nbehrnd
nbehrnd
The string `` seems missing, what is the origin of your data (database / program)? See, for example a run for methanol ```shell $ obabel -:"CO" -h -opdbqt REMARK Name...
It does not seem possible with openbabel (version 3.1.1). For one, there is no explicit option mentioned in the [manual](https://open-babel.readthedocs.io/en/latest/FileFormats/Sybyl_Mol2_format.html). From the section about [SMILES](https://open-babel.readthedocs.io/en/latest/FileFormats/SMILES_format.html) one could infer `-k` would...
An alternative approach is to use openbabel-wheel which equally is available on pypi and hence can be used with pip. Commands and functionality provided by this bypass are the same,...
Re AWK: by default, one space, multiple free spaces, or a tabulator is all one white space. It is one argument e.g. to use [bioawk](https://github.com/vsbuffalo/bioawk-tutorial) to process pdb and FASTA....
@schatzsc Not a solution, only a complementary observation: by default, obabel clearly indicates that the input structure is (in comparison to a "more usual one") problematic e.g., during the conversion...
@schatzsc An other plausible cause for the troubles could be the use of *single bonds* defined between the complex, and the ion to be chelated. Beside bond order of single,...
@schatzsc I redrew the structure on the test page of Marvin JS ([link](https://marvinjs-demo.chemaxon.com/latest/demo.html)) using the coordinate/dative bond. Pt was assigned a positive charge, Br for compensation a negative one: ...
@schatzsc > Maybe some Zoom discussion of software developers together with the IUPAC InChi organometallics team would be helpful to work towards general solutions? Yes I do think it were...
@schatzsc For your information, there is an early note by Greg Landrum (project of RDKit) [here](https://github.com/rdkit/rdkit/discussions/6995) by today, [2023-12-18 Mon]. By your contribution to chemotion_ELN you possibly have a couple...
Each time one wants to report an issue about openbabel here on GitHub, the interface provides you with a template. This is to help you to organize your observation(s), and...