pdbe-molstar 3.11.0 → 3.12.0

package/lib/viewer.js

@@ -143,7 +143,7 @@ class PDBeMolstarPlugin {
                 }
             }),
             /** Change the visibility of a structure.
-             * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
+             * `structureNumberOrId` is either index (numbered from 1!; use negative index to count backwards) or the ID that was provided when loading the structure.
              * If `visibility` is undefined, toggle current visibility state. */
             structureVisibility: (structureNumberOrId, visibility) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 const struct = this.getStructure(structureNumberOrId);
@@ -173,7 +173,7 @@ class PDBeMolstarPlugin {
             }),
             /** Focus (zoom) on the part of the structure defined by `selection`.
              * If `selection` contains more items, focus on the union of those.
-             * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure;
+             * `structureNumberOrId` is either index (numbered from 1!; use negative index to count backwards) or the ID that was provided when loading the structure;
              * if not provided, will use the last added structure. */
             focus: (selection, structureNumberOrId) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 const loci = this.getLociForParams(selection, structureNumberOrId);
@@ -183,7 +183,7 @@ class PDBeMolstarPlugin {
              * This includes behaviors like "show non-covalent interactions" or "show streamed volume data"
              * but not camera adjustment (call `.visual.focus` for that).
              * If `data` contains more items, focus on the union of those.
-             * If `structureId` or `structureNumber` is provided, use the specified structure (numbered from 1!);
+             * If `structureId` or `structureNumber` is provided, use the specified structure (numbered from 1!; use negative index to count backwards);
              * otherwise use the last added structure. */
             interactivityFocus: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a;
@@ -194,7 +194,7 @@ class PDBeMolstarPlugin {
             /** Trigger highlight on the part of the structure defined by `data`
              * (this will look the same as when the user hovers over a part of the structure).
              * If `focus`, also zoom on the highlighted part.
-             * If `structureId` or `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
+             * If `structureId` or `structureNumber` is provided, use the specified structure (numbered from 1!; use negative index to count backwards); otherwise use the last added structure. */
             highlight: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a;
                 const loci = this.getLociForParams(params.data, (_a = params.structureId) !== null && _a !== void 0 ? _a : params.structureNumber);
@@ -218,7 +218,7 @@ class PDBeMolstarPlugin {
              * If any items in `data` contain `opacity`, set opacity accordingly, set opacity to `nonSelectedOpacity` (or 1) for the rest of the structure.
              * If any items in `data` contain `focus`, zoom to the union of these items.
              * If any items in `data` contain `sideChain` or `representation`, add extra representations to them (colored in `representationColor` if provided).
-             * If `structureNumber` is provided, apply to the specified structure (numbered from 1!); otherwise apply to all loaded structures.
+             * If `structureNumber` is provided, apply to the specified structure (numbered from 1!; use negative index to count backwards); otherwise apply to all loaded structures.
              * Remove any previously added coloring, opacity, and/or extra representations, unless `keepColors`, `keepOpacity`, and/or `keepRepresentations` is set. */
             select: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a, _b, _c, _d;
@@ -318,7 +318,7 @@ class PDBeMolstarPlugin {
                 }
             }),
             /** Remove any coloring and extra representations previously added by the `select` method.
-             * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure;
+             * `structureNumberOrId` is either index (numbered from 1!; use negative index to count backwards) or the ID that was provided when loading the structure;
              * if not provided, will apply to all loaded structures.
              * If `keepColors`, current residue coloring is preserved. If `keepOpacity`, current residue opacity is preserved. If `keepRepresentations`, current added representations are preserved. */
             clearSelection: (structureNumberOrId, options) => tslib_1.__awaiter(this, void 0, void 0, function* () {
@@ -349,7 +349,7 @@ class PDBeMolstarPlugin {
                 }
             }),
             /** Color the parts of sequence in the sequence panel defined by `data`. Color the rest of the sequence in `nonSelectedColor` if provided.
-             * If `structureId` or `structureNumber` is provided, apply to the specified structure (`structureNumber` numbered from 1!); otherwise apply to all loaded structures.
+             * If `structureId` or `structureNumber` is provided, apply to the specified structure (`structureNumber` numbered from 1!; use negative index to count backwards); otherwise apply to all loaded structures.
              * Remove any previously added coloring, unless `keepColors` is set. */
             sequenceColor: (params) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 var _a, _b;
@@ -408,7 +408,7 @@ class PDBeMolstarPlugin {
                 yield update.commit();
             }),
             /** Remove any sequence coloring previously added by the `sequenceColor` method.
-             * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure;
+             * `structureNumberOrId` is either index (numbered from 1!; use negative index to count backwards) or the ID that was provided when loading the structure;
              * if not provided, will apply to all loaded structures. */
             clearSequenceColor: (structureNumberOrId) => tslib_1.__awaiter(this, void 0, void 0, function* () {
                 if (typeof structureNumberOrId === 'number')
@@ -925,7 +925,7 @@ class PDBeMolstarPlugin {
         });
     }
     /** Remove loaded structure(s).
-     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
+     * `structureNumberOrId` is either index (numbered from 1!; use negative index to count backwards) or the ID that was provided when loading the structure.
      * If `structureNumberOrId` is undefined, remove all structures.
      * You will likely need to call `await this.visual.reset({ camera: true })` afterwards. */
     deleteStructure(structureNumberOrId) {
@@ -1009,14 +1009,14 @@ class PDBeMolstarPlugin {
     }
     /** Get loci corresponding to a selection within a structure.
      * If `params` contains more items, return loci for the union of the selections.
-     * If `structureNumber` is provided, use the specified structure (numbered from 1!); otherwise use the last added structure. */
+     * If `structureNumber` is provided, use the specified structure (numbered from 1!; use negative index to count backwards); otherwise use the last added structure. */
     getLociForParams(params, structureNumberOrId) {
-        var _a, _b, _c, _d;
+        var _a, _b, _c, _d, _e, _f;
         const struct = (structureNumberOrId !== undefined) ?
             (_b = (_a = this.getStructure(structureNumberOrId)) === null || _a === void 0 ? void 0 : _a.cell.obj) === null || _b === void 0 ? void 0 : _b.data
             : this.assemblyRef ?
                 (_d = (_c = this.plugin.state.data.select(this.assemblyRef)[0]) === null || _c === void 0 ? void 0 : _c.obj) === null || _d === void 0 ? void 0 : _d.data
-                : undefined;
+                : (_f = (_e = this.getStructure(-1)) === null || _e === void 0 ? void 0 : _e.cell.obj) === null || _f === void 0 ? void 0 : _f.data;
         if (!struct)
             return loci_1.EmptyLoci;
         return helpers_1.QueryHelper.getInteractivityLoci(params, struct);
@@ -1055,13 +1055,22 @@ class PDBeMolstarPlugin {
         return (0, helpers_1.normalizeColor)(colorVal, defaultColor);
     }
     /** Get structure ref for a structure with given `structureNumberOrId`.
-     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure.
+     * `structureNumberOrId` is either index (numbered from 1!; use negative index to count backwards) or the ID that was provided when loading the structure.
      * If `structureNumberOrId` is undefined, return refs for all loaded structures. */
     getStructures(structureNumberOrId) {
         const allStructures = this.plugin.managers.structure.hierarchy.current.structures.map((structureRef, i) => ({ structureRef, number: i + 1 }));
         if (typeof structureNumberOrId === 'number') {
-            const theStructure = allStructures[structureNumberOrId - 1];
-            return theStructure ? [theStructure] : [];
+            if (structureNumberOrId > 0) { // count forwards from 1
+                const theStructure = allStructures[structureNumberOrId - 1];
+                return theStructure ? [theStructure] : [];
+            }
+            else if (structureNumberOrId < 0) { // count backwards from -1
+                const theStructure = allStructures[allStructures.length + structureNumberOrId];
+                return theStructure ? [theStructure] : [];
+            }
+            else {
+                throw new Error('0 is not a valid value for structureNumberOrId, as structures are numbered from 1');
+            }
         }
         else if (typeof structureNumberOrId === 'string') {
             const structRef = this.structureRefMap.get(structureNumberOrId);
@@ -1082,7 +1091,7 @@ class PDBeMolstarPlugin {
         }
     }
     /** Get StructureRef for a structure with given `structureNumberOrId`.
-     * `structureNumberOrId` is either index (numbered from 1!) or the ID that was provided when loading the structure. */
+     * `structureNumberOrId` is either index (numbered from 1!; use negative index to count backwards) or the ID that was provided when loading the structure. */
     getStructure(structureNumberOrId) {
         var _a;
         return (_a = this.getStructures(structureNumberOrId)[0]) === null || _a === void 0 ? void 0 : _a.structureRef;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pdbe-molstar",
-  "version": "3.11.0",
+  "version": "3.12.0",
   "description": "Molstar implementation for PDBe",
   "main": "index.js",
   "scripts": {
@@ -80,7 +80,7 @@
     "d3-scale": "^4.0.2",
     "d3-selection": "^3.0.0",
     "lit": "^3.1.1",
-    "molstar": "5.7.0",
+    "molstar": "5.8.0",
     "path-browserify": "^1.0.1",
     "stream-browserify": "^3.0.0",
     "vm-browserify": "^1.1.2"