Adding custom Trajectory rejection thresholds using advanced settings#365
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dbeinhauer wants to merge 2 commits intomartinpacesa:mainfrom
Open
Adding custom Trajectory rejection thresholds using advanced settings#365dbeinhauer wants to merge 2 commits intomartinpacesa:mainfrom
dbeinhauer wants to merge 2 commits intomartinpacesa:mainfrom
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…JSON parameter in advanced settings
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Pull request overview
Adds configurable trajectory rejection thresholds via advanced_settings, enabling users to tune when a trajectory is discarded for clashes, low confidence, or insufficient contacts.
Changes:
- Parameterized CA-clash rejection using
trajectory_max_ca_clashes(default0). - Parameterized pLDDT rejection using
trajectory_min_plddt(default0.7). - Parameterized interface-contact rejection using
trajectory_min_contacts(default3), and documented these new settings in the README.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| functions/colabdesign_utils.py | Uses new advanced_settings keys (with defaults) to control trajectory rejection thresholds. |
| README.md | Documents the three new advanced-settings parameters and their defaults. |
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Adding option to customize Trajectory rejection thresholds by using 3 new arguments in advanced settings json file.
The arguments are:
trajectory_max_ca_clashes- Maximum number of CA clashes allowed before discarding trajectory as Clashing (default: 0)trajectory_min_plddt- Minimum final pLDDT required to keep trajectory, below this it is marked LowConfidence (default: 0.7)trajectory_min_contacts- Minimum number of interface contacts required, below this trajectory is marked LowConfidence (default: 3)