npm - molstar - Versions diffs - 3.6.0 → 3.8.0 - Mend

molstar 3.6.0 → 3.8.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (410) hide show

package/build/viewer/molstar.js.LICENSE.txt CHANGED Viewed

@@ -5,21 +5,6 @@
  * @license  MIT
  */
-/*! *****************************************************************************
-Copyright (c) Microsoft Corporation.
-Permission to use, copy, modify, and/or distribute this software for any
-purpose with or without fee is hereby granted.
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
-AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM
-LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
-OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
-PERFORMANCE OF THIS SOFTWARE.
-***************************************************************************** */
 /*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */
 /*! safe-buffer. MIT License. Feross Aboukhadijeh <https://feross.org/opensource> */

package/lib/apps/docking-viewer/index.html CHANGED Viewed

@@ -1,37 +1,37 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <title>Mol* Docking Viewer</title>
-        <style>
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            function getParam(name, regex) {
-                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
-                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-            }
-            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
-            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
-            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
-                viewer.loadStructuresFromUrlsAndMerge([
-                    { url: pdbqt, format: 'pdbqt' },
-                    { url: mol2, format: 'mol2' }
-                ]);
-            });
-        </script>
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Docking Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+            var pdbqt = getParam('pdbqt', '[^&]+').trim() || '../../examples/ace2.pdbqt';
+            var mol2 = getParam('mol2', '[^&]+').trim() || '../../examples/ace2-hit.mol2';
+            DockingViewer.create('app', [0x33DD22, 0x1133EE], true).then(viewer => {
+                viewer.loadStructuresFromUrlsAndMerge([
+                    { url: pdbqt, format: 'pdbqt' },
+                    { url: mol2, format: 'mol2' }
+                ]);
+            });
+        </script>
+    </body>
 </html>

package/lib/apps/viewer/embedded.html CHANGED Viewed

@@ -1,44 +1,44 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <link rel="icon" href="./favicon.ico" type="image/x-icon">
-        <title>Embedded Mol* Viewer</title>
-        <style>
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            molstar.Viewer.create('app', {
-                layoutIsExpanded: true,
-                layoutShowControls: false,
-                layoutShowRemoteState: false,
-                layoutShowSequence: true,
-                layoutShowLog: false,
-                layoutShowLeftPanel: true,
-                viewportShowExpand: true,
-                viewportShowSelectionMode: false,
-                viewportShowAnimation: false,
-                pdbProvider: 'rcsb',
-                emdbProvider: 'rcsb',
-            }).then(viewer => {
-                viewer.loadPdb('7bv2');
-                viewer.loadEmdb('EMD-30210', { detail: 6 });
-                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
-            });
-        </script>
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Embedded Mol* Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            molstar.Viewer.create('app', {
+                layoutIsExpanded: true,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            }).then(viewer => {
+                viewer.loadPdb('7bv2');
+                viewer.loadEmdb('EMD-30210', { detail: 6 });
+                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+            });
+        </script>
+    </body>
 </html>

package/lib/apps/viewer/index.html CHANGED Viewed

@@ -1,107 +1,107 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <link rel="icon" href="./favicon.ico" type="image/x-icon">
-        <title>Mol* Viewer</title>
-        <style>
-            * {
-                margin: 0;
-                padding: 0;
-                box-sizing: border-box;
-            }
-            html, body {
-                width: 100%;
-                height: 100%;
-                overflow: hidden;
-            }
-            hr {
-                margin: 10px;
-            }
-            h1, h2, h3, h4, h5 {
-                margin-top: 5px;
-                margin-bottom: 3px;
-            }
-            button {
-                padding: 2px;
-            }
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            function getParam(name, regex) {
-                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
-                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
-            }
-            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
-            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
-            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
-            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
-            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
-            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
-            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
-            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
-            var pickScale = getParam('pick-scale', '[^&]+').trim();
-            var pickPadding = getParam('pick-padding', '[^&]+').trim();
-            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
-            molstar.Viewer.create('app', {
-                layoutShowControls: !hideControls,
-                viewportShowExpand: false,
-                collapseLeftPanel: collapseLeftPanel,
-                pdbProvider: pdbProvider || 'pdbe',
-                emdbProvider: emdbProvider || 'pdbe',
-                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
-                    ? 'https://maps.rcsb.org'
-                    : 'https://www.ebi.ac.uk/pdbe/densities',
-                pixelScale: parseFloat(pixelScale) || 1,
-                pickScale: parseFloat(pickScale) || 0.25,
-                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
-                preferWebgl1: preferWebgl1,
-            }).then(viewer => {
-                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
-                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
-                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
-                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
-                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
-                var structureUrl = getParam('structure-url', '[^&]+').trim();
-                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
-                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
-                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
-                var pdb = getParam('pdb', '[^&]+').trim();
-                if (pdb) viewer.loadPdb(pdb);
-                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
-                if (pdbDev) viewer.loadPdbDev(pdbDev);
-                var emdb = getParam('emdb', '[^&]+').trim();
-                if (emdb) viewer.loadEmdb(emdb);
-                var afdb = getParam('afdb', '[^&]+').trim();
-                if (afdb) viewer.loadAlphaFoldDb(afdb);
-                var modelArchive = getParam('model-archive', '[^&]+').trim();
-                if (modelArchive) viewer.loadModelArchive(modelArchive);
-            });
-        </script>
-        <!-- __MOLSTAR_ANALYTICS__ -->
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Mol* Viewer</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            html, body {
+                width: 100%;
+                height: 100%;
+                overflow: hidden;
+            }
+            hr {
+                margin: 10px;
+            }
+            h1, h2, h3, h4, h5 {
+                margin-top: 5px;
+                margin-bottom: 3px;
+            }
+            button {
+                padding: 2px;
+            }
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
+            var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
+            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
+            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
+            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
+            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
+            var pickScale = getParam('pick-scale', '[^&]+').trim();
+            var pickPadding = getParam('pick-padding', '[^&]+').trim();
+            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+            molstar.Viewer.create('app', {
+                layoutShowControls: !hideControls,
+                viewportShowExpand: false,
+                collapseLeftPanel: collapseLeftPanel,
+                pdbProvider: pdbProvider || 'pdbe',
+                emdbProvider: emdbProvider || 'pdbe',
+                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
+                    ? 'https://maps.rcsb.org'
+                    : 'https://www.ebi.ac.uk/pdbe/densities',
+                pixelScale: parseFloat(pixelScale) || 1,
+                pickScale: parseFloat(pickScale) || 0.25,
+                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
+                enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
+                preferWebgl1: preferWebgl1,
+            }).then(viewer => {
+                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
+                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
+                var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
+                var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
+                if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
+                var structureUrl = getParam('structure-url', '[^&]+').trim();
+                var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim();
+                var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1';
+                if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary);
+                var pdb = getParam('pdb', '[^&]+').trim();
+                if (pdb) viewer.loadPdb(pdb);
+                var pdbDev = getParam('pdb-dev', '[^&]+').trim();
+                if (pdbDev) viewer.loadPdbDev(pdbDev);
+                var emdb = getParam('emdb', '[^&]+').trim();
+                if (emdb) viewer.loadEmdb(emdb);
+                var afdb = getParam('afdb', '[^&]+').trim();
+                if (afdb) viewer.loadAlphaFoldDb(afdb);
+                var modelArchive = getParam('model-archive', '[^&]+').trim();
+                if (modelArchive) viewer.loadModelArchive(modelArchive);
+            });
+        </script>
+        <!-- __MOLSTAR_ANALYTICS__ -->
+    </body>
 </html>

package/lib/cli/chem-comp-dict/create-ions.d.ts CHANGED Viewed

@@ -1,7 +1,8 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Josh McMenemy <josh.mcmenemy@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 export {};

package/lib/cli/chem-comp-dict/create-ions.js CHANGED Viewed

@@ -1,8 +1,9 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Josh McMenemy <josh.mcmenemy@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { __awaiter, __generator } from "tslib";
 import * as argparse from 'argparse';
@@ -25,7 +26,7 @@ function extractIonNames(ccd) {
     return ionNames;
 }
 function writeIonNamesFile(filePath, ionNames) {
-    var output = "/**\n * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-table cli\n */\n\nexport const IonNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
+    var output = "/**\n * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-ions cli\n */\n\nexport const IonNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
     writeFile(filePath, output);
 }
 function run(out, forceDownload) {

package/lib/cli/cifschema/index.js CHANGED Viewed

@@ -302,7 +302,7 @@ var MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.di
 var IHM_DIC_PATH = "".concat(DIC_DIR, "/ihm-extension.dic");
 var IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
 var MA_DIC_PATH = "".concat(DIC_DIR, "/ma-extension.dic");
-var MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/MA-dictionary/master/mmcif_ma.dic';
+var MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic';
 var CIF_CORE_DIC_PATH = "".concat(DIC_DIR, "/cif_core.dic");
 var CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic';
 var CIF_CORE_ENUM_PATH = "".concat(DIC_DIR, "/templ_enum.cif");

package/lib/cli/cifschema/util/cif-dic.js CHANGED Viewed

@@ -48,6 +48,7 @@ export function getFieldType(type, description, values, container) {
         case 'operation_expression':
         case 'point_symmetry':
         case '4x3_matrix':
+        case '3x4_matrix':
         case '3x4_matrices':
         case 'point_group':
         case 'point_group_helical':

package/lib/commonjs/cli/chem-comp-dict/create-ions.d.ts CHANGED Viewed

@@ -1,7 +1,8 @@
 #!/usr/bin/env node
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Josh McMenemy <josh.mcmenemy@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 export {};

package/lib/commonjs/cli/chem-comp-dict/create-ions.js CHANGED Viewed

@@ -1,9 +1,10 @@
 #!/usr/bin/env node
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Josh McMenemy <josh.mcmenemy@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
@@ -27,7 +28,7 @@ function extractIonNames(ccd) {
     return ionNames;
 }
 function writeIonNamesFile(filePath, ionNames) {
-    var output = "/**\n * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-table cli\n */\n\nexport const IonNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
+    var output = "/**\n * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-ions cli\n */\n\nexport const IonNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
     writeFile(filePath, output);
 }
 function run(out, forceDownload) {

package/lib/commonjs/cli/cifschema/index.js CHANGED Viewed

@@ -304,7 +304,7 @@ var MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.di
 var IHM_DIC_PATH = "".concat(DIC_DIR, "/ihm-extension.dic");
 var IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic';
 var MA_DIC_PATH = "".concat(DIC_DIR, "/ma-extension.dic");
-var MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/MA-dictionary/master/mmcif_ma.dic';
+var MA_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic';
 var CIF_CORE_DIC_PATH = "".concat(DIC_DIR, "/cif_core.dic");
 var CIF_CORE_DIC_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic';
 var CIF_CORE_ENUM_PATH = "".concat(DIC_DIR, "/templ_enum.cif");

package/lib/commonjs/cli/cifschema/util/cif-dic.js CHANGED Viewed

@@ -51,6 +51,7 @@ function getFieldType(type, description, values, container) {
         case 'operation_expression':
         case 'point_symmetry':
         case '4x3_matrix':
+        case '3x4_matrix':
         case '3x4_matrices':
         case 'point_group':
         case 'point_group_helical':

package/lib/commonjs/examples/alpha-orbitals/index.js CHANGED Viewed

@@ -30,14 +30,14 @@ var AlphaOrbitalsExample = /** @class */ (function () {
         this.currentParams = tslib_1.__assign({}, this.state.value);
     }
     AlphaOrbitalsExample.prototype.init = function (target) {
-        var _a;
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            var defaultSpec, _b;
-            return tslib_1.__generator(this, function (_c) {
-                switch (_c.label) {
+            var defaultSpec, _a;
+            var _this = this;
+            return tslib_1.__generator(this, function (_b) {
+                switch (_b.label) {
                     case 0:
                         defaultSpec = (0, spec_1.DefaultPluginUISpec)();
-                        _b = this;
+                        _a = this;
                         return [4 /*yield*/, (0, react18_1.createPluginUI)(typeof target === 'string' ? document.getElementById(target) : target, tslib_1.__assign(tslib_1.__assign({}, defaultSpec), { layout: {
                                     initial: {
                                         isExpanded: false,
@@ -56,17 +56,22 @@ var AlphaOrbitalsExample = /** @class */ (function () {
                                     [config_1.PluginConfig.Viewport.ShowAnimation, false],
                                 ] }))];
                     case 1:
-                        _b.plugin = _c.sent();
+                        _a.plugin = _b.sent();
                         this.plugin.managers.interactivity.setProps({ granularity: 'element' });
-                        if (!(0, grid3d_1.canComputeGrid3dOnGPU)((_a = this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl)) {
-                            commands_1.PluginCommands.Toast.Show(this.plugin, {
-                                title: 'Error',
-                                message: "Browser/device does not support required WebGL extension (OES_texture_float)."
-                            });
-                            return [2 /*return*/];
-                        }
-                        this.load(tslib_1.__assign({ moleculeSdf: example_data_1.DemoMoleculeSDF }, example_data_1.DemoOrbitals));
-                        (0, controls_1.mountControls)(this, document.getElementById('controls'));
+                        this.plugin.behaviors.canvas3d.initialized.subscribe(function (init) {
+                            var _a;
+                            if (!init)
+                                return;
+                            if (!(0, grid3d_1.canComputeGrid3dOnGPU)((_a = _this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.webgl)) {
+                                commands_1.PluginCommands.Toast.Show(_this.plugin, {
+                                    title: 'Error',
+                                    message: "Browser/device does not support required WebGL extension (OES_texture_float)."
+                                });
+                                return;
+                            }
+                            _this.load(tslib_1.__assign({ moleculeSdf: example_data_1.DemoMoleculeSDF }, example_data_1.DemoOrbitals));
+                            (0, controls_1.mountControls)(_this, document.getElementById('controls'));
+                        });
                         return [2 /*return*/];
                 }
             });

package/lib/commonjs/examples/proteopedia-wrapper/coloring.d.ts CHANGED Viewed

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { Color } from '../../mol-util/color';
-import { ColorTheme } from '../../mol-theme/color';
+import { ColorTheme, LocationColor } from '../../mol-theme/color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../../mol-theme/theme';
 export declare function createProteopediaCustomTheme(colors: number[]): {
@@ -16,11 +16,26 @@ export declare function createProteopediaCustomTheme(colors: number[]): {
         colors: PD.ObjectList<PD.Normalize<{
             color: Color;
         }>>;
-    }>) => ColorTheme<{
-        colors: PD.ObjectList<PD.Normalize<{
-            color: Color;
+    }>) => {
+        readonly granularity: import("../../mol-geo/geometry/color-data").ColorTypeLocation;
+        readonly color: LocationColor;
+    } & {
+        readonly factory: ColorTheme.Factory<{
+            colors: PD.ObjectList<PD.Normalize<{
+                color: Color;
+            }>>;
+        }, import("../../mol-geo/geometry/color-data").ColorTypeLocation>;
+        readonly props: Readonly<PD.Values<{
+            colors: PD.ObjectList<PD.Normalize<{
+                color: Color;
+            }>>;
         }>>;
-    }>;
+        readonly palette?: Readonly<ColorTheme.Palette> | undefined;
+        readonly preferSmoothing?: boolean | undefined;
+        readonly contextHash?: number | undefined;
+        readonly description?: string | undefined;
+        readonly legend?: Readonly<import("../../mol-util/legend").TableLegend | import("../../mol-util/legend").ScaleLegend> | undefined;
+    };
     getParams: (ctx: ThemeDataContext) => {
         colors: PD.ObjectList<PD.Normalize<{
             color: Color;

package/lib/commonjs/extensions/anvil/behavior.d.ts CHANGED Viewed

@@ -42,7 +42,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
-    allowTransparentBackfaces: boolean;
+    transparentBackfaces: string;
     bumpFrequency: number;
     bumpAmplitude: number;
 }>>;