@kent-tokyo/chematic 0.1.4 → 0.1.9

package/package.json

@@ -5,7 +5,7 @@
     "kent-tokyo <kent-tokyo@users.noreply.github.com>"
   ],
   "description": "WebAssembly bindings for chematic — use chematic from JavaScript/TypeScript",
-  "version": "0.1.4",
+  "version": "0.1.9",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",
@@ -14,14 +14,12 @@
   "files": [
     "chematic_wasm_bg.wasm",
     "chematic_wasm.js",
-    "chematic_wasm_bg.js",
     "chematic_wasm.d.ts"
   ],
   "main": "chematic_wasm.js",
   "homepage": "https://github.com/kent-tokyo/chematic",
   "types": "chematic_wasm.d.ts",
   "sideEffects": [
-    "./chematic_wasm.js",
     "./snippets/*"
   ],
   "keywords": [

package/chematic_wasm_bg.js

@@ -1,370 +0,0 @@
-/**
- * A handle to a parsed molecule.  Owns the molecule behind an `Rc` so that
- * it can be cheaply cloned on the JS side without copying atom/bond data.
- */
-export class MolHandle {
-    static __wrap(ptr) {
-        const obj = Object.create(MolHandle.prototype);
-        obj.__wbg_ptr = ptr;
-        MolHandleFinalization.register(obj, obj.__wbg_ptr, obj);
-        return obj;
-    }
-    __destroy_into_raw() {
-        const ptr = this.__wbg_ptr;
-        this.__wbg_ptr = 0;
-        MolHandleFinalization.unregister(this);
-        return ptr;
-    }
-    free() {
-        const ptr = this.__destroy_into_raw();
-        wasm.__wbg_molhandle_free(ptr, 0);
-    }
-    /**
-     * Number of aromatic rings (all ring atoms aromatic).
-     * @returns {number}
-     */
-    aromatic_ring_count() {
-        const ret = wasm.molhandle_aromatic_ring_count(this.__wbg_ptr);
-        return ret >>> 0;
-    }
-    /**
-     * Number of heavy atoms (explicit atoms in the graph; does not count implicit H).
-     * @returns {number}
-     */
-    atom_count() {
-        const ret = wasm.molhandle_atom_count(this.__wbg_ptr);
-        return ret >>> 0;
-    }
-    /**
-     * Number of bonds.
-     * @returns {number}
-     */
-    bond_count() {
-        const ret = wasm.molhandle_bond_count(this.__wbg_ptr);
-        return ret >>> 0;
-    }
-    /**
-     * Canonical SMILES string.
-     * @returns {string}
-     */
-    canonical_smiles() {
-        let deferred1_0;
-        let deferred1_1;
-        try {
-            const ret = wasm.molhandle_canonical_smiles(this.__wbg_ptr);
-            deferred1_0 = ret[0];
-            deferred1_1 = ret[1];
-            return getStringFromWasm0(ret[0], ret[1]);
-        } finally {
-            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
-        }
-    }
-    /**
-     * Monoisotopic (exact) mass.
-     * @returns {number}
-     */
-    exact_mass() {
-        const ret = wasm.molhandle_exact_mass(this.__wbg_ptr);
-        return ret;
-    }
-    /**
-     * Molecular formula string (Hill notation: C first, H second, then alphabetical).
-     * @returns {string}
-     */
-    formula() {
-        let deferred1_0;
-        let deferred1_1;
-        try {
-            const ret = wasm.molhandle_formula(this.__wbg_ptr);
-            deferred1_0 = ret[0];
-            deferred1_1 = ret[1];
-            return getStringFromWasm0(ret[0], ret[1]);
-        } finally {
-            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
-        }
-    }
-    /**
-     * Fraction of sp3 carbons (Fsp3).
-     * @returns {number}
-     */
-    fsp3() {
-        const ret = wasm.molhandle_fsp3(this.__wbg_ptr);
-        return ret;
-    }
-    /**
-     * Number of hydrogen bond acceptors (Lipinski: all N and O atoms).
-     * @returns {number}
-     */
-    hba_count() {
-        const ret = wasm.molhandle_hba_count(this.__wbg_ptr);
-        return ret >>> 0;
-    }
-    /**
-     * Number of hydrogen bond donors (N-H or O-H groups).
-     * @returns {number}
-     */
-    hbd_count() {
-        const ret = wasm.molhandle_hbd_count(this.__wbg_ptr);
-        return ret >>> 0;
-    }
-    /**
-     * Number of non-hydrogen heavy atoms.
-     * @returns {number}
-     */
-    heavy_atom_count() {
-        const ret = wasm.molhandle_heavy_atom_count(this.__wbg_ptr);
-        return ret >>> 0;
-    }
-    /**
-     * Returns `true` if the molecule satisfies Lipinski's Rule of Five.
-     * @returns {boolean}
-     */
-    lipinski_passes() {
-        const ret = wasm.molhandle_lipinski_passes(this.__wbg_ptr);
-        return ret !== 0;
-    }
-    /**
-     * Crippen–Wildman octanol/water partition coefficient (LogP).
-     * @returns {number}
-     */
-    logp_crippen() {
-        const ret = wasm.molhandle_logp_crippen(this.__wbg_ptr);
-        return ret;
-    }
-    /**
-     * Average molecular weight (Da).
-     * @returns {number}
-     */
-    molecular_weight() {
-        const ret = wasm.molhandle_molecular_weight(this.__wbg_ptr);
-        return ret;
-    }
-    /**
-     * Quantitative Estimate of Drug-likeness (QED); range [0, 1].
-     * @returns {number}
-     */
-    qed() {
-        const ret = wasm.molhandle_qed(this.__wbg_ptr);
-        return ret;
-    }
-    /**
-     * Number of rotatable bonds.
-     * @returns {number}
-     */
-    rotatable_bond_count() {
-        const ret = wasm.molhandle_rotatable_bond_count(this.__wbg_ptr);
-        return ret >>> 0;
-    }
-    /**
-     * Topological polar surface area (Ų).
-     * @returns {number}
-     */
-    tpsa() {
-        const ret = wasm.molhandle_tpsa(this.__wbg_ptr);
-        return ret;
-    }
-}
-if (Symbol.dispose) MolHandle.prototype[Symbol.dispose] = MolHandle.prototype.free;
-
-/**
- * Number of BRICS fragments produced by fragmenting the molecule.
- *
- * Returns 1 if no BRICS-breakable bonds exist (whole molecule is one fragment).
- * @param {MolHandle} mol
- * @returns {number}
- */
-export function brics_fragment_count(mol) {
-    _assertClass(mol, MolHandle);
-    const ret = wasm.brics_fragment_count(mol.__wbg_ptr);
-    return ret >>> 0;
-}
-
-/**
- * Compute the ECFP4 fingerprint as a bit-packed byte vector (256 bytes = 2048 bits).
- * @param {MolHandle} mol
- * @returns {Uint8Array}
- */
-export function ecfp4_bitvec(mol) {
-    _assertClass(mol, MolHandle);
-    const ret = wasm.ecfp4_bitvec(mol.__wbg_ptr);
-    var v1 = getArrayU8FromWasm0(ret[0], ret[1]).slice();
-    wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
-    return v1;
-}
-
-/**
- * Parse a SMILES string into a `MolHandle`.
- *
- * Returns a JS error string on parse failure.
- * @param {string} s
- * @returns {MolHandle}
- */
-export function parse_smiles(s) {
-    const ptr0 = passStringToWasm0(s, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
-    const len0 = WASM_VECTOR_LEN;
-    const ret = wasm.parse_smiles(ptr0, len0);
-    if (ret[2]) {
-        throw takeFromExternrefTable0(ret[1]);
-    }
-    return MolHandle.__wrap(ret[0]);
-}
-
-/**
- * Tanimoto similarity between two molecules using AtomPair fingerprints.
- * @param {MolHandle} a
- * @param {MolHandle} b
- * @returns {number}
- */
-export function tanimoto_atom_pair(a, b) {
-    _assertClass(a, MolHandle);
-    _assertClass(b, MolHandle);
-    const ret = wasm.tanimoto_atom_pair(a.__wbg_ptr, b.__wbg_ptr);
-    return ret;
-}
-
-/**
- * Tanimoto similarity between two molecules using ECFP4 fingerprints.
- * @param {MolHandle} a
- * @param {MolHandle} b
- * @returns {number}
- */
-export function tanimoto_ecfp4(a, b) {
-    _assertClass(a, MolHandle);
-    _assertClass(b, MolHandle);
-    const ret = wasm.tanimoto_ecfp4(a.__wbg_ptr, b.__wbg_ptr);
-    return ret;
-}
-
-/**
- * Tanimoto similarity between two molecules using Topological Torsion fingerprints.
- * @param {MolHandle} a
- * @param {MolHandle} b
- * @returns {number}
- */
-export function tanimoto_torsion(a, b) {
-    _assertClass(a, MolHandle);
-    _assertClass(b, MolHandle);
-    const ret = wasm.tanimoto_torsion(a.__wbg_ptr, b.__wbg_ptr);
-    return ret;
-}
-export function __wbg___wbindgen_throw_1506f2235d1bdba0(arg0, arg1) {
-    throw new Error(getStringFromWasm0(arg0, arg1));
-}
-export function __wbindgen_cast_0000000000000001(arg0, arg1) {
-    // Cast intrinsic for `Ref(String) -> Externref`.
-    const ret = getStringFromWasm0(arg0, arg1);
-    return ret;
-}
-export function __wbindgen_init_externref_table() {
-    const table = wasm.__wbindgen_externrefs;
-    const offset = table.grow(4);
-    table.set(0, undefined);
-    table.set(offset + 0, undefined);
-    table.set(offset + 1, null);
-    table.set(offset + 2, true);
-    table.set(offset + 3, false);
-}
-const MolHandleFinalization = (typeof FinalizationRegistry === 'undefined')
-    ? { register: () => {}, unregister: () => {} }
-    : new FinalizationRegistry(ptr => wasm.__wbg_molhandle_free(ptr, 1));
-
-function _assertClass(instance, klass) {
-    if (!(instance instanceof klass)) {
-        throw new Error(`expected instance of ${klass.name}`);
-    }
-}
-
-function getArrayU8FromWasm0(ptr, len) {
-    ptr = ptr >>> 0;
-    return getUint8ArrayMemory0().subarray(ptr / 1, ptr / 1 + len);
-}
-
-function getStringFromWasm0(ptr, len) {
-    return decodeText(ptr >>> 0, len);
-}
-
-let cachedUint8ArrayMemory0 = null;
-function getUint8ArrayMemory0() {
-    if (cachedUint8ArrayMemory0 === null || cachedUint8ArrayMemory0.byteLength === 0) {
-        cachedUint8ArrayMemory0 = new Uint8Array(wasm.memory.buffer);
-    }
-    return cachedUint8ArrayMemory0;
-}
-
-function passStringToWasm0(arg, malloc, realloc) {
-    if (realloc === undefined) {
-        const buf = cachedTextEncoder.encode(arg);
-        const ptr = malloc(buf.length, 1) >>> 0;
-        getUint8ArrayMemory0().subarray(ptr, ptr + buf.length).set(buf);
-        WASM_VECTOR_LEN = buf.length;
-        return ptr;
-    }
-
-    let len = arg.length;
-    let ptr = malloc(len, 1) >>> 0;
-
-    const mem = getUint8ArrayMemory0();
-
-    let offset = 0;
-
-    for (; offset < len; offset++) {
-        const code = arg.charCodeAt(offset);
-        if (code > 0x7F) break;
-        mem[ptr + offset] = code;
-    }
-    if (offset !== len) {
-        if (offset !== 0) {
-            arg = arg.slice(offset);
-        }
-        ptr = realloc(ptr, len, len = offset + arg.length * 3, 1) >>> 0;
-        const view = getUint8ArrayMemory0().subarray(ptr + offset, ptr + len);
-        const ret = cachedTextEncoder.encodeInto(arg, view);
-
-        offset += ret.written;
-        ptr = realloc(ptr, len, offset, 1) >>> 0;
-    }
-
-    WASM_VECTOR_LEN = offset;
-    return ptr;
-}
-
-function takeFromExternrefTable0(idx) {
-    const value = wasm.__wbindgen_externrefs.get(idx);
-    wasm.__externref_table_dealloc(idx);
-    return value;
-}
-
-let cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
-cachedTextDecoder.decode();
-const MAX_SAFARI_DECODE_BYTES = 2146435072;
-let numBytesDecoded = 0;
-function decodeText(ptr, len) {
-    numBytesDecoded += len;
-    if (numBytesDecoded >= MAX_SAFARI_DECODE_BYTES) {
-        cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
-        cachedTextDecoder.decode();
-        numBytesDecoded = len;
-    }
-    return cachedTextDecoder.decode(getUint8ArrayMemory0().subarray(ptr, ptr + len));
-}
-
-const cachedTextEncoder = new TextEncoder();
-
-if (!('encodeInto' in cachedTextEncoder)) {
-    cachedTextEncoder.encodeInto = function (arg, view) {
-        const buf = cachedTextEncoder.encode(arg);
-        view.set(buf);
-        return {
-            read: arg.length,
-            written: buf.length
-        };
-    };
-}
-
-let WASM_VECTOR_LEN = 0;
-
-
-let wasm;
-export function __wbg_set_wasm(val) {
-    wasm = val;
-}