molstar 3.8.2 → 3.9.0

package/lib/commonjs/mol-model/structure/structure/structure.js

@@ -599,7 +599,7 @@ function getEntityIndices(structure) {
     var keys = generic_1.UniqueArray.create();
     for (var _a = 0, units_2 = units; _a < units_2.length; _a++) {
         var unit = units_2[_a];
-        var prop = unit.kind === 0 /* Atomic */ ? properties_1.StructureProperties.entity.key : properties_1.StructureProperties.coarse.entityKey;
+        var prop = unit.kind === 0 /* Unit.Kind.Atomic */ ? properties_1.StructureProperties.entity.key : properties_1.StructureProperties.coarse.entityKey;
         l.unit = unit;
         var elements = unit.elements;
         var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
@@ -925,20 +925,20 @@ function getSerialMapping(structure) {
                     partitionAtomicUnitByResidue(model, elements, builder, multiChain, operator);
                 }
                 else {
-                    builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
+                    builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, elements, multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */);
                 }
             }
             else {
-                builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
+                builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, elements, multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */);
             }
         }
         var cs = model.coarseHierarchy;
         if (cs.isDefined) {
             if (cs.spheres.count > 0) {
-                addCoarseUnits(builder, model, model.coarseHierarchy.spheres, 1 /* Spheres */);
+                addCoarseUnits(builder, model, model.coarseHierarchy.spheres, 1 /* Unit.Kind.Spheres */);
             }
             if (cs.gaussians.count > 0) {
-                addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, 2 /* Gaussians */);
+                addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, 2 /* Unit.Kind.Gaussians */);
             }
         }
         return builder.getStructure();
@@ -957,7 +957,7 @@ function getSerialMapping(structure) {
         var position = { x: x, y: y, z: z, indices: indices };
         var lookup = (0, geometry_1.GridLookup3D)(position, (0, boundary_1.getBoundary)(position), 8192);
         var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
-        var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
+        var traits = (multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */) | (offset.length > 1 ? 2 /* Unit.Trait.Partitioned */ : 0 /* Unit.Trait.None */);
         builder.beginChainGroup();
         for (var i = 0, _i = offset.length; i < _i; i++) {
             var start = offset[i];
@@ -965,7 +965,7 @@ function getSerialMapping(structure) {
             for (var j = 0, _j = count[i]; j < _j; j++) {
                 set[j] = indices[array[start + j]];
             }
-            builder.addUnit(0 /* Atomic */, model, operator, int_1.SortedArray.ofSortedArray(set), traits);
+            builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, int_1.SortedArray.ofSortedArray(set), traits);
         }
         builder.endChainGroup();
     }
@@ -986,7 +986,7 @@ function getSerialMapping(structure) {
         var position = { x: x, y: y, z: z, indices: int_1.SortedArray.ofSortedArray(startIndices) };
         var lookup = (0, geometry_1.GridLookup3D)(position, (0, boundary_1.getBoundary)(position), gridCellCount);
         var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
-        var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
+        var traits = (multiChain ? 1 /* Unit.Trait.MultiChain */ : 0 /* Unit.Trait.None */) | (offset.length > 1 ? 2 /* Unit.Trait.Partitioned */ : 0 /* Unit.Trait.None */);
         builder.beginChainGroup();
         for (var i = 0, _i = offset.length; i < _i; i++) {
             var start = offset[i];
@@ -997,7 +997,7 @@ function getSerialMapping(structure) {
                     set[set.length] = l;
                 }
             }
-            builder.addUnit(0 /* Atomic */, model, operator, int_1.SortedArray.ofSortedArray(new Int32Array(set)), traits);
+            builder.addUnit(0 /* Unit.Kind.Atomic */, model, operator, int_1.SortedArray.ofSortedArray(new Int32Array(set)), traits);
         }
         builder.endChainGroup();
     }
@@ -1005,7 +1005,7 @@ function getSerialMapping(structure) {
         var chainElementSegments = elements.chainElementSegments;
         for (var cI = 0; cI < chainElementSegments.count; cI++) {
             var elements_1 = int_1.SortedArray.ofBounds(chainElementSegments.offsets[cI], chainElementSegments.offsets[cI + 1]);
-            builder.addUnit(kind, model, symmetry_operator_1.SymmetryOperator.Default, elements_1, 0 /* None */);
+            builder.addUnit(kind, model, symmetry_operator_1.SymmetryOperator.Default, elements_1, 0 /* Unit.Trait.None */);
         }
     }
     function transform(s, transform) {
@@ -1282,7 +1282,7 @@ function getSerialMapping(structure) {
         var l = element_1.StructureElement.Location.create(structure);
         for (var _b = 0, _c = structure.units; _b < _c.length; _b++) {
             var unit = _c[_b];
-            if (unit.kind !== 0 /* Atomic */)
+            if (unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;

package/lib/commonjs/mol-model/structure/structure/unit/bonds/inter-compute.js

@@ -159,7 +159,7 @@ function findPairBonds(unitA, unitB, props, builder) {
                 var compIdB = label_comp_idB.value(residueIndexB[bI]);
                 builder.add(_aI, _bI, {
                     order: (0, bonds_1.getInterBondOrderFromTable)(compIdA, compIdB, atomIdA, atomIdB),
-                    flag: (isMetal ? 2 /* MetallicCoordination */ : 1 /* Covalent */) | 32 /* Computed */
+                    flag: (isMetal ? 2 /* BondType.Flag.MetallicCoordination */ : 1 /* BondType.Flag.Covalent */) | 32 /* BondType.Flag.Computed */
                 });
             }
         }
@@ -188,10 +188,10 @@ function computeInterUnitBonds(structure, props) {
     return findBonds(structure, tslib_1.__assign(tslib_1.__assign({}, p), { validUnitPair: (props && props.validUnitPair) || (function (s, a, b) {
             var mtA = a.model.atomicHierarchy.derived.residue.moleculeType;
             var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
-            var notWater = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&
-                (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* Water */));
-            var notIon = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* Ion */) &&
-                (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* Ion */));
+            var notWater = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* MoleculeType.Water */) &&
+                (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* MoleculeType.Water */));
+            var notIon = ((!unit_1.Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* MoleculeType.Ion */) &&
+                (!unit_1.Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* MoleculeType.Ion */));
             return structure_1.Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
         }) }));
 }

package/lib/commonjs/mol-model/structure/structure/unit/bonds/intra-compute.js

@@ -194,9 +194,9 @@ function findBonds(unit, props) {
                     order[order.length] = e.order;
                     var flag = e.flags;
                     if (isMetal) {
-                        if (flag | 1 /* Covalent */)
-                            flag ^= 1 /* Covalent */;
-                        flag |= 2 /* MetallicCoordination */;
+                        if (flag | 1 /* BondType.Flag.Covalent */)
+                            flag ^= 1 /* BondType.Flag.Covalent */;
+                        flag |= 2 /* BondType.Flag.MetallicCoordination */;
                     }
                     flags[flags.length] = flag;
                 }
@@ -210,7 +210,7 @@ function findBonds(unit, props) {
                 atomA[atomA.length] = _aI;
                 atomB[atomB.length] = _bI;
                 order[order.length] = (0, bonds_1.getIntraBondOrderFromTable)(compId, atomIdA, label_atom_id.value(bI));
-                flags[flags.length] = (isMetal ? 2 /* MetallicCoordination */ : 1 /* Covalent */) | 32 /* Computed */;
+                flags[flags.length] = (isMetal ? 2 /* BondType.Flag.MetallicCoordination */ : 1 /* BondType.Flag.Covalent */) | 32 /* BondType.Flag.Computed */;
                 var seqIdB = label_seq_id.value(rbI);
                 if (seqIdA === seqIdB)
                     isDictionaryBased = false;

package/lib/commonjs/mol-model/structure/structure/unit/bonds.js

@@ -129,14 +129,14 @@ var Bond;
             var bonds = location.aUnit.bonds;
             var idx = bonds.getEdgeIndex(location.aIndex, location.bIndex);
             if (idx < 0)
-                return types_1.BondType.create(0 /* None */);
+                return types_1.BondType.create(0 /* BondType.Flag.None */);
             return types_1.BondType.create(bonds.edgeProps.flags[idx]);
         }
         else {
             var bond = structure.interUnitBonds.getBondFromLocation(location);
             if (bond)
                 return types_1.BondType.create(bond.props.flag);
-            return types_1.BondType.create(0 /* None */);
+            return types_1.BondType.create(0 /* BondType.Flag.None */);
         }
     }
     Bond.getType = getType;

package/lib/commonjs/mol-model/structure/structure/unit/resonance.js

@@ -41,7 +41,7 @@ function getDelocalizedTriplets(unit) {
         var deloBonds = [];
         for (var t = offset[i], _t = offset[i + 1]; t < _t; t++) {
             var f = _flags[t];
-            if (!types_1.BondType.is(f, 16 /* Aromatic */))
+            if (!types_1.BondType.is(f, 16 /* BondType.Flag.Aromatic */))
                 continue;
             deloBonds.push(b[t]);
         }

package/lib/commonjs/mol-model/structure/structure/unit/rings/compute.js

@@ -32,8 +32,8 @@ function State(unit, capacity) {
         queue: new Int32Array(capacity),
         pred: new Int32Array(capacity),
         depth: new Int32Array(capacity),
-        left: new Int32Array(5 /* MaxDepth */),
-        right: new Int32Array(5 /* MaxDepth */),
+        left: new Int32Array(5 /* Constants.MaxDepth */),
+        right: new Int32Array(5 /* Constants.MaxDepth */),
         color: new Int32Array(capacity),
         currentColor: 0,
         currentAltLoc: '',
@@ -136,7 +136,7 @@ function addRing(state, a, b, isRingAtom) {
     var pred = state.pred, color = state.color, left = state.left, right = state.right;
     var nc = ++state.currentColor;
     var current = a;
-    for (var t = 0; t < 5 /* MaxDepth */; t++) {
+    for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
         color[current] = nc;
         current = pred[current];
         if (current < 0)
@@ -145,7 +145,7 @@ function addRing(state, a, b, isRingAtom) {
     var leftOffset = 0, rightOffset = 0;
     var found = false, target = 0;
     current = b;
-    for (var t = 0; t < 5 /* MaxDepth */; t++) {
+    for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
         if (color[current] === nc) {
             target = current;
             found = true;
@@ -160,7 +160,7 @@ function addRing(state, a, b, isRingAtom) {
         return false;
     }
     current = a;
-    for (var t = 0; t < 5 /* MaxDepth */; t++) {
+    for (var t = 0; t < 5 /* Constants.MaxDepth */; t++) {
         left[leftOffset++] = current;
         if (target === current)
             break;
@@ -232,7 +232,7 @@ function findRings(state, from, mark) {
                 continue;
             }
             var newDepth = Math.min(depth[other], d + 1);
-            if (newDepth > 5 /* MaxDepth */)
+            if (newDepth > 5 /* Constants.MaxDepth */)
                 continue;
             depth[other] = newDepth;
             marked[other] = mark;

package/lib/commonjs/mol-model/structure/structure/unit/rings.js

@@ -97,11 +97,11 @@ var UnitRing;
     }
     UnitRing.elementFingerprint = elementFingerprint;
     var AromaticRingElements = new Set([
-        "B" /* B */, "C" /* C */, "N" /* N */, "O" /* O */,
-        "SI" /* SI */, "P" /* P */, "S" /* S */,
-        "GE" /* GE */, "AS" /* AS */,
-        "SN" /* SN */, "SB" /* SB */,
-        "BI" /* BI */
+        "B" /* Elements.B */, "C" /* Elements.C */, "N" /* Elements.N */, "O" /* Elements.O */,
+        "SI" /* Elements.SI */, "P" /* Elements.P */, "S" /* Elements.S */,
+        "GE" /* Elements.GE */, "AS" /* Elements.AS */,
+        "SN" /* Elements.SN */, "SB" /* Elements.SB */,
+        "BI" /* Elements.BI */
     ]);
     var AromaticRingPlanarityThreshold = 0.05;
     function isAromatic(unit, ring) {
@@ -119,7 +119,7 @@ var UnitRing;
             }
             for (var j = offset[aI], jl = offset[aI + 1]; j < jl; ++j) {
                 // comes e.g. from `chem_comp_bond.pdbx_aromatic_flag`
-                if (types_1.BondType.is(16 /* Aromatic */, flags[j])) {
+                if (types_1.BondType.is(16 /* BondType.Flag.Aromatic */, flags[j])) {
                     if (int_1.SortedArray.has(ring, b[j]))
                         aromaticBondCount += 1;
                 }

package/lib/commonjs/mol-model/structure/structure/unit.js

@@ -26,19 +26,19 @@ var symmetry_1 = require("../../../mol-model-formats/structure/property/symmetry
 var resonance_1 = require("./unit/resonance");
 var Unit;
 (function (Unit) {
-    function isAtomic(u) { return u.kind === 0 /* Atomic */; }
+    function isAtomic(u) { return u.kind === 0 /* Kind.Atomic */; }
     Unit.isAtomic = isAtomic;
-    function isCoarse(u) { return u.kind === 1 /* Spheres */ || u.kind === 2 /* Gaussians */; }
+    function isCoarse(u) { return u.kind === 1 /* Kind.Spheres */ || u.kind === 2 /* Kind.Gaussians */; }
     Unit.isCoarse = isCoarse;
-    function isSpheres(u) { return u.kind === 1 /* Spheres */; }
+    function isSpheres(u) { return u.kind === 1 /* Kind.Spheres */; }
     Unit.isSpheres = isSpheres;
-    function isGaussians(u) { return u.kind === 2 /* Gaussians */; }
+    function isGaussians(u) { return u.kind === 2 /* Kind.Gaussians */; }
     Unit.isGaussians = isGaussians;
     function create(id, invariantId, chainGroupId, traits, kind, model, operator, elements, props) {
         switch (kind) {
-            case 0 /* Atomic */: return new Atomic(id, invariantId, chainGroupId, traits, model, elements, symmetry_operator_1.SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), props !== null && props !== void 0 ? props : AtomicProperties());
-            case 1 /* Spheres */: return createCoarse(id, invariantId, chainGroupId, traits, model, 1 /* Spheres */, elements, symmetry_operator_1.SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
-            case 2 /* Gaussians */: return createCoarse(id, invariantId, chainGroupId, traits, model, 2 /* Gaussians */, elements, symmetry_operator_1.SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
+            case 0 /* Kind.Atomic */: return new Atomic(id, invariantId, chainGroupId, traits, model, elements, symmetry_operator_1.SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), props !== null && props !== void 0 ? props : AtomicProperties());
+            case 1 /* Kind.Spheres */: return createCoarse(id, invariantId, chainGroupId, traits, model, 1 /* Kind.Spheres */, elements, symmetry_operator_1.SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
+            case 2 /* Kind.Gaussians */: return createCoarse(id, invariantId, chainGroupId, traits, model, 2 /* Kind.Gaussians */, elements, symmetry_operator_1.SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
         }
     }
     Unit.create = create;
@@ -126,7 +126,7 @@ var Unit;
      */
     var Atomic = /** @class */ (function () {
         function Atomic(id, invariantId, chainGroupId, traits, model, elements, conformation, props) {
-            this.kind = 0 /* Atomic */;
+            this.kind = 0 /* Kind.Atomic */;
             this.objectPrimitive = 'atomistic';
             this.id = id;
             this.invariantId = invariantId;
@@ -310,7 +310,7 @@ var Unit;
     var Coarse = /** @class */ (function () {
         function Coarse(id, invariantId, chainGroupId, traits, model, kind, elements, conformation, props) {
             this.kind = kind;
-            this.objectPrimitive = kind === 1 /* Spheres */ ? 'sphere' : 'gaussian';
+            this.objectPrimitive = kind === 1 /* Kind.Spheres */ ? 'sphere' : 'gaussian';
             this.id = id;
             this.invariantId = invariantId;
             this.chainGroupId = chainGroupId;
@@ -318,8 +318,8 @@ var Unit;
             this.model = model;
             this.elements = elements;
             this.conformation = conformation;
-            this.coarseElements = kind === 1 /* Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
-            this.coarseConformation = (kind === 1 /* Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians);
+            this.coarseElements = kind === 1 /* Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
+            this.coarseConformation = (kind === 1 /* Kind.Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians);
             this.props = props;
         }
         Coarse.prototype.getChild = function (elements) {
@@ -408,7 +408,7 @@ var Unit;
         return Coarse;
     }());
     function getCoarseConformation(kind, model) {
-        return kind === 1 /* Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians;
+        return kind === 1 /* Kind.Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians;
     }
     function CoarseProperties() {
         return BaseProperties();
@@ -482,8 +482,8 @@ var Unit;
     }
     Unit.isSameConformation = isSameConformation;
     function getModelConformationOfKind(kind, model) {
-        return kind === 0 /* Atomic */ ? model.atomicConformation :
-            kind === 1 /* Spheres */ ? model.coarseConformation.spheres :
+        return kind === 0 /* Kind.Atomic */ ? model.atomicConformation :
+            kind === 1 /* Kind.Spheres */ ? model.coarseConformation.spheres :
                 model.coarseConformation.gaussians;
     }
     Unit.getModelConformationOfKind = getModelConformationOfKind;
@@ -492,8 +492,8 @@ var Unit;
     }
     Unit.getConformation = getConformation;
     function getModelHierarchyOfKind(kind, model) {
-        return kind === 0 /* Atomic */ ? model.atomicHierarchy :
-            kind === 1 /* Spheres */ ? model.coarseHierarchy.spheres :
+        return kind === 0 /* Kind.Atomic */ ? model.atomicHierarchy :
+            kind === 1 /* Kind.Spheres */ ? model.coarseHierarchy.spheres :
                 model.coarseHierarchy.gaussians;
     }
     Unit.getModelHierarchyOfKind = getModelHierarchyOfKind;

package/lib/commonjs/mol-model/structure/structure/util/superposition-sifts-mapping.js

@@ -109,7 +109,7 @@ function buildIndex(structure, index, sI, traceOnly) {
     var _a;
     for (var _i = 0, _b = structure.units; _i < _b.length; _i++) {
         var unit = _b[_i];
-        if (unit.kind !== 0 /* Atomic */)
+        if (unit.kind !== 0 /* Unit.Kind.Atomic */)
             continue;
         var elements = unit.elements, model = unit.model;
         var map = sifts_mapping_1.SIFTSMapping.Provider.get(model).value;

package/lib/commonjs/mol-model/structure/util.js

@@ -17,17 +17,17 @@ function getCoarseBegCompId(unit, element) {
 exports.getCoarseBegCompId = getCoarseBegCompId;
 function getElementMoleculeType(unit, element) {
     switch (unit.kind) {
-        case 0 /* Atomic */:
+        case 0 /* Unit.Kind.Atomic */:
             return unit.model.atomicHierarchy.derived.residue.moleculeType[unit.residueIndex[element]];
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
+        case 1 /* Unit.Kind.Spheres */:
+        case 2 /* Unit.Kind.Gaussians */:
             // TODO add unit.model.coarseHierarchy.derived.residue.moleculeType
             var compId = getCoarseBegCompId(unit, element);
             var cc = unit.model.properties.chemicalComponentMap.get(compId);
             if (cc)
                 return (0, types_1.getMoleculeType)(cc.type, compId);
     }
-    return 0 /* Unknown */;
+    return 0 /* MoleculeType.Unknown */;
 }
 exports.getElementMoleculeType = getElementMoleculeType;
 function getAtomicMoleculeType(model, rI) {

package/lib/commonjs/mol-model-formats/structure/basic/atomic.js

@@ -98,12 +98,12 @@ function createChainOperatorMappingAndSubstituteNames(hierarchy, format) {
     var labelMap = new Map();
     var authMap = new Map();
     for (var i = 0; i < entries._rowCount; i++) {
-        var assembly = entries.assembly_operator_id.valueKind(i) === 0 /* Present */
+        var assembly = entries.assembly_operator_id.valueKind(i) === 0 /* Column.ValueKind.Present */
             ? { id: entries.assembly_id.value(i), operList: [], operId: entries.assembly_operator_id.value(i) }
             : void 0;
         var operator = geometry_1.SymmetryOperator.create(entries.operator_name.value(i), linear_algebra_1.Mat4.identity(), {
             assembly: assembly,
-            spgrOp: entries.symmetry_operator_index.valueKind(i) === 0 /* Present */ ? entries.symmetry_operator_index.value(i) : void 0,
+            spgrOp: entries.symmetry_operator_index.valueKind(i) === 0 /* Column.ValueKind.Present */ ? entries.symmetry_operator_index.value(i) : void 0,
             hkl: linear_algebra_1.Vec3.ofArray(entries.symmetry_hkl.value(i)),
             ncsId: entries.ncs_id.value(i)
         });

package/lib/commonjs/mol-model-formats/structure/basic/parser.js

@@ -66,12 +66,12 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
     var sequence = (0, sequence_1.getSequence)(data, entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = (0, atomic_ranges_1.getAtomicRanges)(atomic.hierarchy, entities, atomic.conformation, sequence);
     var structAsymMap = (0, properties_1.getStructAsymMap)(atomic.hierarchy);
-    var entry = data.entry.id.valueKind(0) === 0 /* Present */
+    var entry = data.entry.id.valueKind(0) === 0 /* Column.ValueKind.Present */
         ? data.entry.id.value(0) : format.name;
     var label = [];
     if (entry)
         label.push(entry);
-    if (data.struct.title.valueKind(0) === 0 /* Present */)
+    if (data.struct.title.valueKind(0) === 0 /* Column.ValueKind.Present */)
         label.push(data.struct.title.value(0));
     return {
         id: uuid_1.UUID.create22(),
@@ -101,12 +101,12 @@ function createIntegrativeModel(data, ihm, properties, format) {
     var coarse = (0, coarse_1.getCoarse)(ihm, properties.chemicalComponentMap);
     var sequence = (0, sequence_1.getSequence)(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = (0, atomic_ranges_1.getAtomicRanges)(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);
-    var entry = data.entry.id.valueKind(0) === 0 /* Present */
+    var entry = data.entry.id.valueKind(0) === 0 /* Column.ValueKind.Present */
         ? data.entry.id.value(0) : format.name;
     var label = [];
     if (entry)
         label.push(entry);
-    if (data.struct.title.valueKind(0) === 0 /* Present */)
+    if (data.struct.title.valueKind(0) === 0 /* Column.ValueKind.Present */)
         label.push(data.struct.title.value(0));
     if (ihm.model_name)
         label.push(ihm.model_name);

package/lib/commonjs/mol-model-formats/structure/basic/properties.js

@@ -81,7 +81,7 @@ function getSaccharideComponentMap(data) {
             if (constants_1.SaccharideCompIdMap.has(_id)) {
                 map.set(_id, constants_1.SaccharideCompIdMap.get(_id));
             }
-            else if ((0, types_1.getMoleculeType)(_type, _id) === 9 /* Saccharide */) {
+            else if ((0, types_1.getMoleculeType)(_type, _id) === 9 /* MoleculeType.Saccharide */) {
                 map.set(_id, constants_1.UnknownSaccharideComponent);
             }
         }

package/lib/commonjs/mol-model-formats/structure/basic/sort.js

@@ -36,7 +36,7 @@ function sortAtomSite(ctx, atom_site, start, end) {
                     if (!(cI < _cI)) return [3 /*break*/, 7];
                     aI = chainBuckets[cI];
                     // are we in HETATM territory?
-                    if (label_seq_id.valueKind(aI) !== 0 /* Present */)
+                    if (label_seq_id.valueKind(aI) !== 0 /* Column.ValueKind.Present */)
                         return [3 /*break*/, 6];
                     (0, util_1.makeBuckets)(indices, label_seq_id.value, { sort: true, start: aI, end: chainBuckets[cI + 1] });
                     if (!ctx.shouldUpdate) return [3 /*break*/, 6];

package/lib/commonjs/mol-model-formats/structure/basic/util.js

@@ -22,7 +22,7 @@ exports.getModelGroupName = getModelGroupName;
 //
 function hasPresentValues(column) {
     for (var i = 0, il = column.rowCount; i < il; i++) {
-        if (column.valueKind(i) === 0 /* Present */)
+        if (column.valueKind(i) === 0 /* Column.ValueKind.Present */)
             return true;
     }
     return false;

package/lib/commonjs/mol-model-formats/structure/cif-core.js

@@ -131,7 +131,7 @@ function getModels(db, format, ctx) {
                         db.chemical_formula.sum.value(0));
                     entityBuilder = new entity_1.EntityBuilder();
                     entityBuilder.setNames([['MOL', name || 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new component_1.ComponentBuilder(seq_id, db.atom_site.type_symbol);
                     componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
@@ -176,23 +176,23 @@ function getModels(db, format, ctx) {
                                     t = bond_type.str(i);
                                     if (t === 'D') {
                                         order[j] = 2;
-                                        flag[j] = 1 /* Covalent */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */;
                                     }
                                     else if (t === 'A') {
                                         order[j] = 1;
-                                        flag[j] = 1 /* Covalent */ | 16 /* Aromatic */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */ | 16 /* BondType.Flag.Aromatic */;
                                     }
                                     else if (t === 'S') {
                                         order[j] = 1;
-                                        flag[j] = 1 /* Covalent */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */;
                                     }
                                     else {
                                         order[j] = 1;
-                                        flag[j] = 1 /* Covalent */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */;
                                     }
                                 }
                                 else {
-                                    flag[j] = 1 /* Covalent */;
+                                    flag[j] = 1 /* BondType.Flag.Covalent */;
                                     // TODO derive order from bond length if undefined
                                     order[j] = valence.isDefined ? valence.value(i) : 1;
                                 }

package/lib/commonjs/mol-model-formats/structure/common/entity.js

@@ -27,7 +27,7 @@ var EntityBuilder = /** @class */ (function () {
         this.descriptions.push([description]);
     };
     EntityBuilder.prototype.getEntityId = function (compId, moleculeType, chainId, options) {
-        if (moleculeType === 2 /* Water */) {
+        if (moleculeType === 2 /* MoleculeType.Water */) {
             if (this.waterId === undefined) {
                 this.set('water', (options === null || options === void 0 ? void 0 : options.customName) || 'Water');
                 this.waterId = "".concat(this.count);

package/lib/commonjs/mol-model-formats/structure/cube.js

@@ -45,7 +45,7 @@ function getModels(cube, ctx) {
                     }, atoms.count);
                     entityBuilder = new entity_1.EntityBuilder();
                     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);

package/lib/commonjs/mol-model-formats/structure/gro.js

@@ -31,7 +31,7 @@ function getBasic(atoms, modelNum) {
     var currentAsymIndex = 0;
     var currentAsymId = '';
     var currentSeqId = 0;
-    var prevMoleculeType = 0 /* Unknown */;
+    var prevMoleculeType = 0 /* MoleculeType.Unknown */;
     var prevResidueNumber = -1;
     for (var i = 0, il = atoms.count; i < il; ++i) {
         var residueNumber = atoms.residueNumber.value(i);

package/lib/commonjs/mol-model-formats/structure/mol.js

@@ -60,7 +60,7 @@ function getMolModels(mol, format, ctx) {
                     }, atoms.count);
                     entityBuilder = new entity_1.EntityBuilder();
                     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);

package/lib/commonjs/mol-model-formats/structure/mol2.js

@@ -66,7 +66,7 @@ function getModels(mol2, ctx) {
                     }, atoms.count);
                     entityBuilder = new entity_1.EntityBuilder();
                     entityBuilder.setNames([['MOL', molecule.mol_name || 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new component_1.ComponentBuilder(atoms.subst_id, atoms.atom_name);
                     for (i_3 = 0, il_1 = atoms.subst_name.rowCount; i_3 < il_1; ++i_3) {
                         componentBuilder.add(atoms.subst_name.value(i_3), i_3);
@@ -100,13 +100,13 @@ function getModels(mol2, ctx) {
                             switch (x) {
                                 case 'ar': // aromatic
                                 case 'am': // amide
-                                    return 16 /* Aromatic */ | 1 /* Covalent */;
+                                    return 16 /* BondType.Flag.Aromatic */ | 1 /* BondType.Flag.Covalent */;
                                 case 'du': // dummy
                                 case 'nc': // not connected
-                                    return 0 /* None */;
+                                    return 0 /* BondType.Flag.None */;
                                 case 'un': // unknown
                                 default:
-                                    return 1 /* Covalent */;
+                                    return 1 /* BondType.Flag.Covalent */;
                             }
                         }, Int8Array));
                         pairBonds = index_pair_1.IndexPairBonds.fromData({ pairs: { key: key, indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });

package/lib/commonjs/mol-model-formats/structure/prmtop.js

@@ -47,7 +47,7 @@ function getBasic(prmtop) {
     var currentAsymIndex = 0;
     var currentAsymId = '';
     var currentSeqId = 0;
-    var prevMoleculeType = 0 /* Unknown */;
+    var prevMoleculeType = 0 /* MoleculeType.Unknown */;
     var prevResidueNumber = -1;
     for (var i = 0, il = atomCount; i < il; ++i) {
         var residueNumber = residueId.value(i);

package/lib/commonjs/mol-model-formats/structure/property/bonds/chem_comp.js

@@ -67,13 +67,13 @@ var ComponentBond;
             if (entry.id !== id) {
                 entry = addEntry(id);
             }
-            var flags = 1 /* Covalent */;
+            var flags = 1 /* BondType.Flag.Covalent */;
             var ord = 1;
             if (aromatic)
-                flags |= 16 /* Aromatic */;
+                flags |= 16 /* BondType.Flag.Aromatic */;
             switch (order.toLowerCase()) {
                 case 'delo':
-                    flags |= 16 /* Aromatic */;
+                    flags |= 16 /* BondType.Flag.Aromatic */;
                     break;
                 case 'doub':
                     ord = 2;

package/lib/commonjs/mol-model-formats/structure/property/bonds/index-pair.js

@@ -21,7 +21,7 @@ function getGraph(indexA, indexB, props, count) {
         builder.assignProperty(key, props.key ? props.key[i] : -1);
         builder.assignProperty(order, props.order ? props.order[i] : 1);
         builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
-        builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* Covalent */);
+        builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* BondType.Flag.Covalent */);
     }
     return builder.createGraph({ key: key, order: order, distance: distance, flag: flag });
 }

package/lib/commonjs/mol-model-formats/structure/property/bonds/struct_conn.js

@@ -93,7 +93,7 @@ var StructConn;
             symmetry: struct_conn.ptnr2_symmetry
         };
         var _p = function (row, ps) {
-            if (ps.label_asym_id.valueKind(row) !== 0 /* Present */)
+            if (ps.label_asym_id.valueKind(row) !== 0 /* Column.ValueKind.Present */)
                 return void 0;
             var asymId = ps.label_asym_id.value(row);
             var entityIndex = model.atomicHierarchy.index.findEntity(asymId);
@@ -119,7 +119,7 @@ var StructConn;
                 continue;
             var type = conn_type_id.value(i);
             var orderType = (pdbx_value_order.value(i) || '');
-            var flags = 0 /* None */;
+            var flags = 0 /* BondType.Flag.None */;
             var order = 1;
             switch (orderType) {
                 case 'sing':
@@ -139,16 +139,16 @@ var StructConn;
             }
             switch (type) {
                 case 'covale':
-                    flags = 1 /* Covalent */;
+                    flags = 1 /* BondType.Flag.Covalent */;
                     break;
                 case 'disulf':
-                    flags = 1 /* Covalent */ | 8 /* Disulfide */;
+                    flags = 1 /* BondType.Flag.Covalent */ | 8 /* BondType.Flag.Disulfide */;
                     break;
                 case 'hydrog':
-                    flags = 4 /* HydrogenBond */;
+                    flags = 4 /* BondType.Flag.HydrogenBond */;
                     break;
                 case 'metalc':
-                    flags = 2 /* MetallicCoordination */;
+                    flags = 2 /* BondType.Flag.MetallicCoordination */;
                     break;
             }
             entries.push({