>> *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 <lingtrek...@gmail.com> 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 <m...@cresset-group.com> 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...@cresset-group.com <m...@cresset-group.com>* web: >> www.cresset-group.com skype: mark_cresset >> >> >> >> >> >> >> >> *From:* Ling Chan <lingtrek...@gmail.com> >> *Sent:* 31 March 2021 20:56 >> *To:* RDKit <rdkit-discuss@lists.sourceforge.net> >> *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. 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