molstar 2.3.5 → 2.3.9

package/lib/cli/structure-info/model.js

@@ -23,7 +23,7 @@ function downloadFromPdb(pdb) {
         var parsed;
         return __generator(this, function (_a) {
             switch (_a.label) {
-                case 0: return [4 /*yield*/, downloadCif("http://www.ebi.ac.uk/pdbe/static/entry/" + pdb + "_updated.cif", false)];
+                case 0: return [4 /*yield*/, downloadCif("http://www.ebi.ac.uk/pdbe/static/entry/".concat(pdb, "_updated.cif"), false)];
                 case 1:
                     parsed = _a.sent();
                     return [2 /*return*/, parsed.blocks[0]];
@@ -51,7 +51,7 @@ export function atomLabel(model, aI) {
     var label_asym_id = chains.label_asym_id;
     var rI = residueAtomSegments.index[aI];
     var cI = chainAtomSegments.index[aI];
-    return label_asym_id.value(cI) + " " + label_comp_id.value(aI) + " " + label_seq_id.value(rI) + " " + label_atom_id.value(aI);
+    return "".concat(label_asym_id.value(cI), " ").concat(label_comp_id.value(aI), " ").concat(label_seq_id.value(rI), " ").concat(label_atom_id.value(aI));
 }
 export function residueLabel(model, rI) {
     var _a = model.atomicHierarchy, atoms = _a.atoms, residues = _a.residues, chains = _a.chains, residueAtomSegments = _a.residueAtomSegments, chainAtomSegments = _a.chainAtomSegments;
@@ -60,7 +60,7 @@ export function residueLabel(model, rI) {
     var label_asym_id = chains.label_asym_id;
     var aI = residueAtomSegments.offsets[rI];
     var cI = chainAtomSegments.index[aI];
-    return label_asym_id.value(cI) + " " + label_comp_id.value(aI) + " " + label_seq_id.value(rI);
+    return "".concat(label_asym_id.value(cI), " ").concat(label_comp_id.value(aI), " ").concat(label_seq_id.value(rI));
 }
 export function printSecStructure(model) {
     console.log('\nSecondary Structure\n=============');
@@ -78,7 +78,7 @@ export function printSecStructure(model) {
         rI--;
         var e = elements[key[start]];
         if (e.kind !== 'none')
-            console.log(e.kind + ": " + residueLabel(model, start) + " - " + residueLabel(model, rI));
+            console.log("".concat(e.kind, ": ").concat(residueLabel(model, start), " - ").concat(residueLabel(model, rI)));
         rI++;
     }
 }
@@ -98,7 +98,7 @@ export function printBonds(structure, showIntra, showInter) {
                 var x = a[bI], y = b[bI];
                 if (x >= y)
                     continue;
-                console.log(atomLabel(model, elements[x]) + " -- " + atomLabel(model, elements[y]));
+                console.log("".concat(atomLabel(model, elements[x]), " -- ").concat(atomLabel(model, elements[y])));
             }
         }
     }
@@ -116,12 +116,12 @@ export function printBonds(structure, showIntra, showInter) {
                 var unitA = pairBonds.unitA, unitB = pairBonds.unitB, edgeCount = pairBonds.edgeCount;
                 var uA = structure.unitMap.get(unitA);
                 var uB = structure.unitMap.get(unitB);
-                console.log(unitA + " - " + unitB + ": " + edgeCount + " bond(s)");
+                console.log("".concat(unitA, " - ").concat(unitB, ": ").concat(edgeCount, " bond(s)"));
                 for (var _h = 0, _k = pairBonds.connectedIndices; _h < _k.length; _h++) {
                     var aI = _k[_h];
                     for (var _l = 0, _m = pairBonds.getEdges(aI); _l < _m.length; _l++) {
                         var bond = _m[_l];
-                        console.log(atomLabel(uA.model, uA.elements[aI]) + " -- " + atomLabel(uB.model, uB.elements[bond.indexB]));
+                        console.log("".concat(atomLabel(uA.model, uA.elements[aI]), " -- ").concat(atomLabel(uB.model, uB.elements[bond.indexB])));
                     }
                 }
             }
@@ -135,8 +135,8 @@ export function printSequence(model) {
         var key = _b[_a];
         var _c = byEntityKey[+key], sequence = _c.sequence, entityId = _c.entityId;
         var seqId = sequence.seqId, compId = sequence.compId;
-        console.log(entityId + " (" + sequence.kind + " " + seqId.value(0) + ", " + seqId.value(seqId.rowCount - 1) + ") (" + compId.value(0) + ", " + compId.value(compId.rowCount - 1) + ")");
-        console.log("" + Sequence.getSequenceString(sequence));
+        console.log("".concat(entityId, " (").concat(sequence.kind, " ").concat(seqId.value(0), ", ").concat(seqId.value(seqId.rowCount - 1), ") (").concat(compId.value(0), ", ").concat(compId.value(compId.rowCount - 1), ")"));
+        console.log("".concat(Sequence.getSequenceString(sequence)));
     }
     console.log();
 }
@@ -153,7 +153,7 @@ export function printRings(structure) {
         }
         if (all.length > 5)
             fps.push('...');
-        console.log("Unit " + unit.id + ", " + all.length + " ring(s), " + byFingerprint.size + " different fingerprint(s).\n  " + fps.join(', '));
+        console.log("Unit ".concat(unit.id, ", ").concat(all.length, " ring(s), ").concat(byFingerprint.size, " different fingerprint(s).\n  ").concat(fps.join(', ')));
     }
     console.log();
 }
@@ -166,10 +166,10 @@ export function printUnits(structure) {
         var elements = unit.elements;
         var size = OrderedSet.size(elements);
         if (Unit.isAtomic(l.unit)) {
-            console.log("Atomic unit " + unit.id + " " + unit.conformation.operator.name + ": " + size + " elements");
+            console.log("Atomic unit ".concat(unit.id, " ").concat(unit.conformation.operator.name, ": ").concat(size, " elements"));
         }
         else if (Unit.isCoarse(l.unit)) {
-            console.log("Coarse unit " + unit.id + " " + unit.conformation.operator.name + " (" + (Unit.isSpheres(l.unit) ? 'spheres' : 'gaussians') + "): " + size + " elements.");
+            console.log("Coarse unit ".concat(unit.id, " ").concat(unit.conformation.operator.name, " (").concat(Unit.isSpheres(l.unit) ? 'spheres' : 'gaussians', "): ").concat(size, " elements."));
             var props = StructureProperties.coarse;
             var modelSeq = l.unit.model.sequence;
             for (var j = 0, _j = Math.min(size, 3); j < _j; j++) {
@@ -179,7 +179,7 @@ export function printUnits(structure) {
                 var compId = modelSeq.byEntityKey[props.entityKey(l)].sequence.compId.value;
                 for (var e = start; e <= end; e++)
                     residues.push(compId(e));
-                console.log(props.asym_id(l) + ":" + start + "-" + end + " (" + residues.join('-') + ") " + props.asym_id(l) + " [" + props.x(l).toFixed(2) + ", " + props.y(l).toFixed(2) + ", " + props.z(l).toFixed(2) + "]");
+                console.log("".concat(props.asym_id(l), ":").concat(start, "-").concat(end, " (").concat(residues.join('-'), ") ").concat(props.asym_id(l), " [").concat(props.x(l).toFixed(2), ", ").concat(props.y(l).toFixed(2), ", ").concat(props.z(l).toFixed(2), "]"));
             }
             if (size > 3)
                 console.log("...");
@@ -192,10 +192,10 @@ export function printSymmetryInfo(model) {
     if (!symmetry)
         return;
     var _a = symmetry.spacegroup.cell, size = _a.size, anglesInRadians = _a.anglesInRadians;
-    console.log("Spacegroup: " + symmetry.spacegroup.name + " size: " + Vec3.toString(size) + " angles: " + Vec3.toString(anglesInRadians));
-    console.log("Assembly names: " + symmetry.assemblies.map(function (a) { return a.id; }).join(', '));
+    console.log("Spacegroup: ".concat(symmetry.spacegroup.name, " size: ").concat(Vec3.toString(size), " angles: ").concat(Vec3.toString(anglesInRadians)));
+    console.log("Assembly names: ".concat(symmetry.assemblies.map(function (a) { return a.id; }).join(', ')));
     // NCS example: 1auy
-    console.log("NCS operators: " + (symmetry.ncsOperators && symmetry.ncsOperators.map(function (a) { return a.name; }).join(', ')));
+    console.log("NCS operators: ".concat(symmetry.ncsOperators && symmetry.ncsOperators.map(function (a) { return a.name; }).join(', ')));
 }
 export function printModelStats(models) {
     return __awaiter(this, void 0, void 0, function () {
@@ -212,10 +212,10 @@ export function printModelStats(models) {
                 case 2:
                     m = _a.sent();
                     if (m.coarseHierarchy.isDefined) {
-                        console.log(m.label + " " + m.modelNum + ": " + m.atomicHierarchy.atoms._rowCount + " atom(s), " + m.coarseHierarchy.spheres.count + " sphere(s), " + m.coarseHierarchy.gaussians.count + " gaussian(s)");
+                        console.log("".concat(m.label, " ").concat(m.modelNum, ": ").concat(m.atomicHierarchy.atoms._rowCount, " atom(s), ").concat(m.coarseHierarchy.spheres.count, " sphere(s), ").concat(m.coarseHierarchy.gaussians.count, " gaussian(s)"));
                     }
                     else {
-                        console.log(m.label + " " + m.modelNum + ": " + m.atomicHierarchy.atoms._rowCount + " atom(s)");
+                        console.log("".concat(m.label, " ").concat(m.modelNum, ": ").concat(m.atomicHierarchy.atoms._rowCount, " atom(s)"));
                     }
                     _a.label = 3;
                 case 3:

package/lib/cli/structure-info/model.js.map

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package/lib/cli/structure-info/volume.js

@@ -109,5 +109,5 @@ parser.add_argument('--mesh', {
     required: true
 });
 var args = parser.parse_args();
-run("https://ds.litemol.org/em/emd-" + args.emdb + "/cell?detail=4", args.mesh);
+run("https://ds.litemol.org/em/emd-".concat(args.emdb, "/cell?detail=4"), args.mesh);
 //# sourceMappingURL=volume.js.map

package/lib/cli/structure-info/volume.js.map

@@ -1 +1 @@
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+{"version":3,"file":"volume.js","sourceRoot":"","sources":["../../../src/cli/structure-info/volume.ts"],"names":[],"mappings":";AACA;;;;GAIG;;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,QAAQ,MAAM,UAAU,CAAC;AACrC,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAE7B,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAChD,OAAO,EAAE,WAAW,EAAE,MAAM,WAAW,CAAC;AACxC,OAAO,EAAE,GAAG,EAAE,MAAM,yBAAyB,CAAC;AAC9C,OAAO,EAAE,KAAK,EAAE,MAAM,mBAAmB,CAAC;AAC1C,OAAO,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AAC/C,OAAO,EAAE,IAAI,EAAE,MAAM,gBAAgB,CAAC;AACtC,OAAO,EAAE,0BAA0B,EAAE,MAAM,kCAAkC,CAAC;AAC9E,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAC;AAC9C,OAAO,EAAE,2BAA2B,EAAE,WAAW,EAAE,MAAM,+CAA+C,CAAC;AAEzG,OAAO,CAAC,gBAAgB,CAAC,CAAC,IAAI,EAAE,CAAC;AACjC,IAAM,cAAc,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC;AAEpD,SAAe,SAAS,CAAC,GAAW;;;;;wBACpB,qBAAM,WAAW,CAAC,GAAG,EAAE,IAAI,CAAC,EAAA;;oBAAlC,GAAG,GAAG,SAA4B;oBAClC,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,aAAa,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;oBAC9C,qBAAM,2BAA2B,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,EAAA;wBAApD,sBAAO,SAA6C,EAAC;;;;CACxD;AAED,SAAS,KAAK,CAAC,MAAc;IACzB,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC;QAAE,OAAO;IACvC,IAAA,mBAAmB,GAAK,MAAM,CAAC,UAAU,CAAC,IAAI,oBAA3B,CAA4B;IACvD,IAAM,GAAG,GAAG,KAAK,CAAC,MAAM,CAAC,mBAAmB,EAAE,CAAC,CAAC,CAAC;IACjD,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IACjB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;IACnC,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AACnC,CAAC;AAED,SAAe,MAAM,CAAC,MAAc,EAAE,QAAgB;;;;;wBACrC,qBAAM,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,UAAA,OAAO,IAAI,OAAA,0BAA0B,CAAC,EAAE,OAAO,SAAA,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,WAAW,EAAE,EAAE,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC,EAAjH,CAAiH,CAAC,CAAC,GAAG,EAAE,EAAA;;oBAAhK,IAAI,GAAG,SAAyJ;oBACtK,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,IAAI,CAAC,WAAW,EAAE,EAAE,EAAE,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC;oBAGtD,WAAW,GAAoB,IAAI,YAAxB,EAAE,aAAa,GAAK,IAAI,cAAT,CAAU;oBAEtC,EAAE,GAAG,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC;oBACjC,EAAE,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,KAAK,CAAC;oBAEhC,GAAG,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC;oBACnC,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE;wBAClC,aAAa,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;wBAC/B,aAAa,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC;wBAClD,aAAa,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC;wBAC/B,aAAa,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC;wBAClD,aAAa,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC;wBAC/B,aAAa,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC;wBAClD,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;qBAC9B;oBACD,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE;wBACpC,aAAa,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;wBAC/B,aAAa,CAAC,oBAAoB,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;wBAC3D,aAAa,CAAC,oBAAoB,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;wBAC3D,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;wBACnD,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;qBAC9B;oBAED,qBAAM,cAAc,CAAC,QAAQ,EAAE,aAAa,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,EAAA;;oBAA5D,SAA4D,CAAC;;;;;CAChE;AAED,SAAe,GAAG,CAAC,GAAW,EAAE,YAAoB;;;;;wBACjC,qBAAM,SAAS,CAAC,GAAG,CAAC,EAAA;;oBAA7B,MAAM,GAAG,SAAoB;oBACnC,KAAK,CAAC,MAAM,CAAC,CAAC;oBACd,qBAAM,MAAM,CAAC,MAAM,EAAE,YAAY,CAAC,EAAA;;oBAAlC,SAAkC,CAAC;;;;;CACtC;AAED,IAAM,MAAM,GAAG,IAAI,QAAQ,CAAC,cAAc,CAAC;IACvC,QAAQ,EAAE,IAAI;IACd,WAAW,EAAE,6CAA6C;CAC7D,CAAC,CAAC;AACH,MAAM,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,EAAE;IAChC,IAAI,EAAE,2BAA2B;CACpC,CAAC,CAAC;AACH,MAAM,CAAC,YAAY,CAAC,QAAQ,EAAE;IAC1B,IAAI,EAAE,eAAe;IACrB,QAAQ,EAAE,IAAI;CACjB,CAAC,CAAC;AAKH,IAAM,IAAI,GAAS,MAAM,CAAC,UAAU,EAAE,CAAC;AAEvC,GAAG,CAAC,wCAAiC,IAAI,CAAC,IAAI,mBAAgB,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC"}

package/lib/commonjs/apps/docking-viewer/index.js

@@ -110,7 +110,7 @@ var Viewer = /** @class */ (function () {
             ? document.getElementById(elementOrId)
             : elementOrId;
         if (!element)
-            throw new Error("Could not get element with id '" + elementOrId + "'");
+            throw new Error("Could not get element with id '".concat(elementOrId, "'"));
         this.plugin = (0, mol_plugin_ui_1.createPlugin)(element, spec);
         this.plugin.customState = {
             colorPalette: {

package/lib/commonjs/apps/docking-viewer/index.js.map

@@ -1 +1 @@
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