Would this be of any use? https://www.molgen.de/ <https://www.molgen.de/>
It sounded like you were doing something that you want to be fast and in-line, and I don’t know if MOLGEN grants an API that offers that degree of flexibility. People I know who have worked with it say that it is fairly sophisticated in creating physically realizable molecules while still retaining as much combinatorics as possible. Eric > On Oct 13, 2021, at 1:17 AM, Roger Critchlow <r...@elf.org> wrote: > > As long as you stick to basic CNO type chemistry, you can probably figure out > a valid SMILES generator pretty quickly. But it might be easier to work in > the explicit molecule graph instead and just use SMILES as a content name > string. The things that might go wrong after the SMILES input parses > correctly are 1) a ring that's strained because it's too tight a turn, 2) > steric hindrance between bulky sidechains occupying the same space, and 3) > something that no one has any idea how to make. You could probably notice 1) > and 2) if you track the average energy per bond. > > The benzodiazepines are a classic example of structuring the search around a > core framework and substituting side chains onto the core. That's the way > the chemists do it in the wetlab. > > OpenEyes (https://www.eyesopen.com/ > <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.eyesopen.com%2f&c=E,1,_xhq5QreQZB85pzOZP4KFzWNyfJ6g58Ug0kZ0JhX8dk_Swwzs3vVfH3NzcPCYAmGXnfJwwPGIy92mvg8xwUamvtMznmqiBwYIVKPMrP9mxu0PNYU1yT1CA,,&typo=1>) > is running some online events this month that might be interesting. > > -- rec -- > > On Tue, Oct 12, 2021 at 5:44 PM Marcus Daniels <mar...@snoutfarm.com > <mailto:mar...@snoutfarm.com>> wrote: > A search algorithm that, say, proposes a prefix or a suffix to a SMILES > string would need to have a way to autocomplete candidates before it could > use these descriptors to guide an optimization because the parsing step is > non-trivial, never mind the sanitization step (mentioned on that web page). > > > > > I will deflect blame on Jon for changing the topic from music to chemicals, > but presumably with enough debate their aesthetic preferences in music could > be formalized in theory or some rule-based way, as is manifest here. > > > > From: Friam <friam-boun...@redfish.com <mailto:friam-boun...@redfish.com>> On > Behalf Of Roger Critchlow > Sent: Tuesday, October 12, 2021 2:10 PM > To: The Friday Morning Applied Complexity Coffee Group <friam@redfish.com > <mailto:friam@redfish.com>> > Subject: Re: [FRIAM] Schwill Rock? > > > > Hmm, when I was in the drug discovery canal, the "descriptors" that you could > calculate from a SMILES string were legion. > > > > Here's the list for RDKIT, > https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors > > <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.rdkit.org%2fdocs%2fGettingStartedInPython.html%23list-of-available-descriptors&c=E,1,_kV11Wpf_w1jT9C6j7k5J6CtV07T8ZMZLuU_TZVTdAv25WVN3Yk22udDwGD8Ti62gmCqg8x92QOM2UkL6j7n_2jsDLSzmxBHU6BMX2kShuNUW0_oZg,,&typo=1>. > There are one bunch that depend entirely on the formula and molecular > structure. Then there's a whole other bunch you can compute if you generate > 3d structures for the molecules, possibly multiplied by the number of low > energy structures the molecule can adopt. > > > > What kind of plausibility were you looking for? Does the SMILES string > specify a real molecule? That's hard. There are syntax errors in SMILES, > failures to close rings, valency errors, charge errors. But there are lots > of syntactically valid SMILES that won't match any known molecule, either > because they're impossible or as yet to be determined. The pharmas all have > their own lists of molecules of interest, but those are proprietary. Looks > like there are various online databases, none that I'm familiar with. If the > SMILES parses, you can try generating a 2d depiction and a 3d structure. > Those will throw exceptions if things get too weird. > > > > -- rec -- > > > > On Tue, Oct 12, 2021 at 3:22 PM Marcus Daniels <mar...@snoutfarm.com > <mailto:mar...@snoutfarm.com>> wrote: > > I was playing with RDKIT the other day, and it wasn’t obvious how to get a > scalar quantity of plausibility of a molecule. It seems a SMILES string is > right or wrong, and then maybe there are some warnings that can be trapped. > However, the benefits for search or fair sampling are different than the > needs of correctness checks, which is deeper property. That isn’t quite a > fit to the music example where aesthetic considerations are subjective. > > > > From: Friam <friam-boun...@redfish.com <mailto:friam-boun...@redfish.com>> On > Behalf Of Jon Zingale > Sent: Tuesday, October 12, 2021 12:11 PM > To: friam@redfish.com <mailto:friam@redfish.com> > Subject: Re: [FRIAM] Schwill Rock? > > > > "I mean from the perspective of aesthetics. Understanding why Pandora is > messing it up means sampling the deep wells." > > > > Yes, but not more than one has to. This is why I am advocating for methods > like a weighted ensemble. The working analogy for me comes from drug > discovery. 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