feat(phase1): implement all Phase 1 polymer architectures#90
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Peariforme merged 3 commits intomasterfrom Mar 4, 2026
Merged
feat(phase1): implement all Phase 1 polymer architectures#90Peariforme merged 3 commits intomasterfrom
Peariforme merged 3 commits intomasterfrom
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…4.2) ## Nouveaux builders ### LinearBuilder (linear.rs) - US-1.1.1: `random_copolymer(&[f64])` — copolymère statistique avec seed - US-1.1.2: `alternating_copolymer()` — séquence A-B-A-B cyclique - US-1.1.3: `block_copolymer(&[usize])` — diblock/triblock/multiblock - US-1.1.4: `gradient_copolymer(&GradientProfile)` — gradient linéaire ou sigmoïde - US-1.2.5: `cyclic_homopolymer()` — ring closure premier↔dernier atome - US-1.3.3: `with_end_groups()` — préfixe/suffixe BigSMILES inclus dans SMILES + Mn ### BranchedBuilder (branched.rs) - US-1.2.1: `comb_polymer(branch_every)` — peigne régulier backbone+branch - US-1.2.2: `graft_copolymer(graft_fraction, seed)` — greffage aléatoire reproductible - US-1.2.3: `star_polymer(arms)` — étoile 3–12 bras - US-1.2.4: `dendrimer(generation, branching_factor)` — dendrimère G1–G6 ### EnsembleBuilder (ensemble.rs) - `random_copolymer_ensemble`, `alternating_copolymer_ensemble`, `block_copolymer_ensemble`, `gradient_copolymer_ensemble` ## PolymerChain enrichi (US-1.3.1, US-1.3.2) - Nouveau champ `composition: Vec<MonomerUnit>` (fraction molaire par unité) - Nouveau champ `architecture: Architecture` (Linear/Star/Comb/Dendrimer/Cyclic/Gradient/Graft) - API builder fluent: `.with_composition()` et `.with_architecture()` ## CLI (US-1.4.1, US-1.4.2) - `polysim analyze` : `--arch random|alternating|block|gradient` - `polysim generate` : idem + `--gradient-profile linear|sigmoid`, `--gradient-f-start`, `--gradient-f-end` ## Tests: 35 nouveaux tests (tous verts) - `tests/copolymer.rs` : 17 tests random/alternating/block + ensembles - `tests/branched.rs` : 9 tests comb/graft/star/dendrimer - `tests/gradient_cyclic.rs` : 9 tests gradient/cyclic/end-groups Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Vérifie que make_cyclic_smiles ne corrompt pas les atomes bi-lettres comme Cl lors de l'insertion du ring closure. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Polymer Builder Benchmarks
Details
| Benchmark suite | Current: 9fd7da6 | Previous: 8c70235 | Ratio |
|---|---|---|---|
homopolymer/polyethylene/10 |
1664 ns/iter (± 25) |
1633 ns/iter (± 52) |
1.02 |
homopolymer/polyethylene/100 |
12314 ns/iter (± 228) |
12032 ns/iter (± 61) |
1.02 |
homopolymer/polyethylene/1000 |
110712 ns/iter (± 460) |
108414 ns/iter (± 509) |
1.02 |
homopolymer/polyethylene/10000 |
1091913 ns/iter (± 25560) |
1086121 ns/iter (± 88852) |
1.01 |
homopolymer/polystyrene/10 |
8534 ns/iter (± 154) |
8556 ns/iter (± 187) |
1.00 |
homopolymer/polystyrene/100 |
86462 ns/iter (± 343) |
88491 ns/iter (± 396) |
0.98 |
homopolymer/polystyrene/1000 |
847806 ns/iter (± 10543) |
867454 ns/iter (± 3955) |
0.98 |
molecular_weight/average_mass/polyethylene/10 |
1283 ns/iter (± 4) |
1339 ns/iter (± 41) |
0.96 |
molecular_weight/average_mass/polyethylene/100 |
9674 ns/iter (± 46) |
10176 ns/iter (± 67) |
0.95 |
molecular_weight/average_mass/polyethylene/1000 |
88714 ns/iter (± 3158) |
88282 ns/iter (± 2771) |
1.00 |
molecular_weight/average_mass/polystyrene/10 |
7580 ns/iter (± 285) |
7643 ns/iter (± 394) |
0.99 |
molecular_weight/average_mass/polystyrene/100 |
74696 ns/iter (± 407) |
74917 ns/iter (± 659) |
1.00 |
molecular_weight/monoisotopic_mass/polyethylene/10 |
1353 ns/iter (± 8) |
1377 ns/iter (± 17) |
0.98 |
molecular_weight/monoisotopic_mass/polyethylene/100 |
10103 ns/iter (± 244) |
10377 ns/iter (± 153) |
0.97 |
molecular_weight/monoisotopic_mass/polyethylene/1000 |
90793 ns/iter (± 711) |
87936 ns/iter (± 291) |
1.03 |
molecular_weight/by_target_mn/polyethylene/282 |
2941 ns/iter (± 18) |
2938 ns/iter (± 211) |
1.00 |
molecular_weight/by_target_mn/polyethylene/2825 |
13756 ns/iter (± 259) |
13699 ns/iter (± 28) |
1.00 |
molecular_weight/by_target_mn/polyethylene/28255 |
114147 ns/iter (± 422) |
112938 ns/iter (± 1712) |
1.01 |
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Résumé
Implémentation complète de la Phase 1 : Polymer Architectures — 14 user stories, 177 tests verts.
Nouveaux builders
LinearBuilder (
linear.rs)random_copolymer(&[f64])— copolymère statistique avec seedalternating_copolymer()— séquence A-B-A-B-…block_copolymer(&[usize])— diblock / triblock / multiblockgradient_copolymer(&GradientProfile)— gradient linéaire ou sigmoïdecyclic_homopolymer()— ring closure premier ↔ dernier atomeBranchedBuilder (
branched.rs)comb_polymer(branch_every)— peigne régulier backbone + branchgraft_copolymer(fraction, seed)— greffage aléatoire reproductiblestar_polymer(arms)— étoile 3–12 brasdendrimer(generation, branching_factor)— dendrimère G1–G6EnsembleBuilder (
ensemble.rs)random_copolymer_ensemble,alternating_copolymer_ensemble,block_copolymer_ensemble,gradient_copolymer_ensemblePolymerChain enrichi
composition: Vec<MonomerUnit>— fraction molaire par unité de répétitionarchitecture: Architecture— Linear / Star / Comb / Dendrimer / Cyclic / Gradient / GraftCLI
polysim analyze --arch random|alternating|block|gradientpolysim generate+--gradient-profile linear|sigmoid,--gradient-f-start,--gradient-f-endCloses
Closes #9
Closes #10
Closes #11
Closes #12
Closes #13
Closes #14
Closes #15
Closes #16
Closes #17
Closes #18
Closes #19
Closes #20
Closes #21
Closes #22
Plan de test
cargo test: 177 tests, 0 écheccargo clippy: aucun warningcargo fmt --check: formatage conformemake_cyclic_smilesavec atomes bi-lettres (Cl)🤖 Generated with Claude Code