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…angle bending, dihedral angle torsion, inversion)
This commit reverts the series of changes related to the implementation of the internal energy model. While scientifically valuable, this feature introduces significant complexity that is better addressed in a future development cycle. The primary reasons for this temporary rollback are: 1. **Increased Complexity**: Implementing a full topology-based energy calculator (for bonds, angles, dihedrals) is a major undertaking equivalent to building a mini MD engine, which is outside the immediate scope of the current project goals. 2. **Focus on Core Functionality**: The priority is to stabilize and validate the core side-chain placement algorithm based on the non-bonded energy model, which is the foundation of SCREAM.
…atom collection logic
…-type combinations
…esidues and their interactions
…ontributions for accurate results
…nergy to energy terms
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Pull Request Overview
This PR integrates internal non-bonded energy of sidechains into the scoring model to provide more physically accurate energy evaluations. The Empty Lattice (EL) energy now includes both the interaction energy with the fixed environment and the internal VDW/Coulombic energies of the rotamer sidechains themselves.
Key Changes:
- Enhanced EL Energy Calculation: EL energy now includes both interaction and internal energies for rotamer sidechains
- Simplified Fixed Energy Logic: Fixed energy calculation refactored to treat all fixed atoms as a single group
- Updated Test Coverage: Tests modified to reflect the new unified energy calculation approach
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
crates/scream-core/src/engine/tasks/fixed_energy.rs |
Refactored to calculate internal energy of all fixed atoms as a single group, removing separate sidechain/non-sidechain categorization |
crates/scream-core/src/engine/tasks/el_energy.rs |
Enhanced EL energy calculation to include both interaction and internal energies for rotamer sidechains |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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Summary:
Enhances the scoring model by integrating the internal non-bonded energy of sidechains, providing a more physically accurate energy evaluation. Previously, the Empty Lattice (EL) energy only accounted for the interaction of a rotamer with the fixed environment. Now, it also includes the rotamer's own internal VDW and Coulombic energies. This change propagates through the entire
engine, affecting the EL cache generation, total energy calculations, and the final reported energies of solutions. This provides a more complete energy landscape for optimization algorithms to explore.Changes:
tasks/el_energy.rs: The EL energy calculation task now computes both the interaction energy of a rotamer's sidechain with the fixed environment and the internal non-bonded energy of the sidechain itself (score_group_internal). Both components are summed to create the total EL energy value stored in the cache.tasks/fixed_energy.rs: Refactored to calculate the internal energy of the entire fixed portion of the system (backbone and non-mobile sidechains/ligands/etc.) as a single group, simplifying the logic.