molstar 3.7.0 → 3.8.2

package/lib/commonjs/mol-gl/webgl/state.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,12 +11,15 @@ function createState(gl) {
     var currentFrontFace = gl.getParameter(gl.FRONT_FACE);
     var currentCullFace = gl.getParameter(gl.CULL_FACE_MODE);
     var currentDepthMask = gl.getParameter(gl.DEPTH_WRITEMASK);
+    var currentClearDepth = gl.getParameter(gl.DEPTH_CLEAR_VALUE);
+    var currentDepthFunc = gl.getParameter(gl.DEPTH_FUNC);
     var currentColorMask = gl.getParameter(gl.COLOR_WRITEMASK);
     var currentClearColor = gl.getParameter(gl.COLOR_CLEAR_VALUE);
     var currentBlendSrcRGB = gl.getParameter(gl.BLEND_SRC_RGB);
     var currentBlendDstRGB = gl.getParameter(gl.BLEND_DST_RGB);
     var currentBlendSrcAlpha = gl.getParameter(gl.BLEND_SRC_ALPHA);
     var currentBlendDstAlpha = gl.getParameter(gl.BLEND_DST_ALPHA);
+    var currentBlendColor = gl.getParameter(gl.BLEND_COLOR);
     var currentBlendEqRGB = gl.getParameter(gl.BLEND_EQUATION_RGB);
     var currentBlendEqAlpha = gl.getParameter(gl.BLEND_EQUATION_ALPHA);
     var maxVertexAttribs = gl.getParameter(gl.MAX_VERTEX_ATTRIBS);
@@ -61,6 +64,18 @@ function createState(gl) {
                 currentDepthMask = flag;
             }
         },
+        clearDepth: function (depth) {
+            if (depth !== currentClearDepth) {
+                gl.clearDepth(depth);
+                currentClearDepth = depth;
+            }
+        },
+        depthFunc: function (func) {
+            if (func !== currentDepthFunc) {
+                gl.depthFunc(func);
+                currentDepthFunc = func;
+            }
+        },
         colorMask: function (red, green, blue, alpha) {
             if (red !== currentColorMask[0] || green !== currentColorMask[1] || blue !== currentColorMask[2] || alpha !== currentColorMask[3]) {
                 gl.colorMask(red, green, blue, alpha);
@@ -111,6 +126,15 @@ function createState(gl) {
                 currentBlendEqAlpha = modeAlpha;
             }
         },
+        blendColor: function (red, green, blue, alpha) {
+            if (red !== currentBlendColor[0] || green !== currentBlendColor[1] || blue !== currentBlendColor[2] || alpha !== currentBlendColor[3]) {
+                gl.blendColor(red, green, blue, alpha);
+                currentBlendColor[0] = red;
+                currentBlendColor[1] = green;
+                currentBlendColor[2] = blue;
+                currentBlendColor[3] = alpha;
+            }
+        },
         enableVertexAttrib: function (index) {
             gl.enableVertexAttribArray(index);
             vertexAttribsState[index] = 1;
@@ -127,12 +151,15 @@ function createState(gl) {
             currentFrontFace = gl.getParameter(gl.FRONT_FACE);
             currentCullFace = gl.getParameter(gl.CULL_FACE_MODE);
             currentDepthMask = gl.getParameter(gl.DEPTH_WRITEMASK);
+            currentClearDepth = gl.getParameter(gl.DEPTH_CLEAR_VALUE);
+            currentDepthFunc = gl.getParameter(gl.DEPTH_FUNC);
             currentColorMask = gl.getParameter(gl.COLOR_WRITEMASK);
             currentClearColor = gl.getParameter(gl.COLOR_CLEAR_VALUE);
             currentBlendSrcRGB = gl.getParameter(gl.BLEND_SRC_RGB);
             currentBlendDstRGB = gl.getParameter(gl.BLEND_DST_RGB);
             currentBlendSrcAlpha = gl.getParameter(gl.BLEND_SRC_ALPHA);
             currentBlendDstAlpha = gl.getParameter(gl.BLEND_DST_ALPHA);
+            currentBlendColor = gl.getParameter(gl.BLEND_COLOR);
             currentBlendEqRGB = gl.getParameter(gl.BLEND_EQUATION_RGB);
             currentBlendEqAlpha = gl.getParameter(gl.BLEND_EQUATION_ALPHA);
             maxVertexAttribs = gl.getParameter(gl.MAX_VERTEX_ATTRIBS);

package/lib/commonjs/mol-gl/webgl/texture.js

@@ -184,6 +184,9 @@ function createTexture(gl, extensions, kind, _format, _type, _filter) {
         (kind.endsWith('depth') && _type !== 'ushort' && _type !== 'float')) {
         throw new Error("texture kind '".concat(kind, "' and type '").concat(_type, "' are incompatible"));
     }
+    if (!extensions.depthTexture && _format === 'depth') {
+        throw new Error("extension 'WEBGL_depth_texture' needed for 'depth' texture format");
+    }
     var target = getTarget(gl, kind);
     var filter = getFilter(gl, _filter);
     var format = getFormat(gl, _format, _type);

package/lib/commonjs/mol-gl/webgl/uniform.d.ts

@@ -35,6 +35,7 @@ export declare type UniformValues = {
 };
 export declare type UniformsList = [string, ValueCell<UniformType>][];
 export declare function getUniformType(gl: GLRenderingContext, kind: UniformKind): number | undefined;
+export declare function isArrayUniform(kind: UniformKind): boolean;
 export declare type UniformSetter = (gl: GLRenderingContext, location: number, value: any) => void;
 export declare type UniformSetters = {
     [k: string]: UniformSetter;

package/lib/commonjs/mol-gl/webgl/uniform.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.cloneUniformValues = exports.isUniformValueScalar = exports.getUniformGlslType = exports.getUniformSetters = exports.getUniformType = void 0;
+exports.cloneUniformValues = exports.isUniformValueScalar = exports.getUniformGlslType = exports.getUniformSetters = exports.isArrayUniform = exports.getUniformType = void 0;
 var mol_util_1 = require("../../mol-util");
 var object_1 = require("../../mol-util/object");
 function getUniformType(gl, kind) {
@@ -30,6 +30,10 @@ function getUniformType(gl, kind) {
     }
 }
 exports.getUniformType = getUniformType;
+function isArrayUniform(kind) {
+    return kind.endsWith('[]');
+}
+exports.isArrayUniform = isArrayUniform;
 function uniform1f(gl, location, value) { gl.uniform1f(location, value); }
 function uniform1fv(gl, location, value) { gl.uniform1fv(location, value); }
 function uniform1i(gl, location, value) { gl.uniform1i(location, value); }

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/cif/schema/bird.js

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/cif/schema/ccd.js

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,5 +1,5 @@
 /**
- * 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 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
  *

package/lib/commonjs/mol-io/reader/cif/schema/cif-core.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
  *

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */
@@ -903,8 +903,7 @@ export declare const mmCIF_Schema: {
      */
     entity_poly_seq: {
         /**
-         * This data item is a pointer to _entity_poly.entity_id in the
-         * ENTITY_POLY category.
+         * This data item is a pointer to _entity.id in the ENTITY category.
          */
         entity_id: Schema.Str;
         /**
@@ -4926,7 +4925,7 @@ export declare const mmCIF_Schema: {
         /**
          * The type of data held in the dataset.
          */
-        content_type: Schema.Aliased<"target" | "other" | "template structure" | "polymeric template library" | "spatial restraints" | "target-template alignment" | "coevolution MSA" | "model coordinates">;
+        content_type: Schema.Aliased<"target" | "other" | "reference database" | "template structure" | "polymeric template library" | "spatial restraints" | "target-template alignment" | "coevolution MSA" | "model coordinates" | "input structure">;
         /**
          * Details for other content types.
          */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.358, IHM 1.17, MA 1.4.0.
  *
  * @author molstar/ciftools package
  */
@@ -915,8 +915,7 @@ exports.mmCIF_Schema = {
      */
     entity_poly_seq: {
         /**
-         * This data item is a pointer to _entity_poly.entity_id in the
-         * ENTITY_POLY category.
+         * This data item is a pointer to _entity.id in the ENTITY category.
          */
         entity_id: str,
         /**

package/lib/commonjs/mol-io/reader/dx/parser.js

@@ -119,7 +119,7 @@ function parseBinary(taskCtx, data, name) {
     });
 }
 function parseDx(data, name) {
-    return mol_task_1.Task.create('Parse Cube', function (taskCtx) {
+    return mol_task_1.Task.create('Parse DX', function (taskCtx) {
         if (typeof data === 'string')
             return parseText(taskCtx, data, name);
         return parseBinary(taskCtx, data, name);

package/lib/commonjs/mol-math/geometry/lookup3d/grid.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>

package/lib/commonjs/mol-math/geometry/lookup3d/grid.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 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>
@@ -111,12 +111,12 @@ function build(data, boundary, cellSizeOrCount) {
     // need to expand the grid bounds to avoid rounding errors
     var expandedBox = box3d_1.Box3D.expand((0, box3d_1.Box3D)(), boundary.box, linear_algebra_1.Vec3.create(0.5, 0.5, 0.5));
     var indices = data.indices;
-    var S = box3d_1.Box3D.size(linear_algebra_1.Vec3.zero(), expandedBox);
+    var S = box3d_1.Box3D.size((0, linear_algebra_1.Vec3)(), expandedBox);
     var delta, size;
     var elementCount = int_1.OrderedSet.size(indices);
     var cellCount = typeof cellSizeOrCount === 'number' ? cellSizeOrCount : 32;
     var cellSize = Array.isArray(cellSizeOrCount) && cellSizeOrCount;
-    if (cellSize) {
+    if (cellSize && !linear_algebra_1.Vec3.isZero(cellSize)) {
         size = [Math.ceil(S[0] / cellSize[0]), Math.ceil(S[1] / cellSize[1]), Math.ceil(S[2] / cellSize[2])];
         delta = cellSize;
     }

package/lib/commonjs/mol-model/structure/model/properties/seconday-structure.d.ts

@@ -1,10 +1,12 @@
 /**
- * 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>
  */
 import { SecondaryStructureType } from '../types';
 import { ResidueIndex } from '../indexing';
+import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
 /** Secondary structure "indexed" by residues. */
 interface SecondaryStructure {
     readonly type: ArrayLike<SecondaryStructureType>;
@@ -33,7 +35,7 @@ declare namespace SecondaryStructure {
     interface Helix {
         kind: 'helix';
         flags: SecondaryStructureType;
-        type_id: string;
+        type_id: mmCIF_Schema['struct_conf']['conf_type_id']['T'];
         helix_class: string;
         details?: string;
     }

package/lib/commonjs/mol-model/structure/model/properties/seconday-structure.js

@@ -1,8 +1,9 @@
 "use strict";
 /**
- * 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SecondaryStructure = void 0;

package/lib/commonjs/mol-model/structure/model/types/ions.d.ts

@@ -1,8 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Code-generated ion names params file. Names extracted from CCD components.
  *
- * @author molstar/chem-comp-dict/create-table cli
+ * @author molstar/chem-comp-dict/create-ions cli
  */
 export declare const IonNames: Set<string>;

package/lib/commonjs/mol-model/structure/model/types/ions.js

@@ -1,10 +1,10 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * Code-generated ion names params file. Names extracted from CCD components.
  *
- * @author molstar/chem-comp-dict/create-table cli
+ * @author molstar/chem-comp-dict/create-ions cli
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.IonNames = void 0;

package/lib/commonjs/mol-model/structure/model/types/saccharides.js

@@ -8,4 +8,4 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SaccharideNames = void 0;
-exports.SaccharideNames = new Set(['145', '147', '149', '289', '291', '293', '445', '475', '491', '510', '604', '045', '05L', '07E', '07Y', '08U', '09X', '0AT', '0BD', '0H0', '0HX', '0LP', '0MK', '0NZ', '0TS', '0UB', '0V4', '0WK', '0XY', '0YT', '10M', '12E', '14T', '15L', '16F', '16G', '16O', '17T', '18D', '18O', '18T', '1AR', '1BW', '1CF', '1FT', '1GL', '1GN', '1JB', '1LL', '1NA', '1S3', '1S4', '1SD', '1X4', '20S', '20X', '22O', '22S', '23V', '24S', '25E', '26M', '26O', '26Q', '26R', '26V', '26W', '26Y', '27C', '2DG', '2DR', '2F8', '2FG', '2FL', '2FP', '2GL', '2GS', '2H5', '2HA', '2M4', '2M5', '2M8', '2OS', '2WP', '2WS', '32O', '34V', '38J', '3BU', '3CM', '3DO', '3DY', '3FM', '3GR', '3HD', '3J3', '3J4', '3LJ', '3LR', '3MF', '3MG', '3MK', '3R3', '3S6', '3SA', '3YW', '40J', '42D', '44S', '46D', '46M', '46Z', '48Z', '49A', '49S', '49T', '49V', '4AM', '4CQ', '4GC', '4GL', '4GP', '4JA', '4N2', '4NN', '4QY', '4R1', '4RS', '4SG', '4U0', '4U1', '4U2', '4UZ', '4V5', '50A', '51N', '56N', '57S', '5DI', '5GF', '5GO', '5II', '5KQ', '5KS', '5KT', '5KV', '5L2', '5L3', '5LS', '5LT', '5MM', '5N6', '5QP', '5RP', '5SA', '5SP', '5TH', '5TJ', '5TK', '5TM', '61J', '62I', '64K', '66O', '6BG', '6C2', '6DM', '6GB', '6GP', '6GR', '6K3', '6KH', '6KL', '6KS', '6KU', '6KW', '6LA', '6LS', '6LW', '6MJ', '6MN', '6PG', '6PY', '6PZ', '6S2', '6SA', '6UD', '6Y6', '6YR', '6ZC', '73E', '79J', '7CV', '7D1', '7GP', '7JZ', '7K2', '7K3', '7NU', '7SA', '83Y', '89Y', '8B7', '8B9', '8EX', '8GA', '8GG', '8GP', '8LM', '8LR', '8OQ', '8PK', '8S0', '8YV', '95Z', '96O', '9AM', '9C1', '9CD', '9GP', '9KJ', '9MR', '9OK', '9PG', '9QG', '9QZ', '9S7', '9SG', '9SJ', '9SM', '9SP', '9T1', '9T7', '9VP', '9WJ', '9WN', '9WZ', '9YW', 'A0K', 'A1Q', 'A2G', 'A5C', 'A6P', 'AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'AC1', 'ACG', 'ACR', 'ACX', 'ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH', 'AGL', 'AGR', 'AH2', 'AH8', 'AHG', 'AHM', 'AHR', 'AIG', 'ALL', 'ALX', 'AMG', 'AMN', 'AMU', 'AMV', 'ANA', 'AOG', 'AOS', 'AQA', 'ARA', 'ARB', 'ARE', 'ARI', 'ARW', 'ASC', 'ASG', 'ASO', 'AXP', 'AXR', 'AY9', 'AZC', 'B0D', 'B16', 'B1H', 'B1N', 'B2G', 'B4G', 'B6D', 'B7G', 'B8D', 'B9D', 'BBK', 'BBV', 'BCD', 'BCW', 'BDF', 'BDG', 'BDP', 'BDR', 'BDZ', 'BEM', 'BFN', 'BFP', 'BG6', 'BG8', 'BGC', 'BGL', 'BGN', 'BGP', 'BGS', 'BHG', 'BM3', 'BM7', 'BMA', 'BMX', 'BND', 'BNG', 'BNX', 'BO1', 'BOG', 'BQY', 'BRI', 'BS7', 'BTG', 'BTU', 'BWG', 'BXF', 'BXP', 'BXX', 'BXY', 'BZD', 'C3B', 'C3G', 'C3X', 'C4B', 'C4W', 'C4X', 'C5X', 'CAP', 'CBF', 'CBI', 'CBK', 'CDR', 'CE5', 'CE6', 'CE8', 'CEG', 'CEX', 'CEY', 'CEZ', 'CGF', 'CJB', 'CKB', 'CKP', 'CNP', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D0N', 'D1M', 'D5E', 'D6G', 'DAF', 'DAG', 'DAN', 'DDA', 'DDB', 'DDL', 'DEG', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGO', 'DGS', 'DGU', 'DIG', 'DJB', 'DJE', 'DK4', 'DKX', 'DKZ', 'DL6', 'DLD', 'DLF', 'DLG', 'DMU', 'DNO', 'DO8', 'DOM', 'DP5', 'DPC', 'DQQ', 'DQR', 'DR2', 'DR3', 'DR4', 'DR5', 'DRI', 'DSR', 'DT6', 'DVC', 'DYM', 'E3M', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EEN', 'EEQ', 'EGA', 'EJT', 'EMP', 'EMZ', 'EPG', 'EQP', 'EQV', 'ERE', 'ERI', 'ETT', 'EUS', 'F1P', 'F1X', 'F55', 'F58', 'F6P', 'F8X', 'FBP', 'FCA', 'FCB', 'FCT', 'FDP', 'FDQ', 'FFC', 'FFX', 'FIF', 'FIX', 'FK9', 'FKD', 'FMF', 'FMO', 'FNG', 'FNY', 'FRU', 'FSA', 'FSI', 'FSM', 'FSR', 'FSW', 'FU4', 'FUB', 'FUC', 'FUD', 'FUF', 'FUL', 'FUY', 'FVQ', 'FX1', 'FYJ', 'G0S', 'G16', 'G1P', 'G20', 'G28', 'G2F', 'G3F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S', 'G7P', 'G8Z', 'GAA', 'GAC', 'GAD', 'GAF', 'GAL', 'GAT', 'GBH', 'GC1', 'GC4', 'GC9', 'GCB', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU', 'GCV', 'GCW', 'GDA', 'GDL', 'GE1', 'GE3', 'GFP', 'GIV', 'GL0', 'GL1', 'GL2', 'GL4', 'GL5', 'GL6', 'GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS', 'GLT', 'GLW', 'GM0', 'GMB', 'GMH', 'GMT', 'GMZ', 'GN1', 'GN4', 'GNS', 'GNX', 'GP0', 'GP1', 'GP4', 'GPH', 'GPK', 'GPM', 'GPO', 'GPQ', 'GPU', 'GPV', 'GPW', 'GQ1', 'GRF', 'GRX', 'GS1', 'GS4', 'GS9', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTM', 'GTR', 'GU0', 'GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUL', 'GUP', 'GUZ', 'GXL', 'GXV', 'GYE', 'GYG', 'GYP', 'GYU', 'GYV', 'GZL', 'H1M', 'H1S', 'H2P', 'H3S', 'H53', 'H6Q', 'H6Z', 'HBZ', 'HD4', 'HDL', 'HMS', 'HNV', 'HNW', 'HSG', 'HSH', 'HSJ', 'HSQ', 'HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'HTG', 'HTM', 'I57', 'IAB', 'IDC', 'IDF', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU', 'IDX', 'IDY', 'IEM', 'IN1', 'IPT', 'ISD', 'ISL', 'ISX', 'IXD', 'J5B', 'JFZ', 'JHM', 'JLT', 'JRV', 'JS2', 'JSV', 'JV4', 'JVA', 'JVS', 'JZR', 'K5B', 'K99', 'KBA', 'KBG', 'KD5', 'KDA', 'KDB', 'KDD', 'KDE', 'KDF', 'KDM', 'KDN', 'KDO', 'KDR', 'KFN', 'KG1', 'KGM', 'KHP', 'KME', 'KO1', 'KO2', 'KOT', 'KTU', 'L1L', 'L6S', 'L6T', 'LAG', 'LAH', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2', 'LBS', 'LBT', 'LCN', 'LDY', 'LEC', 'LER', 'LFC', 'LFR', 'LGC', 'LGU', 'LKA', 'LKS', 'LM2', 'LMO', 'LMT', 'LMU', 'LNV', 'LOG', 'LOX', 'LPK', 'LRH', 'LSM', 'LTG', 'LTM', 'LVO', 'LVZ', 'LXB', 'LXC', 'LXZ', 'LZ0', 'M1F', 'M1P', 'M2F', 'M3M', 'M3N', 'M55', 'M6D', 'M6P', 'M7B', 'M7P', 'M8C', 'MA1', 'MA2', 'MA3', 'MA8', 'MAB', 'MAF', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBE', 'MBF', 'MBG', 'MCU', 'MDA', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGC', 'MGL', 'MGS', 'MJJ', 'MLB', 'MLR', 'MMA', 'MMN', 'MN0', 'MNA', 'MQG', 'MQT', 'MRH', 'MRP', 'MSX', 'MTT', 'MUB', 'MUG', 'MUR', 'MVP', 'MXY', 'MXZ', 'MYG', 'N1L', 'N9S', 'NA1', 'NAA', 'NAG', 'NBG', 'NBX', 'NBY', 'NDG', 'NED', 'NFG', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGK', 'NGL', 'NGR', 'NGS', 'NGY', 'NGZ', 'NHF', 'NLC', 'NM6', 'NM9', 'NNG', 'NPF', 'NSQ', 'NT1', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'O1G', 'OAK', 'OEL', 'OI7', 'OPM', 'ORP', 'OSU', 'OTG', 'OTN', 'OTU', 'OX2', 'P53', 'P6P', 'P8E', 'PA1', 'PA5', 'PAV', 'PDX', 'PH5', 'PKM', 'PNA', 'PNG', 'PNJ', 'PNW', 'PPC', 'PRP', 'PSG', 'PSJ', 'PSV', 'PTQ', 'PUF', 'PZU', 'QDK', 'QIF', 'QKH', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R2G', 'R5P', 'RAA', 'RAE', 'RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5', 'RG1', 'RGG', 'RHA', 'RHC', 'RI2', 'RIB', 'RIP', 'RM4', 'RNS', 'RNT', 'ROB', 'ROR', 'RP3', 'RP5', 'RP6', 'RPA', 'RR7', 'RRJ', 'RRY', 'RST', 'RTG', 'RTV', 'RUB', 'RUG', 'RUU', 'RV7', 'RVG', 'RVM', 'RWI', 'RY7', 'RZM', 'S6P', 'S7P', 'S81', 'SA0', 'SCG', 'SCR', 'SDD', 'SDY', 'SEJ', 'SF6', 'SF9', 'SFJ', 'SFU', 'SG4', 'SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHD', 'SHG', 'SI3', 'SIA', 'SID', 'SIO', 'SIZ', 'SLB', 'SLM', 'SLT', 'SMD', 'SN5', 'SNG', 'SOE', 'SOG', 'SOL', 'SOR', 'SR1', 'SSG', 'SSH', 'STW', 'STZ', 'SUC', 'SUP', 'SUS', 'SWE', 'SZZ', 'T68', 'T6D', 'T6P', 'T6T', 'TA6', 'TAG', 'TCB', 'TCG', 'TDG', 'TEU', 'TF0', 'TFU', 'TGA', 'TGK', 'TGR', 'TGY', 'TH1', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TNX', 'TOA', 'TOC', 'TQY', 'TRE', 'TRV', 'TS8', 'TT7', 'TTV', 'TTZ', 'TU4', 'TUG', 'TUJ', 'TUP', 'TUR', 'TVD', 'TVG', 'TVM', 'TVS', 'TVV', 'TVY', 'TW7', 'TWA', 'TWD', 'TWG', 'TWJ', 'TWY', 'TXB', 'TYV', 'U1Y', 'U2A', 'U2D', 'U63', 'U8V', 'U97', 'U9A', 'U9D', 'U9G', 'U9J', 'U9M', 'UAP', 'UCD', 'UDC', 'UEA', 'V3M', 'V3P', 'V71', 'VG1', 'VJ1', 'VJ4', 'VKN', 'VTB', 'W9T', 'WIA', 'WOO', 'WUN', 'WZ1', 'WZ2', 'WZ4', 'X0X', 'X1P', 'X1X', 'X2F', 'X2Y', 'X34', 'X4S', 'X5S', 'X6X', 'X6Y', 'XBP', 'XDP', 'XDX', 'XGP', 'XIL', 'XKJ', 'XLF', 'XLS', 'XMM', 'XS2', 'XUL', 'XXM', 'XXR', 'XXX', 'XYB', 'XYF', 'XYL', 'XYP', 'XYS', 'XYT', 'XYZ', 'YDR', 'YIO', 'YJM', 'YKR', 'YO5', 'YX0', 'YX1', 'YYB', 'YYH', 'YYJ', 'YYK', 'YYM', 'YYQ', 'YYR', 'YZ0', 'Z0F', 'Z15', 'Z16', 'Z2D', 'Z2T', 'Z3K', 'Z3L', 'Z3Q', 'Z3U', 'Z4K', 'Z4R', 'Z4S', 'Z4U', 'Z4V', 'Z4W', 'Z4Y', 'Z57', 'Z5J', 'Z5L', 'Z61', 'Z6H', 'Z6J', 'Z6W', 'Z8H', 'Z8T', 'Z9D', 'Z9E', 'Z9H', 'Z9K', 'Z9L', 'Z9M', 'Z9N', 'Z9W', 'ZB0', 'ZB1', 'ZB2', 'ZB3', 'ZCD', 'ZCZ', 'ZD0', 'ZDC', 'ZDM', 'ZDO', 'ZEE', 'ZEL', 'ZGE', 'ZMR', 'UMQ', 'SQD']);
+exports.SaccharideNames = new Set(['145', '147', '149', '289', '291', '293', '445', '475', '491', '510', '604', '045', '05L', '07E', '07Y', '08U', '09X', '0AT', '0BD', '0H0', '0HX', '0LP', '0MK', '0NZ', '0TS', '0UB', '0V4', '0WK', '0XY', '0YT', '10M', '12E', '14T', '15L', '16F', '16G', '16O', '17T', '18D', '18O', '18T', '1AR', '1BW', '1CF', '1FT', '1GL', '1GN', '1JB', '1LL', '1NA', '1S3', '1S4', '1SD', '1X4', '20S', '20X', '22O', '22S', '23V', '24S', '25E', '26M', '26O', '26Q', '26R', '26V', '26W', '26Y', '27C', '2DG', '2DR', '2F8', '2FG', '2FL', '2FP', '2GL', '2GS', '2H5', '2HA', '2M4', '2M5', '2M8', '2OS', '2WP', '2WS', '32O', '34V', '38J', '3BU', '3CM', '3DO', '3DY', '3FM', '3GR', '3HD', '3J3', '3J4', '3LJ', '3LR', '3MF', '3MG', '3MK', '3R3', '3S6', '3SA', '3YW', '40J', '42D', '44S', '46D', '46M', '46Z', '48Z', '49A', '49S', '49T', '49V', '4AM', '4CQ', '4GC', '4GL', '4GP', '4JA', '4N2', '4NN', '4QY', '4R1', '4RS', '4SG', '4U0', '4U1', '4U2', '4UZ', '4V5', '50A', '51N', '56N', '57S', '5DI', '5GF', '5GO', '5II', '5KQ', '5KS', '5KT', '5KV', '5L2', '5L3', '5LS', '5LT', '5MM', '5N6', '5QP', '5RP', '5SA', '5SP', '5TH', '5TJ', '5TK', '5TM', '61J', '62I', '64K', '66O', '6BG', '6C2', '6DM', '6GB', '6GP', '6GR', '6K3', '6KH', '6KL', '6KS', '6KU', '6KW', '6LA', '6LS', '6LW', '6MJ', '6MN', '6PG', '6PY', '6PZ', '6S2', '6SA', '6UD', '6Y6', '6YR', '6ZC', '73E', '79J', '7CV', '7D1', '7GP', '7JZ', '7K2', '7K3', '7NU', '7SA', '83Y', '89Y', '8B7', '8B9', '8EX', '8GA', '8GG', '8GP', '8LM', '8LR', '8OQ', '8PK', '8S0', '8YV', '95Z', '96O', '9AM', '9C1', '9CD', '9GP', '9KJ', '9MR', '9OK', '9PG', '9QG', '9QZ', '9S7', '9SG', '9SJ', '9SM', '9SP', '9T1', '9T7', '9VP', '9WJ', '9WN', '9WZ', '9YW', 'A0K', 'A1Q', 'A2G', 'A5C', 'A6P', 'AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'AC1', 'ACG', 'ACR', 'ACX', 'ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH', 'AGL', 'AGR', 'AH2', 'AH8', 'AHG', 'AHM', 'AHR', 'AIG', 'ALL', 'ALX', 'AMG', 'AMN', 'AMU', 'AMV', 'ANA', 'AOG', 'AOS', 'AQA', 'ARA', 'ARB', 'ARE', 'ARI', 'ARW', 'ASC', 'ASG', 'ASO', 'AXP', 'AXR', 'AY9', 'AZC', 'B0D', 'B16', 'B1H', 'B1N', 'B2G', 'B4G', 'B6D', 'B7G', 'B8D', 'B9D', 'BBK', 'BBV', 'BCD', 'BCW', 'BDF', 'BDG', 'BDP', 'BDR', 'BDZ', 'BEM', 'BFN', 'BFP', 'BG6', 'BG8', 'BGC', 'BGL', 'BGN', 'BGP', 'BGS', 'BHG', 'BM3', 'BM7', 'BMA', 'BMX', 'BND', 'BNG', 'BNX', 'BO1', 'BOG', 'BQY', 'BRI', 'BS7', 'BTG', 'BTU', 'BW3', 'BWG', 'BXF', 'BXP', 'BXX', 'BXY', 'BZD', 'C3B', 'C3G', 'C3X', 'C4B', 'C4W', 'C4X', 'C5X', 'CAP', 'CBF', 'CBI', 'CBK', 'CDR', 'CE5', 'CE6', 'CE8', 'CEG', 'CEX', 'CEY', 'CEZ', 'CGF', 'CJB', 'CKB', 'CKP', 'CNP', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D0N', 'D1M', 'D5E', 'D6G', 'DAF', 'DAG', 'DAN', 'DDA', 'DDB', 'DDL', 'DEG', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGO', 'DGS', 'DGU', 'DIG', 'DJB', 'DJE', 'DK4', 'DKX', 'DKZ', 'DL6', 'DLD', 'DLF', 'DLG', 'DMU', 'DNO', 'DO8', 'DOM', 'DP5', 'DPC', 'DQQ', 'DQR', 'DR2', 'DR3', 'DR4', 'DR5', 'DRI', 'DSR', 'DT6', 'DVC', 'DYM', 'E3M', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EEN', 'EEQ', 'EGA', 'EJT', 'EMP', 'EMZ', 'EPG', 'EQP', 'EQV', 'ERE', 'ERI', 'ETT', 'EUS', 'F1P', 'F1X', 'F55', 'F58', 'F6P', 'F8X', 'FBP', 'FCA', 'FCB', 'FCT', 'FDP', 'FDQ', 'FFC', 'FFX', 'FIF', 'FIX', 'FK9', 'FKD', 'FMF', 'FMO', 'FNG', 'FNY', 'FRU', 'FSA', 'FSI', 'FSM', 'FSR', 'FSW', 'FU4', 'FUB', 'FUC', 'FUD', 'FUF', 'FUL', 'FUY', 'FVQ', 'FX1', 'FYJ', 'G0S', 'G16', 'G1P', 'G20', 'G28', 'G2F', 'G3F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S', 'G7P', 'G8Z', 'GAA', 'GAC', 'GAD', 'GAF', 'GAL', 'GAT', 'GBH', 'GC1', 'GC4', 'GC9', 'GCB', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU', 'GCV', 'GCW', 'GDA', 'GDL', 'GE1', 'GE3', 'GFP', 'GIV', 'GL0', 'GL1', 'GL2', 'GL4', 'GL5', 'GL6', 'GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS', 'GLT', 'GLW', 'GM0', 'GMB', 'GMH', 'GMT', 'GMZ', 'GN1', 'GN4', 'GNS', 'GNX', 'GP0', 'GP1', 'GP4', 'GPH', 'GPK', 'GPM', 'GPO', 'GPQ', 'GPU', 'GPV', 'GPW', 'GQ1', 'GRF', 'GRX', 'GS1', 'GS4', 'GS9', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTM', 'GTR', 'GU0', 'GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUL', 'GUP', 'GUZ', 'GXL', 'GXV', 'GYE', 'GYG', 'GYP', 'GYU', 'GYV', 'GZL', 'H1M', 'H1S', 'H2P', 'H3S', 'H53', 'H6Q', 'H6Z', 'HBZ', 'HD4', 'HDL', 'HMS', 'HNV', 'HNW', 'HSG', 'HSH', 'HSJ', 'HSQ', 'HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'HTG', 'HTM', 'I57', 'IAB', 'IDC', 'IDF', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU', 'IDX', 'IDY', 'IEM', 'IN1', 'IPT', 'ISD', 'ISL', 'ISX', 'IXD', 'J5B', 'JFZ', 'JHM', 'JLT', 'JRV', 'JS2', 'JSV', 'JV4', 'JVA', 'JVS', 'JZR', 'K5B', 'K99', 'KBA', 'KBG', 'KD5', 'KDA', 'KDB', 'KDD', 'KDE', 'KDF', 'KDM', 'KDN', 'KDO', 'KDR', 'KFN', 'KG1', 'KGM', 'KHP', 'KME', 'KO1', 'KO2', 'KOT', 'KTU', 'L1L', 'L6S', 'L6T', 'LAG', 'LAH', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2', 'LBS', 'LBT', 'LCN', 'LDY', 'LEC', 'LER', 'LFC', 'LFR', 'LGC', 'LGU', 'LKA', 'LKS', 'LM2', 'LMO', 'LMT', 'LMU', 'LNV', 'LOG', 'LOX', 'LPK', 'LRH', 'LSM', 'LTG', 'LTM', 'LVO', 'LVZ', 'LXB', 'LXC', 'LXZ', 'LZ0', 'M1F', 'M1P', 'M2F', 'M3M', 'M3N', 'M55', 'M6D', 'M6P', 'M7B', 'M7P', 'M8C', 'MA1', 'MA2', 'MA3', 'MA8', 'MAB', 'MAF', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBE', 'MBF', 'MBG', 'MCU', 'MDA', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGC', 'MGL', 'MGS', 'MJJ', 'MLB', 'MLR', 'MMA', 'MMN', 'MN0', 'MNA', 'MQG', 'MQT', 'MRH', 'MRP', 'MSX', 'MTT', 'MUB', 'MUG', 'MUR', 'MVP', 'MXY', 'MXZ', 'MYG', 'N1L', 'N9S', 'NA1', 'NAA', 'NAG', 'NBG', 'NBX', 'NBY', 'NDG', 'NED', 'NFG', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGK', 'NGL', 'NGR', 'NGS', 'NGY', 'NGZ', 'NHF', 'NLC', 'NM6', 'NM9', 'NNG', 'NPF', 'NSQ', 'NT1', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'O1G', 'OAK', 'OEL', 'OI7', 'OPM', 'ORP', 'OSU', 'OTG', 'OTN', 'OTU', 'OX2', 'P53', 'P6P', 'P8E', 'PA1', 'PA5', 'PAV', 'PDX', 'PH5', 'PKM', 'PNA', 'PNG', 'PNJ', 'PNW', 'PPC', 'PRP', 'PSG', 'PSJ', 'PSV', 'PTQ', 'PUF', 'PZU', 'QDK', 'QIF', 'QKH', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R2G', 'R5P', 'RAA', 'RAE', 'RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5', 'RG1', 'RGG', 'RHA', 'RHC', 'RI2', 'RIB', 'RIP', 'RM4', 'RNS', 'RNT', 'ROB', 'ROR', 'RP3', 'RP5', 'RP6', 'RPA', 'RR7', 'RRJ', 'RRY', 'RST', 'RTG', 'RTV', 'RUB', 'RUG', 'RUU', 'RV7', 'RVG', 'RVM', 'RWI', 'RY7', 'RZM', 'S6P', 'S7P', 'S81', 'SA0', 'SCG', 'SCR', 'SDD', 'SDY', 'SEJ', 'SF6', 'SF9', 'SFJ', 'SFU', 'SG4', 'SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHD', 'SHG', 'SI3', 'SIA', 'SID', 'SIO', 'SIZ', 'SLB', 'SLM', 'SLT', 'SMD', 'SN5', 'SNG', 'SOE', 'SOG', 'SOL', 'SOR', 'SR1', 'SSG', 'SSH', 'STW', 'STZ', 'SUC', 'SUP', 'SUS', 'SWE', 'SZZ', 'T68', 'T6D', 'T6P', 'T6T', 'TA6', 'TAG', 'TCB', 'TCG', 'TDG', 'TEU', 'TF0', 'TFU', 'TGA', 'TGK', 'TGR', 'TGY', 'TH1', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TNX', 'TOA', 'TOC', 'TQY', 'TRE', 'TRV', 'TS8', 'TT7', 'TTV', 'TTZ', 'TU4', 'TUG', 'TUJ', 'TUP', 'TUR', 'TVD', 'TVG', 'TVM', 'TVS', 'TVV', 'TVY', 'TW7', 'TWA', 'TWD', 'TWG', 'TWJ', 'TWY', 'TXB', 'TYV', 'U1Y', 'U2A', 'U2D', 'U63', 'U8V', 'U97', 'U9A', 'U9D', 'U9G', 'U9J', 'U9M', 'UAP', 'UCD', 'UDC', 'UEA', 'V3M', 'V3P', 'V71', 'VG1', 'VJ1', 'VJ4', 'VKN', 'VTB', 'W9T', 'WIA', 'WOO', 'WUN', 'WZ1', 'WZ2', 'WZ4', 'X0X', 'X1P', 'X1X', 'X2F', 'X2Y', 'X34', 'X4S', 'X5S', 'X6X', 'X6Y', 'XBP', 'XDP', 'XDX', 'XGP', 'XIL', 'XKJ', 'XLF', 'XLS', 'XMM', 'XS2', 'XUL', 'XXM', 'XXR', 'XXX', 'XYB', 'XYF', 'XYL', 'XYP', 'XYS', 'XYT', 'XYZ', 'YDR', 'YIO', 'YJM', 'YKR', 'YO5', 'YX0', 'YX1', 'YYB', 'YYH', 'YYJ', 'YYK', 'YYM', 'YYQ', 'YYR', 'YZ0', 'YZT', 'Z0F', 'Z15', 'Z16', 'Z2D', 'Z2T', 'Z3K', 'Z3L', 'Z3Q', 'Z3U', 'Z4K', 'Z4R', 'Z4S', 'Z4U', 'Z4V', 'Z4W', 'Z4Y', 'Z57', 'Z5J', 'Z5L', 'Z61', 'Z6H', 'Z6J', 'Z6W', 'Z8H', 'Z8T', 'Z9D', 'Z9E', 'Z9H', 'Z9K', 'Z9L', 'Z9M', 'Z9N', 'Z9W', 'ZB0', 'ZB1', 'ZB2', 'ZB3', 'ZCD', 'ZCZ', 'ZD0', 'ZDC', 'ZDM', 'ZDO', 'ZEE', 'ZEL', 'ZGE', 'ZMR', 'UMQ', 'SQD']);

package/lib/commonjs/mol-model/structure/model/types.d.ts

@@ -151,7 +151,7 @@ export declare namespace SecondaryStructureType {
         NA = 536870912
     }
     const SecondaryStructureMmcif: {
-        [value: string]: number;
+        [value in mmCIF_Schema['struct_conf']['conf_type_id']['T']]: number;
     };
     const SecondaryStructurePdb: {
         [value: string]: number;

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

@@ -431,47 +431,49 @@ var SecondaryStructureType;
     SecondaryStructureType.is = bit_flags_1.BitFlags.has;
     SecondaryStructureType.create = bit_flags_1.BitFlags.create;
     SecondaryStructureType.SecondaryStructureMmcif = {
-        HELX_LH_27_P: 2 /* Helix */ | 32 /* LeftHanded */ | 1024 /* Helix27 */,
-        HELX_LH_3T_P: 2 /* Helix */ | 32 /* LeftHanded */ | 2048 /* Helix3Ten */,
-        HELX_LH_AL_P: 2 /* Helix */ | 32 /* LeftHanded */ | 4096 /* HelixAlpha */,
-        HELX_LH_A_N: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 524288 /* DoubleHelixA */,
-        HELX_LH_B_N: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 1048576 /* DoubleHelixB */,
-        HELX_LH_GA_P: 2 /* Helix */ | 32 /* LeftHanded */ | 8192 /* HelixGamma */,
-        HELX_LH_N: 1 /* DoubleHelix */ | 32 /* LeftHanded */,
-        HELX_LH_OM_P: 2 /* Helix */ | 32 /* LeftHanded */ | 16384 /* HelixOmega */,
-        HELX_LH_OT_N: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 131072 /* DoubleHelixOther */,
-        HELX_LH_OT_P: 2 /* Helix */ | 32 /* LeftHanded */ | 512 /* HelixOther */,
-        HELX_LH_P: 2 /* Helix */ | 32 /* LeftHanded */,
-        HELX_LH_PI_P: 2 /* Helix */ | 32 /* LeftHanded */ | 32768 /* HelixPi */,
-        HELX_LH_PP_P: 2 /* Helix */ | 32 /* LeftHanded */ | 65536 /* HelixPolyproline */,
-        HELX_LH_Z_N: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 262144 /* DoubleHelixZ */,
-        HELX_N: 1 /* DoubleHelix */,
-        HELX_OT_N: 1 /* DoubleHelix */,
-        HELX_OT_P: 2 /* Helix */,
-        HELX_P: 2 /* Helix */,
-        HELX_RH_27_P: 2 /* Helix */ | 64 /* RightHanded */ | 1024 /* Helix27 */,
-        HELX_RH_3T_P: 2 /* Helix */ | 64 /* RightHanded */ | 2048 /* Helix3Ten */,
-        HELX_RH_AL_P: 2 /* Helix */ | 64 /* RightHanded */ | 4096 /* HelixAlpha */,
-        HELX_RH_A_N: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 524288 /* DoubleHelixA */,
-        HELX_RH_B_N: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 1048576 /* DoubleHelixB */,
-        HELX_RH_GA_P: 2 /* Helix */ | 64 /* RightHanded */ | 8192 /* HelixGamma */,
-        HELX_RH_N: 1 /* DoubleHelix */ | 64 /* RightHanded */,
-        HELX_RH_OM_P: 2 /* Helix */ | 64 /* RightHanded */ | 16384 /* HelixOmega */,
-        HELX_RH_OT_N: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 131072 /* DoubleHelixOther */,
-        HELX_RH_OT_P: 2 /* Helix */ | 64 /* RightHanded */ | 512 /* HelixOther */,
-        HELX_RH_P: 2 /* Helix */ | 64 /* RightHanded */,
-        HELX_RH_PI_P: 2 /* Helix */ | 64 /* RightHanded */ | 32768 /* HelixPi */,
-        HELX_RH_PP_P: 2 /* Helix */ | 64 /* RightHanded */ | 65536 /* HelixPolyproline */,
-        HELX_RH_Z_N: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 262144 /* DoubleHelixZ */,
-        STRN: 4 /* Beta */ | 4194304 /* BetaStrand */,
-        TURN_OT_P: 16 /* Turn */ | 33554432 /* TurnOther */,
-        TURN_P: 16 /* Turn */,
-        TURN_TY1P_P: 16 /* Turn */ | 256 /* InverseTurn */ | 67108864 /* Turn1 */,
-        TURN_TY1_P: 16 /* Turn */ | 128 /* ClassicTurn */ | 67108864 /* Turn1 */,
-        TURN_TY2P_P: 16 /* Turn */ | 256 /* InverseTurn */ | 134217728 /* Turn2 */,
-        TURN_TY2_P: 16 /* Turn */ | 128 /* ClassicTurn */ | 134217728 /* Turn2 */,
-        TURN_TY3P_P: 16 /* Turn */ | 256 /* InverseTurn */ | 268435456 /* Turn3 */,
-        TURN_TY3_P: 16 /* Turn */ | 128 /* ClassicTurn */ | 268435456 /* Turn3 */, // type III turn (protein)
+        helx_lh_27_p: 2 /* Helix */ | 32 /* LeftHanded */ | 1024 /* Helix27 */,
+        helx_lh_3t_p: 2 /* Helix */ | 32 /* LeftHanded */ | 2048 /* Helix3Ten */,
+        helx_lh_al_p: 2 /* Helix */ | 32 /* LeftHanded */ | 4096 /* HelixAlpha */,
+        helx_lh_a_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 524288 /* DoubleHelixA */,
+        helx_lh_b_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 1048576 /* DoubleHelixB */,
+        helx_lh_ga_p: 2 /* Helix */ | 32 /* LeftHanded */ | 8192 /* HelixGamma */,
+        helx_lh_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */,
+        helx_lh_om_p: 2 /* Helix */ | 32 /* LeftHanded */ | 16384 /* HelixOmega */,
+        helx_lh_ot_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 131072 /* DoubleHelixOther */,
+        helx_lh_ot_p: 2 /* Helix */ | 32 /* LeftHanded */ | 512 /* HelixOther */,
+        helx_lh_p: 2 /* Helix */ | 32 /* LeftHanded */,
+        helx_lh_pi_p: 2 /* Helix */ | 32 /* LeftHanded */ | 32768 /* HelixPi */,
+        helx_lh_pp_p: 2 /* Helix */ | 32 /* LeftHanded */ | 65536 /* HelixPolyproline */,
+        helx_lh_z_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 262144 /* DoubleHelixZ */,
+        helx_n: 1 /* DoubleHelix */,
+        helx_ot_n: 1 /* DoubleHelix */,
+        helx_ot_p: 2 /* Helix */,
+        helx_p: 2 /* Helix */,
+        helx_rh_27_p: 2 /* Helix */ | 64 /* RightHanded */ | 1024 /* Helix27 */,
+        helx_rh_3t_p: 2 /* Helix */ | 64 /* RightHanded */ | 2048 /* Helix3Ten */,
+        helx_rh_al_p: 2 /* Helix */ | 64 /* RightHanded */ | 4096 /* HelixAlpha */,
+        helx_rh_a_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 524288 /* DoubleHelixA */,
+        helx_rh_b_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 1048576 /* DoubleHelixB */,
+        helx_rh_ga_p: 2 /* Helix */ | 64 /* RightHanded */ | 8192 /* HelixGamma */,
+        helx_rh_n: 1 /* DoubleHelix */ | 64 /* RightHanded */,
+        helx_rh_om_p: 2 /* Helix */ | 64 /* RightHanded */ | 16384 /* HelixOmega */,
+        helx_rh_ot_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 131072 /* DoubleHelixOther */,
+        helx_rh_ot_p: 2 /* Helix */ | 64 /* RightHanded */ | 512 /* HelixOther */,
+        helx_rh_p: 2 /* Helix */ | 64 /* RightHanded */,
+        helx_rh_pi_p: 2 /* Helix */ | 64 /* RightHanded */ | 32768 /* HelixPi */,
+        helx_rh_pp_p: 2 /* Helix */ | 64 /* RightHanded */ | 65536 /* HelixPolyproline */,
+        helx_rh_z_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 262144 /* DoubleHelixZ */,
+        strn: 4 /* Beta */ | 4194304 /* BetaStrand */,
+        turn_ot_p: 16 /* Turn */ | 33554432 /* TurnOther */,
+        turn_p: 16 /* Turn */,
+        turn_ty1p_p: 16 /* Turn */ | 256 /* InverseTurn */ | 67108864 /* Turn1 */,
+        turn_ty1_p: 16 /* Turn */ | 128 /* ClassicTurn */ | 67108864 /* Turn1 */,
+        turn_ty2p_p: 16 /* Turn */ | 256 /* InverseTurn */ | 134217728 /* Turn2 */,
+        turn_ty2_p: 16 /* Turn */ | 128 /* ClassicTurn */ | 134217728 /* Turn2 */,
+        turn_ty3p_p: 16 /* Turn */ | 256 /* InverseTurn */ | 268435456 /* Turn3 */,
+        turn_ty3_p: 16 /* Turn */ | 128 /* ClassicTurn */ | 268435456 /* Turn3 */,
+        bend: 8 /* Bend */,
+        other: 0 /* None */, // secondary structure type that does not conform to an accepted category, random coil (protein)
     };
     SecondaryStructureType.SecondaryStructurePdb = {
         1: 2 /* Helix */ | 64 /* RightHanded */ | 4096 /* HelixAlpha */,

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

@@ -25,6 +25,8 @@ var FormatRegistry = /** @class */ (function () {
         return this.map.get(kind);
     };
     FormatRegistry.prototype.isApplicable = function (model) {
+        if (!this.map.has(model.sourceData.kind))
+            return false;
         var isApplicable = this.applicable.get(model.sourceData.kind);
         return isApplicable ? isApplicable(model) : true;
     };

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 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>
@@ -66,7 +66,7 @@ function addHelices(cat, coordinates, map, elements) {
         var element = {
             kind: 'helix',
             flags: type,
-            type_id: conf_type_id.valueKind(i) === 0 /* Present */ ? conf_type_id.value(i) : 'HELIX_P',
+            type_id: conf_type_id.valueKind(i) === 0 /* Present */ ? conf_type_id.value(i) : 'helx_p',
             helix_class: pdbx_PDB_helix_class.value(i),
             details: details.valueKind(i) === 0 /* Present */ ? details.value(i) : void 0
         };

package/lib/commonjs/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        /** Precision data the server can show. */
-        label: string;
+        label: string; /** Precision data the server can show. */
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
+        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,6 +23,7 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
+        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;

package/lib/commonjs/mol-plugin-state/helpers/root-structure.js

@@ -16,6 +16,7 @@ var linear_algebra_1 = require("../../mol-math/linear-algebra");
 var symmetry_1 = require("../../mol-model/structure/model/properties/symmetry");
 var objects_1 = require("../objects");
 var symmetry_2 = require("../../mol-model-formats/structure/property/symmetry");
+var type_helpers_1 = require("../../mol-util/type-helpers");
 var CommonStructureParams = {
     dynamicBonds: param_definition_1.ParamDefinition.Optional(param_definition_1.ParamDefinition.Boolean(false, { description: 'Ensure bonds are recalculated upon model changes. Also enables calculation of inter-unit bonds in water molecules and ions.' })),
 };
@@ -198,7 +199,8 @@ var RootStructureDefinition;
                 if (params.name === 'symmetry-assembly') {
                     return [2 /*return*/, buildSymmetryAssembly(ctx, model, params.params.generators, symmetry, props)];
                 }
-                throw new Error("Unknown represetation type: ".concat(params.name));
+                (0, type_helpers_1.assertUnreachable)(params);
+                return [2 /*return*/];
             });
         });
     }

package/lib/commonjs/mol-repr/volume/slice.js

@@ -28,7 +28,7 @@ function createImage(ctx, volume, theme, props, image) {
             _a = volume.grid.cells, space = _a.space, data = _a.data;
             _b = volume.grid.stats, min = _b.min, max = _b.max;
             isoVal = volume_1.Volume.IsoValue.toAbsolute(isoValue, volume.grid.stats).absoluteValue;
-            color = theme.color.color(location_1.NullLocation, false);
+            color = 'color' in theme.color ? theme.color.color(location_1.NullLocation, false) : (0, color_1.Color)(0xffffff);
             _c = color_1.Color.toRgbNormalized(color), r = _c[0], g = _c[1], b = _c[2];
             _d = getSliceInfo(volume.grid, props), width = _d.width, height = _d.height, x = _d.x, y = _d.y, z = _d.z, x0 = _d.x0, y0 = _d.y0, z0 = _d.z0, nx = _d.nx, ny = _d.ny, nz = _d.nz;
             corners = new Float32Array(dim === 'x' ? [x, 0, 0, x, y, 0, x, 0, z, x, y, z] :