npm - molstar - Versions diffs - 2.3.7 → 2.4.1 - Mend

molstar 2.3.7 → 2.4.1

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 (1699) hide show

package/lib/commonjs/mol-script/language/parser.js.map CHANGED Viewed

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1	+ 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package/lib/commonjs/mol-script/language/symbol-table/structure-query.js CHANGED Viewed

@@ -34,10 +34,10 @@ var type = {
     '@header': 'Types',
     elementSymbol: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(type_1.Type.Str) }), Types.ElementSymbol, 'Create element symbol representation from a string value.'),
     atomName: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(type_1.Type.AnyValue) }), Types.AtomName, 'Convert a value to an atom name.'),
-    entityType: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(Types.EntityType) }), Types.EntityType, "Create normalized representation of entity type: " + type_1.Type.oneOfValues(Types.EntityType).join(', ') + "."),
-    bondFlags: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.BondFlag), Types.BondFlags, "Create bond flags representation from a list of strings. Allowed flags: " + type_1.Type.oneOfValues(Types.BondFlag).join(', ') + "."),
+    entityType: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({ 0: (0, symbol_1.Argument)(Types.EntityType) }), Types.EntityType, "Create normalized representation of entity type: ".concat(type_1.Type.oneOfValues(Types.EntityType).join(', '), ".")),
+    bondFlags: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.BondFlag), Types.BondFlags, "Create bond flags representation from a list of strings. Allowed flags: ".concat(type_1.Type.oneOfValues(Types.BondFlag).join(', '), ".")),
     ringFingerprint: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.ElementSymbol, { nonEmpty: true }), Types.RingFingerprint, 'Create ring fingerprint from the supplied atom element list.'),
-    secondaryStructureFlags: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.SecondaryStructureFlag), Types.SecondaryStructureFlags, "Create secondary structure flags representation from a list of strings. Allowed flags: " + type_1.Type.oneOfValues(Types.SecondaryStructureFlag).join(', ') + "."),
+    secondaryStructureFlags: (0, helpers_1.symbol)(symbol_1.Arguments.List(Types.SecondaryStructureFlag), Types.SecondaryStructureFlags, "Create secondary structure flags representation from a list of strings. Allowed flags: ".concat(type_1.Type.oneOfValues(Types.SecondaryStructureFlag).join(', '), ".")),
     authResidueId: (0, helpers_1.symbol)(symbol_1.Arguments.Dictionary({
         0: (0, symbol_1.Argument)(type_1.Type.Str, { description: 'auth_asym_id' }),
         1: (0, symbol_1.Argument)(type_1.Type.Num, { description: 'auth_seq_id' }),

package/lib/commonjs/mol-script/language/symbol-table/structure-query.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-script/language/symbol.js CHANGED Viewed

@@ -41,7 +41,7 @@ function CustomPropSymbol(namespace, name, type, description) {
         return expression_1.Expression.Apply(expression_1.Expression.Symbol(symbol.id), args);
     };
     symbol.info = { namespace: namespace, name: name, description: description };
-    symbol.id = namespace + "." + name;
+    symbol.id = "".concat(namespace, ".").concat(name);
     symbol.args = Arguments.None;
     symbol.type = type;
     return symbol;

package/lib/commonjs/mol-script/language/symbol.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"symbol.js","sourceRoot":"","sources":["../../../../src/mol-script/language/symbol.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAGH,2CAA0C;AAS1C,SAAgB,QAAQ,CAAiB,IAAO,EAAE,MAAoG;IAC5I,IAAA,KAAsF,MAAM,IAAI,EAAE,EAAhG,mBAAoB,EAApB,WAAW,mBAAG,KAAK,CAAC,KAAA,EAAE,kBAAkB,EAAlB,UAAU,mBAAG,KAAK,KAAA,EAAE,cAAc,EAAd,MAAM,mBAAG,KAAK,KAAA,EAAE,oBAAqB,EAArB,YAAY,mBAAG,KAAK,CAAC,KAAiB,CAAC;IACzG,OAAO,EAAE,IAAI,MAAA,EAAE,UAAU,YAAA,EAAE,MAAM,QAAA,EAAE,YAAY,cAAA,EAAE,WAAW,aAAA,EAAE,CAAC;AACnE,CAAC;AAHD,4BAGC;AAMD,IAAiB,SAAS,CAwBzB;AAxBD,WAAiB,SAAS;IACT,cAAI,GAAc,UAAU,CAAC,EAAE,CAAC,CAAC;IAQ9C,SAAgB,UAAU,CAA+C,GAAQ;QAC7E,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,GAAG,KAAA,EAAE,OAAO,EAAE,CAAQ,EAAE,CAAC;IAC1D,CAAC;IAFe,oBAAU,aAEzB,CAAA;IASD,SAAgB,IAAI,CAAiB,IAAO,EAAE,MAA+B;QACjE,IAAA,KAAqB,CAAA,MAAM,IAAI,EAAG,CAAA,SAAlB,EAAhB,QAAQ,mBAAG,KAAK,KAAA,CAAmB;QAC3C,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,MAAA,EAAE,QAAQ,UAAA,EAAE,OAAO,EAAE,CAAQ,EAAE,CAAC;IAC/D,CAAC;IAHe,cAAI,OAGnB,CAAA;AACL,CAAC,EAxBgB,SAAS,GAAT,iBAAS,KAAT,iBAAS,QAwBzB;AAgBD,SAAgB,OAAO,CAAsC,IAAY,EAAE,IAAO,EAAE,IAAO,EAAE,WAAoB;IAC7G,IAAM,MAAM,GAAkB,UAAU,IAAqC;QACzE,OAAO,uBAAU,CAAC,KAAK,CAAC,uBAAU,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,IAAW,CAAC,CAAC;IACvE,CAAQ,CAAC;IACT,MAAM,CAAC,IAAI,GAAG,EAAE,SAAS,EAAE,EAAE,EAAE,IAAI,MAAA,EAAE,WAAW,aAAA,EAAE,CAAC;IACnD,MAAM,CAAC,EAAE,GAAG,EAAE,CAAC;IACf,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;IACnB,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;IACnB,OAAO,MAAM,CAAC;AAClB,CAAC;AATD,0BASC;AAED,SAAgB,gBAAgB,CAAiB,SAAiB,EAAE,IAAY,EAAE,IAAO,EAAE,WAAoB;IAC3G,IAAM,MAAM,GAA8B,UAAU,IAAiD;QACjG,OAAO,uBAAU,CAAC,KAAK,CAAC,uBAAU,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,IAAW,CAAC,CAAC;IACvE,CAAQ,CAAC;IACT,MAAM,CAAC,IAAI,GAAG,EAAE,SAAS,WAAA,EAAE,IAAI,MAAA,EAAE,WAAW,aAAA,EAAE,CAAC;IAC/C,MAAM,CAAC,EAAE,~~GAAM~~,SAAS,~~SAAI~~,~~IAAM~~,CAAC;IACnC,MAAM,CAAC,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;IAC7B,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;IACnB,OAAO,MAAM,CAAC;AAClB,CAAC;AATD,4CASC;AAED,SAAgB,QAAQ,CAAC,CAAM;IAC3B,IAAM,CAAC,GAAG,CAAY,CAAC;IACvB,OAAO,OAAO,CAAC,KAAK,UAAU,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,OAAO,CAAC,CAAC,IAAI,CAAC,SAAS,KAAK,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;AAC/G,CAAC;AAHD,4BAGC"}
1	+ {"version":3,"file":"symbol.js","sourceRoot":"","sources":["../../../../src/mol-script/language/symbol.ts"],"names":[],"mappings":";AAAA;;;;GAIG;;;AAGH,2CAA0C;AAS1C,SAAgB,QAAQ,CAAiB,IAAO,EAAE,MAAoG;IAC5I,IAAA,KAAsF,MAAM,IAAI,EAAE,EAAhG,mBAAoB,EAApB,WAAW,mBAAG,KAAK,CAAC,KAAA,EAAE,kBAAkB,EAAlB,UAAU,mBAAG,KAAK,KAAA,EAAE,cAAc,EAAd,MAAM,mBAAG,KAAK,KAAA,EAAE,oBAAqB,EAArB,YAAY,mBAAG,KAAK,CAAC,KAAiB,CAAC;IACzG,OAAO,EAAE,IAAI,MAAA,EAAE,UAAU,YAAA,EAAE,MAAM,QAAA,EAAE,YAAY,cAAA,EAAE,WAAW,aAAA,EAAE,CAAC;AACnE,CAAC;AAHD,4BAGC;AAMD,IAAiB,SAAS,CAwBzB;AAxBD,WAAiB,SAAS;IACT,cAAI,GAAc,UAAU,CAAC,EAAE,CAAC,CAAC;IAQ9C,SAAgB,UAAU,CAA+C,GAAQ;QAC7E,OAAO,EAAE,IAAI,EAAE,YAAY,EAAE,GAAG,KAAA,EAAE,OAAO,EAAE,CAAQ,EAAE,CAAC;IAC1D,CAAC;IAFe,oBAAU,aAEzB,CAAA;IASD,SAAgB,IAAI,CAAiB,IAAO,EAAE,MAA+B;QACjE,IAAA,KAAqB,CAAA,MAAM,IAAI,EAAG,CAAA,SAAlB,EAAhB,QAAQ,mBAAG,KAAK,KAAA,CAAmB;QAC3C,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,MAAA,EAAE,QAAQ,UAAA,EAAE,OAAO,EAAE,CAAQ,EAAE,CAAC;IAC/D,CAAC;IAHe,cAAI,OAGnB,CAAA;AACL,CAAC,EAxBgB,SAAS,GAAT,iBAAS,KAAT,iBAAS,QAwBzB;AAgBD,SAAgB,OAAO,CAAsC,IAAY,EAAE,IAAO,EAAE,IAAO,EAAE,WAAoB;IAC7G,IAAM,MAAM,GAAkB,UAAU,IAAqC;QACzE,OAAO,uBAAU,CAAC,KAAK,CAAC,uBAAU,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,IAAW,CAAC,CAAC;IACvE,CAAQ,CAAC;IACT,MAAM,CAAC,IAAI,GAAG,EAAE,SAAS,EAAE,EAAE,EAAE,IAAI,MAAA,EAAE,WAAW,aAAA,EAAE,CAAC;IACnD,MAAM,CAAC,EAAE,GAAG,EAAE,CAAC;IACf,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;IACnB,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;IACnB,OAAO,MAAM,CAAC;AAClB,CAAC;AATD,0BASC;AAED,SAAgB,gBAAgB,CAAiB,SAAiB,EAAE,IAAY,EAAE,IAAO,EAAE,WAAoB;IAC3G,IAAM,MAAM,GAA8B,UAAU,IAAiD;QACjG,OAAO,uBAAU,CAAC,KAAK,CAAC,uBAAU,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,IAAW,CAAC,CAAC;IACvE,CAAQ,CAAC;IACT,MAAM,CAAC,IAAI,GAAG,EAAE,SAAS,WAAA,EAAE,IAAI,MAAA,EAAE,WAAW,aAAA,EAAE,CAAC;IAC/C,MAAM,CAAC,EAAE,GAAG,UAAG,SAAS,cAAI,IAAI,CAAE,CAAC;IACnC,MAAM,CAAC,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;IAC7B,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;IACnB,OAAO,MAAM,CAAC;AAClB,CAAC;AATD,4CASC;AAED,SAAgB,QAAQ,CAAC,CAAM;IAC3B,IAAM,CAAC,GAAG,CAAY,CAAC;IACvB,OAAO,OAAO,CAAC,KAAK,UAAU,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,OAAO,CAAC,CAAC,IAAI,CAAC,SAAS,KAAK,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;AAC/G,CAAC;AAHD,4BAGC"}

package/lib/commonjs/mol-script/runtime/query/base.js CHANGED Viewed

@@ -17,7 +17,7 @@ var QueryRuntimeTable = /** @class */ (function () {
     };
     QueryRuntimeTable.prototype.addSymbol = function (runtime) {
         if (this.map.has(runtime.symbol.id)) {
-            console.warn("Symbol '" + runtime.symbol.id + "' already added. Call removeSymbol/removeCustomProps re-adding the symbol.");
+            console.warn("Symbol '".concat(runtime.symbol.id, "' already added. Call removeSymbol/removeCustomProps re-adding the symbol."));
         }
         this.map.set(runtime.symbol.id, runtime);
     };
@@ -163,7 +163,7 @@ function _compile(ctx, expression) {
     }
     var compiler = ctx.table.getRuntime(expression.head.name);
     if (!compiler) {
-        throw new Error("Symbol '" + expression.head.name + "' is not implemented.");
+        throw new Error("Symbol '".concat(expression.head.name, "' is not implemented."));
     }
     return compiler.compile(ctx, expression.args);
 }

package/lib/commonjs/mol-script/runtime/query/base.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/mol-script/script/mol-script/symbols.js CHANGED Viewed

@@ -28,7 +28,7 @@ function Macro(symbol, translate) {
         aliases[_a - 2] = arguments[_a];
     }
     symbol.info.namespace = 'molscript-macro';
-    symbol.id = "molscript-macro." + symbol.info.name;
+    symbol.id = "molscript-macro.".concat(symbol.info.name);
     return { kind: 'macro', symbol: symbol, translate: translate, aliases: (0, tslib_1.__spreadArray)([symbol.info.name], aliases, true) };
 }
 function isMolScriptSymbol(x) {
@@ -245,7 +245,7 @@ exports.SymbolTable = [
             Alias(symbol_table_1.MolScriptSymbolTable.structureQuery.bondProperty.length, 'bond.length'),
             Alias(symbol_table_1.MolScriptSymbolTable.structureQuery.bondProperty.atomA, 'bond.atom-a'),
             Alias(symbol_table_1.MolScriptSymbolTable.structureQuery.bondProperty.atomB, 'bond.atom-b'),
-            Macro((0, symbol_1.MSymbol)('bond.is', symbol_1.Arguments.List(structure_query_1.Types.BondFlag), type_1.Type.Bool, "Test if the current bond has at least one (or all if partial = false) of the specified flags: " + type_1.Type.oneOfValues(structure_query_1.Types.BondFlag).join(', ')), function (args) { return builder_1.MolScriptBuilder.core.flags.hasAny([builder_1.MolScriptBuilder.struct.bondProperty.flags(), builder_1.MolScriptBuilder.struct.type.bondFlags((0, script_macro_1.getPositionalArgs)(args))]); }),
+            Macro((0, symbol_1.MSymbol)('bond.is', symbol_1.Arguments.List(structure_query_1.Types.BondFlag), type_1.Type.Bool, "Test if the current bond has at least one (or all if partial = false) of the specified flags: ".concat(type_1.Type.oneOfValues(structure_query_1.Types.BondFlag).join(', '))), function (args) { return builder_1.MolScriptBuilder.core.flags.hasAny([builder_1.MolScriptBuilder.struct.bondProperty.flags(), builder_1.MolScriptBuilder.struct.type.bondFlags((0, script_macro_1.getPositionalArgs)(args))]); }),
         ]
     ]
 ];
@@ -271,7 +271,7 @@ var normalized = (function () {
             var a = _c[_b];
             symbolList.push([a, s]);
             if (symbolMap[a])
-                throw new Error("Alias '" + a + "' already in use.");
+                throw new Error("Alias '".concat(a, "' already in use."));
             symbolMap[a] = s;
         }
         var args = s.symbol.args;

package/lib/commonjs/mol-script/script/mol-script/symbols.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-state/state/builder.js CHANGED Viewed

@@ -101,7 +101,7 @@ var StateBuilder;
             this.root = root;
             this.ref = ref;
             if (!this.state.tree.transforms.has(ref)) {
-                throw new Error("Could not find node '" + ref + "'.");
+                throw new Error("Could not find node '".concat(ref, "'."));
             }
         }
         Object.defineProperty(To.prototype, "editInfo", {

package/lib/commonjs/mol-state/state/builder.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-state/state.js CHANGED Viewed

@@ -21,7 +21,6 @@ var now_1 = require("../mol-util/now");
 var param_definition_1 = require("../mol-util/param-definition");
 var spine_1 = require("./tree/spine");
 var async_queue_1 = require("../mol-util/async-queue");
-var debug_1 = require("../mol-util/debug");
 var array_1 = require("../mol-util/array");
 var generic_1 = require("../mol-data/generic");
 var object_2 = require("../mol-util/object");
@@ -57,7 +56,7 @@ var State = /** @class */ (function () {
             var _a, _b;
             var ret = (_b = (_a = _this.cells.get(ref)) === null || _a === void 0 ? void 0 : _a.obj) === null || _b === void 0 ? void 0 : _b.data;
             if (!ref)
-                throw new Error("Cell '" + ref + "' data undefined.");
+                throw new Error("Cell '".concat(ref, "' data undefined."));
             return ret;
         };
         this.historyCapacity = 5;
@@ -219,9 +218,9 @@ var State = /** @class */ (function () {
         return mol_task_1.Task.create('Apply Action', function (ctx) {
             var cell = _this.cells.get(ref);
             if (!cell)
-                throw new Error("'" + ref + "' does not exist.");
+                throw new Error("'".concat(ref, "' does not exist."));
             if (cell.status !== 'ok')
-                throw new Error("Action cannot be applied to a cell with status '" + cell.status + "'");
+                throw new Error("Action cannot be applied to a cell with status '".concat(cell.status, "'"));
             return runTask(action.definition.run({ ref: ref, cell: cell, a: cell.obj, params: params, state: _this }, _this.globalContext), ctx);
         });
     };
@@ -260,15 +259,19 @@ var State = /** @class */ (function () {
                         return [4 /*yield*/, this.updateTree(snapshot).runInContext(ctx)];
                     case 6:
                         _a.sent();
-                        this.events.log.next(log_entry_1.LogEntry.error('' + e_1));
+                        this.events.log.next(log_entry_1.LogEntry.error('Error during state transaction, reverting'));
                         _a.label = 7;
                     case 7:
                         if (isNested) {
                             this.inTransactionError = true;
                             throw e_1;
                         }
-                        if (options === null || options === void 0 ? void 0 : options.rethrowErrors)
+                        if (options === null || options === void 0 ? void 0 : options.rethrowErrors) {
                             throw e_1;
+                        }
+                        else {
+                            console.error(e_1);
+                        }
                         return [3 /*break*/, 9];
                     case 8:
                         if (!isNested) {
@@ -801,17 +804,17 @@ function updateSubtree(ctx, root) {
                     if (update_2.action === 'created') {
                         isNull = update_2.obj === object_1.StateObject.Null;
                         if (!isNull && !ctx.options.doNotLogTiming)
-                            ctx.parent.events.log.next(log_entry_1.LogEntry.info("Created " + update_2.obj.label + " in " + (0, now_1.formatTimespan)(time) + "."));
+                            ctx.parent.events.log.next(log_entry_1.LogEntry.info("Created ".concat(update_2.obj.label, " in ").concat((0, now_1.formatTimespan)(time), ".")));
                     }
                     else if (update_2.action === 'updated') {
                         isNull = update_2.obj === object_1.StateObject.Null;
                         if (!isNull && !ctx.options.doNotLogTiming)
-                            ctx.parent.events.log.next(log_entry_1.LogEntry.info("Updated " + update_2.obj.label + " in " + (0, now_1.formatTimespan)(time) + "."));
+                            ctx.parent.events.log.next(log_entry_1.LogEntry.info("Updated ".concat(update_2.obj.label, " in ").concat((0, now_1.formatTimespan)(time), ".")));
                     }
                     else if (update_2.action === 'replaced') {
                         isNull = update_2.obj === object_1.StateObject.Null;
                         if (!isNull && !ctx.options.doNotLogTiming)
-                            ctx.parent.events.log.next(log_entry_1.LogEntry.info("Updated " + update_2.obj.label + " in " + (0, now_1.formatTimespan)(time) + "."));
+                            ctx.parent.events.log.next(log_entry_1.LogEntry.info("Updated ".concat(update_2.obj.label, " in ").concat((0, now_1.formatTimespan)(time), ".")));
                     }
                     return [3 /*break*/, 4];
                 case 3:
@@ -820,8 +823,7 @@ function updateSubtree(ctx, root) {
                     if (!ctx.hadError)
                         ctx.newCurrent = root;
                     doError(ctx, root, e_2, false);
-                    if (!debug_1.isProductionMode)
-                        console.error(e_2);
+                    console.error(e_2);
                     return [2 /*return*/];
                 case 4:
                     children = ctx.tree.children.get(root).values();
@@ -878,7 +880,7 @@ function updateNode(ctx, currentRef) {
                         ? ctx.cells.get(current.transform.parent)
                         : selection_1.StateSelection.findAncestorOfType(tree, ctx.cells, currentRef, transform.transformer.definition.from);
                     if (!parentCell) {
-                        throw new Error("No suitable parent found for '" + currentRef + "'");
+                        throw new Error("No suitable parent found for '".concat(currentRef, "'"));
                     }
                     ctx.spine.current = current;
                     parent = parentCell.obj;