molstar 3.3.1 → 3.6.0

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/chem_comp.js

@@ -63,7 +63,7 @@ var ComponentBond;
             var nameA = atom_id_1.value(i);
             var nameB = atom_id_2.value(i);
             var order = value_order.value(i);
-            var aromatic = pdbx_aromatic_flag.value(i) === 'Y';
+            var aromatic = pdbx_aromatic_flag.value(i) === 'y';
             if (entry.id !== id) {
                 entry = addEntry(id);
             }

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/bonds/struct_conn.js

@@ -118,7 +118,7 @@ var StructConn;
             if (partnerA === undefined || partnerB === undefined)
                 continue;
             var type = conn_type_id.value(i);
-            var orderType = (pdbx_value_order.value(i) || '').toLowerCase();
+            var orderType = (pdbx_value_order.value(i) || '');
             var flags = 0 /* None */;
             var order = 1;
             switch (orderType) {

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>;

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

@@ -0,0 +1,189 @@
+"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.topologyFromTop = exports.TopFormat = 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(top) {
+    var molecules = top.molecules, compounds = top.compounds;
+    var singleResidue = {};
+    var atomCount = 0;
+    for (var i = 0, il = molecules._rowCount; i < il; ++i) {
+        var mol = molecules.compound.value(i);
+        var count = molecules.molCount.value(i);
+        var atoms = compounds[mol].atoms;
+        db_1.Column.asArrayColumn(atoms.atom);
+        db_1.Column.asArrayColumn(atoms.resnr);
+        db_1.Column.asArrayColumn(atoms.residu);
+        atomCount += count * atoms._rowCount;
+        var prevResnr = atoms.resnr.value(0);
+        singleResidue[mol] = true;
+        for (var j = 1, jl = atoms._rowCount; j < jl; ++j) {
+            var resnr = atoms.resnr.value(j);
+            if (resnr !== prevResnr) {
+                singleResidue[mol] = false;
+                break;
+            }
+            prevResnr = resnr;
+        }
+    }
+    //
+    var atomNames = new Array(atomCount);
+    var residueIds = new Uint32Array(atomCount);
+    var residueNames = new Array(atomCount);
+    var k = 0;
+    for (var i = 0, il = molecules._rowCount; i < il; ++i) {
+        var mol = molecules.compound.value(i);
+        var count = molecules.molCount.value(i);
+        var atoms = compounds[mol].atoms;
+        var isSingleResidue = singleResidue[mol];
+        for (var j = 0; j < count; ++j) {
+            for (var l = 0, ll = atoms._rowCount; l < ll; ++l) {
+                atomNames[k] = atoms.atom.value(l);
+                residueIds[k] = atoms.resnr.value(l);
+                residueNames[k] = atoms.residu.value(l);
+                if (isSingleResidue)
+                    residueIds[k] += j;
+                k += 1;
+            }
+        }
+    }
+    var atomName = db_1.Column.ofStringArray(atomNames);
+    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;
+}
+function getBonds(top) {
+    var molecules = top.molecules, compounds = top.compounds;
+    var indexA = [];
+    var indexB = [];
+    var atomOffset = 0;
+    for (var i = 0, il = molecules._rowCount; i < il; ++i) {
+        var mol = molecules.compound.value(i);
+        var count = molecules.molCount.value(i);
+        var _a = compounds[mol], atoms = _a.atoms, bonds = _a.bonds;
+        if (bonds) {
+            for (var j = 0; j < count; ++j) {
+                for (var l = 0, ll = bonds._rowCount; l < ll; ++l) {
+                    indexA.push(bonds.ai.value(l) - 1 + atomOffset);
+                    indexB.push(bonds.aj.value(l) - 1 + atomOffset);
+                }
+                atomOffset += atoms._rowCount;
+            }
+        }
+        else if (mol === 'TIP3') {
+            for (var j = 0; j < count; ++j) {
+                indexA.push(0 + atomOffset);
+                indexB.push(1 + atomOffset);
+                indexA.push(0 + atomOffset);
+                indexB.push(2 + atomOffset);
+                atomOffset += atoms._rowCount;
+            }
+        }
+        else {
+            atomOffset += count * atoms._rowCount;
+        }
+    }
+    return {
+        indexA: db_1.Column.ofIntArray(indexA),
+        indexB: db_1.Column.ofIntArray(indexB),
+        order: db_1.Column.ofConst(1, indexA.length, db_1.Column.Schema.int)
+    };
+}
+var TopFormat;
+(function (TopFormat) {
+    function is(x) {
+        return (x === null || x === void 0 ? void 0 : x.kind) === 'top';
+    }
+    TopFormat.is = is;
+    function fromTop(top) {
+        return { kind: 'top', name: top.system || 'TOP', data: top };
+    }
+    TopFormat.fromTop = fromTop;
+})(TopFormat || (TopFormat = {}));
+exports.TopFormat = TopFormat;
+function topologyFromTop(top) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse TOP', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var format, basic, bonds;
+        return tslib_1.__generator(this, function (_a) {
+            format = TopFormat.fromTop(top);
+            basic = getBasic(top);
+            bonds = getBonds(top);
+            return [2 /*return*/, topology_1.Topology.create(top.system || 'TOP', basic, bonds, format)];
+        });
+    }); });
+}
+exports.topologyFromTop = topologyFromTop;

package/lib/commonjs/mol-model-formats/structure/trr.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 { TrrFile } from '../../mol-io/reader/trr/parser';
+import { Coordinates } from '../../mol-model/structure/coordinates';
+export declare function coordinatesFromTrr(file: TrrFile): Task<Coordinates>;

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

@@ -0,0 +1,46 @@
+"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.coordinatesFromTrr = 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 coordinatesFromTrr(file) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse TRR', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var deltaTime, offsetTime, frames, i, il, box, x, y, z;
+        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.frames.length; i < il; ++i) {
+                        box = file.boxes[i];
+                        x = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 0);
+                        y = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 3);
+                        z = linear_algebra_1.Vec3.fromArray((0, linear_algebra_1.Vec3)(), box, 6);
+                        frames.push({
+                            elementCount: file.frames[i].count,
+                            cell: cell_1.Cell.fromBasis(x, y, z),
+                            x: file.frames[i].x,
+                            y: file.frames[i].y,
+                            z: file.frames[i].z,
+                            xyzOrdering: { isIdentity: true },
+                            time: (0, coordinates_1.Time)(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+                        });
+                    }
+                    return [2 /*return*/, coordinates_1.Coordinates.create(frames, deltaTime, offsetTime)];
+            }
+        });
+    }); });
+}
+exports.coordinatesFromTrr = coordinatesFromTrr;

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

@@ -1,8 +1,8 @@
 /**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Tokens } from '../../mol-io/reader/common/text/tokenizer';
 export declare function guessElementSymbolTokens(tokens: Tokens, str: string, start: number, end: number): void;
-export declare function guessElementSymbolString(str: string): string;
+export declare function guessElementSymbolString(atomId: string, compId: string): string;

package/lib/commonjs/mol-model-formats/structure/util.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -44,35 +44,34 @@ function guessElementSymbolTokens(tokens, str, start, end) {
     tokenizer_1.TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token
 }
 exports.guessElementSymbolTokens = guessElementSymbolTokens;
+var TwoCharElementNames = new Set(['NA', 'CL', 'FE', 'SI', 'BR', 'AS']);
+var OneCharElementNames = new Set(['C', 'H', 'N', 'O', 'P', 'S']);
 var reTrimSpacesAndNumbers = /^[\s\d]+|[\s\d]+$/g;
-function guessElementSymbolString(str) {
+function guessElementSymbolString(atomId, compId) {
     // trim spaces and numbers, convert to upper case
-    str = str.replace(reTrimSpacesAndNumbers, '').toUpperCase();
-    var l = str.length;
+    atomId = atomId.replace(reTrimSpacesAndNumbers, '').toUpperCase();
+    var l = atomId.length;
     if (l === 0)
-        return str; // empty
+        return atomId; // empty
     if (l === 1)
-        return str; // one char
-    if (l === 2) { // two chars
-        if (str === 'NA' || str === 'CL' || str === 'FE' || str === 'SI' ||
-            str === 'BR' || str === 'AS')
-            return str;
-    }
-    if (l === 3) { // three chars
-        if (str === 'SOD')
+        return atomId; // one char
+    if (TwoCharElementNames.has(atomId))
+        return atomId; // two chars
+    // check for Charmm ion names where component and atom id are the same
+    if (l === 3 && compId === atomId) {
+        if (atomId === 'SOD')
             return 'NA';
-        if (str === 'POT')
+        if (atomId === 'POT')
             return 'K';
-        if (str === 'CES')
+        if (atomId === 'CES')
             return 'CS';
-        if (str === 'CAL')
+        if (atomId === 'CAL')
             return 'CA';
-        if (str === 'CLA')
+        if (atomId === 'CLA')
             return 'CL';
     }
-    var c = str[0];
-    if (c === 'C' || c === 'H' || c === 'N' || c === 'O' || c === 'P' || c === 'S')
-        return c;
+    if (OneCharElementNames.has(atomId[0]))
+        return atomId[0];
     return ''; // no reasonable guess, return empty string
 }
 exports.guessElementSymbolString = guessElementSymbolString;

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

@@ -14,9 +14,9 @@ var cell_1 = require("../../mol-math/geometry/spacegroup/cell");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function coordinatesFromXtc(file) {
     var _this = this;
-    return mol_task_1.Task.create('Parse XTC', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse XTC', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var deltaTime, offsetTime, frames, i, il, box, x, y, z;
-        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/xyz.js

@@ -66,12 +66,12 @@ function getModels(mol, ctx) {
     var componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
     componentBuilder.add('MOL', 0);
-    var basics = (0, schema_1.createBasic)({
+    var basic = (0, schema_1.createBasic)({
         entity: entityBuilder.getEntityTable(),
         chem_comp: componentBuilder.getChemCompTable(),
         atom_site: atom_site
     });
-    return (0, parser_1.createModels)(basics, XyzFormat.create(mol), ctx);
+    return (0, parser_1.createModels)(basic, XyzFormat.create(mol), ctx);
 }
 var XyzFormat;
 (function (XyzFormat) {