Re: [Rdkit-discuss] Chemical formula

[Alexey C. <che...@gm...>]

Cool, Thanks Pat. It looks much “pythonic” :)

On Jun 13, 2014, at 16:18 , Patrick Fuller <pat...@gm...> wrote:

> If you’re using Python, I’d recommend using collections.Counter (part of the standard lib). It’s better than rolling out your own parser.
> 
> In [1]: from rdkit import Chem
> In [2]: mol = Chem.AddHs(Chem.MolFromSmiles('C(=O)O'))
> In [3]: from collections import Counter
> In [4]: c = Counter(atom.GetSymbol() for atom in mol.GetAtoms())
> In [5]: c
> Out[5]: Counter({'H': 2, 'O': 2, 'C': 1})
> Counter acts like a dict + some extra methods, and can be converted to a plain dict with d = dict(c).
> 
> Pat
> 
> ​
> 
> 
> On Fri, Jun 13, 2014 at 6:34 AM, Greg Landrum <gre...@gm...> wrote:
> if you want the formula as dictionary of counts instead of a string, you can either parse the string or write a separate calculator.
> Andrew Dalke posted one a while ago: http://sourceforge.net/p/rdkit/mailman/message/21653212/
> 
> -greg
> 
> 
> 
> On Fri, Jun 13, 2014 at 4:49 AM, Alexey Chernobrovkin <che...@gm...> wrote:
> Thanks, Adrian.
> 
> Won’t I reinvent the wheel if I’ll parse the formula to get a dict (element->count)?
> 
> On Jun 13, 2014, at 10:43 , Adrian Jasiński <jas...@gm...> wrote:
> 
>> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdMolDescriptors-module.html#CalcMolFormula
>> 
>>         from rdkit.Chem.rdMolDescriptors import CalcMolFormula
>>         formula = CalcMolFormula(Chem.MolFromSmiles("CCCOC"))
>> 
>> pozdrawiam
>> Adrian
>> 
>> 
>> 2014-06-13 10:20 GMT+02:00 Alexey Chernobrovkin <che...@gm...>:
>> Hi all,
>> 
>> Sorry for stupid question… But what is the simplest way to get chemical formula of a molecule using rdkit?
>> 
>> Cheers,
>> Alex
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