Hi Gyro,
> On Dec 8, 2021, at 11:02, Gyro Funch <gyromagne...@gmail.com> wrote:
>
> My work is in the area of toxicology and I am interested in generating SMILES
> for molecules referred to as 'short chain chlorinated paraffins' (SCCP).
>
> A general definition that is sometimes used is that an SCCP is given by the
> molecular formula
>
> C_{x} H_{2x-y+2} Cl_{y}
>
> where
>
> x = 10-13
> y = 3-12
>
> and the average chlorine content ranges from 40-70% by mass.
>
> -----
>
> Can anyone provide guidance on how to generate the list of SMILES
> corresponding to the above rules?
Here's an alternate approach to the ones presented so far.
https://gist.github.com/adalke/e62df8774032560fef750fa9c88b6516
Like Wim's version, it also generates the SMILES as the syntax level, though by
default it use RDKit to generate canonical SMILES output. (use --no-canonical
to disable the canonicalization step, which is also faster.)
Here it is with 4 carbons and 3 chlorines.
% python sccp_smiles.py --C 4 --Cl 3
Content range not specified. Using --min-content 0.4 and --max-content 0.7.
CCCC(Cl)(Cl)Cl
CCC(Cl)C(Cl)Cl
CCC(Cl)(Cl)CCl
CC(Cl)CC(Cl)Cl
CC(Cl)C(Cl)CCl
CC(Cl)C(C)(Cl)Cl
CC(Cl)(Cl)CCCl
ClCCCC(Cl)Cl
ClCCC(Cl)CCl
The "--C" and "--Cl" are aliases for "--min-C" and "--min-Cl"; if the maximums
are not specified then the maximum is set to the minimum.
Here's a range using all the bells and whistles:
% time python sccp_smiles.py --min-C 10 --max-C 13 --min-Cl 3 --max-Cl 12
--max-Cl-per-atom 2 --min-content 0.4 --max-content 0.7 --no-canonicalize >
example.smi
2.030u 0.156s 0:02.44 89.3% 0+0k 0+0io 0pf+0w
% wc -l example.smi
440334 example.smi
Wim reported 437001 for the same configuration. I haven't figured out if the
difference is due simply to differences in the molecular weight values.
I couldn't canonicalize and pin down the differences in part because Wim's
output generates SMILES strings that RDKit cannot parse:
% grep '^[(]' CSSP.smi | head -4
(Cl)C(Cl)(Cl)CCCCCCCCC(Cl)(Cl)
(Cl)C(Cl)(Cl)CCCCCCCC(Cl)C(Cl)(Cl)
(Cl)C(Cl)(Cl)CCCCCCCC(Cl)(Cl)C(Cl)(Cl)
(Cl)C(Cl)(Cl)CCCCCCC(Cl)CC(Cl)(Cl)
>>> from rdkit import Chem
>>> Chem.CanonSmiles("(Cl)C(Cl)(Cl)CCCCCCC(Cl)CC(Cl)(Cl)")
[14:31:12] SMILES Parse Error: syntax error while parsing:
(Cl)C(Cl)(Cl)CCCCCCC(Cl)CC(Cl)(Cl)
My code isn't well tested, but perhaps enough to get you on the way.
Cheers,
Andrew
da...@dalkescientific.com
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