#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum SupportStatus {
Supported,
SupportedWithRdkitParity { rdkit_version: &'static str },
PreservedOnly,
Experimental,
Unsupported { reason: &'static str },
}
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum FeatureCategory {
Core,
TopologyOperation,
Io,
Fingerprint,
Drawing,
Stereo,
Valence,
Batch,
BioHierarchy,
BioCoordinate,
BioSelection,
}
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub struct FeatureSpec {
pub name: &'static str,
pub category: FeatureCategory,
pub status: SupportStatus,
pub parity_sensitive: bool,
pub docs: &'static str,
}
impl FeatureSpec {
#[must_use]
pub const fn unsupported(
name: &'static str,
category: FeatureCategory,
parity_sensitive: bool,
reason: &'static str,
docs: &'static str,
) -> Self {
Self {
name,
category,
status: SupportStatus::Unsupported { reason },
parity_sensitive,
docs,
}
}
}
#[derive(Debug, Clone, PartialEq, Eq, thiserror::Error)]
#[error("unsupported feature {feature}: {reason}")]
pub struct UnsupportedFeatureError {
pub feature: &'static str,
pub reason: &'static str,
}
impl UnsupportedFeatureError {
#[must_use]
pub const fn from_spec(feature: &'static FeatureSpec) -> Self {
let reason = match feature.status {
SupportStatus::Unsupported { reason } => reason,
_ => "feature is not available in this build",
};
Self {
feature: feature.name,
reason,
}
}
}
pub const SMILES_PARSE_FEATURE: FeatureSpec = FeatureSpec {
name: "smiles.parse",
category: FeatureCategory::Io,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Parse SMILES into Molecule with sanitize integration through registered operations (kekulize, valence, aromaticity, rings). RDKit-aligned postprocessing includes first-2D/first-3D conformer selection, wedged/3D stereo assignment (including non-tetrahedral branches), atropisomer chirality mutation paths, CX wiggly-bond direction cleanup, and _NeedsQueryScan ring/non-ring query completion. CX extensions (coords, labels, values, props, radicals, stereo, SGroups, hierarchy, polymer, linknodes) are parsed. Remove-H isotope tracking and the targeted fixture-backed reader parity gaps from the current checklist are closed, but the reader is not marker-complete: `notation/smiles.rs` still contains 1 `RDKit❌❌`, 2 `RDKit❗❗`, 14 `RDKit✔️❌`, and 713 `RDKit❗✔️` copied-source lines across the remaining parser/helper blockers tracked by the gap report. Remaining unported or unresolved branches fail closed or remain explicitly tracked by gap reports.",
};
pub const SMILES_WRITE_FEATURE: FeatureSpec = FeatureSpec {
name: "smiles.write",
category: FeatureCategory::Io,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Plain SMILES output (canonical and noncanonical) is implemented, including the checklist-closed parity cases for noncanonical/rooted/connected/ring/fused/CIP-tie double-bond direction output and non-tetrahedral class emission/permutation recomputation. Aromatic atoms (lowercase) and BondOrder::Aromatic bonds are supported. CX writer blocks are implemented for bond wedge/dash config, ring-bond cis/trans config, linknodes, polymer SGroups, SGroup hierarchy, atropisomer bonds, atom labels, molfile values, 2D coordinates, radicals, atom properties, enhanced stereo groups, and coordinate/hydrogen/zero bonds. Writer behavior depends on the chemistry-core sanitize/valence/kekulize/ring state pipeline, and writer-internal unsupported stage guards were replaced by concrete invariant/validation errors where reachable. The frozen writer file is marker-closed for the current checklist scope, but the feature remains experimental and depends on broader parser/chemistry parity surfaces that are still open elsewhere.",
};
pub const MOLBLOCK_IO_FEATURE: FeatureSpec = FeatureSpec {
name: "molblock.io",
category: FeatureCategory::Io,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental V2000/V3000 MolBlock/SDF writer with parity flag, bond-stereo, SGroup, RGroup, alias, value lines, and aromatic-bond bookkeeping. Reader has partial V2000 parsing. The writer and reader remain dependent on explicit valence/kekulize/ring state management. Unsupported branches (complex SMARTS queries, atropisomer wedge-bonds) fail closed.",
};
pub const MOL2_READ_FEATURE: FeatureSpec = FeatureSpec {
name: "mol2.read",
category: FeatureCategory::Io,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "RDKit-compatible Tripos MOL2 reading is source-ported from `Mol2FileParser.cpp` for the exposed `Mol2FileToMol`/`Mol2BlockToMol` profile, including `Mol2ParserParams` controls for sanitize, removeHs, CORINA variant, and cleanupSubstructures. The feature remains experimental while broader fixture parity and marker audit work continues.",
};
pub const HYDROGENS_FEATURE: FeatureSpec = FeatureSpec {
name: "molecule.hydrogens",
category: FeatureCategory::TopologyOperation,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental value-style explicit hydrogen operations. Remove-H is being ported through the operation-contract path and depends on valence/kekulize/ring state being available; unsupported source branches fail closed.",
};
pub const COORDINATE_2D_FEATURE: FeatureSpec = FeatureSpec {
name: "coordinates.2d",
category: FeatureCategory::TopologyOperation,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental RDKit-aligned 2D depiction surface with value semantics. The active Rust path includes parameterized compute2DCoords entrypoints, preferCoordGen/forceRDKit routing, ring-template registry loading, mimic-distance embedding, constrained 2D/3D depiction matching, normalize/straighten helpers, and registered with_2d_coordinates exposure used by batch, MolBlock, and drawing callers. CoordGen-backed runtime branches are not available in this build and fail explicitly instead of silently diverging; final whole-surface audit/validation remains tracked separately.",
};
pub const CONFORMER_GENERATION_FEATURE: FeatureSpec = FeatureSpec {
name: "coordinates.3d.conformer_generation",
category: FeatureCategory::TopologyOperation,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental RDKit-aligned distance-geometry conformer generation. The exposed surface uses the source-ported EmbedParameters presets, DG/KDG/ETDG/ETKDG entry points, source-backed seeded and unseeded RNG setup, deterministic explicit-seed single-conformer path, deterministic batch seed policy for multi-conformer generation, pruning, terminal-group symmetrization during symmetry-aware pruning, coordMap, CPCI, custom bounds-matrix size validation, stereo/chiral checks, macrocycle and small-ring torsion paths. Final marker audit: no first-axis `RDKit❌❌` block remains in the audited conformer-generation path; residual `RDKit✔️❌`, `RDKit✔️❗`, and `RDKit❗✔️` markers remain in the bounds-builder helper surface and should not be overstated as blanket parity closure.",
};
pub const SANITIZE_FEATURE: FeatureSpec = FeatureSpec {
name: "molecule.sanitize",
category: FeatureCategory::TopologyOperation,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Run supported RDKit-aligned sanitization steps as a weak topology-state operation, sequencing the explicit valence/kekulize/ring handoff used by the SMILES reader and other operations. Full RDKit flag/error/cleanup closure is still pending in the broader operation-orchestration surface: `operations/ops.rs` still contains 216 `RDKit✔️❌` copied-source lines across the remaining sanitize/property/cleanup orchestration blocks and helper routines tracked by the gap report. Unported requested steps fail closed.",
};
pub const KEKULIZE_FEATURE: FeatureSpec = FeatureSpec {
name: "molecule.with_kekulized_bonds",
category: FeatureCategory::TopologyOperation,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental operation-pipeline for kekulized bond rewriting. This is the dependency used by fused aromatic assignment and KekulizeIfPossible restoration. Fragment filtering, fused aromatic candidate selection, worker ordering/backtracking, dummy-question permutation, and value-style `KekulizeIfPossible` restoration have focused regression coverage, but broader operation-state interaction closure is still pending and `chemistry/kekulize.rs` still contains 397 `RDKit✔️❌` copied-source lines in the current frozen-scope audit; unsupported branches fail closed.",
};
pub const FINGERPRINT_FEATURE: FeatureSpec = FeatureSpec {
name: "fingerprint.morgan",
category: FeatureCategory::Fingerprint,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Compute Morgan-style fingerprints with connectivity invariants (RDKit component-vector hash style). Environment propagation uses RDKit's seed=layer + sorted neighbor-pair hashing. Chirality support, feature invariants (element/property classification), custom atom/bond invariants, count-simulation with configurable bounds. Hash-value alignment is structurally compatible but not bit-identical (uses own hash_combine instead of gboost::hash).",
};
pub const DRAWING_FEATURE: FeatureSpec = FeatureSpec {
name: "drawing.depiction",
category: FeatureCategory::Drawing,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "SVG/PNG molecule renderer ported from RDKit MolDraw2D. \
Includes atom labels (isotope/charge/H/map), bond geometry \
(single/double/triple/wedge/aromatic/dative), radical dots, clash \
detection, scale calculation, and smoothed bond joins. \
Annotations: CIP codes (R/S, E/Z), atom notes, bond notes, \
SGroup data, brackets, variable bonds, link nodes, close-contact \
markers, and highlights. SVG metadata, data-tag attributes, and \
CSS class output for atoms/bonds. \
SVG output via native XML; PNG via usvg+resvg rasterization.",
};
pub const STEREO_FEATURE: FeatureSpec = FeatureSpec {
name: "stereo.perception",
category: FeatureCategory::Stereo,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Tetrahedral stereo detection from typed state (ChiralTag + chiral_permutation). \
CIP ranking system (assignAtomCIPRanks with iterative neighbor-rank refinement) ported. \
R/S label assignment (assignAtomChiralCodes) from ChiralTag + permutation. \
Double-bond E/Z potential detection. Pseudo-3D wedge-based chiral tag detection \
(atomChiralTypeFromBondDirPseudo3D). Full non-tetrahedral stereo infrastructure \
(SquarePlanar, TrigonalBipyramidal, Octahedral swap tables and across-atom lookup). \
Ring stereochemistry special-case detection. Full CIP-based bond stereo codes \
and assignLegacyCIPLabels dispatcher ported. assignAtomChiralTagsFromStructure \
(full 3D coordinate-based ChiralTag assignment) remains blocked on Conformer \
infrastructure completeness.",
};
pub const VALENCE_FEATURE: FeatureSpec = FeatureSpec {
name: "valence.assignment",
category: FeatureCategory::Valence,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental RDKit-aligned valence and implicit hydrogen assignment. This is a shared dependency for sanitize, kekulize, and SMILES postprocessing. `chemistry/valence.rs` now only retains 4 `RDKit✔️❌` copied-source lines in `ValenceContext::new`, and remaining work is concentrated in property-cache maintenance, radicals, dative/query edge cases, and broader entrypoint/orchestration logic in `operations/ops.rs`. Unsupported branches fail closed.",
};
pub const RINGS_FEATURE: FeatureSpec = FeatureSpec {
name: "rings.symm_sssr",
category: FeatureCategory::TopologyOperation,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental RDKit-aligned SSSR, symmetrized SSSR, fast ring traversal, and URF-enabled ring-family/relevant-cycle perception via `cosmolkit_ringdecomposer`. SSSR active-bond filtering, D2 duplicate-candidate handling, D3/extra-ring discovery, symmetrized K4 storage, fastFindRings DFS traversal, and the URF-enabled ring-family/relevant-cycle path have focused regression coverage. The frozen ring-perception file is marker-closed for the current checklist scope, but the feature remains experimental and is not a blanket claim of complete RDKit ring parity outside that audited scope.",
};
pub const AROMATICITY_FEATURE: FeatureSpec = FeatureSpec {
name: "aromaticity.assignment",
category: FeatureCategory::TopologyOperation,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental RDKit-aligned aromaticity assignment scaffold with fail-closed unsupported branches.",
};
pub const BATCH_FEATURE: FeatureSpec = FeatureSpec {
name: "batch.operations",
category: FeatureCategory::Batch,
status: SupportStatus::Experimental,
parity_sensitive: false,
docs: "Batch construction from SMILES list, ordered transformations via registered molecule operations, \
error modes (Strict/KeepErrors), valid mask, filter valid, SMILES export with params, \
and PNG image export. Batch scheduling and parallel execution are not yet implemented.",
};
pub const BIO_STRUCTURE_FEATURE: FeatureSpec = FeatureSpec {
name: "bio.structure",
category: FeatureCategory::BioHierarchy,
status: SupportStatus::Experimental,
parity_sensitive: false,
docs: "Experimental flat-row BioStructure hierarchy and coordinate storage. This is COSMolKit's single public structural model for protein/PDB/mmCIF work. Public access is read-only; mutation must go through crate-internal builders or registered BioStructure operations.",
};
pub const BIO_PDB_COORDINATE_SUBSET_READ_FEATURE: FeatureSpec = FeatureSpec {
name: "bio.pdb.coordinate_subset.read",
category: FeatureCategory::Io,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental Gemmi-aligned PDB structural reader into BioStructure. This is the structural IO path and the required front end for future RDKit-compatible molecule input. The public feature name keeps the historical subset label for API stability, but the current reader surface covers ATOM/HETATM, MODEL/ENDMDL, ANISOU, residue and chain identity, TER semantics, SEQRES entities, DBREF, SSBOND/LINK/CISPEP, MODRES, selected header metadata, AUTHOR, CRYST1, SCALE, ORIGX, and MTRIX/NCS records. Remaining unsupported Gemmi branches fail explicitly and stay marked in io::bio.",
};
pub const BIO_MMCIF_ATOM_SITE_SUBSET_READ_FEATURE: FeatureSpec = FeatureSpec {
name: "bio.mmcif.atom_site_subset.read",
category: FeatureCategory::Io,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental Gemmi-aligned mmCIF/mmJSON structural reader into BioStructure. This is the structural IO path and the required front end for any future molecule compatibility input. The public feature name keeps the historical atom-site subset label for API stability, but the current reader surface also covers mmJSON dispatch, _entity, _entity_poly, _entity_poly_seq, _struct_ref/_struct_ref_seq, _struct_asym, _struct_conn, _struct_mon_prot_cis, _pdbx_struct_mod_residue, _pdbx_struct_assembly*, _pdbx_sifts_xref_db, _struct_ncs_oper, crystallographic transforms, and chem-comp CIF handoff through the same dispatch path. RDKit-derived macromolecular parser work remains deferred unless a Molecule compatibility need is approved. Remaining unsupported Gemmi branches fail explicitly and stay marked in io::bio.",
};
pub const PUBLIC_FEATURES: &[&FeatureSpec] = &[
&SMILES_PARSE_FEATURE,
&SMILES_WRITE_FEATURE,
&MOLBLOCK_IO_FEATURE,
&MOL2_READ_FEATURE,
&HYDROGENS_FEATURE,
&COORDINATE_2D_FEATURE,
&CONFORMER_GENERATION_FEATURE,
&SANITIZE_FEATURE,
&KEKULIZE_FEATURE,
&FINGERPRINT_FEATURE,
&DRAWING_FEATURE,
&STEREO_FEATURE,
&VALENCE_FEATURE,
&RINGS_FEATURE,
&AROMATICITY_FEATURE,
&BATCH_FEATURE,
&DG_BOUNDS_FEATURE,
&BIO_STRUCTURE_FEATURE,
&BIO_PDB_COORDINATE_SUBSET_READ_FEATURE,
&BIO_MMCIF_ATOM_SITE_SUBSET_READ_FEATURE,
&BIO_SELECTION_FEATURE,
];
pub const DG_BOUNDS_FEATURE: FeatureSpec = FeatureSpec {
name: "distgeom.bounds_matrix",
category: FeatureCategory::Core,
status: SupportStatus::Experimental,
parity_sensitive: true,
docs: "Experimental distance-geometry bounds matrix generation. The current Rust DG bounds surface is \
source-backed across the selected RDKit baseline: raw BoundsMatrix upper/lower triangle storage, \
triangle smoothing, 1-2/1-3/1-4/1-5 bound setting, VDW lower bounds, collectBondsAndAngles, \
both setTopolBounds overloads, and GetMoleculeBoundsMatrix-style wrapper defaults are implemented \
with focused strict tests. The final DG bounds audit found no remaining first-axis `RDKit❌*` \
gap in the audited call chain, but deliberate `RDKit✔️❌`, `RDKit✔️❗`, and `RDKit❗✔️` markers \
remain visible for performance and helper-abstraction caveats. This is a port-closure statement \
for the audited DG bounds scope, not a blanket RDKit parity guarantee for every possible \
molecule/input outside that baseline.",
};
pub const BIO_SELECTION_FEATURE: FeatureSpec = FeatureSpec {
name: "bio.selection",
category: FeatureCategory::BioSelection,
status: SupportStatus::Experimental,
parity_sensitive: false,
docs: "Experimental BioStructure selection and filtering operations (e.g. remove_waters).",
};