Re: [Rdkit-discuss] Leaky Memory?

[Greg L. <gre...@gm...>]

On Wed, Jun 11, 2014 at 4:35 AM, Nicholas Firth <Nic...@ic...>
wrote:

> I want to show some numbers from a compatible fragmentation scheme to my
> own one. Which means generating all the leaves from the hierarchy and then
> doing some post processing to merge these fragments. This isn't a problem
> on some of the more drug like data sets, however with ChEMBL this is
> causing me some stress.
>

If you're ok using BRICS instead of RECAP, you can do something like this:

In [24]: mol = Chem.MolFromSmiles('CC[C@H](C)[C@H](NC(=O)[C@H
](CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](N)CCSC)[C@@H](C)O)C(=O)NCC(=O)N[C@
@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@
@H](CC(=O)N)C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@
@H](CCC(=O)N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@
@H](CCCN=C(N)N)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@
@H](CCCN=C(N)N)C(=O)NCC(=O)N[C@@H](CCC(=O)N)C(=O)N[C@
@H](CC(C)C)C(=O)NCC(=O)N2CCC[C@H]2C(=O)N3CCC[C@H]3C(=O)NCC(=O)N[C@
@H](CO)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N')

In [25]: frags =
Chem.GetMolFrags(Chem.FragmentOnBRICSBonds(mol),asMols=True)

In [26]: smis = set([Chem.MolToSmiles(x,True) for x in frags])

In [27]: len(smis)
Out[27]: 17

In [28]: smis
Out[28]:
{'[1*]C(=O)C[4*]',
 '[1*]C(=O)[C@@H](N)CC[4*]',
 '[1*]C(=O)[C@@H]([4*])C',
 '[1*]C(=O)[C@@H]([4*])CC(C)C',
 '[1*]C(=O)[C@@H]([4*])CC(N)=O',
 '[1*]C(=O)[C@@H]([4*])CCC(N)=O',
 '[1*]C(=O)[C@@H]([4*])CCCN=C(N)N',
 '[1*]C(=O)[C@@H]([4*])CO',
 '[1*]C(=O)[C@@H]([4*])C[8*]',
 '[1*]C(=O)[C@H]([4*])[C@@H](C)CC',
 '[1*]C(=O)[C@H]([4*])[C@@H](C)O',
 '[1*]C([6*])=O',
 '[11*]SC',
 '[14*]c1c[nH]cn1',
 '[4*][C@@H](CCCN=C(N)N)C(N)=O',
 '[5*]N1CCC[C@@H]1[13*]',
 '[5*]N[5*]'}


Doing the same thing with the RECAP rules is not quite as trivial, but
should be doable

-greg