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Hydra-Powered YAML Configuration and Enhanced File Support in HelixFold3 #321

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wants to merge 42 commits into from
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Hydra-Powered YAML Configuration and Enhanced File Support in HelixFold3 #321

wants to merge 42 commits into from

Commits on Aug 17, 2024

  1. chore: hydra and pip

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  2. use reduced bfd

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  3. disable no MSA mode (PaddlePaddle#312)

    @RyanGarciaLI @YaoYinYing
    RyanGarciaLI authored and YaoYinYing committed Aug 17, 2024
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  4. add override flag

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  5. add configs

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  6. fix:config

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  7. fix: maxit path

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  8. fix: maxit run with env

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  9. fix: maxit run with env

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  10. copy of license

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  11. fix: obabel bin resolve

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  12. doc: use conda prefix

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  13. doc: merge to readme

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  14. fix: imports

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  15. fix: config overriden

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  16. doc: update for cli

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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  17. doc: update for cli

    @YaoYinYing
    YaoYinYing committed Aug 17, 2024
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Commits on Aug 18, 2024

  1. fix: msa parallel for bfd

    @YaoYinYing
    YaoYinYing committed Aug 18, 2024
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  2. fix: multimer msa parallel

    @YaoYinYing
    YaoYinYing committed Aug 18, 2024
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  3. fix: multimer msa parallel

    @YaoYinYing
    YaoYinYing committed Aug 18, 2024
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  4. drop: buildin logger

    @YaoYinYing
    YaoYinYing committed Aug 18, 2024
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Commits on Aug 19, 2024

  1. fix: nested parallel runs for protein chains

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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  2. refactor: deduplicate code

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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  3. fix: hetatm input raise and dialognoses

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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  4. fix: hetatm input raise from smiles

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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  5. feat: ligand: support obable readable files

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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  6. fix: output logs

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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  7. fix: template try-except bugs

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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  8. docs: sm file inputs

    @YaoYinYing
    YaoYinYing committed Aug 19, 2024
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Commits on Aug 20, 2024

  1. drop: buildin logger

    @YaoYinYing
    YaoYinYing committed Aug 20, 2024
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  2. drop: buildin logger

    @YaoYinYing
    YaoYinYing committed Aug 20, 2024
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  3. add: use_3d opt for ligand

    @YaoYinYing
    YaoYinYing committed Aug 20, 2024
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  4. fix: enable mutiple config overrides

    @YaoYinYing
    YaoYinYing committed Aug 20, 2024
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Commits on Aug 24, 2024

  1. dev:major: covalent bond

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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  2. fix: covalent bond

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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  3. doc: covalently

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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  4. Update README.md

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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  5. feat: disulfide bonding

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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  6. feat: disulfide bonding

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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  7. case: metalc

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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  8. Update pipeline_conf_bonds.py

    @YaoYinYing
    YaoYinYing committed Aug 24, 2024
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Commits on Aug 26, 2024

  1. chore: cpu only for msa only

    @YaoYinYing
    YaoYinYing committed Aug 26, 2024
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