Hi Paul,
On Fri, Nov 9, 2012 at 1:54 PM, <[email protected]> wrote:
>
> I'm wondering about the total number of accessible descriptors in RDKit:
>
> This is is my code:
> "
> import sys
> from rdkit import Chem
> from rdkit.Chem import Descriptors
> from rdkit.ML.Descriptors import MoleculeDescriptors
>
> file_in = sys.argv[1]
> file_out = file_in+".descr.sdf"
> ms = [x for x in Chem.SDMolSupplier(file_in) if x is not None]
> ms_wr = Chem.SDWriter(file_out)
>
> nms=[x[0] for x in Descriptors._descList]
> #nms.remove('MolecularFormula')
> print len(Descriptors._descList)
>
>
> calc = MoleculeDescriptors.MolecularDescriptorCalculator(nms)
>
> for i in range(len(ms)):
> descrs = calc.CalcDescriptors(ms[i])
> for x in range(len(descrs)):
> ms[i].SetProp(str(nms[x]),str(descrs[x]))
> ms_wr.write(ms[i])
> "
>
> This gives me 93 descriptors in total.
>
> A brief look and count in the Python API
> http://www.rdkit.org/docs/api/rdkit.Chem.Descriptors-module.html
> ends up in more than 170 descriptors.
>
> Another brief look (no time to grasp in more depth) reveals that apparently
> the fr_* descriptors have not been calculated.
>
> What did I do wrong?
I don't see anything obvious, but you are definitely getting incorrect results.
Here's what I see:
In [16]: from rdkit import Chem
In [17]: from rdkit.ML.Descriptors import MoleculeDescriptors
In [18]: from rdkit.Chem import Descriptors
In [19]: len(Descriptors._descList)
Out[19]: 177
In [20]: calc =
MoleculeDescriptors.MolecularDescriptorCalculator([x[0] for x in
Descriptors._descList])
In [21]: len(calc.GetDescriptorNames())
Out[21]: 177
In [22]: m = Chem.MolFromSmiles('c1ccccc1OC')
In [23]: ds = calc.CalcDescriptors(m)
In [24]: len(ds)
Out[24]: 177
Just to eliminate some uncertainty, can you please try the above
commands and, if you don't see 177, add this:
In [25]: from rdkit import rdBase
In [26]: rdBase.rdkitVersion
Out[26]: '2012.12.1pre'
Thanks.
-greg
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