molstar 3.3.1 → 3.6.0

package/lib/mol-io/writer/mol/encoder.js

@@ -48,7 +48,7 @@ var MolEncoder = /** @class */ (function (_super) {
             StringBuilder.writeSafe(ctab, '  0');
             StringBuilder.writeIntegerPadLeft(ctab, _this.mapCharge(charge), 3);
             StringBuilder.writeSafe(ctab, '  0  0  0  0  0  0  0  0  0  0\n');
-            if (stereo_config !== 'N')
+            if (stereo_config !== 'n')
                 chiral = true;
             // no data for metal ions
             if (!(bondMap === null || bondMap === void 0 ? void 0 : bondMap.map))

package/lib/mol-math/geometry/common.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 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>
@@ -24,6 +24,7 @@ export declare type DensityData = {
     field: Tensor;
     idField: Tensor;
     resolution: number;
+    maxRadius: number;
 };
 export declare type DensityTextureData = {
     transform: Mat4;

package/lib/mol-math/geometry/common.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 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/mol-math/geometry/gaussian-density/cpu.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-math/geometry/gaussian-density/cpu.js

@@ -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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -127,7 +127,7 @@ export function GaussianDensityCPU(ctx, position, box, radius, props) {
                     transform = Mat4.identity();
                     Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
                     Mat4.setTranslation(transform, expandedBox.min);
-                    return [2 /*return*/, { field: field, idField: idField, transform: transform, radiusFactor: 1, resolution: resolution }];
+                    return [2 /*return*/, { field: field, idField: idField, transform: transform, radiusFactor: 1, resolution: resolution, maxRadius: maxRadius }];
             }
         });
     });

package/lib/mol-math/geometry/gaussian-density/gpu.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>

package/lib/mol-math/geometry/gaussian-density/gpu.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
@@ -56,11 +56,11 @@ export function GaussianDensityGPU(position, box, radius, props, webgl) {
     // it's faster than texture3d
     // console.time('GaussianDensityTexture2d')
     var tmpTexture = getTexture('tmp', webgl, 'image-uint8', 'rgba', 'ubyte', 'linear');
-    var _a = calcGaussianDensityTexture2d(webgl, position, box, radius, false, props, tmpTexture), scale = _a.scale, bbox = _a.bbox, texture = _a.texture, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
+    var _a = calcGaussianDensityTexture2d(webgl, position, box, radius, false, props, tmpTexture), scale = _a.scale, bbox = _a.bbox, texture = _a.texture, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
     // webgl.waitForGpuCommandsCompleteSync()
     // console.timeEnd('GaussianDensityTexture2d')
     var _b = fieldFromTexture2d(webgl, texture, gridDim, gridTexDim), field = _b.field, idField = _b.idField;
-    return { field: field, idField: idField, transform: getTransform(scale, bbox), radiusFactor: radiusFactor, resolution: resolution };
+    return { field: field, idField: idField, transform: getTransform(scale, bbox), radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 export function GaussianDensityTexture(webgl, position, box, radius, props, oldTexture) {
     return webgl.isWebGL2 ?
@@ -74,8 +74,8 @@ export function GaussianDensityTexture3d(webgl, position, box, radius, props, ol
     return finalizeGaussianDensityTexture(calcGaussianDensityTexture3d(webgl, position, box, radius, props, oldTexture));
 }
 function finalizeGaussianDensityTexture(_a) {
-    var texture = _a.texture, scale = _a.scale, bbox = _a.bbox, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, gridTexScale = _a.gridTexScale, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
-    return { transform: getTransform(scale, bbox), texture: texture, bbox: bbox, gridDim: gridDim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution };
+    var texture = _a.texture, scale = _a.scale, bbox = _a.bbox, gridDim = _a.gridDim, gridTexDim = _a.gridTexDim, gridTexScale = _a.gridTexScale, radiusFactor = _a.radiusFactor, resolution = _a.resolution, maxRadius = _a.maxRadius;
+    return { transform: getTransform(scale, bbox), texture: texture, bbox: bbox, gridDim: gridDim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 function getTransform(scale, bbox) {
     var transform = Mat4.identity();
@@ -151,7 +151,7 @@ function calcGaussianDensityTexture2d(webgl, position, box, radius, powerOfTwo,
         render(texture, false);
     }
     // printTexture(webgl, minDistTex, 0.75);
-    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution };
+    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: gridTexDim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 function calcGaussianDensityTexture3d(webgl, position, box, radius, props, texture) {
     // console.log('3d');
@@ -195,7 +195,7 @@ function calcGaussianDensityTexture3d(webgl, position, box, radius, props, textu
     render(minDistTex, true);
     setupGroupIdRendering(webgl, renderable);
     render(texture, false);
-    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: dim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution };
+    return { texture: texture, scale: scale, bbox: expandedBox, gridDim: dim, gridTexDim: dim, gridTexScale: gridTexScale, radiusFactor: radiusFactor, resolution: resolution, maxRadius: maxRadius };
 }
 //
 function prepareGaussianDensityData(position, box, radius, props) {

package/lib/mol-math/geometry/gaussian-density.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -16,11 +16,11 @@ export declare const DefaultGaussianDensityProps: {
 export declare type GaussianDensityProps = typeof DefaultGaussianDensityProps;
 export declare type GaussianDensityData = {
     radiusFactor: number;
-    resolution: number;
 } & DensityData;
 export declare type GaussianDensityTextureData = {
     radiusFactor: number;
     resolution: number;
+    maxRadius: number;
 } & DensityTextureData;
 export declare function computeGaussianDensity(position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps): Task<GaussianDensityData>;
 export declare function computeGaussianDensityTexture(position: PositionData, box: Box3D, radius: (index: number) => number, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<GaussianDensityTextureData>;

package/lib/mol-math/geometry/gaussian-density.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-math/geometry/molecular-surface.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 Fred Ludlow <fred.ludlow@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -29,4 +29,5 @@ export declare function calcMolecularSurface(ctx: RuntimeContext, position: Requ
     idField: Tensor;
     transform: Mat4;
     resolution: number;
+    maxRadius: number;
 }>;

package/lib/mol-math/geometry/molecular-surface.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 Fred Ludlow <fred.ludlow@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -345,7 +345,7 @@ export function calcMolecularSurface(ctx, position, boundary, maxRadius, box, pr
                     Mat4.fromScaling(transform, Vec3.create(resolution, resolution, resolution));
                     Mat4.setTranslation(transform, expandedBox.min);
                     // console.log({ field, idField, transform, updateChunk })
-                    return [2 /*return*/, { field: field, idField: idField, transform: transform, resolution: resolution }];
+                    return [2 /*return*/, { field: field, idField: idField, transform: transform, resolution: resolution, maxRadius: maxRadius }];
             }
         });
     });

package/lib/mol-math/geometry/primitives/box3d.js

@@ -27,8 +27,9 @@ function Box3D() {
     Box3D.clone = clone;
     /** Get box from sphere, uses extrema if available */
     function fromSphere3D(out, sphere) {
-        if (Sphere3D.hasExtrema(sphere))
+        if (Sphere3D.hasExtrema(sphere) && sphere.extrema.length >= 14) { // 14 extrema with coarse boundary helper
             return fromVec3Array(out, sphere.extrema);
+        }
         var r = Vec3.create(sphere.radius, sphere.radius, sphere.radius);
         Vec3.sub(out.min, sphere.center, r);
         Vec3.add(out.max, sphere.center, r);

package/lib/mol-math/geometry/primitives/sphere3d.js

@@ -202,15 +202,21 @@ function Sphere3D() {
             var axes_1 = PrincipalAxes.calculateMomentsAxes(positions);
             Axes3D.scale(axes_1, Axes3D.normalize(axes_1, axes_1), delta);
             setExtrema(out, sphere.extrema.map(function (e) {
-                Vec3.sub(tmpDir, e, sphere.center);
-                var out = Vec3.clone(e);
+                Vec3.normalize(tmpDir, Vec3.sub(tmpDir, e, sphere.center));
+                var o = Vec3.clone(e);
                 var sA = Vec3.dot(tmpDir, axes_1.dirA) < 0 ? -1 : 1;
-                Vec3.scaleAndAdd(out, out, axes_1.dirA, sA);
+                Vec3.scaleAndAdd(o, o, axes_1.dirA, sA);
                 var sB = Vec3.dot(tmpDir, axes_1.dirB) < 0 ? -1 : 1;
-                Vec3.scaleAndAdd(out, out, axes_1.dirB, sB);
+                Vec3.scaleAndAdd(o, o, axes_1.dirB, sB);
                 var sC = Vec3.dot(tmpDir, axes_1.dirC) < 0 ? -1 : 1;
-                Vec3.scaleAndAdd(out, out, axes_1.dirC, sC);
-                return out;
+                Vec3.scaleAndAdd(o, o, axes_1.dirC, sC);
+                if (Vec3.distance(out.center, o) > out.radius) {
+                    if (sphere.extrema.length >= 14) { // 14 extrema with coarse boundary helper
+                        Vec3.normalize(tmpDir, Vec3.sub(tmpDir, o, sphere.center));
+                    }
+                    Vec3.scaleAndAdd(o, out.center, tmpDir, out.radius);
+                }
+                return o;
             }));
         }
         return out;

package/lib/mol-model/sequence/sequence.js

@@ -6,6 +6,7 @@
  */
 import { getProteinOneLetterCode, getRnaOneLetterCode, getDnaOneLetterCode } from './constants';
 import { Column } from '../../mol-data/db';
+import { assertUnreachable } from '../../mol-util/type-helpers';
 var Sequence;
 (function (Sequence) {
     function getSequenceString(seq) {
@@ -40,7 +41,7 @@ var Sequence;
             case "generic" /* Generic */:
                 code = function () { return 'X'; };
                 break;
-            default: throw new Error("unknown kind '".concat(kind, "'"));
+            default: assertUnreachable(kind);
         }
         if (map && map.size > 0) {
             return function (name) {

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

@@ -18,6 +18,7 @@ import { ModelSymmetry } from '../../../mol-model-formats/structure/property/sym
 import { Column } from '../../../mol-data/db';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
 import { ArrayTrajectory } from '../trajectory';
+import { ModelSecondaryStructure } from '../../../mol-model-formats/structure/property/secondary-structure';
 { }
 export var Model;
 (function (Model) {
@@ -28,8 +29,12 @@ export var Model;
         var isIdentity = Column.isIdentity(srcIndex);
         var srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
         var coarseGrained = isCoarseGrained(model);
+        var elementCount = model.atomicHierarchy.atoms._rowCount;
         for (var i = 0, il = frames.length; i < il; ++i) {
             var f = frames[i];
+            if (f.elementCount !== elementCount) {
+                throw new Error("Frame element count mismatch, got ".concat(f.elementCount, " but expected ").concat(elementCount, "."));
+            }
             var m = __assign(__assign({}, model), { id: UUID.create22(), modelNum: i, atomicConformation: Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray), 
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
@@ -215,7 +220,7 @@ export var Model;
             return false;
         var db = model.sourceData.data.db;
         for (var i = 0, il = db.database_2.database_id.rowCount; i < il; ++i) {
-            if (db.database_2.database_id.value(i) === 'PDB')
+            if (db.database_2.database_id.value(i) === 'pdb')
                 return true;
         }
         return false;
@@ -232,11 +237,14 @@ export var Model;
     }
     Model.hasPdbId = hasPdbId;
     function hasSecondaryStructure(model) {
-        if (!MmcifFormat.is(model.sourceData))
-            return false;
-        var db = model.sourceData.data.db;
-        return (db.struct_conf.id.isDefined ||
-            db.struct_sheet_range.id.isDefined);
+        if (MmcifFormat.is(model.sourceData)) {
+            var db = model.sourceData.data.db;
+            return (db.struct_conf.id.isDefined ||
+                db.struct_sheet_range.id.isDefined);
+        }
+        else {
+            return ModelSecondaryStructure.Provider.isApplicable(model);
+        }
     }
     Model.hasSecondaryStructure = hasSecondaryStructure;
     var tmpAngles90 = Vec3.create(1.5707963, 1.5707963, 1.5707963); // in radians

package/lib/mol-model/structure/model/properties/common.js

@@ -5,4 +5,4 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { Column } from '../../../../mol-data/db';
-export var EntitySubtype = Column.Schema.Aliased(Column.Schema.Str(''));
+export var EntitySubtype = Column.Schema.Aliased(Column.Schema.Str());

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

@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 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/cli/chem-comp-dict/create-saccharides
+ */
+export declare const SaccharideNames: Set<string>;

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

@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 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/cli/chem-comp-dict/create-saccharides
+ */
+export var 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']);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -62,32 +62,33 @@ export declare const PolymerTypeAtomRoleId: {
 };
 export declare const ProteinBackboneAtoms: Set<string>;
 export declare const NucleicBackboneAtoms: Set<string>;
+declare type ChemCompType = mmCIF_chemComp_schema['type']['T'];
 /** Chemical component type names for D-linked protein */
-export declare const DProteinComponentTypeNames: Set<string>;
+export declare const DProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for L-linked protein */
-export declare const LProteinComponentTypeNames: Set<string>;
+export declare const LProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for gamma protein, overlaps with D/L-linked */
-export declare const GammaProteinComponentTypeNames: Set<string>;
+export declare const GammaProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for beta protein, overlaps with D/L-linked */
-export declare const BetaProteinComponentTypeNames: Set<string>;
+export declare const BetaProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for protein termini, overlaps with D/L-linked */
-export declare const ProteinTerminusComponentTypeNames: Set<string>;
+export declare const ProteinTerminusComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for peptide-like protein */
-export declare const OtherProteinComponentTypeNames: Set<string>;
+export declare const OtherProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for protein */
-export declare const ProteinComponentTypeNames: Set<string>;
+export declare const ProteinComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for DNA */
-export declare const DNAComponentTypeNames: Set<string>;
+export declare const DNAComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for RNA */
-export declare const RNAComponentTypeNames: Set<string>;
+export declare const RNAComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for saccharide */
 export declare const SaccharideComponentTypeNames: Set<string>;
 /** Chemical component type names for other */
-export declare const OtherComponentTypeNames: Set<string>;
+export declare const OtherComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for ion (extension to mmcif) */
-export declare const IonComponentTypeNames: Set<string>;
+export declare const IonComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Chemical component type names for lipid (extension to mmcif) */
-export declare const LipidComponentTypeNames: Set<string>;
+export declare const LipidComponentTypeNames: Set<"other" | "d-peptide linking" | "l-peptide linking" | "d-peptide nh3 amino terminus" | "l-peptide nh3 amino terminus" | "d-peptide cooh carboxy terminus" | "l-peptide cooh carboxy terminus" | "dna linking" | "rna linking" | "l-rna linking" | "l-dna linking" | "dna oh 5 prime terminus" | "rna oh 5 prime terminus" | "dna oh 3 prime terminus" | "rna oh 3 prime terminus" | "d-saccharide, beta linking" | "d-saccharide, alpha linking" | "l-saccharide, beta linking" | "l-saccharide, alpha linking" | "l-saccharide" | "d-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "l-gamma-peptide, c-delta linking" | "d-gamma-peptide, c-delta linking" | "l-beta-peptide, c-gamma linking" | "d-beta-peptide, c-gamma linking" | "ion" | "lipid">;
 /** Common names for water molecules */
 export declare const WaterNames: Set<string>;
 export declare const AminoAcidNamesL: Set<string>;
@@ -103,12 +104,12 @@ export declare const isPurineBase: (compId: string) => boolean;
 export declare const isPyrimidineBase: (compId: string) => boolean;
 export declare const PolymerNames: Set<string>;
 /** get the molecule type from component type and id */
-export declare function getMoleculeType(compType: string, compId: string): MoleculeType;
-export declare function getPolymerType(compType: string, molType: MoleculeType): PolymerType;
-export declare function getComponentType(compId: string): mmCIF_chemComp_schema['type']['T'];
+export declare function getMoleculeType(compType: ChemCompType, compId: string): MoleculeType;
+export declare function getPolymerType(compType: ChemCompType, molType: MoleculeType): PolymerType;
+export declare function getComponentType(compId: string): ChemCompType;
 export declare function getDefaultChemicalComponent(compId: string): ChemicalComponent;
 export declare function getEntityType(compId: string): mmCIF_Schema['entity']['type']['T'];
-export declare function getEntitySubtype(compId: string, compType: string): EntitySubtype;
+export declare function getEntitySubtype(compId: string, compType: ChemCompType): EntitySubtype;
 export declare function isPolymer(moleculeType: MoleculeType): boolean;
 export declare function isNucleic(moleculeType: MoleculeType): boolean;
 export declare function isProtein(moleculeType: MoleculeType): boolean;
@@ -259,3 +260,4 @@ export declare const ResidueHydrophobicity: {
     HIP: number[];
 };
 export declare const DefaultResidueHydrophobicity: number[];
+export {};

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -117,63 +117,65 @@ export var NucleicBackboneAtoms = new Set([
 ]);
 /** Chemical component type names for D-linked protein */
 export var DProteinComponentTypeNames = new Set([
-    'D-PEPTIDE LINKING', 'D-PEPTIDE NH3 AMINO TERMINUS',
-    'D-PEPTIDE COOH CARBOXY TERMINUS', 'D-GAMMA-PEPTIDE, C-DELTA LINKING',
-    'D-BETA-PEPTIDE, C-GAMMA LINKING'
+    'd-peptide linking', 'd-peptide nh3 amino terminus',
+    'd-peptide cooh carboxy terminus', 'd-gamma-peptide, c-delta linking',
+    'd-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for L-linked protein */
 export var LProteinComponentTypeNames = new Set([
-    'L-PEPTIDE LINKING', 'L-PEPTIDE NH3 AMINO TERMINUS',
-    'L-PEPTIDE COOH CARBOXY TERMINUS', 'L-GAMMA-PEPTIDE, C-DELTA LINKING',
-    'L-BETA-PEPTIDE, C-GAMMA LINKING'
+    'l-peptide linking', 'l-peptide nh3 amino terminus',
+    'l-peptide cooh carboxy terminus', 'l-gamma-peptide, c-delta linking',
+    'l-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for gamma protein, overlaps with D/L-linked */
 export var GammaProteinComponentTypeNames = new Set([
-    'D-GAMMA-PEPTIDE, C-DELTA LINKING', 'L-GAMMA-PEPTIDE, C-DELTA LINKING'
+    'd-gamma-peptide, c-delta linking', 'l-gamma-peptide, c-delta linking'
 ]);
 /** Chemical component type names for beta protein, overlaps with D/L-linked */
 export var BetaProteinComponentTypeNames = new Set([
-    'D-BETA-PEPTIDE, C-GAMMA LINKING', 'L-BETA-PEPTIDE, C-GAMMA LINKING'
+    'd-beta-peptide, c-gamma linking', 'l-beta-peptide, c-gamma linking'
 ]);
 /** Chemical component type names for protein termini, overlaps with D/L-linked */
 export var ProteinTerminusComponentTypeNames = new Set([
-    'D-PEPTIDE NH3 AMINO TERMINUS', 'D-PEPTIDE COOH CARBOXY TERMINUS',
-    'L-PEPTIDE NH3 AMINO TERMINUS', 'L-PEPTIDE COOH CARBOXY TERMINUS'
+    'd-peptide nh3 amino terminus', 'd-peptide cooh carboxy terminus',
+    'l-peptide nh3 amino terminus', 'l-peptide cooh carboxy terminus'
 ]);
 /** Chemical component type names for peptide-like protein */
 export var OtherProteinComponentTypeNames = new Set([
-    'PEPTIDE LINKING', 'PEPTIDE-LIKE',
+    'peptide linking', 'peptide-like',
 ]);
 /** Chemical component type names for protein */
 export var ProteinComponentTypeNames = SetUtils.unionMany(DProteinComponentTypeNames, LProteinComponentTypeNames, OtherProteinComponentTypeNames);
 /** Chemical component type names for DNA */
 export var DNAComponentTypeNames = new Set([
-    'DNA LINKING', 'L-DNA LINKING', 'DNA OH 5 PRIME TERMINUS', 'DNA OH 3 PRIME TERMINUS',
+    'dna linking', 'l-dna linking', 'dna oh 5 prime terminus', 'dna oh 3 prime terminus',
 ]);
 /** Chemical component type names for RNA */
 export var RNAComponentTypeNames = new Set([
-    'RNA LINKING', 'L-RNA LINKING', 'RNA OH 5 PRIME TERMINUS', 'RNA OH 3 PRIME TERMINUS',
+    'rna linking', 'l-rna linking', 'rna oh 5 prime terminus', 'rna oh 3 prime terminus',
 ]);
 /** Chemical component type names for saccharide */
-export var SaccharideComponentTypeNames = new Set([
-    'D-SACCHARIDE, BETA LINKING', 'L-SACCHARIDE, BETA LINKING',
-    'D-SACCHARIDE, ALPHA LINKING', 'L-SACCHARIDE, ALPHA LINKING',
-    'L-SACCHARIDE', 'D-SACCHARIDE', 'SACCHARIDE',
-    // the following four are marked to be deprecated in the mmCIF dictionary
-    'D-SACCHARIDE 1,4 AND 1,4 LINKING', 'L-SACCHARIDE 1,4 AND 1,4 LINKING',
-    'D-SACCHARIDE 1,4 AND 1,6 LINKING', 'L-SACCHARIDE 1,4 AND 1,6 LINKING',
-]);
+export var SaccharideComponentTypeNames = SetUtils.unionMany(new Set([
+    'd-saccharide, beta linking', 'l-saccharide, beta linking',
+    'd-saccharide, alpha linking', 'l-saccharide, alpha linking',
+    'l-saccharide', 'd-saccharide', 'saccharide',
+]), 
+// deprecated in the mmCIF dictionary, kept for backward compatibility
+new Set([
+    'd-saccharide 1,4 and 1,4 linking', 'l-saccharide 1,4 and 1,4 linking',
+    'd-saccharide 1,4 and 1,6 linking', 'l-saccharide 1,4 and 1,6 linking'
+]));
 /** Chemical component type names for other */
 export var OtherComponentTypeNames = new Set([
-    'NON-POLYMER', 'OTHER'
+    'non-polymer', 'other'
 ]);
 /** Chemical component type names for ion (extension to mmcif) */
 export var IonComponentTypeNames = new Set([
-    'ION'
+    'ion'
 ]);
 /** Chemical component type names for lipid (extension to mmcif) */
 export var LipidComponentTypeNames = new Set([
-    'LIPID'
+    'lipid'
 ]);
 /** Common names for water molecules */
 export var WaterNames = new Set([
@@ -230,7 +232,6 @@ export var isPyrimidineBase = function (compId) { return PyrimidineBaseNames.has
 export var PolymerNames = SetUtils.unionMany(AminoAcidNames, BaseNames);
 /** get the molecule type from component type and id */
 export function getMoleculeType(compType, compId) {
-    compType = compType.toUpperCase();
     compId = compId.toUpperCase();
     if (PeptideBaseNames.has(compId)) {
         return 8 /* PNA */;
@@ -258,7 +259,7 @@ export function getMoleculeType(compType, compId) {
     }
     else if (OtherComponentTypeNames.has(compType)) {
         if (SaccharideCompIdMap.has(compId)) {
-            // trust our saccharide table more than given 'non-polymer' or 'other' component type
+            // trust our saccharide table more than given 'NON-POLYMER' or 'OTHER' component type
             return 9 /* Saccharide */;
         }
         else if (AminoAcidNames.has(compId)) {
@@ -279,7 +280,6 @@ export function getMoleculeType(compType, compId) {
     }
 }
 export function getPolymerType(compType, molType) {
-    compType = compType.toUpperCase();
     if (molType === 5 /* Protein */) {
         if (GammaProteinComponentTypeNames.has(compType)) {
             return 2 /* GammaProtein */;
@@ -313,10 +313,10 @@ export function getComponentType(compId) {
         return 'peptide linking';
     }
     else if (RnaBaseNames.has(compId)) {
-        return 'RNA linking';
+        return 'rna linking';
     }
     else if (DnaBaseNames.has(compId)) {
-        return 'DNA linking';
+        return 'dna linking';
     }
     else if (SaccharideCompIdMap.has(compId)) {
         return 'saccharide';
@@ -355,7 +355,6 @@ export function getEntityType(compId) {
 }
 export function getEntitySubtype(compId, compType) {
     compId = compId.toUpperCase();
-    compType = compType.toUpperCase();
     if (LProteinComponentTypeNames.has(compType)) {
         return 'polypeptide(L)';
     }

package/lib/mol-model/structure/query/queries/generators.js

@@ -320,7 +320,7 @@ export function bondedAtomicPairs(bondTest) {
             atomicBond.a.unit = structure.unitMap.get(bond.unitA);
             atomicBond.a.element = atomicBond.a.unit.elements[bond.indexA];
             atomicBond.aIndex = bond.indexA;
-            atomicBond.b.unit = structure.unitMap.get(bond.unitA);
+            atomicBond.b.unit = structure.unitMap.get(bond.unitB);
             atomicBond.b.element = atomicBond.b.unit.elements[bond.indexB];
             atomicBond.bIndex = bond.indexB;
             atomicBond.order = bond.props.order;

package/lib/mol-model/structure/structure/carbohydrates/constants.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 Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>