Parity ledger
Per-capability promotion status from beta to exercised, with the golden workflow and external reference that justify each promotion.
Parity ledger
Every row of the capability register starts at β: native code, covered by
tests, with no external differential evidence. A row moves to ✓ only when it
names a golden workflow (GW-NNN) whose test pins values from a named external
library at a stated version, with a stated tolerance. crates/molframe/tests/parity_ledger.rs
fails when a ✓ row has no GW, or when a named GW has no gw_NNN_ test.
| Status | Meaning |
|---|---|
✓ | Native, backed by a golden workflow with pinned external evidence |
β | Native, covered by tests, not yet pinned to an external reference |
– | Another domain; the argument is in the Evidence column |
· | The reference libraries do not have this |
Blocked
These golden workflows cannot be promoted until their reference prerequisites are reproducible.
- GW-031:
complex_infois not pinned and runnable in the reference workflow. Sources exist in the local siblingligare/deleteme/complex_info; the supplied executable targets Linux x86-64. - GW-032: ATPTS is not pinned and runnable in the reference workflow. Driver sources, templates and examples exist in the local sibling
ligare/deleteme/atpts. - GW-044 to GW-047: the OpenStructure, Graphein and Geomstats pins and their corpora are not selected.
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
✓ | β | — | Not yet promoted | |
≈ | β | — | Not yet promoted | |
β | β | — | Not yet promoted | |
– | β | — | Not yet promoted | |
· | β | — | Not yet promoted |
1. Formats — reading
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| PDBx/mmCIF | β | molframe-cif | — | Not yet promoted |
| mmCIF unknown-category preservation | β | molframe-cif | — | Not yet promoted |
| BinaryCIF | β | molframe-bcif | — | Not yet promoted |
| Legacy PDB | β | molframe-pdb | — | Not yet promoted |
| PDB hybrid-36 | β | molframe-pdb | — | Not yet promoted |
| PDB header records (full set) | β | molframe-pdb | — | Not yet promoted |
| PDBML / XML | β | molframe-cif | — | Not yet promoted |
| ModelCIF | β | molframe-modelcif | — | Not yet promoted |
| PDB-IHM | β | molframe-modelcif | — | Not yet promoted |
| MMTF | β | molframe-pdb | — | Not yet promoted |
| PQR | β | molframe-pdb | — | Not yet promoted |
| PDBQT | β | molframe-pdb | — | Not yet promoted |
| MOL / SDF | β | molframe-chem | — | Not yet promoted |
| MOL2 | β | molframe-chem | — | Not yet promoted |
| Small-molecule CIF | β | molframe-cif | — | Not yet promoted |
| CCD | β | molframe-chem | — | Not yet promoted |
| Monomer restraint library | β | molframe-xtal | — | Not yet promoted |
| gzip / zstd transparent | β | molframe-core | — | Not yet promoted |
| Memory-mapped input | β | molframe-core | — | Not yet promoted |
| Streaming input | β | molframe-core | — | Not yet promoted |
| Diagnostics returned with success | β | molframe-core | — | Not yet promoted |
| Record/category skip filters | β | molframe-cif | — | Not yet promoted |
2. Formats — writing
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| mmCIF canonical write | β | molframe-cif | — | Not yet promoted |
| mmCIF document-preserving write | β | molframe-cif | — | Not yet promoted |
| BinaryCIF write | β | molframe-bcif | — | Not yet promoted |
| BinaryCIF encoding optimisation | β | molframe-bcif | — | Not yet promoted |
| Legacy PDB write | β | molframe-pdb | — | Not yet promoted |
| Refuse lossy PDB write | β | molframe-pdb | — | Not yet promoted |
Selective write (Select protocol) | β | molframe-core | — | Not yet promoted |
| ModelCIF write | β | molframe-modelcif | — | Not yet promoted |
| MMTF write | β | molframe-pdb | — | Not yet promoted |
3. Trajectory formats
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| XTC | β | molframe-traj | — | Not yet promoted |
| TRR | β | molframe-traj | — | Not yet promoted |
| TNG | β | molframe-traj | — | Not yet promoted |
| DCD (CHARMM/NAMD) | β | molframe-traj | — | Not yet promoted |
| DCD (LAMMPS) | β | molframe-traj | — | Not yet promoted |
| NetCDF / AMBER | β | molframe-traj | — | Not yet promoted |
| AMBER ASCII trj | β | molframe-traj | — | Not yet promoted |
| AMBER inpcrd/restart | β | molframe-traj | — | Not yet promoted |
| GRO | β | molframe-traj | — | Not yet promoted |
| XYZ | β | molframe-traj | — | Not yet promoted |
| Tinker TXYZ / ARC | β | molframe-traj | — | Not yet promoted |
| CHARMM CARD (CRD) | β | molframe-traj | — | Not yet promoted |
| DESRES DMS | β | molframe-traj | — | Not yet promoted |
| TRZ | β | molframe-traj | — | Not yet promoted |
| GROMOS11 TRC | β | molframe-traj | — | Not yet promoted |
| HOOMD GSD | β | molframe-traj | — | Not yet promoted |
| H5MD | β | molframe-traj | — | Not yet promoted |
| NAMD binary | β | molframe-traj | — | Not yet promoted |
| FHI-AIMS | β | molframe-traj | — | Not yet promoted |
| DL_POLY CONFIG/HISTORY | β | molframe-traj | — | Not yet promoted |
| GAMESS | β | molframe-traj | — | Not yet promoted |
| LAMMPS dump | β | molframe-traj | — | Not yet promoted |
| In-memory array source | β | molframe-traj | — | Not yet promoted |
| Multi-file chaining | β | molframe-traj | — | Not yet promoted |
| Random frame access | β | molframe-traj | — | Not yet promoted |
| Frame slicing / index lists | β | molframe-traj | — | Not yet promoted |
| Streaming (IMD) | β | molframe-traj | — | Not yet promoted |
4. Simulation topology formats
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| CHARMM/XPLOR/NAMD PSF | β | molframe-traj | — | Not yet promoted |
| Gromacs TPR | β | molframe-traj | — | Not yet promoted |
| Gromacs ITP | β | molframe-traj | — | Not yet promoted |
| AMBER prmtop / parm7 | β | molframe-traj | — | Not yet promoted |
| LAMMPS data | β | molframe-traj | — | Not yet promoted |
| HOOMD XML | β | molframe-traj | — | Not yet promoted |
| Minimal (atom count only) | β | molframe-traj | — | Not yet promoted |
5. Data model
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Hierarchical API | β | molframe-core | — | Not yet promoted |
| Columnar storage | β | molframe-core | — | Not yet promoted |
| Both, over one store | β | molframe-core | — | Not yet promoted |
| Zero-copy views | β | molframe-core | — | Not yet promoted |
| Topology / coordinate separation | β | molframe-core | — | Not yet promoted |
| Dense multi-model | β | molframe-core | — | Not yet promoted |
| Ragged ensembles | β | molframe-core | — | Not yet promoted |
| Entity as a first-class table | β | molframe-core | — | Not yet promoted |
| Both identifier namespaces | β | molframe-core | — | Not yet promoted |
| Namespace as a policy field | β | molframe-core | — | Not yet promoted |
| Insertion codes | β | molframe-core | — | Not yet promoted |
| Extended (12-char) PDB IDs | β | molframe-core | — | Not yet promoted |
| Altlocs preserved | β | molframe-core | — | Not yet promoted |
| Altloc resolution as a policy | β | molframe-core | — | Not yet promoted |
| Conformer-consistent altloc selection | β | molframe-core | — | Not yet promoted |
| Immutable + transactional edit | β | molframe-core | — | Not yet promoted |
| Copy-on-write overlay | β | molframe-core | — | Not yet promoted |
| Coordinate generation tracking | β | molframe-core | — | Not yet promoted |
| Custom per-atom annotations | β | molframe-core | — | Not yet promoted |
| Structure merging | β | molframe-core | — | Not yet promoted |
6. Selection
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Textual selection language | β | molframe-query | — | Not yet promoted |
| Typed builder | β | molframe-query | — | Not yet promoted |
| Pre-compiled reusable queries | β | molframe-query | — | Not yet promoted |
| Boolean composition | β | molframe-query | — | Not yet promoted |
and tighter than or | β | molframe-query | — | Not yet promoted; MD gives both precedence 3; divergence documented |
| Glob name matching | β | molframe-query | — | Not yet promoted |
| Glob resolved at plan time | β | molframe-query | — | Not yet promoted |
within / around / beyond | β | molframe-query | — | Not yet promoted |
sphzone / sphlayer / isolayer | β | molframe-query | — | Not yet promoted |
cyzone / cylayer | β | molframe-query | — | Not yet promoted |
point | β | molframe-query | — | Not yet promoted |
same X as | β | molframe-query | — | Not yet promoted |
byres | β | molframe-query | — | Not yet promoted |
bonded | β | molframe-query | — | Not yet promoted |
global | β | molframe-query | — | Not yet promoted |
group (external set) | β | molframe-query | — | Not yet promoted |
prop comparisons | β | molframe-query | — | Not yet promoted |
resid with insertion codes | β | molframe-query | — | Not yet promoted |
| Macros (protein, backbone, …) | β | molframe-query | — | Not yet promoted |
| Macros derived from chemistry | β | molframe-query | — | Not yet promoted; MD uses hard-coded residue lists |
label_* / auth_* selectors | β | molframe-query | — | Not yet promoted; Unique to molframe |
altloc / model / entity / assembly | β | molframe-query | — | Not yet promoted |
| SMARTS | β | molframe-query | — | Not yet promoted; Native parser and CCD-backed structure matcher; RDKit adapter remains phase 4 |
| Chirality / aromatic / formal charge | β | molframe-query | — | Not yet promoted |
| Updating selections | β | molframe-query | — | Not yet promoted |
| Logical / physical plan separation | β | molframe-query | — | Not yet promoted |
| Chunk pruning by statistics | β | molframe-query | — | Not yet promoted |
| Adaptive result representation | β | molframe-query | — | Not yet promoted |
| Late materialization | β | molframe-query | — | Not yet promoted |
7. Spatial search
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Cell list | β | molframe-spatial | — | Not yet promoted |
| k-d tree | β | molframe-spatial | — | Not yet promoted |
| Brute force (SIMD) | β | molframe-spatial | — | Not yet promoted |
| Verlet neighbour list | β | molframe-spatial | — | Not yet promoted |
| Cost-based backend selection | β | molframe-spatial | — | Not yet promoted |
| Periodic boundaries (orthorhombic) | β | molframe-spatial | — | Not yet promoted |
| Periodic boundaries (triclinic) | β | molframe-spatial | — | Not yet promoted |
| Minimum image convention | β | molframe-spatial | — | Not yet promoted |
| Crystallographic images | β | molframe-spatial | — | Not yet promoted |
| Assembly transforms | β | molframe-spatial | — | Not yet promoted |
| k-nearest neighbours | β | molframe-spatial | — | Not yet promoted |
| Unique pairs / self-exclusion | β | molframe-spatial | — | Not yet promoted |
| Index caching by generation | β | molframe-spatial | — | Not yet promoted |
| Minimum-image lattice shift and flat-torus interpolation | β | molframe-spatial | — | Not yet promoted |
8. Geometry
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Distances, angles, dihedrals | β | molframe-geom | — | Not yet promoted |
| Distance matrices | β | molframe-geom | — | Not yet promoted |
| Centroid, centre of mass | β | molframe-geom | — | Not yet promoted |
| Rigid transforms | β | molframe-geom | — | Not yet promoted |
| Kabsch superposition | β | molframe-geom | — | Not yet promoted |
| QCP superposition | β | molframe-geom | — | Not yet promoted |
| RMSD | β | molframe-geom | — | Not yet promoted |
| RMSF | β | molframe-geom | — | Not yet promoted |
| Radius of gyration | β | molframe-geom | — | Not yet promoted |
| Inertia tensor / principal axes | β | molframe-geom | — | Not yet promoted |
| Asphericity, shape parameter | β | molframe-geom | — | Not yet promoted |
| Backbone torsions | β | molframe-geom | — | Not yet promoted |
| Side-chain torsions | β | molframe-geom | — | Not yet promoted |
| Nucleic torsions / pucker | β | molframe-analysis | — | Not yet promoted |
| Ramachandran classification | β | molframe-validate | — | Not yet promoted |
| Internal coordinates | β | molframe-ic | — | Not yet promoted |
| Rebuild from internal coordinates | β | molframe-ic | — | Not yet promoted |
| Bond-angle-torsion coordinates | β | molframe-ic | — | Not yet promoted |
| Periodic angles and circular statistics | β | molframe-geom | — | Not yet promoted |
| Weighted torus distance and Fréchet summaries | β | molframe-geom | — | Not yet promoted |
| Validated SO(3) rotations, geodesics and interpolation | β | molframe-geom | — | Not yet promoted |
| Intrinsic SO(3) mean with non-uniqueness reporting | β | molframe-geom | — | Not yet promoted |
| Discrete Cα frames and HELANAL geometry | β | molframe-geom | — | Not yet promoted |
9. Surfaces and interactions
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| SASA (Shrake–Rupley) | ✓ | molframe-surface | GW-013 | biotite 1.7.1 on 1CRN and 1UBQ (water excluded), Bondi radii, probe 1.4 Å, 960 points; per-atom bound 1/√960 of the sphere area, totals within 0.5% (tests/reference/sasa_biotite_1.7.1.json) |
| SASA (Lee–Richards) | β | molframe-surface | — | Not yet promoted |
| SES / Connolly surface | β | molframe-surface | — | Not yet promoted |
| Buried surface (two-group SASA) | β | molframe-surface | — | Not yet promoted |
| Buried SES with molecule roles | β | molframe-surface | — | Not yet promoted |
| Surface points with normals | β | molframe-surface | — | Not yet promoted |
| Cavity detection | β | molframe-surface | — | Not yet promoted |
| Residue depth | β | molframe-surface | — | Not yet promoted |
| Half-sphere exposure | β | molframe-analysis | — | Not yet promoted |
| Contacts (distance) | β | molframe-analysis | — | Not yet promoted |
| Contacts (surface-based) | β | molframe-analysis | — | Not yet promoted |
| Contact maps | β | molframe-analysis | — | Not yet promoted |
| Native contacts / Q | β | molframe-analysis | — | Not yet promoted |
| Hydrogen bonds | β | molframe-analysis | — | Not yet promoted |
| Water bridges | β | molframe-analysis | — | Not yet promoted |
| Salt bridges | β | molframe-analysis | — | Not yet promoted |
| π-stacking / cation-π | β | molframe-analysis | — | Not yet promoted |
| Clashes | β | molframe-validate | — | Not yet promoted |
| Interfaces | β | molframe-analysis | — | Not yet promoted |
| Secondary structure (native) | β | molframe-analysis | — | Not yet promoted |
| Secondary structure (DSSP binary) | β | molframe-analysis | — | Not yet promoted |
| Base pairs / stacking | β | molframe-analysis | — | Not yet promoted |
| PEOE charge equalisation (hybridisation-aware) | β | molframe-chem | — | Not yet promoted |
| Indexed oriented surface mesh and quality diagnostics | β | molframe-surface | — | Not yet promoted |
| Edge-geodesic distances and intrinsic patches | β | molframe-surface | — | Not yet promoted |
| Discrete mean/Gaussian/principal surface curvature | β | molframe-surface | — | Not yet promoted |
10. Chemistry
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| CCD integration | β | molframe-chem | — | Not yet promoted |
| Pluggable component provider | β | molframe-chem | — | Not yet promoted |
| Bond table | β | molframe-chem | — | Not yet promoted |
| Bond provenance | β | molframe-chem | — | Not yet promoted |
| Bonds from file records | β | molframe-chem | — | Not yet promoted |
| Bonds from CCD | β | molframe-chem | — | Not yet promoted |
| Bond inference by distance | β | molframe-chem | — | Not yet promoted |
| Element data / radii sets | ✓ | molframe-chem | GW-045 | The atomic weights are the CIAAW 2021 conventional values. gemmi 0.7.5 still carries pre-2021 Ge (72.64) and Se (78.96), so it is not the reference for those two, and molframe matches CIAAW (tests/reference/atomic_weights_ciaaw_2021.json) |
| Named, versioned radii sets | β | molframe-chem | — | Not yet promoted |
| Atom equivalence (CCD symmetry) | β | molframe-chem | — | Not yet promoted |
| Valence checking | β | molframe-validate | — | Not yet promoted |
| Stereochemistry | β | molframe-validate | — | Not yet promoted |
| Residue classification from chemistry | β | molframe-chem | — | Not yet promoted |
| Modified-residue parent mapping | β | molframe-chem | — | Not yet promoted |
| Full cheminformatics | – | — | — | Argued exclusion: general cheminformatics (conformers, tautomers, reactions, descriptors) is another domain; no RDKit bridge ships. |
11. Assemblies, symmetry, crystallography
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Assembly definitions | β | molframe-xtal | — | Not yet promoted |
| Operator expression parsing | β | molframe-xtal | — | Not yet promoted |
| Lazy assembly instances | β | molframe-xtal | — | Not yet promoted |
| Assembly materialisation | β | molframe-xtal | — | Not yet promoted |
| Unit cell | β | molframe-xtal | — | Not yet promoted |
| Space groups (all 230, all settings) | ✓ | molframe-xtal | GW-041, GW-042 | All 530 Hall settings, keyed by Hall symbol, carry gemmi 0.7.5's operator count and international number, and every operator takes two probe points to gemmi's own images modulo 1 (tests/reference/space_groups_gemmi_0.7.5.json) |
| Symmetry operators stored | β | molframe-xtal | — | Not yet promoted |
| Fractional ↔ Cartesian | ✓ | molframe-xtal | GW-043 | Four cells (triclinic, orthorhombic, hexagonal, acute) reproduce gemmi 0.7.5's orthogonalize to 3.6e-15 Å, and each round-trips to 1.1e-16 |
| Crystal neighbour search | β | molframe-xtal | — | Not yet promoted |
| NCS operators | β | molframe-xtal | — | Not yet promoted |
| MTZ reflections | β | molframe-xtal | — | Not yet promoted |
| Structure-factor mmCIF | β | molframe-xtal | — | Not yet promoted |
| CCP4/MRC maps | β | molframe-xtal | — | Not yet promoted |
| Map sampling at coordinates | β | molframe-xtal | — | Not yet promoted |
| Real-space correlation | β | molframe-validate | — | Not yet promoted |
| Crystallographic refinement | – | — | — | Argued exclusion: refinement is another domain. |
12. Trajectories
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Streaming (memory independent of frames) | β | molframe-traj | — | Not yet promoted |
| Random frame access | β | molframe-traj | — | Not yet promoted |
| Declared random-access capability | β | molframe-traj | — | Not yet promoted |
| On-the-fly transformations | β | molframe-traj | — | Not yet promoted |
| Unwrap / wrap / centre / fit | β | molframe-traj | — | Not yet promoted |
| Reusable neighbour lists | β | molframe-traj | — | Not yet promoted |
| Frame analysis framework | β | molframe-traj | — | Not yet promoted |
| Parallel frame analysis | β | molframe-traj | — | Not yet promoted |
| Deterministic parallel merge | β | molframe-traj | — | Not yet promoted |
| Auxiliary data streams | β | molframe-traj | — | Not yet promoted |
| Trajectory writing | β | molframe-traj | — | Not yet promoted |
| Generalized Procrustes mean | β | molframe-traj | — | Not yet promoted |
| Cartesian PCA with explicit fit policy | β | molframe-traj | — | Not yet promoted |
| Dihedral PCA with circular features | β | molframe-traj | — | Not yet promoted |
| Reusable fitted-RMSD and torus distance matrices | β | molframe-traj | — | Not yet promoted |
| Diffusion maps | β | molframe-traj | — | Not yet promoted |
13. Comparison
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Sequence↔structure mapping | β | molframe-compare | — | Not yet promoted |
| Chain mapping (homomeric search) | β | molframe-compare | — | Not yet promoted |
| Atom mapping with equivalence | β | molframe-compare | — | Not yet promoted |
| Ligand symmetry-aware comparison | β | molframe-compare | — | Not yet promoted |
| RMSD family | β | molframe-compare | — | Not yet promoted |
| GDT-TS / GDT-HA | ✓ | molframe-compare | GW-046 | Match the Zemla 2003 definition exactly at the least-squares superposition, and that superposition's RMSD equals TM-align's to 6.5e-08 Å |
| TM-score | β | molframe-compare | GW-044 | Every case agrees with TM-align (tmtools 0.3.0) on the 1UBQ Cα trace — exact for a rigid displacement, 1e-5 for 0.5 Å noise. On a hinge or a displaced tail the fixed-correspondence fit reads about 0.04 and 0.015 lower, because TM-align re-pairs residues as well as moves them; the limitation is recorded in tests/reference/tm_score_tmalign_0.3.0.json |
| lDDT | β | molframe-compare | — | Not yet promoted |
| DockQ | ✓ | molframe-compare | GW-046 | Score and all three components (fnat, LRMSD, iRMSD) recomputed from the Basu & Wallner 2016 definition at three displacements on 4HHB chains A/B; agree to 1e-15 |
| CAD-score | β | molframe-compare | — | Not yet promoted |
| QS-score | β | molframe-compare | — | Not yet promoted |
| Contact-map similarity | β | molframe-compare | — | Not yet promoted |
| CE structural alignment | β | molframe-compare | — | Not yet promoted |
| Mapping/alignment/measure/verdict split | β | molframe-compare | — | Not yet promoted |
14. Validation
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Bond length / angle deviation | β | molframe-validate | — | Not yet promoted |
| Torsion outliers | β | molframe-validate | — | Not yet promoted |
| Rotamer outliers | β | molframe-validate | — | Not yet promoted |
| Planarity | β | molframe-validate | — | Not yet promoted |
| Chirality | β | molframe-validate | — | Not yet promoted |
| Clashes | β | molframe-validate | — | Not yet promoted |
| Cis-peptide detection | β | molframe-validate | — | Not yet promoted |
| Nucleic acid geometry | β | molframe-validate | — | Not yet promoted |
| Ligand geometry | β | molframe-validate | — | Not yet promoted |
| Occupancy / B-factor checks | β | molframe-validate | — | Not yet promoted |
| Altloc occupancy sums | β | molframe-validate | — | Not yet promoted |
| B-factor distribution / explicit TLS consistency | β | molframe-validate | — | Not yet promoted |
| Explicit non-aromatic plane restraints | β | molframe-validate | — | Not yet promoted |
| CCD missing atoms per residue | β | molframe-validate | — | Not yet promoted |
| Completeness vs canonical sequence | β | molframe-validate | — | Not yet promoted |
| Per-item detail, not only aggregates | β | molframe-validate | — | Not yet promoted |
| Versioned reference distributions | β | molframe-validate | — | Not yet promoted |
15. Sequence
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Alphabets / encoded sequences | β | molframe-seq | — | Not yet promoted |
| Global / local / semi-global alignment | ✓ | molframe-seq | GW-047 | Global and local affine-gap scores match biopython 1.88's PairwiseAligner exactly, on seven pairs including end gaps, an internal gap and a tandem repeat |
| Banded alignment | β | molframe-seq | — | Not yet promoted |
| Affine gaps, substitution matrices | ✓ | molframe-seq | GW-047 | BLOSUM62, BLOSUM50 and PAM250 agree with biopython 1.88 entry for entry, and a zero-cost-gap scheme agrees too |
| Multiple sequence alignment (guide-tree progressive + refinement) | β | molframe-seq | — | Not yet promoted |
| k-mer tables / bucketed tables / spaced seeds / minimizers | β | molframe-seq | — | Not yet promoted |
| Seed-and-extend search | β | molframe-seq | — | Not yet promoted |
| Phylogenetics (NJ, UPGMA, reroot, ladderise, traverse) | ✓ | molframe-seq | GW-047 | On a matrix whose closest pair is (A,B), both UPGMA and neighbour joining produce a tree with that pair as a cherry and equal branch lengths |
| Newick I/O | β | molframe-seq | — | Not yet promoted |
| FASTA / FASTQ / Stockholm / Clustal / PHYLIP / A2M / A3M | β | molframe-seq | — | Not yet promoted |
| Observed vs canonical vs reference sequence | β | molframe-seq | — | Not yet promoted |
| Database-scale search | – | molframe-seq | — | Argued exclusion: archive-scale search infrastructure is another domain; pairwise and small-set alignment is in scope. |
16. Interoperability
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| NumPy coordinate view | β | molframe-py | — | Not yet promoted |
| Read-only by default | β | molframe-py | — | Not yet promoted |
| Scoped coordinate mutation | β | molframe-py | — | Not yet promoted |
| Arrow C-stream export | β | molframe-interop | — | Not yet promoted |
| Arrow extension types | β | molframe-interop | — | Not yet promoted |
| Polars / pandas dataframes | β | molframe-interop | — | Not yet promoted |
| DLPack / PyTorch / JAX | β | molframe-interop | — | Not yet promoted |
| Graph export (PyG / DGL) | β | molframe-interop | — | Not yet promoted |
| Dataset abstraction | β | molframe-interop | — | Not yet promoted |
| Leakage-aware splitting | β | molframe-interop | — | Not yet promoted |
| Canonical mmCIF exchange contract | β | molframe-cif | — | Not yet promoted |
| BinaryCIF exchange contract | β | molframe-bcif | — | Not yet promoted |
| Arrow C Stream consumer contract | β | molframe-interop | — | Not yet promoted |
| Owned NumPy input contract | β | molframe-py | — | Not yet promoted |
| Forward-only trajectory stream contract | β | molframe-traj | — | Not yet promoted |
| Caller-owned frame batch contract | β | molframe-traj | — | Not yet promoted |
| Project-external differential harness contract | β | external | — | Not yet promoted |
| Simulation-topology file exchange | β | molframe-traj | — | Not yet promoted |
| Trajectory-file exchange | β | molframe-traj | — | Not yet promoted |
| Neutral array and table consumer protocol | β | molframe-interop | — | Not yet promoted |
17. Contracts and research — unique to pdbiox
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
AnalysisPolicy | β | molframe-core | — | Not yet promoted |
| Named, versioned default profile | β | molframe-core | — | Not yet promoted |
Analysis<T> enriched results | β | molframe-core | — | Not yet promoted |
Status including Indeterminate | β | molframe-core | — | Not yet promoted |
Coverage against CCD-expected composition | β | molframe-core | — | Not yet promoted |
| Full provenance record | β | molframe-core | — | Not yet promoted |
| Provenance serialisation (JSON + mmCIF) | β | molframe-core | — | Not yet promoted |
| Versioned verdict profiles | β | molframe-fx | — | Not yet promoted |
| Policy sensitivity audit | β | molframe-audit | — | Per-universe policy reads and consistent declared estimands checked; external domain and runner pilot evidence recorded in the study README. Not yet promoted. |
| PDB-scale audit study | · | molframe-audit | — | Reference-library column is ·; this is external evidence work, not missing library code. |
| Declarative motif specification | β | molframe-fx | — | Not yet promoted |
| Chemistry-aware motif mapping | β | molframe-fx | — | Not yet promoted |
| Four-stage evaluation split | β | molframe-fx | — | Not yet promoted |
| Decomposed functional results | β | molframe-fx | — | Not yet promoted |
| MotifBench / AME compatibility profiles | β | molframe-fx | — | Not yet promoted |
| Reproducible-from-provenance re-execution | β | molframe-core | — | Not yet promoted |
18. Surfaces
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| Rust API | β | molframe | — | Not yet promoted |
| Python API | β | molframe-py | — | Not yet promoted |
| Typed Python stubs | β | molframe-py | — | Not yet promoted |
| Zero logic in the binding layer | β | molframe-py | — | Not yet promoted |
| CLI | β | molframe-cli | — | Not yet promoted |
| CLI tabular output formats | β | molframe-cli | — | Not yet promoted |
| Compatibility shims | β | molframe-py | — | Not yet promoted |
| Capability | molframe | Crate | GW | Evidence |
|---|---|---|---|---|
| 1 | β | — | Not yet promoted | |
| 2 | β | — | Not yet promoted | |
| 3 | β | — | Not yet promoted | |
| 4 | β | — | Not yet promoted | |
| 5 | β | — | Not yet promoted | |
| 6 | β | — | Not yet promoted | |
| 7 | β | — | Not yet promoted | |
| 8 | β | — | Not yet promoted | |
– | β | — | Not yet promoted | |
| Total | β | — | Not yet promoted |