Re: [Rdkit-discuss] read SD file with hydrogens

[Peter S. <psc...@ub...>]

Hey Greg,

thanks for the reply. Mea culpa, indeed, I have to get used to the C++
oriented API doc (I'm more used into Pythonic docs, the reason why I did
not look into the constructor arguments).

Cheers.

Peter

Greg Landrum wrote:
> Dear Peter,
>
> On Tue, Sep 28, 2010 at 1:32 AM, Peter Schmidtke <psc...@ub...> wrote:
>   
>> I'd like to read several molecules from a SD file (created with MOE).
>> These molecules have already added H's and I'd like to keep them as they
>> are (so not readd them in rdkit after reading). How can I do this with
>> the SDMolSupplier...right now I get the impression that he reads
>> everything but H's.
>>     
>
> By default the RDKit removes Hs from molecules. To keep them you need
> to use the optional "removeHs" argument when constructing your
> SDMolSupplier:
> In [11]: suppl = Chem.SDMolSupplier('blah.sdf',removeHs=False)
> In [12]: ms = [x for x in suppl]
> In [13]: ms[0].Debug()
> Atoms:
>         0 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
>         1 6 C chg: 0  deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0
>         2 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
>         3 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
>         4 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
>         5 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
>         6 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
>         7 1 H chg: 0  deg: 1 exp: 1 imp: 0 hyb: 1 arom?: 0 chi: 0
> Bonds:
>         0 0->1 order: 1 conj?: 0 aromatic?: 0
>         1 0->2 order: 1 conj?: 0 aromatic?: 0
>         2 0->3 order: 1 conj?: 0 aromatic?: 0
>         3 0->4 order: 1 conj?: 0 aromatic?: 0
>         4 1->5 order: 1 conj?: 0 aromatic?: 0
>         5 1->6 order: 1 conj?: 0 aromatic?: 0
>         6 1->7 order: 1 conj?: 0 aromatic?: 0
>
> Best Regards,
> -greg
>   


-- 

Peter Schmidtke
PhD Student
Dept. Physical Chemistry
Faculty of Pharmacy
University of Barcelona