Revisions for paper#35

Merged

hllelli2 merged 43 commits intomainfrom

singularity_support

May 28, 2025

Commits on Apr 29, 2025

Updated Boltz version to 1.0.0, this allows us to use Boltz-1x
hlasimpk
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Commits on May 7, 2025

Added initial support for af3 singularity image
hlasimpk
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Fixed issue with run_alphafold.py path
hlasimpk
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Modified check install to use .sif file and updated tests
hlasimpk
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Added ptm and iptm scores to the output page
hlasimpk
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Changed parse score function to use correct instances
hlasimpk
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Updated the readme with .sif info and some other fixes mentioned by reviewers
hlasimpk
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Rounded ptm/iptm scores to 2 decimal places
hlasimpk
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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
hlasimpk
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Commits on May 9, 2025

Updated readme and added command to make run dir for boltz/chai if saving the input
hlasimpk
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Fixes to chai output issues
hlasimpk
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Commits on May 12, 2025

Updated the help descriptions of the input arguments
hlasimpk
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Added warning about pairedMSA with mmseqs2
hlasimpk
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Commits on May 14, 2025

Added in something about boltz limitations
hlasimpk
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Added type checker to input_json argument
hlasimpk
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Added a legend to make it clear you can show/hide the methods
hlasimpk
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Commits on May 16, 2025

preliminary commit to add local mmseqs support
hlasimpk
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Commits on May 19, 2025

Added code to add in the a3m lines
hlasimpk
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Commits on May 20, 2025

Fixed a3m path
hlasimpk
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Commits on May 21, 2025

Added template support and fixed broken test
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Fixed get_templates bug
hlasimpk
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Fixed another get_templates issue
hlasimpk
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Add check to iptm score parse to avoid monomer error
hlasimpk
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Fix issue with square brackets causing problems in the input yaml
hllelli2
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Update the readme and add the script to download MMseqs2 databases
hlasimpk
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Merge remote-tracking branch 'origin/boltz_update_version' into singularity_support
hlasimpk
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Merge remote-tracking branch 'origin/boltz_update_version' into singularity_support
hlasimpk
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Fixed test
hlasimpk
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Commits on May 22, 2025

Fixed bug in iptm/ptm scores
hlasimpk
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Fix for nucleotide plddt score issue - this needs refining
hlasimpk
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Fixed test changes by luc's boltz fix
hlasimpk
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Commits on May 23, 2025

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
hlasimpk
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Updated version number
hlasimpk
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fixed flake8 error
hlasimpk
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other precommit change
hlasimpk
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Fixing tests
hlasimpk
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fix?
hlasimpk
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Commits on May 25, 2025

fixed issue in superposition
hlasimpk
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hlasimpk
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Commits on May 27, 2025

Added some changes suggested by Luc
hlasimpk
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Commits on May 28, 2025