nbehrnd

I speculate your setup attempts to fetch openbabel from pypi.org instead of the OS' package manager. If this is the case, check if the by bypass with openbabel-wheel equally works...

The following can only cover some parts. Inferring from Linux Debian, Linux CentOS provides *some basic* support of Python; mainly to support the operating system itself. And if you perform...

@merkys A possible bypass is to request all hydrogens to be processed as explicit, i.e. ```shell $ obabel -:"[OH2].[OH2]" -h -ocan --append formula O.O H4O2 1 molecule converted ``` with...

@vaitkus I'm unable to answer how `-h` eventually completes the Hill formula at level of the source code. It were a speculation if functions defined in path `include/openbabel` (e.g., files...

Agreed, `[CH2]` stays CH2 e.g., in [CDK Depict](https://www.simolecule.com/cdkdepict/depict.html) and is not methane represented as `C`; with one explicit hydrogen `[H]C`, or `C[H]`, nor depicted with two explicit hydrogens, `[H]C[H]`. This...

@AlexisGeorgiou There is a technique called `sanitize SMILES strings`. This is to validate SMILES strings (as Geoffrey mentioned, to identify and sort out e.g. pentavalent carbons early), but not limited...

@JSLJ23 The following is not a solution to openbabel, however suggests a bypass relying on RDKit. Based on `xyz2mol` by the Jensen group, I forked [xyz2mol_b](https://github.com/nbehrnd/xyz2mol_b) which is capable to...

@JSLJ23 Well, was is a typical .xyz you want to pass? Starting in line 50, the moderator script includes a `try/except ValueError` clause: ```python try: rdkit.Chem.rdDetermineBonds.DetermineBonds(mol, charge=args.charge) print(Chem.MolToMolBlock(mol)) except ValueError:...

@e-kwsm Complementary observation: entry VS001, spiro[4.5]dec-2-ene in the [cipvalidationsuite](https://cipvalidationsuite.github.io/ValidationSuite/) compiled by Robert Hanson *et al.* equally is assigned by them by the SMILES string `C1[C@]2(CCCC1)CC=CC2`. However, the submission of their...

About two years after the initial post to suggest the addition of DataWarrior's `idcode`, openbabel 3.1.1 apparently does not offer this as input/output format, too. I would like to renew...