Hi Joss,
Yes there is an easier way, by using substructure search, i.e. do a
substructure search for [C] and then get the number of matches.
Hope this example to be readable and answer your question.
In [1]:
from rdkit import rdBase
print rdBase.rdkitVersion
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
2014.09.2
In [2]:
m = Chem.MolFromSmiles("CCCCCCCCc1ccccc1")
m
Out[2]:
[image: Inline images 1]
In [3]:
patt= Chem.MolFromSmarts("[C]")
print Chem.MolToSmarts(patt)
C
In [4]:
pm = m.GetSubstructMatches(patt)
print len(pm)
8
Regards,
Christos
Christos Kannas
Researcher
Ph.D Student
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On 7 October 2015 at 10:12, Joos Kiener <joos.kie...@gmail.com> wrote:
> Hi all,
>
> is there an easy way I'm missing to get the number of C-Atoms in a
> molecule?
>
> Currently I iterate all atoms and check if it's symbol is C. Doesn't seem
> very efficient.
>
> Best Regards,
>
> Joos Kiener
>
>
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