molstar 3.3.1 → 3.6.0

package/lib/mol-io/reader/cif/schema/mmcif.js

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2017-2020 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.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
  *
  * @author molstar/ciftools package
  */
@@ -14,6 +14,7 @@ var coord = Schema.coord;
 var Aliased = Schema.Aliased;
 var Matrix = Schema.Matrix;
 var Vector = Schema.Vector;
+var lstr = Schema.lstr;
 var List = Schema.List;
 export var mmCIF_Schema = {
     /**
@@ -508,7 +509,7 @@ export var mmCIF_Schema = {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Aliased(str),
+        mon_nstd_flag: Aliased(lstr),
         /**
          * The full name of the component.
          */
@@ -519,7 +520,7 @@ export var mmCIF_Schema = {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Synonym list for the component.
          */
@@ -556,7 +557,7 @@ export var mmCIF_Schema = {
          * bond associated with the specified atoms, expressed as a bond
          * order.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * Ordinal index for the component bond list.
          */
@@ -564,11 +565,11 @@ export var mmCIF_Schema = {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Aliased(str),
+        pdbx_stereo_config: Aliased(lstr),
         /**
          * A flag indicating an aromatic bond.
          */
-        pdbx_aromatic_flag: Aliased(str),
+        pdbx_aromatic_flag: Aliased(lstr),
     },
     /**
      * Data items in the CITATION category record details about the
@@ -700,7 +701,7 @@ export var mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased(str),
+        database_id: Aliased(lstr),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -763,7 +764,7 @@ export var mmCIF_Schema = {
          * manipulated sources are expected to have further information in
          * the ENTITY_SRC_GEN category.
          */
-        src_method: Aliased(str),
+        src_method: Aliased(lstr),
         /**
          * Defines the type of the entity.
          *
@@ -776,7 +777,7 @@ export var mmCIF_Schema = {
          * Water entities are not expected to have corresponding
          * entries in the ENTITY category.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A description of the entity.
          *
@@ -816,12 +817,12 @@ export var mmCIF_Schema = {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Aliased(str),
+        nstd_linkage: Aliased(lstr),
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Aliased(str),
+        nstd_monomer: Aliased(lstr),
         /**
          * The type of the polymer.
          */
@@ -890,6 +891,10 @@ export var mmCIF_Schema = {
          * parent is not specified. Deoxynucleotides are
          * represented by their canonical one-letter codes of A,
          * C, G, or T.
+         *
+         * For modifications with several parent amino acids,
+         * all corresponding parent amino acid codes will be listed
+         * (ex. chromophores).
          */
         pdbx_seq_one_letter_code_can: str,
         /**
@@ -915,7 +920,7 @@ export var mmCIF_Schema = {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -992,7 +997,7 @@ export var mmCIF_Schema = {
          * The classification of the software according to the most
          * common types.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * The version of the software.
          */
@@ -1115,7 +1120,7 @@ export var mmCIF_Schema = {
          * This data item is a pointer to _struct_conf_type.id in the
          * STRUCT_CONF_TYPE category.
          */
-        conf_type_id: Aliased(str),
+        conf_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the conformation assignment.
          */
@@ -1215,7 +1220,7 @@ export var mmCIF_Schema = {
          * This data item is a pointer to _struct_conn_type.id in the
          * STRUCT_CONN_TYPE category.
          */
-        conn_type_id: Aliased(str),
+        conn_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the connection.
          */
@@ -1435,7 +1440,7 @@ export var mmCIF_Schema = {
          * The chemical bond order associated with the specified atoms in
          * this contact.
          */
-        pdbx_value_order: Aliased(str),
+        pdbx_value_order: Aliased(lstr),
     },
     /**
      * Data items in the STRUCT_CONN_TYPE category record details
@@ -1450,7 +1455,7 @@ export var mmCIF_Schema = {
         /**
          * The chemical or structural type of the interaction.
          */
-        id: Aliased(str),
+        id: Aliased(lstr),
         /**
          * A reference that specifies the criteria used to define the
          * interaction.
@@ -1804,7 +1809,7 @@ export var mmCIF_Schema = {
         /**
          * The cell settings for this space-group symmetry.
          */
-        cell_setting: Aliased(str),
+        cell_setting: Aliased(lstr),
         /**
          * Space-group number from International Tables for Crystallography
          * Vol. A (2002).
@@ -1864,7 +1869,7 @@ export var mmCIF_Schema = {
          * This code indicates whether the entry belongs to
          * Structural Genomics Project.
          */
-        SG_entry: Aliased(str),
+        SG_entry: Aliased(lstr),
         /**
          * The site where the file was deposited.
          */
@@ -1888,7 +1893,7 @@ export var mmCIF_Schema = {
          * A value of 'N' indicates that the no PDB format data file is
          * corresponding to this entry is available in the PDB archive.
          */
-        pdb_format_compatible: Aliased(str),
+        pdb_format_compatible: Aliased(lstr),
     },
     /**
      * The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
@@ -2041,7 +2046,7 @@ export var mmCIF_Schema = {
          * The value of polymer flag indicates whether the unobserved or
          * zero occupancy residue is part of a polymer chain or not
          */
-        polymer_flag: Aliased(str),
+        polymer_flag: Aliased(lstr),
         /**
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
@@ -2294,7 +2299,7 @@ export var mmCIF_Schema = {
         /**
          * Defines the polymer characteristic of the entity.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Additional details about this entity.
          */
@@ -2389,7 +2394,7 @@ export var mmCIF_Schema = {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * The entity component identifier for the first of two entities containing the linkage.
          */
@@ -2475,7 +2480,7 @@ export var mmCIF_Schema = {
         /**
          * The bond order target for the non-standard linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_MOLECULE category identify reference molecules
@@ -2510,11 +2515,11 @@ export var mmCIF_Schema = {
         /**
          * Broadly defines the function of the molecule.
          */
-        class: Aliased(str),
+        class: Aliased(lstr),
         /**
          * Defines the structural classification of the molecule.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A name of the molecule.
          */
@@ -2661,7 +2666,7 @@ export var mmCIF_Schema = {
         /**
          * This data item contains the descriptor type.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * This data item contains the name of the program
          * or library used to compute the descriptor.
@@ -2736,7 +2741,7 @@ export var mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2808,7 +2813,7 @@ export var mmCIF_Schema = {
         /**
          * The chiral configuration of the first atom making the linkage.
          */
-        atom_stereo_config_1: Aliased(str),
+        atom_stereo_config_1: Aliased(lstr),
         /**
          * The atom identifier/name for the second atom making the linkage.
          */
@@ -2820,11 +2825,11 @@ export var mmCIF_Schema = {
         /**
          * The chiral configuration of the second atom making the linkage.
          */
-        atom_stereo_config_2: Aliased(str),
+        atom_stereo_config_2: Aliased(lstr),
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_ENTITY_BRANCH category specify the list
@@ -2855,7 +2860,7 @@ export var mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3328,15 +3333,15 @@ export var mmCIF_Schema = {
         /**
          * A flag to indicate if the modeling is multi scale.
          */
-        multi_scale_flag: Aliased(str),
+        multi_scale_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling is multi state.
          */
-        multi_state_flag: Aliased(str),
+        multi_state_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling involves an ensemble ordered by time or other order.
          */
-        ordered_flag: Aliased(str),
+        ordered_flag: Aliased(lstr),
         /**
          * The file id corresponding to the script used in the modeling protocol step.
          * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
@@ -3625,7 +3630,7 @@ export var mmCIF_Schema = {
          * A flag that indicates whether the dataset is archived in
          * an IHM related database or elsewhere.
          */
-        database_hosted: Aliased(str),
+        database_hosted: Aliased(lstr),
     },
     /**
      * Category to define groups or collections of input datasets.
@@ -4232,7 +4237,7 @@ export var mmCIF_Schema = {
          * whether the whole image is used or only a portion of it is used (by masking
          * or by other means) as restraint in the modeling.
          */
-        image_segment_flag: Aliased(str),
+        image_segment_flag: Aliased(lstr),
         /**
          * Number of 2D projections of the model used in the fitting.
          */
@@ -4385,7 +4390,7 @@ export var mmCIF_Schema = {
          * whether the whole SAS profile is used or only a portion of it is used
          * (by masking or by other means) as restraint in the modeling.
          */
-        profile_segment_flag: Aliased(str),
+        profile_segment_flag: Aliased(lstr),
         /**
          * The type of atoms in the model fit to the SAS data.
          */

package/lib/mol-io/reader/cif/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 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/mol-io/reader/cif/schema.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 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>
@@ -42,13 +42,33 @@ export function toTable(schema, category) {
 }
 function getColumnCtor(t) {
     switch (t.valueType) {
-        case 'str': return function (f, c, k) { return createColumn(t, f, f.str, f.toStringArray); };
+        case 'str': return function (f, c, k) { return createStringColumn(t, f, f.str, f.toStringArray); };
         case 'int': return function (f, c, k) { return createColumn(t, f, f.int, f.toIntArray); };
         case 'float': return function (f, c, k) { return createColumn(t, f, f.float, f.toFloatArray); };
         case 'list': throw new Error('Use createListColumn instead.');
         case 'tensor': throw new Error('Use createTensorColumn instead.');
     }
 }
+function createStringColumn(schema, field, value, toArray) {
+    return {
+        schema: schema,
+        __array: field.__array,
+        isDefined: field.isDefined,
+        rowCount: field.rowCount,
+        value: schema.transform === 'lowercase'
+            ? function (row) { return value(row).toLowerCase(); }
+            : schema.transform === 'uppercase'
+                ? function (row) { return value(row).toUpperCase(); }
+                : value,
+        valueKind: field.valueKind,
+        areValuesEqual: field.areValuesEqual,
+        toArray: schema.transform === 'lowercase'
+            ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toLowerCase(); }); }
+            : schema.transform === 'uppercase'
+                ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toUpperCase(); }); }
+                : toArray,
+    };
+}
 function createColumn(schema, field, value, toArray) {
     return {
         schema: schema,

package/lib/mol-io/reader/nctraj/parser.d.ts

@@ -0,0 +1,18 @@
+/**
+ * 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 { ReaderResult as Result } from '../result';
+export interface NctrajFile {
+    coordinates: number[][];
+    velocities?: number[][];
+    forces?: number[][];
+    cell_lengths?: number[][];
+    cell_angles?: number[][];
+    time?: number[];
+    timeOffset: number;
+    deltaTime: number;
+}
+export declare function parseNctraj(data: Uint8Array): Task<Result<NctrajFile>>;

package/lib/mol-io/reader/nctraj/parser.js

@@ -0,0 +1,97 @@
+/**
+ * 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 { NetcdfReader } from '../../common/netcdf/reader';
+import { ReaderResult as Result } from '../result';
+function parseInternal(data) {
+    return __awaiter(this, void 0, void 0, function () {
+        var nc, f, _i, _a, c, velocities, _b, _c, v, forces, _d, _e, f_1, cell_lengths, _f, _g, l, cell_angles, _h, _j, a, time, _k, _l, t;
+        return __generator(this, function (_m) {
+            nc = new NetcdfReader(data);
+            f = {
+                coordinates: [],
+                time: [],
+                timeOffset: 0,
+                deltaTime: 1
+            };
+            for (_i = 0, _a = nc.getDataVariable('coordinates'); _i < _a.length; _i++) {
+                c = _a[_i];
+                f.coordinates.push(c);
+            }
+            if (nc.hasDataVariable('velocities')) {
+                velocities = [];
+                for (_b = 0, _c = nc.getDataVariable('velocities'); _b < _c.length; _b++) {
+                    v = _c[_b];
+                    velocities.push(v);
+                }
+                f.velocities = velocities;
+            }
+            if (nc.hasDataVariable('forces')) {
+                forces = [];
+                for (_d = 0, _e = nc.getDataVariable('forces'); _d < _e.length; _d++) {
+                    f_1 = _e[_d];
+                    forces.push(f_1);
+                }
+                f.forces = forces;
+            }
+            if (nc.hasDataVariable('cell_lengths')) {
+                cell_lengths = [];
+                for (_f = 0, _g = nc.getDataVariable('cell_lengths'); _f < _g.length; _f++) {
+                    l = _g[_f];
+                    cell_lengths.push(l);
+                }
+                f.cell_lengths = cell_lengths;
+            }
+            if (nc.hasDataVariable('cell_angles')) {
+                cell_angles = [];
+                for (_h = 0, _j = nc.getDataVariable('cell_angles'); _h < _j.length; _h++) {
+                    a = _j[_h];
+                    cell_angles.push(a);
+                }
+                f.cell_angles = cell_angles;
+            }
+            if (nc.hasDataVariable('time')) {
+                time = [];
+                for (_k = 0, _l = nc.getDataVariable('time'); _k < _l.length; _k++) {
+                    t = _l[_k];
+                    time.push(t);
+                }
+                f.time = time;
+            }
+            if (f.time) {
+                if (f.time.length >= 1) {
+                    f.timeOffset = f.time[0];
+                }
+                if (f.time.length >= 2) {
+                    f.deltaTime = f.time[1] - f.time[0];
+                }
+            }
+            return [2 /*return*/, f];
+        });
+    });
+}
+export function parseNctraj(data) {
+    var _this = this;
+    return Task.create('Parse NCTRAJ', function (ctx) { return __awaiter(_this, void 0, void 0, function () {
+        var file, e_1;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    _a.trys.push([0, 2, , 3]);
+                    ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
+                    return [4 /*yield*/, parseInternal(data)];
+                case 1:
+                    file = _a.sent();
+                    return [2 /*return*/, Result.success(file)];
+                case 2:
+                    e_1 = _a.sent();
+                    return [2 /*return*/, Result.error('' + e_1)];
+                case 3: return [2 /*return*/];
+            }
+        });
+    }); });
+}

package/lib/mol-io/reader/prmtop/parser.d.ts

@@ -0,0 +1,58 @@
+/**
+ * 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 { ReaderResult as Result } from '../result';
+import { Column } from '../../../mol-data/db';
+declare const Pointers: {
+    NATOM: string;
+    NTYPES: string;
+    NBONH: string;
+    MBONA: string;
+    NTHETH: string;
+    MTHETA: string;
+    NPHIH: string;
+    MPHIA: string;
+    NHPARM: string;
+    NPARM: string;
+    NNB: string;
+    NRES: string;
+    NBONA: string;
+    NTHETA: string;
+    NPHIA: string;
+    NUMBND: string;
+    NUMANG: string;
+    NPTRA: string;
+    NATYP: string;
+    NPHB: string;
+    IFPERT: string;
+    NBPER: string;
+    NGPER: string;
+    NDPER: string;
+    MBPER: string;
+    MGPER: string;
+    MDPER: string;
+    IFBOX: string;
+    NMXRS: string;
+    IFCAP: string;
+    NUMEXTRA: string;
+    NCOPY: string;
+};
+declare type PointerName = keyof typeof Pointers;
+export interface PrmtopFile {
+    readonly version: string;
+    readonly title: ReadonlyArray<string>;
+    readonly pointers: Readonly<Record<PointerName, number>>;
+    readonly atomName: Column<string>;
+    readonly charge: Column<number>;
+    readonly mass: Column<number>;
+    readonly residueLabel: Column<string>;
+    readonly residuePointer: Column<number>;
+    readonly bondsIncHydrogen: Column<number>;
+    readonly bondsWithoutHydrogen: Column<number>;
+    readonly radii: Column<number>;
+}
+export declare function parsePrmtop(data: string): Task<Result<PrmtopFile>>;
+export {};