Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule
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Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule
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From: Pavel P. <pav...@uk...> - 2021-04-02 05:22:06
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Hi Ling, this can be a workaround if RDKit does not have a built-in function to extract a submolecule by atom ids. You may assign atom property labels to these atoms and then looping over atoms in EditableMol remove those ones which do not have this property assigned. Kind regards, Pavel. On 02/04/2021 02:30, Ling Chan wrote: > Yes, Kangway, that was what I first tried, as mentioned in the first > post. I did not have any problem with obtaining the primary fragments > (applying all cuts) . Just that I have not yet figured out how to > obtain the secondary fragments, either from recombining the > primary fragments, or from fragmenting from the initial molecule (by > not applying all cuts). > > Chuang, Kangway <Kan...@uc... > <mailto:Kan...@uc...>> 於 2021年4月1日週四 下午5:20寫道： > > Hi Ling, > > I think I've run into something similar before, have you tried > using FragmentOnBonds followed by Chem.GetMolFrags? GetMolFrags > lets you toggle a few things (e.g. (bool)asMols=False [, > (bool)sanitizeFrags=True) to provide some workarounds with > sanitization. > > Best, > Kangway > ------------------------------------------------------------------------ > *From:* Ling Chan <lin...@gm... > <mailto:lin...@gm...>> > *Sent:* Thursday, April 1, 2021 5:08 PM > *To:* Mark Mackey <ma...@cr... > <mailto:ma...@cr...>> > *Cc:* RDKit <rdk...@li... > <mailto:rdk...@li...>> > *Subject:* Re: [Rdkit-discuss] rejoining pairs of fragments after > fragmenting a molecule > >> /I did manage to achieve what I want by going > through Chem.MolFragmentToSmiles and then convert the Smiles back > to a Mol. But is there a neater way?/ > > Oops, I wrote too soon. Actually I did not achieve what I want. > The conversion from the smiles from Chem.MolFragmentToSmiles > sometimes crashes, because of Sanitization problem. > > > Ling Chan <lin...@gm... <mailto:lin...@gm...>> 於 > 2021年4月1日週四 下午4:11寫道： > > Thank you Mark for your suggestion. It sounds good and I gave > it a try. However, this leads to another question that may > sound dumb. > > I have the atom indices of a fragment. For example, the > fragment comes from atoms [3,4,5,9,10,11,14] of the original > molecule. How can I extract this fragment from the molecule? > I tried > > (1) using EditableMol and deleting atoms one by one using > RemoveAtom. But this does not work since the atom numbering > changes after each deletion. > (2) going through FragmentOnBonds. But the output of > FragmentOnBonds have the atom indices reshuffled so I cannot > directly use my index list to fish out my fragment. > > I did manage to achieve what I want by going > through Chem.MolFragmentToSmiles and then convert the Smiles > back to a Mol. But is there a neater way? Basically, is there > a Chem.MolFragmentToMol function? > > Thank you again. > > Ling > > > Mark Mackey <ma...@cr... > <mailto:ma...@cr...>> 於 2021年4月1日週四 > 上午1:58寫道： > > Hi Ling, > > Having done something similar (but not in RDKit), I would > suggest a different algorithm. I think that fragmenting > the molecule first and then stitching the bits together is > always going to be very complicated. Instead, just > fragment the molecule in the ways that you want: > > - Find the set B of all breakable bonds according to your > rules. I’m assuming here that B contains only acyclic bonds. > > - To get all of the pairwise pieces, for each element b of > B break all bonds in B _except_ b. Keep the fragment > containing b, and clean up. > > - To get all of the triplets, for each tuple (b1, b2) in > B, break all bonds in B except b1 and b2. Keep the > fragment containing b1 only if it also contains b2. > > Regards, > > Mark > > ** > > *-- * > > *Mark Mackey* > > *Chief Scientific Officer* > > *Cresset* > > New Cambridge House, Bassingbourn Road, Litlington, > Cambridgeshire, SG8 0SS, UK > > tel: +44 (0)1223 858890 mobile: +44 (0)7595 > 099165 fax: +44 (0)1223 853667 > > email:_m...@cr... > <mailto:ma...@cr...>_web:www.cresset-group.com > <https://urldefense.com/v3/__http://www.cresset-group.com/__;!!LQC6Cpwp!_TcJCf-sigb7LDzkbKrsrFcW9tvIZeaipJYFoxrlJcJu_i7ISOrtBw_r-FiTOxLSLc3HOA$> > skype: mark_cresset > > *From:*Ling Chan <lin...@gm... > <mailto:lin...@gm...>> > *Sent:* 31 March 2021 20:56 > *To:* RDKit <rdk...@li... > <mailto:rdk...@li...>> > *Subject:* [Rdkit-discuss] rejoining pairs of fragments > after fragmenting a molecule > > Dear Colleagues, > > I am trying to do something that I think is quite simple, > but I have not figured out a simple way. Don't know if I > am missing something. I am sure that ultimately I can > figure it out, but I wonder if there is a good way. > > I fragmented a molecule with some rules, using > FragmentOnBonds. I did get a list of primary fragments. > > I wish to recombine pairs (and triplets, but no bigger) of > these primary fragments, but only if the resulting > fragment is part of the original molecule. I.e. I want to > undo some of the cuttings. (FragmentOnSomeBonds does not > help, since you cannot ensure that the resulting fragments > consist only of pairs of primary fragments.) > > What is the best way to do this? The following is what I > am trying. > > I see that you can mark the original cut points using the > dummyLabels argument in FragmentOnBonds. So I converted > the primary fragments to smiles. I looked for the two > sides of the original cut point and substituted the two > dummyLables to [2H] and [3H]. I then tried to rejoin the > fragments using a reaction string > "[*:1][2H].[*:2][3H]>>[*:1][*:2]". Unfortunately the > ReactionFromSmarts function does not accept this string. > So I'll have to use Smarts search to look for [2H] and > [3H], then create an editable molecule from the two > primary fragments, look for neighbours of [2H] and [3H], > add a bond, then delete the atoms [2H] and [3H], then > sanitize. > > Thank you for your ideas. > > Ling > > > This email has been sent from Cresset BioMolecular > Discovery Limited, registered in England and Wales, > Company Number: 04151475. The information in this email > and any attachments are confidential and may be > privileged. It is intended solely for the addressee and > access to this email by anyone else is unauthorised. If an > addressing or transmission error has misdirected this > email, please notify the author by replying to this email. > If you are not the intended recipient you must not use, > disclose, distribute, store or copy the information in any > medium. Although this e-mail and any attachments are > believed to be free from any virus or other defect which > might affect any system into which they are opened or > received, it is the responsibility of the recipient to > check that they are virus-free and that they will in no > way affect systems and data. No responsibility is accepted > by Cresset BioMolecular Discovery Limited for any loss or > damage arising in any way from their receipt, opening or > use. Privacy notice > <https://urldefense.com/v3/__https://www.cresset-group.com/privacy/__;!!LQC6Cpwp!_TcJCf-sigb7LDzkbKrsrFcW9tvIZeaipJYFoxrlJcJu_i7ISOrtBw_r-FiTOxJWf9Hoxw$> > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss |
