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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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Biopython has made some significant changes in recent versions, the most important of which for our purposes is the handling of alphabets.
chg60 updated
2 years ago
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The following has been deprecated from the BioPython repo
`from Bio.SubsMat.MatrixInfo import blosum62`
One way to fix it is to replace with
```
# from Bio.SubsMat.MatrixInfo import blosum62
from…
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Hello,
I have created a conda environment with (what I think) all the requisite programs with:
```
conda activate trans2express
mamba install -y diamond beautifulsoup4 biopython biothings_clie…
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See https://github.com/peterjc/peterjc.github.io/blob/master/wiki/Biopython.md vs https://github.com/peterjc/peterjc.github.io/blob/master/wiki/Biopython.mediawiki
See https://github.com/peterjc/pete…
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Biopython and pysam have iterators for some of the objects implemented in SC Tools.
See if those tools are more efficient than the ones implemented here, and if so, determine how difficult it woul…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
import sys; print(sys.version)
import platform; print(platform.python_imp…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
import sys; print(sys.version)
import platform; print(platform.python_imp…
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Hi everyone,
Hope you'll help me. I uploaded VAPiD and all necessary modules. Unfortunately, I couldn't start.
Here, the result with my own files.
PS C:\Users\shank\PycharmProjects\BioPython_Tr…
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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…