molstar 3.3.0 → 3.5.0

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

@@ -0,0 +1,146 @@
+"use strict";
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from NGL.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseTrr = void 0;
+var tslib_1 = require("tslib");
+var mol_task_1 = require("../../../mol-task");
+var result_1 = require("../result");
+function parseInternal(data) {
+    return tslib_1.__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 tslib_1.__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];
+        });
+    });
+}
+function parseTrr(data) {
+    var _this = this;
+    return mol_task_1.Task.create('Parse TRR', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        var file, e_1;
+        return tslib_1.__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_1.ReaderResult.success(file)];
+                case 2:
+                    e_1 = _a.sent();
+                    return [2 /*return*/, result_1.ReaderResult.error('' + e_1)];
+                case 3: return [2 /*return*/];
+            }
+        });
+    }); });
+}
+exports.parseTrr = parseTrr;

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

@@ -141,9 +141,9 @@ function undefinedError() {
     throw new Error('(xdrfile error) Undefined error.');
 }
 function parseInternal(ctx, data) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var dv, f, coordinates, boxes, times, minMaxInt, sizeint, bitsizeint, sizesmall, thiscoord, prevcoord, offset, buf, frameCoords, natoms, box, i, i, lfp, lsize, precision, bitsize, smallidx, tmpIdx, smaller, smallnum, adz, invPrecision, run_1, i, flag, isSmaller, k, tmpSwap, c;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     dv = new DataView(data.buffer, data.byteOffset);
@@ -354,9 +354,9 @@ function parseInternal(ctx, data) {
 }
 function parseXtc(data) {
     var _this = this;
-    return mol_task_1.Task.create('Parse XTC', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse XTC', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var file, e_1;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     _a.trys.push([0, 2, , 3]);

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

@@ -51,8 +51,8 @@ function parseInternal(data) {
 }
 function parseXyz(data) {
     var _this = this;
-    return mol_task_1.Task.create('Parse Mol', function () { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return mol_task_1.Task.create('Parse Mol', function () { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, parseInternal(data)];
         });
     }); });

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

@@ -10,6 +10,7 @@ exports.Encoder = exports.Category = exports.Field = void 0;
 var tslib_1 = require("tslib");
 var iterator_1 = require("../../../mol-data/iterator");
 var binary_cif_1 = require("../../common/binary-cif");
+var type_helpers_1 = require("../../../mol-util/type-helpers");
 var Field;
 (function (Field) {
     function str(name, value, params) {
@@ -199,7 +200,7 @@ function columnTensorValue(k) {
     }
     return function (i, d) {
         var _a;
-        return (_a = d[k].schema.space).get.apply(_a, (0, tslib_1.__spreadArray)([d[k].value(i)], coords, false));
+        return (_a = d[k].schema.space).get.apply(_a, tslib_1.__spreadArray([d[k].value(i)], coords, false));
     };
 }
 function columnValueKind(k) {
@@ -262,7 +263,7 @@ function cifFieldsFromTableSchema(schema) {
             fields.push.apply(fields, getTensorDefinitions(k, t.space));
         }
         else {
-            throw new Error("Unknown valueType ".concat(t.valueType));
+            (0, type_helpers_1.assertUnreachable)(t.valueType);
         }
     }
     return fields;

package/lib/commonjs/mol-io/writer/cif.js

@@ -10,7 +10,7 @@ exports.CifWriter = void 0;
 var tslib_1 = require("tslib");
 var text_1 = require("./cif/encoder/text");
 var binary_1 = require("./cif/encoder/binary");
-var _Encoder = (0, tslib_1.__importStar)(require("./cif/encoder"));
+var _Encoder = tslib_1.__importStar(require("./cif/encoder"));
 var binary_cif_1 = require("../common/binary-cif");
 var CifWriter;
 (function (CifWriter) {

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

@@ -9,7 +9,7 @@ exports.LigandEncoder = void 0;
 var tslib_1 = require("tslib");
 var mol_util_1 = require("../../mol-util");
 function Atom(partial) {
-    return (0, tslib_1.__assign)({}, partial);
+    return tslib_1.__assign({}, partial);
 }
 var LigandEncoder = /** @class */ (function () {
     function LigandEncoder(encoder, metaInformation, hydrogens) {

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

@@ -13,7 +13,7 @@ var ligand_encoder_1 = require("../ligand-encoder");
 // specification: http://c4.cabrillo.edu/404/ctfile.pdf
 // SDF wraps MOL and allows for multiple molecules per file as well as additional properties
 var MolEncoder = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(MolEncoder, _super);
+    tslib_1.__extends(MolEncoder, _super);
     function MolEncoder(encoder, metaInformation, hydrogens, terminator) {
         if (terminator === void 0) { terminator = ''; }
         var _this = _super.call(this, encoder, metaInformation, hydrogens) || this;

package/lib/commonjs/mol-io/writer/mol2/encoder.js

@@ -16,7 +16,7 @@ var types_1 = require("../../../mol-model/structure/model/types");
 var NON_METAL_ATOMS = 'H D B C N O F Si P S Cl As Se Br Te I At He Ne Ar Kr Xe Rn'.split(' ');
 // specification: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
 var Mol2Encoder = /** @class */ (function (_super) {
-    (0, tslib_1.__extends)(Mol2Encoder, _super);
+    tslib_1.__extends(Mol2Encoder, _super);
     function Mol2Encoder(encoder, metaInformation, hydrogens) {
         var _this = _super.call(this, encoder, metaInformation, hydrogens) || this;
         _this.out = mol_util_1.StringBuilder.create();

package/lib/commonjs/mol-math/geometry/boundary-helper.js

@@ -88,7 +88,7 @@ var BoundaryHelper = /** @class */ (function () {
         this.centroidHelper.radiusSphereStep(center, radius);
     };
     BoundaryHelper.prototype.getSphere = function (sphere) {
-        return geometry_1.Sphere3D.setExtrema(this.centroidHelper.getSphere(sphere), (0, tslib_1.__spreadArray)([], this.extrema, true));
+        return geometry_1.Sphere3D.setExtrema(this.centroidHelper.getSphere(sphere), tslib_1.__spreadArray([], this.extrema, true));
     };
     BoundaryHelper.prototype.getBox = function (box) {
         return box3d_1.Box3D.fromVec3Array(box || (0, box3d_1.Box3D)(), this.extrema);
@@ -109,16 +109,16 @@ function getEposDir(quality) {
     var dir;
     switch (quality) {
         case '6':
-            dir = (0, tslib_1.__spreadArray)([], Type001, true);
+            dir = tslib_1.__spreadArray([], Type001, true);
             break;
         case '14':
-            dir = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Type001, true), Type111, true);
+            dir = tslib_1.__spreadArray(tslib_1.__spreadArray([], Type001, true), Type111, true);
             break;
         case '26':
-            dir = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Type001, true), Type111, true), Type011, true);
+            dir = tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([], Type001, true), Type111, true), Type011, true);
             break;
         case '98':
-            dir = (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], Type001, true), Type111, true), Type011, true), Type012, true), Type112, true), Type122, true);
+            dir = tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray(tslib_1.__spreadArray([], Type001, true), Type111, true), Type011, true), Type012, true), Type112, true), Type122, true);
             break;
     }
     return dir.map(function (a) {

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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/commonjs/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/commonjs/mol-math/geometry/gaussian-density/cpu.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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -12,7 +12,7 @@ var linear_algebra_1 = require("../../linear-algebra");
 var int_1 = require("../../../mol-data/int");
 var approx_1 = require("../../approx");
 function GaussianDensityCPU(ctx, position, box, radius, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         function accumulateRange(begI, endI) {
             for (var i = begI; i < endI; ++i) {
                 var j = int_1.OrderedSet.getAt(indices, i);
@@ -63,9 +63,9 @@ function GaussianDensityCPU(ctx, position, box, radius, props) {
             }
         }
         function accumulate() {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var i;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             i = 0;
@@ -87,7 +87,7 @@ function GaussianDensityCPU(ctx, position, box, radius, props) {
             });
         }
         var resolution, radiusOffset, smoothness, scaleFactor, indices, x, y, z, id, n, radii, maxRadius, i, r, pad, expandedBox, min, scaledBox, dim, space, data, field, idData, idField, dimX, dimY, dimZ, iu, iv, iuv, gridx, gridy, gridz, densData, alpha, updateChunk, transform;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     resolution = props.resolution, radiusOffset = props.radiusOffset, smoothness = props.smoothness;
@@ -130,7 +130,7 @@ function GaussianDensityCPU(ctx, position, box, radius, props) {
                     transform = linear_algebra_1.Mat4.identity();
                     linear_algebra_1.Mat4.fromScaling(transform, linear_algebra_1.Vec3.create(resolution, resolution, resolution));
                     linear_algebra_1.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/commonjs/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/commonjs/mol-math/geometry/gaussian-density/gpu.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -59,11 +59,11 @@ 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 };
 }
 exports.GaussianDensityGPU = GaussianDensityGPU;
 function GaussianDensityTexture(webgl, position, box, radius, props, oldTexture) {
@@ -81,8 +81,8 @@ function GaussianDensityTexture3d(webgl, position, box, radius, props, oldTextur
 }
 exports.GaussianDensityTexture3d = GaussianDensityTexture3d;
 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 = linear_algebra_1.Mat4.identity();
@@ -158,7 +158,7 @@ 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');
@@ -202,7 +202,7 @@ 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) {
@@ -287,7 +287,7 @@ function createGaussianDensityRenderable(webgl, drawCount, positions, radii, gro
         dGridTexType: mol_util_1.ValueCell.create(minDistanceTexture.getDepth() > 0 ? '3d' : '2d'),
         dCalcType: mol_util_1.ValueCell.create('density'),
     };
-    var schema = (0, tslib_1.__assign)({}, GaussianDensitySchema);
+    var schema = tslib_1.__assign({}, GaussianDensitySchema);
     var shaderCode = (0, shader_code_1.ShaderCode)(GaussianDensityName, gaussian_density_vert_1.gaussianDensity_vert, gaussian_density_frag_1.gaussianDensity_frag);
     var renderItem = (0, render_item_1.createComputeRenderItem)(webgl, 'points', shaderCode, schema, values);
     return (0, renderable_1.createComputeRenderable)(renderItem, values);

package/lib/commonjs/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/commonjs/mol-math/geometry/gaussian-density.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>
  */
@@ -17,8 +17,8 @@ exports.DefaultGaussianDensityProps = {
 };
 function computeGaussianDensity(position, box, radius, props) {
     var _this = this;
-    return task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return task_1.Task.create('Gaussian Density', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, (0, cpu_1.GaussianDensityCPU)(ctx, position, box, radius, props)];
                 case 1: return [2 /*return*/, _a.sent()];
@@ -41,8 +41,8 @@ function computeGaussianDensityTexture3d(position, box, radius, props, webgl, te
 exports.computeGaussianDensityTexture3d = computeGaussianDensityTexture3d;
 function _computeGaussianDensityTexture(type, position, box, radius, props, webgl, texture) {
     var _this = this;
-    return task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return task_1.Task.create('Gaussian Density', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
+        return tslib_1.__generator(this, function (_a) {
             return [2 /*return*/, type === '2d' ?
                     (0, gpu_1.GaussianDensityTexture2d)(webgl, position, box, radius, false, props, texture) :
                     (0, gpu_1.GaussianDensityTexture3d)(webgl, position, box, radius, props, texture)];

package/lib/commonjs/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/commonjs/mol-math/geometry/molecular-surface.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
@@ -44,12 +44,12 @@ function getAngleTables(probePositions) {
 //
 exports.MolecularSurfaceCalculationParams = {
     probeRadius: param_definition_1.ParamDefinition.Numeric(1.4, { min: 0, max: 10, step: 0.1 }, { description: 'Radius of the probe tracing the molecular surface.' }),
-    resolution: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.01, max: 20, step: 0.01 }, (0, tslib_1.__assign)({ description: 'Grid resolution/cell spacing.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
-    probePositions: param_definition_1.ParamDefinition.Numeric(36, { min: 12, max: 90, step: 1 }, (0, tslib_1.__assign)({ description: 'Number of positions tested for probe target intersection.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
+    resolution: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0.01, max: 20, step: 0.01 }, tslib_1.__assign({ description: 'Grid resolution/cell spacing.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
+    probePositions: param_definition_1.ParamDefinition.Numeric(36, { min: 12, max: 90, step: 1 }, tslib_1.__assign({ description: 'Number of positions tested for probe target intersection.' }, base_1.BaseGeometry.CustomQualityParamInfo)),
 };
 exports.DefaultMolecularSurfaceCalculationProps = param_definition_1.ParamDefinition.getDefaultValues(exports.MolecularSurfaceCalculationParams);
 function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         /**
          * Is the point at x,y,z obscured by any of the atoms specifeid by indices in neighbours.
          * Ignore indices a and b (these are the relevant atoms in projectPoints/Torii)
@@ -157,9 +157,9 @@ function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
             }
         }
         function projectPoints() {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var i;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             i = 0;
@@ -267,9 +267,9 @@ function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
             }
         }
         function projectTorii() {
-            return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+            return tslib_1.__awaiter(this, void 0, void 0, function () {
                 var i;
-                return (0, tslib_1.__generator)(this, function (_a) {
+                return tslib_1.__generator(this, function (_a) {
                     switch (_a.label) {
                         case 0:
                             i = 0;
@@ -291,7 +291,7 @@ function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
             });
         }
         var lastClip, atob, mid, n1, n2, resolution, probeRadius, probePositions, scaleFactor, ngTorus, cellSize, lookup3d, neighbours, indices, px, py, pz, id, radius, n, pad, expandedBox, _a, minX, minY, minZ, scaledBox, dim, dimX, dimY, dimZ, iu, iv, iuv, _b, cosTable, sinTable, space, data, idData, gridx, gridy, gridz, updateChunk, field, idField, transform;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     lastClip = -1;
@@ -348,7 +348,7 @@ function calcMolecularSurface(ctx, position, boundary, maxRadius, box, props) {
                     mat4_1.Mat4.fromScaling(transform, linear_algebra_1.Vec3.create(resolution, resolution, resolution));
                     mat4_1.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/commonjs/mol-math/geometry/primitives/box3d.js

@@ -31,8 +31,9 @@ exports.Box3D = Box3D;
     Box3D.clone = clone;
     /** Get box from sphere, uses extrema if available */
     function fromSphere3D(out, sphere) {
-        if (sphere3d_1.Sphere3D.hasExtrema(sphere))
+        if (sphere3d_1.Sphere3D.hasExtrema(sphere) && sphere.extrema.length >= 14) { // 14 extrema with coarse boundary helper
             return fromVec3Array(out, sphere.extrema);
+        }
         var r = linear_algebra_1.Vec3.create(sphere.radius, sphere.radius, sphere.radius);
         linear_algebra_1.Vec3.sub(out.min, sphere.center, r);
         linear_algebra_1.Vec3.add(out.max, sphere.center, r);

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

@@ -183,7 +183,7 @@ exports.Sphere3D = Sphere3D;
         linear_algebra_1.Vec3.copy(out.center, sphere.center);
         out.radius = Math.max(sphere.radius, linear_algebra_1.Vec3.distance(sphere.center, by.center) + by.radius);
         if (hasExtrema(sphere) && hasExtrema(by)) {
-            setExtrema(out, (0, tslib_1.__spreadArray)((0, tslib_1.__spreadArray)([], sphere.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true), by.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true));
+            setExtrema(out, tslib_1.__spreadArray(tslib_1.__spreadArray([], sphere.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true), by.extrema.map(function (e) { return linear_algebra_1.Vec3.clone(e); }), true));
         }
         return out;
     }
@@ -206,15 +206,21 @@ exports.Sphere3D = Sphere3D;
             var axes_1 = principal_axes_1.PrincipalAxes.calculateMomentsAxes(positions);
             axes3d_1.Axes3D.scale(axes_1, axes3d_1.Axes3D.normalize(axes_1, axes_1), delta);
             setExtrema(out, sphere.extrema.map(function (e) {
-                linear_algebra_1.Vec3.sub(tmpDir, e, sphere.center);
-                var out = linear_algebra_1.Vec3.clone(e);
+                linear_algebra_1.Vec3.normalize(tmpDir, linear_algebra_1.Vec3.sub(tmpDir, e, sphere.center));
+                var o = linear_algebra_1.Vec3.clone(e);
                 var sA = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirA) < 0 ? -1 : 1;
-                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirA, sA);
+                linear_algebra_1.Vec3.scaleAndAdd(o, o, axes_1.dirA, sA);
                 var sB = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirB) < 0 ? -1 : 1;
-                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirB, sB);
+                linear_algebra_1.Vec3.scaleAndAdd(o, o, axes_1.dirB, sB);
                 var sC = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirC) < 0 ? -1 : 1;
-                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirC, sC);
-                return out;
+                linear_algebra_1.Vec3.scaleAndAdd(o, o, axes_1.dirC, sC);
+                if (linear_algebra_1.Vec3.distance(out.center, o) > out.radius) {
+                    if (sphere.extrema.length >= 14) { // 14 extrema with coarse boundary helper
+                        linear_algebra_1.Vec3.normalize(tmpDir, linear_algebra_1.Vec3.sub(tmpDir, o, sphere.center));
+                    }
+                    linear_algebra_1.Vec3.scaleAndAdd(o, out.center, tmpDir, out.radius);
+                }
+                return o;
             }));
         }
         return out;

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

@@ -7,11 +7,11 @@
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 var tslib_1 = require("tslib");
-(0, tslib_1.__exportStar)(require("./geometry/common"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/symmetry-operator"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/spacegroup/construction"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/lookup3d/common"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/lookup3d/grid"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/primitives/box3d"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/primitives/sphere3d"), exports);
-(0, tslib_1.__exportStar)(require("./geometry/primitives/axes3d"), exports);
+tslib_1.__exportStar(require("./geometry/common"), exports);
+tslib_1.__exportStar(require("./geometry/symmetry-operator"), exports);
+tslib_1.__exportStar(require("./geometry/spacegroup/construction"), exports);
+tslib_1.__exportStar(require("./geometry/lookup3d/common"), exports);
+tslib_1.__exportStar(require("./geometry/lookup3d/grid"), exports);
+tslib_1.__exportStar(require("./geometry/primitives/box3d"), exports);
+tslib_1.__exportStar(require("./geometry/primitives/sphere3d"), exports);
+tslib_1.__exportStar(require("./geometry/primitives/axes3d"), exports);