[Rdkit-discuss] PandasTools LoadSDF: Different treatment of SMILES depending on presence of 'MOL' column?

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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] Help mapping atoms between two files

fferent way to get the atom mapping between the two molecules? Thanks a lot, -- Gustavo Seabra a1.pdb Description: Binary data a2.pdb Description: Binary data ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] RDKit Chem.MolFromPDBFile ignores some files...

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 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https:

Re: [Rdkit-discuss] RDKit Chem.MolFromPDBFile ignores some files...

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

[Rdkit-discuss] Multiline legend in MolsToGridImage

angle in place of the \n or \r symbols... (see picture) Are there any ideas? Thanks, -- Gustavo Seabra. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Converting csv/xls file containing SMILES to .sdf

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

[Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

r if this is a limitation of the InChI Key definition, or an implementation issue. Thanks a lot, -- Gustavo Seabra. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

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

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

. 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

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

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

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

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

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

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

Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key

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

[Rdkit-discuss] Partial substructure match?

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! -- Gustavo Seabra ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourc

Re: [Rdkit-discuss] Partial substructure match?

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

Re: [Rdkit-discuss] Partial substructure match?

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

Re: [Rdkit-discuss] Applying Lipinsky filter on ligand data set

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

Re: [Rdkit-discuss] Applying Lipinsky filter on ligand data set

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

Re: [Rdkit-discuss] activate my-rdkit-env from python script

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:

Re: [Rdkit-discuss] Applying Lipinsky filter on ligand data set

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

Re: [Rdkit-discuss] activate my-rdkit-env from python script

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

[Rdkit-discuss] Get conformers as independent mols?

://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

Re: [Rdkit-discuss] 2021.03.1 RDKit Release

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

Re: [Rdkit-discuss] Autodock Vina

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

[Rdkit-discuss] Maximum Common Substructure using SMARTS

bility (similar to AtomCompare.CompareAny) only for a portion of the molecule and still enforce specific atoms in another portion? Thank you so much! -- Gustavo Seabra. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Maximum Common Substructure using SMARTS

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]

Re: [Rdkit-discuss] Maximum Common Substructure using SMARTS

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

Re: [Rdkit-discuss] Maximum Common Substructure using SMARTS

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

Re: [Rdkit-discuss] Maximum Common Substructure using SMARTS

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

Re: [Rdkit-discuss] Generating 3D molecules for docking

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 (

[Rdkit-discuss] Problems reading XYZ file

27;rdkit_mol.xyz') mol2 [image: image.png] Is there a bug on the XYZ code, or am I missing something? Thanks! -- Gustavo Seabra. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] Problems reading XYZ file

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')