nx_chem_smiles.nx

nx_chem_smiles.nx -- C2.1 + C2.2 milestones: basic SMILES parser. Parses the organic-subset SMILES grammar (Daylight 1988 / OpenSMILES 2016) into the MolGraph type from nx_chem_molecule.nx. Memory-safe by construction: every read is bounded against the input length; every error path sets is_valid=0 + structured err_code + err_pos. Supported (C2.1 + C2.2): - Organic-subset aliphatic atoms outside brackets: B, C, N, O, P, S, F, Cl, Br, I - Aromatic lowercase atoms outside brackets: b, c, n, o, p, s - Wildcard: * - **Full 118-element bracket atoms** (C2.2): H..Og, all IUPAC element symbols - Bracket attributes: isotope -- leading digits, e.g. [13C] chirality -- @ (CCW) or @@ (CW) on atom; stored in Atom.stereo (C2.2) H count -- H[count], e.g. [CH4], [NH4+] charge -- +, -, ++, --, +n, -n atom map -- :n, stored in Atom.map_num (C2.2) - Bond types: -, =, #, :, . (default = single between aliphatic, aromatic between two aromatics) - **Bond stereo: /, \\** -- stored in Bond.stereo as NX_BSTEREO_UP/DOWN (C2.2) - Branches: ( and ) - **Ring closures: 0..9 + %nn (two-digit, 00..99)** (C2.2) Honest gaps (deferred to C2.3+): - E/Z resolution from /, \\ (C2.1 stores raw UP/DOWN; CIP-rule resolution is C2.3) - Atropisomer + enhanced-stereo (C2.4) - Implicit-H valence inference (C2.3 -- h_count stays -1 for non-bracket atoms) - 6-aromaticity-tuple model dispatch (C2.5 -- this milestone sets one Daylight bit; tuple slot present) - Canonical SMILES output (C2.3) - Fuzzer 10^9 harness (C2.9) EXCEED axes hit (landscape doc references): E2 -- memory-safe parser by construction (bounded buffer reads + structured error paths) E4 -- per-atom + per-bond stereo slots populated from SMILES input (C2.2) E7 -- first-class radicals + charges + isotopes + full 118-element bracket support E11 -- no format lock-in (output is native MolGraph) nx_safety_envelope: intended_use: SMILES -> MolGraph parser for cheminformatics pipeline sil_target: SIL1