Revisions for paper#35
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…ssue when trying to open the output file from the output page
added 7 commits
May 22, 2025 14:23
…e first in the list. Also fixed an indexing error in add_mmseqs_msa and a seperate broken test
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May 25, 2025 10:24
hllelli2
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May 26, 2025
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hllelli2
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Nice work! Thank you for getting these done. The only thing that I think needs adding are tests for the superpose function. As this is a useful addition, we should ensure it always works correctly.
…n of af3_error.log, this wasn't happening. Instead new test read the log file and passes if it's the right error message.
SergeiNikolenko
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Mar 22, 2026
* Updated Boltz version to 1.0.0, this allows us to use Boltz-1x * Added initial support for af3 singularity image * Fixed issue with run_alphafold.py path * Modified check install to use .sif file and updated tests * Added ptm and iptm scores to the output page * Changed parse score function to use correct instances * Updated the readme with .sif info and some other fixes mentioned by reviewers * Rounded ptm/iptm scores to 2 decimal places * Clarified how to run open_output.py in the readme and fixed pathing issue when trying to open the output file from the output page * Updated readme and added command to make run dir for boltz/chai if saving the input * Fixes to chai output issues * Updated the help descriptions of the input arguments * Added warning about pairedMSA with mmseqs2 * Added in something about boltz limitations * Added type checker to input_json argument * Added a legend to make it clear you can show/hide the methods * preliminary commit to add local mmseqs support * Added code to add in the a3m lines * Fixed a3m path * Added template support and fixed broken test * Fixed get_templates bug * Fixed another get_templates issue * Add check to iptm score parse to avoid monomer error * Fix issue with square brackets causing problems in the input yaml * Update the readme and add the script to download MMseqs2 databases * Fixed test * Fixed bug in iptm/ptm scores * Fix for nucleotide plddt score issue - this needs refining * Fixed test changes by luc's boltz fix * Added in code to make an output folder and superpose all models to the first in the list. Also fixed an indexing error in add_mmseqs_msa and a seperate broken test * Updated version number * fixed flake8 error * other precommit change * Fixing tests * fix? * fixed issue in superposition * ... * ... * Added some changes suggested by Luc * Local AF3 test was waiting for sub process call error but with addtion of af3_error.log, this wasn't happening. Instead new test read the log file and passes if it's the right error message. * Fixed superpose test --------- Co-authored-by: hlasimpk <hlasimpk@liverpool.ac.uk> Co-authored-by: hllelli2 <hllelli2@liverpool.ac.uk>
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Lots of added features