molstar 3.0.0-dev.7 → 3.0.1

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

@@ -1,339 +0,0 @@
-"use strict";
-/**
- * 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>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.StructureSymmetry = void 0;
-var tslib_1 = require("tslib");
-var int_1 = require("../../../mol-data/int");
-var util_1 = require("../../../mol-data/util");
-var geometry_1 = require("../../../mol-math/geometry");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var mol_task_1 = require("../../../mol-task");
-var model_1 = require("../model");
-var query_1 = require("../query");
-var structure_1 = require("./structure");
-var unit_1 = require("./unit");
-var symmetry_1 = require("../../../mol-model-formats/structure/property/symmetry");
-var properties_1 = require("./properties");
-var StructureSymmetry;
-(function (StructureSymmetry) {
-    function buildAssembly(structure, asmName) {
-        var _this = this;
-        return mol_task_1.Task.create('Build Assembly', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            var models, assembly, coordinateSystem, assembler, queryCtx, _i, _a, g, selection, units, _b, _c, oper, _d, units_1, unit;
-            return (0, tslib_1.__generator)(this, function (_e) {
-                models = structure.models;
-                if (models.length !== 1)
-                    throw new Error('Can only build assemblies from structures based on 1 model.');
-                assembly = model_1.Symmetry.findAssembly(models[0], asmName);
-                if (!assembly)
-                    throw new Error("Assembly '".concat(asmName, "' is not defined."));
-                coordinateSystem = geometry_1.SymmetryOperator.create(assembly.id, linear_algebra_1.Mat4.identity(), { assembly: { id: assembly.id, operId: 0, operList: [] } });
-                assembler = structure_1.Structure.Builder({
-                    coordinateSystem: coordinateSystem,
-                    label: structure.label,
-                    dynamicBonds: structure.dynamicBonds
-                });
-                queryCtx = new query_1.QueryContext(structure);
-                for (_i = 0, _a = assembly.operatorGroups; _i < _a.length; _i++) {
-                    g = _a[_i];
-                    selection = g.selector(queryCtx);
-                    if (query_1.StructureSelection.structureCount(selection) === 0) {
-                        continue;
-                    }
-                    units = query_1.StructureSelection.unionStructure(selection).units;
-                    for (_b = 0, _c = g.operators; _b < _c.length; _b++) {
-                        oper = _c[_b];
-                        for (_d = 0, units_1 = units; _d < units_1.length; _d++) {
-                            unit = units_1[_d];
-                            assembler.addWithOperator(unit, oper);
-                        }
-                    }
-                }
-                return [2 /*return*/, assembler.getStructure()];
-            });
-        }); });
-    }
-    StructureSymmetry.buildAssembly = buildAssembly;
-    function buildSymmetryAssembly(structure, generators, symmetry) {
-        var _this = this;
-        return mol_task_1.Task.create('Build Symmetry Assembly', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-            var models, modelCenter, assembler, queryCtx, _i, generators_1, g, selector, selection, units, _a, _b, _c, index, _d, i, j, k, operators, _e, units_2, unit, _f, operators_1, op;
-            return (0, tslib_1.__generator)(this, function (_g) {
-                models = structure.models;
-                if (models.length !== 1)
-                    throw new Error('Can only build symmetry assemblies from structures based on 1 model.');
-                modelCenter = (0, linear_algebra_1.Vec3)();
-                assembler = structure_1.Structure.Builder({
-                    label: structure.label,
-                    representativeModel: models[0],
-                    dynamicBonds: structure.dynamicBonds
-                });
-                queryCtx = new query_1.QueryContext(structure);
-                for (_i = 0, generators_1 = generators; _i < generators_1.length; _i++) {
-                    g = generators_1[_i];
-                    selector = getSelector(g.asymIds);
-                    selection = selector(queryCtx);
-                    if (query_1.StructureSelection.structureCount(selection) === 0) {
-                        continue;
-                    }
-                    units = query_1.StructureSelection.unionStructure(selection).units;
-                    for (_a = 0, _b = g.operators; _a < _b.length; _a++) {
-                        _c = _b[_a], index = _c.index, _d = _c.shift, i = _d[0], j = _d[1], k = _d[2];
-                        operators = getOperatorsForIndex(symmetry, index, i, j, k, modelCenter);
-                        for (_e = 0, units_2 = units; _e < units_2.length; _e++) {
-                            unit = units_2[_e];
-                            for (_f = 0, operators_1 = operators; _f < operators_1.length; _f++) {
-                                op = operators_1[_f];
-                                assembler.addWithOperator(unit, op);
-                            }
-                        }
-                    }
-                }
-                return [2 /*return*/, assembler.getStructure()];
-            });
-        }); });
-    }
-    StructureSymmetry.buildSymmetryAssembly = buildSymmetryAssembly;
-    function builderSymmetryMates(structure, radius) {
-        return mol_task_1.Task.create('Find Symmetry Mates', function (ctx) { return findMatesRadius(ctx, structure, radius); });
-    }
-    StructureSymmetry.builderSymmetryMates = builderSymmetryMates;
-    function buildSymmetryRange(structure, ijkMin, ijkMax) {
-        return mol_task_1.Task.create('Build Symmetry', function (ctx) { return findSymmetryRange(ctx, structure, ijkMin, ijkMax); });
-    }
-    StructureSymmetry.buildSymmetryRange = buildSymmetryRange;
-    /** Builds NCS structure, returns the original if NCS operators are not present. */
-    function buildNcs(structure) {
-        return mol_task_1.Task.create('Build NCS', function (ctx) { return _buildNCS(ctx, structure); });
-    }
-    StructureSymmetry.buildNcs = buildNcs;
-    function areUnitsEquivalent(a, b) {
-        return a.invariantId === b.invariantId && a.model.id === b.model.id && int_1.SortedArray.areEqual(a.elements, b.elements);
-    }
-    StructureSymmetry.areUnitsEquivalent = areUnitsEquivalent;
-    function UnitEquivalenceBuilder() {
-        return (0, util_1.EquivalenceClasses)(unit_1.Unit.hashUnit, areUnitsEquivalent);
-    }
-    StructureSymmetry.UnitEquivalenceBuilder = UnitEquivalenceBuilder;
-    function computeTransformGroups(s) {
-        var groups = UnitEquivalenceBuilder();
-        for (var _i = 0, _a = s.units; _i < _a.length; _i++) {
-            var u = _a[_i];
-            groups.add(u.id, u);
-        }
-        var ret = [];
-        for (var _b = 0, _c = groups.groups; _b < _c.length; _b++) {
-            var eqUnits = _c[_b];
-            ret.push(unit_1.Unit.SymmetryGroup(eqUnits.map(function (id) { return s.unitMap.get(id); })));
-        }
-        return ret;
-    }
-    StructureSymmetry.computeTransformGroups = computeTransformGroups;
-    /** Checks if transform groups are equal up to their unit's transformations */
-    function areTransformGroupsEquivalent(a, b) {
-        if (a.length !== b.length)
-            return false;
-        for (var i = 0, il = a.length; i < il; ++i) {
-            var au = a[i].units, bu = b[i].units;
-            if (au.length !== bu.length)
-                return false;
-            if (a[i].hashCode !== b[i].hashCode)
-                return false;
-            for (var j = 0, _j = au.length; j < _j; j++) {
-                if (au[j].conformation !== bu[j].conformation)
-                    return false;
-            }
-        }
-        return true;
-    }
-    StructureSymmetry.areTransformGroupsEquivalent = areTransformGroupsEquivalent;
-})(StructureSymmetry || (StructureSymmetry = {}));
-exports.StructureSymmetry = StructureSymmetry;
-function getSelector(asymIds) {
-    return query_1.Queries.generators.atoms({ chainTest: query_1.Queries.pred.and(query_1.Queries.pred.eq(function (ctx) { return properties_1.StructureProperties.unit.operator_name(ctx.element); }, geometry_1.SymmetryOperator.DefaultName), query_1.Queries.pred.inSet(function (ctx) { return properties_1.StructureProperties.chain.label_asym_id(ctx.element); }, asymIds)) });
-}
-function getOperatorsForIndex(symmetry, index, i, j, k, modelCenter) {
-    var spacegroup = symmetry.spacegroup, ncsOperators = symmetry.ncsOperators;
-    var operators = [];
-    var toFractional = spacegroup.cell.toFractional;
-    var ref = linear_algebra_1.Vec3.transformMat4((0, linear_algebra_1.Vec3)(), modelCenter, toFractional);
-    var symOp = geometry_1.Spacegroup.getSymmetryOperatorRef(spacegroup, index, i, j, k, ref);
-    if (ncsOperators && ncsOperators.length) {
-        for (var u = 0, ul = ncsOperators.length; u < ul; ++u) {
-            var ncsOp = ncsOperators[u];
-            var matrix = linear_algebra_1.Mat4.mul((0, linear_algebra_1.Mat4)(), symOp.matrix, ncsOp.matrix);
-            var operator = geometry_1.SymmetryOperator.create("".concat(symOp.name, " ").concat(ncsOp.name), matrix, {
-                assembly: symOp.assembly,
-                ncsId: ncsOp.ncsId,
-                hkl: symOp.hkl,
-                spgrOp: symOp.spgrOp
-            });
-            operators.push(operator);
-        }
-    }
-    else {
-        operators.push(symOp);
-    }
-    return operators;
-}
-function getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter) {
-    var spacegroup = symmetry.spacegroup, ncsOperators = symmetry.ncsOperators;
-    var ncsCount = (ncsOperators && ncsOperators.length) || 0;
-    var operators = [];
-    if (!ncsCount &&
-        ijkMin[0] <= 0 && ijkMax[0] >= 0 &&
-        ijkMin[1] <= 0 && ijkMax[1] >= 0 &&
-        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++) {
-                for (var k = ijkMin[2]; k <= ijkMax[2]; k++) {
-                    // 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));
-                }
-            }
-        }
-    }
-    return operators;
-}
-function getOperatorsCached333(symmetry, ref) {
-    if (symmetry._operators_333 && linear_algebra_1.Vec3.equals(ref, symmetry._operators_333.ref)) {
-        return symmetry._operators_333.operators;
-    }
-    symmetry._operators_333 = {
-        ref: linear_algebra_1.Vec3.clone(ref),
-        operators: getOperatorsForRange(symmetry, linear_algebra_1.Vec3.create(-3, -3, -3), linear_algebra_1.Vec3.create(3, 3, 3), ref)
-    };
-    return symmetry._operators_333.operators;
-}
-function assembleOperators(structure, operators) {
-    var assembler = structure_1.Structure.Builder({
-        label: structure.label,
-        dynamicBonds: structure.dynamicBonds
-    });
-    var units = structure.units;
-    for (var _i = 0, operators_2 = operators; _i < operators_2.length; _i++) {
-        var oper = operators_2[_i];
-        for (var _a = 0, units_3 = units; _a < units_3.length; _a++) {
-            var unit = units_3[_a];
-            assembler.addWithOperator(unit, oper);
-        }
-    }
-    return assembler.getStructure();
-}
-function _buildNCS(ctx, structure) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var models, symmetry, operators;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            models = structure.models;
-            if (models.length !== 1)
-                throw new Error('Can only build NCS from structures based on 1 model.');
-            symmetry = symmetry_1.ModelSymmetry.Provider.get(models[0]);
-            if (!symmetry)
-                return [2 /*return*/, structure];
-            operators = symmetry.ncsOperators;
-            if (!operators || !operators.length)
-                return [2 /*return*/, structure];
-            return [2 /*return*/, assembleOperators(structure, operators)];
-        });
-    });
-}
-function findSymmetryRange(ctx, structure, ijkMin, ijkMax) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var models, symmetry, spacegroup, modelCenter, operators;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            models = structure.models;
-            if (models.length !== 1)
-                throw new Error('Can only build symmetries from structures based on 1 model.');
-            symmetry = symmetry_1.ModelSymmetry.Provider.get(models[0]);
-            if (!symmetry)
-                return [2 /*return*/, structure];
-            spacegroup = symmetry.spacegroup;
-            if (geometry_1.SpacegroupCell.isZero(spacegroup.cell))
-                return [2 /*return*/, structure];
-            modelCenter = model_1.Model.getCenter(models[0]);
-            operators = getOperatorsForRange(symmetry, ijkMin, ijkMax, modelCenter);
-            return [2 /*return*/, assembleOperators(structure, operators)];
-        });
-    });
-}
-function findMatesRadius(ctx, structure, radius) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        function hash(unit, oper) {
-            return "".concat(unit.invariantId, "|").concat(oper.name);
-        }
-        var models, symmetry, spacegroup, modelCenter, operators, lookup, added, assembler, units, center, _i, operators_3, oper, _a, units_4, unit, boundingSphere, closeUnits, uI, _uI, closeUnit, h;
-        return (0, tslib_1.__generator)(this, function (_b) {
-            switch (_b.label) {
-                case 0:
-                    models = structure.models;
-                    if (models.length !== 1)
-                        throw new Error('Can only build symmetries from structures based on 1 model.');
-                    symmetry = symmetry_1.ModelSymmetry.Provider.get(models[0]);
-                    if (!symmetry)
-                        return [2 /*return*/, structure];
-                    spacegroup = symmetry.spacegroup;
-                    if (geometry_1.SpacegroupCell.isZero(spacegroup.cell))
-                        return [2 /*return*/, structure];
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 2];
-                    return [4 /*yield*/, ctx.update('Initialing...')];
-                case 1:
-                    _b.sent();
-                    _b.label = 2;
-                case 2:
-                    modelCenter = model_1.Model.getCenter(models[0]);
-                    operators = getOperatorsCached333(symmetry, modelCenter);
-                    lookup = structure.lookup3d;
-                    added = new Set();
-                    assembler = structure_1.Structure.Builder({
-                        label: structure.label,
-                        dynamicBonds: structure.dynamicBonds
-                    });
-                    units = structure.units;
-                    center = linear_algebra_1.Vec3.zero();
-                    _i = 0, operators_3 = operators;
-                    _b.label = 3;
-                case 3:
-                    if (!(_i < operators_3.length)) return [3 /*break*/, 6];
-                    oper = operators_3[_i];
-                    for (_a = 0, units_4 = units; _a < units_4.length; _a++) {
-                        unit = units_4[_a];
-                        boundingSphere = unit.lookup3d.boundary.sphere;
-                        linear_algebra_1.Vec3.transformMat4(center, boundingSphere.center, oper.matrix);
-                        closeUnits = lookup.findUnitIndices(center[0], center[1], center[2], boundingSphere.radius + radius);
-                        for (uI = 0, _uI = closeUnits.count; uI < _uI; uI++) {
-                            closeUnit = units[closeUnits.indices[uI]];
-                            if (!closeUnit.lookup3d.check(center[0], center[1], center[2], boundingSphere.radius + radius))
-                                continue;
-                            h = hash(unit, oper);
-                            if (!added.has(h)) {
-                                assembler.addWithOperator(unit, oper);
-                                added.add(h);
-                            }
-                        }
-                    }
-                    if (!ctx.shouldUpdate) return [3 /*break*/, 5];
-                    return [4 /*yield*/, ctx.update('Building symmetry...')];
-                case 4:
-                    _b.sent();
-                    _b.label = 5;
-                case 5:
-                    _i++;
-                    return [3 /*break*/, 3];
-                case 6: return [2 /*return*/, assembler.getStructure()];
-            }
-        });
-    });
-}
-//# sourceMappingURL=symmetry.js.map

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

@@ -1,20 +0,0 @@
-/**
- * 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>
- */
-import { ElementSymbol } from '../../../model/types';
-/** Default for atomic bonds */
-export declare const DefaultBondMaxRadius = 4;
-export interface BondComputationProps {
-    forceCompute: boolean;
-    noCompute: boolean;
-    maxRadius: number;
-}
-export declare const DefaultBondComputationProps: BondComputationProps;
-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 isHydrogen(i: number): boolean;

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

@@ -1,113 +0,0 @@
-"use strict";
-/**
- * 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>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isHydrogen = exports.getElementThreshold = exports.getElementPairThreshold = exports.getElementIdx = exports.MetalsSet = exports.DefaultBondComputationProps = exports.DefaultBondMaxRadius = void 0;
-/** Default for atomic bonds */
-exports.DefaultBondMaxRadius = 4;
-exports.DefaultBondComputationProps = {
-    forceCompute: false,
-    noCompute: false,
-    maxRadius: exports.DefaultBondMaxRadius,
-};
-// H,D,T are all mapped to H
-var __ElementIndex = { 'H': 0, 'h': 0, 'D': 0, 'd': 0, 'T': 0, 't': 0, 'He': 2, 'HE': 2, 'he': 2, 'Li': 3, 'LI': 3, 'li': 3, 'Be': 4, 'BE': 4, 'be': 4, 'B': 5, 'b': 5, 'C': 6, 'c': 6, 'N': 7, 'n': 7, 'O': 8, 'o': 8, 'F': 9, 'f': 9, 'Ne': 10, 'NE': 10, 'ne': 10, 'Na': 11, 'NA': 11, 'na': 11, 'Mg': 12, 'MG': 12, 'mg': 12, 'Al': 13, 'AL': 13, 'al': 13, 'Si': 14, 'SI': 14, 'si': 14, 'P': 15, 'p': 15, 'S': 16, 's': 16, 'Cl': 17, 'CL': 17, 'cl': 17, 'Ar': 18, 'AR': 18, 'ar': 18, 'K': 19, 'k': 19, 'Ca': 20, 'CA': 20, 'ca': 20, 'Sc': 21, 'SC': 21, 'sc': 21, 'Ti': 22, 'TI': 22, 'ti': 22, 'V': 23, 'v': 23, 'Cr': 24, 'CR': 24, 'cr': 24, 'Mn': 25, 'MN': 25, 'mn': 25, 'Fe': 26, 'FE': 26, 'fe': 26, 'Co': 27, 'CO': 27, 'co': 27, 'Ni': 28, 'NI': 28, 'ni': 28, 'Cu': 29, 'CU': 29, 'cu': 29, 'Zn': 30, 'ZN': 30, 'zn': 30, 'Ga': 31, 'GA': 31, 'ga': 31, 'Ge': 32, 'GE': 32, 'ge': 32, 'As': 33, 'AS': 33, 'as': 33, 'Se': 34, 'SE': 34, 'se': 34, 'Br': 35, 'BR': 35, 'br': 35, 'Kr': 36, 'KR': 36, 'kr': 36, 'Rb': 37, 'RB': 37, 'rb': 37, 'Sr': 38, 'SR': 38, 'sr': 38, 'Y': 39, 'y': 39, 'Zr': 40, 'ZR': 40, 'zr': 40, 'Nb': 41, 'NB': 41, 'nb': 41, 'Mo': 42, 'MO': 42, 'mo': 42, 'Tc': 43, 'TC': 43, 'tc': 43, 'Ru': 44, 'RU': 44, 'ru': 44, 'Rh': 45, 'RH': 45, 'rh': 45, 'Pd': 46, 'PD': 46, 'pd': 46, 'Ag': 47, 'AG': 47, 'ag': 47, 'Cd': 48, 'CD': 48, 'cd': 48, 'In': 49, 'IN': 49, 'in': 49, 'Sn': 50, 'SN': 50, 'sn': 50, 'Sb': 51, 'SB': 51, 'sb': 51, 'Te': 52, 'TE': 52, 'te': 52, 'I': 53, 'i': 53, 'Xe': 54, 'XE': 54, 'xe': 54, 'Cs': 55, 'CS': 55, 'cs': 55, 'Ba': 56, 'BA': 56, 'ba': 56, 'La': 57, 'LA': 57, 'la': 57, 'Ce': 58, 'CE': 58, 'ce': 58, 'Pr': 59, 'PR': 59, 'pr': 59, 'Nd': 60, 'ND': 60, 'nd': 60, 'Pm': 61, 'PM': 61, 'pm': 61, 'Sm': 62, 'SM': 62, 'sm': 62, 'Eu': 63, 'EU': 63, 'eu': 63, 'Gd': 64, 'GD': 64, 'gd': 64, 'Tb': 65, 'TB': 65, 'tb': 65, 'Dy': 66, 'DY': 66, 'dy': 66, 'Ho': 67, 'HO': 67, 'ho': 67, 'Er': 68, 'ER': 68, 'er': 68, 'Tm': 69, 'TM': 69, 'tm': 69, 'Yb': 70, 'YB': 70, 'yb': 70, 'Lu': 71, 'LU': 71, 'lu': 71, 'Hf': 72, 'HF': 72, 'hf': 72, 'Ta': 73, 'TA': 73, 'ta': 73, 'W': 74, 'w': 74, 'Re': 75, 'RE': 75, 're': 75, 'Os': 76, 'OS': 76, 'os': 76, 'Ir': 77, 'IR': 77, 'ir': 77, 'Pt': 78, 'PT': 78, 'pt': 78, 'Au': 79, 'AU': 79, 'au': 79, 'Hg': 80, 'HG': 80, 'hg': 80, 'Tl': 81, 'TL': 81, 'tl': 81, 'Pb': 82, 'PB': 82, 'pb': 82, 'Bi': 83, 'BI': 83, 'bi': 83, 'Po': 84, 'PO': 84, 'po': 84, 'At': 85, 'AT': 85, 'at': 85, 'Rn': 86, 'RN': 86, 'rn': 86, 'Fr': 87, 'FR': 87, 'fr': 87, 'Ra': 88, 'RA': 88, 'ra': 88, 'Ac': 89, 'AC': 89, 'ac': 89, 'Th': 90, 'TH': 90, 'th': 90, 'Pa': 91, 'PA': 91, 'pa': 91, 'U': 92, 'u': 92, 'Np': 93, 'NP': 93, 'np': 93, 'Pu': 94, 'PU': 94, 'pu': 94, 'Am': 95, 'AM': 95, 'am': 95, 'Cm': 96, 'CM': 96, 'cm': 96, 'Bk': 97, 'BK': 97, 'bk': 97, 'Cf': 98, 'CF': 98, 'cf': 98, 'Es': 99, 'ES': 99, 'es': 99, 'Fm': 100, 'FM': 100, 'fm': 100, 'Md': 101, 'MD': 101, 'md': 101, 'No': 102, 'NO': 102, 'no': 102, 'Lr': 103, 'LR': 103, 'lr': 103, 'Rf': 104, 'RF': 104, 'rf': 104, 'Db': 105, 'DB': 105, 'db': 105, 'Sg': 106, 'SG': 106, 'sg': 106, 'Bh': 107, 'BH': 107, 'bh': 107, 'Hs': 108, 'HS': 108, 'hs': 108, 'Mt': 109, 'MT': 109, 'mt': 109 };
-// Increased P (15) threshold from 1.9 to 2.0 (e.g. for G16 in 1O08)
-var __ElementBondThresholds = { 0: 1.42, 1: 1.42, 3: 2.7, 4: 2.7, 6: 1.75, 7: 1.6, 8: 1.52, 11: 2.7, 12: 2.7, 13: 2.7, 14: 1.9, 15: 2.0, 16: 1.9, 17: 1.8, 19: 2.7, 20: 2.7, 21: 2.7, 22: 2.7, 23: 2.7, 24: 2.7, 25: 2.7, 26: 2.7, 27: 2.7, 28: 2.7, 29: 2.7, 30: 2.7, 31: 2.7, 33: 2.68, 37: 2.7, 38: 2.7, 39: 2.7, 40: 2.7, 41: 2.7, 42: 2.7, 43: 2.7, 44: 2.7, 45: 2.7, 46: 2.7, 47: 2.7, 48: 2.7, 49: 2.7, 50: 2.7, 55: 2.7, 56: 2.7, 57: 2.7, 58: 2.7, 59: 2.7, 60: 2.7, 61: 2.7, 62: 2.7, 63: 2.7, 64: 2.7, 65: 2.7, 66: 2.7, 67: 2.7, 68: 2.7, 69: 2.7, 70: 2.7, 71: 2.7, 72: 2.7, 73: 2.7, 74: 2.7, 75: 2.7, 76: 2.7, 77: 2.7, 78: 2.7, 79: 2.7, 80: 2.7, 81: 2.7, 82: 2.7, 83: 2.7, 87: 2.7, 88: 2.7, 89: 2.7, 90: 2.7, 91: 2.7, 92: 2.7, 93: 2.7, 94: 2.7, 95: 2.7, 96: 2.7, 97: 2.7, 98: 2.7, 99: 2.7, 100: 2.7, 101: 2.7, 102: 2.7, 103: 2.7, 104: 2.7, 105: 2.7, 106: 2.7, 107: 2.7, 108: 2.7, 109: 2.88 };
-/**
- * Added O-S (316) as 1.8
- * N-O-S bridge (e.g. LYS-CSO in 7B0L, 6ZWJ, 6ZWH)
- * (https://www.nature.com/articles/s41586-021-03513-3?s=09)
- *
- * Increased N-N (112) threshold from 1.55 to 1.6 (e.g. for 0QH in 1BMA)
- *
- * More experimentally observed bond length here (https://cccbdb.nist.gov/expbondlengths1x.asp)
- *
- * H-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rHH)
- * - 0.741
- *
- * Changed C-H (27) to 1.2
- * C-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rCH)
- * - Average    1.091 (+/- 0.017)
- * - Min        0.931
- * - Max        1.140
- *
- * Changed N-H (35) to 1.15
- * N-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rNH)
- * - Average    1.009 (+/- 0.043)
- * - Min        0.836
- * - Max        1.090
- *
- * Changed O-H (44) to 1.1
- * O-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rOH)
- * - Average    0.967 (+/- 0.022)
- * - Min        0.912
- * - Max        1.033
- *
- * Added P-H (135) as 1.47
- * P-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rPH)
- * - Average    1.423 ((+/- 0.007)
- * - Min        1.414
- * - Max        1.435
- *
- * Added S-H (152) as 1.45
- * S-H (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rSH)
- * - Average    1.345 (+/- 0.020)
- * - Min        1.322
- * - Max        1.400
- *
- * Added Si-Si (420) as 2.37
- * (https://cccbdb.nist.gov/expbondlengths2x.asp?descript=rSiSi)
- */
-var __ElementPairThresholds = { 0: 0.8, 20: 1.31, 27: 1.2, 35: 1.15, 44: 1.1, 54: 1, 60: 1.84, 72: 1.88, 84: 1.75, 85: 1.56, 86: 1.76, 98: 1.6, 99: 1.68, 100: 1.63, 112: 1.6, 113: 1.59, 114: 1.36, 129: 1.45, 135: 1.47, 144: 1.6, 152: 1.45, 170: 1.4, 180: 1.55, 202: 2.4, 222: 2.24, 224: 1.91, 225: 1.98, 243: 2.02, 269: 2, 293: 1.9, 316: 1.8, 420: 2.37, 480: 2.3, 512: 2.3, 544: 2.3, 612: 2.1, 629: 1.54, 665: 1, 813: 2.6, 854: 2.27, 894: 1.93, 896: 2.1, 937: 2.05, 938: 2.06, 981: 1.62, 1258: 2.68, 1309: 2.33, 1484: 1, 1763: 2.14, 1823: 2.48, 1882: 2.1, 1944: 1.72, 2380: 2.34, 3367: 2.44, 3733: 2.11, 3819: 2.6, 3821: 2.36, 4736: 2.75, 5724: 2.73, 5959: 2.63, 6519: 2.84, 6750: 2.87, 8991: 2.81 };
-var __DefaultBondingRadius = 2.001;
-exports.MetalsSet = (function () {
-    var metals = ['LI', 'NA', 'K', 'RB', 'CS', 'FR', 'BE', 'MG', 'CA', 'SR', 'BA', 'RA', 'AL', 'GA', 'IN', 'SN', 'TL', 'PB', 'BI', 'SC', 'TI', 'V', 'CR', 'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', 'Y', 'ZR', 'NB', 'MO', 'TC', 'RU', 'RH', 'PD', 'AG', 'CD', 'LA', 'HF', 'TA', 'W', 'RE', 'OS', 'IR', 'PT', 'AU', 'HG', 'AC', 'RF', 'DB', 'SG', 'BH', 'HS', 'MT', 'CE', 'PR', 'ND', 'PM', 'SM', 'EU', 'GD', 'TB', 'DY', 'HO', 'ER', 'TM', 'YB', 'LU', 'TH', 'PA', 'U', 'NP', 'PU', 'AM', 'CM', 'BK', 'CF', 'ES', 'FM', 'MD', 'NO', 'LR'];
-    var set = new Set();
-    for (var _i = 0, metals_1 = metals; _i < metals_1.length; _i++) {
-        var m = metals_1[_i];
-        set.add(__ElementIndex[m]);
-    }
-    return set;
-})();
-function pair(a, b) {
-    if (a < b)
-        return (a + b) * (a + b + 1) / 2 + b;
-    else
-        return (a + b) * (a + b + 1) / 2 + a;
-}
-function getElementIdx(e) {
-    var i = __ElementIndex[e];
-    if (i === void 0)
-        return -1;
-    return i;
-}
-exports.getElementIdx = getElementIdx;
-function getElementPairThreshold(i, j) {
-    if (i < 0 || j < 0)
-        return -1;
-    var r = __ElementPairThresholds[pair(i, j)];
-    if (r === void 0)
-        return -1;
-    return r;
-}
-exports.getElementPairThreshold = getElementPairThreshold;
-function getElementThreshold(i) {
-    if (i < 0)
-        return __DefaultBondingRadius;
-    var r = __ElementBondThresholds[i];
-    if (r === void 0)
-        return __DefaultBondingRadius;
-    return r;
-}
-exports.getElementThreshold = getElementThreshold;
-var H_ID = __ElementIndex['H'];
-function isHydrogen(i) {
-    return i === H_ID;
-}
-exports.isHydrogen = isHydrogen;
-//# sourceMappingURL=common.js.map

package/lib/commonjs/mol-model/structure/structure/unit/bonds/data.js

@@ -1,46 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017-2020 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>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.InterUnitBonds = exports.IntraUnitBonds = void 0;
-var tslib_1 = require("tslib");
-var graph_1 = require("../../../../../mol-math/graph");
-var unit_1 = require("../../unit");
-var inter_unit_graph_1 = require("../../../../../mol-math/graph/inter-unit-graph");
-var IntraUnitBonds;
-(function (IntraUnitBonds) {
-    IntraUnitBonds.Empty = graph_1.IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });
-})(IntraUnitBonds || (IntraUnitBonds = {}));
-exports.IntraUnitBonds = IntraUnitBonds;
-var InterUnitBonds = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(InterUnitBonds, _super);
-    function InterUnitBonds() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    /** Get inter-unit bond given a bond-location */
-    InterUnitBonds.prototype.getBondFromLocation = function (l) {
-        return unit_1.Unit.isAtomic(l.aUnit) && unit_1.Unit.isAtomic(l.bUnit) ? this.getEdge(l.aIndex, l.aUnit.id, l.bIndex, l.bUnit.id) : undefined;
-    };
-    /** Get inter-unit bond index given a bond-location */
-    InterUnitBonds.prototype.getBondIndexFromLocation = function (l) {
-        return unit_1.Unit.isAtomic(l.aUnit) && unit_1.Unit.isAtomic(l.bUnit) ? this.getEdgeIndex(l.aIndex, l.aUnit.id, l.bIndex, l.bUnit.id) : -1;
-    };
-    return InterUnitBonds;
-}(inter_unit_graph_1.InterUnitGraph));
-exports.InterUnitBonds = InterUnitBonds;
-(function (InterUnitBonds) {
-    var UnitPairBonds = /** @class */ (function (_super) {
-        (0, tslib_1.__extends)(UnitPairBonds, _super);
-        function UnitPairBonds() {
-            return _super !== null && _super.apply(this, arguments) || this;
-        }
-        return UnitPairBonds;
-    }(inter_unit_graph_1.InterUnitGraph.UnitPairEdges));
-    InterUnitBonds.UnitPairBonds = UnitPairBonds;
-})(InterUnitBonds || (InterUnitBonds = {}));
-exports.InterUnitBonds = InterUnitBonds;
-//# sourceMappingURL=data.js.map

package/lib/commonjs/mol-model/structure/structure/unit/bonds/element-set-intra-bond-cache.js

@@ -1,50 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ElementSetIntraBondCache = void 0;
-var int_1 = require("../../../../../mol-data/int");
-var ElementSetIntraBondCache = /** @class */ (function () {
-    function ElementSetIntraBondCache() {
-        this.data = new Map();
-    }
-    ElementSetIntraBondCache.prototype.get = function (xs) {
-        var hash = int_1.SortedArray.hashCode(xs);
-        if (!this.data.has(hash))
-            return void 0;
-        for (var _i = 0, _a = this.data.get(hash); _i < _a.length; _i++) {
-            var _b = _a[_i], s = _b[0], b = _b[1];
-            if (int_1.SortedArray.areEqual(xs, s))
-                return b;
-        }
-    };
-    ElementSetIntraBondCache.prototype.set = function (xs, bonds) {
-        var hash = int_1.SortedArray.hashCode(xs);
-        if (this.data.has(hash)) {
-            var es = this.data.get(hash);
-            for (var _i = 0, es_1 = es; _i < es_1.length; _i++) {
-                var e = es_1[_i];
-                if (int_1.SortedArray.areEqual(xs, e[0])) {
-                    e[1] = bonds;
-                    return;
-                }
-            }
-            es.push([xs, bonds]);
-        }
-        else {
-            this.data.set(hash, [[xs, bonds]]);
-        }
-    };
-    ElementSetIntraBondCache.get = function (model) {
-        if (!model._dynamicPropertyData.ElementSetIntraBondCache) {
-            model._dynamicPropertyData.ElementSetIntraBondCache = new ElementSetIntraBondCache();
-        }
-        return model._dynamicPropertyData.ElementSetIntraBondCache;
-    };
-    return ElementSetIntraBondCache;
-}());
-exports.ElementSetIntraBondCache = ElementSetIntraBondCache;
-//# sourceMappingURL=element-set-intra-bond-cache.js.map