Re: [Rdkit-discuss] descriptor calculation - fragment counts & Co.

[<Pau...@me...>]

> > 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

Hi Greg,

here we go:


In [4]: from rdkit import Chem
        from rdkit import rdBase
        from rdkit.ML.Descriptors import MoleculeDescriptors
        from rdkit.Chem import Descriptors
        len(Descriptors._descList)

Out[4]: 93


In [6]: calc = MoleculeDescriptors.MolecularDescriptorCalculator([x[0] for
x in Descriptors._descList])
        len (calc.GetDescriptorNames())

Out[6]: 93


In [7]: m = Chem.MolFromSmiles('c1ccccc1OC')
        ds = calc.CalcDescriptors(m)
        len(ds)

Out[7]: 93

In [8]: print rdBase.rdkitVersion
        2012.09.1beta


Now you see that we are still using the Q3 beta :)

Only solution: Upgrading to the stable version? Or is there a workaround
available in conjunction with the Q3 beta?


Cheers & Thanks,
Paul

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