nbehrnd
nbehrnd
Unable to recall if you or an other leading developer of openbabel attended the virtual meeting «InChI Days 2022» in April by [InChI trust](https://www.inchi-trust.org/) or/and are subscriber to the (low...
There are at least two solutions to resolve the issue reported. Either - with file `test.smi` you present, provide the instruction in a *different sequence*, i.e. `obabel -ismi test.smi -osmi...
@vaitkus True, the first suggestion boils down to not use `cat` and `|`. When I moderate OpenBabel with Python's `subprocess` module, using `Popen` to work with input data which are...
@e-kwsm Affirmative, it is an interesting observation. Addition of two blank lines in the input file alters OpenBabel's output from ``` [Na] #1 1 molecule converted ``` into ``` [Na]...
PubChem's entry #962 about [water](https://pubchem.ncbi.nlm.nih.gov/compound/water) holds in section 3.3 *a link* to SpringerMaterials about the dielectric constant, but not the value of the dielectric constant itself ([their page](https://materials.springer.com/substanceprofile/docs/smsid_uatzaqfmzswvnmaj)). And SpringerMaterials...
As an observation: Processing the .pdb about [4gq6](https://www.rcsb.org/structure/4gq6) by RCSB, Openbabel has difficulties to perceive bond orders: ```bash obabel -ipdb 4gq6.pdb -opdb -O 4gq6_out.pdb ============================== *** Open Babel Warning in...
The change I referred to was in the columns after the label about arginine/alanine and prior to the atom's coordinates:  Re the `.pdb` file, the most relevant entry to...
I doubt the file `src/formats/fastaformats.cpp` would be the file defining the assignments of the three letter codes, though e.g., line 3071 has a block reading as ``` { 'A', "ALA",...
The `.mol` file submitted to openbabel misses an indication that the molecule is a radical (`RAD`); otherwise, the algorithm seems to work fine. This applies at least for openbabel 3.1.1...
May you please clarify what represents for you a «3D builder»? *Assuming* this refers to a program to set up a computation in a program like Gaussian, Gamess-UK, Games-US, etc....