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 <[email protected]> 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 ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
