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As of 19 Feb 2024, af2_binder_design.yml will install biopython 1.83, resulting in the following error during test `ImportError: cannot import name 'SCOPData' from 'Bio.Data' (~/.conda/envs/af2_binder…
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### Expected and Actual
The standard API documentation on https://biopython.org/docs/latest/api suggests showing the input and return, even if it is not on the function's detail page.
For exampl…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```
3.10.0 (default, Nov 10 2021, 13:28:23) [Clang 12.0.0 ]
CPython
macOS-14.0-arm…
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Looks like you may need to pin BioPython or update the imports. On a new environment I installed fanc with lead to Biopython being installed with version 1.83 where GC has changed to gc_fraction (sinc…
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Hi
I've installed all required dependencies and databases for use with gutSMASH, but when I come to run the program I get the following error.
Bio.Alphabet has been removed from Biopython. In ma…
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Right now, it is hard to write content for the Biopython Tutorial because there is not much documentation on the tools and conventions used.
I can work on adding some of this documentation to Contr…
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Hello,
I'm wondering if it would be useful to make a similar package to `Bio.Entrez`, but for UniProtKB/TrEMBL records.
There's good support for parsing UniProt records with the `Bio.UniProt` pa…
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After running the first code cell block we get this warning:
/usr/local/lib/python3.10/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we int…
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Having just submitted a pull request to one of the data carpentry lessons, I was surprised to see there were no continuous integration tests run automatically (by attempting to build the lessons, or a…
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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…