feat(polymers): add native and CGSmiles authoring - #83
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Add mBuild-to-OpenFF conversion as the canonical chemistry boundary for atomistic polymer fragments, with OpenFF/SDF adapters feeding existing conjugation fragment models. Add static ACB parity coverage independent of Polymerist runtime, including graph, SMIRNOFF labels, NAGL charges, and OpenMM energy checks.
Preserve unchanged default config routing through bundled native methacrylate generation. Add deterministic random-walk mBuild assembly, OpenFF charging/cache artifacts, and a custom .rxn legacy Polymerist warning.
Add native linear fragment assembly with mBuild Port and force_overlap stitching, plus additive fixed and probabilistic provided charged SDF molecule pools. Preserve deprecated sdf_directory compatibility with warnings, update templates/docs, and cover behavior with focused tests.
Add the init-scaffolded simple notebook for offline CGSmiles polymer authoring. Support mBuild/OpenFF export with provided-only mode for generated charged SDFs. Remove Polymerist-backed generation paths and legacy reaction files. Pin the authoring stack in the project environments and lockfile.
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Summary
.rxnbackend path and document migration to native default methacrylate generation,polymers.fragments, the CGSmiles notebook, orpolymers.provided_molecules.Limitations
Glycan/protein handoff status
The notebook currently produces a charged SDF and a config snippet. Verified config/API support in this stack covers using that SDF as a free/additive polymer molecule through
polymers.provided_molecules/generation_mode: provided. The config-driven conjugation moiety provider still supportsattachment.moiety.polymer_recipeand SMILES/residue-name sources, and explicitly rejectsattachment.moiety.input_path; therefore automatic glycan attachment from the notebook SDF is not claimed here. Testing the notebook-to-branched-glycan/protein handoff remains the primary manual target for this PR.Validation
Fresh-checkout manual test
pixi install -e buildpixi run -e build polyzymd init <project-dir>pixi run -e build jupyter lab <project-dir>/notebooks/cgsmiles_polymer_scaffold.ipynbStacked commits included