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refactor(core): Refactor Core Models with SlotMap for Stability and Mutability #8

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TKanX merged 20 commits into from
Jul 3, 2025
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refactor(core): Refactor Core Models with SlotMap for Stability and Mutability #8

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6850367
chore(package): Add slotmap dependency for enhanced data structure su…
TKanX Jul 3, 2025
cf36a49
feat(core): Introduce new key types for AtomId, ResidueId, and ChainI…
TKanX Jul 3, 2025
116d8e3
refactor(core): Simplify Atom struct by removing unused fields and up…
TKanX Jul 3, 2025
00e8b71
test(core): Add unit tests for Atom struct and its flags operations
TKanX Jul 3, 2025
bfd3048
refactor(core): Update Residue struct to include chain_id and change …
TKanX Jul 3, 2025
7614a6b
test(core): Add unit tests for Residue struct methods
TKanX Jul 3, 2025
ac61635
refactor(core): Update Chain struct to use ResidueId and simplify res…
TKanX Jul 3, 2025
c18bbab
test(core): Add unit tests for ChainType parsing and Chain creation
TKanX Jul 3, 2025
62fe7a8
refactor(core): Update Bond struct to use AtomId for atom identification
TKanX Jul 3, 2025
3daa711
test(core): Add comprehensive tests for Bond and BondOrder functionality
TKanX Jul 3, 2025
f118a90
refactor(core): Revise MolecularSystem structure for improved data ma…
TKanX Jul 3, 2025
bc3af3e
test(core): Add unit tests for MolecularSystem functionality includin…
TKanX Jul 3, 2025
3aeede3
refactor(core): Remove unused AtomFlags import and adjust test module…
TKanX Jul 3, 2025
d3b8428
refactor(core): Remove builder module from core models
TKanX Jul 3, 2025
6b7a564
refactor(core): Use BufWriter for improved file writing in MolecularF…
TKanX Jul 3, 2025
8ba1d14
refactor(core): Improve bond addition logic and enhance atom removal …
TKanX Jul 3, 2025
dbdf873
refactor(core): Replace MolecularSystemBuilder with direct MolecularS…
TKanX Jul 3, 2025
8eee55a
test(core): Add unit tests for BgfFile read_from and write_to methods
TKanX Jul 3, 2025
1bdc944
feat(core): Ensure consistent atom ordering in Bond struct initializa…
TKanX Jul 3, 2025
74b04e1
refactor(core): Simplify chain residue access in add_residue method
TKanX Jul 3, 2025
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16 changes: 16 additions & 0 deletions Cargo.lock
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1 change: 1 addition & 0 deletions crates/scream-core/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,4 +10,5 @@ edition.workspace = true
[dependencies]
bitflags = "2.9.1"
nalgebra = "0.33.2"
slotmap = "1.0.7"
thiserror = "2.0.12"
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