molstar 3.8.2 → 3.9.0

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

@@ -40,11 +40,11 @@ var ModelSecondaryStructure;
 exports.ModelSecondaryStructure = ModelSecondaryStructure;
 function getCoordinateType(conf, sheetRange) {
     if (conf._rowCount > 0) {
-        if (conf.beg_label_seq_id.valueKind(0) !== 0 /* Present */ || conf.end_label_seq_id.valueKind(0) !== 0 /* Present */)
+        if (conf.beg_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */ || conf.end_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */)
             return 'auth';
     }
     else if (sheetRange) {
-        if (sheetRange.beg_label_seq_id.valueKind(0) !== 0 /* Present */ || sheetRange.end_label_seq_id.valueKind(0) !== 0 /* Present */)
+        if (sheetRange.beg_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */ || sheetRange.end_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */)
             return 'auth';
     }
     return 'label';
@@ -58,17 +58,17 @@ function addHelices(cat, coordinates, map, elements) {
     var beg_seq_id = coordinates === 'label' ? beg_label_seq_id : beg_auth_seq_id;
     var end_seq_id = coordinates === 'label' ? end_label_seq_id : end_auth_seq_id;
     for (var i = 0, _i = cat._rowCount; i < _i; i++) {
-        var type = types_1.SecondaryStructureType.create(pdbx_PDB_helix_class.valueKind(i) === 0 /* Present */
+        var type = types_1.SecondaryStructureType.create(pdbx_PDB_helix_class.valueKind(i) === 0 /* Column.ValueKind.Present */
             ? types_1.SecondaryStructureType.SecondaryStructurePdb[pdbx_PDB_helix_class.value(i)]
-            : conf_type_id.valueKind(i) === 0 /* Present */
+            : conf_type_id.valueKind(i) === 0 /* Column.ValueKind.Present */
                 ? types_1.SecondaryStructureType.SecondaryStructureMmcif[conf_type_id.value(i)]
-                : 536870912 /* NA */);
+                : 536870912 /* SecondaryStructureType.Flag.NA */);
         var element = {
             kind: 'helix',
             flags: type,
-            type_id: conf_type_id.valueKind(i) === 0 /* Present */ ? conf_type_id.value(i) : 'helx_p',
+            type_id: conf_type_id.valueKind(i) === 0 /* Column.ValueKind.Present */ ? conf_type_id.value(i) : 'helx_p',
             helix_class: pdbx_PDB_helix_class.value(i),
-            details: details.valueKind(i) === 0 /* Present */ ? details.value(i) : void 0
+            details: details.valueKind(i) === 0 /* Column.ValueKind.Present */ ? details.value(i) : void 0
         };
         var entry = {
             startSeqId: beg_seq_id.value(i),
@@ -113,7 +113,7 @@ function addSheets(cat, coordinates, map, sheetCount, elements) {
             key = currentKey++;
             sheet_id_key.set(id, key);
         }
-        var type = types_1.SecondaryStructureType.create(4 /* Beta */ | 8388608 /* BetaSheet */);
+        var type = types_1.SecondaryStructureType.create(4 /* SecondaryStructureType.Flag.Beta */ | 8388608 /* SecondaryStructureType.Flag.BetaSheet */);
         var element = {
             kind: 'sheet',
             flags: type,

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

@@ -29,7 +29,7 @@ function getBasic(atoms) {
     var currentAsymId = '';
     var currentSeqId = 0;
     var currentSegmentName = atoms.segmentName.value(0), segmentChanged = false;
-    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.residueId.value(i);

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

@@ -74,7 +74,7 @@ function getBasic(top) {
     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/xyz.js

@@ -62,7 +62,7 @@ function getModels(mol, ctx) {
     }, count);
     var entityBuilder = new entity_1.EntityBuilder();
     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
-    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
     var componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
     componentBuilder.add('MOL', 0);

package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js

@@ -46,7 +46,7 @@ function assignRadiusForHeavyAtoms(ctx) {
             var atomId = label_atom_id(l);
             var moleculeType = (0, util_1.getElementMoleculeType)(unit, eI);
             // skip water and optionally non-polymer groups
-            if (moleculeType === 2 /* Water */ || (!ctx.nonPolymer && !(0, types_1.isPolymer)(moleculeType))) {
+            if (moleculeType === 2 /* MoleculeType.Water */ || (!ctx.nonPolymer && !(0, types_1.isPolymer)(moleculeType))) {
                 atomRadiusType[mj] = 0;
                 serialResidueIndex[mj] = -1;
                 continue;
@@ -60,7 +60,7 @@ function assignRadiusForHeavyAtoms(ctx) {
             if ((0, types_1.isNucleic)(moleculeType)) {
                 atomRadiusType[mj] = determineRadiusNucl(atomId, element, compId);
             }
-            else if (moleculeType === 5 /* Protein */) {
+            else if (moleculeType === 5 /* MoleculeType.Protein */) {
                 atomRadiusType[mj] = determineRadiusAmino(atomId, element, compId);
             }
             else {

package/lib/commonjs/mol-model-props/computed/accessible-surface-area/shrake-rupley.js

@@ -111,9 +111,9 @@ var AccessibleSurfaceArea;
     AccessibleSurfaceArea.getNormalizedValue = getNormalizedValue;
     function getFlag(location, accessibleSurfaceArea) {
         var value = getNormalizedValue(location, accessibleSurfaceArea);
-        return value === -1 ? 0 /* NA */ :
-            value < 0.16 ? 1 /* Buried */ :
-                2 /* Accessible */;
+        return value === -1 ? 0 /* Flag.NA */ :
+            value < 0.16 ? 1 /* Flag.Buried */ :
+                2 /* Flag.Accessible */;
     }
     AccessibleSurfaceArea.getFlag = getFlag;
 })(AccessibleSurfaceArea || (AccessibleSurfaceArea = {}));

package/lib/commonjs/mol-model-props/computed/accessible-surface-area.js

@@ -24,7 +24,7 @@ exports.AccessibleSurfaceAreaSymbols = {
         var accessibleSurfaceArea = exports.AccessibleSurfaceAreaProvider.get(ctx.element.structure).value;
         if (!accessibleSurfaceArea)
             return false;
-        return shrake_rupley_1.AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 1 /* Buried */;
+        return shrake_rupley_1.AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 1 /* AccessibleSurfaceArea.Flag.Buried */;
     }),
     isAccessible: compiler_1.QuerySymbolRuntime.Dynamic((0, symbol_1.CustomPropSymbol)('computed', 'accessible-surface-area.is-accessible', type_1.Type.Bool), function (ctx) {
         if (!structure_1.Unit.isAtomic(ctx.element.unit))
@@ -32,7 +32,7 @@ exports.AccessibleSurfaceAreaSymbols = {
         var accessibleSurfaceArea = exports.AccessibleSurfaceAreaProvider.get(ctx.element.structure).value;
         if (!accessibleSurfaceArea)
             return false;
-        return shrake_rupley_1.AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 2 /* Accessible */;
+        return shrake_rupley_1.AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 2 /* AccessibleSurfaceArea.Flag.Accessible */;
     }),
 };
 exports.AccessibleSurfaceAreaProvider = custom_structure_property_1.CustomStructureProperty.createProvider({

package/lib/commonjs/mol-model-props/computed/chemistry/functional-group.js

@@ -13,7 +13,7 @@ function isAromatic(unit, index) {
     // TODO also extend unit.rings with geometry/composition-based aromaticity detection and use it here in addition
     var _a = unit.bonds, offset = _a.offset, edgeProps = _a.edgeProps;
     for (var i = offset[index], il = offset[index + 1]; i < il; ++i) {
-        if (types_2.BondType.is(16 /* Aromatic */, edgeProps.flags[i]))
+        if (types_2.BondType.is(16 /* BondType.Flag.Aromatic */, edgeProps.flags[i]))
             return true;
     }
     return false;
@@ -31,16 +31,16 @@ function bondToCarbonylCount(structure, unit, index) {
  * Nitrogen in a quaternary amine
  */
 function isQuaternaryAmine(structure, unit, index) {
-    return ((0, util_1.typeSymbol)(unit, index) === "N" /* N */ &&
+    return ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
         (0, util_1.bondCount)(structure, unit, index) === 4 &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */) === 0);
+        (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 0);
 }
 exports.isQuaternaryAmine = isQuaternaryAmine;
 /**
  * Nitrogen in a tertiary amine
  */
 function isTertiaryAmine(structure, unit, index, idealValence) {
-    return ((0, util_1.typeSymbol)(unit, index) === "N" /* N */ &&
+    return ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
         (0, util_1.bondCount)(structure, unit, index) === 4 &&
         idealValence === 3);
 }
@@ -50,8 +50,8 @@ exports.isTertiaryAmine = isTertiaryAmine;
  */
 function isImide(structure, unit, index) {
     var flag = false;
-    if ((0, util_1.typeSymbol)(unit, index) === "N" /* N */ &&
-        ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */)) === 2) {
+    if ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
+        ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */)) === 2) {
         flag = bondToCarbonylCount(structure, unit, index) === 2;
     }
     return flag;
@@ -62,8 +62,8 @@ exports.isImide = isImide;
  */
 function isAmide(structure, unit, index) {
     var flag = false;
-    if ((0, util_1.typeSymbol)(unit, index) === "N" /* N */ &&
-        ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */)) === 2) {
+    if ((0, util_1.typeSymbol)(unit, index) === "N" /* Elements.N */ &&
+        ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */)) === 2) {
         flag = bondToCarbonylCount(structure, unit, index) === 1;
     }
     return flag;
@@ -73,33 +73,33 @@ exports.isAmide = isAmide;
  * Sulfur in a sulfonium group
  */
 function isSulfonium(structure, unit, index) {
-    return ((0, util_1.typeSymbol)(unit, index) === "S" /* S */ &&
+    return ((0, util_1.typeSymbol)(unit, index) === "S" /* Elements.S */ &&
         (0, util_1.bondCount)(structure, unit, index) === 3 &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */) === 0);
+        (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 0);
 }
 exports.isSulfonium = isSulfonium;
 /**
  * Sulfur in a sulfonic acid or sulfonate group
  */
 function isSulfonicAcid(structure, unit, index) {
-    return ((0, util_1.typeSymbol)(unit, index) === "S" /* S */ &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* O */) === 3);
+    return ((0, util_1.typeSymbol)(unit, index) === "S" /* Elements.S */ &&
+        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === 3);
 }
 exports.isSulfonicAcid = isSulfonicAcid;
 /**
  * Sulfur in a sulfate group
  */
 function isSulfate(structure, unit, index) {
-    return ((0, util_1.typeSymbol)(unit, index) === "S" /* S */ &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* O */) === 4);
+    return ((0, util_1.typeSymbol)(unit, index) === "S" /* Elements.S */ &&
+        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === 4);
 }
 exports.isSulfate = isSulfate;
 /**
  * Phosphor in a phosphate group
  */
 function isPhosphate(structure, unit, index) {
-    return ((0, util_1.typeSymbol)(unit, index) === "P" /* P */ &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* O */) === (0, util_1.bondCount)(structure, unit, index));
+    return ((0, util_1.typeSymbol)(unit, index) === "P" /* Elements.P */ &&
+        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === (0, util_1.bondCount)(structure, unit, index));
 }
 exports.isPhosphate = isPhosphate;
 /**
@@ -108,7 +108,7 @@ exports.isPhosphate = isPhosphate;
 function isHalocarbon(structure, unit, index) {
     return ((0, types_1.isHalogen)((0, util_1.typeSymbol)(unit, index)) &&
         (0, util_1.bondCount)(structure, unit, index) === 1 &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "C" /* C */) === 1);
+        (0, util_1.bondToElementCount)(structure, unit, index, "C" /* Elements.C */) === 1);
 }
 exports.isHalocarbon = isHalocarbon;
 /**
@@ -118,10 +118,10 @@ exports.isHalocarbon = isHalocarbon;
  */
 function isCarbonyl(structure, unit, index) {
     var flag = false;
-    if ((0, util_1.typeSymbol)(unit, index) === "C" /* C */) {
+    if ((0, util_1.typeSymbol)(unit, index) === "C" /* Elements.C */) {
         var _a = unit.bonds, offset = _a.offset, edgeProps = _a.edgeProps, b = _a.b;
         for (var i = offset[index], il = offset[index + 1]; i < il; ++i) {
-            if (edgeProps.order[i] === 2 && (0, util_1.typeSymbol)(unit, b[i]) === "O" /* O */) {
+            if (edgeProps.order[i] === 2 && (0, util_1.typeSymbol)(unit, b[i]) === "O" /* Elements.O */) {
                 flag = true;
                 break;
             }
@@ -135,12 +135,12 @@ exports.isCarbonyl = isCarbonyl;
  */
 function isCarboxylate(structure, unit, index) {
     var terminalOxygenCount = 0;
-    if ((0, util_1.typeSymbol)(unit, index) === "C" /* C */ &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* O */) === 2 &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "C" /* C */) === 1) {
+    if ((0, util_1.typeSymbol)(unit, index) === "C" /* Elements.C */ &&
+        (0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === 2 &&
+        (0, util_1.bondToElementCount)(structure, unit, index, "C" /* Elements.C */) === 1) {
         (0, util_1.eachBondedAtom)(structure, unit, index, function (unit, index) {
-            if ((0, util_1.typeSymbol)(unit, index) === "O" /* O */ &&
-                (0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */) === 1) {
+            if ((0, util_1.typeSymbol)(unit, index) === "O" /* Elements.O */ &&
+                (0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 1) {
                 terminalOxygenCount += 1;
             }
         });
@@ -153,11 +153,11 @@ exports.isCarboxylate = isCarboxylate;
  */
 function isGuanidine(structure, unit, index) {
     var terminalNitrogenCount = 0;
-    if ((0, util_1.typeSymbol)(unit, index) === "C" /* C */ &&
+    if ((0, util_1.typeSymbol)(unit, index) === "C" /* Elements.C */ &&
         (0, util_1.bondCount)(structure, unit, index) === 3 &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "N" /* N */) === 3) {
+        (0, util_1.bondToElementCount)(structure, unit, index, "N" /* Elements.N */) === 3) {
         (0, util_1.eachBondedAtom)(structure, unit, index, function (unit, index) {
-            if ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */) === 1) {
+            if ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 1) {
                 terminalNitrogenCount += 1;
             }
         });
@@ -170,12 +170,12 @@ exports.isGuanidine = isGuanidine;
  */
 function isAcetamidine(structure, unit, index) {
     var terminalNitrogenCount = 0;
-    if ((0, util_1.typeSymbol)(unit, index) === "C" /* C */ &&
+    if ((0, util_1.typeSymbol)(unit, index) === "C" /* Elements.C */ &&
         (0, util_1.bondCount)(structure, unit, index) === 3 &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "N" /* N */) === 2 &&
-        (0, util_1.bondToElementCount)(structure, unit, index, "C" /* C */) === 1) {
+        (0, util_1.bondToElementCount)(structure, unit, index, "N" /* Elements.N */) === 2 &&
+        (0, util_1.bondToElementCount)(structure, unit, index, "C" /* Elements.C */) === 1) {
         (0, util_1.eachBondedAtom)(structure, unit, index, function (unit, index) {
-            if ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */) === 1) {
+            if ((0, util_1.bondCount)(structure, unit, index) - (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 1) {
                 terminalNitrogenCount += 1;
             }
         });

package/lib/commonjs/mol-model-props/computed/chemistry/geometry.js

@@ -12,43 +12,43 @@ var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var util_1 = require("./util");
 function geometryLabel(geometry) {
     switch (geometry) {
-        case 0 /* Spherical */:
+        case 0 /* AtomGeometry.Spherical */:
             return 'Spherical';
-        case 1 /* Terminal */:
+        case 1 /* AtomGeometry.Terminal */:
             return 'Terminal';
-        case 2 /* Linear */:
+        case 2 /* AtomGeometry.Linear */:
             return 'Linear';
-        case 3 /* Trigonal */:
+        case 3 /* AtomGeometry.Trigonal */:
             return 'Trigonal';
-        case 4 /* Tetrahedral */:
+        case 4 /* AtomGeometry.Tetrahedral */:
             return 'Tetrahedral';
-        case 5 /* TrigonalBiPyramidal */:
+        case 5 /* AtomGeometry.TrigonalBiPyramidal */:
             return 'Trigonal Bi-Pyramidal';
-        case 6 /* Octahedral */:
+        case 6 /* AtomGeometry.Octahedral */:
             return 'Octahedral';
-        case 7 /* SquarePlanar */:
+        case 7 /* AtomGeometry.SquarePlanar */:
             return 'Square Planar';
-        case 8 /* Unknown */:
+        case 8 /* AtomGeometry.Unknown */:
             return 'Unknown';
     }
 }
 exports.geometryLabel = geometryLabel;
 function assignGeometry(totalCoordination) {
     switch (totalCoordination) {
-        case 0: return 0 /* Spherical */;
-        case 1: return 1 /* Terminal */;
-        case 2: return 2 /* Linear */;
-        case 3: return 3 /* Trigonal */;
-        case 4: return 4 /* Tetrahedral */;
-        default: return 8 /* Unknown */;
+        case 0: return 0 /* AtomGeometry.Spherical */;
+        case 1: return 1 /* AtomGeometry.Terminal */;
+        case 2: return 2 /* AtomGeometry.Linear */;
+        case 3: return 3 /* AtomGeometry.Trigonal */;
+        case 4: return 4 /* AtomGeometry.Tetrahedral */;
+        default: return 8 /* AtomGeometry.Unknown */;
     }
 }
 exports.assignGeometry = assignGeometry;
 exports.AtomGeometryAngles = new Map([
-    [2 /* Linear */, (0, misc_1.degToRad)(180)],
-    [3 /* Trigonal */, (0, misc_1.degToRad)(120)],
-    [4 /* Tetrahedral */, (0, misc_1.degToRad)(109.4721)],
-    [6 /* Octahedral */, (0, misc_1.degToRad)(90)]
+    [2 /* AtomGeometry.Linear */, (0, misc_1.degToRad)(180)],
+    [3 /* AtomGeometry.Trigonal */, (0, misc_1.degToRad)(120)],
+    [4 /* AtomGeometry.Tetrahedral */, (0, misc_1.degToRad)(109.4721)],
+    [6 /* AtomGeometry.Octahedral */, (0, misc_1.degToRad)(90)]
 ]);
 // tmp objects for `calcAngles` and `calcPlaneAngle`
 var tmpDir1 = (0, linear_algebra_1.Vec3)();
@@ -65,7 +65,7 @@ function calcAngles(structure, unitA, indexA, unitB, indexB) {
     unitB.conformation.position(unitB.elements[indexB], tmpPosB);
     linear_algebra_1.Vec3.sub(tmpDir1, tmpPosB, tmpPosA);
     (0, util_1.eachBondedAtom)(structure, unitA, indexA, function (unitX, indexX) {
-        if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* H */) {
+        if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* Elements.H */) {
             unitX.conformation.position(unitX.elements[indexX], tmpPosX);
             linear_algebra_1.Vec3.sub(tmpDir2, tmpPosX, tmpPosA);
             angles.push(linear_algebra_1.Vec3.angle(tmpDir1, tmpDir2));
@@ -92,7 +92,7 @@ function calcPlaneAngle(structure, unitA, indexA, unitB, indexB) {
     (0, util_1.eachBondedAtom)(structure, unitA, indexA, function (unitX, indexX) {
         if (ni > 1)
             return;
-        if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* H */) {
+        if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* Elements.H */) {
             unitX1 = unitX;
             indexX1 = indexX;
             unitX.conformation.position(unitX.elements[indexX], tmpPosX);
@@ -105,7 +105,7 @@ function calcPlaneAngle(structure, unitA, indexA, unitB, indexB) {
                 return;
             if (unitX === unitA && indexX === indexA)
                 return;
-            if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* H */) {
+            if ((0, util_1.typeSymbol)(unitX, indexX) !== "H" /* Elements.H */) {
                 unitX.conformation.position(unitX.elements[indexX], tmpPosX);
                 linear_algebra_1.Vec3.sub(neighbours[ni++], tmpPosX, tmpPosA);
             }

package/lib/commonjs/mol-model-props/computed/chemistry/valence-model.js

@@ -37,7 +37,7 @@ var tmpConjBondItB = new structure_1.Bond.ElementBondIterator();
  */
 function isConjugated(structure, unit, index) {
     var element = (0, util_1.typeSymbol)(unit, index);
-    var hetero = element === "O" /* O */ || element === "N" /* N */;
+    var hetero = element === "O" /* Elements.O */ || element === "N" /* Elements.N */;
     if (hetero && (0, util_1.bondCount)(structure, unit, index) === 4)
         return false;
     tmpConjBondItA.setElement(structure, unit, index);
@@ -51,8 +51,8 @@ function isConjugated(structure, unit, index) {
             while (tmpConjBondItB.hasNext) {
                 var bB = tmpConjBondItB.move();
                 if (bB.order > 1) {
-                    if ((elementB === "P" /* P */ || elementB === "S" /* S */) &&
-                        (0, util_1.typeSymbol)(bB.otherUnit, bB.otherIndex) === "O" /* O */) {
+                    if ((elementB === "P" /* Elements.P */ || elementB === "S" /* Elements.S */) &&
+                        (0, util_1.typeSymbol)(bB.otherUnit, bB.otherIndex) === "O" /* Elements.O */) {
                         continue;
                     }
                     return true;
@@ -93,7 +93,7 @@ var tmpChargeBondItB = new structure_1.Bond.ElementBondIterator();
  * a much simpler view and deduces one from the other
  */
 function calculateHydrogensCharge(structure, unit, index, props) {
-    var hydrogenCount = (0, util_1.bondToElementCount)(structure, unit, index, "H" /* H */);
+    var hydrogenCount = (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */);
     var element = (0, util_1.typeSymbol)(unit, index);
     var charge = (0, util_1.formalCharge)(unit, index);
     var assignCharge = (props.assignCharge === 'always' || (props.assignCharge === 'auto' && charge === 0));
@@ -103,21 +103,21 @@ function calculateHydrogensCharge(structure, unit, index, props) {
     var conjugated = isConjugated(structure, unit, index);
     var multiBond = (valence - degree > 0);
     var implicitHCount = 0;
-    var geom = 8 /* Unknown */;
+    var geom = 8 /* AtomGeometry.Unknown */;
     switch (element) {
-        case "H" /* H */:
+        case "H" /* Elements.H */:
             if (assignCharge) {
                 if (degree === 0) {
                     charge = 1;
-                    geom = 0 /* Spherical */;
+                    geom = 0 /* AtomGeometry.Spherical */;
                 }
                 else if (degree === 1) {
                     charge = 0;
-                    geom = 1 /* Terminal */;
+                    geom = 1 /* AtomGeometry.Terminal */;
                 }
             }
             break;
-        case "C" /* C */:
+        case "C" /* Elements.C */:
             // TODO: Isocyanide?
             if (assignCharge) {
                 charge = 0; // Assume carbon always neutral
@@ -129,7 +129,7 @@ function calculateHydrogensCharge(structure, unit, index, props) {
             // Carbocation is planar, carbanion is tetrahedral
             geom = (0, geometry_1.assignGeometry)(degree + implicitHCount + Math.max(0, -charge));
             break;
-        case "N" /* N */:
+        case "N" /* Elements.N */:
             if (assignCharge) {
                 if (!assignH) { // Trust input H explicitly:
                     charge = valence - 3;
@@ -151,7 +151,7 @@ function calculateHydrogensCharge(structure, unit, index, props) {
                     while (tmpChargeBondItA.hasNext) {
                         var b = tmpChargeBondItA.move();
                         var elementB = (0, util_1.typeSymbol)(b.otherUnit, b.otherIndex);
-                        if (elementB === "S" /* S */ || (0, types_1.isMetal)(elementB)) {
+                        if (elementB === "S" /* Elements.S */ || (0, types_1.isMetal)(elementB)) {
                             charge = 0;
                             break;
                         }
@@ -177,7 +177,7 @@ function calculateHydrogensCharge(structure, unit, index, props) {
                 geom = (0, geometry_1.assignGeometry)(degree + implicitHCount + 1 - charge);
             }
             break;
-        case "O" /* O */:
+        case "O" /* Elements.O */:
             if (assignCharge) {
                 if (!assignH) {
                     charge = valence - 2;
@@ -190,7 +190,7 @@ function calculateHydrogensCharge(structure, unit, index, props) {
                         while (tmpChargeBondItB.hasNext) {
                             var bB = tmpChargeBondItB.move();
                             if (!(bB.otherUnit === unit && bB.otherIndex === index) &&
-                                (0, util_1.typeSymbol)(bB.otherUnit, bB.otherIndex) === "O" /* O */ &&
+                                (0, util_1.typeSymbol)(bB.otherUnit, bB.otherIndex) === "O" /* Elements.O */ &&
                                 bB.order === 2) {
                                 charge = -1;
                                 break b1;
@@ -214,10 +214,10 @@ function calculateHydrogensCharge(structure, unit, index, props) {
             break;
         // Only handles thiols/thiolates/thioether/sulfonium. Sulfoxides and higher
         // oxidiation states are assumed neutral S (charge carried on O if required)
-        case "S" /* S */:
+        case "S" /* Elements.S */:
             if (assignCharge) {
                 if (!assignH) {
-                    if (valence <= 3 && (0, util_1.bondToElementCount)(structure, unit, index, "O" /* O */) === 0) {
+                    if (valence <= 3 && (0, util_1.bondToElementCount)(structure, unit, index, "O" /* Elements.O */) === 0) {
                         charge = valence - 2; // e.g. explicitly deprotonated thiol
                     }
                     else {
@@ -235,32 +235,32 @@ function calculateHydrogensCharge(structure, unit, index, props) {
                 geom = (0, geometry_1.assignGeometry)(degree + implicitHCount - charge + 2);
             }
             break;
-        case "F" /* F */:
-        case "CL" /* CL */:
-        case "BR" /* BR */:
-        case "I" /* I */:
-        case "AT" /* AT */:
+        case "F" /* Elements.F */:
+        case "CL" /* Elements.CL */:
+        case "BR" /* Elements.BR */:
+        case "I" /* Elements.I */:
+        case "AT" /* Elements.AT */:
             // Never implicitly protonate halides
             if (assignCharge) {
                 charge = valence - 1;
             }
             break;
-        case "LI" /* LI */:
-        case "NA" /* NA */:
-        case "K" /* K */:
-        case "RB" /* RB */:
-        case "CS" /* CS */:
-        case "FR" /* FR */:
+        case "LI" /* Elements.LI */:
+        case "NA" /* Elements.NA */:
+        case "K" /* Elements.K */:
+        case "RB" /* Elements.RB */:
+        case "CS" /* Elements.CS */:
+        case "FR" /* Elements.FR */:
             if (assignCharge) {
                 charge = 1 - valence;
             }
             break;
-        case "BE" /* BE */:
-        case "MG" /* MG */:
-        case "CA" /* CA */:
-        case "SR" /* SR */:
-        case "BA" /* BA */:
-        case "RA" /* RA */:
+        case "BE" /* Elements.BE */:
+        case "MG" /* Elements.MG */:
+        case "CA" /* Elements.CA */:
+        case "SR" /* Elements.SR */:
+        case "BA" /* Elements.BA */:
+        case "RA" /* Elements.RA */:
             if (assignCharge) {
                 charge = 2 - valence;
             }