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…ibrary if specified in config
…ing missing atoms and restructuring bond reconstruction
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Pull Request Overview
This PR fixes a critical crash when using the include-input-conformation option by ensuring that rotamers extracted from the live system are properly parameterized. The root cause was that system-derived rotamers lacked essential data like atom roles and forcefield parameters, leading to failures in placement and scoring operations.
- Moved the system conformation inclusion logic to occur after the
Parameterizeris created, allowing proper parameterization of extracted rotamers - Enhanced the
include_system_conformationsmethod to accept aParameterizerinstance and explicitly parameterize each extracted rotamer - Improved the robustness of the rotamer extraction process to handle edge cases and missing atoms more gracefully
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| crates/scream-core/src/workflows/place.rs | Moved system conformation inclusion after parameterizer creation and updated function signatures |
| crates/scream-core/src/core/rotamers/library.rs | Added parameterization to extracted rotamers and improved extraction logic with better error handling |
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Summary:
Fixes a critical crash that occurred when using the
include-input-conformationoption. The root cause was that rotamers extracted from the live system were not being parameterized, leaving them without essential data like atom roles and cached forcefield parameters, which led to failures in subsequent placement and scoring operations. The fix ensures these system-derived rotamers are fully parameterized, making them consistent with those loaded from the library. Additionally, the extraction logic has been made more robust.Changes:
Parameterized System-Extracted Rotamers:
include_system_conformationsfunction in theRotamerLibrarynow accepts aParameterizerinstance.Improved Rotamer Extraction Logic:
extract_rotamer_from_systemfunction was refactored for greater robustness.