molstar 3.1.0 → 3.2.0

package/lib/mol-plugin-ui/skin/colors/blue.scss

@@ -1,24 +1,24 @@
-$default-background:         #2D3E50;
-$font-color:                 #EDF1F2; 
-$hover-font-color:           #3B9AD9;
-$entity-current-font-color:  #FFFFFF;
-$msp-btn-remove-background:      #BF3A31;
-$msp-btn-remove-hover-font-color:#ffffff;
-$msp-btn-commit-on-font-color:   #ffffff; 
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #2D3E50;
+$font-color:                 #EDF1F2; 
+$hover-font-color:           #3B9AD9;
+$entity-current-font-color:  #FFFFFF;
+$msp-btn-remove-background:      #BF3A31;
+$msp-btn-remove-hover-font-color:#ffffff;
+$msp-btn-commit-on-font-color:   #ffffff; 
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/dark.scss

@@ -1,24 +1,24 @@
-$default-background:         #111318;
-$font-color:                 #ccd4e0;
-$hover-font-color:           #51A2FB;
-$entity-current-font-color:  #68BEFD;
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-$msp-btn-commit-on-font-color:   #68BEFD;
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #111318;
+$font-color:                 #ccd4e0;
+$hover-font-color:           #51A2FB;
+$entity-current-font-color:  #68BEFD;
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+$msp-btn-commit-on-font-color:   #68BEFD;
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/light.scss

@@ -1,30 +1,30 @@
-// this is complement of the dark theme
-
-@function compl($color) {
-    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
-}
-
-$default-background:         compl(#111318);
-$font-color:                 compl(#ccd4e0);
-$hover-font-color:           compl(#51A2FB);
-$entity-current-font-color:  compl(#68BEFD);
-$msp-btn-commit-on-font-color:   compl(#68BEFD);
-$entity-badge-font-color:    lighten(#ccd4e0,10%);
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: compl(#111318);
-
-@function color-lower-contrast($color, $amount) {
-    @return lighten($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return darken($color, $amount);
+// this is complement of the dark theme
+
+@function compl($color) {
+    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
+}
+
+$default-background:         compl(#111318);
+$font-color:                 compl(#ccd4e0);
+$hover-font-color:           compl(#51A2FB);
+$entity-current-font-color:  compl(#68BEFD);
+$msp-btn-commit-on-font-color:   compl(#68BEFD);
+$entity-badge-font-color:    lighten(#ccd4e0,10%);
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: compl(#111318);
+
+@function color-lower-contrast($color, $amount) {
+    @return lighten($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return darken($color, $amount);
 }

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

@@ -1,2 +1,2 @@
-@import 'colors/dark';
+@import 'colors/dark';
 @import 'base/base';

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

@@ -1,2 +1,2 @@
-@import 'colors/light';
+@import 'colors/light';
 @import 'base/base';

package/lib/mol-plugin-ui/structure/superposition.d.ts

@@ -1,7 +1,8 @@
 /**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 /// <reference types="react" />
 import { CollapsableControls, PurePluginUIComponent } from '../base';
@@ -26,6 +27,7 @@ export declare class StructureSuperpositionControls extends CollapsableControls
 }
 export declare const StructureSuperpositionParams: {
     alignSequences: PD.BooleanParam;
+    traceOnly: PD.BooleanParam;
 };
 export declare type StructureSuperpositionOptions = PD.ValuesFor<typeof StructureSuperpositionParams>;
 declare type SuperpositionControlsState = {
@@ -50,6 +52,7 @@ export declare class SuperpositionControls extends PurePluginUIComponent<{}, Sup
     superposeChains: () => Promise<void>;
     superposeAtoms: () => Promise<void>;
     superposeDb: () => Promise<void>;
+    cameraReset(): Promise<void>;
     toggleByChains: () => void;
     toggleByAtoms: () => void;
     toggleOptions: () => void;

package/lib/mol-plugin-ui/structure/superposition.js

@@ -1,9 +1,10 @@
 import { __assign, __awaiter, __extends, __generator } from "tslib";
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 /**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 import { CollapsableControls, PurePluginUIComponent } from '../base';
 import { Icon, ArrowUpwardSvg, ArrowDownwardSvg, DeleteOutlinedSvg, HelpOutlineSvg, TuneSvg, SuperposeAtomsSvg, SuperposeChainsSvg, SuperpositionSvg } from '../controls/icons';
@@ -18,9 +19,9 @@ import { structureElementStatsLabel, elementLabel } from '../../mol-theme/label'
 import { ParameterControls } from '../controls/parameters';
 import { stripTags } from '../../mol-util/string';
 import { ToggleSelectionModeButton } from './selection';
-import { alignAndSuperposeWithBestDatabaseMapping } from '../../mol-model/structure/structure/util/superposition-db-mapping';
+import { alignAndSuperposeWithSIFTSMapping } from '../../mol-model/structure/structure/util/superposition-sifts-mapping';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { BestDatabaseSequenceMapping } from '../../mol-model-props/sequence/best-database-mapping';
+import { SIFTSMapping } from '../../mol-model-props/sequence/sifts-mapping';
 var StructureSuperpositionControls = /** @class */ (function (_super) {
     __extends(StructureSuperpositionControls, _super);
     function StructureSuperpositionControls() {
@@ -47,7 +48,8 @@ var StructureSuperpositionControls = /** @class */ (function (_super) {
 }(CollapsableControls));
 export { StructureSuperpositionControls };
 export var StructureSuperpositionParams = {
-    alignSequences: PD.Boolean(true, { isEssential: true, description: 'Perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    alignSequences: PD.Boolean(true, { isEssential: true, description: 'For Chain-based 3D superposition, perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    traceOnly: PD.Boolean(true, { description: 'For Chain- and Uniprot-based 3D superposition, base superposition only on CA (and equivalent) atoms.' })
 };
 var DefaultStructureSuperpositionOptions = PD.getDefaultValues(StructureSuperpositionParams);
 var SuperpositionTag = 'SuperpositionTransform';
@@ -64,14 +66,14 @@ var SuperpositionControls = /** @class */ (function (_super) {
             options: DefaultStructureSuperpositionOptions
         };
         _this.superposeChains = function () { return __awaiter(_this, void 0, void 0, function () {
-            var query, entries, traceLocis, transforms, eA, i, il, eB, _a, bTransform, rmsd, labelA, labelB;
+            var query, entries, locis, transforms, eA, i, il, eB, _a, bTransform, rmsd, labelA, labelB;
             var _this = this;
             return __generator(this, function (_b) {
                 switch (_b.label) {
                     case 0:
-                        query = StructureSelectionQueries.trace.query;
+                        query = (this.state.options.traceOnly ? StructureSelectionQueries.trace : StructureSelectionQueries.polymer).query;
                         entries = this.chainEntries;
-                        traceLocis = entries.map(function (e, i) {
+                        locis = entries.map(function (e, i) {
                             var s = StructureElement.Loci.toStructure(e.loci);
                             var loci = StructureSelection.toLociWithSourceUnits(query(new QueryContext(s)));
                             return StructureElement.Loci.remap(loci, i === 0
@@ -79,10 +81,10 @@ var SuperpositionControls = /** @class */ (function (_super) {
                                 : loci.structure.root);
                         });
                         transforms = this.state.options.alignSequences
-                            ? alignAndSuperpose(traceLocis)
-                            : superpose(traceLocis);
+                            ? alignAndSuperpose(locis)
+                            : superpose(locis);
                         eA = entries[0];
-                        i = 1, il = traceLocis.length;
+                        i = 1, il = locis.length;
                         _b.label = 1;
                     case 1:
                         if (!(i < il)) return [3 /*break*/, 4];
@@ -98,7 +100,10 @@ var SuperpositionControls = /** @class */ (function (_super) {
                     case 3:
                         ++i;
                         return [3 /*break*/, 1];
-                    case 4: return [2 /*return*/];
+                    case 4: return [4 /*yield*/, this.cameraReset()];
+                    case 5:
+                        _b.sent();
+                        return [2 /*return*/];
                 }
             });
         }); };
@@ -133,39 +138,57 @@ var SuperpositionControls = /** @class */ (function (_super) {
                     case 3:
                         ++i;
                         return [3 /*break*/, 1];
-                    case 4: return [2 /*return*/];
+                    case 4: return [4 /*yield*/, this.cameraReset()];
+                    case 5:
+                        _b.sent();
+                        return [2 /*return*/];
                 }
             });
         }); };
         _this.superposeDb = function () { return __awaiter(_this, void 0, void 0, function () {
-            var input, transforms, rmsd, _i, transforms_1, xform;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
+            var input, traceOnly, structures, _a, entries, failedPairs, zeroOverlapPairs, rmsd, _i, entries_1, xform, formatPairs;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
                     case 0:
                         input = this.plugin.managers.structure.hierarchy.behaviors.selection.value.structures;
-                        transforms = alignAndSuperposeWithBestDatabaseMapping(input.map(function (s) { var _a; return (_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data; }));
+                        traceOnly = this.state.options.traceOnly;
+                        structures = input.map(function (s) { var _a; return (_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data; });
+                        _a = alignAndSuperposeWithSIFTSMapping(structures, { traceOnly: traceOnly }), entries = _a.entries, failedPairs = _a.failedPairs, zeroOverlapPairs = _a.zeroOverlapPairs;
                         rmsd = 0;
-                        _i = 0, transforms_1 = transforms;
-                        _a.label = 1;
+                        _i = 0, entries_1 = entries;
+                        _b.label = 1;
                     case 1:
-                        if (!(_i < transforms_1.length)) return [3 /*break*/, 4];
-                        xform = transforms_1[_i];
+                        if (!(_i < entries_1.length)) return [3 /*break*/, 4];
+                        xform = entries_1[_i];
                         return [4 /*yield*/, this.transform(input[xform.other].cell, xform.transform.bTransform)];
                     case 2:
-                        _a.sent();
+                        _b.sent();
                         rmsd += xform.transform.rmsd;
-                        _a.label = 3;
+                        _b.label = 3;
                     case 3:
                         _i++;
                         return [3 /*break*/, 1];
                     case 4:
-                        rmsd /= Math.max(transforms.length - 1, 1);
-                        this.plugin.log.info("Superposed ".concat(input.length, " structures with avg. RMSD ").concat(rmsd.toFixed(2), " \u00C5."));
-                        return [4 /*yield*/, new Promise(function (res) { return requestAnimationFrame(res); })];
+                        rmsd /= Math.max(entries.length - 1, 1);
+                        formatPairs = function (pairs) {
+                            return "[".concat(pairs.map(function (_a) {
+                                var i = _a[0], j = _a[1];
+                                return "(".concat(structures[i].models[0].entryId, ", ").concat(structures[j].models[0].entryId, ")");
+                            }).join(', '), "]");
+                        };
+                        if (zeroOverlapPairs.length) {
+                            this.plugin.log.warn("Superposition: No UNIPROT mapping overlap between structures ".concat(formatPairs(zeroOverlapPairs), "."));
+                        }
+                        if (failedPairs.length) {
+                            this.plugin.log.error("Superposition: Failed to superpose structures ".concat(formatPairs(failedPairs), "."));
+                        }
+                        if (!entries.length) return [3 /*break*/, 6];
+                        this.plugin.log.info("Superposed ".concat(entries.length + 1, " structures with avg. RMSD ").concat(rmsd.toFixed(2), " \u00C5."));
+                        return [4 /*yield*/, this.cameraReset()];
                     case 5:
-                        _a.sent();
-                        PluginCommands.Camera.Reset(this.plugin);
-                        return [2 /*return*/];
+                        _b.sent();
+                        _b.label = 6;
+                    case 6: return [2 /*return*/];
                 }
             });
         }); };
@@ -189,7 +212,7 @@ var SuperpositionControls = /** @class */ (function (_super) {
             _this.setState({ isBusy: v });
         });
         this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, function (sel) {
-            _this.setState({ canUseDb: sel.structures.every(function (s) { var _a; return !!((_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data) && s.cell.obj.data.models.some(function (m) { return BestDatabaseSequenceMapping.Provider.isApplicable(m); }); }) });
+            _this.setState({ canUseDb: sel.structures.every(function (s) { var _a; return !!((_a = s.cell.obj) === null || _a === void 0 ? void 0 : _a.data) && s.cell.obj.data.models.some(function (m) { return SIFTSMapping.Provider.isApplicable(m); }); }) });
         });
     };
     Object.defineProperty(SuperpositionControls.prototype, "selection", {
@@ -227,6 +250,19 @@ var SuperpositionControls = /** @class */ (function (_super) {
             });
         });
     };
+    SuperpositionControls.prototype.cameraReset = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, new Promise(function (res) { return requestAnimationFrame(res); })];
+                    case 1:
+                        _a.sent();
+                        PluginCommands.Camera.Reset(this.plugin);
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
     SuperpositionControls.prototype.highlight = function (loci) {
         this.plugin.managers.interactivity.lociHighlights.highlightOnly({ loci: loci }, false);
     };
@@ -318,7 +354,7 @@ var SuperpositionControls = /** @class */ (function (_super) {
         return _jsxs(_Fragment, { children: [entries.length > 0 && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: entries.map(function (e, i) { return _this.atomsLociEntry(e, i); }) }), void 0), entries.length < 2 && _jsx("div", __assign({ className: 'msp-control-offset msp-help-text' }, { children: _jsxs("div", __assign({ className: 'msp-help-description' }, { children: [_jsx(Icon, { svg: HelpOutlineSvg, inline: true }, void 0), "Add 1 or more selections (toggle ", _jsx(ToggleSelectionModeButton, { inline: true }, void 0), " mode) from separate structures. Selections must be limited to single atoms."] }), void 0) }), void 0), entries.length > 1 && _jsx(Button, __assign({ title: 'Superpose structures by selected atoms.', className: 'msp-btn-commit msp-btn-commit-on', onClick: this.superposeAtoms, style: { marginTop: '1px' } }, { children: "Superpose" }), void 0)] }, void 0);
     };
     SuperpositionControls.prototype.superposeByDbMapping = function () {
-        return _jsx(_Fragment, { children: _jsx(Button, __assign({ icon: SuperposeChainsSvg, title: 'Superpose structures using database mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px' }, disabled: this.state.isBusy }, { children: "DB" }), void 0) }, void 0);
+        return _jsx(_Fragment, { children: _jsx(Button, __assign({ icon: SuperposeChainsSvg, title: 'Superpose structures using intersection of residues from SIFTS UNIPROT mapping.', className: 'msp-btn msp-btn-block', onClick: this.superposeDb, style: { marginTop: '1px' }, disabled: this.state.isBusy }, { children: "Uniprot" }), void 0) }, void 0);
     };
     SuperpositionControls.prototype.render = function () {
         return _jsxs(_Fragment, { children: [_jsxs("div", __assign({ className: 'msp-flex-row' }, { children: [_jsx(ToggleButton, { icon: SuperposeChainsSvg, label: 'Chains', toggle: this.toggleByChains, isSelected: this.state.action === 'byChains', disabled: this.state.isBusy }, void 0), _jsx(ToggleButton, { icon: SuperposeAtomsSvg, label: 'Atoms', toggle: this.toggleByAtoms, isSelected: this.state.action === 'byAtoms', disabled: this.state.isBusy }, void 0), this.state.canUseDb && this.superposeByDbMapping(), _jsx(ToggleButton, { icon: TuneSvg, label: '', title: 'Options', toggle: this.toggleOptions, isSelected: this.state.action === 'options', disabled: this.state.isBusy, style: { flex: '0 0 40px', padding: 0 } }, void 0)] }), void 0), this.state.action === 'byChains' && this.addByChains(), this.state.action === 'byAtoms' && this.addByAtoms(), this.state.action === 'options' && _jsx("div", __assign({ className: 'msp-control-offset' }, { children: _jsx(ParameterControls, { params: StructureSuperpositionParams, values: this.state.options, onChangeValues: this.setOptions, isDisabled: this.state.isBusy }, void 0) }), void 0)] }, void 0);

package/lib/mol-script/language/builder.d.ts

@@ -10,6 +10,7 @@ export declare namespace MolScriptBuilder {
         '@header': string;
         type: {
             '@header': string;
+            /** atom macromolecular property set */
             bool: MSymbol<import("./symbol").Arguments<import("./symbol").Arguments.PropTypes<{
                 0: import("./symbol").Argument<import("./type").Type.AnyValue>;
             }>>, import("./type").Type.OneOf<boolean>>;