fingerprints
-greg
On Tue, May 18, 2021 at 12:34 PM Nils Weskamp
wrote:
> Hi Din,
>
> to the best of my knowledge, the "RDKit" fingerprints are a path-based
> ("Daylight-like") fingerprint as described in slide 7 of that presentation.
>
> You may want to have a look at
>
> https://www.daylight.com/dayhtml/doc/theory/theory.finger.html
>
> for a more detailed description.
>
> Best,
> Nils
>
> Am 18.05.2021 um 12:27 schrieb דין עזרא:
> > Hi Nils,
> >
> > Thanks for your mail !
> > So if I understand correctly, the function of the fingerprint is related
> > to the topological fingerprint in the document?
> >
> > Thanks,
> > Din
> > On 18 May 2021, 13:10 +0300, Nils Weskamp ,
> wrote:
> >>
> >> There may be more recent sources available.
>
>
>
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Re: [Rdkit-discuss] rdkit and pip
Hi Marco, On Wed, May 26, 2021 at 2:37 PM Marco Stenta wrote: > Dear Colleagues, > I recently came across this > https://pypi.org/project/rdkit-pypi/ > > is pip going to be supported officially by the dev community? any plan? > I'm not quite sure yet. I believe that at the moment the pip images are still missing the extra data files that the RDKit requires in order to correctly function. After that's taken care of, we'll need one or more volunteers to make sure that the rdkit-pypi images stay up to date. Just like the conda-forge packages, this will be something that's community maintained, not something the development team takes care of. > getting out of the conda dependency might be beneficial to get > slightly slimmer docker images. > If this is something you actually care about, you can just create a docker image which has a local RDKit build matching the version of Python used in the container. -greg ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
