molstar 3.3.0 → 3.5.0

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

@@ -0,0 +1,142 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from NGL.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __awaiter, __generator } from "tslib";
+import { Task } from '../../../mol-task';
+import { ReaderResult as Result } from '../result';
+function parseInternal(data) {
+    return __awaiter(this, void 0, void 0, function () {
+        var dv, f, coordinates, boxes, times, offset, versionSize, boxSize, virSize, presSize, coordSize, velocitySize, forceSize, natoms, floatSize, natoms3, box, i, i, x, y, z, i, tmp, i, value, frameCoords, i;
+        return __generator(this, function (_a) {
+            dv = new DataView(data.buffer);
+            f = {
+                frames: [],
+                boxes: [],
+                times: [],
+                timeOffset: 0,
+                deltaTime: 0
+            };
+            coordinates = f.frames;
+            boxes = f.boxes;
+            times = f.times;
+            offset = 0;
+            while (true) {
+                // const magicnum = dv.getInt32(offset)
+                // const i1 = dv.getFloat32(offset + 4)
+                offset += 8;
+                versionSize = dv.getInt32(offset);
+                offset += 4;
+                offset += versionSize;
+                boxSize = dv.getInt32(offset + 8);
+                virSize = dv.getInt32(offset + 12);
+                presSize = dv.getInt32(offset + 16);
+                coordSize = dv.getInt32(offset + 28);
+                velocitySize = dv.getInt32(offset + 32);
+                forceSize = dv.getInt32(offset + 36);
+                natoms = dv.getInt32(offset + 40);
+                // const step = dv.getInt32(offset + 44)
+                // const nre = dv.getInt32(offset + 48)
+                offset += 52;
+                floatSize = boxSize / 9;
+                natoms3 = natoms * 3;
+                // let lambda
+                if (floatSize === 8) {
+                    times.push(dv.getFloat64(offset));
+                    // lambda = dv.getFloat64(offset + 8)
+                }
+                else {
+                    times.push(dv.getFloat32(offset));
+                    // lambda = dv.getFloat32(offset + 4)
+                }
+                offset += 2 * floatSize;
+                if (boxSize) {
+                    box = new Float32Array(9);
+                    if (floatSize === 8) {
+                        for (i = 0; i < 9; ++i) {
+                            box[i] = dv.getFloat64(offset) * 10;
+                            offset += 8;
+                        }
+                    }
+                    else {
+                        for (i = 0; i < 9; ++i) {
+                            box[i] = dv.getFloat32(offset) * 10;
+                            offset += 4;
+                        }
+                    }
+                    boxes.push(box);
+                }
+                // ignore, unused
+                offset += virSize;
+                // ignore, unused
+                offset += presSize;
+                if (coordSize) {
+                    x = new Float32Array(natoms);
+                    y = new Float32Array(natoms);
+                    z = new Float32Array(natoms);
+                    if (floatSize === 8) {
+                        for (i = 0; i < natoms; ++i) {
+                            x[i] = dv.getFloat64(offset) * 10;
+                            y[i] = dv.getFloat64(offset + 8) * 10;
+                            z[i] = dv.getFloat64(offset + 16) * 10;
+                            offset += 24;
+                        }
+                    }
+                    else {
+                        tmp = new Uint32Array(data.buffer, offset, natoms3);
+                        for (i = 0; i < natoms3; ++i) {
+                            value = tmp[i];
+                            tmp[i] = (((value & 0xFF) << 24) | ((value & 0xFF00) << 8) |
+                                ((value >> 8) & 0xFF00) | ((value >> 24) & 0xFF));
+                        }
+                        frameCoords = new Float32Array(data.buffer, offset, natoms3);
+                        for (i = 0; i < natoms; ++i) {
+                            x[i] = frameCoords[i * 3] * 10;
+                            y[i] = frameCoords[i * 3 + 1] * 10;
+                            z[i] = frameCoords[i * 3 + 2] * 10;
+                            offset += 12;
+                        }
+                    }
+                    coordinates.push({ count: natoms, x: x, y: y, z: z });
+                }
+                // ignore, unused
+                offset += velocitySize;
+                // ignore, unused
+                offset += forceSize;
+                if (offset >= data.byteLength)
+                    break;
+            }
+            if (times.length >= 1) {
+                f.timeOffset = times[0];
+            }
+            if (times.length >= 2) {
+                f.deltaTime = times[1] - times[0];
+            }
+            return [2 /*return*/, f];
+        });
+    });
+}
+export function parseTrr(data) {
+    var _this = this;
+    return Task.create('Parse TRR', 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/writer/cif/encoder.js

@@ -7,6 +7,7 @@
 import { __spreadArray } from "tslib";
 import { Iterator } from '../../../mol-data/iterator';
 import { ArrayEncoding } from '../../common/binary-cif';
+import { assertUnreachable } from '../../../mol-util/type-helpers';
 export var Field;
 (function (Field) {
     function str(name, value, params) {
@@ -259,7 +260,7 @@ function cifFieldsFromTableSchema(schema) {
             fields.push.apply(fields, getTensorDefinitions(k, t.space));
         }
         else {
-            throw new Error("Unknown valueType ".concat(t.valueType));
+            assertUnreachable(t.valueType);
         }
     }
     return fields;

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/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/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>

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

@@ -1,11 +1,12 @@
 /**
- * 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>
  */
 var _a, _b;
 import { ColorMap } from '../../../../mol-util/color';
+import { SaccharideNames } from '../../model/types/saccharides';
 export var SaccharideColors = ColorMap({
     Blue: 0x0090bc,
     Green: 0x00a651,
@@ -262,11 +263,6 @@ var CommonSaccharideNames = {
     Sor: ['SOE', 'UEA'],
     Psi: ['PSV', 'SF6', 'SF9', 'TTV'],
 };
-var UnknownSaccharideNames = [
-    'NGZ',
-    'LAT',
-    'PUF', 'GDA', '9WJ', // via updated CCD
-];
 /**
  * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
  */
@@ -309,8 +305,9 @@ export var SaccharideCompIdMap = (function () {
             }
         }
     }
-    for (var i = 0, il = UnknownSaccharideNames.length; i < il; ++i) {
-        map.set(UnknownSaccharideNames[i], UnknownSaccharideComponent);
-    }
+    SaccharideNames.forEach(function (name) {
+        if (!map.has(name))
+            map.set(name, UnknownSaccharideComponent);
+    });
     return map;
 })();

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

@@ -280,7 +280,10 @@ var Structure = /** @class */ (function () {
                 this.state.interUnitBonds = new InterUnitBonds(new Map());
             }
             else {
-                this.state.interUnitBonds = computeInterUnitBonds(this, { ignoreWater: !this.dynamicBonds });
+                this.state.interUnitBonds = computeInterUnitBonds(this, {
+                    ignoreWater: !this.dynamicBonds,
+                    ignoreIon: !this.dynamicBonds,
+                });
             }
             return this.state.interUnitBonds;
         },

package/lib/mol-model/structure/structure/unit/bonds/inter-compute.d.ts

@@ -11,6 +11,7 @@ import { InterUnitBonds } from './data';
 export interface InterBondComputationProps extends BondComputationProps {
     validUnitPair: (structure: Structure, unitA: Unit, unitB: Unit) => boolean;
     ignoreWater: boolean;
+    ignoreIon: boolean;
 }
 declare function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondComputationProps>): InterUnitBonds;
 export { computeInterUnitBonds };

package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js

@@ -163,7 +163,7 @@ function findPairBonds(unitA, unitB, props, builder) {
     }
     builder.finishUnitPair();
 }
-var DefaultInterBondComputationProps = __assign(__assign({}, DefaultBondComputationProps), { ignoreWater: true });
+var DefaultInterBondComputationProps = __assign(__assign({}, DefaultBondComputationProps), { ignoreWater: true, ignoreIon: true });
 function findBonds(structure, props) {
     var builder = new InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return IndexPairBonds.Provider.get(m); });
@@ -189,7 +189,9 @@ function computeInterUnitBonds(structure, props) {
             var mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
             var notWater = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 2 /* Water */) &&
                 (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 2 /* Water */));
-            return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater);
+            var notIon = ((!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== 3 /* Ion */) &&
+                (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== 3 /* Ion */));
+            return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
         }) }));
 }
 export { computeInterUnitBonds };

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

@@ -21,8 +21,6 @@ import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bo
 import { ElementSetIntraBondCache } from './unit/bonds/element-set-intra-bond-cache';
 import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
 import { getResonance } from './unit/resonance';
-// avoiding namespace lookup improved performance in Chrome (Aug 2020)
-var v3add = Vec3.add;
 var Unit;
 (function (Unit) {
     function isAtomic(u) { return u.kind === 0 /* Atomic */; }
@@ -155,22 +153,7 @@ var Unit;
                         ? undefined
                         : tryRemapBonds(this, this.props.bonds, model, dynamicBonds) });
                 if (!Unit.isSameConformation(this, model)) {
-                    var b = props.boundary;
-                    if (b) {
-                        var elements = this.elements;
-                        var pos = this.conformation.invariantPosition;
-                        var v = Vec3();
-                        var center = Vec3();
-                        for (var i = 0, il = elements.length; i < il; i++) {
-                            pos(elements[i], v);
-                            v3add(center, center, v);
-                        }
-                        Vec3.scale(center, center, 1 / elements.length);
-                        // only invalidate boundary if sphere has changed too much
-                        if (Vec3.distance(center, b.sphere.center) / b.sphere.radius >= 1.0) {
-                            props.boundary = undefined;
-                        }
-                    }
+                    props.boundary = undefined;
                     props.lookup3d = undefined;
                     props.principalAxes = undefined;
                 }

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

package/lib/mol-model-formats/structure/basic/atomic.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -37,14 +37,6 @@ function findHierarchyOffsets(atom_site) {
     }
     return { residues: residues, chains: chains };
 }
-function substUndefinedColumn(table, a, b) {
-    if (!table[a].isDefined) {
-        table[a] = table[b];
-    }
-    if (!table[b].isDefined) {
-        table[b] = table[a];
-    }
-}
 function createHierarchyData(atom_site, sourceIndex, offsets) {
     var atoms = Table.ofColumns(AtomsSchema, {
         type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased(Column.Schema.str) }),
@@ -74,11 +66,6 @@ function createHierarchyData(atom_site, sourceIndex, offsets) {
     // Optimize the numeric columns
     Table.columnToArray(residues, 'label_seq_id', Int32Array);
     Table.columnToArray(residues, 'auth_seq_id', Int32Array);
-    // Fix possibly missing auth_/label_ columns
-    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
-    substUndefinedColumn(atoms, 'label_comp_id', 'auth_comp_id');
-    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
-    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
     return { atoms: atoms, residues: residues, chains: chains, atomSourceIndex: sourceIndex };
 }
 function getConformation(atom_site) {

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

package/lib/mol-model-formats/structure/basic/parser.js

@@ -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.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>