feat(pack): Implement Core Sidechain Packing Algorithm#6
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…rogen torsion symmetry
…r instead of vdw_cutoff
…`neighbor_edges` method
…of for atom count
…pdate tests accordingly
…gyTable and PairEnergyTable
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Pull request overview
Implements the core sidechain packing pipeline to solve for a GMEC using a multi-phase workflow (sampling → graph → pruning → pair energies → DEE → DP), with Rayon-based parallelization and new packing-scope selection during IO conversion.
Changes:
- Added rotamer sampling (Dunbrack + polar-H sampling) and contact-graph construction, plus self/pair energy computation and pruning.
- Implemented DEE (Goldstein + Split) and a tree-decomposition DP solver with edge decomposition fallback.
- Introduced parallel spatial indexing and IO-level
PackingScope(Full/Pocket/Interface/List), plus new pack configuration and constants.
Reviewed changes
Copilot reviewed 25 out of 25 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| src/pack/phase/sample.rs | Rotamer/polar-H conformation sampling (parallel). |
| src/pack/phase/graph.rs | Builds contact graph using spatial grid queries. |
| src/pack/phase/prune.rs | Computes self energies vs fixed atoms and threshold-prunes candidates. |
| src/pack/phase/pair.rs | Computes pairwise SC–SC energy matrices for contact edges. |
| src/pack/phase/dee.rs | Dead-End Elimination (Goldstein + Split) with absorption of fixed slots. |
| src/pack/phase/dp.rs | Tree-decomposition dynamic programming GMEC solver with edge decomposition fallback. |
| src/pack/phase/mod.rs | Orchestrates the 6-phase pack pipeline and writes back best conformers. |
| src/pack/model/spatial.rs | Parallel SpatialGrid build (AtomicU32) + query iterator changes. |
| src/pack/model/graph.rs | ContactGraph now tracks edge indices; adds neighbor_edges() iterator. |
| src/pack/model/energy.rs | Introduces PRUNED sentinel; adjusts energy table APIs/tests. |
| src/pack/model/conformation.rs | Removes n_atoms() accessor; tests updated to use coords_of().len(). |
| src/pack/model/mod.rs | Removes junction module export. |
| src/pack/model/junction.rs | Deleted junction tree implementation (superseded by DP code in phase). |
| src/pack/energy.rs | Adds VdW/HBond/Coulomb kernels and helpers (dreid-kernel integration). |
| src/pack/constant.rs | Adds cutoffs/constants and max_interaction_cutoff(). |
| src/pack/config.rs | Adds PackConfig defaults and parameters. |
| src/pack/mod.rs | Exposes PackConfig and pack(); internalizes pack submodules. |
| src/model/system.rs | Adds residue ω angle and plumbs it through Residue::new() and accessors. |
| src/model/residue.rs | Updates is_packable() and adds polar_h_period() used by sampling. |
| src/io/config.rs | Adds PackingScope to ReadConfig. |
| src/io/convert.rs | Applies packing scope selection; computes φ/ψ/ω; builds mobile residues accordingly. |
| src/io/error.rs | Adds Error::Scope for packing-scope configuration failures. |
| src/io/mod.rs | Re-exports PackingScope and updates module docs. |
| Cargo.toml | Bumps/sets kernel + rotamer versions and adds rayon. |
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TKanX
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Summary:
Implemented the complete high-performance sidechain packing pipeline to resolve the Global Minimum Energy Conformation (GMEC). The system introduces a highly parallelized 6-phase workflow (Sample, Graph, Prune, Pair, DEE, DP), integrating
rayonfor concurrency, spatial hashing for interaction graphs, anddreid-kernelfor physical energy evaluations. Flexible packing scopes (Pocket, Interface, List) were also added for targeted region repacking.Changes:
phase/): Developed the corepackorchestrator executing 6 parallelized phases:sample,graph,prune(self-energy),pair(pair-energy),dee, anddp.dee.rswith Goldstein and Split criteria) and Tree-Decomposition Dynamic Programming (dp.rswith rank-1 edge decomposition) to exactly or near-exactly solve for the GMEC.sample.rs): Integrated the Dunbrack rotamer library (viarotamercrate) with support for backbonepolar_h_period).energy.rs): Integrateddreid-kernelfor vectorized evaluation of VdW (Lennard-Jones/Buckingham), Hydrogen Bonds, and distance-dependent Coulomb electrostatics.config.rs,convert.rs): AddedPackingScope(Full, Pocket, Interface, List) utilizingrayondependency. UpgradedSpatialGridconstruction (usingAtomicU32) and energy/graph calculations to leverage multi-threading.