-
This script fails:
```
import pybel
mymol=pybel.readstring('smi','CCOC(=O)C')
mymol.addh()
mymol.make3D()
print mymol.write(format='mol2')
```
```
Traceback (most recent call last):
File "…
-
- [x] I believe this to be a bug with Open Babel
## Environment Information
Open Babel version: 3.1.1 (`master`)
Operating system and version: Ubuntu 20.04
## Expected Behavior
Calling the `.…
-
I was doing some tests with a file for a software I'm developing, and when I did certain unrelated changes, the HBA calculation went crazy.
I haven't been able to reproduce the normal behaviour, on…
-
BioDati upload is already available since PyBEL v0.14.6 or 14.7, so just reorganize the output to go right there. Make sure the right metadata is inside!
-
- [x] I believe this to be a bug with Open Babel
- [ ] This is a feature request
## Environment Information
Python version: 3.6.7
Open Babel version: 2.4.1
Operating system and version: Ma…
-
Of course there's a command-line for getting partial charges:
```
obabel CF2Cl2.g03 -onul --partialcharge eem --print
```
Replace `eem` with `gasteiger` or `mmff94` or whatever you want.
-
## Environment Information
Open Babel version: 3.1.0
Operating system and version: windows 11 running ubuntu in WSL running Anaconda3
## Expected Behavior
I am running the script prepareCova…
-
[pdb_data.csv](https://github.com/openbabel/openbabel/files/10087372/pdb_data.csv)
Environment Information:
Open Babel version: 3.1.0 from conda-forge, python 3.9.13
Operating system and version:…
-
Example from EMMAA covid model:
WARNING: [2021-08-17 14:29:41] indra.assemblers.pybel.assembler - Node should not have variants: bp(MESH:D019895 ! Transposases), [{'kind': 'hgvs', 'hgvs': 'p.?'}]
-
Dear Administrator,
scPDB dataset provides protein structures by mol2 format.
To generate machine learning features I used pybel, but Segmentation fault has been occurred for large protein file.
…