molstar 3.0.0-dev.6 → 3.0.0

package/lib/commonjs/mol-io/reader/mol/parser.js

@@ -1,22 +1,70 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseMol = exports.handleBonds = exports.handleAtoms = void 0;
+exports.parseMol = exports.handlePropertiesBlock = exports.handleFormalCharges = exports.handleBonds = exports.handleAtoms = exports.formalChargeMapper = void 0;
 var tslib_1 = require("tslib");
 var db_1 = require("../../../mol-data/db");
 var mol_task_1 = require("../../../mol-task");
 var token_1 = require("../common/text/column/token");
 var tokenizer_1 = require("../common/text/tokenizer");
 var result_1 = require("../result");
+/*
+    The atom lines in a .mol file have the following structure:
+
+    xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
+    ---------------------------------------------------------------------
+
+    Below is a breakdown of each component and its start/end indices:
+
+    xxxxx.xxxx  (X COORDINATE, 1-10)
+    yyyyy.yyyy  (Y COORDINATE, 10-20)
+    zzzzz.zzzz  (Z COORDINATE, 20-30)
+    _           (30 IS EMPTY)
+    aaa         (ATOM SYMBOL, 31-34)
+    dd          (MASS DIFF, 34-36)
+    ccc         (FORMAL CHARGE, 36-39)
+    sss         (ATOM STEREO PARITY, 39-42)
+    hhh         (HYDROGEN COUNT+1, 42-45)
+    bbb         (STEREO CARE BOX, 45-48)
+    vvv         (VALENCE, 48-51)
+    HHH         (H0 DESIGNATOR, 51-54)
+    rrr         (UNUSED, 54-57)
+    iii         (UNUSED, 57-60)
+    mmm         (ATOM-ATOM MAPPING NUMBER, 60-63)
+    nnn         (INVERSION/RETENTION FLAG, 63-66)
+    eee         (EXACT CHANGE FLAG, 66-69)
+*/
+/**
+ * @param key - The value found at the atom block.
+ * @returns The actual formal charge based on the mapping.
+ */
+function formalChargeMapper(key) {
+    switch (key) {
+        case 7: return -3;
+        case 6: return -2;
+        case 5: return -1;
+        case 0: return 0;
+        case 3: return 1;
+        case 2: return 2;
+        case 1: return 3;
+        case 4: return 0;
+        default:
+            console.error("Value ".concat(key, " is outside the 0-7 range, defaulting to 0."));
+            return 0;
+    }
+}
+exports.formalChargeMapper = formalChargeMapper;
 function handleAtoms(tokenizer, count) {
     var x = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     var y = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     var z = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     var type_symbol = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
+    var formal_charge = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     for (var i = 0; i < count; ++i) {
         tokenizer_1.Tokenizer.markLine(tokenizer);
         var s = tokenizer.tokenStart, position = tokenizer.position;
@@ -28,6 +76,8 @@ function handleAtoms(tokenizer, count) {
         tokenizer_1.TokenBuilder.addUnchecked(z, tokenizer.tokenStart, tokenizer.tokenEnd);
         tokenizer_1.Tokenizer.trim(tokenizer, s + 31, s + 34);
         tokenizer_1.TokenBuilder.addUnchecked(type_symbol, tokenizer.tokenStart, tokenizer.tokenEnd);
+        tokenizer_1.Tokenizer.trim(tokenizer, s + 36, s + 39);
+        tokenizer_1.TokenBuilder.addUnchecked(formal_charge, tokenizer.tokenStart, tokenizer.tokenEnd);
         tokenizer.position = position;
     }
     return {
@@ -35,7 +85,8 @@ function handleAtoms(tokenizer, count) {
         x: (0, token_1.TokenColumnProvider)(x)(db_1.Column.Schema.float),
         y: (0, token_1.TokenColumnProvider)(y)(db_1.Column.Schema.float),
         z: (0, token_1.TokenColumnProvider)(z)(db_1.Column.Schema.float),
-        type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str)
+        type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str),
+        formal_charge: (0, token_1.TokenColumnProvider)(formal_charge)(db_1.Column.Schema.int)
     };
 }
 exports.handleAtoms = handleAtoms;
@@ -62,6 +113,65 @@ function handleBonds(tokenizer, count) {
     };
 }
 exports.handleBonds = handleBonds;
+function handleFormalCharges(tokenizer, lineStart, formalCharges) {
+    tokenizer_1.Tokenizer.trim(tokenizer, lineStart + 6, lineStart + 9);
+    var numOfCharges = parseInt(tokenizer_1.Tokenizer.getTokenString(tokenizer));
+    for (var i = 0; i < numOfCharges; ++i) {
+        /*
+        M  CHG  3   1  -1   2   0   2  -1
+                |   |   |   |   |
+                |   |   |   |   |__charge2 (etc.)
+                |   |   |   |
+                |   |   |   |__atomIdx2
+                |   |   |
+                |   |   |__charge1
+                |   |
+                |   |__atomIdx1 (cursor at position 12)
+                |
+                |___numOfCharges
+        */
+        var offset = 9 + (i * 8);
+        tokenizer_1.Tokenizer.trim(tokenizer, lineStart + offset, lineStart + offset + 4);
+        var _atomIdx = tokenizer_1.Tokenizer.getTokenString(tokenizer);
+        formalCharges.atomIdx.push(+_atomIdx);
+        tokenizer_1.Tokenizer.trim(tokenizer, lineStart + offset + 4, lineStart + offset + 8);
+        var _charge = tokenizer_1.Tokenizer.getTokenString(tokenizer);
+        formalCharges.charge.push(+_charge);
+    }
+    /* Once the line is read, move to the next one. */
+    tokenizer_1.Tokenizer.eatLine(tokenizer);
+}
+exports.handleFormalCharges = handleFormalCharges;
+/** Call an appropriate handler based on the property type.
+ * (For now it only calls the formal charge handler, additional handlers can
+ * be added for other properties.)
+ */
+function handlePropertiesBlock(tokenizer) {
+    var _atomIdx = [];
+    var _charge = [];
+    var _formalCharges = { atomIdx: _atomIdx, charge: _charge };
+    while (tokenizer.position < tokenizer.length) {
+        var s = tokenizer.position;
+        tokenizer_1.Tokenizer.trim(tokenizer, s + 3, s + 6);
+        var propertyType = tokenizer_1.Tokenizer.getTokenString(tokenizer);
+        if (propertyType === 'END')
+            break;
+        tokenizer_1.Tokenizer.eatLine(tokenizer);
+        switch (propertyType) {
+            case 'CHG':
+                handleFormalCharges(tokenizer, s, _formalCharges);
+                break;
+            default:
+                break;
+        }
+    }
+    var formalCharges = {
+        atomIdx: db_1.Column.ofIntArray(_formalCharges.atomIdx),
+        charge: db_1.Column.ofIntArray(_formalCharges.charge)
+    };
+    return formalCharges;
+}
+exports.handlePropertiesBlock = handlePropertiesBlock;
 function parseInternal(data) {
     var tokenizer = (0, tokenizer_1.Tokenizer)(data);
     var title = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
@@ -71,12 +181,14 @@ function parseInternal(data) {
     var atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
     var atoms = handleAtoms(tokenizer, atomCount);
     var bonds = handleBonds(tokenizer, bondCount);
+    var formalCharges = handlePropertiesBlock(tokenizer);
     var result = {
         title: title,
         program: program,
         comment: comment,
         atoms: atoms,
-        bonds: bonds
+        bonds: bonds,
+        formalCharges: formalCharges,
     };
     return result_1.ReaderResult.success(result);
 }

package/lib/commonjs/mol-io/reader/mol2/parser.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/commonjs/mol-io/reader/mol2/parser.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -244,9 +244,38 @@ function handleBonds(state) {
         });
     });
 }
+function handleCrysin(state) {
+    var tokenizer = state.tokenizer;
+    while (tokenizer.position < tokenizer.data.length) {
+        var l = getTokenString(tokenizer);
+        if (l === '@<TRIPOS>MOLECULE') {
+            return;
+        }
+        else if (l === '@<TRIPOS>CRYSIN') {
+            break;
+        }
+        else {
+            markLine(tokenizer);
+        }
+    }
+    if (tokenizer.position >= tokenizer.data.length)
+        return;
+    markLine(tokenizer);
+    var values = getTokenString(tokenizer).trim().split(reWhitespace);
+    return {
+        a: parseFloat(values[0]),
+        b: parseFloat(values[1]),
+        c: parseFloat(values[2]),
+        alpha: parseFloat(values[3]),
+        beta: parseFloat(values[4]),
+        gamma: parseFloat(values[5]),
+        spaceGroup: parseInt(values[6], 10),
+        setting: parseInt(values[7], 10),
+    };
+}
 function parseInternal(ctx, data, name) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var tokenizer, structures, state, atoms, bonds, result;
+        var tokenizer, structures, state, atoms, bonds, crysin, result;
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -264,7 +293,8 @@ function parseInternal(ctx, data, name) {
                     return [4 /*yield*/, handleBonds(state)];
                 case 3:
                     bonds = _a.sent();
-                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds });
+                    crysin = handleCrysin(state);
+                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds, crysin: crysin });
                     skipWhitespace(tokenizer);
                     while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
                         markLine(tokenizer);

package/lib/commonjs/mol-io/reader/mol2/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,10 +37,21 @@ export interface Mol2Bonds {
     bond_type: Column<string>;
     status_bits: Column<string>;
 }
+export interface Mol2Crysin {
+    a: number;
+    b: number;
+    c: number;
+    alpha: number;
+    beta: number;
+    gamma: number;
+    spaceGroup: number;
+    setting: number;
+}
 export interface Mol2Structure {
     molecule: Readonly<Mol2Molecule>;
     atoms: Readonly<Mol2Atoms>;
     bonds: Readonly<Mol2Bonds>;
+    crysin?: Readonly<Mol2Crysin>;
 }
 export interface Mol2File {
     name: string;

package/lib/commonjs/mol-io/reader/mol2/schema.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.d.ts

@@ -1,3 +1,9 @@
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 import { MolFile } from '../mol/parser';
 import { Tokenizer } from '../common/text/tokenizer';
 export declare function isV3(versionLine: string): boolean;

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js

@@ -1,4 +1,10 @@
 "use strict";
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.handleBondsV3 = exports.handleAtomsV3 = exports.handleCountsV3 = exports.isV3 = void 0;
 var db_1 = require("../../../mol-data/db");
@@ -49,6 +55,9 @@ function handleAtomsV3(tokenizer, atomCount) {
         y: (0, token_1.TokenColumnProvider)(y)(db_1.Column.Schema.float),
         z: (0, token_1.TokenColumnProvider)(z)(db_1.Column.Schema.float),
         type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str),
+        /* No support for formal charge parsing in V3000 molfiles at the moment,
+        so all charges default to 0.*/
+        formal_charge: db_1.Column.ofConst(0, atomCount, db_1.Column.Schema.int)
     };
 }
 exports.handleAtomsV3 = handleAtomsV3;

package/lib/commonjs/mol-io/reader/sdf/parser.d.ts

@@ -1,8 +1,10 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { Column } from '../../../mol-data/db';
 import { MolFile } from '../mol/parser';

package/lib/commonjs/mol-io/reader/sdf/parser.js

@@ -1,9 +1,11 @@
 "use strict";
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseSdf = void 0;
@@ -72,11 +74,18 @@ function handleMolFile(tokenizer) {
         }
         return;
     }
+    /* No support for formal charge parsing in V3000 molfiles at the moment,
+    so all charges default to 0.*/
+    var nullFormalCharges = {
+        atomIdx: db_1.Column.ofConst(0, atomCount, db_1.Column.Schema.int),
+        charge: db_1.Column.ofConst(0, atomCount, db_1.Column.Schema.int)
+    };
     var atoms = molIsV3 ? (0, parser_v3_util_1.handleAtomsV3)(tokenizer, atomCount) : (0, parser_1.handleAtoms)(tokenizer, atomCount);
     var bonds = molIsV3 ? (0, parser_v3_util_1.handleBondsV3)(tokenizer, bondCount) : (0, parser_1.handleBonds)(tokenizer, bondCount);
+    var formalCharges = molIsV3 ? nullFormalCharges : (0, parser_1.handlePropertiesBlock)(tokenizer);
     var dataItems = handleDataItems(tokenizer);
     return {
-        molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds },
+        molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds, formalCharges: formalCharges },
         dataItems: dataItems
     };
 }

package/lib/commonjs/mol-io/writer/cif/encoder/binary.js

@@ -173,8 +173,15 @@ function getFieldData(field, arrayCtor, totalCount, data) {
                 allPresent = false;
             }
             else {
-                mask[offset] = 0 /* Present */;
-                array[offset] = getter(key, d, offset);
+                var value = getter(key, d, offset);
+                if (typeof value === 'string' && !value) {
+                    mask[offset] = 1 /* NotPresent */;
+                    allPresent = false;
+                }
+                else {
+                    mask[offset] = 0 /* Present */;
+                }
+                array[offset] = value;
             }
             offset++;
         }

package/lib/commonjs/mol-math/geometry/gaussian-density/gpu.js

@@ -13,7 +13,7 @@ var int_1 = require("../../../mol-data/int");
 var linear_algebra_1 = require("../../linear-algebra");
 var mol_util_1 = require("../../../mol-util");
 var renderable_1 = require("../../../mol-gl/renderable");
-var float_packing_1 = require("../../../mol-util/float-packing");
+var number_packing_1 = require("../../../mol-util/number-packing");
 var shader_code_1 = require("../../../mol-gl/shader-code");
 var render_item_1 = require("../../../mol-gl/webgl/render-item");
 var schema_1 = require("../../../mol-gl/renderable/schema");
@@ -378,7 +378,7 @@ function fieldFromTexture2d(ctx, texture, dim, texDim) {
             for (var ix = 0; ix < dx; ++ix) {
                 var idx = 4 * (tmpCol * dx + (iy + tmpRow) * width + ix);
                 data[j] = image[idx + 3] / 255;
-                idData[j] = (0, float_packing_1.decodeFloatRGB)(image[idx], image[idx + 1], image[idx + 2]);
+                idData[j] = (0, number_packing_1.unpackRGBToInt)(image[idx], image[idx + 1], image[idx + 2]);
                 j++;
             }
         }

package/lib/commonjs/mol-math/geometry/symmetry-operator.d.ts

@@ -42,7 +42,7 @@ declare namespace SymmetryOperator {
         hkl?: Vec3;
         spgrOp?: number;
     };
-    function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator;
+    function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator;
     function checkIfRotationAndTranslation(rot: Mat3, offset: Vec3): boolean;
     function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3, ncsId?: number): SymmetryOperator;
     function lerpFromIdentity(out: Mat4, op: SymmetryOperator, t: number): Mat4;

package/lib/commonjs/mol-math/geometry/symmetry-operator.js

@@ -22,8 +22,9 @@ var SymmetryOperator;
         var _hkl = hkl ? vec3_1.Vec3.clone(hkl) : (0, vec3_1.Vec3)();
         spgrOp = (0, mol_util_1.defaults)(spgrOp, -1);
         ncsId = ncsId || -1;
-        var suffix = getSuffix(info);
-        if (mat4_1.Mat4.isIdentity(matrix))
+        var isIdentity = mat4_1.Mat4.isIdentity(matrix);
+        var suffix = getSuffix(info, isIdentity);
+        if (isIdentity)
             return { name: name, assembly: assembly, matrix: matrix, inverse: mat4_1.Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
         if (!mat4_1.Mat4.isRotationAndTranslation(matrix, SymmetryOperator.RotationTranslationEpsilon)) {
             console.warn("Symmetry operator (".concat(name, ") should be a composition of rotation and translation."));
@@ -31,11 +32,16 @@ var SymmetryOperator;
         return { name: name, assembly: assembly, matrix: matrix, inverse: mat4_1.Mat4.invert((0, mat4_1.Mat4)(), matrix), isIdentity: false, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
     }
     SymmetryOperator.create = create;
-    function getSuffix(info) {
+    function isSymmetryOperator(x) {
+        return !!x && !!x.matrix && !!x.inverse && typeof x.name === 'string';
+    }
+    function getSuffix(info, isIdentity) {
         if (!info)
             return '';
         if (info.assembly) {
-            return "_".concat(info.assembly.operId);
+            if (isSymmetryOperator(info))
+                return info.suffix;
+            return isIdentity ? '' : "_".concat(info.assembly.operId);
         }
         if (typeof info.spgrOp !== 'undefined' && typeof info.hkl !== 'undefined' && info.spgrOp !== -1) {
             var _a = info.hkl, i = _a[0], j = _a[1], k = _a[2];

package/lib/commonjs/mol-math/linear-algebra/3d/quat.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -70,6 +70,14 @@ declare namespace Quat {
     function fromArray(a: Quat, array: NumberArray, offset: number): Quat;
     function copy(out: Quat, a: Quat): Quat;
     function set(out: Quat, x: number, y: number, z: number, w: number): Quat;
+    /**
+     * Returns whether or not the quaternions have exactly the same elements in the same position (when compared with ===)
+     */
+    function exactEquals(a: Quat, b: Quat): boolean;
+    /**
+     * Returns whether or not the quaternions have approximately the same elements in the same position.
+     */
+    function equals(a: Quat, b: Quat): boolean;
     function add(out: Quat, a: Quat, b: Quat): Quat;
     function normalize(out: Quat, a: Quat): Quat;
     function rotationTo(out: Quat, a: Vec3, b: Vec3): Quat;

package/lib/commonjs/mol-math/linear-algebra/3d/quat.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -315,6 +315,25 @@ exports.Quat = Quat;
         return out;
     }
     Quat.set = set;
+    /**
+     * Returns whether or not the quaternions have exactly the same elements in the same position (when compared with ===)
+     */
+    function exactEquals(a, b) {
+        return a[0] === b[0] && a[1] === b[1] && a[2] === b[2] && a[3] === b[3];
+    }
+    Quat.exactEquals = exactEquals;
+    /**
+     * Returns whether or not the quaternions have approximately the same elements in the same position.
+     */
+    function equals(a, b) {
+        var a0 = a[0], a1 = a[1], a2 = a[2], a3 = a[3];
+        var b0 = b[0], b1 = b[1], b2 = b[2], b3 = b[3];
+        return (Math.abs(a0 - b0) <= common_1.EPSILON * Math.max(1.0, Math.abs(a0), Math.abs(b0)) &&
+            Math.abs(a1 - b1) <= common_1.EPSILON * Math.max(1.0, Math.abs(a1), Math.abs(b1)) &&
+            Math.abs(a2 - b2) <= common_1.EPSILON * Math.max(1.0, Math.abs(a2), Math.abs(b2)) &&
+            Math.abs(a3 - b3) <= common_1.EPSILON * Math.max(1.0, Math.abs(a3), Math.abs(b3)));
+    }
+    Quat.equals = equals;
     function add(out, a, b) {
         out[0] = a[0] + b[0];
         out[1] = a[1] + b[1];

package/lib/commonjs/mol-model/structure/export/mmcif.d.ts

@@ -28,5 +28,5 @@ declare type encode_mmCIF_categories_Params = {
 };
 /** Doesn't start a data block */
 export declare function encode_mmCIF_categories(encoder: CifWriter.Encoder, structures: Structure | Structure[], params?: encode_mmCIF_categories_Params): void;
-declare function to_mmCIF(name: string, structure: Structure, asBinary?: boolean): string | Uint8Array;
+declare function to_mmCIF(name: string, structure: Structure, asBinary?: boolean, params?: encode_mmCIF_categories_Params): string | Uint8Array;
 export { to_mmCIF };

package/lib/commonjs/mol-model/structure/export/mmcif.js

@@ -40,6 +40,9 @@ var _entity = {
 function isWithoutSymmetry(structure) {
     return structure.units.every(function (u) { return u.conformation.operator.isIdentity; });
 }
+function isWithoutOperator(structure) {
+    return isWithoutSymmetry(structure) && structure.units.every(function (u) { return !u.conformation.operator.assembly && !u.conformation.operator.suffix; });
+}
 var Categories = [
     // Basics
     (0, utils_1.copy_mmCif_category)('entry'),
@@ -49,9 +52,9 @@ var Categories = [
     (0, utils_1.copy_mmCif_category)('cell', isWithoutSymmetry),
     (0, utils_1.copy_mmCif_category)('symmetry', isWithoutSymmetry),
     // Assemblies
-    (0, utils_1.copy_mmCif_category)('pdbx_struct_assembly', isWithoutSymmetry),
-    (0, utils_1.copy_mmCif_category)('pdbx_struct_assembly_gen', isWithoutSymmetry),
-    (0, utils_1.copy_mmCif_category)('pdbx_struct_oper_list', isWithoutSymmetry),
+    (0, utils_1.copy_mmCif_category)('pdbx_struct_assembly', isWithoutOperator),
+    (0, utils_1.copy_mmCif_category)('pdbx_struct_assembly_gen', isWithoutOperator),
+    (0, utils_1.copy_mmCif_category)('pdbx_struct_oper_list', isWithoutOperator),
     // Secondary structure
     secondary_structure_1._struct_conf,
     secondary_structure_1._struct_sheet_range,
@@ -233,11 +236,11 @@ function encode_mmCIF_categories_copyAll(encoder, ctx, params) {
             encoder.writeCategory(info[0], info[1], info[2]);
     });
 }
-function to_mmCIF(name, structure, asBinary) {
+function to_mmCIF(name, structure, asBinary, params) {
     if (asBinary === void 0) { asBinary = false; }
     var enc = cif_1.CifWriter.createEncoder({ binary: asBinary });
     enc.startDataBlock(name);
-    encode_mmCIF_categories(enc, structure);
+    encode_mmCIF_categories(enc, structure, params);
     return enc.getData();
 }
 exports.to_mmCIF = to_mmCIF;

package/lib/commonjs/mol-model/structure/model/properties/common.d.ts

@@ -13,7 +13,7 @@ export declare const EntitySubtype: Column.Schema.Aliased<EntitySubtype>;
 export interface Entities {
     data: mmCIF_Database['entity'];
     subtype: Column<EntitySubtype>;
-    prd_id: Column<string>;
+    prd_id?: Column<string>;
     getEntityIndex(id: string): EntityIndex;
 }
 export declare type ChemicalComponent = Table.Row<mmCIF_chemComp_schema>;

package/lib/commonjs/mol-model/structure/structure/element/stats.js

@@ -52,6 +52,7 @@ var Stats;
         }
         else if (size === 1) {
             if (unit_1.Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
+                // handled in `handleUnitChainsSimple`
                 return;
             }
             else {
@@ -177,6 +178,13 @@ var Stats;
                     location_1.Location.set(stats.firstChainLoc, structure, unit, offsets[cI]);
                 }
             }
+            else if (size === 1) {
+                // need to handle here, skipped in `handleElement`
+                stats.elementCount += 1;
+                if (stats.elementCount === 1) {
+                    location_1.Location.set(stats.firstElementLoc, structure, unit, eI);
+                }
+            }
         }
     }
     function handleUnitChainsPartitioned(stats, structure, lociElements, start, end) {

package/lib/commonjs/mol-model/structure/structure/properties.d.ts

@@ -87,6 +87,7 @@ declare const StructureProperties: {
         y: StructureElement.Property<number>;
         z: StructureElement.Property<number>;
         asym_id: StructureElement.Property<string>;
+        entity_id: StructureElement.Property<string>;
         seq_id_begin: StructureElement.Property<number>;
         seq_id_end: StructureElement.Property<number>;
         sphere_radius: StructureElement.Property<number>;

package/lib/commonjs/mol-model/structure/structure/properties.js

@@ -114,6 +114,7 @@ var coarse = {
     y: atom.y,
     z: atom.z,
     asym_id: p(function (l) { return !unit_1.Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.asym_id.value(l.element); }),
+    entity_id: p(function (l) { return !unit_1.Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entity_id.value(l.element); }),
     seq_id_begin: p(function (l) { return !unit_1.Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_begin.value(l.element); }),
     seq_id_end: p(function (l) { return !unit_1.Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_end.value(l.element); }),
     sphere_radius: p(function (l) { return !unit_1.Unit.isSpheres(l.unit) ? notCoarse('spheres') : l.unit.coarseConformation.radius[l.element]; }),
@@ -144,7 +145,7 @@ var entity = {
     pdbx_fragment: p(function (l) { return l.unit.model.entities.data.pdbx_fragment.value(eK(l)); }),
     pdbx_ec: p(function (l) { return l.unit.model.entities.data.pdbx_ec.value(eK(l)); }),
     subtype: p(function (l) { return l.unit.model.entities.subtype.value(eK(l)); }),
-    prd_id: p(function (l) { return l.unit.model.entities.prd_id.value(eK(l)); }),
+    prd_id: p(function (l) { var _a, _b; return (_b = (_a = l.unit.model.entities.prd_id) === null || _a === void 0 ? void 0 : _a.value(eK(l))) !== null && _b !== void 0 ? _b : ''; }),
 };
 var _emptyList = [];
 var unit = {

package/lib/commonjs/mol-model/structure/structure/symmetry.js

@@ -191,8 +191,6 @@ function getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter) {
         ijkMin[2] <= 0 && ijkMax[2] >= 0) {
         operators[0] = geometry_1.Spacegroup.getSymmetryOperator(spacegroup, 0, 0, 0, 0);
     }
-    var toFractional = spacegroup.cell.toFractional;
-    var ref = linear_algebra_1.Vec3.transformMat4((0, linear_algebra_1.Vec3)(), modelCenter, toFractional);
     for (var op = 0; op < spacegroup.operators.length; op++) {
         for (var i = ijkMin[0]; i <= ijkMax[0]; i++) {
             for (var j = ijkMin[1]; j <= ijkMax[1]; j++) {
@@ -200,7 +198,7 @@ function getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter) {
                     // check if we have added identity as the 1st operator.
                     if (!ncsCount && op === 0 && i === 0 && j === 0 && k === 0)
                         continue;
-                    operators.push.apply(operators, getOperatorsForIndex(symmetry, op, i, j, k, ref));
+                    operators.push.apply(operators, getOperatorsForIndex(symmetry, op, i, j, k, modelCenter));
                 }
             }
         }

package/lib/commonjs/mol-model/structure/structure/unit/bonds/common.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -17,4 +17,5 @@ export declare const MetalsSet: Set<number>;
 export declare function getElementIdx(e: ElementSymbol): number;
 export declare function getElementPairThreshold(i: number, j: number): number;
 export declare function getElementThreshold(i: number): number;
+export declare function getPairingThreshold(elementIndexA: number, elementIndexB: number, thresholdA: number, thresholdB: number): number;
 export declare function isHydrogen(i: number): boolean;