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 <greg.land...@gmail.com>
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 <
> chernobrov...@gmail.com> 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 <jasinski.adr...@gmail.com>
>> 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 <chernobrov...@gmail.com>
>> :
>>
>>> 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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>>
>>
>>
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>
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> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
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http://p.sf.net/sfu/hpccsystems
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