@kent-tokyo/chematic 0.16.0 → 0.18.0

package/README.md

@@ -24,6 +24,8 @@ npm install @kent-tokyo/chematic
 - ECFP4/6, AtomPair, Torsion, and path fingerprints with Tanimoto similarity
 - BRICS fragment count
 - SDF/MOL block parsing
+- PDBx/mmCIF, PQR, QCSchema JSON, ORCA input/output, Gaussian Cube, OpenDX,
+  and LAMMPS data/dump I/O (JSON-based bindings; see `format_io.rs`)
 - Topological descriptors: Wiener index, Hall-Kier κ, χ connectivity indices, Bertz CT
 - Shape descriptors (with 3D coordinates): PMI, NPR, radius of gyration, asphericity
 - 2D SVG depiction with CPK colors and atom/bond highlighting

package/chematic_wasm.d.ts

@@ -660,6 +660,30 @@ export function conformer_ensemble_json(mol: MolHandle, n: number, rmsd_threshol
  */
 export function cpk_color(element_symbol: string): string;
 
+/**
+ * Parse a Gaussian Cube file and return its full [`chematic_mol::VolumetricGrid`]
+ * as JSON: `{"origin":[x,y,z],"axes":[[..],[..],[..]],"shape":[nx,ny,nz],
+ * "values":[...flat, row-major third-axis-fastest...],
+ * "atoms":[{"element":"C","charge":6.0,"position":[x,y,z]}],
+ * "units":"bohr"|"angstrom"}`. See module docs for the perf tradeoff of a
+ * full `values` JSON round trip on a large grid.
+ */
+export function cube_grid_json(text: string): string;
+
+/**
+ * `[nx, ny, nz]` for a Gaussian Cube file's grid, as a `Uint32Array`.
+ */
+export function cube_shape_u32(text: string): Uint32Array;
+
+/**
+ * Flat `values` from a Gaussian Cube file's grid, as a `Float64Array` --
+ * same data [`cube_grid_json`]'s `"values"` field carries (row-major,
+ * third-axis-fastest order -- see `chematic_mol::volumetric`'s module
+ * docs for the exact index formula), as a real typed array instead of a
+ * JSON number array.
+ */
+export function cube_values_f64(text: string): Float64Array;
+
 /**
  * Compute structured depiction data for `mol` as a JSON object.
  *
@@ -1118,6 +1142,114 @@ export function is_valid_smiles(s: string): boolean;
  */
 export function labute_asa_per_atom_json(mol: MolHandle): string;
 
+/**
+ * Parse a LAMMPS data file (`read_data` format) and return every section
+ * as JSON: `{"counts":[["atoms",120],["atom types",4],...],
+ * "atom_style":"atomic"|"charge"|"molecular"|"full"|"<other>",
+ * "simulation_box":{"lo":[x,y,z],"hi":[x,y,z],"tilt":[xy,xz,yz]|null},
+ * "masses":[{"atom_type":N,"mass":N}],
+ * "atoms":[{"id":N,"molecule_id":N|null,"atom_type":N,"charge":N|null,"x":N,"y":N,"z":N,"image":[ix,iy,iz]|null}],
+ * "velocities":[{"atom_id":N,"vx":N,"vy":N,"vz":N}],
+ * "bonds":[{"id":N,"bond_type":N,"atom1":N,"atom2":N}],
+ * "unparsed_sections":[["Angles","<raw row text>"],...]}`. `atom_type`
+ * must be exactly `"atomic"`/`"charge"`/`"molecular"`/`"full"` -- LAMMPS's
+ * atom style is not recoverable from the file itself (see
+ * [`chematic_mol::LammpsData`]'s module doc comment); any other value is
+ * rejected with a JS error, matching
+ * [`chematic_mol::LammpsDataError::UnsupportedAtomStyle`].
+ *
+ * This module has no bond-perception step of its own: `Angles`/
+ * `Dihedrals`/`Impropers`/`*Coeffs`/any other section not listed above
+ * are preserved verbatim (byte-for-byte, `#` comments included) in
+ * `unparsed_sections`, not modeled field-by-field.
+ */
+export function lammps_data_to_json(text: string, atom_style: string): string;
+
+/**
+ * Like [`lammps_dump_cartesian_positions_json`], but returns a flat
+ * `Float64Array` (`[x0,y0,z0,x1,y1,z1,...]`, 3 values per atom) instead
+ * of a JSON `[[x,y,z],...]` array.
+ *
+ * **Behavioral difference from the JSON sibling**: when the frame has no
+ * recognized coordinate columns, [`lammps_dump_cartesian_positions_json`]
+ * returns JSON `null`; a `Float64Array` has no `null`, so this function
+ * returns `Err` instead, with a message naming the columns it looked for.
+ */
+export function lammps_dump_cartesian_positions_f64(frame_json: string): Float64Array;
+
+/**
+ * Real Cartesian positions for a LAMMPS dump frame (in the JSON shape
+ * [`lammps_dump_frame_to_json_str`] returns), resolved by delegating
+ * directly to [`chematic_mol::LammpsDumpFrame::cartesian_positions`] --
+ * this function does not reimplement any part of the box-bounds or
+ * scaled-coordinate math itself; that method is the single place this
+ * crate gets the (orthogonal or triclinic) transform right, and every
+ * WASM caller must go through it rather than re-deriving the transform in
+ * JS (the same reasoning behind this crate's OpenDX fail-closed unit
+ * handling and QCSchema's single Bohr<->Ångström conversion point).
+ *
+ * - `x y z` columns: passed straight through.
+ * - `xs ys zs` columns: transformed through `frame.box_bounds` (including
+ *   the triclinic shear terms when a tilt is present).
+ * - Neither present (including an `xu yu zu`-only frame -- "unwrapped" is
+ *   a materially different physical quantity from a scaled coordinate,
+ *   never resolved by this method): returns JSON `null`, not an error and
+ *   not an empty array, matching
+ *   [`chematic_mol::LammpsDumpFrame::cartesian_positions`]'s own
+ *   `Option` semantics exactly.
+ *
+ * Returns JSON `[[x,y,z],...]` on success, in the same atom order as
+ * `frame.rows`. See [`lammps_dump_cartesian_positions_f64`] for a flat
+ * `Float64Array` sibling -- note its `null` case becomes an `Err` there
+ * instead, a disclosed, real API-shape difference (a typed array has no
+ * `null`).
+ */
+export function lammps_dump_cartesian_positions_json(frame_json: string): string;
+
+/**
+ * Parse a single LAMMPS dump/trajectory frame and return it as JSON:
+ * `{"timestep":N,"num_atoms":N,
+ * "box_bounds":{"lo":[x,y,z],"hi":[x,y,z],"tilt":[xy,xz,yz]|null},
+ * "boundary_flags":["pp","pp","pp"],"column_names":[...],
+ * "rows":[[...values, one per column_names entry...],...]}`.
+ * `box_bounds` is already the resolved TRUE simulation box (the parser
+ * applies [`chematic_mol::box_bounds_to_true`] internally before
+ * `LammpsDumpFrame` is ever built) -- not the file's raw
+ * `xlo_bound`/`xhi_bound`/... values. `rows` is the raw per-atom column
+ * data as declared by `column_names`, which may be `x y z`
+ * (already-Cartesian), `xs ys zs` (box-scaled), `xu yu zu` (unwrapped), or
+ * any other dump-command column -- use
+ * [`lammps_dump_cartesian_positions_json`] to resolve real Cartesian
+ * positions from whichever convention is present, rather than
+ * reimplementing that resolution/transform in JS.
+ */
+export function lammps_dump_frame_to_json_str(text: string): string;
+
+/**
+ * Flattens a LAMMPS dump frame's `rows` (JSON shape
+ * [`lammps_dump_frame_to_json_str`] returns) into a single flat
+ * `Float64Array`, row-major (atom 0's `column_names.len()` values, then
+ * atom 1's, ...). The caller already has `column_names` from
+ * [`lammps_dump_frame_to_json_str`] and can compute the row length
+ * itself (`column_names.length`); no separate row-length accessor is
+ * provided here.
+ */
+export function lammps_dump_rows_f64(frame_json: string): Float64Array;
+
+/**
+ * Parse every frame of a LAMMPS dump/trajectory file and return them as a
+ * JSON array (same per-frame shape as [`lammps_dump_frame_to_json_str`]).
+ *
+ * This reads the whole input, parses it fully, and returns every frame at
+ * once -- [`chematic_mol::LammpsDumpReader`]'s per-frame streaming
+ * iteration (reading one frame at a time from a `BufRead` without holding
+ * the whole trajectory in memory) has no natural equivalent across the
+ * JS/WASM boundary in this first pass and is deliberately not exposed
+ * here, not silently dropped: a JS caller with a truly large trajectory
+ * that needs bounded memory should process it server-side instead.
+ */
+export function lammps_trajectory_to_json(text: string): string;
+
 /**
  * Return the largest fragment of `mol` (salt/solvent stripping).
  *
@@ -1222,6 +1354,24 @@ export function minimize_mmff94_lbfgs_json(mol: MolHandle, max_iter: number): st
  */
 export function minimize_uff_json(smiles: string, coords_json: string, max_iter: number): string;
 
+/**
+ * Cartesian coordinates from an mmCIF file, in the SAME atom order
+ * [`mol_from_mmcif`] returns topology for. Returns JSON `[[x,y,z],...]`
+ * (Å).
+ */
+export function mmcif_coords_json(text: string): string;
+
+/**
+ * Parse an mmCIF file and return every `_atom_site` field (occupancy,
+ * B-factor, chain/residue bookkeeping, formal charge, model number, ...),
+ * the unit cell, space group, and any loop column this reader saw but
+ * does not model, as JSON: `{"atoms":[{...}],"cell":{...}|null,
+ * "space_group":"..."|null,"unhandled_columns":[...]}`. See
+ * [`chematic_mol::MmcifAtomRecord`]'s doc comment for each atom field's
+ * exact source column and defaulting rule.
+ */
+export function mmcif_to_json(text: string): string;
+
 /**
  * MMFF94 partial charges (BCI table, ±0.1e accuracy) as a JSON array of f64.
  *
@@ -1348,6 +1498,14 @@ export function mol_from_cdxml(cdxml: string): MolHandle;
  */
 export function mol_from_cml(cml: string): MolHandle;
 
+/**
+ * Parse a Gaussian Cube file and return a `MolHandle` (topology only --
+ * element list, no bonds; Cube carries no bond table). Use
+ * [`cube_grid_json`] to recover coordinates, the scalar field, and the
+ * grid geometry.
+ */
+export function mol_from_cube(text: string): MolHandle;
+
 /**
  * Parse an Extended XYZ (extxyz) frame and return a `MolHandle` (topology +
  * element/position only; use [`extxyz_frame_json`] to recover coordinates,
@@ -1361,6 +1519,15 @@ export function mol_from_cml(cml: string): MolHandle;
  */
 export function mol_from_extxyz(text: string): MolHandle;
 
+/**
+ * Parse an mmCIF file and return a `MolHandle` (topology only -- element
+ * list, no bonds; mmCIF's `_atom_site` category carries no connectivity).
+ * Includes every model's atoms if the file has more than one -- use
+ * [`mmcif_to_json`] to get each atom's `model_num` for filtering. Use
+ * [`mmcif_coords_json`] to recover coordinates in the same atom order.
+ */
+export function mol_from_mmcif(text: string): MolHandle;
+
 /**
  * Parse a MolJSON string into a `MolHandle`.
  *
@@ -1369,6 +1536,18 @@ export function mol_from_extxyz(text: string): MolHandle;
  */
 export function mol_from_moljson(json: string): MolHandle;
 
+/**
+ * Parse an ORCA input file (`.inp`) and return a `MolHandle` (topology
+ * only -- element list, no bonds; ORCA input carries no bond table).
+ * Returns a JS error unless the file's coordinate block is an embedded
+ * `* xyz ... *` block -- `xyzfile`/`gzmtfile`/`int` (Z-matrix) blocks
+ * carry no atom list to convert, or none is present at all. Use
+ * [`orca_input_coords_json`] to recover coordinates + charge +
+ * multiplicity in the same atom order, or [`orca_input_to_json`] for the
+ * full input (comments/keywords/blocks/any coordinate-block kind).
+ */
+export function mol_from_orca_input(text: string): MolHandle;
+
 /**
  * Parse a PDB file and return a `MolHandle` (topology only; coordinates are
  * discarded -- use [`pdb_coords_json`] to recover them in the SAME atom
@@ -1380,6 +1559,24 @@ export function mol_from_moljson(json: string): MolHandle;
  */
 export function mol_from_pdb(pdb: string): MolHandle;
 
+/**
+ * Parse a PQR file and return a `MolHandle` (topology only -- element
+ * list inferred per-atom, no bonds; PQR carries no connectivity). Use
+ * [`pqr_coords_json`] to recover coordinates in the same atom order.
+ */
+export function mol_from_pqr(text: string): MolHandle;
+
+/**
+ * Parse a QCSchema `qcschema_molecule` JSON document and return a
+ * `MolHandle` (topology + `atomic_numbers`-derived isotopes -- no bonds
+ * unless the document's optional `connectivity` list is present, in which
+ * case those bond orders are mapped onto the nearest
+ * [`chematic_core::BondOrder`]). Use [`qcschema_molecule_coords_json`] to
+ * recover coordinates (converted Bohr -> Å) plus molecular
+ * charge/multiplicity, in the same atom order.
+ */
+export function mol_from_qcschema_molecule(json: string): MolHandle;
+
 /**
  * Parse a MOL V2000 block and return a `MolHandle`.
  *
@@ -1519,6 +1716,58 @@ export function normalize_cxsmiles(s: string): string;
  */
 export function normalize_reaction_smiles(rxn_smiles: string): string;
 
+/**
+ * Parse an OpenDX (APBS scalar-field subset) file and return its full
+ * [`chematic_mol::VolumetricGrid`] as JSON (same shape as
+ * [`cube_grid_json`]; `atoms` is always empty -- OpenDX has no atom
+ * section). No `mol_from_opendx` is provided: an OpenDX grid never carries
+ * atoms, so a `MolHandle` from one would always be empty and is not a
+ * useful binding.
+ */
+export function opendx_grid_json(text: string): string;
+
+/**
+ * `[nx, ny, nz]` for an OpenDX file's grid, as a `Uint32Array`.
+ */
+export function opendx_shape_u32(text: string): Uint32Array;
+
+/**
+ * Flat `values` from an OpenDX file's grid, as a `Float64Array` -- same
+ * data [`opendx_grid_json`]'s `"values"` field carries.
+ */
+export function opendx_values_f64(text: string): Float64Array;
+
+/**
+ * Coordinates + charge + multiplicity from an ORCA input file's embedded
+ * `* xyz ... *` block, in the SAME atom order [`mol_from_orca_input`]
+ * returns topology for. Returns JSON
+ * `{"coords":[[x,y,z],...],"charge":0,"multiplicity":1}`, or a JS error
+ * under the same conditions as [`mol_from_orca_input`].
+ */
+export function orca_input_coords_json(text: string): string;
+
+/**
+ * Parse an ORCA input file and return every field as JSON:
+ * `{"comments":[...],"keywords":[...],
+ * "blocks":[{"name":"scf","raw":"...","has_end":true},...],
+ * "coords":{"type":"xyz"|"xyzfile"|"gzmtfile"|"internal",...}|null}`.
+ * See [`chematic_mol::OrcaInput`]'s doc comment for each field's meaning.
+ */
+export function orca_input_to_json(text: string): string;
+
+/**
+ * Parse an ORCA output file (`.out`/`.log`) and return every extracted
+ * field as JSON: `{"charge":N|null,"multiplicity":N|null,
+ * "final_energy_hartree":N|null,
+ * "trajectory":[{"elements":[...],"coords":[[x,y,z],...]},...],
+ * "frequencies_cm1":[...],
+ * "termination":{"kind":"normal"|"error"|"incomplete","detail":"..."?},
+ * "optimization_convergence":"not_requested"|"converged"|"not_converged"|"unknown"}`.
+ * No writer is provided -- an ORCA output file is a job log, not a
+ * document this crate constructs.
+ */
+export function orca_output_to_json(text: string): string;
+
 /**
  * PAINS structural alert names matched by `mol` as a JSON array.
  *
@@ -1586,6 +1835,26 @@ export function pharmacophore_fp_2d_summary(mol: MolHandle): string;
  */
 export function pharmacophore_fp_3d_summary(mol: MolHandle): string;
 
+/**
+ * Cartesian coordinates from a PQR file, in the SAME atom order
+ * [`mol_from_pqr`] returns topology for. Returns JSON `[[x,y,z],...]` (Å).
+ */
+export function pqr_coords_json(text: string): string;
+
+/**
+ * Infer an element from a PQR atom name (see
+ * [`chematic_mol::infer_element`]'s doc comment for the heuristic).
+ * Returns `undefined` (JS) / `None` if no element could be inferred.
+ */
+export function pqr_infer_element(group_pdb: string, res_name: string, atom_name: string): string | undefined;
+
+/**
+ * Parse a PQR file and return every field (charge, radius, chain,
+ * residue, inferred element, ...) as JSON: `{"atoms":[{...}]}`. See
+ * [`chematic_mol::PqrAtomRecord`]'s doc comment for each field's meaning.
+ */
+export function pqr_to_json(text: string): string;
+
 /**
  * Predict pKa for all ionizable sites in a molecule.
  *
@@ -1595,6 +1864,34 @@ export function pharmacophore_fp_3d_summary(mol: MolHandle): string;
  */
 export function predict_pka_json(smiles: string): string;
 
+/**
+ * Coordinates (Å) plus molecular charge/multiplicity from a QCSchema
+ * `qcschema_molecule` document, in the SAME atom order
+ * [`mol_from_qcschema_molecule`] returns topology for. Returns JSON
+ * `{"coords":[[x,y,z],...],"molecular_charge":0.0,"molecular_multiplicity":1}`.
+ */
+export function qcschema_molecule_coords_json(json: string): string;
+
+/**
+ * Parse a QCSchema `qcschema_input`/`qc_schema_input` JSON document
+ * (molecule + driver + model + keywords) and re-emit it, validating and
+ * canonicalizing field defaults in the process (e.g. a missing
+ * `schema_name`/`schema_version` is filled in). Job-level fields
+ * (`driver`, `model`, `keywords`, `protocols`, `extras`) are round-tripped
+ * opaquely -- this binding validates/reformats the document; it does not
+ * expose a separate JS-facing accessor for each field (out of scope for
+ * this first pass, see module docs' "None of these formats carry a bond
+ * table" section for the analogous molecule-centric scope choice made
+ * elsewhere in this file).
+ */
+export function qcschema_validate_atomic_input(json: string): string;
+
+/**
+ * Like [`qcschema_validate_atomic_input`], for a QCSchema
+ * `qcschema_output`/`qc_schema_output` (`AtomicResult`) document.
+ */
+export function qcschema_validate_atomic_result(json: string): string;
+
 /**
  * Generate `count` random SMILES from a SMILES string using the given seed.
  * Atoms are permuted based on xorshift64 RNG. Each variant should parse back
@@ -2022,6 +2319,16 @@ export function to_mol_v3000_block(mol: MolHandle): string;
  */
 export function to_moljson(mol: MolHandle): string;
 
+/**
+ * Serialize a `MolHandle` + coordinates (Å) + molecular charge/multiplicity
+ * as a QCSchema `qcschema_molecule` JSON document (coordinates converted
+ * to Bohr).
+ *
+ * `coords_json`: `[[x,y,z],...]` (Å), same order and length as `mol`'s
+ * atoms.
+ */
+export function to_qcschema_molecule_json(mol: MolHandle, coords_json: string, charge: number, multiplicity: bigint): string;
+
 /**
  * Serialize a molecule to XYZ format.
  *
@@ -2060,6 +2367,76 @@ export function whim_descriptors_json(mol: MolHandle): string;
  */
 export function whim_getaway_combined_json(mol: MolHandle): string;
 
+/**
+ * Write a grid (in the JSON shape [`cube_grid_json`] returns) as a
+ * Gaussian Cube file.
+ */
+export function write_cube_json(grid_json: string): string;
+
+/**
+ * Write a LAMMPS data file from the JSON shape [`lammps_data_to_json`]
+ * returns.
+ */
+export function write_lammps_data_json(json: string): string;
+
+/**
+ * Write a single LAMMPS dump frame from the JSON shape
+ * [`lammps_dump_frame_to_json_str`] returns.
+ */
+export function write_lammps_dump_frame_json(json: string): string;
+
+/**
+ * Write a LAMMPS trajectory (N frames concatenated back to back, matching
+ * [`chematic_mol::write_lammps_trajectory`]) from a JSON array of frames
+ * in the shape [`lammps_dump_frame_to_json_str`] returns.
+ */
+export function write_lammps_trajectory_json(json: string): string;
+
+/**
+ * Write an mmCIF file from atom records in the JSON shape
+ * [`mmcif_to_json`]'s `"atoms"` array uses (a full record per atom, not
+ * just element+coordinates -- mmCIF has no equivalent of "build from a
+ * bare `MolHandle`", since occupancy/B-factor/chain/residue fields have no
+ * source in a plain [`MolHandle`]).
+ *
+ * `cell_json`: `"null"` or `{"a":...,"b":...,"c":...,"alpha":...,"beta":...,"gamma":...}`.
+ * `space_group`: pass `""` for none.
+ */
+export function write_mmcif_json(records_json: string, cell_json: string, space_group: string, data_block_name: string): string;
+
+/**
+ * Write a grid as an OpenDX file. Fails closed for a
+ * [`chematic_mol::GridUnits::Bohr`]-tagged grid (OpenDX has no unit tag of
+ * its own and is universally read back as Ångström -- see
+ * `chematic_mol::opendx`'s module docs) and for a grid carrying any atoms
+ * (OpenDX has no atom section). Use [`write_opendx_lossy_json`] to opt
+ * into an explicit Bohr->Ångström conversion instead of failing.
+ */
+export function write_opendx_json(grid_json: string): string;
+
+/**
+ * Like [`write_opendx_json`], but a [`chematic_mol::GridUnits::Bohr`] grid
+ * has its `origin`/`axes` explicitly converted to Ångström rather than
+ * rejected (`values` -- the scalar-field samples themselves -- are never
+ * rescaled; see `write_opendx_lossy`'s doc comment). Still fails for a
+ * grid carrying any atoms.
+ */
+export function write_opendx_lossy_json(grid_json: string): string;
+
+/**
+ * Write an ORCA input file from the JSON shape [`orca_input_to_json`]
+ * returns.
+ */
+export function write_orca_input_json(json: string): string;
+
+/**
+ * Write a PQR file from atom records in the JSON shape [`pqr_to_json`]'s
+ * `"atoms"` array uses. Each atom's `chain_id` independently controls
+ * whether that line is written with or without the (optional) chain
+ * column.
+ */
+export function write_pqr_json(records_json: string): string;
+
 /**
  * Non-canonical SMILES for `mol`.
  *
@@ -2120,6 +2497,9 @@ export interface InitOutput {
     readonly conformerhandle_new: (a: number, b: number) => [number, number, number];
     readonly conformerhandle_remove_conformer: (a: number, b: number) => number;
     readonly cpk_color: (a: number, b: number) => [number, number];
+    readonly cube_grid_json: (a: number, b: number) => [number, number, number, number];
+    readonly cube_shape_u32: (a: number, b: number) => [number, number, number];
+    readonly cube_values_f64: (a: number, b: number) => [number, number, number];
     readonly depict_data_json: (a: number) => [number, number];
     readonly depict_data_with_coords_json: (a: number, b: number, c: number) => [number, number];
     readonly depict_reaction_svg: (a: number, b: number) => [number, number, number, number];
@@ -2181,6 +2561,12 @@ export interface InitOutput {
     readonly invert_stereocenter_at: (a: number, b: number) => [number, number, number];
     readonly is_valid_smiles: (a: number, b: number) => number;
     readonly labute_asa_per_atom_json: (a: number) => [number, number];
+    readonly lammps_data_to_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly lammps_dump_cartesian_positions_f64: (a: number, b: number) => [number, number, number];
+    readonly lammps_dump_cartesian_positions_json: (a: number, b: number) => [number, number, number, number];
+    readonly lammps_dump_frame_to_json_str: (a: number, b: number) => [number, number, number, number];
+    readonly lammps_dump_rows_f64: (a: number, b: number) => [number, number, number];
+    readonly lammps_trajectory_to_json: (a: number, b: number) => [number, number, number, number];
     readonly largest_fragment: (a: number) => number;
     readonly logp_per_atom_json: (a: number) => [number, number];
     readonly maccs_bitvec: (a: number) => [number, number];
@@ -2198,6 +2584,8 @@ export interface InitOutput {
     readonly minimize_mmff94_json: (a: number, b: number) => [number, number];
     readonly minimize_mmff94_lbfgs_json: (a: number, b: number) => [number, number];
     readonly minimize_uff_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
+    readonly mmcif_coords_json: (a: number, b: number) => [number, number, number, number];
+    readonly mmcif_to_json: (a: number, b: number) => [number, number, number, number];
     readonly mmff94_charges_json: (a: number) => [number, number];
     readonly mmff94_charges_typed_json: (a: number) => [number, number];
     readonly mmff94_energy_breakdown_from_coords_json: (a: number, b: number, c: number) => [number, number];
@@ -2210,9 +2598,14 @@ export interface InitOutput {
     readonly mol_block_stereo_diagnostics_json: (a: number, b: number) => [number, number, number, number];
     readonly mol_from_cdxml: (a: number, b: number) => [number, number, number];
     readonly mol_from_cml: (a: number, b: number) => [number, number, number];
+    readonly mol_from_cube: (a: number, b: number) => [number, number, number];
     readonly mol_from_extxyz: (a: number, b: number) => [number, number, number];
+    readonly mol_from_mmcif: (a: number, b: number) => [number, number, number];
     readonly mol_from_moljson: (a: number, b: number) => [number, number, number];
+    readonly mol_from_orca_input: (a: number, b: number) => [number, number, number];
     readonly mol_from_pdb: (a: number, b: number) => number;
+    readonly mol_from_pqr: (a: number, b: number) => [number, number, number];
+    readonly mol_from_qcschema_molecule: (a: number, b: number) => [number, number, number];
     readonly mol_from_sdf_block: (a: number, b: number) => [number, number, number];
     readonly mol_from_v3000_block: (a: number, b: number) => [number, number, number];
     readonly mol_from_xyz: (a: number, b: number) => [number, number, number];
@@ -2304,6 +2697,12 @@ export interface InitOutput {
     readonly neutralize_charges: (a: number) => number;
     readonly normalize_cxsmiles: (a: number, b: number) => [number, number, number, number];
     readonly normalize_reaction_smiles: (a: number, b: number) => [number, number, number, number];
+    readonly opendx_grid_json: (a: number, b: number) => [number, number, number, number];
+    readonly opendx_shape_u32: (a: number, b: number) => [number, number, number];
+    readonly opendx_values_f64: (a: number, b: number) => [number, number, number];
+    readonly orca_input_coords_json: (a: number, b: number) => [number, number, number, number];
+    readonly orca_input_to_json: (a: number, b: number) => [number, number, number, number];
+    readonly orca_output_to_json: (a: number, b: number) => [number, number, number, number];
     readonly pains_matches_json: (a: number) => [number, number];
     readonly parse_cxsmarts_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_cxsmiles_json: (a: number, b: number) => [number, number, number, number];
@@ -2313,7 +2712,13 @@ export interface InitOutput {
     readonly pharmacophore_features_json: (a: number) => [number, number];
     readonly pharmacophore_fp_2d_summary: (a: number) => [number, number];
     readonly pharmacophore_fp_3d_summary: (a: number) => [number, number];
+    readonly pqr_coords_json: (a: number, b: number) => [number, number, number, number];
+    readonly pqr_infer_element: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number];
+    readonly pqr_to_json: (a: number, b: number) => [number, number, number, number];
     readonly predict_pka_json: (a: number, b: number) => [number, number];
+    readonly qcschema_molecule_coords_json: (a: number, b: number) => [number, number, number, number];
+    readonly qcschema_validate_atomic_input: (a: number, b: number) => [number, number, number, number];
+    readonly qcschema_validate_atomic_result: (a: number, b: number) => [number, number, number, number];
     readonly random_smiles_json: (a: number, b: number, c: number, d: bigint) => [number, number, number, number];
     readonly rdkit_ecfp4_bitvec: (a: number) => [number, number, number, number];
     readonly rdkit_ecfp4_detail_json: (a: number) => [number, number, number, number];
@@ -2358,11 +2763,21 @@ export interface InitOutput {
     readonly to_mol_block: (a: number) => [number, number];
     readonly to_mol_v3000_block: (a: number) => [number, number];
     readonly to_moljson: (a: number) => [number, number];
+    readonly to_qcschema_molecule_json: (a: number, b: number, c: number, d: number, e: bigint) => [number, number, number, number];
     readonly to_xyz: (a: number) => [number, number];
     readonly torsion_bitvec: (a: number) => [number, number];
     readonly virtual_screen_ecfp4_json: (a: number, b: number, c: number, d: number, e: number) => [number, number];
     readonly whim_descriptors_json: (a: number) => [number, number];
     readonly whim_getaway_combined_json: (a: number) => [number, number];
+    readonly write_cube_json: (a: number, b: number) => [number, number, number, number];
+    readonly write_lammps_data_json: (a: number, b: number) => [number, number, number, number];
+    readonly write_lammps_dump_frame_json: (a: number, b: number) => [number, number, number, number];
+    readonly write_lammps_trajectory_json: (a: number, b: number) => [number, number, number, number];
+    readonly write_mmcif_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number) => [number, number, number, number];
+    readonly write_opendx_json: (a: number, b: number) => [number, number, number, number];
+    readonly write_opendx_lossy_json: (a: number, b: number) => [number, number, number, number];
+    readonly write_orca_input_json: (a: number, b: number) => [number, number, number, number];
+    readonly write_pqr_json: (a: number, b: number) => [number, number, number, number];
     readonly write_smiles: (a: number) => [number, number];
     readonly xlogp3_json: (a: number) => [number, number];
     readonly xlogp3_per_atom_json: (a: number) => [number, number];