molstar 3.0.0 → 3.0.1

package/lib/commonjs/cli/cifschema/util/schema.d.ts

@@ -1,70 +0,0 @@
-/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export interface Database {
-    tables: {
-        [tableName: string]: Table;
-    };
-    aliases: {
-        [path: string]: string[];
-    };
-}
-export interface Table {
-    description: string;
-    key: Set<string>;
-    columns: {
-        [columnName: string]: Column;
-    };
-}
-export declare type Column = IntCol | StrCol | FloatCol | CoordCol | EnumCol | VectorCol | MatrixCol | ListCol;
-declare type BaseCol = {
-    description: string;
-};
-export declare type IntCol = {
-    type: 'int';
-} & BaseCol;
-export declare function IntCol(description: string): IntCol;
-export declare type StrCol = {
-    type: 'str';
-} & BaseCol;
-export declare function StrCol(description: string): StrCol;
-export declare type FloatCol = {
-    type: 'float';
-} & BaseCol;
-export declare function FloatCol(description: string): FloatCol;
-export declare type CoordCol = {
-    type: 'coord';
-} & BaseCol;
-export declare function CoordCol(description: string): CoordCol;
-export declare type EnumCol = {
-    type: 'enum';
-    subType: 'int' | 'str';
-    values: string[];
-} & BaseCol;
-export declare function EnumCol(values: string[], subType: 'int' | 'str', description: string): EnumCol;
-export declare type VectorCol = {
-    type: 'vector';
-    length: number;
-} & BaseCol;
-export declare function VectorCol(length: number, description: string): VectorCol;
-export declare type MatrixCol = {
-    type: 'matrix';
-    rows: number;
-    columns: number;
-} & BaseCol;
-export declare function MatrixCol(columns: number, rows: number, description: string): MatrixCol;
-export declare type ListCol = {
-    type: 'list';
-    subType: 'int' | 'str' | 'float' | 'coord';
-    separator: string;
-} & BaseCol;
-export declare function ListCol(subType: 'int' | 'str' | 'float' | 'coord', separator: string, description: string): ListCol;
-export declare type Filter = {
-    [table: string]: {
-        [column: string]: true;
-    };
-};
-export declare function mergeFilters(...filters: Filter[]): Filter;
-export {};

package/lib/commonjs/cli/cifschema/util/schema.js

@@ -1,64 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017-2019 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.mergeFilters = exports.ListCol = exports.MatrixCol = exports.VectorCol = exports.EnumCol = exports.CoordCol = exports.FloatCol = exports.StrCol = exports.IntCol = void 0;
-function IntCol(description) { return { type: 'int', description: description }; }
-exports.IntCol = IntCol;
-function StrCol(description) { return { type: 'str', description: description }; }
-exports.StrCol = StrCol;
-function FloatCol(description) { return { type: 'float', description: description }; }
-exports.FloatCol = FloatCol;
-function CoordCol(description) { return { type: 'coord', description: description }; }
-exports.CoordCol = CoordCol;
-function EnumCol(values, subType, description) {
-    return { type: 'enum', description: description, values: values, subType: subType };
-}
-exports.EnumCol = EnumCol;
-function VectorCol(length, description) {
-    return { type: 'vector', description: description, length: length };
-}
-exports.VectorCol = VectorCol;
-function MatrixCol(columns, rows, description) {
-    return { type: 'matrix', description: description, columns: columns, rows: rows };
-}
-exports.MatrixCol = MatrixCol;
-function ListCol(subType, separator, description) {
-    return { type: 'list', description: description, separator: separator, subType: subType };
-}
-exports.ListCol = ListCol;
-function mergeFilters() {
-    var filters = [];
-    for (var _i = 0; _i < arguments.length; _i++) {
-        filters[_i] = arguments[_i];
-    }
-    var n = filters.length;
-    var mergedFilter = {};
-    var fields = new Map();
-    filters.forEach(function (filter) {
-        Object.keys(filter).forEach(function (category) {
-            Object.keys(filter[category]).forEach(function (field) {
-                var key = "".concat(category, ".").concat(field);
-                var value = fields.get(key) || 0;
-                fields.set(key, value + 1);
-            });
-        });
-    });
-    fields.forEach(function (v, k) {
-        if (v !== n)
-            return;
-        var _a = k.split('.'), categoryName = _a[0], fieldName = _a[1];
-        if (categoryName in mergedFilter) {
-            mergedFilter[categoryName][fieldName] = true;
-        }
-        else {
-            mergedFilter[categoryName] = { fieldName: true };
-        }
-    });
-    return mergedFilter;
-}
-exports.mergeFilters = mergeFilters;
-//# sourceMappingURL=schema.js.map

package/lib/commonjs/cli/lipid-params/index.d.ts

@@ -1,7 +0,0 @@
-#!/usr/bin/env node
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-export {};

package/lib/commonjs/cli/lipid-params/index.js

@@ -1,104 +0,0 @@
-#!/usr/bin/env node
-"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 });
-var tslib_1 = require("tslib");
-var argparse = (0, tslib_1.__importStar)(require("argparse"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var path = (0, tslib_1.__importStar)(require("path"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
-var generic_1 = require("../../mol-data/generic");
-var LIPIDS_DIR = path.resolve(__dirname, '../../../../build/lipids/');
-var MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
-var MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';
-function ensureAvailable(path, url) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var name_1, data, _a, _b, _c;
-        return (0, tslib_1.__generator)(this, function (_d) {
-            switch (_d.label) {
-                case 0:
-                    if (!(FORCE_DOWNLOAD || !fs.existsSync(path))) return [3 /*break*/, 3];
-                    name_1 = url.substr(url.lastIndexOf('/') + 1);
-                    console.log("downloading ".concat(name_1, "..."));
-                    return [4 /*yield*/, (0, node_fetch_1.default)(url)];
-                case 1:
-                    data = _d.sent();
-                    if (!fs.existsSync(LIPIDS_DIR)) {
-                        fs.mkdirSync(LIPIDS_DIR);
-                    }
-                    _b = (_a = fs).writeFileSync;
-                    _c = [path];
-                    return [4 /*yield*/, data.text()];
-                case 2:
-                    _b.apply(_a, _c.concat([_d.sent()]));
-                    console.log("done downloading ".concat(name_1));
-                    _d.label = 3;
-                case 3: return [2 /*return*/];
-            }
-        });
-    });
-}
-function ensureLipidsAvailable() {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () { return (0, tslib_1.__generator)(this, function (_a) {
-        switch (_a.label) {
-            case 0: return [4 /*yield*/, ensureAvailable(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL)];
-            case 1:
-                _a.sent();
-                return [2 /*return*/];
-        }
-    }); });
-}
-var extraLipids = ['DMPC'];
-function run(out) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var lipidsItpStr, lipids, reLipid, m, v, _i, extraLipids_1, v, lipidNames, output;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, ensureLipidsAvailable()];
-                case 1:
-                    _a.sent();
-                    lipidsItpStr = fs.readFileSync(MARTINI_LIPIDS_PATH, 'utf8');
-                    lipids = generic_1.UniqueArray.create();
-                    reLipid = /\[moleculetype\]\n; molname      nrexcl\n +([a-zA-Z]{3,5})/g;
-                    while ((m = reLipid.exec(lipidsItpStr)) !== null) {
-                        v = m[0].substr(m[0].lastIndexOf(' ') + 1);
-                        generic_1.UniqueArray.add(lipids, v, v);
-                    }
-                    for (_i = 0, extraLipids_1 = extraLipids; _i < extraLipids_1.length; _i++) {
-                        v = extraLipids_1[_i];
-                        generic_1.UniqueArray.add(lipids, v, v);
-                    }
-                    lipidNames = JSON.stringify(lipids.array);
-                    if (out) {
-                        output = "/**\n * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated lipid params file. Names extracted from Martini FF lipids itp.\n *\n * @author molstar/lipid-params cli\n */\n\nexport const LipidNames = new Set(".concat(lipidNames.replace(/"/g, "'").replace(/,/g, ', '), ");\n");
-                        fs.writeFileSync(out, output);
-                    }
-                    else {
-                        console.log(lipidNames);
-                    }
-                    return [2 /*return*/];
-            }
-        });
-    });
-}
-var parser = new argparse.ArgumentParser({
-    add_help: true,
-    description: 'Create lipid params (from martini lipids itp)'
-});
-parser.add_argument('--out', '-o', {
-    help: 'Generated lipid params output path, if not given printed to stdout'
-});
-parser.add_argument('--forceDownload', '-f', {
-    action: 'store_true',
-    help: 'Force download of martini lipids itp'
-});
-var args = parser.parse_args();
-var FORCE_DOWNLOAD = args.forceDownload;
-run(args.out || '').catch(function (e) {
-    console.error(e);
-});
-//# sourceMappingURL=index.js.map

package/lib/commonjs/cli/state-docs/index.js

@@ -1,64 +0,0 @@
-#!/usr/bin/env node
-"use strict";
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-var tslib_1 = require("tslib");
-var _ = (0, tslib_1.__importStar)(require("../../mol-plugin-state/transforms"));
-var mol_state_1 = require("../../mol-state");
-var mol_util_1 = require("../../mol-util");
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var pd_to_md_1 = require("./pd-to-md");
-var context_1 = require("../../mol-plugin/context");
-var param_definition_1 = require("../../mol-util/param-definition");
-// force the transform to be evaluated
-_.StateTransforms.Data.Download.id;
-// Empty plugin context
-var ctx = new context_1.PluginContext({
-    behaviors: []
-});
-var builder = mol_util_1.StringBuilder.create();
-function typeToString(o) {
-    if (o.length === 0)
-        return '()';
-    return o.map(function (o) { return o.name; }).join(' | ');
-}
-function writeTransformer(t) {
-    mol_util_1.StringBuilder.write(builder, "## <a name=\"".concat(t.id.replace('.', '-'), "\"></a>").concat(t.id, " :: ").concat(typeToString(t.definition.from), " -> ").concat(typeToString(t.definition.to)));
-    mol_util_1.StringBuilder.newline(builder);
-    if (t.definition.display.description) {
-        mol_util_1.StringBuilder.write(builder, "*".concat(t.definition.display.description, "*"));
-        mol_util_1.StringBuilder.newline(builder);
-    }
-    mol_util_1.StringBuilder.newline(builder);
-    if (t.definition.params) {
-        var params = t.definition.params(void 0, ctx);
-        mol_util_1.StringBuilder.write(builder, "### Parameters");
-        mol_util_1.StringBuilder.newline(builder);
-        mol_util_1.StringBuilder.write(builder, (0, pd_to_md_1.paramsToMd)(params));
-        mol_util_1.StringBuilder.newline(builder);
-        mol_util_1.StringBuilder.write(builder, "### Default Parameters");
-        mol_util_1.StringBuilder.newline(builder);
-        mol_util_1.StringBuilder.write(builder, "```js\n".concat(JSON.stringify(param_definition_1.ParamDefinition.getDefaultValues(params), null, 2), "\n```"));
-        mol_util_1.StringBuilder.newline(builder);
-    }
-    mol_util_1.StringBuilder.write(builder, '----------------------------');
-    mol_util_1.StringBuilder.newline(builder);
-}
-var transformers = mol_state_1.StateTransformer.getAll();
-mol_util_1.StringBuilder.write(builder, '# Mol* Plugin State Transformer Reference');
-mol_util_1.StringBuilder.newline(builder);
-mol_util_1.StringBuilder.newline(builder);
-transformers.forEach(function (t) {
-    mol_util_1.StringBuilder.write(builder, "* [".concat(t.id, "](#").concat(t.id.replace('.', '-'), ")"));
-    mol_util_1.StringBuilder.newline(builder);
-});
-mol_util_1.StringBuilder.newline(builder);
-mol_util_1.StringBuilder.write(builder, '----------------------------');
-mol_util_1.StringBuilder.newline(builder);
-transformers.forEach(function (t) { return writeTransformer(t); });
-fs.writeFileSync("docs/state/transforms.md", mol_util_1.StringBuilder.getString(builder));
-//# sourceMappingURL=index.js.map

package/lib/commonjs/cli/state-docs/pd-to-md.js

@@ -1,80 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 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.paramsToMd = void 0;
-var param_definition_1 = require("../../mol-util/param-definition");
-function paramsToMd(params) {
-    return getParams(params, 0);
-}
-exports.paramsToMd = paramsToMd;
-function paramInfo(param, offset) {
-    switch (param.type) {
-        case 'value': return 'Value';
-        case 'boolean': return 'true/false';
-        case 'number': return 'Numeric value';
-        case 'converted': return paramInfo(param.converted, offset);
-        case 'conditioned': return getParams(param.conditionParams, offset);
-        case 'multi-select': return "Array of ".concat(oToS(param.options));
-        case 'color': return 'Color as 0xrrggbb';
-        case 'color-list': return "A list of colors as 0xrrggbb";
-        case 'vec3': return "3D vector [x, y, z]";
-        case 'mat4': return "4x4 transformation matrix";
-        case 'url': return "URL couple with unique identifier";
-        case 'file': return "JavaScript File Handle";
-        case 'file-list': return "JavaScript FileList Handle";
-        case 'select': return "One of ".concat(oToS(param.options));
-        case 'value-ref': return "Reference to a runtime defined value.";
-        case 'data-ref': return "Reference to a computed data value.";
-        case 'text': return 'String';
-        case 'interval': return "Interval [min, max]";
-        case 'group': return "Object with:\n".concat(getParams(param.params, offset + 2));
-        case 'mapped': return "Object { name: string, params: object } where name+params are:\n".concat(getMapped(param, offset + 2));
-        case 'line-graph': return "A list of 2d vectors [xi, yi][]";
-        case 'object-list': return "Array of\n".concat(paramInfo(param_definition_1.ParamDefinition.Group(param.element), offset + 2));
-        // TODO: support more languages
-        case 'script': return "An expression in the specified language { language: 'mol-script', expressiong: string }";
-        default:
-            var _ = param;
-            console.warn("".concat(_, " has no associated UI component"));
-            return '';
-    }
-}
-function oToS(options) {
-    return options.map(function (o) { return "'".concat(o[0], "'"); }).join(', ');
-}
-function offsetS(n) {
-    return new Array(n + 1).join(' ') + '- ';
-}
-function getMapped(param, offset) {
-    var ret = '';
-    for (var _i = 0, _a = param.select.options; _i < _a.length; _i++) {
-        var n = _a[_i][0];
-        ret += offsetS(offset);
-        ret += "**".concat(n, "**:\n");
-        ret += paramInfo(param.map(n), offset + 2);
-        ret += '\n';
-    }
-    return ret;
-}
-function getParams(params, offset) {
-    var ret = '';
-    for (var _i = 0, _a = Object.keys(params); _i < _a.length; _i++) {
-        var k = _a[_i];
-        var param = params[k];
-        ret += offsetS(offset);
-        ret += "**".concat(k, "**").concat(param.isOptional ? '?:' : ':', " ").concat(paramInfo(param, offset));
-        // if (param.defaultValue) {
-        //     ret += ` = ${JSON.stringify(param.defaultValue)}`;
-        // }
-        if (param.description) {
-            ret += " *(".concat(param.description, ")*");
-        }
-        ret += '\n';
-    }
-    return ret;
-}
-//# sourceMappingURL=pd-to-md.js.map

package/lib/commonjs/cli/structure-info/helpers.d.ts

@@ -1,7 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-export declare function openCif(path: string): Promise<import("../../mol-io/reader/cif").CifFile>;
-export declare function downloadCif(url: string, isBinary: boolean): Promise<import("../../mol-io/reader/cif").CifFile>;

package/lib/commonjs/cli/structure-info/helpers.js

@@ -1,92 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018 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.downloadCif = exports.openCif = void 0;
-var tslib_1 = require("tslib");
-var util = (0, tslib_1.__importStar)(require("util"));
-var fs = (0, tslib_1.__importStar)(require("fs"));
-var node_fetch_1 = (0, tslib_1.__importDefault)(require("node-fetch"));
-require('util.promisify').shim();
-var cif_1 = require("../../mol-io/reader/cif");
-var mol_task_1 = require("../../mol-task");
-var readFileAsync = util.promisify(fs.readFile);
-function readFile(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var input, data, i;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    if (!path.match(/\.bcif$/)) return [3 /*break*/, 2];
-                    return [4 /*yield*/, readFileAsync(path)];
-                case 1:
-                    input = _a.sent();
-                    data = new Uint8Array(input.byteLength);
-                    for (i = 0; i < input.byteLength; i++)
-                        data[i] = input[i];
-                    return [2 /*return*/, data];
-                case 2: return [2 /*return*/, readFileAsync(path, 'utf8')];
-            }
-        });
-    });
-}
-function parseCif(data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var comp, parsed;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    comp = cif_1.CIF.parse(data);
-                    return [4 /*yield*/, comp.run(function (p) { return console.log(mol_task_1.Progress.format(p)); }, 250)];
-                case 1:
-                    parsed = _a.sent();
-                    if (parsed.isError)
-                        throw parsed;
-                    return [2 /*return*/, parsed.result];
-            }
-        });
-    });
-}
-function openCif(path) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var data;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, readFile(path)];
-                case 1:
-                    data = _a.sent();
-                    return [2 /*return*/, parseCif(data)];
-            }
-        });
-    });
-}
-exports.openCif = openCif;
-function downloadCif(url, isBinary) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var data, _a, _b, _c;
-        return (0, tslib_1.__generator)(this, function (_d) {
-            switch (_d.label) {
-                case 0: return [4 /*yield*/, (0, node_fetch_1.default)(url)];
-                case 1:
-                    data = _d.sent();
-                    _a = parseCif;
-                    if (!isBinary) return [3 /*break*/, 3];
-                    _c = Uint8Array.bind;
-                    return [4 /*yield*/, data.arrayBuffer()];
-                case 2:
-                    _b = new (_c.apply(Uint8Array, [void 0, _d.sent()]))();
-                    return [3 /*break*/, 5];
-                case 3: return [4 /*yield*/, data.text()];
-                case 4:
-                    _b = _d.sent();
-                    _d.label = 5;
-                case 5: return [2 /*return*/, _a.apply(void 0, [_b])];
-            }
-        });
-    });
-}
-exports.downloadCif = downloadCif;
-//# sourceMappingURL=helpers.js.map