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This my smile structure 'C1(=[C][C]=C([C]=[C]1)[C]N1[C][C][C][C][C]1)C1=[N]=C2C(=[C][C]=[C][C]2)O1' and when I a calculating the molecular descriptors the following error ocurs for Descriptors.Balaban…
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In the module chemml.chem.magpie_python.CompositionEntry there is one line saying "import pybel". However, in the new version of openbabel, this syntax is no longer supported and it must read "from op…
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Hello guys.
You have the next dependency:
pybel==0.14.1
And
'bio2bel_chebi>=0.1.0',
If you will take a look at the dependency list of a latest bio2bel_chebi package (https://github.com…
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## Feature description
One easy check is to run charge equilibration. If we have crazy numbers there's likely something wrong.
This was already used in https://www.nature.com/articles/s41467-020-17…
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```python
WARNING: autodoc: failed to import module 'bel.processor' from module 'indra.sources'; the following exception was raised:
Traceback (most recent call last):
File "/home/docs/checkouts/…
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Hi @cthoyt
I tried Daniel's KEGG to BEL notebook, and was able to generate a BEL script. However, converting to indra statements fails:
```python
----------------------------------------------…
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Blocked by:
- [x] Upgrade Bio2BEL with PyBEL 14 https://github.com/bio2bel/bio2bel/pull/24
- [x] Upgrade ComPath Utils with new PyBEL/Bio2BEL https://github.com/ComPath/ComPath-Utils/issues/5
- [ …
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To have a more robust implementation of the SMILES converter
conversion should be first tried via rdkit via a try---except
and then via openbabel.
For some strange reason the present versions of …
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Hi guys,
I am experiencing problems using function `getVoxelDescriptors()`
`~/anaconda3/lib/python3.7/site-packages/moleculekit/tools/atomtyper.py in getProperties(mol)
78 from o…
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It appears that there are some issues with none-types when processing content from Reactome. It can be reproduced with (pybiopax==0.0.4, indra==1.18.0):
```python
import pybiopax
import indra.sou…