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Hello,
I have written a script which uses biopython, obabel and pymol to loop over RNA-small molecule complexes and extracts the binding pocket and prepared the pdbqt fies for docking (Python 3.9.1…
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This is not necessarily a huge issue ,but neither Biopython nor the actual BLAST API mentioned parameters such as Max target sequence which is a parameter in the blastp Algorithm parameters section on…
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Biopython is unable to parse the latest version of UniProt. This is a known issue and is due to a change in the feature (FT) lines of the UniProt file.
See issue #4021 from the biopython GitHub rep…
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`import phylopandas as ph`
raises error
```python
---------------------------------------------------------------------------
ImportError Traceback (most recent c…
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something like `Tree.from_biopython(...)` and `Tree.as_biopython(...)`
1) The method should accept/return biopython Tree instances.
2) Is it possible to avoid newick serialisation?
3) any special at…
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I wasn't aware of any limitation on locus identifier length in the imaginary genbank specification, but there you go!
> Traceback (most recent call last):
...
> File "/home/gibthon/site/gibthon/gib…
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# My error
## Generate the ESM2 embeddings for the proteins:
```python
python datasets/esm_embedding_preparation.py
```
I downloaded the BindingMOAD dataset and extracted it into the "/data/Bin…
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[Pyfastx](https://pypi.org/project/pyfastx/) is faster than Biopython.
**Warning**
- pyfastx is 1-offset based (i.e. sequence start index is 1), biopython is 0-offset
- sequence end is included i…
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When fetching, it checks for BioPython being installed. On MSI's setup, this breaks the script as it won't fetch on LAB and LOGIN doesn't have BioPython readily available.
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I just freshly set up the environment and the version of biopython installed was 1.83 where GC has changed to gc_fraction (since 1.80) - I received the below error and had to force install biopython 1…