Hi Guys,
I'm sorry it took me this long to try it... But I could finally get to it,
and it works well now. Thanks for your help!
--
Gustavo Seabra.
On Tue, Apr 11, 2023 at 3:19 AM Jan Halborg Jensen
wrote:
> Hi Gustavo
>
> raw_mol = Chem.MolFromXYZFile('acetate.xyz')
27;rdkit_mol.xyz')
mol2
[image: image.png]
Is there a bug on the XYZ code, or am I missing something?
Thanks!
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Gustavo Seabra.
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omol2 -Omol2_file.mol2 -m
The -m tells obabel to split the multimolecule file into individual
molecules.
--
Gustavo Seabra.
On Tue, Jul 27, 2021 at 1:37 PM Francesca Magarotto -
francesca.magarot...@studio.unibo.it
wrote:
> Hi,
> after a cluster analysis using a dataset of compounds from ZINC15 (
On Fri, Jul 23, 2021 at 4:53 AM Paolo Tosco
wrote:
>
> # here there seems to a be a bug with the 2D depiction, but that's another
> story
>
> template
>
> [image: image.png]
>
>
Just a quick thing: I don't know if this is supposed to be a bug or a
feature, but I noticed that this seems to be cau
Thanks a lot!
--
Gustavo Seabra.
On Fri, Jul 23, 2021 at 12:18 PM Paolo Tosco
wrote:
> Hi Gustavo,
>
> Chem.Atom.HasQuery() and Chem.Bond.HasQuery() return True when the
> underlying atom (or bond) is an instance of Chem.QueryAtom (or Chem.
> QueryBond).
> Query atoms and b
This works perfectly!
I could understand most of what you did there ;-), but what does the
".HasQuery()" mean? The RDKit API is not very clear about it: "Returns
whether or not the atom has an associated query". Is this described
anywhere else?
Thank you so much!
--
Gustavo S
idering a match on the
sulfone only if it really is there. (e.g., CF3 should *not* match.) Does it
make sense?
Thanks a lot!
--
Gustavo Seabra.
On Thu, Jul 22, 2021 at 4:52 PM Andrew Dalke
wrote:
> Hi Gustavo,
>
>
> > template =
> Chem.MolFromSmarts('[a]1(-[S](-*)(=[O]
bility (similar to
AtomCompare.CompareAny) only for a portion of the molecule and still
enforce specific atoms in another portion?
Thank you so much!
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qt -m")
Then you'll have the files you need. Of course, you will still need to
build the pdbqt file for the target and the vina_config file, but that you
only need to do once.
All the best,
--
Gustavo Seabra.
On Tue, Jun 22, 2021 at 4:08 AM Velik Velikov wrote:
> Dear all,
>
&g
Thak a lot to Greg and all contributors for the continuing development of
this project!
--
Gustavo Seabra.
On Fri, Mar 26, 2021 at 11:16 AM Greg Landrum
wrote:
> Dear all,
>
> I'm pleased to announce that the 2021.03 version of the RDKit is released.
> We actually manag
://github.com/nglviewer/nglview), but it
only shows what I believe is the first conformer in the molecule. How can I
change the conformer shown? or maybe is there a way to convert the
conformers to Mol objects?
Any idea would be greatly appreciated.
Thank you!
--
Gustavo Seabra
ed to change environment during runtime, it just means that
your environment is missing something...
--
Gustavo Seabra
From: Jeff Saxon
Sent: Wednesday, December 2, 2020 9:29:37 AM
To: Gustavo Seabra ;
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-di
w thread for it)
All the best,
Gustavo.
--
Gustavo Seabra
From: Jeff Saxon
Sent: Wednesday, December 2, 2020 9:37:01 AM
To: Gustavo Seabra ;
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Applying Lipinsky filter on ligand data set
Thank you
I don't believe that it is possible. You have to run your script from within
the environment where you installed rdkit.
What I actually do is to have a work environment, and then install all the
packages I need in this same env.
--
Gustavo Seabra
From:
ndas. SDF is a
better format for small molecules, anyway.
All the best,
--
Gustavo Seabra
____
From: Jeff Saxon
Sent: Wednesday, December 2, 2020 4:53:05 AM
To: Gustavo Seabra ;
rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Applying Lipinsky filter
ipinskyHBA','LipinskyHBD','ROMol
']]
return df
df = load_sdf_file("chembl-26_phase-1.sdf","ChEMBL_Phase-1","ID")
df.head() #Should show the top of the DataFrame, with the properties and the
structures.
All the best,
--
Gus
Chem.MolFromSmiles(template_smiles)
core = MurckoScaffold.GetScaffoldForMol(template_mol)
scaffold = Chem.MolToSmiles(core)
match = scaffold_matching(query_smiles,scaffold)
--
Gustavo Seabra
From: Andrew Dalke
Sent: Monday, November 23, 2020 7:59 AM
To: Gustavo Seabra
Cc: rd
stavo.
--
Gustavo Seabra
From: Adelene LAI
Sent: Friday, November 20, 2020 9:13:15 AM
To: Dan Nealschneider ; Gustavo Seabra
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Partial substructure match?
Hi Dan and Gustavo,
MCSS sounds good, but depends on the
is a naphthalene and the molecule to
search has a benzene, that would count as a 60% match.
Is there a way to do that in RDKit?
Thanks a lot!
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plicate molecules from my
database. I'm using a Pandas DataFrame and, with the more recent versions
of Pandas, the following works fine:
> df['InChI Key'] = df[mol_col].progress_apply(Chem.MolToInchiKey,
options="/FixedH")
> df.drop_duplicates(subset=['InChI
Aha! Fantastic!
Thanks a lot!!
Gustavo.
--
Gustavo Seabra
From: Paolo Tosco
Sent: Thursday, October 29, 2020 5:13:33 PM
To: Gustavo Seabra
Cc: Igor Pletnev ; RDKit Discuss
Subject: Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key
Hi Gustavo
Ok, thanks!
--
Gustavo Seabra.
On Thu, Oct 29, 2020 at 4:33 PM Igor Pletnev wrote:
> > Is this "/FixedH" an option in RDKit? How to use that? (I don't see it
> in the docs).
>
> Sorry, I am not so proficient in RDKit and can not answer exactly. Anyway,
> this
That does make sense, I understand it now, thanks!
Is this "/FixedH" an option in RDKit? How to use that? (I don't see it in
the docs).
Thanks,
--
Gustavo Seabra.
On Wed, Oct 28, 2020 at 6:10 PM Igor Pletnev wrote:
> Hi Gustavo,
>
> > ... I was generating the InCh
. On the bright side, I won't lose
time generating InChIs...
Can I trust that the same molecule will always get the same canonical
SMILES from RDKit, independent of how it is read? (Different SDF files,
geometries, atom orders, etc.?)
All the best,
Gustavo.
--
Gustavo Seabra.
On Sun, O
Thanks for looking into it. I'm happy to see.it wasn't just a mistake by me ;-)
I hope we can find what's wrong there.
Best,
Gustavo.
--
Gustavo Seabra
From: Adelene LAI
Sent: Friday, October 23, 2020 11:28:55 PM
To: Gustavo Seabra ; RDKit Di
r if this is a limitation of the InChI Key definition, or an
implementation issue.
Thanks a lot,
--
Gustavo Seabra.
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You can open the csv file directly into Schrodinger's Maestro. The free version
can open CSV files.
--
Gustavo Seabra
From: ITS RDC
Sent: Thursday, May 28, 2020 9:11:42 AM
To: RDKit Discuss
Subject: [Rdkit-discuss] Converting csv/xls file containing SMIL
angle in place of the
\n or \r symbols... (see picture)
Are there any ideas?
Thanks,
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Gustavo Seabra.
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Thanks. Yes, I too understood that it should get the connectivity from the
distances.
I'm using PDB for it being the output from another program.
I'll see what I can change then.
Thanks,
Gustavo.
--
Gustavo Seabra
From: Alan Kerstjens Medina
Se
s file?
I can open it regularly in other programs. Is there any way to "force" rdkit
to recognize the file?
Thanks,
--
Gustavo Seabra
a3.pdb
Description: Binary data
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https:
fferent way to get the atom mapping between
the two molecules?
Thanks a lot,
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a1.pdb
Description: Binary data
a2.pdb
Description: Binary data
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h files here, I put a test database and a Jupyter Notebook
with the example in here:
https://www.dropbox.com/s/v8kf7vzpmrjkidl/RDKit_test.zip?dl=0
Thanks a lot!
--
Gustavo Seabra
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