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History / Run AlphaPulldown Python Command Line Interface

Revisions

  • Document AlphaFold3 JSON feature names

    @DimaMolod DimaMolod committed May 4, 2026
    18f7bf9

  • Sync wiki with README: fold_backend values, APLit HTTPS install, AlphaJudge/Snakemake CSV inputs

    @DimaMolod DimaMolod committed Apr 13, 2026
    a74bbe4

  • Document new interaction-network rendering and label policy - Explain --label_top_n behavior: all nodes are drawn, but only the top-N (by degree then best score) get text labels by design, to keep dense screens legible - Document new visual encoding: viridis edge colour with colorbar, uniform node fill (no more component rainbow), self-interaction outer ring, two-node horizontal pairs, components sorted by size and strength - Document --max_edges cap and the stderr report when it triggers - Add a Recommended workflow tip block: defaults first, always export --edges_out CSV, tighten thresholds, raise --label_top_n for small focused subsets Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

    @DimaMolod DimaMolod committed Apr 13, 2026
    e97a4b6

  • Updated Run AlphaPulldown Python Command Line Interface (markdown)

    @DimaMolod DimaMolod committed Apr 13, 2026
    38e919a

  • Audit fixes plus AlphaJudge / APLit references - Fix --fold_backend default (alphafold → alphafold2) in both flag lists - Add accepted values for --fold_backend (alphafold2, alphafold3, alphalink) - Replace bogus --[no]no_pair_msa entry with --[no]pair_msa (default True) and clarify that --pair_msa=False is required for skip-MSA features - Fix --[no]remove_result_pickles default (true → False) - Add Companion tools section to Home: link AlphaJudge and APLit - Add Companion tools section to Downstream-Analysis: link AlphaJudge and APLit Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

    @DimaMolod DimaMolod committed Apr 13, 2026
    25fbb19

  • Document skip-MSA mode, diagnostics plots, interaction network, and AF Server JSON exporter - Add --skip_msa flag description in section 1.1 FLAGS list - Add section 1.5: Skip-MSA mode (query-only features without DB search) - Add section 2.7: generate_alphafold_server_json.py for AF Server batch JSON export - Add section 3: Diagnostics Plots (plot_diagnostics.py, ColabFold-style MSA/PAE/pLDDT/distogram) - Add section 3: Interaction Network (plot_interaction_network.py, force-layout from score CSV) - Mirror Diagnostics Plots and Interaction Network stubs in Downstream-Analysis.md Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

    @DimaMolod DimaMolod committed Apr 13, 2026
    2af9a53

  • af2 and af3 installations

    @DimaMolod DimaMolod committed Apr 1, 2026
    6949149

  • Document test layout and coverage workflow

    @DimaMolod DimaMolod committed Mar 27, 2026
    e53ef14

  • Updated Run AlphaPulldown Python Command Line Interface (markdown)

    @DimaMolod DimaMolod committed Mar 24, 2026
    cd870fb

  • Updated Run AlphaPulldown Python Command Line Interface (markdown)

    @DimaMolod DimaMolod committed Nov 24, 2025
    98ebe78

  • Updated Run AlphaPulldown Python Command Line Interface (markdown)

    @amrismil amrismil committed Oct 28, 2025
    5c6e955

  • Updated Run AlphaPulldown Python Command Line Interface (markdown)

    @amrismil amrismil committed Oct 28, 2025
    474d615

  • Created Run AlphaPulldown Python Command Line Interface (markdown)

    @amrismil amrismil committed Oct 28, 2025
    bb1c358