openbabel

openbabel copied to clipboard

InChI additional arguments silently ignored

14

When generating an InChI key for a molecule with incomplete valence (e.g., CH3 radical), `openbabel` always generates the InChI key corresponding to the molecule with additional hydrogens, even with the...

RaphaelRobidas

Feature Request: Incorporate the GAMESS US Z-Matrix Format

3

As the title says: Would it be possible to implement conversion from xyz to the GAMESS US Z-Matrix format with the zmat section?

ocelotStride

Rigid fragment XXXX in rigid-fragments.txt has all zero coordinates

2

--> - [x] I believe this to be a bug with Open Babel - [ ] This is a feature request ## Environment Information Open Babel version: Open Babel 3.1.1...

teriken

installing openbabel with Python bindings

2

Hi, I am trying to run a script for generating slabs and I use pymatgen and openbeabel at some point. But I get this error: ------------------ Writing surface slab to...

Rojaettfolk

Cannot SetOutputStream in Python

2

## Environment Information Open Babel version: 3.1.1 - installed with apt Operating system and version: Ubuntu 22.04, Python 3.10.4 ## Expected Behavior I want to redirect the output stream in...

xrobin

Open Babel Error in OpenBabel::OBBuilder::GetFragmentCoord Rigid fragment C1CCCNC1 in rigid-fragments.txt has all zero coordinates

8

- [x] I believe this to be a bug with Open Babel - [ ] This is a feature request ## Environment Information Open Babel version: ```3.1.0``` Operating system and...

StashOfCode

Reimplement OpenBabel::OBRandom as a wrapper of std::mt19937_64

8

Mersenne twister is one of high-quality PRNGs and available on all platforms since C++11.

e-kwsm

Comment out unused parameters

5

e-kwsm

Arginine fix

3

Fix issue with protonating charged ARG OB was placing a third H on NH1 using a random bond vector. The AssignBonds, which is suppose to match known protein residue bonding...

dkoes

ROOT in pdb to pdbqt conversion

2

Hi, I am converting the RNA PDB file built by Maestro to pdbqt. `ls 1KOC_clean.pdb | xargs /usr/local/bin/obabel -xcr -ipdb -opdbqt | tee receptor.pdbqt` However, this conversion prints the "ROOT"...

mandar5335