molstar 3.0.0-dev.6 → 3.0.0

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

@@ -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>
@@ -241,9 +241,38 @@ 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 __awaiter(this, void 0, void 0, function () {
-        var tokenizer, structures, state, atoms, bonds, result;
+        var tokenizer, structures, state, atoms, bonds, crysin, result;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -261,7 +290,8 @@ 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/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/mol-io/reader/mol2/schema.js

@@ -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>
  */

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

@@ -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 { Column } from '../../../mol-data/db';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
@@ -44,6 +50,9 @@ export function handleAtomsV3(tokenizer, atomCount) {
         y: TokenColumn(y)(Column.Schema.float),
         z: TokenColumn(z)(Column.Schema.float),
         type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+        /* No support for formal charge parsing in V3000 molfiles at the moment,
+        so all charges default to 0.*/
+        formal_charge: Column.ofConst(0, atomCount, Column.Schema.int)
     };
 }
 export function handleBondsV3(tokenizer, bondCount) {

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

@@ -1,12 +1,14 @@
 /**
- * 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 { __awaiter, __generator } from "tslib";
 import { Column } from '../../../mol-data/db';
-import { handleAtoms, handleBonds } from '../mol/parser';
+import { handleAtoms, handleBonds, handlePropertiesBlock } from '../mol/parser';
 import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
@@ -69,11 +71,18 @@ 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: Column.ofConst(0, atomCount, Column.Schema.int),
+        charge: Column.ofConst(0, atomCount, Column.Schema.int)
+    };
     var atoms = molIsV3 ? handleAtomsV3(tokenizer, atomCount) : handleAtoms(tokenizer, atomCount);
     var bonds = molIsV3 ? handleBondsV3(tokenizer, bondCount) : handleBonds(tokenizer, bondCount);
+    var formalCharges = molIsV3 ? nullFormalCharges : 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/mol-io/writer/cif/encoder/binary.js

@@ -170,8 +170,15 @@ 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/mol-math/geometry/gaussian-density/gpu.js

@@ -10,7 +10,7 @@ import { OrderedSet } from '../../../mol-data/int';
 import { Vec3, Tensor, Mat4, Vec2 } from '../../linear-algebra';
 import { ValueCell } from '../../../mol-util';
 import { createComputeRenderable } from '../../../mol-gl/renderable';
-import { decodeFloatRGB } from '../../../mol-util/float-packing';
+import { unpackRGBToInt } from '../../../mol-util/number-packing';
 import { ShaderCode } from '../../../mol-gl/shader-code';
 import { createComputeRenderItem } from '../../../mol-gl/webgl/render-item';
 import { ValueSpec, AttributeSpec, UniformSpec, TextureSpec, DefineSpec } from '../../../mol-gl/renderable/schema';
@@ -371,7 +371,7 @@ 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] = decodeFloatRGB(image[idx], image[idx + 1], image[idx + 2]);
+                idData[j] = unpackRGBToInt(image[idx], image[idx + 1], image[idx + 2]);
                 j++;
             }
         }

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

@@ -19,8 +19,9 @@ var SymmetryOperator;
         var _hkl = hkl ? Vec3.clone(hkl) : Vec3();
         spgrOp = defaults(spgrOp, -1);
         ncsId = ncsId || -1;
-        var suffix = getSuffix(info);
-        if (Mat4.isIdentity(matrix))
+        var isIdentity = Mat4.isIdentity(matrix);
+        var suffix = getSuffix(info, isIdentity);
+        if (isIdentity)
             return { name: name, assembly: assembly, matrix: matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
         if (!Mat4.isRotationAndTranslation(matrix, SymmetryOperator.RotationTranslationEpsilon)) {
             console.warn("Symmetry operator (".concat(name, ") should be a composition of rotation and translation."));
@@ -28,11 +29,16 @@ var SymmetryOperator;
         return { name: name, assembly: assembly, matrix: matrix, inverse: Mat4.invert(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/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/mol-math/linear-algebra/3d/quat.js

@@ -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>
@@ -311,6 +311,25 @@ function 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) <= EPSILON * Math.max(1.0, Math.abs(a0), Math.abs(b0)) &&
+            Math.abs(a1 - b1) <= EPSILON * Math.max(1.0, Math.abs(a1), Math.abs(b1)) &&
+            Math.abs(a2 - b2) <= EPSILON * Math.max(1.0, Math.abs(a2), Math.abs(b2)) &&
+            Math.abs(a3 - b3) <= 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/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/mol-model/structure/export/mmcif.js

@@ -37,6 +37,9 @@ 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
     copy_mmCif_category('entry'),
@@ -46,9 +49,9 @@ var Categories = [
     copy_mmCif_category('cell', isWithoutSymmetry),
     copy_mmCif_category('symmetry', isWithoutSymmetry),
     // Assemblies
-    copy_mmCif_category('pdbx_struct_assembly', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_oper_list', isWithoutSymmetry),
+    copy_mmCif_category('pdbx_struct_assembly', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_oper_list', isWithoutOperator),
     // Secondary structure
     _struct_conf,
     _struct_sheet_range,
@@ -229,11 +232,11 @@ 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 = CifWriter.createEncoder({ binary: asBinary });
     enc.startDataBlock(name);
-    encode_mmCIF_categories(enc, structure);
+    encode_mmCIF_categories(enc, structure, params);
     return enc.getData();
 }
 export { to_mmCIF };

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

@@ -49,6 +49,7 @@ export var Stats;
         }
         else if (size === 1) {
             if (Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
+                // handled in `handleUnitChainsSimple`
                 return;
             }
             else {
@@ -174,6 +175,13 @@ export var Stats;
                     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.set(stats.firstElementLoc, structure, unit, eI);
+                }
+            }
         }
     }
     function handleUnitChainsPartitioned(stats, structure, lociElements, start, end) {

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

@@ -111,6 +111,7 @@ var coarse = {
     y: atom.y,
     z: atom.z,
     asym_id: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.asym_id.value(l.element); }),
+    entity_id: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entity_id.value(l.element); }),
     seq_id_begin: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_begin.value(l.element); }),
     seq_id_end: p(function (l) { return !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_end.value(l.element); }),
     sphere_radius: p(function (l) { return !Unit.isSpheres(l.unit) ? notCoarse('spheres') : l.unit.coarseConformation.radius[l.element]; }),
@@ -141,7 +142,7 @@ 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/mol-model/structure/structure/symmetry.js

@@ -187,8 +187,6 @@ function getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter) {
         ijkMin[2] <= 0 && ijkMax[2] >= 0) {
         operators[0] = Spacegroup.getSymmetryOperator(spacegroup, 0, 0, 0, 0);
     }
-    var toFractional = spacegroup.cell.toFractional;
-    var ref = Vec3.transformMat4(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++) {
@@ -196,7 +194,7 @@ 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/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;

package/lib/mol-model/structure/structure/unit/bonds/common.js

@@ -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>
@@ -99,6 +99,14 @@ export function getElementThreshold(i) {
         return __DefaultBondingRadius;
     return r;
 }
+export function getPairingThreshold(elementIndexA, elementIndexB, thresholdA, thresholdB) {
+    var thresholdAB = getElementPairThreshold(elementIndexA, elementIndexB);
+    return thresholdAB > 0
+        ? thresholdAB
+        : elementIndexB < 0
+            ? thresholdA
+            : (thresholdA + thresholdB) / 1.95; // not sure if avg or min but max is too big
+}
 var H_ID = __ElementIndex['H'];
 export function isHydrogen(i) {
     return i === H_ID;

package/lib/mol-model/structure/structure/unit/bonds/inter-compute.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>

package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js

@@ -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>
@@ -7,7 +7,7 @@
 import { __assign } from "tslib";
 import { Structure } from '../../structure';
 import { Unit } from '../../unit';
-import { getElementIdx, getElementPairThreshold, getElementThreshold, isHydrogen, MetalsSet, DefaultBondComputationProps } from './common';
+import { getElementIdx, getElementThreshold, isHydrogen, MetalsSet, DefaultBondComputationProps, getPairingThreshold } from './common';
 import { InterUnitBonds } from './data';
 import { SortedArray } from '../../../../../mol-data/int';
 import { Vec3, Mat4 } from '../../../../../mol-math/linear-algebra';
@@ -67,11 +67,26 @@ function findPairBonds(unitA, unitB, props, builder) {
                 var _bI = SortedArray.indexOf(unitB.elements, bI);
                 if (_bI < 0)
                     continue;
-                if (type_symbolA.value(aI) === 'H' && type_symbolB.value(bI) === 'H')
-                    continue;
+                var aeI_1 = getElementIdx(type_symbolA.value(aI));
+                var beI = getElementIdx(type_symbolA.value(bI));
                 var d = distance[i];
                 var dist = getDistance(unitA, aI, unitB, bI);
-                if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
+                var add = false;
+                if (d >= 0) {
+                    add = equalEps(dist, d, 0.3);
+                }
+                else if (maxDistance >= 0) {
+                    add = dist < maxDistance;
+                }
+                else {
+                    var pairingThreshold = getPairingThreshold(aeI_1, beI, getElementThreshold(aeI_1), getElementThreshold(beI));
+                    add = dist < pairingThreshold;
+                    if (isHydrogen(aeI_1) && isHydrogen(beI)) {
+                        // TODO handle molecular hydrogen
+                        add = false;
+                    }
+                }
+                if (add) {
                     builder.add(_aI, _bI, { order: order[i], flag: flag[i] });
                 }
             }
@@ -135,12 +150,7 @@ function findPairBonds(unitA, unitB, props, builder) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = getElementPairThreshold(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + getElementThreshold(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = getPairingThreshold(aeI, beI, thresholdA, getElementThreshold(beI));
             if (dist <= pairingThreshold) {
                 var atomIdB = label_atom_idB.value(bI);
                 var compIdB = label_comp_idB.value(residueIndexB[bI]);

package/lib/mol-model/structure/structure/unit/bonds/intra-compute.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>

package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js

@@ -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>
@@ -7,7 +7,7 @@
 import { __assign } from "tslib";
 import { IntraUnitBonds } from './data';
 import { IntAdjacencyGraph } from '../../../../../mol-math/graph';
-import { getElementIdx, MetalsSet, getElementThreshold, isHydrogen, getElementPairThreshold, DefaultBondComputationProps } from './common';
+import { getElementIdx, MetalsSet, getElementThreshold, isHydrogen, DefaultBondComputationProps, getPairingThreshold } from './common';
 import { SortedArray } from '../../../../../mol-data/int';
 import { getIntraBondOrderFromTable } from '../../../model/properties/atomic/bonds';
 import { IndexPairBonds } from '../../../../../mol-model-formats/structure/property/bonds/index-pair';
@@ -50,7 +50,8 @@ function findIndexPairBonds(unit) {
     var orders = [];
     for (var _aI = 0; _aI < atomCount; _aI++) {
         var aI = atoms[_aI];
-        var isHa = type_symbol.value(aI) === 'H';
+        var aeI = getElementIdx(type_symbol.value(aI));
+        var isHa = isHydrogen(aeI);
         var srcA = sourceIndex.value(aI);
         for (var i = offset[srcA], il = offset[srcA + 1]; i < il; ++i) {
             var bI = invertedIndex[b[i]];
@@ -59,11 +60,25 @@ function findIndexPairBonds(unit) {
             var _bI = SortedArray.indexOf(unit.elements, bI);
             if (_bI < 0)
                 continue;
-            if (isHa && type_symbol.value(bI) === 'H')
-                continue;
+            var beI = getElementIdx(type_symbol.value(bI));
             var d = distance[i];
             var dist = getDistance(unit, aI, bI);
-            if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
+            var add = false;
+            if (d >= 0) {
+                add = equalEps(dist, d, 0.3);
+            }
+            else if (maxDistance >= 0) {
+                add = dist < maxDistance;
+            }
+            else {
+                var pairingThreshold = getPairingThreshold(aeI, beI, getElementThreshold(aeI), getElementThreshold(beI));
+                add = dist < pairingThreshold;
+                if (isHa && isHydrogen(beI)) {
+                    // TODO handle molecular hydrogen
+                    add = false;
+                }
+            }
+            if (add) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
                 orders[orders.length] = order[i];
@@ -187,12 +202,7 @@ function findBonds(unit, props) {
             var dist = Math.sqrt(squaredDistances[ni]);
             if (dist === 0)
                 continue;
-            var thresholdAB = getElementPairThreshold(aeI, beI);
-            var pairingThreshold = thresholdAB > 0
-                ? thresholdAB
-                : beI < 0
-                    ? thresholdA
-                    : (thresholdA + getElementThreshold(beI)) / 1.95; // not sure if avg or min but max is too big
+            var pairingThreshold = getPairingThreshold(aeI, beI, thresholdA, getElementThreshold(beI));
             if (dist <= pairingThreshold) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;