Unmasking interchain contacts for complexes and fixing hardcoded paths#13
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gezmi wants to merge 3 commits intoMingchenchen:mainfrom
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Unmasking interchain contacts for complexes and fixing hardcoded paths#13gezmi wants to merge 3 commits intoMingchenchen:mainfrom
gezmi wants to merge 3 commits intoMingchenchen:mainfrom
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added 3 commits
February 17, 2026 12:18
This commit adds support for using inter-chain template information when scoring protein complexes, enabling AF2Rank-style evaluation. Changes: - Add allow_interchain_templates parameter to Diffuser, Evoformer, and _embed_template_pair in model.py - When True, template embeddings include both intra-chain and inter-chain distances. When False (default), only intra-chain template features are used (standard AF3 behavior) - Add --allow_interchain_templates CLI flag to run_af3score.py - Thread parameter through full call chain: CLI → process_fold_input → predict_structure → run_inference → model Use case: For scoring existing structures (--init_guess=true --diffusion_steps=0), this allows the template structure's full complex geometry (including interface contacts) to inform confidence predictions. Backward compatible: defaults to False to preserve standard AF3 behavior.
- Add command-line argument parsing to all 4 example scripts - Scripts now accept -i/--input_dir and -o/--output_dir flags - Remove hardcoded paths (./pdb, ./complex_chain_cifs, etc.) - Enables flexible directory structure for pipeline scripts - 1_extract_chains.py: Supports both PDB and CIF input files - 3_generate_json.py: Added -c/--csv_path flag for CSV input - 4_extract_iptm-ipae-pae-interaction.py: Modified update_sc_file() to accept parameters
- 1_extract_chains.py: Save complex_chain_sequences.csv to output directory instead of working directory - 4_extract_iptm-ipae-pae-interaction.py: Save failed_records.txt to same directory as output file
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