Re: [Rdkit-discuss] Fragmentation Help

[Paolo T. <pao...@gm...>]

Hi Ben,

you could use SMARTS queries to do that, e.g.:

from  rdkit  import  Chem
from  rdkit.Chem.Draw  import  IPythonConsole

RDKit WARNING: [19:50:41] Enabling RDKit 2020.03.1dev1 jupyter extensions

sucrose  =  "O1[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O[C@@]2(O[C@@H]([C@@H](O)[C@@H]2O)CO)CO"

sucrose_mol  =  Chem.MolFromSmiles(sucrose)

sucrose_mol

primary_alcohol  =  Chem.MolFromSmarts("[CH2][OH1]")

sucrose_mol.GetSubstructMatches(primary_alcohol)

((2, 3), (19, 20), (21, 22))

secondary_alcohol  =  Chem.MolFromSmarts("[CH1][OH1]")

sucrose_mol.GetSubstructMatches(secondary_alcohol)

((4, 5), (6, 7), (8, 9), (15, 16), (17, 18))

I hope this helps, cheers
p.

On 16/11/2019 22:02, Ben Davidson wrote:
> Hi, I am using RDKit to basically identify the oxygenated groups in 
> complex biomass. The ether, ester, ketone, and aldehyde getfrag 
> commands are amazing. I am wondering if it is possible to identify the 
> different types of alcohols in a molecule ie, primary, secondary, and 
> finally tertiary. For example in sucrose, there are 8 alcohols, 5 
> secondary and 3 primary, is it possible to have RDKit identify that 
> for me? if you would like to see any code feel free to email me at 
> dav...@gm... <mailto:dav...@gm...>
> Any help would be greatly appreciated.
> -Ben
>
>
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