Re: [Rdkit-discuss] Count-based fingerprints of molecules with and without starred atoms

It is encoded as an atom with element number 0, and unless you specify otherwise 0 mass, 0 charge. Steve On Sun, 19 Sep 2021, 17:06 Gianmarco Ghiandoni, wrote: > I have a question for the RDKit community that regards count-based RDKit > fingerprints. During a test, I have noticed that the

Re: [Rdkit-discuss] Strange core dump with Morgan fingerprints with Java

Hi Tim, You mentioned the calculation is done using Java streams. Have you tried calling #sequential() on your stream to force it to run single threaded from the Java side? Steve On Wed, 3 Feb 2021, 12:58 Greg Landrum, wrote: > Given the fun that threading is, this isn't necessarily

Re: [Rdkit-discuss] proper technical term for generating virtual compounds with rdkit and smarts

I recall the first time I heard the term was in a project meeting in RiboTargets back in around 1999/2000. One of our modelling group used it after hearing discussion of results of in vitro and in vivo studies being discussed. My recollection is that there was a certain amount of amusement at

Re: [Rdkit-discuss] Are atom and bond indexes deterministic?

It looks like it should be deterministic, in that it always loops through the existing non-hydrogen atoms in their internal order, adding H's to each in turn. https://github.com/rdkit/rdkit/blob/ffc123a6659705adae33a6f5bf3913d65aa7b54d/Code/GraphMol/AddHs.cpp Steve On Wed, 3 Oct 2018 at 21:23,

Re: [Rdkit-discuss] GetMolFrags asMols with persistent atom indexes

You could try looping over all your atoms and calling setIntProp on each one to set a property with the original index, then get that property value back rather than the new atom indices. Steve On Mon, 2 Jul 2018, 17:43 Joshua Meyers, wrote: > Hey Again, > > Back to this problem because I

Re: [Rdkit-discuss] Make chain atoms not match ring atoms

Axel, You need to use a SMARTS query: q = Chem.MolFromSmarts("[CR0][CR0][CR0]") Have a look at http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html Steve On 29 June 2018 at 08:04, Axel Pahl wrote: > Dear all, > > my google-fu is failing is me. > Is it possible in substructure

Re: [Rdkit-discuss] RDKit Reaction gives disconnected components

Steve From: Brian Kelley [fustiga...@gmail.com] Sent: 30 March 2017 17:59 To: Stephen Roughley Cc: RDKit Discuss (rdkit-discuss@lists.sourceforge.net) Subject: Re: [Rdkit-discuss] RDKit Reaction gives disconnected components Correction here, you are not maki

[Rdkit-discuss] RDKit Reaction gives disconnected components

Dear Greg/RDKitters, This may be user error, or misunderstanding of rSMARTS, so can anyone throw some light on the following behaviour? First example works as expected - there are 2× Ph in m4, so we end up with 2×2×2 copies of the expected product:

Re: [Rdkit-discuss] mass replacement of External R-groups with many substituents

You can match a dummy atom (*) with the SMARTS [#0] Steve On 16 Mar 2017 16:43, "Chris Earnshaw" wrote: > Hi Brian > > I'm by no means an expert in RDKit with Python, but until someone else > comes along, here are a few thoughts. > > Your reaction SMARTS specifically

Re: [Rdkit-discuss] RDKit conformer handling possible bug?

Thanks Greg. For completeness, for anyone trying this from the Java wrappers, the relevant methods are mol.clearConformers(); and mol.addConformer(conf, true); Steve From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 11 January 2017 11:01 To: Stephen Roughley Cc: RDKit Discuss Subject

Re: [Rdkit-discuss] RDKit conformer handling possible bug?

[mailto:greg.land...@gmail.com] Sent: 11 January 2017 07:24 To: Stephen Roughley; RDKit Discuss Subject: Re: RDKit conformer handling possible bug? Hi Steve, [A general request: please send RDKit questions/comments to the rdkit-discuss mailing list so that others can see the questions and answers. I'm