npm - molstar - Versions diffs - 3.26.0 → 3.28.0 - Mend

molstar 3.26.0 → 3.28.0

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 (499) 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;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
     ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
@@ -34,6 +35,7 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
     ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{

package/lib/apps/docking-viewer/viewport.js CHANGED Viewed

@@ -40,6 +40,7 @@ function occlusionStyle(plugin) {
                         scale: 1.0,
                         threshold: 0.33,
                         color: Color(0x0000),
+                        includeTransparent: true,
                     } }, shadow: { name: 'off', params: {} } })
         } });
 }

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

@@ -23,7 +23,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "backgrounds" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    extensions: ("cellpack" | "g3d" | "volseg" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "backgrounds" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -54,6 +54,7 @@ declare const DefaultViewerOptions: {
     pdbProvider: "rcsb" | "pdbe" | "pdbj" | undefined;
     emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
     saccharideCompIdMapType: SaccharideCompIdMapType;
+    volumesAndSegmentationsDefaultServer: string | undefined;
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 export declare class Viewer {
@@ -211,6 +212,7 @@ export interface LoadTrajectoryParams {
 }
 export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
     ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{

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

@@ -9,6 +9,7 @@ import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
 import { CellPack } from '../../extensions/cellpack';
 import { DnatcoConfalPyramids } from '../../extensions/dnatco';
 import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { Volseg, VolsegVolumeServerConfig } from '../../extensions/volumes-and-segmentations';
 import { GeometryExport } from '../../extensions/geo-export';
 import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
@@ -41,6 +42,7 @@ var CustomFormats = [
     ['g3d', G3dProvider]
 ];
 var Extensions = {
+    'volseg': PluginSpec.Behavior(Volseg),
     'backgrounds': PluginSpec.Behavior(Backgrounds),
     'cellpack': PluginSpec.Behavior(CellPack),
     'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
@@ -88,6 +90,7 @@ var DefaultViewerOptions = {
     pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
     saccharideCompIdMapType: 'default',
+    volumesAndSegmentationsDefaultServer: VolsegVolumeServerConfig.DefaultServer.defaultValue,
 };
 var Viewer = /** @class */ (function () {
     function Viewer(plugin) {
@@ -155,6 +158,7 @@ var Viewer = /** @class */ (function () {
                                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                                 [PluginConfig.Structure.DefaultRepresentationPreset, ViewerAutoPreset.id],
                                 [PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
+                                [VolsegVolumeServerConfig.DefaultServer, o.volumesAndSegmentationsDefaultServer],
                             ]
                         };
                         element = typeof elementOrId === 'string'

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

@@ -1,53 +1,53 @@
-<!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' } } })
-                // viewer.loadStructureFromUrl('my url', 'pdb', false, {
-                //     representationParams: {
-                //         theme: {
-                //             globalName: 'uniform',
-                //             globalColorParams: { value: 0xff0000 }
-                //         }
-                //     },
-                //     label: 'my structure'
-                // });
-            });
-        </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' } } })
+                // viewer.loadStructureFromUrl('my url', 'pdb', false, {
+                //     representationParams: {
+                //         theme: {
+                //             globalName: 'uniform',
+                //             globalColorParams: { value: 0xff0000 }
+                //         }
+                //     },
+                //     label: 'my structure'
+                // });
+            });
+        </script>
+    </body>
 </html>

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

@@ -1,116 +1,116 @@
-<!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);
-            var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
-            if (timingMode) molstar.setTimingMode(timingMode);
-            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 enableDpoit = getParam('enable-dpoit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
-            var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
-            var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
-            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 || enableDpoit) ? false : void 0, // use default value if disable-wboit is not set
-                enableDpoit: enableDpoit ? true : void 0,
-                preferWebgl1: preferWebgl1,
-                allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
-                powerPreference: powerPreference || 'high-performance',
-            }).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);
+            var timingMode = getParam('timing-mode', '[^&]+').trim() === '1';
+            if (timingMode) molstar.setTimingMode(timingMode);
+            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 enableDpoit = getParam('enable-dpoit', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+            var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
+            var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();
+            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 || enableDpoit) ? false : void 0, // use default value if disable-wboit is not set
+                enableDpoit: enableDpoit ? true : void 0,
+                preferWebgl1: preferWebgl1,
+                allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
+                powerPreference: powerPreference || 'high-performance',
+            }).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/structure-info/volume.js CHANGED Viewed

@@ -48,7 +48,7 @@ function doMesh(volume, filename) {
         var mesh, vertexCount, triangleCount, vs, ts, obj, i, i;
         return __generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, Task.create('', function (runtime) { return createVolumeIsosurfaceMesh({ runtime: runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) }); }).run()];
+                case 0: return [4 /*yield*/, Task.create('', function (runtime) { return createVolumeIsosurfaceMesh({ runtime: runtime }, volume, -1, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) }); }).run()];
                 case 1:
                     mesh = _a.sent();
                     console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });

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;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
     ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
@@ -34,6 +35,7 @@ export declare const StructurePreset: StructureRepresentationPresetProvider<{
 }>;
 export declare const IllustrativePreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
     ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{

package/lib/commonjs/apps/docking-viewer/viewport.js CHANGED Viewed

@@ -43,6 +43,7 @@ function occlusionStyle(plugin) {
                         scale: 1.0,
                         threshold: 0.33,
                         color: (0, color_1.Color)(0x0000),
+                        includeTransparent: true,
                     } }, shadow: { name: 'off', params: {} } })
         } });
 }

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

@@ -23,7 +23,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode, setTimingMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("cellpack" | "g3d" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "backgrounds" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
+    extensions: ("cellpack" | "g3d" | "volseg" | "geo-export" | "model-export" | "mp4-export" | "pdbe-structure-quality-report" | "zenodo-import" | "backgrounds" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "ma-quality-assessment")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -54,6 +54,7 @@ declare const DefaultViewerOptions: {
     pdbProvider: "rcsb" | "pdbe" | "pdbj" | undefined;
     emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
     saccharideCompIdMapType: SaccharideCompIdMapType;
+    volumesAndSegmentationsDefaultServer: string | undefined;
 };
 type ViewerOptions = typeof DefaultViewerOptions;
 export declare class Viewer {
@@ -211,6 +212,7 @@ export interface LoadTrajectoryParams {
 }
 export declare const ViewerAutoPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
     ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: import("../../mol-util/param-definition").ParamDefinition.Normalize<{

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

@@ -12,6 +12,7 @@ var behavior_1 = require("../../extensions/anvil/behavior");
 var cellpack_1 = require("../../extensions/cellpack");
 var dnatco_1 = require("../../extensions/dnatco");
 var format_1 = require("../../extensions/g3d/format");
+var volumes_and_segmentations_1 = require("../../extensions/volumes-and-segmentations");
 var geo_export_1 = require("../../extensions/geo-export");
 var behavior_2 = require("../../extensions/model-archive/quality-assessment/behavior");
 var behavior_3 = require("../../extensions/model-archive/quality-assessment/behavior");
@@ -48,6 +49,7 @@ var CustomFormats = [
     ['g3d', format_1.G3dProvider]
 ];
 var Extensions = {
+    'volseg': spec_2.PluginSpec.Behavior(volumes_and_segmentations_1.Volseg),
     'backgrounds': spec_2.PluginSpec.Behavior(backgrounds_1.Backgrounds),
     'cellpack': spec_2.PluginSpec.Behavior(cellpack_1.CellPack),
     'dnatco-confal-pyramids': spec_2.PluginSpec.Behavior(dnatco_1.DnatcoConfalPyramids),
@@ -95,6 +97,7 @@ var DefaultViewerOptions = {
     pdbProvider: config_1.PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: config_1.PluginConfig.Download.DefaultEmdbProvider.defaultValue,
     saccharideCompIdMapType: 'default',
+    volumesAndSegmentationsDefaultServer: volumes_and_segmentations_1.VolsegVolumeServerConfig.DefaultServer.defaultValue,
 };
 var Viewer = /** @class */ (function () {
     function Viewer(plugin) {
@@ -162,6 +165,7 @@ var Viewer = /** @class */ (function () {
                                 [config_1.PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
                                 [config_1.PluginConfig.Structure.DefaultRepresentationPreset, exports.ViewerAutoPreset.id],
                                 [config_1.PluginConfig.Structure.SaccharideCompIdMapType, o.saccharideCompIdMapType],
+                                [volumes_and_segmentations_1.VolsegVolumeServerConfig.DefaultServer, o.volumesAndSegmentationsDefaultServer],
                             ]
                         };
                         element = typeof elementOrId === 'string'

package/lib/commonjs/cli/structure-info/volume.js CHANGED Viewed

@@ -50,7 +50,7 @@ function doMesh(volume, filename) {
         var mesh, vertexCount, triangleCount, vs, ts, obj, i, i;
         return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, mol_task_1.Task.create('', function (runtime) { return (0, isosurface_1.createVolumeIsosurfaceMesh)({ runtime: runtime }, volume, theme_1.Theme.createEmpty(), { isoValue: volume_1.Volume.IsoValue.absolute(1.5) }); }).run()];
+                case 0: return [4 /*yield*/, mol_task_1.Task.create('', function (runtime) { return (0, isosurface_1.createVolumeIsosurfaceMesh)({ runtime: runtime }, volume, -1, theme_1.Theme.createEmpty(), { isoValue: volume_1.Volume.IsoValue.absolute(1.5) }); }).run()];
                 case 1:
                     mesh = _a.sent();
                     console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });

package/lib/commonjs/examples/lighting/index.js CHANGED Viewed

@@ -18,7 +18,7 @@ var Canvas3DPresets = {
         canvas3d: {
             postprocessing: {
                 occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
-                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: (0, color_1.Color)(0x000000) } },
+                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: (0, color_1.Color)(0x000000), includeTransparent: true, } },
                 shadow: { name: 'off', params: {} },
             },
             renderer: {

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

@@ -49,6 +49,7 @@ declare const MembraneOrientation3D: StateTransformer<PluginStateObject.Molecule
 }>>;
 export declare const MembraneOrientationPreset: StructureRepresentationPresetProvider<{
     ignoreHydrogens: boolean | undefined;
+    ignoreHydrogensVariant: "all" | "non-polar" | undefined;
     ignoreLight: boolean | undefined;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
     theme: PD.Normalize<{