molstar 4.3.0 → 4.4.1

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

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromPDB = exports.PdbFormat = void 0;
+exports.PdbFormat = void 0;
+exports.trajectoryFromPDB = trajectoryFromPDB;
 const to_cif_1 = require("./pdb/to-cif");
 const mol_task_1 = require("../../mol-task");
 const mmcif_1 = require("./mmcif");
@@ -55,4 +56,3 @@ function trajectoryFromPDB(pdb) {
         return models;
     });
 }
-exports.trajectoryFromPDB = trajectoryFromPDB;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.topologyFromPrmtop = exports.PrmtopFormat = void 0;
+exports.PrmtopFormat = void 0;
+exports.topologyFromPrmtop = topologyFromPrmtop;
 const db_1 = require("../../mol-data/db");
 const types_1 = require("../../mol-model/structure/model/types");
 const topology_1 = require("../../mol-model/structure/topology/topology");
@@ -138,4 +139,3 @@ function topologyFromPrmtop(prmtop) {
         return topology_1.Topology.create(prmtop.title.join(' ') || 'PRMTOP', basic, bonds, format);
     });
 }
-exports.topologyFromPrmtop = topologyFromPrmtop;

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

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getMatrices = exports.operatorGroupsProvider = exports.createAssemblies = void 0;
+exports.createAssemblies = createAssemblies;
+exports.operatorGroupsProvider = operatorGroupsProvider;
+exports.getMatrices = getMatrices;
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 const symmetry_operator_1 = require("../../../mol-math/geometry/symmetry-operator");
 const symmetry_1 = require("../../../mol-model/structure/model/properties/symmetry");
@@ -21,7 +23,6 @@ function createAssemblies(pdbx_struct_assembly, pdbx_struct_assembly_gen, pdbx_s
     }
     return assemblies;
 }
-exports.createAssemblies = createAssemblies;
 function createAssembly(pdbx_struct_assembly, pdbx_struct_assembly_gen, index, matrices) {
     const id = pdbx_struct_assembly.id.value(index);
     const details = pdbx_struct_assembly.details.value(index);
@@ -54,7 +55,6 @@ function operatorGroupsProvider(generators, matrices) {
         return groups;
     };
 }
-exports.operatorGroupsProvider = operatorGroupsProvider;
 function getMatrices(pdbx_struct_oper_list) {
     const { id, matrix, vector, _schema } = pdbx_struct_oper_list;
     const matrices = new Map();
@@ -68,7 +68,6 @@ function getMatrices(pdbx_struct_oper_list) {
     }
     return matrices;
 }
-exports.getMatrices = getMatrices;
 function expandOperators(operatorList) {
     const ops = [];
     const currentOp = [];

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.topologyFromPsf = exports.PsfFormat = void 0;
+exports.PsfFormat = void 0;
+exports.topologyFromPsf = topologyFromPsf;
 const db_1 = require("../../mol-data/db");
 const types_1 = require("../../mol-model/structure/model/types");
 const topology_1 = require("../../mol-model/structure/topology/topology");
@@ -115,4 +116,3 @@ function topologyFromPsf(psf) {
         return topology_1.Topology.create(psf.id, basic, bonds, format);
     });
 }
-exports.topologyFromPsf = topologyFromPsf;

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

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromSdf = exports.SdfFormat = void 0;
+exports.SdfFormat = void 0;
+exports.trajectoryFromSdf = trajectoryFromSdf;
 const mol_task_1 = require("../../mol-task");
 const mol_1 = require("./mol");
 var SdfFormat;
@@ -22,4 +23,3 @@ var SdfFormat;
 function trajectoryFromSdf(mol) {
     return mol_task_1.Task.create('Parse SDF', ctx => (0, mol_1.getMolModels)(mol.molFile, SdfFormat.create(mol), ctx));
 }
-exports.trajectoryFromSdf = trajectoryFromSdf;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.topologyFromTop = exports.TopFormat = void 0;
+exports.TopFormat = void 0;
+exports.topologyFromTop = topologyFromTop;
 const db_1 = require("../../mol-data/db");
 const types_1 = require("../../mol-model/structure/model/types");
 const topology_1 = require("../../mol-model/structure/topology/topology");
@@ -180,4 +181,3 @@ function topologyFromTop(top) {
         return topology_1.Topology.create(top.system || 'TOP', basic, bonds, format);
     });
 }
-exports.topologyFromTop = topologyFromTop;

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

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.coordinatesFromTrr = void 0;
+exports.coordinatesFromTrr = coordinatesFromTrr;
 const mol_task_1 = require("../../mol-task");
 const coordinates_1 = require("../../mol-model/structure/coordinates");
 const cell_1 = require("../../mol-math/geometry/spacegroup/cell");
@@ -34,4 +34,3 @@ function coordinatesFromTrr(file) {
         return coordinates_1.Coordinates.create(frames, deltaTime, offsetTime);
     });
 }
-exports.coordinatesFromTrr = coordinatesFromTrr;

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

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.guessElementSymbolString = exports.guessElementSymbolTokens = void 0;
+exports.guessElementSymbolTokens = guessElementSymbolTokens;
+exports.guessElementSymbolString = guessElementSymbolString;
 const tokenizer_1 = require("../../mol-io/reader/common/text/tokenizer");
 function guessElementSymbolTokens(tokens, str, start, end) {
     let s = start, e = end - 1;
@@ -43,7 +44,6 @@ function guessElementSymbolTokens(tokens, str, start, end) {
         return tokenizer_1.TokenBuilder.add(tokens, s, s + 1);
     tokenizer_1.TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token
 }
-exports.guessElementSymbolTokens = guessElementSymbolTokens;
 const TwoCharElementNames = new Set(['NA', 'CL', 'FE', 'SI', 'BR', 'AS', 'LI']);
 const OneCharElementNames = new Set(['C', 'H', 'N', 'O', 'P', 'S', 'F', 'B']);
 const reTrimSpacesAndNumbers = /^[\s\d]+|[\s\d]+$/g;
@@ -74,4 +74,3 @@ function guessElementSymbolString(atomId, compId) {
         return atomId[0];
     return ''; // no reasonable guess, return empty string
 }
-exports.guessElementSymbolString = guessElementSymbolString;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.coordinatesFromXtc = void 0;
+exports.coordinatesFromXtc = coordinatesFromXtc;
 const mol_task_1 = require("../../mol-task");
 const coordinates_1 = require("../../mol-model/structure/coordinates");
 const cell_1 = require("../../mol-math/geometry/spacegroup/cell");
@@ -35,4 +35,3 @@ function coordinatesFromXtc(file) {
         return coordinates_1.Coordinates.create(frames, deltaTime, offsetTime);
     });
 }
-exports.coordinatesFromXtc = coordinatesFromXtc;

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

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.trajectoryFromXyz = exports.XyzFormat = void 0;
+exports.XyzFormat = void 0;
+exports.trajectoryFromXyz = trajectoryFromXyz;
 const db_1 = require("../../mol-data/db");
 const mol_task_1 = require("../../mol-task");
 const parser_1 = require("./basic/parser");
@@ -85,4 +86,3 @@ var XyzFormat;
 function trajectoryFromXyz(mol) {
     return mol_task_1.Task.create('Parse XYZ', ctx => getModels(mol, ctx));
 }
-exports.trajectoryFromXyz = trajectoryFromXyz;

package/lib/commonjs/mol-model-formats/volume/ccp4.js

@@ -5,7 +5,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Ccp4Format = exports.volumeFromCcp4 = exports.getCcp4Origin = void 0;
+exports.Ccp4Format = void 0;
+exports.getCcp4Origin = getCcp4Origin;
+exports.volumeFromCcp4 = volumeFromCcp4;
 const mol_task_1 = require("../../mol-task");
 const geometry_1 = require("../../mol-math/geometry");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
@@ -23,7 +25,6 @@ function getCcp4Origin(header) {
         return linear_algebra_1.Vec3.create(header.originX / (header.xLength / header.NX), header.originY / (header.yLength / header.NY), header.originZ / (header.zLength / header.NZ));
     }
 }
-exports.getCcp4Origin = getCcp4Origin;
 function getTypedArrayCtor(header) {
     const valueType = (0, parser_1.getCcp4ValueType)(header);
     switch (valueType) {
@@ -79,7 +80,6 @@ function volumeFromCcp4(source, params) {
         };
     });
 }
-exports.volumeFromCcp4 = volumeFromCcp4;
 var Ccp4Format;
 (function (Ccp4Format) {
     function is(x) {

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

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CubeFormat = exports.volumeFromCube = void 0;
+exports.CubeFormat = void 0;
+exports.volumeFromCube = volumeFromCube;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const mol_task_1 = require("../../mol-task");
 const array_1 = require("../../mol-util/array");
@@ -56,7 +57,6 @@ function volumeFromCube(source, params) {
         };
     });
 }
-exports.volumeFromCube = volumeFromCube;
 var CubeFormat;
 (function (CubeFormat) {
     function is(x) {

package/lib/commonjs/mol-model-formats/volume/density-server.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DscifFormat = exports.volumeFromDensityServerData = void 0;
+exports.DscifFormat = void 0;
+exports.volumeFromDensityServerData = volumeFromDensityServerData;
 const mol_task_1 = require("../../mol-task");
 const geometry_1 = require("../../mol-math/geometry");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
@@ -42,7 +43,6 @@ function volumeFromDensityServerData(source, params) {
         };
     });
 }
-exports.volumeFromDensityServerData = volumeFromDensityServerData;
 var DscifFormat;
 (function (DscifFormat) {
     function is(x) {

package/lib/commonjs/mol-model-formats/volume/dsn6.js

@@ -5,7 +5,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Dsn6Format = exports.volumeFromDsn6 = void 0;
+exports.Dsn6Format = void 0;
+exports.volumeFromDsn6 = volumeFromDsn6;
 const mol_task_1 = require("../../mol-task");
 const geometry_1 = require("../../mol-math/geometry");
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
@@ -46,7 +47,6 @@ function volumeFromDsn6(source, params) {
         };
     });
 }
-exports.volumeFromDsn6 = volumeFromDsn6;
 var Dsn6Format;
 (function (Dsn6Format) {
     function is(x) {

package/lib/commonjs/mol-model-formats/volume/dx.js

@@ -5,7 +5,8 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DxFormat = exports.volumeFromDx = void 0;
+exports.DxFormat = void 0;
+exports.volumeFromDx = volumeFromDx;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const mol_task_1 = require("../../mol-task");
 const array_1 = require("../../mol-util/array");
@@ -37,7 +38,6 @@ function volumeFromDx(source, params) {
         };
     });
 }
-exports.volumeFromDx = volumeFromDx;
 var DxFormat;
 (function (DxFormat) {
     function is(x) {

package/lib/commonjs/mol-model-formats/volume/segmentation.js

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SegcifFormat = exports.volumeFromSegmentationData = void 0;
+exports.SegcifFormat = void 0;
+exports.volumeFromSegmentationData = volumeFromSegmentationData;
 const volume_1 = require("../../mol-model/volume");
 const mol_task_1 = require("../../mol-task");
 const geometry_1 = require("../../mol-math/geometry");
@@ -120,7 +121,6 @@ function volumeFromSegmentationData(source, params) {
         return v;
     });
 }
-exports.volumeFromSegmentationData = volumeFromSegmentationData;
 var SegcifFormat;
 (function (SegcifFormat) {
     function is(x) {

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.computeArea = void 0;
+exports.computeArea = computeArea;
 const common_1 = require("./common");
 // TODO
 // - iterate over units and elements
@@ -23,7 +23,6 @@ async function computeArea(runtime, ctx) {
         computeRange(ctx, i, Math.min(i + updateChunk, atomRadius.length));
     }
 }
-exports.computeArea = computeArea;
 function computeRange(ctx, begin, end) {
     const { structure, atomRadiusType, serialResidueIndex, area, spherePoints, scalingConstant, maxLookupRadius, probeSize } = ctx;
     const { lookup3d, serialMapping, unitIndexMap, units } = structure;

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

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.assignRadiusForHeavyAtoms = void 0;
+exports.assignRadiusForHeavyAtoms = assignRadiusForHeavyAtoms;
 const common_1 = require("./common");
 const common_2 = require("../../../../mol-model/structure/structure/unit/bonds/common");
 const types_1 = require("../../../../mol-model/structure/model/types");
@@ -71,7 +71,6 @@ function assignRadiusForHeavyAtoms(ctx) {
         m += elements.length;
     }
 }
-exports.assignRadiusForHeavyAtoms = assignRadiusForHeavyAtoms;
 /**
  * Gets the van der Waals radius of the given atom following the values defined by Chothia (1976)
  * J.Mol.Biol.105,1-14. NOTE: the vdw values defined by the paper assume no Hydrogens and thus "inflates" slightly

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

@@ -5,7 +5,22 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.hasAromaticNeighbour = exports.hasPolarNeighbour = exports.isPolar = exports.isAcetamidine = exports.isGuanidine = exports.isCarboxylate = exports.isCarbonyl = exports.isHalocarbon = exports.isPhosphate = exports.isSulfate = exports.isSulfonicAcid = exports.isSulfonium = exports.isAmide = exports.isImide = exports.isTertiaryAmine = exports.isQuaternaryAmine = void 0;
+exports.isQuaternaryAmine = isQuaternaryAmine;
+exports.isTertiaryAmine = isTertiaryAmine;
+exports.isImide = isImide;
+exports.isAmide = isAmide;
+exports.isSulfonium = isSulfonium;
+exports.isSulfonicAcid = isSulfonicAcid;
+exports.isSulfate = isSulfate;
+exports.isPhosphate = isPhosphate;
+exports.isHalocarbon = isHalocarbon;
+exports.isCarbonyl = isCarbonyl;
+exports.isCarboxylate = isCarboxylate;
+exports.isGuanidine = isGuanidine;
+exports.isAcetamidine = isAcetamidine;
+exports.isPolar = isPolar;
+exports.hasPolarNeighbour = hasPolarNeighbour;
+exports.hasAromaticNeighbour = hasAromaticNeighbour;
 const types_1 = require("../../../mol-model/structure/model/properties/atomic/types");
 const types_2 = require("../../../mol-model/structure/model/types");
 const util_1 = require("./util");
@@ -35,7 +50,6 @@ function isQuaternaryAmine(structure, unit, index) {
         (0, util_1.bondCount)(structure, unit, index) === 4 &&
         (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 0);
 }
-exports.isQuaternaryAmine = isQuaternaryAmine;
 /**
  * Nitrogen in a tertiary amine
  */
@@ -44,7 +58,6 @@ function isTertiaryAmine(structure, unit, index, idealValence) {
         (0, util_1.bondCount)(structure, unit, index) === 4 &&
         idealValence === 3);
 }
-exports.isTertiaryAmine = isTertiaryAmine;
 /**
  * Nitrogen in an imide
  */
@@ -56,7 +69,6 @@ function isImide(structure, unit, index) {
     }
     return flag;
 }
-exports.isImide = isImide;
 /**
  * Nitrogen in an amide
  */
@@ -68,7 +80,6 @@ function isAmide(structure, unit, index) {
     }
     return flag;
 }
-exports.isAmide = isAmide;
 /**
  * Sulfur in a sulfonium group
  */
@@ -77,7 +88,6 @@ function isSulfonium(structure, unit, index) {
         (0, util_1.bondCount)(structure, unit, index) === 3 &&
         (0, util_1.bondToElementCount)(structure, unit, index, "H" /* Elements.H */) === 0);
 }
-exports.isSulfonium = isSulfonium;
 /**
  * Sulfur in a sulfonic acid or sulfonate group
  */
@@ -85,7 +95,6 @@ function isSulfonicAcid(structure, unit, index) {
     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
  */
@@ -93,7 +102,6 @@ function isSulfate(structure, unit, index) {
     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
  */
@@ -101,7 +109,6 @@ function isPhosphate(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;
 /**
  * Halogen with one bond to a carbon
  */
@@ -110,7 +117,6 @@ function isHalocarbon(structure, unit, index) {
         (0, util_1.bondCount)(structure, unit, index) === 1 &&
         (0, util_1.bondToElementCount)(structure, unit, index, "C" /* Elements.C */) === 1);
 }
-exports.isHalocarbon = isHalocarbon;
 /**
  * Carbon in a carbonyl/acyl group
  *
@@ -129,7 +135,6 @@ function isCarbonyl(structure, unit, index) {
     }
     return flag;
 }
-exports.isCarbonyl = isCarbonyl;
 /**
  * Carbon in a carboxylate group
  */
@@ -147,7 +152,6 @@ function isCarboxylate(structure, unit, index) {
     }
     return terminalOxygenCount === 2;
 }
-exports.isCarboxylate = isCarboxylate;
 /**
  * Carbon in a guanidine group
  */
@@ -164,7 +168,6 @@ function isGuanidine(structure, unit, index) {
     }
     return terminalNitrogenCount === 2;
 }
-exports.isGuanidine = isGuanidine;
 /**
  * Carbon in a acetamidine group
  */
@@ -182,10 +185,8 @@ function isAcetamidine(structure, unit, index) {
     }
     return terminalNitrogenCount === 2;
 }
-exports.isAcetamidine = isAcetamidine;
 const PolarElements = new Set(['N', 'O', 'S', 'F', 'CL', 'BR', 'I']);
 function isPolar(element) { return PolarElements.has(element); }
-exports.isPolar = isPolar;
 function hasPolarNeighbour(structure, unit, index) {
     let flag = false;
     (0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
@@ -194,7 +195,6 @@ function hasPolarNeighbour(structure, unit, index) {
     });
     return flag;
 }
-exports.hasPolarNeighbour = hasPolarNeighbour;
 function hasAromaticNeighbour(structure, unit, index) {
     let flag = false;
     (0, util_1.eachBondedAtom)(structure, unit, index, (unit, index) => {
@@ -203,4 +203,3 @@ function hasAromaticNeighbour(structure, unit, index) {
     });
     return flag;
 }
-exports.hasAromaticNeighbour = hasAromaticNeighbour;

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

@@ -6,7 +6,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.calcPlaneAngle = exports.calcAngles = exports.AtomGeometryAngles = exports.assignGeometry = exports.geometryLabel = exports.AtomGeometry = void 0;
+exports.AtomGeometryAngles = exports.AtomGeometry = void 0;
+exports.geometryLabel = geometryLabel;
+exports.assignGeometry = assignGeometry;
+exports.calcAngles = calcAngles;
+exports.calcPlaneAngle = calcPlaneAngle;
 const misc_1 = require("../../../mol-math/misc");
 const linear_algebra_1 = require("../../../mol-math/linear-algebra");
 const util_1 = require("./util");
@@ -48,7 +52,6 @@ function geometryLabel(geometry) {
             return 'Unknown';
     }
 }
-exports.geometryLabel = geometryLabel;
 function assignGeometry(totalCoordination) {
     switch (totalCoordination) {
         case 0: return AtomGeometry.Spherical;
@@ -59,7 +62,6 @@ function assignGeometry(totalCoordination) {
         default: return AtomGeometry.Unknown;
     }
 }
-exports.assignGeometry = assignGeometry;
 exports.AtomGeometryAngles = new Map([
     [AtomGeometry.Linear, (0, misc_1.degToRad)(180)],
     [AtomGeometry.Trigonal, (0, misc_1.degToRad)(120)],
@@ -89,7 +91,6 @@ function calcAngles(structure, unitA, indexA, unitB, indexB) {
     });
     return angles;
 }
-exports.calcAngles = calcAngles;
 /**
  * Find two neighbours of ap1 to define a plane (if possible) and
  * measure angle out of plane to ap2
@@ -133,4 +134,3 @@ function calcPlaneAngle(structure, unitA, indexA, unitB, indexB) {
     linear_algebra_1.Vec3.cross(tmpDir2, neighbours[0], neighbours[1]);
     return Math.abs((Math.PI / 2) - linear_algebra_1.Vec3.angle(tmpDir2, tmpDir1));
 }
-exports.calcPlaneAngle = calcPlaneAngle;

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

@@ -5,29 +5,39 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.eachResidueAtom = exports.eachBondedAtom = exports.eachIntraBondedAtom = exports.eachInterBondedAtom = exports.connectedTo = exports.interConnectedTo = exports.intraConnectedTo = exports.bondToElementCount = exports.bondCount = exports.intraBondCount = exports.interBondCount = exports.compId = exports.altLoc = exports.atomId = exports.formalCharge = exports.typeSymbol = void 0;
+exports.typeSymbol = typeSymbol;
+exports.formalCharge = formalCharge;
+exports.atomId = atomId;
+exports.altLoc = altLoc;
+exports.compId = compId;
+exports.interBondCount = interBondCount;
+exports.intraBondCount = intraBondCount;
+exports.bondCount = bondCount;
+exports.bondToElementCount = bondToElementCount;
+exports.intraConnectedTo = intraConnectedTo;
+exports.interConnectedTo = interConnectedTo;
+exports.connectedTo = connectedTo;
+exports.eachInterBondedAtom = eachInterBondedAtom;
+exports.eachIntraBondedAtom = eachIntraBondedAtom;
+exports.eachBondedAtom = eachBondedAtom;
+exports.eachResidueAtom = eachResidueAtom;
 const types_1 = require("../../../mol-model/structure/model/types");
 const int_1 = require("../../../mol-data/int");
 function typeSymbol(unit, index) {
     return unit.model.atomicHierarchy.atoms.type_symbol.value(unit.elements[index]);
 }
-exports.typeSymbol = typeSymbol;
 function formalCharge(unit, index) {
     return unit.model.atomicHierarchy.atoms.pdbx_formal_charge.value(unit.elements[index]);
 }
-exports.formalCharge = formalCharge;
 function atomId(unit, index) {
     return unit.model.atomicHierarchy.atoms.label_atom_id.value(unit.elements[index]);
 }
-exports.atomId = atomId;
 function altLoc(unit, index) {
     return unit.model.atomicHierarchy.atoms.label_alt_id.value(unit.elements[index]);
 }
-exports.altLoc = altLoc;
 function compId(unit, index) {
     return unit.model.atomicHierarchy.atoms.label_comp_id.value(unit.elements[index]);
 }
-exports.compId = compId;
 //
 function interBondCount(structure, unit, index) {
     let count = 0;
@@ -39,7 +49,6 @@ function interBondCount(structure, unit, index) {
     }
     return count;
 }
-exports.interBondCount = interBondCount;
 function intraBondCount(unit, index) {
     let count = 0;
     const { offset, edgeProps: { flags } } = unit.bonds;
@@ -49,11 +58,9 @@ function intraBondCount(unit, index) {
     }
     return count;
 }
-exports.intraBondCount = intraBondCount;
 function bondCount(structure, unit, index) {
     return interBondCount(structure, unit, index) + intraBondCount(unit, index);
 }
-exports.bondCount = bondCount;
 function bondToElementCount(structure, unit, index, element) {
     let count = 0;
     eachBondedAtom(structure, unit, index, (unit, index) => {
@@ -62,7 +69,6 @@ function bondToElementCount(structure, unit, index, element) {
     });
     return count;
 }
-exports.bondToElementCount = bondToElementCount;
 //
 function intraConnectedTo(unit, indexA, indexB) {
     const { offset, b, edgeProps: { flags } } = unit.bonds;
@@ -73,16 +79,13 @@ function intraConnectedTo(unit, indexA, indexB) {
     }
     return false;
 }
-exports.intraConnectedTo = intraConnectedTo;
 function interConnectedTo(structure, unitA, indexA, unitB, indexB) {
     const b = structure.interUnitBonds.getEdge(indexA, unitA.id, indexB, unitB.id);
     return b && types_1.BondType.isCovalent(b.props.flag);
 }
-exports.interConnectedTo = interConnectedTo;
 function connectedTo(structure, unitA, indexA, unitB, indexB) {
     return unitA === unitB ? intraConnectedTo(unitA, indexA, indexB) : interConnectedTo(structure, unitA, indexA, unitB, indexB);
 }
-exports.connectedTo = connectedTo;
 //
 function eachInterBondedAtom(structure, unit, index, cb) {
     const indices = structure.interUnitBonds.getEdgeIndices(index, unit.id);
@@ -93,7 +96,6 @@ function eachInterBondedAtom(structure, unit, index, cb) {
             cb(uB, b.indexB);
     }
 }
-exports.eachInterBondedAtom = eachInterBondedAtom;
 function eachIntraBondedAtom(unit, index, cb) {
     const { offset, b, edgeProps: { flags } } = unit.bonds;
     for (let i = offset[index], il = offset[index + 1]; i < il; ++i) {
@@ -101,12 +103,10 @@ function eachIntraBondedAtom(unit, index, cb) {
             cb(unit, b[i]);
     }
 }
-exports.eachIntraBondedAtom = eachIntraBondedAtom;
 function eachBondedAtom(structure, unit, index, cb) {
     eachInterBondedAtom(structure, unit, index, cb);
     eachIntraBondedAtom(unit, index, cb);
 }
-exports.eachBondedAtom = eachBondedAtom;
 //
 function eachResidueAtom(unit, index, cb) {
     const { offsets } = unit.model.atomicHierarchy.residueAtomSegments;
@@ -118,4 +118,3 @@ function eachResidueAtom(unit, index, cb) {
             cb(idx);
     }
 }
-exports.eachResidueAtom = eachResidueAtom;

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

@@ -6,7 +6,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.calcValenceModel = exports.ValenceModelParams = exports.calculateHydrogensCharge = exports.explicitValence = void 0;
+exports.ValenceModelParams = void 0;
+exports.explicitValence = explicitValence;
+exports.calculateHydrogensCharge = calculateHydrogensCharge;
+exports.calcValenceModel = calcValenceModel;
 const structure_1 = require("../../../mol-model/structure");
 const types_1 = require("../../../mol-model/structure/model/properties/atomic/types");
 const geometry_1 = require("./geometry");
@@ -77,7 +80,6 @@ function explicitValence(structure, unit, index) {
     });
     return v;
 }
-exports.explicitValence = explicitValence;
 const tmpChargeBondItA = new structure_1.Bond.ElementBondIterator();
 const tmpChargeBondItB = new structure_1.Bond.ElementBondIterator();
 /**
@@ -271,7 +273,6 @@ function calculateHydrogensCharge(structure, unit, index, props) {
     }
     return [charge, implicitHCount, implicitHCount + hydrogenCount, geom];
 }
-exports.calculateHydrogensCharge = calculateHydrogensCharge;
 function calcUnitValenceModel(structure, unit, props) {
     const n = unit.elements.length;
     const charge = new Int8Array(n);
@@ -316,4 +317,3 @@ async function calcValenceModel(ctx, structure, props) {
     }
     return map;
 }
-exports.calcValenceModel = calcValenceModel;