molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js

@@ -1,117 +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.ComponentBond = void 0;
-var mmcif_1 = require("../../../../mol-io/reader/cif/schema/mmcif");
-var cif_1 = require("../../../../mol-io/writer/cif");
-var db_1 = require("../../../../mol-data/db");
-var property_1 = require("../../common/property");
-var ComponentBond;
-(function (ComponentBond) {
-    ComponentBond.Descriptor = {
-        name: 'chem_comp_bond',
-        cifExport: {
-            prefix: '',
-            categories: [{
-                    name: 'chem_comp_bond',
-                    instance: function (ctx) {
-                        var p = ComponentBond.Provider.get(ctx.firstModel);
-                        if (!p)
-                            return cif_1.CifWriter.Category.Empty;
-                        var chem_comp_bond = p.data;
-                        if (!chem_comp_bond)
-                            return cif_1.CifWriter.Category.Empty;
-                        var comp_names = ctx.structures[0].uniqueResidueNames;
-                        var comp_id = chem_comp_bond.comp_id, _rowCount = chem_comp_bond._rowCount;
-                        var indices = [];
-                        for (var i = 0; i < _rowCount; i++) {
-                            if (comp_names.has(comp_id.value(i)))
-                                indices[indices.length] = i;
-                        }
-                        return cif_1.CifWriter.Category.ofTable(chem_comp_bond, indices);
-                    }
-                }]
-        }
-    };
-    ComponentBond.Provider = property_1.FormatPropertyProvider.create(ComponentBond.Descriptor);
-    function chemCompBondFromTable(model, table) {
-        return db_1.Table.pick(table, mmcif_1.mmCIF_Schema.chem_comp_bond, function (i) {
-            return model.properties.chemicalComponentMap.has(table.comp_id.value(i));
-        });
-    }
-    ComponentBond.chemCompBondFromTable = chemCompBondFromTable;
-    function getEntriesFromChemCompBond(data) {
-        var entries = new Map();
-        function addEntry(id) {
-            // weird behavior when 'PRO' is requested - will report a single bond between N and H because a later operation would override real content
-            if (entries.has(id)) {
-                return entries.get(id);
-            }
-            var e = new Entry(id);
-            entries.set(id, e);
-            return e;
-        }
-        var comp_id = data.comp_id, atom_id_1 = data.atom_id_1, atom_id_2 = data.atom_id_2, value_order = data.value_order, pdbx_aromatic_flag = data.pdbx_aromatic_flag, _rowCount = data._rowCount;
-        var entry = addEntry(comp_id.value(0));
-        for (var i = 0; i < _rowCount; i++) {
-            var id = comp_id.value(i);
-            var nameA = atom_id_1.value(i);
-            var nameB = atom_id_2.value(i);
-            var order = value_order.value(i);
-            var aromatic = pdbx_aromatic_flag.value(i) === 'Y';
-            if (entry.id !== id) {
-                entry = addEntry(id);
-            }
-            var flags = 1 /* Covalent */;
-            var ord = 1;
-            if (aromatic)
-                flags |= 16 /* Aromatic */;
-            switch (order.toLowerCase()) {
-                case 'doub':
-                case 'delo':
-                    ord = 2;
-                    break;
-                case 'trip':
-                    ord = 3;
-                    break;
-                case 'quad':
-                    ord = 4;
-                    break;
-            }
-            entry.add(nameA, nameB, ord, flags);
-        }
-        return entries;
-    }
-    ComponentBond.getEntriesFromChemCompBond = getEntriesFromChemCompBond;
-    var Entry = /** @class */ (function () {
-        function Entry(id) {
-            this.id = id;
-            this.map = new Map();
-        }
-        Entry.prototype.add = function (a, b, order, flags, swap) {
-            if (swap === void 0) { swap = true; }
-            var e = this.map.get(a);
-            if (e !== void 0) {
-                var f = e.get(b);
-                if (f === void 0) {
-                    e.set(b, { order: order, flags: flags });
-                }
-            }
-            else {
-                var map = new Map();
-                map.set(b, { order: order, flags: flags });
-                this.map.set(a, map);
-            }
-            if (swap)
-                this.add(b, a, order, flags, false);
-        };
-        return Entry;
-    }());
-    ComponentBond.Entry = Entry;
-})(ComponentBond = exports.ComponentBond || (exports.ComponentBond = {}));
-//# sourceMappingURL=chem_comp.js.map

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js

@@ -1,62 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.IndexPairBonds = void 0;
-var tslib_1 = require("tslib");
-var graph_1 = require("../../../../mol-math/graph");
-var property_1 = require("../../common/property");
-function getGraph(indexA, indexB, props, count) {
-    var builder = new graph_1.IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
-    var key = new Int32Array(builder.slotCount);
-    var order = new Int8Array(builder.slotCount);
-    var distance = new Array(builder.slotCount);
-    var flag = new Array(builder.slotCount);
-    for (var i = 0, _i = builder.edgeCount; i < _i; i++) {
-        builder.addNextEdge();
-        builder.assignProperty(key, props.key ? props.key[i] : -1);
-        builder.assignProperty(order, props.order ? props.order[i] : 1);
-        builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
-        builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* Covalent */);
-    }
-    return builder.createGraph({ key: key, order: order, distance: distance, flag: flag });
-}
-var IndexPairBonds;
-(function (IndexPairBonds) {
-    IndexPairBonds.Descriptor = {
-        name: 'index_pair_bonds',
-    };
-    IndexPairBonds.Provider = property_1.FormatPropertyProvider.create(IndexPairBonds.Descriptor);
-    IndexPairBonds.DefaultProps = {
-        /**
-         * If negative, test using element-based threshold, otherwise distance in Angstrom.
-         *
-         * This option exists to handle bonds in periodic cells. For systems that are
-         * made from beads (as opposed to atomic elements), set to a specific distance.
-         *
-         * Note that `Data` has a `distance` field which allows specifying a distance
-         * for each bond individually which takes precedence over this option.
-         */
-        maxDistance: -1
-    };
-    function fromData(data, props) {
-        if (props === void 0) { props = {}; }
-        var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, IndexPairBonds.DefaultProps), props);
-        var pairs = data.pairs, count = data.count;
-        var indexA = pairs.indexA.toArray();
-        var indexB = pairs.indexB.toArray();
-        var key = pairs.key && pairs.key.toArray();
-        var order = pairs.order && pairs.order.toArray();
-        var distance = pairs.distance && pairs.distance.toArray();
-        var flag = pairs.flag && pairs.flag.toArray();
-        return {
-            bonds: getGraph(indexA, indexB, { key: key, order: order, distance: distance, flag: flag }, count),
-            maxDistance: p.maxDistance
-        };
-    }
-    IndexPairBonds.fromData = fromData;
-})(IndexPairBonds = exports.IndexPairBonds || (exports.IndexPairBonds = {}));
-//# sourceMappingURL=index-pair.js.map

package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js

@@ -1,167 +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.StructConn = void 0;
-var int_1 = require("../../../../mol-data/int");
-var cif_1 = require("../../../../mol-io/writer/cif");
-var bonds_1 = require("../../../../mol-model/structure/model/properties/atomic/bonds");
-var property_1 = require("../../common/property");
-var StructConn;
-(function (StructConn) {
-    StructConn.Descriptor = {
-        name: 'struct_conn',
-        cifExport: {
-            prefix: '',
-            categories: [{
-                    name: 'struct_conn',
-                    instance: function (ctx) {
-                        var p = StructConn.Provider.get(ctx.firstModel);
-                        if (!p || p.entries.length === 0)
-                            return cif_1.CifWriter.Category.Empty;
-                        var structure = ctx.structures[0];
-                        var indices = [];
-                        for (var _a = 0, _b = p.entries; _a < _b.length; _a++) {
-                            var e = _b[_a];
-                            if (hasAtom(structure, e.partnerA.atomIndex) &&
-                                hasAtom(structure, e.partnerB.atomIndex)) {
-                                indices[indices.length] = e.rowIndex;
-                            }
-                        }
-                        return cif_1.CifWriter.Category.ofTable(p.data, indices);
-                    }
-                }]
-        }
-    };
-    StructConn.Provider = property_1.FormatPropertyProvider.create(StructConn.Descriptor);
-    /**
-     * Heuristic to test if StructConn likely provides all atomic bonds by
-     * checking if the fraction of bonds and atoms is high (> 0.95).
-     */
-    function isExhaustive(model) {
-        var structConn = StructConn.Provider.get(model);
-        return !!structConn && (structConn.data.id.rowCount / model.atomicConformation.atomId.rowCount) > 0.95;
-    }
-    StructConn.isExhaustive = isExhaustive;
-    function hasAtom(_a, element) {
-        var units = _a.units;
-        for (var i = 0, _i = units.length; i < _i; i++) {
-            if (int_1.SortedArray.indexOf(units[i].elements, element) >= 0)
-                return true;
-        }
-        return false;
-    }
-    function getAtomIndexFromEntries(entries) {
-        var m = new Map();
-        for (var _a = 0, entries_1 = entries; _a < entries_1.length; _a++) {
-            var e = entries_1[_a];
-            var iA = e.partnerA.atomIndex, iB = e.partnerB.atomIndex;
-            if (m.has(iA))
-                m.get(iA).push(e);
-            else
-                m.set(iA, [e]);
-            if (m.has(iB))
-                m.get(iB).push(e);
-            else
-                m.set(iB, [e]);
-        }
-        return m;
-    }
-    StructConn.getAtomIndexFromEntries = getAtomIndexFromEntries;
-    function getEntriesFromStructConn(struct_conn, model) {
-        var conn_type_id = struct_conn.conn_type_id, pdbx_dist_value = struct_conn.pdbx_dist_value, pdbx_value_order = struct_conn.pdbx_value_order;
-        var p1 = {
-            label_asym_id: struct_conn.ptnr1_label_asym_id,
-            label_seq_id: struct_conn.ptnr1_label_seq_id,
-            auth_seq_id: struct_conn.ptnr1_auth_seq_id,
-            label_atom_id: struct_conn.ptnr1_label_atom_id,
-            label_alt_id: struct_conn.pdbx_ptnr1_label_alt_id,
-            ins_code: struct_conn.pdbx_ptnr1_PDB_ins_code,
-            symmetry: struct_conn.ptnr1_symmetry
-        };
-        var p2 = {
-            label_asym_id: struct_conn.ptnr2_label_asym_id,
-            label_seq_id: struct_conn.ptnr2_label_seq_id,
-            auth_seq_id: struct_conn.ptnr2_auth_seq_id,
-            label_atom_id: struct_conn.ptnr2_label_atom_id,
-            label_alt_id: struct_conn.pdbx_ptnr2_label_alt_id,
-            ins_code: struct_conn.pdbx_ptnr2_PDB_ins_code,
-            symmetry: struct_conn.ptnr2_symmetry
-        };
-        var _p = function (row, ps) {
-            if (ps.label_asym_id.valueKind(row) !== 0 /* Present */)
-                return void 0;
-            var asymId = ps.label_asym_id.value(row);
-            var entityIndex = model.atomicHierarchy.index.findEntity(asymId);
-            if (entityIndex < 0)
-                return void 0;
-            var residueIndex = model.atomicHierarchy.index.findResidue(model.entities.data.id.value(entityIndex), asymId, ps.auth_seq_id.value(row), ps.ins_code.value(row));
-            if (residueIndex < 0)
-                return void 0;
-            var atomName = ps.label_atom_id.value(row);
-            // turns out "mismat" records might not have atom name value
-            if (!atomName)
-                return void 0;
-            var atomIndex = model.atomicHierarchy.index.findAtomOnResidue(residueIndex, atomName, ps.label_alt_id.value(row));
-            if (atomIndex < 0)
-                return void 0;
-            return { residueIndex: residueIndex, atomIndex: atomIndex, symmetry: ps.symmetry.value(row) };
-        };
-        var entries = [];
-        for (var i = 0; i < struct_conn._rowCount; i++) {
-            var partnerA = _p(i, p1);
-            var partnerB = _p(i, p2);
-            if (partnerA === undefined || partnerB === undefined)
-                continue;
-            var type = conn_type_id.value(i);
-            var orderType = (pdbx_value_order.value(i) || '').toLowerCase();
-            var flags = 0 /* None */;
-            var order = 1;
-            switch (orderType) {
-                case 'sing':
-                    order = 1;
-                    break;
-                case 'doub':
-                    order = 2;
-                    break;
-                case 'trip':
-                    order = 3;
-                    break;
-                case 'quad':
-                    order = 4;
-                    break;
-                default:
-                    order = (0, bonds_1.getInterBondOrderFromTable)(struct_conn.ptnr1_label_comp_id.value(i), struct_conn.ptnr1_label_atom_id.value(i), struct_conn.ptnr2_label_comp_id.value(i), struct_conn.ptnr2_label_atom_id.value(i));
-            }
-            switch (type) {
-                case 'covale':
-                    flags = 1 /* Covalent */;
-                    break;
-                case 'disulf':
-                    flags = 1 /* Covalent */ | 8 /* Disulfide */;
-                    break;
-                case 'hydrog':
-                    flags = 4 /* HydrogenBond */;
-                    break;
-                case 'metalc':
-                    flags = 2 /* MetallicCoordination */;
-                    break;
-            }
-            entries.push({
-                rowIndex: i,
-                flags: flags,
-                order: order,
-                distance: pdbx_dist_value.value(i),
-                partnerA: partnerA,
-                partnerB: partnerB
-            });
-        }
-        return entries;
-    }
-    StructConn.getEntriesFromStructConn = getEntriesFromStructConn;
-})(StructConn = exports.StructConn || (exports.StructConn = {}));
-//# sourceMappingURL=struct_conn.js.map

package/lib/commonjs/mol-model-formats/structure/property/partial-charge.js

@@ -1,18 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AtomPartialCharge = void 0;
-var property_1 = require("../common/property");
-var AtomPartialCharge;
-(function (AtomPartialCharge) {
-    AtomPartialCharge.Descriptor = {
-        name: 'atom_partial_charge',
-    };
-    AtomPartialCharge.Provider = property_1.FormatPropertyProvider.create(AtomPartialCharge.Descriptor);
-})(AtomPartialCharge || (AtomPartialCharge = {}));
-exports.AtomPartialCharge = AtomPartialCharge;
-//# sourceMappingURL=partial-charge.js.map

package/lib/commonjs/mol-model-formats/structure/property/secondary-structure.js

@@ -1,190 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 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.ModelSecondaryStructure = void 0;
-var types_1 = require("../../../mol-model/structure/model/types");
-var atomic_1 = require("../../../mol-model/structure/model/properties/atomic");
-var seconday_structure_1 = require("../../../mol-model/structure/model/properties/seconday-structure");
-var property_1 = require("../common/property");
-var ModelSecondaryStructure;
-(function (ModelSecondaryStructure) {
-    ModelSecondaryStructure.Descriptor = {
-        name: 'model_secondary_structure',
-    };
-    ModelSecondaryStructure.Provider = property_1.FormatPropertyProvider.create(ModelSecondaryStructure.Descriptor);
-    function fromStruct(conf, sheetRange, hierarchy) {
-        var map = new Map();
-        var elements = [{ kind: 'none' }];
-        var coordinates = getCoordinateType(conf, sheetRange);
-        addHelices(conf, coordinates, map, elements);
-        // must add Helices 1st because of 'key' value assignment.
-        addSheets(sheetRange, coordinates, map, conf._rowCount, elements);
-        var n = hierarchy.residues._rowCount;
-        var getIndex = function (rI) { return rI; };
-        var secStruct = {
-            type: new Int32Array(n),
-            key: new Int32Array(n),
-            elements: elements
-        };
-        if (map.size > 0)
-            assignSecondaryStructureRanges(hierarchy, coordinates, map, secStruct);
-        return (0, seconday_structure_1.SecondaryStructure)(secStruct.type, secStruct.key, secStruct.elements, getIndex);
-    }
-    ModelSecondaryStructure.fromStruct = fromStruct;
-})(ModelSecondaryStructure || (ModelSecondaryStructure = {}));
-exports.ModelSecondaryStructure = ModelSecondaryStructure;
-function getCoordinateType(conf, sheetRange) {
-    if (conf._rowCount > 0) {
-        if (conf.beg_label_seq_id.valueKind(0) !== 0 /* Present */ || conf.end_label_seq_id.valueKind(0) !== 0 /* Present */)
-            return 'auth';
-    }
-    else if (sheetRange) {
-        if (sheetRange.beg_label_seq_id.valueKind(0) !== 0 /* Present */ || sheetRange.end_label_seq_id.valueKind(0) !== 0 /* Present */)
-            return 'auth';
-    }
-    return 'label';
-}
-function addHelices(cat, coordinates, map, elements) {
-    if (!cat._rowCount)
-        return;
-    var beg_label_asym_id = cat.beg_label_asym_id, beg_label_seq_id = cat.beg_label_seq_id, beg_auth_seq_id = cat.beg_auth_seq_id, pdbx_beg_PDB_ins_code = cat.pdbx_beg_PDB_ins_code;
-    var end_label_seq_id = cat.end_label_seq_id, end_auth_seq_id = cat.end_auth_seq_id, pdbx_end_PDB_ins_code = cat.pdbx_end_PDB_ins_code;
-    var pdbx_PDB_helix_class = cat.pdbx_PDB_helix_class, conf_type_id = cat.conf_type_id, details = cat.details;
-    var beg_seq_id = coordinates === 'label' ? beg_label_seq_id : beg_auth_seq_id;
-    var end_seq_id = coordinates === 'label' ? end_label_seq_id : end_auth_seq_id;
-    for (var i = 0, _i = cat._rowCount; i < _i; i++) {
-        var type = types_1.SecondaryStructureType.create(pdbx_PDB_helix_class.valueKind(i) === 0 /* Present */
-            ? types_1.SecondaryStructureType.SecondaryStructurePdb[pdbx_PDB_helix_class.value(i)]
-            : conf_type_id.valueKind(i) === 0 /* Present */
-                ? types_1.SecondaryStructureType.SecondaryStructureMmcif[conf_type_id.value(i)]
-                : 536870912 /* NA */);
-        var element = {
-            kind: 'helix',
-            flags: type,
-            type_id: conf_type_id.valueKind(i) === 0 /* Present */ ? conf_type_id.value(i) : 'HELIX_P',
-            helix_class: pdbx_PDB_helix_class.value(i),
-            details: details.valueKind(i) === 0 /* Present */ ? details.value(i) : void 0
-        };
-        var entry = {
-            startSeqId: beg_seq_id.value(i),
-            startInsCode: pdbx_beg_PDB_ins_code.value(i),
-            endSeqId: end_seq_id.value(i),
-            endInsCode: pdbx_end_PDB_ins_code.value(i),
-            type: type,
-            key: elements.length
-        };
-        elements[elements.length] = element;
-        var asymId = beg_label_asym_id.value(i);
-        if (map.has(asymId)) {
-            var entries = map.get(asymId);
-            if (entries.has(entry.startSeqId)) {
-                entries.get(entry.startSeqId).push(entry);
-            }
-            else {
-                entries.set(entry.startSeqId, [entry]);
-            }
-        }
-        else {
-            map.set(asymId, new Map([[entry.startSeqId, [entry]]]));
-        }
-    }
-}
-function addSheets(cat, coordinates, map, sheetCount, elements) {
-    if (!cat._rowCount)
-        return;
-    var beg_label_asym_id = cat.beg_label_asym_id, beg_label_seq_id = cat.beg_label_seq_id, beg_auth_seq_id = cat.beg_auth_seq_id, pdbx_beg_PDB_ins_code = cat.pdbx_beg_PDB_ins_code;
-    var end_label_seq_id = cat.end_label_seq_id, end_auth_seq_id = cat.end_auth_seq_id, pdbx_end_PDB_ins_code = cat.pdbx_end_PDB_ins_code;
-    var sheet_id = cat.sheet_id;
-    var beg_seq_id = coordinates === 'label' ? beg_label_seq_id : beg_auth_seq_id;
-    var end_seq_id = coordinates === 'label' ? end_label_seq_id : end_auth_seq_id;
-    var sheet_id_key = new Map();
-    var currentKey = sheetCount + 1;
-    for (var i = 0, _i = cat._rowCount; i < _i; i++) {
-        var id = sheet_id.value(i);
-        var key = void 0;
-        if (sheet_id_key.has(id))
-            key = sheet_id_key.get(id);
-        else {
-            key = currentKey++;
-            sheet_id_key.set(id, key);
-        }
-        var type = types_1.SecondaryStructureType.create(4 /* Beta */ | 8388608 /* BetaSheet */);
-        var element = {
-            kind: 'sheet',
-            flags: type,
-            sheet_id: id,
-            symmetry: void 0
-        };
-        var entry = {
-            startSeqId: beg_seq_id.value(i),
-            startInsCode: pdbx_beg_PDB_ins_code.value(i),
-            endSeqId: end_seq_id.value(i),
-            endInsCode: pdbx_end_PDB_ins_code.value(i),
-            type: type,
-            key: elements.length
-        };
-        elements[elements.length] = element;
-        var asymId = beg_label_asym_id.value(i);
-        if (map.has(asymId)) {
-            var entries = map.get(asymId);
-            if (entries.has(entry.startSeqId)) {
-                entries.get(entry.startSeqId).push(entry);
-            }
-            else {
-                entries.set(entry.startSeqId, [entry]);
-            }
-        }
-        else {
-            map.set(asymId, new Map([[entry.startSeqId, [entry]]]));
-        }
-    }
-    return;
-}
-function assignSecondaryStructureEntry(hierarchy, coordinates, entry, resStart, resEnd, data) {
-    var _a = hierarchy.residues, auth_seq_id = _a.auth_seq_id, label_seq_id = _a.label_seq_id, pdbx_PDB_ins_code = _a.pdbx_PDB_ins_code;
-    var endSeqId = entry.endSeqId, endInsCode = entry.endInsCode, key = entry.key, type = entry.type;
-    var seq_id = coordinates === 'label' ? label_seq_id : auth_seq_id;
-    var rI = resStart;
-    while (rI < resEnd) {
-        var seqNumber = seq_id.value(rI);
-        data.type[rI] = type;
-        data.key[rI] = key;
-        if ((seqNumber > endSeqId) ||
-            (seqNumber === endSeqId && pdbx_PDB_ins_code.value(rI) === endInsCode)) {
-            break;
-        }
-        rI++;
-    }
-}
-function assignSecondaryStructureRanges(hierarchy, coordinates, map, data) {
-    var chainCount = hierarchy.chainAtomSegments.count;
-    var label_asym_id = hierarchy.chains.label_asym_id;
-    var _a = hierarchy.residues, auth_seq_id = _a.auth_seq_id, label_seq_id = _a.label_seq_id, pdbx_PDB_ins_code = _a.pdbx_PDB_ins_code;
-    var seq_id = coordinates === 'label' ? label_seq_id : auth_seq_id;
-    for (var cI = 0; cI < chainCount; cI++) {
-        var resStart = atomic_1.AtomicHierarchy.chainStartResidueIndex(hierarchy, cI), resEnd = atomic_1.AtomicHierarchy.chainEndResidueIndexExcl(hierarchy, cI);
-        var asymId = label_asym_id.value(cI);
-        if (map.has(asymId)) {
-            var entries = map.get(asymId);
-            for (var rI = resStart; rI < resEnd; rI++) {
-                var seqId = seq_id.value(rI);
-                if (entries.has(seqId)) {
-                    var entryList = entries.get(seqId);
-                    for (var _b = 0, entryList_1 = entryList; _b < entryList_1.length; _b++) {
-                        var entry = entryList_1[_b];
-                        var insCode = pdbx_PDB_ins_code.value(rI);
-                        if (entry.startInsCode !== insCode)
-                            continue;
-                        assignSecondaryStructureEntry(hierarchy, coordinates, entry, rI, resEnd, data);
-                    }
-                }
-            }
-        }
-    }
-}
-//# sourceMappingURL=secondary-structure.js.map

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

@@ -1,77 +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.ModelSymmetry = void 0;
-var mmcif_1 = require("../../../mol-io/reader/cif/schema/mmcif");
-var geometry_1 = require("../../../mol-math/geometry");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var assembly_1 = require("./assembly");
-var property_1 = require("../common/property");
-var ModelSymmetry;
-(function (ModelSymmetry) {
-    ModelSymmetry.Descriptor = {
-        name: 'model_symmetry',
-    };
-    ModelSymmetry.Provider = property_1.FormatPropertyProvider.create(ModelSymmetry.Descriptor);
-    function fromData(data) {
-        var assemblies = (0, assembly_1.createAssemblies)(data.pdbx_struct_assembly, data.pdbx_struct_assembly_gen, data.pdbx_struct_oper_list);
-        var spacegroup = getSpacegroup(data.symmetry, data.cell);
-        var isNonStandardCrystalFrame = checkNonStandardCrystalFrame(data.atom_sites, spacegroup);
-        return { assemblies: assemblies, spacegroup: spacegroup, isNonStandardCrystalFrame: isNonStandardCrystalFrame, ncsOperators: getNcsOperators(data.struct_ncs_oper) };
-    }
-    ModelSymmetry.fromData = fromData;
-    function fromCell(size, anglesInRadians) {
-        var spaceCell = geometry_1.SpacegroupCell.create('P 1', size, anglesInRadians);
-        var spacegroup = geometry_1.Spacegroup.create(spaceCell);
-        return { assemblies: [], spacegroup: spacegroup, isNonStandardCrystalFrame: false };
-    }
-    ModelSymmetry.fromCell = fromCell;
-})(ModelSymmetry || (ModelSymmetry = {}));
-exports.ModelSymmetry = ModelSymmetry;
-function checkNonStandardCrystalFrame(atom_sites, spacegroup) {
-    if (atom_sites._rowCount === 0)
-        return false;
-    // TODO: parse atom_sites transform and check if it corresponds to the toFractional matrix
-    return false;
-}
-function getSpacegroupNameOrNumber(symmetry) {
-    var groupNumber = symmetry['Int_Tables_number'].value(0);
-    var groupName = symmetry['space_group_name_H-M'].value(0);
-    if (!symmetry['Int_Tables_number'].isDefined)
-        return groupName;
-    if (!symmetry['space_group_name_H-M'].isDefined)
-        return groupNumber;
-    return groupName;
-}
-function getSpacegroup(symmetry, cell) {
-    if (symmetry._rowCount === 0 || cell._rowCount === 0)
-        return geometry_1.Spacegroup.ZeroP1;
-    var nameOrNumber = getSpacegroupNameOrNumber(symmetry);
-    var spaceCell = geometry_1.SpacegroupCell.create(nameOrNumber, linear_algebra_1.Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)), linear_algebra_1.Vec3.scale(linear_algebra_1.Vec3.zero(), linear_algebra_1.Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
-    return geometry_1.Spacegroup.create(spaceCell);
-}
-function getNcsOperators(struct_ncs_oper) {
-    if (struct_ncs_oper._rowCount === 0)
-        return void 0;
-    var id = struct_ncs_oper.id, matrix = struct_ncs_oper.matrix, vector = struct_ncs_oper.vector;
-    var matrixSpace = mmcif_1.mmCIF_Schema.struct_ncs_oper.matrix.space, vectorSpace = mmcif_1.mmCIF_Schema.struct_ncs_oper.vector.space;
-    var opers = [];
-    for (var i = 0; i < struct_ncs_oper._rowCount; i++) {
-        var m = linear_algebra_1.Tensor.toMat3((0, linear_algebra_1.Mat3)(), matrixSpace, matrix.value(i));
-        var v = linear_algebra_1.Tensor.toVec3((0, linear_algebra_1.Vec3)(), vectorSpace, vector.value(i));
-        if (!geometry_1.SymmetryOperator.checkIfRotationAndTranslation(m, v))
-            continue;
-        // ignore non-identity 'given' NCS operators
-        if (struct_ncs_oper.code.value(i) === 'given' && !linear_algebra_1.Mat3.isIdentity(m) && !linear_algebra_1.Vec3.isZero(v))
-            continue;
-        var ncsId = id.value(i);
-        opers[opers.length] = geometry_1.SymmetryOperator.ofRotationAndOffset("ncs_".concat(ncsId), m, v, ncsId);
-    }
-    return opers;
-}
-//# sourceMappingURL=symmetry.js.map

package/lib/commonjs/mol-model-formats/structure/psf.d.ts

@@ -1,16 +0,0 @@
-/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { PsfFile } from '../../mol-io/reader/psf/parser';
-import { Topology } from '../../mol-model/structure/topology/topology';
-import { Task } from '../../mol-task';
-import { ModelFormat } from '../format';
-export { PsfFormat };
-declare type PsfFormat = ModelFormat<PsfFile>;
-declare namespace PsfFormat {
-    function is(x?: ModelFormat): x is PsfFormat;
-    function fromPsf(psf: PsfFile): PsfFormat;
-}
-export declare function topologyFromPsf(psf: PsfFile): Task<Topology>;