Hi Markus, I'm puzzled for two reasons:
+ My first guess was that the atom block were incomplete -- not because of the missing charge (even the old V2000 format presented by Dalby et al. J. Chem. Inf. Comput. Sci. 32, 1992, 244--255 allowed charges), but by number of columns. Thus, I passed your input .sdf to openbabel to write a new .sdf file. openbabel's .sdf indeed contains more columns in the atom block. The insertion of this as input in your Jupyter notebook still yields the same issue -- displaying the protonated N in the formula, postponing the information about the charge to the properties block. + More puzzling were my attempts to read SMILES strings of ions which equally were displayed as expected, i.e. with charge in the structure formulae. Here, the export of the atom block contains a charge identification (attached notebook); yet if I convert the same strings with openbabel, the openbabel .sdf use both other columns to note the charge and (apparently) an other key cipher to denote the charge which however seem to be a closer match to reference[1]. Perhaps relevant for comparison, I still use rdkit 2019.09.1 and openbabel 3.1.0. This e-mail contains as attachment both a Jupyter notebook (6.1.3) with the two worked examples of thiophenolate and protonated phenylalanine, as well as the two .sdf of these molecules written by openbabel. Norwid [1] http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx On Fri, 2 Oct 2020 10:56:07 -0700 Markus Metz <metm...@gmail.com> wrote: > Hello everybody: > I have a question to the sd file format. > When I write charged molecules via rdkit I noticed that the charge definition > in the atom block is not written. > The charge is written at the end of the entry.
thiophenolate_via_openbabel.sdf
Description: application/vnd.openmolecules.sdf
protonated_phenylalanine_via_openbabel.sdf
Description: application/vnd.openmolecules.sdf
thiophenolate_from_smiles.ipynb
Description: application/ipynb
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