npm - molstar - Versions diffs - 2.3.6 → 2.4.0 - Mend

molstar 2.3.6 → 2.4.0

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 (1610) hide show

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/lib/cli/structure-info/volume.js CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/apps/docking-viewer/index.ts"],"names":[],"mappings":";AAAA;;;;;GAKG;;;;AAEH,uDAAsD;AAEtD,0DAAgG;AAChG,qDAAmD;AAGnD,iDAA6E;AAC7E,sDAA4D;AAC5D,sDAA2D;AAC3D,kDAAuD;AACvD,8CAAmD;AACnD,6CAA8C;AAC9C,2CAAsC;AACtC,8CAA6C;AAC7C,oDAAwD;AACxD,oEAAwE;AACxE,mCAAiC;AACjC,4DAAyD;AACzD,wBAAsB;AACtB,uCAA6E;AAE7E,OAAO,CAAC,+BAA+B,CAAC,CAAC;AAEzC,oDAAqE;AAA5D,kGAAA,cAAc,OAAW;AAClC,8CAAuE;AAA9D,qGAAA,YAAY,OAAA;AAAE,0GAAA,iBAAiB,OAAA;AAGxC,IAAM,oBAAoB,GAAG;IACzB,UAAU,EAAE,IAAA,yBAAU,EAAC,EAAE,CAAC;IAC1B,gBAAgB,EAAE,IAAI;IACtB,kBAAkB,EAAE,IAAI;IACxB,qBAAqB,EAAE,IAAI;IAC3B,qBAAqB,EAAE,UAAyC;IAChE,kBAAkB,EAAE,IAAI;IACxB,aAAa,EAAE,IAAI;IACnB,mBAAmB,EAAE,IAAI;IAEzB,kBAAkB,EAAE,qBAAY,CAAC,QAAQ,CAAC,UAAU,CAAC,YAAY;IACjE,oBAAoB,EAAE,qBAAY,CAAC,QAAQ,CAAC,YAAY,CAAC,YAAY;IACrE,oBAAoB,EAAE,qBAAY,CAAC,QAAQ,CAAC,YAAY,CAAC,YAAY;IACrE,yBAAyB,EAAE,qBAAY,CAAC,QAAQ,CAAC,iBAAiB,CAAC,YAAY;IAC/E,qBAAqB,EAAE,qBAAY,CAAC,QAAQ,CAAC,aAAa,CAAC,YAAY;IACvE,iBAAiB,EAAE,qBAAY,CAAC,KAAK,CAAC,aAAa,CAAC,YAAY;IAChE,qBAAqB,EAAE,qBAAY,CAAC,eAAe,CAAC,aAAa,CAAC,YAAY;IAC9E,WAAW,EAAE,qBAAY,CAAC,QAAQ,CAAC,kBAAkB,CAAC,YAAY;IAClE,YAAY,EAAE,qBAAY,CAAC,QAAQ,CAAC,mBAAmB,CAAC,YAAY;CACvE,CAAC;AAEF;IAGI,gBAAY,WAAiC,EAAE,MAA2C,EAAE,WAAkB;QAA9G,iBA4FC;QA5F8C,uBAAA,EAAA,UAAU,IAAA,aAAK,EAAC,QAAQ,CAAC,EAAE,IAAA,aAAK,EAAC,QAAQ,CAAC,CAAC;QAAE,4BAAA,EAAA,kBAAkB;;QAC1G,IAAM,CAAC,mDAAQ,oBAAoB,GAAK;YACpC,gBAAgB,EAAE,KAAK;YACvB,kBAAkB,EAAE,KAAK;YACzB,qBAAqB,EAAE,KAAK;YAC5B,kBAAkB,EAAE,IAAI;YACxB,aAAa,EAAE,KAAK;YACpB,mBAAmB,EAAE,IAAI;YAEzB,kBAAkB,EAAE,IAAI;YACxB,oBAAoB,EAAE,KAAK;YAC3B,oBAAoB,EAAE,KAAK;YAC3B,yBAAyB,EAAE,KAAK;YAChC,qBAAqB,EAAE,KAAK;SAC/B,CAAE,CAAC;QACJ,IAAM,WAAW,GAAG,IAAA,0BAAmB,GAAE,CAAC;QAE1C,IAAM,IAAI,GAAiB;YACvB,OAAO,EAAE,WAAW,CAAC,OAAO;YAC5B,SAAS,EAAE;gBACP,iBAAU,CAAC,QAAQ,CAAC,0BAAe,CAAC,cAAc,CAAC,aAAa,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC;gBAClF,iBAAU,CAAC,QAAQ,CAAC,0BAAe,CAAC,cAAc,CAAC,wBAAwB,CAAC;gBAC5E,iBAAU,CAAC,QAAQ,CAAC,0BAAe,CAAC,MAAM,CAAC,SAAS,CAAC;gBAErD,iBAAU,CAAC,QAAQ,CAAC,0BAAe,CAAC,WAAW,CAAC,aAAa,CAAC;gBAC9D,iBAAU,CAAC,QAAQ,CAAC,0BAAe,CAAC,WAAW,CAAC,YAAY,CAAC;gBAC7D,iBAAU,CAAC,QAAQ,CAAC,0BAAe,CAAC,WAAW,CAAC,kBAAkB,CAAC;aACtE;YACD,UAAU,EAAE,WAAW,CAAC,UAAU;YAClC,kBAAkB,EAAE,WAAW,CAAC,kBAAkB;YAClD,MAAM,EAAE;gBACJ,OAAO,EAAE;oBACL,UAAU,EAAE,CAAC,CAAC,gBAAgB;oBAC9B,YAAY,EAAE,CAAC,CAAC,kBAAkB;oBAClC,eAAe,EAAE,CAAC,CAAC,qBAAqB;iBAC3C;aACJ;YACD,UAAU,kDACH,WAAW,CAAC,UAAU,KACzB,QAAQ,kDACD,MAAA,WAAW,CAAC,UAAU,0CAAE,QAAQ,KACnC,GAAG,EAAE,CAAC,CAAC,kBAAkB,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,EAC9C,MAAM,EAAE,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,EAC5C,IAAI,EAAE,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,KAEpD,WAAW,EAAE,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,EACzD,QAAQ,EAAE;oBACN,IAAI,EAAE,4BAAiB;iBAC1B,GACJ;YACD,MAAM,EAAE;gBACJ,CAAC,qBAAY,CAAC,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAC,kBAAkB,CAAC;gBACxD,CAAC,qBAAY,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,CAAC,oBAAoB,CAAC;gBAC5D,CAAC,qBAAY,CAAC,QAAQ,CAAC,YAAY,EAAE,CAAC,CAAC,oBAAoB,CAAC;gBAC5D,CAAC,qBAAY,CAAC,QAAQ,CAAC,iBAAiB,EAAE,CAAC,CAAC,yBAAyB,CAAC;gBACtE,CAAC,qBAAY,CAAC,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC,qBAAqB,CAAC;gBAC9D,CAAC,qBAAY,CAAC,KAAK,CAAC,aAAa,EAAE,CAAC,CAAC,iBAAiB,CAAC;gBACvD,CAAC,qBAAY,CAAC,KAAK,CAAC,aAAa,EAAE,CAAC,CAAC,iBAAiB,CAAC;gBACvD,CAAC,qBAAY,CAAC,eAAe,CAAC,aAAa,EAAE,CAAC,CAAC,qBAAqB,CAAC;gBACrE,CAAC,qBAAY,CAAC,QAAQ,CAAC,kBAAkB,EAAE,CAAC,CAAC,WAAW,CAAC;gBACzD,CAAC,qBAAY,CAAC,QAAQ,CAAC,mBAAmB,EAAE,CAAC,CAAC,YAAY,CAAC;gBAC3D,CAAC,sBAAW,EAAE,WAAW,CAAC;aAC7B;SACJ,CAAC;QAEF,IAAM,OAAO,GAAG,OAAO,WAAW,KAAK,QAAQ;YAC3C,CAAC,CAAC,QAAQ,CAAC,cAAc,CAAC,WAAW,CAAC;YACtC,CAAC,CAAC,WAAW,CAAC;QAClB,IAAI,CAAC,OAAO;YAAE,MAAM,IAAI,KAAK,CAAC,yCAAkC,WAAW,MAAG,CAAC,CAAC;QAChF,IAAI,CAAC,MAAM,GAAG,IAAA,4BAAY,EAAC,OAAO,EAAE,IAAI,CAAC,CAAC;QAEzC,IAAI,CAAC,MAAM,CAAC,WAAmB,GAAG;YAC/B,YAAY,EAAE;gBACV,IAAI,EAAE,QAAQ;gBACd,MAAM,EAAE,EAAE,IAAI,EAAE,EAAE,MAAM,QAAA,EAAE,EAAE;aAC/B;SACJ,CAAC;QAEF,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,QAAQ,CAAC,WAAW,CAAC,SAAS,CAAC,UAAA,CAAC;YAClD,IAAI,CAAC,EAAE;gBACH,yBAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,KAAI,CAAC,MAAM,EAAE,EAAE,QAAQ,EAAE;wBACzD,QAAQ,kDACD,KAAI,CAAC,MAAM,CAAC,QAAS,CAAC,KAAK,CAAC,QAAQ,KACvC,eAAe,EAAE,kBAAU,CAAC,KAAK,GACpC;wBACD,MAAM,kDACC,KAAI,CAAC,MAAM,CAAC,QAAS,CAAC,KAAK,CAAC,MAAM,KACrC,MAAM,EAAE,EAAE,IAAI,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,EAAE,EAAE,GAChD;qBACJ,EAAE,CAAC,CAAC;aACR;QACL,CAAC,CAAC,CAAC;IACP,CAAC;IAEK,+CAA8B,GAApC,UAAqC,OAA+E;;;;;;;wBAC1G,UAAU,GAAsB,EAAE,CAAC;8BACM,EAAP,mBAAO;;;6BAAP,CAAA,qBAAO,CAAA;wBAApC,kBAAyB,EAAvB,GAAG,SAAA,EAAE,MAAM,YAAA,EAAE,QAAQ,cAAA;wBACjB,qBAAM,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,GAAG,KAAA,EAAE,QAAQ,UAAA,EAAE,CAAC,EAAA;;wBAAlE,SAAO,SAA2D;wBACrD,qBAAM,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,eAAe,CAAC,MAAI,EAAE,MAAM,CAAC,EAAA;;wBAA/E,UAAU,GAAG,SAAkE;wBACvE,qBAAM,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,CAAC,EAAA;;wBAApE,KAAK,GAAG,SAA4D;wBAClD,qBAAM,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,qBAAqB,CAAC,KAAK,CAAC,EAAA;;wBAAnF,eAA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package/lib/commonjs/apps/viewer/index.d.ts CHANGED Viewed

@@ -24,7 +24,7 @@ export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setDebugMode, setProductionMode } from '../../mol-util/debug';
 declare const DefaultViewerOptions: {
     customFormats: [string, DataFormatProvider<any, any, any>][];
-    extensions: ("geo-export" | "g3d" | "cellpack" | "dnatco-confal-pyramids" | "pdbe-structure-quality-report" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "mp4-export")[];
+    extensions: ("pdbe-structure-quality-report" | "g3d" | "cellpack" | "dnatco-confal-pyramids" | "rcsb-assembly-symmetry" | "rcsb-validation-report" | "anvil-membrane-orientation" | "mp4-export" | "geo-export")[];
     layoutIsExpanded: boolean;
     layoutShowControls: boolean;
     layoutShowRemoteState: boolean;
@@ -47,7 +47,7 @@ declare const DefaultViewerOptions: {
     pluginStateServer: string | undefined;
     volumeStreamingServer: string | undefined;
     volumeStreamingDisabled: boolean;
-    pdbProvider: "rcsb" | "pdbe" | undefined;
+    pdbProvider: "pdbe" | "rcsb" | undefined;
     emdbProvider: import("../../mol-plugin-state/actions/volume").EmdbDownloadProvider | undefined;
 };
 declare type ViewerOptions = typeof DefaultViewerOptions;
@@ -130,7 +130,7 @@ export declare class Viewer {
             unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
             structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
             structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
-            representation: {
+            representation: {} | {
                 components?: undefined;
                 representations?: undefined;
             } | {
@@ -188,7 +188,7 @@ export declare class Viewer {
                 representations: {
                     all: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
                 };
-            } | {} | {
+            } | {
                 components?: undefined;
                 representations?: undefined;
             } | {
@@ -213,7 +213,7 @@ export declare class Viewer {
             unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
             structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
             structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
-            representation: {
+            representation: {} | {
                 components?: undefined;
                 representations?: undefined;
             } | {
@@ -271,7 +271,7 @@ export declare class Viewer {
                 representations: {
                     all: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
                 };
-            } | {} | {
+            } | {
                 components?: undefined;
                 representations?: undefined;
             } | {
@@ -290,7 +290,7 @@ export declare class Viewer {
             unitcell: StateObjectSelector<PluginStateObject.Shape.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | undefined;
             structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
             structureProperties: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
-            representation: {
+            representation: {} | {
                 components?: undefined;
                 representations?: undefined;
             } | {
@@ -348,7 +348,7 @@ export declare class Viewer {
                 representations: {
                     all: StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>;
                 };
-            } | {} | {
+            } | {
                 components?: undefined;
                 representations?: undefined;
             } | {

package/lib/commonjs/apps/viewer/index.js CHANGED Viewed

@@ -129,11 +129,11 @@ 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);
     }
     Viewer.prototype.setRemoteSnapshot = function (id) {
-        var url = this.plugin.config.get(config_1.PluginConfig.State.CurrentServer) + "/get/" + id;
+        var url = "".concat(this.plugin.config.get(config_1.PluginConfig.State.CurrentServer), "/get/").concat(id);
         return commands_1.PluginCommands.State.Snapshots.Fetch(this.plugin, { url: url });
     };
     Viewer.prototype.loadSnapshotFromUrl = function (url, type) {
@@ -294,7 +294,7 @@ var Viewer = /** @class */ (function () {
             return (0, tslib_1.__generator)(this, function (_b) {
                 plugin = this.plugin;
                 if (!plugin.dataFormats.get(format)) {
-                    throw new Error("Unknown density format: " + format);
+                    throw new Error("Unknown density format: ".concat(format));
                 }
                 if (options === null || options === void 0 ? void 0 : options.isLazy) {
                     update = this.plugin.build();

package/lib/commonjs/apps/viewer/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/cli/chem-comp-dict/create-ions.js CHANGED Viewed

@@ -27,7 +27,7 @@ function extractIonNames(ccd) {
     return ionNames;
 }
 function writeIonNamesFile(filePath, ionNames) {
-    var output = "/**\n * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-table cli\n */\n\nexport const IonNames = new Set(" + JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ') + ");\n";
+    var output = "/**\n * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * Code-generated ion names params file. Names extracted from CCD components.\n *\n * @author molstar/chem-comp-dict/create-table cli\n */\n\nexport const IonNames = new Set(".concat(JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', '), ");\n");
     writeFile(filePath, output);
 }
 function run(out, forceDownload) {

package/lib/commonjs/cli/chem-comp-dict/create-ions.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/cli/chem-comp-dict/create-table.js CHANGED Viewed

@@ -20,10 +20,10 @@ var mmcif_extras_1 = require("../../mol-io/reader/cif/schema/mmcif-extras");
 var ccd_extras_1 = require("../../mol-io/reader/cif/schema/ccd-extras");
 var util_1 = require("./util");
 function ccbKey(compId, atomId1, atomId2) {
-    return atomId1 < atomId2 ? compId + ":" + atomId1 + "-" + atomId2 : compId + ":" + atomId2 + "-" + atomId1;
+    return atomId1 < atomId2 ? "".concat(compId, ":").concat(atomId1, "-").concat(atomId2) : "".concat(compId, ":").concat(atomId2, "-").concat(atomId1);
 }
 function ccaKey(compId, atomId) {
-    return compId + ":" + atomId;
+    return "".concat(compId, ":").concat(atomId);
 }
 function addChemCompBondToSet(set, ccb) {
     for (var i = 0, il = ccb._rowCount; i < il; ++i) {
@@ -68,7 +68,7 @@ function checkAddingBondsFromPVCD(pvcd) {
                     extraBonds.forEach(function (bk) {
                         var _a = bk.split('|'), a1 = _a[0], a2 = _a[1];
                         if (entryAtoms.has(a1) && entryAtoms.has(a2)) {
-                            console.error("Adding all PVCD bonds would wrongly add bond " + bk + " for " + k);
+                            console.error("Adding all PVCD bonds would wrongly add bond ".concat(bk, " for ").concat(k));
                         }
                     });
                 };

package/lib/commonjs/cli/chem-comp-dict/create-table.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/cli/chem-comp-dict/util.js CHANGED Viewed

@@ -27,7 +27,7 @@ function ensureAvailable(path, url, forceDownload) {
             switch (_g.label) {
                 case 0:
                     if (!(forceDownload || !fs.existsSync(path))) return [3 /*break*/, 8];
-                    console.log("downloading " + url + "...");
+                    console.log("downloading ".concat(url, "..."));
                     return [4 /*yield*/, (0, node_fetch_1.default)(url)];
                 case 1:
                     data = _g.sent();
@@ -52,7 +52,7 @@ function ensureAvailable(path, url, forceDownload) {
                     _g.sent();
                     _g.label = 7;
                 case 7:
-                    console.log("done downloading " + url);
+                    console.log("done downloading ".concat(url));
                     _g.label = 8;
                 case 8: return [2 /*return*/];
             }

package/lib/commonjs/cli/chem-comp-dict/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/cli/cif2bcif/converter.js CHANGED Viewed

@@ -17,8 +17,8 @@ var mol_task_1 = require("../../mol-task");
 var binary_cif_1 = require("../../mol-io/common/binary-cif");
 var encoder_1 = require("../../mol-io/writer/cif/encoder");
 function showProgress(p) {
-    process.stdout.write("\r" + new Array(80).join(' '));
-    process.stdout.write("\r" + mol_task_1.Progress.format(p));
+    process.stdout.write("\r".concat(new Array(80).join(' ')));
+    process.stdout.write("\r".concat(mol_task_1.Progress.format(p)));
 }
 var readFileAsync = util.promisify(fs.readFile);
 var unzipAsync = util.promisify(zlib.unzip);