molstar 3.3.1 → 3.4.0

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

@@ -0,0 +1,144 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __awaiter, __generator } from "tslib";
+import { Column, Table } from '../../mol-data/db';
+import { getMoleculeType } from '../../mol-model/structure/model/types';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { getChainId } from './common/util';
+import { guessElementSymbolString } from './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 = Column.ofIntArray(residueIds);
+    var residueName = 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 EntityBuilder();
+    var componentBuilder = new 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 = getMoleculeType(componentBuilder.add(compId, i).type, compId);
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = 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 = Column.ofIntArray(ids);
+    var asym_id = Column.ofStringArray(asymIds);
+    //
+    var type_symbol = new Array(atomCount);
+    for (var i = 0; i < atomCount; ++i) {
+        type_symbol[i] = guessElementSymbolString(atomName.value(i), residueName.value(i));
+    }
+    var atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: Column.asArrayColumn(id),
+        label_asym_id: asym_id,
+        label_atom_id: Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: Column.ofIntArray(seqIds),
+        label_entity_id: Column.ofStringArray(entityIds),
+        occupancy: Column.ofConst(1, atomCount, Column.Schema.float),
+        type_symbol: Column.ofStringArray(type_symbol),
+        pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
+    }, atomCount);
+    var basic = createBasic({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site: atom_site
+    });
+    return basic;
+}
+//
+export { PrmtopFormat };
+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 = {}));
+export function topologyFromPrmtop(prmtop) {
+    var _this = this;
+    return Task.create('Parse PRMTOP', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
+        var format, basic, _a, NBONH, NBONA, bondsIncHydrogen, bondsWithoutHydrogen, bondCount, bonds;
+        return __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: Column.ofLambda({
+                    value: function (row) {
+                        return row < NBONH
+                            ? bondsIncHydrogen.value(row * 3) / 3
+                            : bondsWithoutHydrogen.value((row - NBONH) * 3) / 3;
+                    },
+                    rowCount: bondCount,
+                    schema: Column.Schema.int,
+                }),
+                indexB: Column.ofLambda({
+                    value: function (row) {
+                        return row < NBONH
+                            ? bondsIncHydrogen.value(row * 3 + 1) / 3
+                            : bondsWithoutHydrogen.value((row - NBONH) * 3 + 1) / 3;
+                    },
+                    rowCount: bondCount,
+                    schema: Column.Schema.int,
+                }),
+                order: Column.ofConst(1, bondCount, Column.Schema.int)
+            };
+            return [2 /*return*/, Topology.create(prmtop.title.join(' ') || 'PRMTOP', basic, bonds, format)];
+        });
+    }); });
+}

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

@@ -48,8 +48,18 @@ function getSpacegroupNameOrNumber(symmetry) {
 function getSpacegroup(symmetry, cell) {
     if (symmetry._rowCount === 0 || cell._rowCount === 0)
         return 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 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 Spacegroup.ZeroP1;
     var nameOrNumber = getSpacegroupNameOrNumber(symmetry);
-    var spaceCell = SpacegroupCell.create(nameOrNumber, Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)), Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+    var spaceCell = SpacegroupCell.create(nameOrNumber, Vec3.create(a, b, c), Vec3.scale(Vec3(), Vec3.create(alpha, beta, gamma), Math.PI / 180));
     return Spacegroup.create(spaceCell);
 }
 function getNcsOperators(struct_ncs_oper) {

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

@@ -18,6 +18,7 @@ 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 EntityBuilder();
     var componentBuilder = new ComponentBuilder(atoms.residueId, atoms.atomName);
     var currentEntityId = '';
@@ -57,6 +58,7 @@ function getBasic(atoms) {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
     }
     var atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
         auth_asym_id: atoms.segmentName,
@@ -70,7 +72,7 @@ function getBasic(atoms) {
         label_seq_id: Column.ofIntArray(seqIds),
         label_entity_id: Column.ofStringArray(entityIds),
         occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, function (s) { return guessElementSymbolString(s); })),
+        type_symbol: Column.ofStringArray(typeSymbol),
         pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
     }, atoms.count);
     return createBasic({

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

@@ -0,0 +1,186 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __awaiter, __generator } from "tslib";
+import { Column, Table } from '../../mol-data/db';
+import { getMoleculeType } from '../../mol-model/structure/model/types';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { getChainId } from './common/util';
+import { guessElementSymbolString } from './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;
+        Column.asArrayColumn(atoms.atom);
+        Column.asArrayColumn(atoms.resnr);
+        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 = Column.ofStringArray(atomNames);
+    var residueId = Column.ofIntArray(residueIds);
+    var residueName = 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 EntityBuilder();
+    var componentBuilder = new 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 = getMoleculeType(componentBuilder.add(compId, i).type, compId);
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = 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 = Column.ofIntArray(ids);
+    var asym_id = Column.ofStringArray(asymIds);
+    //
+    var type_symbol = new Array(atomCount);
+    for (var i = 0; i < atomCount; ++i) {
+        type_symbol[i] = guessElementSymbolString(atomName.value(i), residueName.value(i));
+    }
+    var atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: Column.asArrayColumn(id),
+        label_asym_id: asym_id,
+        label_atom_id: Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: Column.ofIntArray(seqIds),
+        label_entity_id: Column.ofStringArray(entityIds),
+        occupancy: Column.ofConst(1, atomCount, Column.Schema.float),
+        type_symbol: Column.ofStringArray(type_symbol),
+        pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
+    }, atomCount);
+    var basic = 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: Column.ofIntArray(indexA),
+        indexB: Column.ofIntArray(indexB),
+        order: Column.ofConst(1, indexA.length, Column.Schema.int)
+    };
+}
+//
+export { TopFormat };
+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 = {}));
+export function topologyFromTop(top) {
+    var _this = this;
+    return Task.create('Parse TOP', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
+        var format, basic, bonds;
+        return __generator(this, function (_a) {
+            format = TopFormat.fromTop(top);
+            basic = getBasic(top);
+            bonds = getBonds(top);
+            return [2 /*return*/, Topology.create(top.system || 'TOP', basic, bonds, format)];
+        });
+    }); });
+}

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

@@ -0,0 +1,42 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __awaiter, __generator } from "tslib";
+import { Task } from '../../mol-task';
+import { Coordinates, Time } from '../../mol-model/structure/coordinates';
+import { Cell } from '../../mol-math/geometry/spacegroup/cell';
+import { Vec3 } from '../../mol-math/linear-algebra';
+export function coordinatesFromTrr(file) {
+    var _this = this;
+    return Task.create('Parse TRR', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
+        var deltaTime, offsetTime, frames, i, il, box, x, y, z;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
+                case 1:
+                    _a.sent();
+                    deltaTime = Time(file.deltaTime, 'step');
+                    offsetTime = Time(file.timeOffset, deltaTime.unit);
+                    frames = [];
+                    for (i = 0, il = file.frames.length; i < il; ++i) {
+                        box = file.boxes[i];
+                        x = Vec3.fromArray(Vec3(), box, 0);
+                        y = Vec3.fromArray(Vec3(), box, 3);
+                        z = Vec3.fromArray(Vec3(), box, 6);
+                        frames.push({
+                            elementCount: file.frames[i].count,
+                            cell: Cell.fromBasis(x, y, z),
+                            x: file.frames[i].x,
+                            y: file.frames[i].y,
+                            z: file.frames[i].z,
+                            xyzOrdering: { isIdentity: true },
+                            time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+                        });
+                    }
+                    return [2 /*return*/, Coordinates.create(frames, deltaTime, offsetTime)];
+            }
+        });
+    }); });
+}

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

@@ -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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -40,34 +40,33 @@ export function guessElementSymbolTokens(tokens, str, start, end) {
         return TokenBuilder.add(tokens, s, s + 1);
     TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token
 }
+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;
-export function guessElementSymbolString(str) {
+export 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
 }

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

@@ -63,12 +63,12 @@ function getModels(mol, ctx) {
     var componentBuilder = new ComponentBuilder(seq_id, type_symbol);
     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
     componentBuilder.add('MOL', 0);
-    var basics = createBasic({
+    var basic = createBasic({
         entity: entityBuilder.getEntityTable(),
         chem_comp: componentBuilder.getChemCompTable(),
         atom_site: atom_site
     });
-    return createModels(basics, XyzFormat.create(mol), ctx);
+    return createModels(basic, XyzFormat.create(mol), ctx);
 }
 //
 export { XyzFormat };

package/lib/mol-plugin/context.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -143,6 +143,7 @@ export declare class PluginContext {
     readonly customModelProperties: CustomProperty.Registry<Model>;
     readonly customStructureProperties: CustomProperty.Registry<Structure>;
     readonly customStructureControls: Map<string, new () => any>;
+    readonly customImportControls: Map<string, new () => any>;
     readonly genericRepresentationControls: Map<string, (selection: StructureHierarchyManager['selection']) => [StructureHierarchyRef[], string]>;
     /**
      * Used to store application specific custom state which is then available

package/lib/mol-plugin/context.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -156,6 +156,7 @@ var PluginContext = /** @class */ (function () {
         this.customModelProperties = new CustomProperty.Registry();
         this.customStructureProperties = new CustomProperty.Registry();
         this.customStructureControls = new Map();
+        this.customImportControls = new Map();
         this.genericRepresentationControls = new Map();
         /**
          * Used to store application specific custom state which is then available
@@ -291,8 +292,8 @@ var PluginContext = /** @class */ (function () {
         this.state.dispose();
         this.managers.task.dispose();
         this.helpers.substructureParent.dispose();
-        objectForEach(this.managers, function (m) { var _a, _b; return (_b = (_a = m) === null || _a === void 0 ? void 0 : _a.dispose) === null || _b === void 0 ? void 0 : _b.call(_a); });
-        objectForEach(this.managers.structure, function (m) { var _a, _b; return (_b = (_a = m) === null || _a === void 0 ? void 0 : _a.dispose) === null || _b === void 0 ? void 0 : _b.call(_a); });
+        objectForEach(this.managers, function (m) { var _a; return (_a = m === null || m === void 0 ? void 0 : m.dispose) === null || _a === void 0 ? void 0 : _a.call(m); });
+        objectForEach(this.managers.structure, function (m) { var _a; return (_a = m === null || m === void 0 ? void 0 : m.dispose) === null || _a === void 0 ? void 0 : _a.call(m); });
         this.disposed = true;
     };
     PluginContext.prototype.initBehaviorEvents = function () {

package/lib/mol-plugin/spec.js

@@ -33,10 +33,10 @@ var PluginSpec;
 export var DefaultPluginSpec = function () { return ({
     actions: [
         PluginSpec.Action(StateActions.Structure.DownloadStructure),
-        PluginSpec.Action(StateActions.Structure.AddTrajectory),
         PluginSpec.Action(StateActions.Volume.DownloadDensity),
         PluginSpec.Action(StateActions.DataFormat.DownloadFile),
         PluginSpec.Action(StateActions.DataFormat.OpenFiles),
+        PluginSpec.Action(StateActions.Structure.LoadTrajectory),
         PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
         PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),
         // Volume streaming

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.3.1';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1646016251962);
+export var PLUGIN_VERSION = '3.4.0';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1647202245473);

package/lib/mol-plugin-state/actions/file.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */