molstar 3.8.2 → 3.10.0

package/lib/mol-plugin-state/formats/volume.js

@@ -1,8 +1,9 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Aliaksei Chareshneu <chareshneu.tech@gmail.com>
  */
 import { __awaiter, __generator, __spreadArray } from "tslib";
 import { StateTransforms } from '../transforms';
@@ -243,35 +244,41 @@ export var DscifProvider = DataFormatProvider({
     },
     parse: function (plugin, data, params) { return __awaiter(void 0, void 0, void 0, function () {
         var cifCell, b, blocks, volumes, i, _i, blocks_1, block, entryId, _a, volumes_1, v;
-        return __generator(this, function (_b) {
-            switch (_b.label) {
+        var _b;
+        return __generator(this, function (_c) {
+            switch (_c.label) {
                 case 0: return [4 /*yield*/, plugin.build().to(data).apply(StateTransforms.Data.ParseCif).commit()];
                 case 1:
-                    cifCell = _b.sent();
+                    cifCell = _c.sent();
                     b = plugin.build().to(cifCell);
-                    blocks = cifCell.obj.data.blocks.slice(1);
-                    if (blocks.length !== 1 && blocks.length !== 2)
-                        throw new Error('unknown number of blocks');
+                    blocks = cifCell.obj.data.blocks;
+                    if (blocks.length === 0)
+                        throw new Error('no data blocks');
                     volumes = [];
                     i = 0;
                     for (_i = 0, blocks_1 = blocks; _i < blocks_1.length; _i++) {
                         block = blocks_1[_i];
+                        // Skip "server" data block.
+                        if (block.header.toUpperCase() === 'SERVER')
+                            continue;
                         entryId = Array.isArray(params === null || params === void 0 ? void 0 : params.entryId) ? params === null || params === void 0 ? void 0 : params.entryId[i] : params === null || params === void 0 ? void 0 : params.entryId;
-                        volumes.push(b.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId: entryId }).selector);
-                        i++;
+                        if (((_b = block.categories['volume_data_3d_info']) === null || _b === void 0 ? void 0 : _b.rowCount) > 0) {
+                            volumes.push(b.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId: entryId }).selector);
+                            i++;
+                        }
                     }
                     return [4 /*yield*/, b.commit()];
                 case 2:
-                    _b.sent();
+                    _c.sent();
                     _a = 0, volumes_1 = volumes;
-                    _b.label = 3;
+                    _c.label = 3;
                 case 3:
                     if (!(_a < volumes_1.length)) return [3 /*break*/, 6];
                     v = volumes_1[_a];
                     return [4 /*yield*/, tryObtainRecommendedIsoValue(plugin, v.data)];
                 case 4:
-                    _b.sent();
-                    _b.label = 5;
+                    _c.sent();
+                    _c.label = 5;
                 case 5:
                     _a++;
                     return [3 /*break*/, 3];

package/lib/mol-plugin-state/helpers/structure-selection-query.js

@@ -221,7 +221,7 @@ var helix = StructureSelectionQuery('Helix', MS.struct.modifier.union([
         'entity-test': _proteinEntityTest,
         'residue-test': MS.core.flags.hasAny([
             MS.ammp('secondaryStructureFlags'),
-            MS.core.type.bitflags([2 /* Helix */])
+            MS.core.type.bitflags([2 /* SecondaryStructureType.Flag.Helix */])
         ])
     })
 ]), {
@@ -235,7 +235,7 @@ var beta = StructureSelectionQuery('Beta Strand/Sheet', MS.struct.modifier.union
         'entity-test': _proteinEntityTest,
         'residue-test': MS.core.flags.hasAny([
             MS.ammp('secondaryStructureFlags'),
-            MS.core.type.bitflags([4 /* Beta */])
+            MS.core.type.bitflags([4 /* SecondaryStructureType.Flag.Beta */])
         ])
     })
 ]), {
@@ -338,7 +338,7 @@ var ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', MS.st
                 'bond-test': MS.core.flags.hasAny([
                     MS.struct.bondProperty.flags(),
                     MS.core.type.bitflags([
-                        1 /* Covalent */ | 2 /* MetallicCoordination */
+                        1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
                     ])
                 ])
             })
@@ -382,7 +382,7 @@ var disulfideBridges = StructureSelectionQuery('Disulfide Bridges', MS.struct.mo
                     MS.struct.generator.bondedAtomicPairs({
                         0: MS.core.flags.hasAny([
                             MS.struct.bondProperty.flags(),
-                            MS.core.type.bitflags([8 /* Disulfide */])
+                            MS.core.type.bitflags([8 /* BondType.Flag.Disulfide */])
                         ])
                     })
                 ])
@@ -500,7 +500,7 @@ var covalentlyOrMetallicBonded = StructureSelectionQuery('Residues with Cov. or
         'bond-test': MS.core.flags.hasAny([
             MS.struct.bondProperty.flags(),
             MS.core.type.bitflags([
-                1 /* Covalent */ | 2 /* MetallicCoordination */
+                1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
             ])
         ])
     })

package/lib/mol-plugin-state/transforms/representation.js

@@ -657,7 +657,7 @@ var ClippingStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn({
         }, function (e) { return "".concat(Clipping.Groups.toNames(e.groups).length, " group(s)"); }, {
             defaultValue: [{
                     script: Script('(sel.atom.all)', 'mol-script'),
-                    groups: 0 /* None */,
+                    groups: 0 /* Clipping.Groups.Flag.None */,
                 }]
         }),
     }); }
@@ -705,7 +705,7 @@ var ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn({
         }, function (e) { return "".concat(Clipping.Groups.toNames(e.groups).length, " group(s)"); }, {
             defaultValue: [{
                     bundle: StructureElement.Bundle.Empty,
-                    groups: 0 /* None */,
+                    groups: 0 /* Clipping.Groups.Flag.None */,
                 }],
             isHidden: true
         }),

package/lib/mol-plugin-ui/controls/parameters.d.ts

@@ -94,7 +94,7 @@ export declare class LineGraphControl extends React.PureComponent<ParamProps<PD.
         isOverPoint: boolean;
         message: string;
     };
-    onHover: (point?: Vec2 | undefined) => void;
+    onHover: (point?: Vec2) => void;
     onDrag: (point: Vec2) => void;
     onChange: (value: PD.LineGraph['defaultValue']) => void;
     toggleExpanded: (e: React.MouseEvent<HTMLButtonElement>) => void;

package/lib/mol-plugin-ui/controls.js

@@ -74,7 +74,7 @@ var TrajectoryViewportControls = /** @class */ (function (_super) {
     };
     TrajectoryViewportControls.prototype.render = function () {
         var isAnimating = this.plugin.behaviors.state.isAnimating.value;
-        if (!this.state.show || (isAnimating && !this.state.label))
+        if (!this.state.show || (isAnimating && !this.state.label) || !this.plugin.config.get(PluginConfig.Viewport.ShowTrajectoryControls))
             return null;
         return _jsxs("div", __assign({ className: 'msp-traj-controls' }, { children: [!isAnimating && _jsx(IconButton, { svg: SkipPreviousSvg, title: 'First Model', onClick: this.reset, disabled: isAnimating }), !isAnimating && _jsx(IconButton, { svg: NavigateBeforeSvg, title: 'Previous Model', onClick: this.prev, disabled: isAnimating }), !isAnimating && _jsx(IconButton, { svg: NavigateNextSvg, title: 'Next Model', onClick: this.next, disabled: isAnimating }), !!this.state.label && _jsx("span", { children: this.state.label })] }));
     };

package/lib/mol-plugin-ui/sequence/polymer.js

@@ -94,7 +94,7 @@ function createResidueQuery(chainGroupId, operatorName, label_seq_id) {
                 SP.unit.operator_name(ctx.element) === operatorName);
         },
         residueTest: function (ctx) {
-            if (ctx.element.unit.kind === 0 /* Atomic */) {
+            if (ctx.element.unit.kind === 0 /* Unit.Kind.Atomic */) {
                 return SP.residue.label_seq_id(ctx.element) === label_seq_id;
             }
             else {

package/lib/mol-plugin-ui/sequence/sequence.js

@@ -93,7 +93,7 @@ var Sequence = /** @class */ (function (_super) {
                 _this.lastMouseOverSeqIdx = seqIdx;
                 if (_this.mouseDownLoci !== undefined) {
                     var loci = _this.getLoci(seqIdx);
-                    _this.hover(loci, 0 /* None */, 0 /* None */, __assign(__assign({}, modifiers), { shift: true }));
+                    _this.hover(loci, 0 /* ButtonsType.Flag.None */, 0 /* ButtonsType.Flag.None */, __assign(__assign({}, modifiers), { shift: true }));
                 }
                 else {
                     _this.highlightQueue.next({ seqIdx: seqIdx, buttons: buttons, button: button, modifiers: modifiers });

package/lib/mol-plugin-ui/skin/base/base.scss

@@ -1,33 +1,33 @@
-
-@mixin user-select($select) {
-  -webkit-user-select: $select;
-     -moz-user-select: $select;
-      -ms-user-select: $select; // IE10+
-          user-select: $select;
-}
-
-.msp-plugin {
-    font-family: "Helvetica Neue", "Segoe UI", Helvetica, "Source Sans Pro", Arial, sans-serif;
-    font-size: 14px;
-    line-height: 1.42857143;
-
-    position: absolute;
-    left: 0;
-    top: 0;
-    right: 0;
-    bottom: 0;
-
-    @import 'variables';
-
-    @import "normalize";
-
-    @import 'layout';
-    @import 'ui';
-    @import 'logo';
-
-    .msp-plugin-content {
-        color: $font-color;
-    }
-
-    background: $default-background;
+
+@mixin user-select($select) {
+  -webkit-user-select: $select;
+     -moz-user-select: $select;
+      -ms-user-select: $select; // IE10+
+          user-select: $select;
+}
+
+.msp-plugin {
+    font-family: "Helvetica Neue", "Segoe UI", Helvetica, "Source Sans Pro", Arial, sans-serif;
+    font-size: 14px;
+    line-height: 1.42857143;
+
+    position: absolute;
+    left: 0;
+    top: 0;
+    right: 0;
+    bottom: 0;
+
+    @import 'variables';
+
+    @import "normalize";
+
+    @import 'layout';
+    @import 'ui';
+    @import 'logo';
+
+    .msp-plugin-content {
+        color: $font-color;
+    }
+
+    background: $default-background;
 }