molstar 2.3.5 → 2.3.9

package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone-iterator.js

@@ -1,116 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 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.CoarsePolymerBackboneIterator = exports.AtomicPolymerBackboneIterator = exports.PolymerBackboneIterator = void 0;
-var structure_1 = require("../../../../../mol-model/structure");
-var int_1 = require("../../../../../mol-data/int");
-var sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges");
-var polymer_1 = require("../polymer");
-/** Iterates over consecutive pairs of residues/coarse elements in polymers */
-function PolymerBackboneIterator(structure, unit) {
-    switch (unit.kind) {
-        case 0 /* Atomic */: return new AtomicPolymerBackboneIterator(structure, unit);
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
-            return new CoarsePolymerBackboneIterator(structure, unit);
-    }
-}
-exports.PolymerBackboneIterator = PolymerBackboneIterator;
-function createPolymerBackbonePair(structure, unit) {
-    return {
-        centerA: structure_1.StructureElement.Location.create(structure, unit),
-        centerB: structure_1.StructureElement.Location.create(structure, unit),
-    };
-}
-var AtomicPolymerBackboneIterator = /** @class */ (function () {
-    function AtomicPolymerBackboneIterator(structure, unit) {
-        this.unit = unit;
-        this.state = 0 /* nextPolymer */;
-        this.hasNext = false;
-        this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex; // can assume it won't be -1 for polymer residues
-        this.polymerIt = sorted_ranges_1.SortedRanges.transientSegments(polymer_1.getPolymerRanges(unit), unit.elements);
-        this.residueIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
-        this.value = createPolymerBackbonePair(structure, unit);
-        this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext;
-    }
-    AtomicPolymerBackboneIterator.prototype.move = function () {
-        if (this.state === 0 /* nextPolymer */) {
-            while (this.polymerIt.hasNext) {
-                this.residueIt.setSegment(this.polymerIt.move());
-                if (this.residueIt.hasNext) {
-                    this.residueSegment = this.residueIt.move();
-                    this.value.centerB.element = this.traceElementIndex[this.residueSegment.index];
-                    this.state = 2 /* nextResidue */;
-                    break;
-                }
-            }
-        }
-        if (this.state === 2 /* nextResidue */) {
-            this.residueSegment = this.residueIt.move();
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.traceElementIndex[this.residueSegment.index];
-            if (!this.residueIt.hasNext) {
-                if (this.unit.model.atomicRanges.cyclicPolymerMap.has(this.residueSegment.index)) {
-                    this.state = 3 /* cycle */;
-                }
-                else {
-                    // TODO need to advance to a polymer that has two or more residues (can't assume it has)
-                    this.state = 0 /* nextPolymer */;
-                }
-            }
-        }
-        else if (this.state === 3 /* cycle */) {
-            var cyclicPolymerMap = this.unit.model.atomicRanges.cyclicPolymerMap;
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.traceElementIndex[cyclicPolymerMap.get(this.residueSegment.index)];
-            // TODO need to advance to a polymer that has two or more residues (can't assume it has)
-            this.state = 0 /* nextPolymer */;
-        }
-        this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext || this.state === 3 /* cycle */;
-        return this.value;
-    };
-    return AtomicPolymerBackboneIterator;
-}());
-exports.AtomicPolymerBackboneIterator = AtomicPolymerBackboneIterator;
-var CoarsePolymerBackboneIterator = /** @class */ (function () {
-    function CoarsePolymerBackboneIterator(structure, unit) {
-        this.unit = unit;
-        this.state = 0 /* nextPolymer */;
-        this.hasNext = false;
-        this.polymerIt = sorted_ranges_1.SortedRanges.transientSegments(polymer_1.getPolymerRanges(unit), unit.elements);
-        this.value = createPolymerBackbonePair(structure, unit);
-        this.hasNext = this.polymerIt.hasNext;
-    }
-    CoarsePolymerBackboneIterator.prototype.move = function () {
-        if (this.state === 0 /* nextPolymer */) {
-            if (this.polymerIt.hasNext) {
-                this.polymerSegment = this.polymerIt.move();
-                this.elementIndex = this.polymerSegment.start;
-                if (this.elementIndex + 1 < this.polymerSegment.end) {
-                    this.value.centerB.element = this.unit.elements[this.elementIndex];
-                    this.state = 1 /* nextElement */;
-                }
-                else {
-                    this.state = 0 /* nextPolymer */;
-                }
-            }
-        }
-        if (this.state === 1 /* nextElement */) {
-            this.elementIndex += 1;
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.unit.elements[this.elementIndex];
-            if (this.elementIndex + 1 >= this.polymerSegment.end) {
-                this.state = 0 /* nextPolymer */;
-            }
-        }
-        this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || this.polymerIt.hasNext;
-        return this.value;
-    };
-    return CoarsePolymerBackboneIterator;
-}());
-exports.CoarsePolymerBackboneIterator = CoarsePolymerBackboneIterator;
-//# sourceMappingURL=backbone-iterator.js.map

package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone-iterator.js.map

@@ -1 +0,0 @@
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package/lib/commonjs/mol-script/util/residue-list.d.ts

@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { StructureQuery } from '../../mol-model/structure/query';
-export declare function compileResidueListSelection(input: string, idType: 'auth' | 'label'): StructureQuery;

package/lib/commonjs/mol-script/util/residue-list.js

@@ -1,63 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2021 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.compileResidueListSelection = void 0;
-var builder_1 = require("../language/builder");
-var base_1 = require("../runtime/query/base");
-function entriesToQuery(xs, kind) {
-    var _a;
-    var groups = [];
-    var asym_id_key = kind === 'auth' ? 'auth_asym_id' : 'label_asym_id';
-    var seq_id_key = kind === 'auth' ? 'auth_seq_id' : 'label_seq_id';
-    for (var _i = 0, xs_1 = xs; _i < xs_1.length; _i++) {
-        var x = xs_1[_i];
-        if (x.kind === 'range') {
-            groups.push(builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp(asym_id_key), x.asym_id]),
-                'residue-test': builder_1.MolScriptBuilder.core.rel.inRange([builder_1.MolScriptBuilder.ammp(seq_id_key), x.seq_id_beg, x.seq_id_end])
-            }));
-        }
-        else {
-            var ins_code = ((_a = x.ins_code) !== null && _a !== void 0 ? _a : '').trim();
-            groups.push(builder_1.MolScriptBuilder.struct.generator.atomGroups({
-                'chain-test': builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp(asym_id_key), x.asym_id]),
-                'residue-test': builder_1.MolScriptBuilder.core.logic.and([
-                    builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp(seq_id_key), x.seq_id]),
-                    builder_1.MolScriptBuilder.core.rel.eq([builder_1.MolScriptBuilder.ammp('pdbx_PDB_ins_code'), ins_code])
-                ])
-            }));
-        }
-    }
-    var query = builder_1.MolScriptBuilder.struct.combinator.merge(groups);
-    return base_1.compile(query);
-}
-function parseRange(c, s, e) {
-    if (!c || s.length === 0 || Number.isNaN(+s[0]))
-        return;
-    if (Number.isNaN(e)) {
-        return { kind: 'single', asym_id: c, seq_id: +s[0], ins_code: s[1] };
-    }
-    return { kind: 'range', asym_id: c, seq_id_beg: +s[0], seq_id_end: e };
-}
-function parseInsCode(e) {
-    if (!e)
-        return [];
-    return e.split(':');
-}
-function parseResidueListSelection(input) {
-    return input.split(',') // A 1-3, B 3 => [A 1-3, B 3]
-        .map(function (e) { return e.trim().split(/\s+|[-]/g).filter(function (e) { return !!e; }); }) // [A 1-3, B 3] => [[A, 1, 3], [B, 3]]
-        .map(function (e) { return parseRange(e[0], parseInsCode(e[1]), +e[2]); })
-        .filter(function (e) { return !!e; });
-}
-// parses a list of residue ranges, e.g. A 10-100, B 30, C 12:i
-function compileResidueListSelection(input, idType) {
-    var entries = parseResidueListSelection(input);
-    return entriesToQuery(entries, idType);
-}
-exports.compileResidueListSelection = compileResidueListSelection;
-//# sourceMappingURL=residue-list.js.map

package/lib/commonjs/mol-script/util/residue-list.js.map

@@ -1 +0,0 @@
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package/lib/mol-gl/shader/chunks/wboit-params.glsl.d.ts

@@ -1 +0,0 @@
-export declare const wboit_params = "\n#if defined(dRenderVariant_colorWboit)\n    #if !defined(dRenderMode_volume) && !defined(dRenderMode_isosurface)\n        uniform sampler2D tDepth;\n        uniform vec2 uDrawingBufferSize;\n\n        float getDepth(const in vec2 coords) {\n            // always packed due to merged depth from primitives and volumes\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\n    #endif\n#endif\n\nuniform bool uRenderWboit;\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n";

package/lib/mol-gl/shader/chunks/wboit-params.glsl.js

@@ -1,2 +0,0 @@
-export var wboit_params = "\n#if defined(dRenderVariant_colorWboit)\n    #if !defined(dRenderMode_volume) && !defined(dRenderMode_isosurface)\n        uniform sampler2D tDepth;\n        uniform vec2 uDrawingBufferSize;\n\n        float getDepth(const in vec2 coords) {\n            // always packed due to merged depth from primitives and volumes\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\n    #endif\n#endif\n\nuniform bool uRenderWboit;\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n";
-//# sourceMappingURL=wboit-params.glsl.js.map

package/lib/mol-gl/shader/chunks/wboit-params.glsl.js.map

@@ -1 +0,0 @@
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package/lib/mol-model/structure/model/properties/utils/guess-element.d.ts

@@ -1,6 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export declare function guessElement(str: string): string;

package/lib/mol-model/structure/model/properties/utils/guess-element.js

@@ -1,36 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-var elm1 = ['H', 'C', 'O', 'N', 'S', 'P'];
-var elm2 = ['NA', 'CL', 'FE'];
-function charAtIsNumber(str, index) {
-    var code = str.charCodeAt(index);
-    return code >= 48 && code <= 57;
-}
-export function guessElement(str) {
-    var at = str.trim().toUpperCase();
-    if (charAtIsNumber(at, 0))
-        at = at.substr(1);
-    // parse again to check for a second integer
-    if (charAtIsNumber(at, 0))
-        at = at.substr(1);
-    var n = at.length;
-    if (n === 0)
-        return '';
-    if (n === 1)
-        return at;
-    if (n === 2) {
-        if (elm2.indexOf(at) !== -1)
-            return at;
-        if (elm1.indexOf(at[0]) !== -1)
-            return at[0];
-    }
-    if (n >= 3) {
-        if (elm1.indexOf(at[0]) !== -1)
-            return at[0];
-    }
-    return '';
-}
-//# sourceMappingURL=guess-element.js.map

package/lib/mol-model/structure/model/properties/utils/guess-element.js.map

@@ -1 +0,0 @@
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package/lib/mol-model-formats/structure/mol copy.d.ts

@@ -1,17 +0,0 @@
-/**
- * Copyright (c) 2019-2020 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>
- */
-import { MolFile } from '../../mol-io/reader/mol/parser';
-import { Task } from '../../mol-task';
-import { ModelFormat } from '../format';
-import { Trajectory } from '../../mol-model/structure';
-export { MolFormat };
-declare type MolFormat = ModelFormat<MolFile>;
-declare namespace MolFormat {
-    function is(x?: ModelFormat): x is MolFormat;
-    function create(mol: MolFile): MolFormat;
-}
-export declare function trajectoryFromMol(mol: MolFile): Task<Trajectory>;

package/lib/mol-model-formats/structure/mol copy.js

@@ -1,86 +0,0 @@
-/**
- * Copyright (c) 2019-2020 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>
- */
-import { __awaiter, __generator } from "tslib";
-import { Column, Table } from '../../mol-data/db';
-import { Task } from '../../mol-task';
-import { createModels } from './basic/parser';
-import { BasicSchema, createBasic } from './basic/schema';
-import { ComponentBuilder } from './common/component';
-import { EntityBuilder } from './common/entity';
-import { IndexPairBonds } from './property/bonds/index-pair';
-function getModels(mol, ctx) {
-    return __awaiter(this, void 0, void 0, function () {
-        var atoms, bonds, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    atoms = mol.atoms, bonds = mol.bonds;
-                    MOL = Column.ofConst('MOL', mol.atoms.count, Column.Schema.str);
-                    A = Column.ofConst('A', mol.atoms.count, Column.Schema.str);
-                    type_symbol = Column.asArrayColumn(atoms.type_symbol);
-                    seq_id = Column.ofConst(1, atoms.count, Column.Schema.int);
-                    atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
-                        auth_asym_id: A,
-                        auth_atom_id: type_symbol,
-                        auth_comp_id: MOL,
-                        auth_seq_id: seq_id,
-                        Cartn_x: Column.asArrayColumn(atoms.x, Float32Array),
-                        Cartn_y: Column.asArrayColumn(atoms.y, Float32Array),
-                        Cartn_z: Column.asArrayColumn(atoms.z, Float32Array),
-                        id: Column.range(0, atoms.count - 1),
-                        label_asym_id: A,
-                        label_atom_id: type_symbol,
-                        label_comp_id: MOL,
-                        label_seq_id: seq_id,
-                        label_entity_id: Column.ofConst('1', atoms.count, Column.Schema.str),
-                        occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-                        type_symbol: type_symbol,
-                        pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
-                    }, atoms.count);
-                    entityBuilder = new EntityBuilder();
-                    entityBuilder.setNames([['MOL', 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
-                    componentBuilder = new ComponentBuilder(seq_id, type_symbol);
-                    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
-                    componentBuilder.add('MOL', 0);
-                    basics = createBasic({
-                        entity: entityBuilder.getEntityTable(),
-                        chem_comp: componentBuilder.getChemCompTable(),
-                        atom_site: atom_site
-                    });
-                    return [4 /*yield*/, createModels(basics, MolFormat.create(mol), ctx)];
-                case 1:
-                    models = _a.sent();
-                    if (models.frameCount > 0) {
-                        indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, function (x) { return x - 1; }, Int32Array));
-                        indexB = Column.ofIntArray(Column.mapToArray(bonds.atomIdxB, function (x) { return x - 1; }, Int32Array));
-                        order = Column.asArrayColumn(bonds.order, Int32Array);
-                        pairBonds = IndexPairBonds.fromData({ pairs: { indexA: indexA, indexB: indexB, order: order }, count: atoms.count });
-                        IndexPairBonds.Provider.set(models.representative, pairBonds);
-                    }
-                    return [2 /*return*/, models];
-            }
-        });
-    });
-}
-//
-export { MolFormat };
-var MolFormat;
-(function (MolFormat) {
-    function is(x) {
-        return (x === null || x === void 0 ? void 0 : x.kind) === 'mol';
-    }
-    MolFormat.is = is;
-    function create(mol) {
-        return { kind: 'mol', name: mol.title, data: mol };
-    }
-    MolFormat.create = create;
-})(MolFormat || (MolFormat = {}));
-export function trajectoryFromMol(mol) {
-    return Task.create('Parse MOL', function (ctx) { return getModels(mol, ctx); });
-}
-//# sourceMappingURL=mol%20copy.js.map

package/lib/mol-model-formats/structure/mol copy.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"mol copy.js","sourceRoot":"","sources":["../../../src/mol-model-formats/structure/mol copy.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;;AAEH,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,mBAAmB,CAAC;AAGlD,OAAO,EAAkB,IAAI,EAAE,MAAM,gBAAgB,CAAC;AACtD,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAC9C,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAC1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAEhD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAG7D,SAAe,SAAS,CAAC,GAAY,EAAE,GAAmB;;;;;;oBAC9C,KAAK,GAAY,GAAG,MAAf,EAAE,KAAK,GAAK,GAAG,MAAR,CAAS;oBAEvB,GAAG,GAAG,MAAM,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;oBAChE,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;oBAC5D,WAAW,GAAG,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC;oBACtD,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;oBAE3D,SAAS,GAAG,KAAK,CAAC,gBAAgB,CAAC,WAAW,CAAC,SAAS,EAAE;wBAC5D,YAAY,EAAE,CAAC;wBACf,YAAY,EAAE,WAAW;wBACzB,YAAY,EAAE,GAAG;wBACjB,WAAW,EAAE,MAAM;wBACnB,OAAO,EAAE,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC;wBACpD,OAAO,EAAE,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC;wBACpD,OAAO,EAAE,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC;wBACpD,EAAE,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;wBAEpC,aAAa,EAAE,CAAC;wBAChB,aAAa,EAAE,WAAW;wBAC1B,aAAa,EAAE,GAAG;wBAClB,YAAY,EAAE,MAAM;wBACpB,eAAe,EAAE,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC;wBAEpE,SAAS,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,KAAK,CAAC;wBAC9D,WAAW,aAAA;wBAEX,kBAAkB,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,KAAK,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC;qBACxE,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC;oBAEV,aAAa,GAAG,IAAI,aAAa,EAAE,CAAC;oBAC1C,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,EAAE,gBAAgB,CAAC,CAAC,CAAC,CAAC;oBACpD,aAAa,CAAC,WAAW,CAAC,KAAK,mBAAwB,GAAG,CAAC,CAAC;oBAEtD,gBAAgB,GAAG,IAAI,gBAAgB,CAAC,MAAM,EAAE,WAAW,CAAC,CAAC;oBACnE,gBAAgB,CAAC,QAAQ,CAAC,CAAC,CAAC,KAAK,EAAE,kBAAkB,CAAC,CAAC,CAAC,CAAC;oBACzD,gBAAgB,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;oBAEzB,MAAM,GAAG,WAAW,CAAC;wBACvB,MAAM,EAAE,aAAa,CAAC,cAAc,EAAE;wBACtC,SAAS,EAAE,gBAAgB,CAAC,gBAAgB,EAAE;wBAC9C,SAAS,WAAA;qBACZ,CAAC,CAAC;oBAEY,qBAAM,YAAY,CAAC,MAAM,EAAE,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,EAAA;;oBAA/D,MAAM,GAAG,SAAsD;oBAErE,IAAI,MAAM,CAAC,UAAU,GAAG,CAAC,EAAE;wBACjB,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,QAAQ,EAAE,UAAA,CAAC,IAAI,OAAA,CAAC,GAAG,CAAC,EAAL,CAAK,EAAE,UAAU,CAAC,CAAC,CAAC;wBACtF,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,QAAQ,EAAE,UAAA,CAAC,IAAI,OAAA,CAAC,GAAG,CAAC,EAAL,CAAK,EAAE,UAAU,CAAC,CAAC,CAAC;wBACtF,KAAK,GAAG,MAAM,CAAC,aAAa,CAAC,KAAK,CAAC,KAAK,EAAE,UAAU,CAAC,CAAC;wBACtD,SAAS,GAAG,cAAc,CAAC,QAAQ,CAAC,EAAE,KAAK,EAAE,EAAE,MAAM,QAAA,EAAE,MAAM,QAAA,EAAE,KAAK,OAAA,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;wBACpG,cAAc,CAAC,QAAQ,CAAC,GAAG,CAAC,MAAM,CAAC,cAAc,EAAE,SAAS,CAAC,CAAC;qBACjE;oBAED,sBAAO,MAAM,EAAC;;;;CACjB;AAED,EAAE;AAEF,OAAO,EAAE,SAAS,EAAE,CAAC;AAIrB,IAAU,SAAS,CAQlB;AARD,WAAU,SAAS;IACf,SAAgB,EAAE,CAAC,CAAe;QAC9B,OAAO,CAAA,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,IAAI,MAAK,KAAK,CAAC;IAC7B,CAAC;IAFe,YAAE,KAEjB,CAAA;IAED,SAAgB,MAAM,CAAC,GAAY;QAC/B,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,GAAG,CAAC,KAAK,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;IACvD,CAAC;IAFe,gBAAM,SAErB,CAAA;AACL,CAAC,EARS,SAAS,KAAT,SAAS,QAQlB;AAED,MAAM,UAAU,iBAAiB,CAAC,GAAY;IAC1C,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,UAAA,GAAG,IAAI,OAAA,SAAS,CAAC,GAAG,EAAE,GAAG,CAAC,EAAnB,CAAmB,CAAC,CAAC;AAChE,CAAC"}

package/lib/mol-repr/structure/visual/aromatic-ring-mesh.js

@@ -1,3 +0,0 @@
-"use strict";
-// TODO
-//# sourceMappingURL=aromatic-ring-mesh.js.map

package/lib/mol-repr/structure/visual/aromatic-ring-mesh.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"aromatic-ring-mesh.js","sourceRoot":"","sources":["../../../../src/mol-repr/structure/visual/aromatic-ring-mesh.ts"],"names":[],"mappings":";AAAA,OAAO"}

package/lib/mol-repr/structure/visual/util/polymer/backbone-iterator.d.ts

@@ -1,37 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { Unit, Structure, StructureElement } from '../../../../../mol-model/structure';
-import { Iterator } from '../../../../../mol-data/iterator';
-/** Iterates over consecutive pairs of residues/coarse elements in polymers */
-export declare function PolymerBackboneIterator(structure: Structure, unit: Unit): Iterator<PolymerBackbonePair>;
-interface PolymerBackbonePair {
-    centerA: StructureElement.Location;
-    centerB: StructureElement.Location;
-}
-export declare class AtomicPolymerBackboneIterator implements Iterator<PolymerBackbonePair> {
-    private unit;
-    private traceElementIndex;
-    private value;
-    private polymerIt;
-    private residueIt;
-    private state;
-    private residueSegment;
-    hasNext: boolean;
-    move(): PolymerBackbonePair;
-    constructor(structure: Structure, unit: Unit.Atomic);
-}
-export declare class CoarsePolymerBackboneIterator implements Iterator<PolymerBackbonePair> {
-    private unit;
-    private value;
-    private polymerIt;
-    private polymerSegment;
-    private state;
-    private elementIndex;
-    hasNext: boolean;
-    move(): PolymerBackbonePair;
-    constructor(structure: Structure, unit: Unit.Spheres | Unit.Gaussians);
-}
-export {};

package/lib/mol-repr/structure/visual/util/polymer/backbone-iterator.js

@@ -1,112 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { StructureElement } from '../../../../../mol-model/structure';
-import { Segmentation } from '../../../../../mol-data/int';
-import { SortedRanges } from '../../../../../mol-data/int/sorted-ranges';
-import { getPolymerRanges } from '../polymer';
-/** Iterates over consecutive pairs of residues/coarse elements in polymers */
-export function PolymerBackboneIterator(structure, unit) {
-    switch (unit.kind) {
-        case 0 /* Atomic */: return new AtomicPolymerBackboneIterator(structure, unit);
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
-            return new CoarsePolymerBackboneIterator(structure, unit);
-    }
-}
-function createPolymerBackbonePair(structure, unit) {
-    return {
-        centerA: StructureElement.Location.create(structure, unit),
-        centerB: StructureElement.Location.create(structure, unit),
-    };
-}
-var AtomicPolymerBackboneIterator = /** @class */ (function () {
-    function AtomicPolymerBackboneIterator(structure, unit) {
-        this.unit = unit;
-        this.state = 0 /* nextPolymer */;
-        this.hasNext = false;
-        this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex; // can assume it won't be -1 for polymer residues
-        this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
-        this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
-        this.value = createPolymerBackbonePair(structure, unit);
-        this.hasNext = this.residueIt.hasNext && this.polymerIt.hasNext;
-    }
-    AtomicPolymerBackboneIterator.prototype.move = function () {
-        if (this.state === 0 /* nextPolymer */) {
-            while (this.polymerIt.hasNext) {
-                this.residueIt.setSegment(this.polymerIt.move());
-                if (this.residueIt.hasNext) {
-                    this.residueSegment = this.residueIt.move();
-                    this.value.centerB.element = this.traceElementIndex[this.residueSegment.index];
-                    this.state = 2 /* nextResidue */;
-                    break;
-                }
-            }
-        }
-        if (this.state === 2 /* nextResidue */) {
-            this.residueSegment = this.residueIt.move();
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.traceElementIndex[this.residueSegment.index];
-            if (!this.residueIt.hasNext) {
-                if (this.unit.model.atomicRanges.cyclicPolymerMap.has(this.residueSegment.index)) {
-                    this.state = 3 /* cycle */;
-                }
-                else {
-                    // TODO need to advance to a polymer that has two or more residues (can't assume it has)
-                    this.state = 0 /* nextPolymer */;
-                }
-            }
-        }
-        else if (this.state === 3 /* cycle */) {
-            var cyclicPolymerMap = this.unit.model.atomicRanges.cyclicPolymerMap;
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.traceElementIndex[cyclicPolymerMap.get(this.residueSegment.index)];
-            // TODO need to advance to a polymer that has two or more residues (can't assume it has)
-            this.state = 0 /* nextPolymer */;
-        }
-        this.hasNext = this.residueIt.hasNext || this.polymerIt.hasNext || this.state === 3 /* cycle */;
-        return this.value;
-    };
-    return AtomicPolymerBackboneIterator;
-}());
-export { AtomicPolymerBackboneIterator };
-var CoarsePolymerBackboneIterator = /** @class */ (function () {
-    function CoarsePolymerBackboneIterator(structure, unit) {
-        this.unit = unit;
-        this.state = 0 /* nextPolymer */;
-        this.hasNext = false;
-        this.polymerIt = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
-        this.value = createPolymerBackbonePair(structure, unit);
-        this.hasNext = this.polymerIt.hasNext;
-    }
-    CoarsePolymerBackboneIterator.prototype.move = function () {
-        if (this.state === 0 /* nextPolymer */) {
-            if (this.polymerIt.hasNext) {
-                this.polymerSegment = this.polymerIt.move();
-                this.elementIndex = this.polymerSegment.start;
-                if (this.elementIndex + 1 < this.polymerSegment.end) {
-                    this.value.centerB.element = this.unit.elements[this.elementIndex];
-                    this.state = 1 /* nextElement */;
-                }
-                else {
-                    this.state = 0 /* nextPolymer */;
-                }
-            }
-        }
-        if (this.state === 1 /* nextElement */) {
-            this.elementIndex += 1;
-            this.value.centerA.element = this.value.centerB.element;
-            this.value.centerB.element = this.unit.elements[this.elementIndex];
-            if (this.elementIndex + 1 >= this.polymerSegment.end) {
-                this.state = 0 /* nextPolymer */;
-            }
-        }
-        this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || this.polymerIt.hasNext;
-        return this.value;
-    };
-    return CoarsePolymerBackboneIterator;
-}());
-export { CoarsePolymerBackboneIterator };
-//# sourceMappingURL=backbone-iterator.js.map

package/lib/mol-repr/structure/visual/util/polymer/backbone-iterator.js.map

@@ -1 +0,0 @@
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package/lib/mol-script/util/residue-list.d.ts

@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { StructureQuery } from '../../mol-model/structure/query';
-export declare function compileResidueListSelection(input: string, idType: 'auth' | 'label'): StructureQuery;

package/lib/mol-script/util/residue-list.js

@@ -1,59 +0,0 @@
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-import { MolScriptBuilder as MS } from '../language/builder';
-import { compile } from '../runtime/query/base';
-function entriesToQuery(xs, kind) {
-    var _a;
-    var groups = [];
-    var asym_id_key = kind === 'auth' ? 'auth_asym_id' : 'label_asym_id';
-    var seq_id_key = kind === 'auth' ? 'auth_seq_id' : 'label_seq_id';
-    for (var _i = 0, xs_1 = xs; _i < xs_1.length; _i++) {
-        var x = xs_1[_i];
-        if (x.kind === 'range') {
-            groups.push(MS.struct.generator.atomGroups({
-                'chain-test': MS.core.rel.eq([MS.ammp(asym_id_key), x.asym_id]),
-                'residue-test': MS.core.rel.inRange([MS.ammp(seq_id_key), x.seq_id_beg, x.seq_id_end])
-            }));
-        }
-        else {
-            var ins_code = ((_a = x.ins_code) !== null && _a !== void 0 ? _a : '').trim();
-            groups.push(MS.struct.generator.atomGroups({
-                'chain-test': MS.core.rel.eq([MS.ammp(asym_id_key), x.asym_id]),
-                'residue-test': MS.core.logic.and([
-                    MS.core.rel.eq([MS.ammp(seq_id_key), x.seq_id]),
-                    MS.core.rel.eq([MS.ammp('pdbx_PDB_ins_code'), ins_code])
-                ])
-            }));
-        }
-    }
-    var query = MS.struct.combinator.merge(groups);
-    return compile(query);
-}
-function parseRange(c, s, e) {
-    if (!c || s.length === 0 || Number.isNaN(+s[0]))
-        return;
-    if (Number.isNaN(e)) {
-        return { kind: 'single', asym_id: c, seq_id: +s[0], ins_code: s[1] };
-    }
-    return { kind: 'range', asym_id: c, seq_id_beg: +s[0], seq_id_end: e };
-}
-function parseInsCode(e) {
-    if (!e)
-        return [];
-    return e.split(':');
-}
-function parseResidueListSelection(input) {
-    return input.split(',') // A 1-3, B 3 => [A 1-3, B 3]
-        .map(function (e) { return e.trim().split(/\s+|[-]/g).filter(function (e) { return !!e; }); }) // [A 1-3, B 3] => [[A, 1, 3], [B, 3]]
-        .map(function (e) { return parseRange(e[0], parseInsCode(e[1]), +e[2]); })
-        .filter(function (e) { return !!e; });
-}
-// parses a list of residue ranges, e.g. A 10-100, B 30, C 12:i
-export function compileResidueListSelection(input, idType) {
-    var entries = parseResidueListSelection(input);
-    return entriesToQuery(entries, idType);
-}
-//# sourceMappingURL=residue-list.js.map

package/lib/mol-script/util/residue-list.js.map

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