@kent-tokyo/chematic 1.1.4 → 1.1.5

package/README.md

@@ -4,7 +4,7 @@ WebAssembly bindings for [chematic](https://github.com/kent-tokyo/chematic), a p
 
 Published to npm as [`@kent-tokyo/chematic`](https://www.npmjs.com/package/@kent-tokyo/chematic).
 
-The current workspace line is 1.1.4. The binding keeps bounded parsing,
+The current workspace line is 1.1.5. The binding keeps bounded parsing,
 typed failures, and opt-in `embed_pipeline_v2_json`; 3D/MMFF94 behavior remains
 Experimental and is not a claim of full RDKit parity.
 

package/chematic_wasm.d.ts

@@ -480,6 +480,15 @@ export class MolHandle {
      * diagonal and lower bounds below it. At most 512 atoms are accepted.
      */
     rdkit_bounds_matrix_json(set15bounds: boolean, do_triangle_smoothing: boolean, use_macrocycle_14_config: boolean): string;
+    /**
+     * Distance-geometry bounds with user bond-length, angle and torsion
+     * constraints injected before triangle smoothing.
+     *
+     * `constraintsJson` contains optional camelCase arrays `bondLengths`,
+     * `bondAngles`, and `torsions`; atom indices are zero based. Lengths use
+     * angstrom and angles use degrees.
+     */
+    rdkit_bounds_matrix_with_constraints_json(constraints_json: string, set15bounds: boolean, do_triangle_smoothing: boolean, use_macrocycle_14_config: boolean): string;
     /**
      * RDKit `CalcRMS`, bounded by `max_matches <= 1_000_000`.
      */
@@ -492,11 +501,21 @@ export class MolHandle {
      * RDKit-compatible CXSMARTS.
      */
     rdkit_cx_smarts(): string;
+    /**
+     * Checked 3D matrix in prepared RDKit atom order. JSON has one [x,y,z]
+     * row per prepared atom; malformed/nonfinite/unrepresentable input refuses.
+     */
+    rdkit_distance_matrix_3d_checked_json(coords_json: string, use_atom_wts: boolean): string;
     /**
      * Seeded RDKit ETKDGv3 coordinates as JSON. Call on an
      * explicit-hydrogen molecule. At most 512 atoms are accepted.
      */
     rdkit_embed_json(random_seed: number, max_iterations: number): string;
+    /**
+     * Seeded ETKDG embedding using constraints injected before triangle
+     * smoothing. Returns one `[x,y,z]` row per atom as JSON.
+     */
+    rdkit_embed_with_constraints_json(constraints_json: string, random_seed: number, max_iterations: number): string;
     /**
      * RDKit MolHash by case-insensitive function name.
      */
@@ -1979,6 +1998,12 @@ export function mol_block_stereo_diagnostics_json(mol_block: string): string;
  */
 export function mol_block_stereo_loss_json(mol: MolHandle): string;
 
+/**
+ * Project explicit CCD topology. Unassigned stereo annotations require
+ * explicit loss consent; coordinates remain in parse_ccd_json's record.
+ */
+export function mol_from_ccd(text: string, allow_stereo_loss: boolean): MolHandle;
+
 /**
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
@@ -2321,6 +2346,12 @@ export function orca_output_to_json(text: string): string;
  */
 export function pains_matches_json(mol: MolHandle): string;
 
+/**
+ * One CCD template including source IDs, charges, explicit bonds, optional
+ * coordinates and unassigned stereo labels. No atom_site bond perception.
+ */
+export function parse_ccd_json(text: string): string;
+
 /**
  * Inspect strictly validated CJSON with exact source and opaque field paths.
  */
@@ -2342,6 +2373,11 @@ export function parse_cxsmarts_json(s: string): string;
  */
 export function parse_cxsmiles_json(s: string): string;
 
+/**
+ * Inspect the bounded HIN record, including literal aromatic bonds and charges.
+ */
+export function parse_hin_record_json(text: string): string;
+
 /**
  * Inspect partial charges, atom types and source retention for MOL2.
  */
@@ -2757,6 +2793,11 @@ export function ring_families_json(mol: MolHandle): string;
  */
 export function roundtrip_cjson_record(text: string): string;
 
+/**
+ * Validate a single HIN record and retain exact source text and line endings.
+ */
+export function roundtrip_hin_record(text: string): string;
+
 /**
  * Validate one MOL2 record and preserve its exact source, including metadata.
  */
@@ -3561,6 +3602,7 @@ export interface InitOutput {
     readonly mol_block_from_smiles: (a: number, b: number) => [number, number, number, number];
     readonly mol_block_stereo_diagnostics_json: (a: number, b: number) => [number, number, number, number];
     readonly mol_block_stereo_loss_json: (a: number) => [number, number];
+    readonly mol_from_ccd: (a: number, b: number, c: number) => [number, number, number];
     readonly mol_from_cdxml: (a: number, b: number) => [number, number, number];
     readonly mol_from_cjson: (a: number, b: number) => [number, number, number];
     readonly mol_from_cml: (a: number, b: number) => [number, number, number];
@@ -3662,10 +3704,13 @@ export interface InitOutput {
     readonly molhandle_rdkit_best_alignment_json: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number) => [number, number, number, number];
     readonly molhandle_rdkit_best_rms: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number) => [number, number, number];
     readonly molhandle_rdkit_bounds_matrix_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
+    readonly molhandle_rdkit_bounds_matrix_with_constraints_json: (a: number, b: number, c: number, d: number, e: number, f: number) => [number, number, number, number];
     readonly molhandle_rdkit_calc_rms: (a: number, b: number, c: number, d: number, e: number, f: number, g: number, h: number, i: number) => [number, number, number];
     readonly molhandle_rdkit_chiral_centers_json: (a: number, b: number) => [number, number, number, number];
     readonly molhandle_rdkit_cx_smarts: (a: number) => [number, number, number, number];
+    readonly molhandle_rdkit_distance_matrix_3d_checked_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly molhandle_rdkit_embed_json: (a: number, b: number, c: number) => [number, number, number, number];
+    readonly molhandle_rdkit_embed_with_constraints_json: (a: number, b: number, c: number, d: number, e: number) => [number, number, number, number];
     readonly molhandle_rdkit_mol_hash: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly molhandle_rdkit_morgan_bit_info_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly molhandle_rdkit_murcko_scaffold: (a: number) => [number, number, number, number];
@@ -3700,9 +3745,11 @@ export interface InitOutput {
     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_ccd_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_cjson_record_json: (a: number, b: number) => [number, 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];
+    readonly parse_hin_record_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_mol2_record_json: (a: number, b: number) => [number, number, number, number];
     readonly parse_smiles: (a: number, b: number) => [number, number, number];
     readonly pdb_coords_json: (a: number, b: number) => [number, number];
@@ -3759,6 +3806,7 @@ export interface InitOutput {
     readonly rgroup_decompose_json: (a: number, b: number, c: number, d: number) => [number, number, number, number];
     readonly ring_families_json: (a: number) => [number, number, number, number];
     readonly roundtrip_cjson_record: (a: number, b: number) => [number, number, number, number];
+    readonly roundtrip_hin_record: (a: number, b: number) => [number, number, number, number];
     readonly roundtrip_mol2_record: (a: number, b: number) => [number, number, number, number];
     readonly roundtrip_mol_v3000_block: (a: number, b: number) => [number, number, number, number];
     readonly run_reactants: (a: number, b: number, c: number, d: number) => [number, number, number, number];

package/chematic_wasm.js

@@ -1243,6 +1243,39 @@ export class MolHandle {
             wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
         }
     }
+    /**
+     * Distance-geometry bounds with user bond-length, angle and torsion
+     * constraints injected before triangle smoothing.
+     *
+     * `constraintsJson` contains optional camelCase arrays `bondLengths`,
+     * `bondAngles`, and `torsions`; atom indices are zero based. Lengths use
+     * angstrom and angles use degrees.
+     * @param {string} constraints_json
+     * @param {boolean} set15bounds
+     * @param {boolean} do_triangle_smoothing
+     * @param {boolean} use_macrocycle_14_config
+     * @returns {string}
+     */
+    rdkit_bounds_matrix_with_constraints_json(constraints_json, set15bounds, do_triangle_smoothing, use_macrocycle_14_config) {
+        let deferred3_0;
+        let deferred3_1;
+        try {
+            const ptr0 = passStringToWasm0(constraints_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len0 = WASM_VECTOR_LEN;
+            const ret = wasm.molhandle_rdkit_bounds_matrix_with_constraints_json(this.__wbg_ptr, ptr0, len0, set15bounds, do_triangle_smoothing, use_macrocycle_14_config);
+            var ptr2 = ret[0];
+            var len2 = ret[1];
+            if (ret[3]) {
+                ptr2 = 0; len2 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred3_0 = ptr2;
+            deferred3_1 = len2;
+            return getStringFromWasm0(ptr2, len2);
+        } finally {
+            wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+        }
+    }
     /**
      * RDKit `CalcRMS`, bounded by `max_matches <= 1_000_000`.
      * @param {string} probe_coords_json
@@ -1310,6 +1343,33 @@ export class MolHandle {
             wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
         }
     }
+    /**
+     * Checked 3D matrix in prepared RDKit atom order. JSON has one [x,y,z]
+     * row per prepared atom; malformed/nonfinite/unrepresentable input refuses.
+     * @param {string} coords_json
+     * @param {boolean} use_atom_wts
+     * @returns {string}
+     */
+    rdkit_distance_matrix_3d_checked_json(coords_json, use_atom_wts) {
+        let deferred3_0;
+        let deferred3_1;
+        try {
+            const ptr0 = passStringToWasm0(coords_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len0 = WASM_VECTOR_LEN;
+            const ret = wasm.molhandle_rdkit_distance_matrix_3d_checked_json(this.__wbg_ptr, ptr0, len0, use_atom_wts);
+            var ptr2 = ret[0];
+            var len2 = ret[1];
+            if (ret[3]) {
+                ptr2 = 0; len2 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred3_0 = ptr2;
+            deferred3_1 = len2;
+            return getStringFromWasm0(ptr2, len2);
+        } finally {
+            wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+        }
+    }
     /**
      * Seeded RDKit ETKDGv3 coordinates as JSON. Call on an
      * explicit-hydrogen molecule. At most 512 atoms are accepted.
@@ -1335,6 +1395,34 @@ export class MolHandle {
             wasm.__wbindgen_free(deferred2_0, deferred2_1, 1);
         }
     }
+    /**
+     * Seeded ETKDG embedding using constraints injected before triangle
+     * smoothing. Returns one `[x,y,z]` row per atom as JSON.
+     * @param {string} constraints_json
+     * @param {number} random_seed
+     * @param {number} max_iterations
+     * @returns {string}
+     */
+    rdkit_embed_with_constraints_json(constraints_json, random_seed, max_iterations) {
+        let deferred3_0;
+        let deferred3_1;
+        try {
+            const ptr0 = passStringToWasm0(constraints_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            const len0 = WASM_VECTOR_LEN;
+            const ret = wasm.molhandle_rdkit_embed_with_constraints_json(this.__wbg_ptr, ptr0, len0, random_seed, max_iterations);
+            var ptr2 = ret[0];
+            var len2 = ret[1];
+            if (ret[3]) {
+                ptr2 = 0; len2 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred3_0 = ptr2;
+            deferred3_1 = len2;
+            return getStringFromWasm0(ptr2, len2);
+        } finally {
+            wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+        }
+    }
     /**
      * RDKit MolHash by case-insensitive function name.
      * @param {string} _function
@@ -5386,6 +5474,23 @@ export function mol_block_stereo_loss_json(mol) {
     }
 }
 
+/**
+ * Project explicit CCD topology. Unassigned stereo annotations require
+ * explicit loss consent; coordinates remain in parse_ccd_json's record.
+ * @param {string} text
+ * @param {boolean} allow_stereo_loss
+ * @returns {MolHandle}
+ */
+export function mol_from_ccd(text, allow_stereo_loss) {
+    const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.mol_from_ccd(ptr0, len0, allow_stereo_loss);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return MolHandle.__wrap(ret[0]);
+}
+
 /**
  * Only the first molecular fragment in the document is returned.
  * Returns a JS error if the document cannot be parsed.
@@ -6276,6 +6381,33 @@ export function pains_matches_json(mol) {
     }
 }
 
+/**
+ * One CCD template including source IDs, charges, explicit bonds, optional
+ * coordinates and unassigned stereo labels. No atom_site bond perception.
+ * @param {string} text
+ * @returns {string}
+ */
+export function parse_ccd_json(text) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.parse_ccd_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
 /**
  * Inspect strictly validated CJSON with exact source and opaque field paths.
  * @param {string} text
@@ -6360,6 +6492,32 @@ export function parse_cxsmiles_json(s) {
     }
 }
 
+/**
+ * Inspect the bounded HIN record, including literal aromatic bonds and charges.
+ * @param {string} text
+ * @returns {string}
+ */
+export function parse_hin_record_json(text) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.parse_hin_record_json(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
 /**
  * Inspect partial charges, atom types and source retention for MOL2.
  * @param {string} text
@@ -7545,6 +7703,32 @@ export function roundtrip_cjson_record(text) {
     }
 }
 
+/**
+ * Validate a single HIN record and retain exact source text and line endings.
+ * @param {string} text
+ * @returns {string}
+ */
+export function roundtrip_hin_record(text) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.roundtrip_hin_record(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
 /**
  * Validate one MOL2 record and preserve its exact source, including metadata.
  * @param {string} text

package/package.json

@@ -5,7 +5,7 @@
     "Kentaro Tanabe (kent-tokyo) <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "1.1.4",
+  "version": "1.1.5",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",