Hi Marco,
Welcome to the mailing list!
The trick in this particular case is that you want to do a maxDepth of 0
(that means a single iteration) and to tell BRICSBuild that you're willing
to see incomplete molecules (i.e. molecules that still contain a dummy
atom):
In [22]: from rdkit import Chem
...: from rdkit.Chem import BRICS
...: frags = ['[8*]C(C)(C)C', '[16*]c1ccc2occ([16*])c2c1']
...: molfrags = [Chem.MolFromSmiles(f) for f in frags]
...: print(list(Chem.MolToSmiles(x) for x in BRICS.BRICSBuild(molfrags,
onlyCompleteMols=False, maxDepth=0)))
['[16*]c1coc2ccc(-c3ccc4occ([16*])c4c3)cc12',
'[16*]c1ccc2occ(-c3ccc4occ([16*])c4c3)c2c1',
'[16*]c1ccc2occ(-c3coc4ccc([16*])cc34)c2c1',
'[16*]c1coc2ccc(C(C)(C)C)cc12', '[16*]c1ccc2occ(C(C)(C)C)c2c1']
The results with two [16*] attachment points happen because there's a rule
that allows [16*] - [[16*] bonds to be formed. This wasn't in the original
BRICS paper but it is consistent with the rest of the rules, so we added it.
I hope this helps,
-greg
On Mon, Mar 11, 2019 at 3:37 PM Marco Podda <marcopodda1...@gmail.com>
wrote:
> Hello,
> first of all, many thanks for this awesome library.
>
> I have little to none knowledge of chemistry, so I hope you'll excuse me
> if I say some chemical nonsense below.
>
> I have a fragmented molecule (fragmentation being done with the BRICS
> implementation in rdkit) which (for example) looks like this:
>
> frags = ['[8*]C(C)(C)C', '[16*]c1ccc2occ([16*])c2c1']
>
> Say I want to join the two fragments in the list. Then, I would write:
>
> from rdkit import Chem
> from rdkit.Chem import BRICS
> frags = ['[8*]C(C)(C)C', '[16*]c1ccc2occ([16*])c2c1']
> molfrags = [Chem.MolFromSmiles(f) for f in frags]
> combined = list(BRICS.BRICSBuild(molfrags, maxDepth=1))[0] # maxDepth=1
> gives me 1 result in this case
> print(Chem.MolToSmiles(combined, True)) # 'CC(C)(C)c1ccc2occ(C(C)(C)C)c2c1'
>
> If I understood this code correctly, BRICSBuild has reacted both dummy
> spots in the second fragment with the dummy spot in the first fragment.
> However, I would like to perform a partial join, meaning joining the first
> fragment only with one of the two dummy spots in the second fragment. In
> practice, I'm looking for a result like this:
>
> 'CC(C)(C)c1ccc2occ([16*])c2c1'
> or
> [16*]c1ccc2occ(C(C)(C)C)c2c1'
>
> Is there a way in rdkit to achieve this?
> Again, sorry for the poor chemical jargon and if I make not much sense
> from a chemical point of view.
>
> Thank you.
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