npm - molstar - Versions diffs - 3.0.0 → 3.2.0 - Mend

molstar 3.0.0 → 3.2.0

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 (256) hide show

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/docking-viewer/viewport.d.ts CHANGED Viewed

@@ -9,6 +9,7 @@ import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy
 import { PluginUIComponent } from '../../mol-plugin-ui/base';
 export declare const StructurePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;
@@ -31,6 +32,7 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/apps/viewer/app.d.ts CHANGED Viewed

@@ -202,6 +202,7 @@ export interface LoadTrajectoryParams {
 }
 export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/apps/viewer/app.js CHANGED Viewed

@@ -17,6 +17,7 @@ import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { Volume } from '../../mol-model/volume';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
@@ -361,7 +362,7 @@ var Viewer = /** @class */ (function () {
                     return [2 /*return*/, update.commit()];
                 }
                 return [2 /*return*/, plugin.dataTransaction(function () { return __awaiter(_this, void 0, void 0, function () {
-                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso;
+                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso, volume, volumeData;
                         var _a, _b, _c, _d;
                         return __generator(this, function (_e) {
                             switch (_e.label) {
@@ -377,11 +378,13 @@ var Viewer = /** @class */ (function () {
                                     repr = plugin.build();
                                     for (_i = 0, isovalues_1 = isovalues; _i < isovalues_1.length; _i++) {
                                         iso = isovalues_1[_i];
+                                        volume = (_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume;
+                                        volumeData = volume.cell.obj.data;
                                         repr
-                                            .to((_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume)
+                                            .to(volume)
                                             .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data, {
                                             type: 'isosurface',
-                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
                                             color: 'uniform',
                                             colorParams: { value: iso.color }
                                         }));

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 ? true : 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 ? true : 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/commonjs/apps/docking-viewer/viewport.d.ts CHANGED Viewed

@@ -9,6 +9,7 @@ import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy
 import { PluginUIComponent } from '../../mol-plugin-ui/base';
 export declare const StructurePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;
@@ -31,6 +32,7 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/commonjs/apps/viewer/app.d.ts CHANGED Viewed

@@ -202,6 +202,7 @@ export interface LoadTrajectoryParams {
 }
 export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
         globalName: any;

package/lib/commonjs/apps/viewer/app.js CHANGED Viewed

@@ -20,8 +20,9 @@ var model_export_1 = require("../../extensions/model-export");
 var mp4_export_1 = require("../../extensions/mp4-export");
 var pdbe_1 = require("../../extensions/pdbe");
 var rcsb_1 = require("../../extensions/rcsb");
+var volume_1 = require("../../mol-model/volume");
 var structure_1 = require("../../mol-plugin-state/actions/structure");
-var volume_1 = require("../../mol-plugin-state/actions/volume");
+var volume_2 = require("../../mol-plugin-state/actions/volume");
 var representation_preset_1 = require("../../mol-plugin-state/builder/structure/representation-preset");
 var volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
 var transforms_1 = require("../../mol-plugin-state/transforms");
@@ -269,7 +270,7 @@ var Viewer = /** @class */ (function () {
     Viewer.prototype.loadEmdb = function (emdb, options) {
         var _a;
         var provider = this.plugin.config.get(config_1.PluginConfig.Download.DefaultEmdbProvider);
-        return this.plugin.runTask(this.plugin.state.data.applyAction(volume_1.DownloadDensity, {
+        return this.plugin.runTask(this.plugin.state.data.applyAction(volume_2.DownloadDensity, {
             source: {
                 name: 'pdb-emd-ds',
                 params: {
@@ -367,7 +368,7 @@ var Viewer = /** @class */ (function () {
                     return [2 /*return*/, update.commit()];
                 }
                 return [2 /*return*/, plugin.dataTransaction(function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso;
+                        var data, parsed, firstVolume, repr, _i, isovalues_1, iso, volume, volumeData;
                         var _a, _b, _c, _d;
                         return (0, tslib_1.__generator)(this, function (_e) {
                             switch (_e.label) {
@@ -383,11 +384,13 @@ var Viewer = /** @class */ (function () {
                                     repr = plugin.build();
                                     for (_i = 0, isovalues_1 = isovalues; _i < isovalues_1.length; _i++) {
                                         iso = isovalues_1[_i];
+                                        volume = (_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume;
+                                        volumeData = volume.cell.obj.data;
                                         repr
-                                            .to((_c = (_a = parsed.volumes) === null || _a === void 0 ? void 0 : _a[(_b = iso.volumeIndex) !== null && _b !== void 0 ? _b : 0]) !== null && _c !== void 0 ? _c : parsed.volume)
+                                            .to(volume)
                                             .apply(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, (0, volume_representation_params_1.createVolumeRepresentationParams)(this.plugin, firstVolume.data, {
                                             type: 'isosurface',
-                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                                            typeParams: { alpha: (_d = iso.alpha) !== null && _d !== void 0 ? _d : 1, isoValue: volume_1.Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
                                             color: 'uniform',
                                             colorParams: { value: iso.color }
                                         }));

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

@@ -47,6 +47,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
 }>>;
 export declare const MembraneOrientationPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;

package/lib/commonjs/extensions/dnatco/confal-pyramids/behavior.d.ts CHANGED Viewed

@@ -9,6 +9,7 @@ import { StructureRepresentationPresetProvider } from '../../../mol-plugin-state
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 export declare const DnatcoConfalPyramidsPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;

package/lib/commonjs/extensions/model-archive/quality-assessment/behavior.d.ts CHANGED Viewed

@@ -12,6 +12,7 @@ export declare const MAQualityAssessment: import("../../../mol-state/transformer
 }>;
 export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;
@@ -40,6 +41,7 @@ export declare const QualityAssessmentPLDDTPreset: StructureRepresentationPreset
 }>;
 export declare const QualityAssessmentQmeanPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts CHANGED Viewed

@@ -43,11 +43,12 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
 }>>;
 export declare const AssemblySymmetryPresetParams: {
     ignoreHydrogens: PD.Base<boolean | undefined>;
+    ignoreLight: PD.Base<boolean | undefined>;
     quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
     theme: PD.Base<PD.Normalize<{
-        globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+        globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
         carbonColor: "element-symbol" | "chain-id" | "operator-name" | undefined;
-        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "entity-source" | "entity-id" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
+        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "shape-group" | "uncertainty" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "entity-id" | "entity-source" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "unit-index" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "volume-value" | undefined;
         focus: PD.Normalize<{
             name: any;
             params: any;
@@ -56,6 +57,7 @@ export declare const AssemblySymmetryPresetParams: {
 };
 export declare const AssemblySymmetryPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{
         globalName: any;

package/lib/commonjs/extensions/rcsb/graphql/types.d.ts CHANGED Viewed

@@ -12854,21 +12854,21 @@ export declare type AssemblySymmetryQuery = {
         readonly rcsb_struct_symmetry?: ReadonlyArray<{
             readonly kind: string;
             readonly oligomeric_state: string;
-            readonly stoichiometry: ReadonlyArray<string | null | undefined>;
+            readonly stoichiometry: ReadonlyArray<string | null>;
             readonly symbol: string;
             readonly type: string;
             readonly clusters: ReadonlyArray<{
-                readonly avg_rmsd?: number | null | undefined;
+                readonly avg_rmsd?: number | null;
                 readonly members: ReadonlyArray<{
                     readonly asym_id: string;
-                    readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null | undefined> | null | undefined;
-                } | null | undefined>;
-            } | null | undefined>;
+                    readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null> | null;
+                } | null>;
+            } | null>;
             readonly rotation_axes?: ReadonlyArray<{
-                readonly order?: number | null | undefined;
-                readonly start: ReadonlyArray<number | null | undefined>;
-                readonly end: ReadonlyArray<number | null | undefined>;
-            } | null | undefined> | null | undefined;
-        } | null | undefined> | null | undefined;
-    } | null | undefined;
+                readonly order?: number | null;
+                readonly start: ReadonlyArray<number | null>;
+                readonly end: ReadonlyArray<number | null>;
+            } | null> | null;
+        } | null> | null;
+    } | null;
 };