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. It doesn't make a lot of sense to probe the same old sites and the > same old conformations. > > > .-- .- -. - / .- -.-. - .. --- -. ..--.. / -.-. --- -. .--- ..- --. .- - . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn UTC-6 bit.ly/virtualfriam > <http://bit.ly/virtualfriam> > un/subscribe http://redfish.com/mailman/listinfo/friam_redfish.com > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,kAEQVqygw-mklC6UzbbrvFqhvMSszsFykfEAr20R02FDJR4m_r4IBO71CKTc3BdTs5S-5Wf6J3avuTUYvk5hFvKuoGvPoMd1MKhLv_Ts6B4Bc2N6TGcdxG_qxrIj&typo=1> > FRIAM-COMIC http://friam-comic.blogspot.com/ > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,_qKIclWboq6eryGEjSyfIE-qwCg6WC8-eDHMypbep_QZKNW-OaiW9VTwtjuzBFAslwp5PZ8np10L-fCwwWwCO0TyPgku_T-lXXiWZVYNSRg72vRYqff3eDw,&typo=1> > archives: > 5/2017 thru present https://redfish.com/pipermail/friam_redfish.com/ > <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fredfish.com%2fpipermail%2ffriam_redfish.com%2f&c=E,1,oAHgPoDoLaUeb8920Laf41onFQbRDR4QMgTbRpcGeKTEq5lBB5iFIfX4rnSHeu6uO7glgVXQc2bXhyF7a58GGJrjK4s3PmUOvlw1YytDjJxaTZDSQ1lERSjqaXde&typo=1> > 1/2003 thru 6/2021 http://friam.383.s1.nabble.com/ > <http://friam.383.s1.nabble.com/> > .-- .- -. - / .- -.-. - .. --- -. ..--.. / -.-. --- -. .--- ..- --. .- - . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn UTC-6 bit.ly/virtualfriam > <http://bit.ly/virtualfriam> > un/subscribe http://redfish.com/mailman/listinfo/friam_redfish.com > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,gWfkgKf-PuOkcHJvAZ588kXqzytuPowg2rtDPj_r_THM-EJOjIU357mKqxOGFr_RO_JC2ofIkIBawyiVyes3hGTIsn3nEX1xL5-mNb0fJw,,&typo=1> > FRIAM-COMIC http://friam-comic.blogspot.com/ > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,H5Y8mKdfAoW6w8roMiiK2wvkR1uDfGGiXm9oGFAZC3xrwX3ocGXGeU8robt_HQBXPShiE02IJJl_6Eg1pybkph6Y2p7cmXixiR1AftVfN6-F2w,,&typo=1> > archives: > 5/2017 thru present https://redfish.com/pipermail/friam_redfish.com/ > <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fredfish.com%2fpipermail%2ffriam_redfish.com%2f&c=E,1,_vfY1Z3NVF8sL8-JjNOd3_NLM5QrG86_7zZd8MF4Dv6iPYrbsCV_Yu6IPpzqvtKzHYnnSXjFwg30MzRdYCiPRkLSfVZLWujHSCuasYsMocpT&typo=1> > 1/2003 thru 6/2021 http://friam.383.s1.nabble.com/ > <http://friam.383.s1.nabble.com/> > > .-- .- -. - / .- -.-. - .. --- -. ..--.. / -.-. --- -. .--- ..- --. .- - . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn UTC-6 bit.ly/virtualfriam > un/subscribe > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,0lqPD06aA9PWXkU2fYWCaqLSikddQZe80PLaUZeu5FviFGeVFNJOWUS-ojJgAhZPBqzb1CSzVpDEgSSd97X-0yMyJT0Ifp6g5zZsMluwCJvPQJDo&typo=1 > FRIAM-COMIC > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,IIJT1XMEIpixe9hmK9RgGG-RCx-58qn9yflxV_UPIoBfA9m_5ZL1vp1ZBM_jtQ3JtRRCuWHZL3XktDbmoP_PNQTrbYJIbASZn-tjECMkL_fF&typo=1 > archives: > 5/2017 thru present > https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fredfish.com%2fpipermail%2ffriam_redfish.com%2f&c=E,1,uLozJkxopu31LHxRrhRpWQtadMzQFFxqD3RcqHq6qkqbVwXWNTeGHvkK6o69I1-IQJFtwpW7zSk162gTTSRMq9tfsf8gR28jX1grDxHhCNG0thc_dlJAGoFoCEY,&typo=1 > 1/2003 thru 6/2021 http://friam.383.s1.nabble.com/
.-- .- -. - / .- -.-. - .. --- -. ..--.. / -.-. --- -. .--- ..- --. .- - . FRIAM Applied Complexity Group listserv Zoom Fridays 9:30a-12p Mtn UTC-6 bit.ly/virtualfriam un/subscribe http://redfish.com/mailman/listinfo/friam_redfish.com FRIAM-COMIC http://friam-comic.blogspot.com/ archives: 5/2017 thru present https://redfish.com/pipermail/friam_redfish.com/ 1/2003 thru 6/2021 http://friam.383.s1.nabble.com/