Re: [Rdkit-discuss] Best practice: which (database) fingerprints to use ?

Hi JeanPaul, The difference between featmorganbv and morganbv is that the first one uses pharmacophore features for atom descriptions whereas the other one atom types (it essentially corresponds to the ECFP descriptors). I would suggest to use featmorganbv_fp only if you want to do more fuzzy

Re: [Rdkit-discuss] Write SDF as a string instead of two file

Hi JP, Maybe a comment since I ran into this before - you will loose the properties of a molecule when just using the MolBlock. Cheers Nik -Original Message- From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: Tuesday, May 17, 2011 6:10 AM To: JP Cc:

Re: [Rdkit-discuss] calculation of number of chiral centres in a mol

If you'd have 3D molecules you could use the AllChem.AssignAtomChiralTagsFromStructure() ... but that's only if you have 3D molecules. Nik -Original Message- From: JP [mailto:jeanpaul.ebe...@inhibox.com] Sent: Thursday, May 19, 2011 1:27 PM To: Greg Landrum Cc:

Re: [Rdkit-discuss] how to come to a good model

Hi Paul, I'd agree on Greg's comment - if this is for a hErg model then you will not have a lot of luck to make a reasonable model purely with physchem properties. I guess having information on ionizability could be of help. Another one to test - in case you need to make a 3 class model -

Re: [Rdkit-discuss] multiprocessing rdkit

Hi Paul, When I look at your definition below and the one that worked there is a slight difference. In fps_calc you are passing a molecule and then you try to iterate over it (in fps = [GetMorganFingerprint(x,3) for x in m] ). Whereas in generateconformations(m) you also pass a single

Re: [Rdkit-discuss] Mol2 Format problem ? Can't kekulize mol -- but with a twist.

fix. Unfortunately, but the mol2 file format (documentation) is such a pain in general and the multiple different implementations doesn't make it any better. Sorry Nik From: JP [mailto:jeanpaul.ebe...@inhibox.com] Sent: Thursday, January 12, 2012 3:33 PM To: Stiefl, Nikolaus Cc: rdkit-discuss

Re: [Rdkit-discuss] improving substructure search behavior with real molecules

Hi Greg, Personally I like your suggestion of the behaviour similar to SMARTS. That way one can decide to whwat level of granularity one wants. Obviously it also means that we have to think a bit more about our queries and database preparations - I am sure though this will only improve our

Re: [Rdkit-discuss] Detecting rings and bond types from PDB HETATM record

Hi JP, Not sure if this is of any help. If it's an pdb file from rcsb or an in-house one where you have a corresponding smiles available maybe you could use this information to properly setup the bond types using bond matches? I know the components.cif file still has quite a few errors - however,

Re: [Rdkit-discuss] matching substructures to molecules

Hi Gonzalo, SmilesToMol has a sanitize flag which you can set to False. However - I am not sure how well you molecule fingerprints will work with an unsanitized molecule. I would imagine that you will run into all sorts of funny problems wrt aromaticity detection etc. Not sure if this helps

Re: [Rdkit-discuss] fdef files

Hi James, Yes – I just checked the files I generated for the ph4 definitions and they definitely do not have the tautomer recognition (guess I am just not SMART enough for this ;-). I will follow up with Greg and see how quickly we can get the fdef file as a contribution so people can start to

Re: [Rdkit-discuss] non-smallest rings

do you just have to check if an atom is in a 6-membered ring? If so then In [8]: m = Chem.MolFromSmiles('COc1ccc(cc1O[C@H]1C[C@@H]2CC[C@H]1C2)C1CNC(=O)NC1') In [9]: [a.IsInRingSize(6) for a in m.GetAtoms()] Out[9]: [False, False, True, True, True, True, True, True, False, False,

Re: [Rdkit-discuss] Volume Overlap using RDKit

Hi JP, Do you want to do a shape align or just any sort of alignment? There is a MolAlign in All.Chem which will give you an RMSD align. This works well if you have reasonably similar molecules (do a GetSubstructMatch before to get the atom list). Don't think there is a shape alignment for

Re: [Rdkit-discuss] SmilesWriter

Hmm, I don't know if there is a predefined option in RDKit but if you have a list of properties (say propertyList) you want to pick you could write directly to a text file something along those lines: w.write(%s\t%s%(Chem.MolToSmiles(m),\t.join([m.GetProp(p) for p in propertyList if

Re: [Rdkit-discuss] RDkit user beginner.

Hi - welcome to the community You have a typo there GenMACCSkeys Should actually be GenMACCSKeys (ie an uppercase K in Keys) Try ipython (with the ipython notebook) then autocomplete will solve those issues for you more or less. The notebook is cool and there is some info in the mailing

Re: [Rdkit-discuss] Chemistry 101 question...

Hi James, Interesting. I wonder if this is also dependent on the transport phase that was used. Do you have any info on that? Was it a typical 10% MeOH or more something with dichlormethane? Cheers Nik From: James Davidson j.david...@vernalis.commailto:j.david...@vernalis.com Date: Tuesday,

Re: [Rdkit-discuss] Load mol2 file with partial charges

Hi Gaetano The properties of the mol2 file are stored as atom properties. Here is an example (sorry - the only thing I have at hand right now is a benzene mol2 file created with moe - note the mol2 file parser was tested on corina mol2 files) Here is the file

Re: [Rdkit-discuss] creating new properties on a molecule

Hi Chris No - that should just work: m = Chem.MolFromSmiles("CC") list(m.GetPropNames()) [] m.SetProp("NewProp","TheNewProp") list(m.GetPropNames()) ['NewProp'] m.GetProp("NewProp") 'TheNewProp' Ciao Nik From: chris dalton > Date: Monday 14

Re: [Rdkit-discuss] Corresponding Features to Mol2 file

Hi Nick What you are after is (based on your example below) feat = feats[0] feat.GetAtomIds() (here for the first feature. In addition you might also want to check out for a better understanding what is what: feat.GetFamiliy() feat.GetType() Ciao Nik From: Nicholas Michelarakis

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

Then I guess Greg’s solution is the better suited one since you don’t have to specify a list of isotopes (assuming that your input compounds will not have things like 12C specified). Minor modification: In [23]: q = rdqueries.IsotopeGreaterQueryAtom(1) In [24]: atomNums = [1,6,7,8,15,16] In

Re: [Rdkit-discuss] Check for Heavy Isotopes using RdKit

Hi Maybe this is much less efficient but I guess if you need it for specific isotopes then you could try using a smarts pattern and check for that? In [20]: q = Chem.MolFromSmarts("[13C,14C,2H,3H,15N,24P,46P,33S,34S,36S]") In [21]: m = Chem.MolFromSmiles('CC[15NH2]') In [22]:

Re: [Rdkit-discuss] elimination of small fragments

Even better ☺ From: Greg Landrum Date: Friday 29 June 2018 at 18:04 To: GMCProfile Cc: "rdkit-discuss@lists.sourceforge.net" Subject: Re: [Rdkit-discuss] elimination of small fragments How about just GetLargestFragment()? On Fri, 29 Jun 2018 at 16:45, Stiefl, Nikolaus mailto:ni

Re: [Rdkit-discuss] elimination of small fragments

Quick question – mostly to the core developers I guess: I just checked and have that kind of thing in my code in at least 5 different places - wouldn’t it make sense to have that kind of functionality as a convenience function as part of the GetMolFrags method? Something along the lines of

[Rdkit-discuss] RGroup matching in RGroup decomposition code

Hi all, I was playing around with the RGroup decomposition code and must say that I am pretty impressed by it. The fact that one can directly work with a MDL R-group file and that the output is a pandasDataFrame makes analysis really slick - well done ! However, one thing that irritates me is

Re: [Rdkit-discuss] RGroup matching in RGroup decomposition code

Kelley and he suggested to fix it in the underlying codebase so I hope this will be fixed in the next version :) Cheers Nik From: Paolo Tosco Sent: Thursday, December 13, 2018 11:09 AM To: Stiefl, Nikolaus ; RDKit Discuss Subject: Re: [Rdkit-discuss] RGroup matching in RGroup decomposition code

[Rdkit-discuss] CIx position at NIBR Cambridge, US

Dear all, I wanted to bring to your attention that our position for a cheminformatics expert in the CADD group in our global chemistry community at NIBR is opened again. https://www.novartis.com/careers/career-search/job-details/288340BR If you feel like you want to apply your skill set to

Re: [Rdkit-discuss] Cheminformatics Graduate School Recommendations?

Hi Patrick, Sorry yet another non US-based lab but I will still throw in Sereina Riniker’s group (Riniker, Sereina, Prof. Dr. | ETH Zurich) who recently attracted quite some talent ;-) Ciao Nik From: