fix: correct BindCraft settings JSON format across use cases#2
Open
wanghan0501 wants to merge 5 commits intoMacromNex:mainfrom
Open
fix: correct BindCraft settings JSON format across use cases#2wanghan0501 wants to merge 5 commits intoMacromNex:mainfrom
wanghan0501 wants to merge 5 commits intoMacromNex:mainfrom
Conversation
wanghan0501
commented
Mar 16, 2026
wanghan0501
commented
- Update field names in generate_target_settings() to match run_bindcraft.py expectations:
- "output_dir" → "design_path"
- "target_pdb" → "starting_pdb"
- "target_chains" → "chains"
- "hotspot" → "target_hotspot_residues"
- "binder_length" → "lengths" array format
- "num_designs" → "number_of_final_designs"
- Add absolute path handling for settings files
- Update .gitignore to exclude .omc/ directory
- Improve docstrings with correct field descriptions
- Update field names in generate_target_settings() to match run_bindcraft.py expectations: - "output_dir" → "design_path" - "target_pdb" → "starting_pdb" - "target_chains" → "chains" - "hotspot" → "target_hotspot_residues" - "binder_length" → "lengths" array format - "num_designs" → "number_of_final_designs" - Add absolute path handling for settings files - Update .gitignore to exclude .omc/ directory - Improve docstrings with correct field descriptions Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add HTTP_PROXY, HTTPS_PROXY, NO_PROXY build arguments - Configure proxy in builder and runtime stages - Reset proxy after build to avoid leaking config - Update README with proxy build instructions
Add build-arg based proxy configuration for apt, conda, pip, git, and wget. Proxy settings are cleared after build to keep runtime environment clean.
- Add HTTP/HTTPS proxy support via build-arg - Configure USTC mirrors for conda and pip by default - Reset proxy variables after build to keep runtime clean - Update README with proxy build instructions Usage: docker build -t bindcraft_mcp:latest . docker build --build-arg HTTP_PROXY=http://proxy:7890 -t bindcraft_mcp:latest .
- Add HTTP/HTTPS proxy support via build-arg - Configure USTC mirrors for conda and pip by default - Reset proxy variables after build to keep runtime clean - Update README with proxy build instructions Usage: docker build -t bindcraft_mcp:latest . docker build --build-arg HTTP_PROXY=http://proxy:7890 -t bindcraft_mcp:latest .
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.