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Does anybody is planning to port "atoms" to Larch? If not, I could probably invest some time in this. I never went through the source code of atoms itself, so the ideas I have in mind on how to implem…
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Hello,
I am trying to plot a graph from BioPAX file.
While I am executing below code I got an error 'UnicodeDecodeError: 'charmap' codec can't decode byte 0x8d in position 8815866: character ma…
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Hi,
I am trying to read a bunch of pdbs for receptor and ligands to generated the PLEC fingerprint.
If i were to use
`fname = fname = "./ligands/ligand_ZINC1184910816.pdb"`
and then use
`ligand…
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Hi,
I am trying to use simple_fit.py and test_dkoes_simple_fit.py to obtain a molecules from a grid. I tried the following setting for the input path of sdf file:
--for simple_fit.py, I used the ex…
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- [x] I believe this to be a bug with Open Babel
- [ ] This is a feature request
## Environment Information
Open Babel version: 2.4.1
Operating system and version: CentOS 7
## Expected Be…
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I'm unable to load chemml after following install instructions:
```
from openbabel import pybel, openbabel
from chemml.chem import Molecule
```
The error message:
```
------------------------…
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Dear Developers,
I just found that if I install the new open babel version with conda from the conda-forge channel, I got errors in importing pybel.
However, if I install the deprecated version …
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My molecules are stored in XYZ format in a pandas DataFrame and I'm trying to iterate them to chemml, It looks like I can not pass a string directly and I was with the impresison that this was possibl…
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As brought up by @chrisiacovella in a recent meeting, the SMILES --> 3d structure functionality does not generate the same 3d structure each time. I've dug around `openbabel` a little bit, but I haven…
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Python 3.6.9
Ubuntu 18.04
installing with `pip3 install bio2bel_reactome` raises the following error
```
>>> import bio2bel_reactome
Traceback (most recent call last):
File "", line 1, in…