molstar 3.3.1 → 3.4.0

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

@@ -10,6 +10,7 @@ var db_1 = require("../../../mol-data/db");
 var types_1 = require("../../../mol-model/structure/model/types");
 var set_1 = require("../../../mol-util/set");
 var schema_1 = require("../basic/schema");
+var constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants");
 var ProteinAtomIdsList = [
     new Set(['CA']),
     new Set(['C']),
@@ -27,7 +28,7 @@ var DnaAtomIdsList = [
 ];
 /** Used to reduce false positives for atom name-based type guessing */
 var NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP' // Mononucleotides
+    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP', // Mononucleotides
 ]);
 var StandardComponents = (function () {
     var map = new Map();
@@ -154,6 +155,9 @@ var ComponentBuilder = /** @class */ (function () {
             else if (NonPolymerNames.has(compId.toUpperCase())) {
                 this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
             }
+            else if (constants_1.SaccharideCompIdMap.has(compId.toUpperCase())) {
+                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'saccharide' });
+            }
             else {
                 var atomIds = this.getAtomIds(index);
                 if (atomIds.size === 1 && CharmmIonComponents.has(compId)) {

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

@@ -15,9 +15,9 @@ var schema_1 = require("./basic/schema");
 var component_1 = require("./common/component");
 var entity_1 = require("./common/entity");
 function getModels(cube, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics;
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basic;
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     atoms = cube.atoms;
@@ -49,12 +49,12 @@ function getModels(cube, ctx) {
                     componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = (0, schema_1.createBasic)({
+                    basic = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, MolFormat.create(cube), ctx)];
+                    return [4 /*yield*/, (0, parser_1.createModels)(basic, MolFormat.create(cube), ctx)];
                 case 1: return [2 /*return*/, _a.sent()];
             }
         });

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

@@ -16,9 +16,9 @@ var common_1 = require("../../mol-math/linear-algebra/3d/common");
 var charmmTimeUnitFactor = 20.45482949774598;
 function coordinatesFromDcd(dcdFile) {
     var _this = this;
-    return mol_task_1.Task.create('Parse DCD', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse DCD', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, deltaTime, offsetTime, frames, i, il, dcdFrame, frame, c;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
                 case 1:

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

@@ -24,6 +24,7 @@ function getBasic(atoms, modelNum) {
     var asymIds = new Array(atoms.count);
     var seqIds = new Uint32Array(atoms.count);
     var ids = new Uint32Array(atoms.count);
+    var typeSymbol = new Array(atoms.count);
     var entityBuilder = new entity_1.EntityBuilder();
     var componentBuilder = new component_1.ComponentBuilder(atoms.residueNumber, atoms.atomName);
     var currentEntityId = '';
@@ -53,6 +54,7 @@ function getBasic(atoms, modelNum) {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+        typeSymbol[i] = (0, util_1.guessElementSymbolString)(atoms.atomName.value(i), atoms.residueName.value(i));
     }
     var auth_asym_id = db_1.Column.ofStringArray(asymIds);
     var atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
@@ -70,7 +72,7 @@ function getBasic(atoms, modelNum) {
         label_seq_id: db_1.Column.ofIntArray(seqIds),
         label_entity_id: db_1.Column.ofStringArray(entityIds),
         occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
-        type_symbol: db_1.Column.ofStringArray(db_1.Column.mapToArray(atoms.atomName, function (s) { return (0, util_1.guessElementSymbolString)(s); })),
+        type_symbol: db_1.Column.ofStringArray(typeSymbol),
         pdbx_PDB_model_num: db_1.Column.ofConst(modelNum, atoms.count, db_1.Column.Schema.int),
     }, atoms.count);
     return (0, schema_1.createBasic)({
@@ -95,9 +97,9 @@ exports.GroFormat = GroFormat;
 //      need to pass all gro.structures as one table into createModels
 function trajectoryFromGRO(gro) {
     var _this = this;
-    return mol_task_1.Task.create('Parse GRO', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse GRO', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var format, models, i, il, basic, m;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = GroFormat.fromGro(gro);

package/lib/commonjs/mol-model-formats/structure/mmcif.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -17,6 +17,7 @@ var anisotropic_1 = require("./property/anisotropic");
 var chem_comp_1 = require("./property/bonds/chem_comp");
 var struct_conn_1 = require("./property/bonds/struct_conn");
 var global_transform_1 = require("../../mol-model/structure/model/properties/global-transform");
+var schema_1 = require("./basic/schema");
 function modelSymmetryFromMmcif(model) {
     if (!MmcifFormat.is(model.sourceData))
         return;
@@ -87,6 +88,7 @@ var MmcifFormat;
 exports.MmcifFormat = MmcifFormat;
 function trajectoryFromMmCIF(frame) {
     var format = MmcifFormat.fromFrame(frame);
-    return mol_task_1.Task.create('Create mmCIF Model', function (ctx) { return (0, parser_1.createModels)(format.data.db, format, ctx); });
+    var basic = (0, schema_1.createBasic)(format.data.db, true);
+    return mol_task_1.Task.create('Create mmCIF Model', function (ctx) { return (0, parser_1.createModels)(basic, format, ctx); });
 }
 exports.trajectoryFromMmCIF = trajectoryFromMmCIF;

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

@@ -18,9 +18,9 @@ var component_1 = require("./common/component");
 var entity_1 = require("./common/entity");
 var index_pair_1 = require("./property/bonds/index-pair");
 function getMolModels(mol, format, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basic, models, indexA, indexB, order, pairBonds;
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     atoms = mol.atoms, bonds = mol.bonds, formalCharges = mol.formalCharges;
@@ -64,12 +64,12 @@ function getMolModels(mol, format, ctx) {
                     componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = (0, schema_1.createBasic)({
+                    basic = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_2.createModels)(basics, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
+                    return [4 /*yield*/, (0, parser_2.createModels)(basic, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
                 case 1:
                     models = _a.sent();
                     if (models.frameCount > 0) {

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

@@ -21,9 +21,9 @@ var symmetry_1 = require("./property/symmetry");
 var geometry_1 = require("../../mol-math/geometry");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function getModels(mol2, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basics, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
-        return (0, tslib_1.__generator)(this, function (_b) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basic, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     models = [];
@@ -44,7 +44,7 @@ function getModels(mol2, ctx) {
                     for (i_2 = 0; i_2 < atoms.count; ++i_2) {
                         type_symbol[i_2] = hasAtomType
                             ? atoms.atom_type.value(i_2).split('.')[0].toUpperCase()
-                            : (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_2));
+                            : (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_2), atoms.subst_name.value(i_2));
                     }
                     atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
                         auth_asym_id: A,
@@ -71,12 +71,12 @@ function getModels(mol2, ctx) {
                     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);
                     }
-                    basics = (0, schema_1.createBasic)({
+                    basic = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, Mol2Format.create(mol2), ctx)];
+                    return [4 /*yield*/, (0, parser_1.createModels)(basic, Mol2Format.create(mol2), ctx)];
                 case 2:
                     _models = _b.sent();
                     if (_models.frameCount > 0) {

package/lib/commonjs/mol-model-formats/structure/nctraj.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Task } from '../../mol-task';
+import { NctrajFile } from '../../mol-io/reader/nctraj/parser';
+import { Coordinates } from '../../mol-model/structure/coordinates';
+export declare function coordinatesFromNctraj(file: NctrajFile): Task<Coordinates>;

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

@@ -0,0 +1,60 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.coordinatesFromNctraj = void 0;
+var tslib_1 = require("tslib");
+var mol_task_1 = require("../../mol-task");
+var coordinates_1 = require("../../mol-model/structure/coordinates");
+var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
+var linear_algebra_1 = require("../../mol-math/linear-algebra");
+function coordinatesFromNctraj(file) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse NCTRAJ', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var deltaTime, offsetTime, frames, i, il, c, elementCount, x, y, z, j, jl, frame, lengths, x_1, y_1, z_1;
+        return tslib_1.__generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
+                case 1:
+                    _a.sent();
+                    deltaTime = (0, coordinates_1.Time)(file.deltaTime, 'step');
+                    offsetTime = (0, coordinates_1.Time)(file.timeOffset, deltaTime.unit);
+                    frames = [];
+                    for (i = 0, il = file.coordinates.length; i < il; ++i) {
+                        c = file.coordinates[i];
+                        elementCount = c.length / 3;
+                        x = new Float32Array(elementCount);
+                        y = new Float32Array(elementCount);
+                        z = new Float32Array(elementCount);
+                        for (j = 0, jl = c.length; j < jl; j += 3) {
+                            x[j / 3] = c[j];
+                            y[j / 3] = c[j + 1];
+                            z[j / 3] = c[j + 2];
+                        }
+                        frame = {
+                            elementCount: elementCount,
+                            x: x,
+                            y: y,
+                            z: z,
+                            xyzOrdering: { isIdentity: true },
+                            time: (0, coordinates_1.Time)(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+                        };
+                        // TODO: handle case where cell_lengths and cell_angles are set, i.e., angles not 90deg
+                        if (file.cell_lengths) {
+                            lengths = file.cell_lengths[i];
+                            x_1 = linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.unitX, lengths[0]);
+                            y_1 = linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.unitY, lengths[1]);
+                            z_1 = linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.unitZ, lengths[2]);
+                            frame.cell = cell_1.Cell.fromBasis(x_1, y_1, z_1);
+                        }
+                        frames.push(frame);
+                    }
+                    return [2 /*return*/, coordinates_1.Coordinates.create(frames, deltaTime, offsetTime)];
+            }
+        });
+    }); });
+}
+exports.coordinatesFromNctraj = coordinatesFromNctraj;

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

@@ -23,9 +23,9 @@ var anisotropic_1 = require("./anisotropic");
 var conect_1 = require("./conect");
 var debug_1 = require("../../../mol-util/debug");
 function pdbToMmCif(pdb) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var lines, data, indices, tokenizer, isPdbqt, atomCount, anisotropicCount, i, _i, s, e, atomSite, anisotropic, entityBuilder, helperCategories, heteroNames, modelNum, modelStr, conectRange, i, _i, s, e, j, j, j, j, j, j, j, seqIds, atomIds, compIds, asymIds, componentBuilder, i, il, compId, moleculeType, atom_site, categories, _a, helperCategories_1, c;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             lines = pdb.lines;
             data = lines.data, indices = lines.indices;
             tokenizer = (0, tokenizer_1.Tokenizer)(data);

package/lib/commonjs/mol-model-formats/structure/pdb.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -14,6 +14,7 @@ var mmcif_1 = require("./mmcif");
 var parser_1 = require("./basic/parser");
 var db_1 = require("../../mol-data/db");
 var partial_charge_1 = require("./property/partial-charge");
+var schema_1 = require("./basic/schema");
 var PdbFormat;
 (function (PdbFormat) {
     function is(x) {
@@ -28,10 +29,10 @@ var PdbFormat;
 exports.PdbFormat = PdbFormat;
 function trajectoryFromPDB(pdb) {
     var _this = this;
-    return mol_task_1.Task.create('Parse PDB', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        var cif, format, models, partial_charge, first, srcIndex, isIdentity, srcIndexArray, q_1, partialCharge;
+    return mol_task_1.Task.create('Parse PDB', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var cif, format, basic, models, partial_charge, first, srcIndex, isIdentity, srcIndexArray, q_1, partialCharge;
         var _a;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0: return [4 /*yield*/, ctx.update('Converting to mmCIF')];
                 case 1:
@@ -40,7 +41,8 @@ function trajectoryFromPDB(pdb) {
                 case 2:
                     cif = _b.sent();
                     format = mmcif_1.MmcifFormat.fromFrame(cif, undefined, PdbFormat.create(pdb));
-                    return [4 /*yield*/, (0, parser_1.createModels)(format.data.db, format, ctx)];
+                    basic = (0, schema_1.createBasic)(format.data.db, true);
+                    return [4 /*yield*/, (0, parser_1.createModels)(basic, format, ctx)];
                 case 3:
                     models = _b.sent();
                     partial_charge = (_a = cif.categories['atom_site']) === null || _a === void 0 ? void 0 : _a.getField('partial_charge');

package/lib/commonjs/mol-model-formats/structure/prmtop.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { PrmtopFile } from '../../mol-io/reader/prmtop/parser';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+export { PrmtopFormat };
+declare type PrmtopFormat = ModelFormat<PrmtopFile>;
+declare namespace PrmtopFormat {
+    function is(x?: ModelFormat): x is PrmtopFormat;
+    function fromPrmtop(prmtop: PrmtopFile): PrmtopFormat;
+}
+export declare function topologyFromPrmtop(prmtop: PrmtopFile): Task<Topology>;

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

@@ -0,0 +1,147 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.topologyFromPrmtop = exports.PrmtopFormat = void 0;
+var tslib_1 = require("tslib");
+var db_1 = require("../../mol-data/db");
+var types_1 = require("../../mol-model/structure/model/types");
+var topology_1 = require("../../mol-model/structure/topology/topology");
+var mol_task_1 = require("../../mol-task");
+var schema_1 = require("./basic/schema");
+var component_1 = require("./common/component");
+var entity_1 = require("./common/entity");
+var util_1 = require("./common/util");
+var util_2 = require("./util");
+function getBasic(prmtop) {
+    var pointers = prmtop.pointers, residuePointer = prmtop.residuePointer, residueLabel = prmtop.residueLabel, atomName = prmtop.atomName;
+    var atomCount = pointers.NATOM;
+    var residueCount = pointers.NRES;
+    //
+    var residueIds = new Uint32Array(atomCount);
+    var residueNames = [];
+    var addResidue = function (i, from, to) {
+        var rn = residueLabel.value(i);
+        for (var j = from, jl = to; j < jl; ++j) {
+            residueIds[j] = i + 1;
+            residueNames[j] = rn;
+        }
+    };
+    for (var i = 0, il = residueCount - 1; i < il; ++i) {
+        addResidue(i, residuePointer.value(i) - 1, residuePointer.value(i + 1) - 1);
+    }
+    addResidue(residueCount - 1, residuePointer.value(residueCount - 1) - 1, atomCount);
+    var residueId = db_1.Column.ofIntArray(residueIds);
+    var residueName = db_1.Column.ofStringArray(residueNames);
+    //
+    var entityIds = new Array(atomCount);
+    var asymIds = new Array(atomCount);
+    var seqIds = new Uint32Array(atomCount);
+    var ids = new Uint32Array(atomCount);
+    var entityBuilder = new entity_1.EntityBuilder();
+    var componentBuilder = new component_1.ComponentBuilder(residueId, atomName);
+    var currentEntityId = '';
+    var currentAsymIndex = 0;
+    var currentAsymId = '';
+    var currentSeqId = 0;
+    var prevMoleculeType = 0 /* Unknown */;
+    var prevResidueNumber = -1;
+    for (var i = 0, il = atomCount; i < il; ++i) {
+        var residueNumber = residueId.value(i);
+        if (residueNumber !== prevResidueNumber) {
+            var compId = residueName.value(i);
+            var moleculeType = (0, types_1.getMoleculeType)(componentBuilder.add(compId, i).type, compId);
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = (0, util_1.getChainId)(currentAsymIndex);
+                currentAsymIndex += 1;
+                currentSeqId = 0;
+            }
+            currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId);
+            currentSeqId += 1;
+            prevResidueNumber = residueNumber;
+            prevMoleculeType = moleculeType;
+        }
+        entityIds[i] = currentEntityId;
+        asymIds[i] = currentAsymId;
+        seqIds[i] = currentSeqId;
+        ids[i] = i;
+    }
+    var id = db_1.Column.ofIntArray(ids);
+    var asym_id = db_1.Column.ofStringArray(asymIds);
+    //
+    var type_symbol = new Array(atomCount);
+    for (var i = 0; i < atomCount; ++i) {
+        type_symbol[i] = (0, util_2.guessElementSymbolString)(atomName.value(i), residueName.value(i));
+    }
+    var atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: db_1.Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: db_1.Column.asArrayColumn(id),
+        label_asym_id: asym_id,
+        label_atom_id: db_1.Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: db_1.Column.ofIntArray(seqIds),
+        label_entity_id: db_1.Column.ofStringArray(entityIds),
+        occupancy: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.float),
+        type_symbol: db_1.Column.ofStringArray(type_symbol),
+        pdbx_PDB_model_num: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.int),
+    }, atomCount);
+    var basic = (0, schema_1.createBasic)({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site: atom_site
+    });
+    return basic;
+}
+var PrmtopFormat;
+(function (PrmtopFormat) {
+    function is(x) {
+        return (x === null || x === void 0 ? void 0 : x.kind) === 'prmtop';
+    }
+    PrmtopFormat.is = is;
+    function fromPrmtop(prmtop) {
+        return { kind: 'prmtop', name: prmtop.title.join(' ') || 'PRMTOP', data: prmtop };
+    }
+    PrmtopFormat.fromPrmtop = fromPrmtop;
+})(PrmtopFormat || (PrmtopFormat = {}));
+exports.PrmtopFormat = PrmtopFormat;
+function topologyFromPrmtop(prmtop) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse PRMTOP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var format, basic, _a, NBONH, NBONA, bondsIncHydrogen, bondsWithoutHydrogen, bondCount, bonds;
+        return tslib_1.__generator(this, function (_b) {
+            format = PrmtopFormat.fromPrmtop(prmtop);
+            basic = getBasic(prmtop);
+            _a = prmtop.pointers, NBONH = _a.NBONH, NBONA = _a.NBONA, bondsIncHydrogen = prmtop.bondsIncHydrogen, bondsWithoutHydrogen = prmtop.bondsWithoutHydrogen;
+            bondCount = NBONH + NBONA;
+            bonds = {
+                indexA: db_1.Column.ofLambda({
+                    value: function (row) {
+                        return row < NBONH
+                            ? bondsIncHydrogen.value(row * 3) / 3
+                            : bondsWithoutHydrogen.value((row - NBONH) * 3) / 3;
+                    },
+                    rowCount: bondCount,
+                    schema: db_1.Column.Schema.int,
+                }),
+                indexB: db_1.Column.ofLambda({
+                    value: function (row) {
+                        return row < NBONH
+                            ? bondsIncHydrogen.value(row * 3 + 1) / 3
+                            : bondsWithoutHydrogen.value((row - NBONH) * 3 + 1) / 3;
+                    },
+                    rowCount: bondCount,
+                    schema: db_1.Column.Schema.int,
+                }),
+                order: db_1.Column.ofConst(1, bondCount, db_1.Column.Schema.int)
+            };
+            return [2 /*return*/, topology_1.Topology.create(prmtop.title.join(' ') || 'PRMTOP', basic, bonds, format)];
+        });
+    }); });
+}
+exports.topologyFromPrmtop = topologyFromPrmtop;

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

@@ -45,7 +45,7 @@ var IndexPairBonds;
     };
     function fromData(data, props) {
         if (props === void 0) { props = {}; }
-        var p = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, IndexPairBonds.DefaultProps), props);
+        var p = tslib_1.__assign(tslib_1.__assign({}, IndexPairBonds.DefaultProps), props);
         var pairs = data.pairs, count = data.count;
         var indexA = pairs.indexA.toArray();
         var indexB = pairs.indexB.toArray();

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

@@ -51,8 +51,18 @@ function getSpacegroupNameOrNumber(symmetry) {
 function getSpacegroup(symmetry, cell) {
     if (symmetry._rowCount === 0 || cell._rowCount === 0)
         return geometry_1.Spacegroup.ZeroP1;
+    var a = cell.length_a.value(0);
+    var b = cell.length_b.value(0);
+    var c = cell.length_c.value(0);
+    if (a === 0 || b === 0 || c === 0)
+        return geometry_1.Spacegroup.ZeroP1;
+    var alpha = cell.angle_alpha.value(0);
+    var beta = cell.angle_beta.value(0);
+    var gamma = cell.angle_gamma.value(0);
+    if (alpha === 0 || beta === 0 || gamma === 0)
+        return geometry_1.Spacegroup.ZeroP1;
     var nameOrNumber = getSpacegroupNameOrNumber(symmetry);
-    var spaceCell = geometry_1.SpacegroupCell.create(nameOrNumber, linear_algebra_1.Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)), linear_algebra_1.Vec3.scale(linear_algebra_1.Vec3.zero(), linear_algebra_1.Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+    var spaceCell = geometry_1.SpacegroupCell.create(nameOrNumber, linear_algebra_1.Vec3.create(a, b, c), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.create(alpha, beta, gamma), Math.PI / 180));
     return geometry_1.Spacegroup.create(spaceCell);
 }
 function getNcsOperators(struct_ncs_oper) {

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

@@ -21,6 +21,7 @@ function getBasic(atoms) {
     var asymIds = new Array(atoms.count);
     var seqIds = new Uint32Array(atoms.count);
     var ids = new Uint32Array(atoms.count);
+    var typeSymbol = new Array(atoms.count);
     var entityBuilder = new entity_1.EntityBuilder();
     var componentBuilder = new component_1.ComponentBuilder(atoms.residueId, atoms.atomName);
     var currentEntityId = '';
@@ -60,6 +61,7 @@ function getBasic(atoms) {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+        typeSymbol[i] = (0, util_2.guessElementSymbolString)(atoms.atomName.value(i), atoms.residueName.value(i));
     }
     var atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
         auth_asym_id: atoms.segmentName,
@@ -73,7 +75,7 @@ function getBasic(atoms) {
         label_seq_id: db_1.Column.ofIntArray(seqIds),
         label_entity_id: db_1.Column.ofStringArray(entityIds),
         occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
-        type_symbol: db_1.Column.ofStringArray(db_1.Column.mapToArray(atoms.atomName, function (s) { return (0, util_2.guessElementSymbolString)(s); })),
+        type_symbol: db_1.Column.ofStringArray(typeSymbol),
         pdbx_PDB_model_num: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.int),
     }, atoms.count);
     return (0, schema_1.createBasic)({
@@ -96,9 +98,9 @@ var PsfFormat;
 exports.PsfFormat = PsfFormat;
 function topologyFromPsf(psf) {
     var _this = this;
-    return mol_task_1.Task.create('Parse PSF', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse PSF', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var format, basic, _a, atomIdA, atomIdB, bonds;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             format = PsfFormat.fromPsf(psf);
             basic = getBasic(psf.atoms);
             _a = psf.bonds, atomIdA = _a.atomIdA, atomIdB = _a.atomIdB;

package/lib/commonjs/mol-model-formats/structure/top.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { TopFile } from '../../mol-io/reader/top/parser';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+export { TopFormat };
+declare type TopFormat = ModelFormat<TopFile>;
+declare namespace TopFormat {
+    function is(x?: ModelFormat): x is TopFormat;
+    function fromTop(top: TopFile): TopFormat;
+}
+export declare function topologyFromTop(top: TopFile): Task<Topology>;