Sean
Sean
## Expected Behavior Accession-number-sequence associations should be the same between metaclust and colabfold_envdb ## Current Behavior The metaclust id seems to be correct. colabfold_envdb seems to have scrambled the name-sequence...
- [X] I hereby agree to dual licence this and any previous contributions under both the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_. - [X] I have read the...
Here is some code for coloring the structures based on PAE, which I think is useful for visualizing domain boundaries. Maybe others will also find it useful. The legend code...
**Bug description** **Reproduction steps** ```python import esm model, alphabet = esm.pretrained.esm_msa1b_t12_100M_UR50S() batch_converter = alphabet.get_batch_converter() batch_size=5 padded_msa = [('0', 'AAA'), ('1', 'ACC'), ('2', 'ACDE')] labels, strs, tokens = batch_converter([padded_msa] * batch_size)...
It would be nice to be able to skip the `.git` folders but not skip all non-tracked files. In my case, I have some singularity `.sif` containers which are the...
I'm using a slightly modified version of parse_hhr in a currently private repo. I'd like to make that repo public and Open Source. But I want to use a permissive...
## Expected Behavior Include a brief description of the database hits in the html and tabular output files from a search. ## Current Behavior The Foldseek web server includes some...
What is the best way to control memory usage for foldseek searches with big databases. In particular, I'm searching the full UniProt database with the following command: `foldseek easy-search "query.pdb"...
I'm trying to predict structures for a bunch of sequences from the same family. For this reason, I don't need to search against the entire uniprot30 or envdb. I just...
I wrote a package to run the Viterbi hmm-profile alignment algorithm on hmmer3 profiles. The package uses pyhmmer to parse the hmm files and get numpy arrays from the values....