History / Run AlphaPulldown Python Command Line Interface

CLI: --allow_resume (AlphaFold 3 from 2.11.0), --debug_msas/--debug_templates, the alphapulldown/ and debug/ subdirectories Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

DimaMolod committed Oct 14, 2026

CLI: --fast_kernels and the compile cache; local MMseqs2 covers AlphaFold 2 - Document --fast_kernels and --jax_compilation_cache_dir (2.10.0) in the prediction flags, with a short tip on both. - Local MMseqs2 (sections 1.3 and 1.6) serves AlphaFold 2 since 2.9.0: finalize with --data_pipeline alphafold2; the AF2 benchmark; updated links to the renamed sections. - UniFold is disabled: say so in the backend and UniFold flags. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

DimaMolod committed Oct 8, 2026

Document the batched local MMseqs2 path for AlphaFold 3 Section 1.3 claimed AlphaPulldown provides no interface for running MMseqs2 locally. That stopped being true in 2.8.0, which searches your own databases as part of the AlphaFold 3 feature pipeline. Correct the claim, scope it to the ColabFold route it still describes, and document the built-in path beside it: databases, RNA chains, running the scripts, tuning and caveats. The README now carries only the config switches; the how-to lives here.

DimaMolod committed Sep 8, 2026

Document local MMseqs2 features and batched structure prediction The wiki covered neither of the new runnable scripts. Adds section 1.6 for create_batch_msas.py / finalize_batch_features.py / create_batch_features.py / compare_msa_backends.py, and section 2.8 for run_structure_prediction_batch.py, each with the measured behaviour that decides whether they are worth using. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

DimaMolod committed Sep 5, 2026

Document the HHblits patch needed for AlphaFold2 features

DimaMolod committed Aug 21, 2026

Document AlphaFold3 JSON feature names

DimaMolod committed May 4, 2026

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

DimaMolod committed Apr 13, 2026

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 committed Apr 13, 2026

Updated Run AlphaPulldown Python Command Line Interface (markdown)

DimaMolod committed Apr 13, 2026

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 committed Apr 13, 2026

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 committed Apr 13, 2026

af2 and af3 installations

DimaMolod committed Apr 1, 2026

Document test layout and coverage workflow

DimaMolod committed Mar 27, 2026

Updated Run AlphaPulldown Python Command Line Interface (markdown)

DimaMolod committed Mar 24, 2026

Updated Run AlphaPulldown Python Command Line Interface (markdown)

DimaMolod committed Nov 24, 2025

Updated Run AlphaPulldown Python Command Line Interface (markdown)

amrismil committed Oct 28, 2025

Updated Run AlphaPulldown Python Command Line Interface (markdown)

amrismil committed Oct 28, 2025

Created Run AlphaPulldown Python Command Line Interface (markdown)

amrismil committed Oct 28, 2025