molstar 2.3.7 → 2.4.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.3.7",
+  "version": "2.4.1",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -89,52 +89,51 @@
   "license": "MIT",
   "devDependencies": {
     "@graphql-codegen/add": "^3.1.0",
-    "@graphql-codegen/cli": "^2.2.0",
+    "@graphql-codegen/cli": "^2.3.0",
     "@graphql-codegen/time": "^3.1.0",
-    "@graphql-codegen/typescript": "^2.2.2",
+    "@graphql-codegen/typescript": "^2.4.1",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.1.0",
-    "@graphql-codegen/typescript-graphql-request": "^4.1.4",
-    "@graphql-codegen/typescript-operations": "^2.1.6",
+    "@graphql-codegen/typescript-graphql-request": "^4.3.1",
+    "@graphql-codegen/typescript-operations": "^2.2.1",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
-    "@types/jest": "^27.0.2",
-    "@typescript-eslint/eslint-plugin": "^4.32.0",
-    "@typescript-eslint/parser": "^4.32.0",
+    "@types/jest": "^27.0.3",
+    "@typescript-eslint/eslint-plugin": "^5.4.0",
+    "@typescript-eslint/parser": "^5.4.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^6.3.0",
+    "concurrently": "^6.4.0",
     "cpx2": "^4.0.0",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.3.0",
-    "eslint": "^7.32.0",
+    "css-loader": "^6.5.1",
+    "eslint": "^8.3.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.0.0",
-    "graphql": "^15.6.0",
-    "http-server": "^13.0.2",
-    "jest": "^27.2.4",
-    "mini-css-extract-plugin": "^2.3.0",
-    "node-sass": "^6.0.1",
+    "graphql": "^15.7.2",
+    "http-server": "^14.0.0",
+    "jest": "^27.3.1",
+    "mini-css-extract-plugin": "^2.4.5",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass-loader": "^12.1.0",
-    "simple-git": "^2.46.0",
+    "sass": "^1.43.5",
+    "sass-loader": "^12.3.0",
+    "simple-git": "^2.47.0",
     "stream-browserify": "^3.0.0",
-    "style-loader": "^3.3.0",
-    "ts-jest": "^27.0.5",
-    "typescript": "^4.4.3",
-    "webpack": "^5.56.0",
-    "webpack-cli": "^4.8.0",
-    "webpack-version-file-plugin": "^0.4.0"
+    "style-loader": "^3.3.1",
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.5.2",
+    "webpack": "^5.64.4",
+    "webpack-cli": "^4.9.1"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.10.2",
+    "@types/node": "^16.11.10",
     "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.27",
-    "@types/react-dom": "^17.0.9",
+    "@types/react": "^17.0.37",
+    "@types/react-dom": "^17.0.11",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
     "body-parser": "^1.19.0",
@@ -142,13 +141,13 @@
     "cors": "^2.8.5",
     "express": "^4.17.1",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.6",
+    "immer": "^9.0.7",
     "immutable": "^3.8.2",
     "node-fetch": "^2.6.2",
     "react": "^17.0.2",
     "react-dom": "^17.0.2",
-    "rxjs": "^7.3.1",
-    "swagger-ui-dist": "^3.52.3",
+    "rxjs": "^7.4.0",
+    "swagger-ui-dist": "^4.1.1",
     "tslib": "^2.3.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"

package/CHANGELOG.md

@@ -1,191 +0,0 @@
-# Change Log
-All notable changes to this project will be documented in this file, following the suggestions of [Keep a CHANGELOG](http://keepachangelog.com/). This project adheres to [Semantic Versioning](http://semver.org/) for its most widely used - and defacto - public interfaces.
-
-Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
-
-
-## [Unreleased]
-
-- Added ``ViewerOptions.collapseRightPanel``
-- Added ``Viewer.loadTrajectory`` to support loading "composed" trajectories (e.g. from gro + xtc)
-- Fix: handle parent in Structure.remapModel
-- Add ``rounded`` and ``square`` helix profile options to Cartoon representation (in addition to the default ``elliptical``)
-
-## [v2.3.6] - 2021-11-8
-
-- Add additional measurement controls: orientation (box, axes, ellipsoid) & plane (best fit)
-- Improve aromatic bond visuals (add ``aromaticScale``, ``aromaticSpacing``, ``aromaticDashCount`` params)
-- [Breaking] Change ``adjustCylinderLength`` default to ``false`` (set to true for focus representation)
-- Fix marker highlight color overriding select color
-- CellPack extension update
-    - add binary model support
-    - add compartment (including membrane) geometry support
-    - add latest mycoplasma model example
-- Prefer WebGL1 in Safari 15.1.
-
-## [v2.3.5] - 2021-10-19
-
-- Fix sequence viewer for PDB files with COMPND record and multichain entities.
-- Fix index pair bonds order assignment
-
-## [v2.3.4] - 2021-10-12
-
-- Fix pickScale not taken into account in line/point shader
-- Add pixel-scale, pick-scale & pick-padding GET params to Viewer app
-- Fix selecting bonds not adding their atoms in selection manager
-- Add ``preferAtoms`` option to SelectLoci/HighlightLoci behaviors
-- Make the implicit atoms of bond visuals pickable
-    - Add ``preferAtomPixelPadding`` to Canvas3dInteractionHelper
-- Add points & crosses visuals to Line representation
-- Add ``pickPadding`` config option (look around in case target pixel is empty)
-- Add ``multipleBonds`` param to bond visuals with options: off, symmetric, offset
-- Fix ``argparse`` config in servers.
-
-## [v2.3.3] - 2021-10-01
-
-- Fix direct volume shader
-
-## [v2.3.2] - 2021-10-01
-
-- Prefer WebGL1 on iOS devices until WebGL2 support has stabilized.
-
-## [v2.3.1] - 2021-09-28
-
-- Add Charmm saccharide names
-- Treat missing occupancy column as occupancy of 1
-- Fix line shader not accounting for aspect ratio
-- [Breaking] Fix point repr & shader
-    - Was unusable with ``wboit``
-    - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
-    - Set ``pointSizeAttenuation`` to false by default
-    - Set ``sizeTheme`` to ``uniform`` by default
-- Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
-- Add support support for ``chem_comp_bond`` and ``struct_conn`` categories (fixes ModelServer behavior where these categories should have been present)
-- Model and VolumeServer: fix argparse config
-
-## [v2.3.0] - 2021-09-06
-
-- Take include/exclude flags into account when displaying aromatic bonds
-- Improve marking performance
-    - Avoid unnecessary draw calls/ui updates when marking
-    - Check if loci is superset of visual
-    - Check if loci overlaps with unit visual
-    - Ensure ``Interval`` is used for ranges instead of ``SortedArray``
-    - Add uniform marker type
-    - Special case for reversing previous mark
-- Add optional marking pass
-    - Outlines visible and hidden parts of highlighted/selected groups
-    - Add highlightStrength/selectStrength renderer params
-
-## [v2.2.3] - 2021-08-25
-
-- Add ``invertCantorPairing`` helper function
-- Add ``Mesh`` processing helper ``.smoothEdges``
-- Smooth border of molecular-surface with ``includeParent`` enabled
-- Hide ``includeParent`` option from gaussian-surface visuals (not particularly useful)
-- Improved ``StructureElement.Loci.size`` performance (for marking large cellpack models)
-- Fix new ``TransformData`` issues (camera/bounding helper not showing up)
-- Improve marking performance (avoid superfluous calls to ``StructureElement.Loci.isWholeStructure``)
-
-## [v2.2.2] - 2021-08-11
-
-- Fix ``TransformData`` issues [#133](https://github.com/molstar/molstar/issues/133)
-- Fix ``mol-script`` query compiler const expression recognition.
-
-## [v2.2.1] - 2021-08-02
-
-- Add surrounding atoms (5 Angstrom) structure selection query
-- [Breaking] Add maxDistance prop to ``IndexPairBonds``
-- Fix coordinateSystem not handled in ``Structure.asParent``
-- Add ``dynamicBonds`` to ``Structure`` props (force re-calc on model change)
-    - Expose as optional param in root structure transform helper
-- Add overpaint support to geometry exporters
-- ``InputObserver`` improvements
-  - normalize wheel speed across browsers/platforms
-  - support Safari gestures (used by ``TrackballControls``)
-  - ``PinchInput.fractionDelta`` and use it in ``TrackballControls``
-
-## [v2.2.0] - 2021-07-31
-
-- Add ``tubularHelices`` parameter to Cartoon representation
-- Add ``SdfFormat`` and update SDF parser to be able to parse data headers according to spec (hopefully :)) #230
-- Fix mononucleotides detected as polymer components (#229)
-- Set default outline scale back to 1
-- Improved DCD reader cell angle handling (interpret near 0 angles as 90 deg)
-- Handle more residue/atom names commonly used in force-fields
-- Add USDZ support to ``geo-export`` extension.
-- Fix ``includeParent`` support for multi-instance bond visuals.
-- Add ``operator`` Loci granularity, selecting everything with the same operator name.
-- Prefer ``_label_seq_id`` fields in secondary structure assignment.
-- Support new EMDB API (https://www.ebi.ac.uk/emdb/api/entry/map/[EMBD-ID]) for EM volume contour levels.
-- ``Canvas3D`` tweaks:
-    - Update ``forceDraw`` logic.
-    - Ensure the scene is re-rendered when viewport size changes.
-    - Support ``noDraw`` mode in ``PluginAnimationLoop``.
-
-## [v2.1.0] - 2021-07-05
-
-- Add parameter for to display aromatic bonds as dashes next to solid cylinder/line.
-- Add backbone representation
-- Fix outline in orthographic mode and set default scale to 2.
-
-## [v2.0.7] - 2021-06-23
-
-- Add ability to specify ``volumeIndex`` in ``Viewer.loadVolumeFromUrl`` to better support Volume Server inputs.
-- Support in-place reordering for trajectory ``Frame.x/y/z`` arrays for better memory efficiency.
-- Fixed text CIF encoder edge cases (most notably single whitespace not being escaped).
-
-## [v2.0.6] - 2021-06-01
-
-- Add glTF (GLB) and STL support to ``geo-export`` extension.
-- Protein crosslink improvements
-    - Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
-    - Added NOS-bridges query & improved disulfide-bridges query
-- Fix #178: ``IndexPairBonds`` for non-single residue structures (bug due to atom reordering).
-- Add volumetric color smoothing for MolecularSurface and GaussianSurface representations (#173)
-- Fix nested 3d grid lookup that caused results being overwritten in non-covalent interactions computation.
-- Basic implementation of ``BestDatabaseSequenceMapping`` (parse from CIF, color theme, superposition).
-- Add atom id ranges support to Selection UI.
-
-## [v2.0.5] - 2021-04-26
-
-- Ability to pass ``Canvas3DContext`` to ``PluginContext.fromCanvas``.
-- Relative frame support for ``Canvas3D`` viewport.
-- Fix bug in screenshot copy UI.
-- Add ability to select residues from a list of identifiers to the Selection UI.
-- Fix SSAO bugs when used with ``Canvas3D`` viewport.
-- Support for  full pausing (no draw) rendering: ``Canvas3D.pause(true)``.
-- Add ``MeshBuilder.addMesh``.
-- Add ``Torus`` primitive.
-- Lazy volume loading support.
-- [Breaking] ``Viewer.loadVolumeFromUrl`` signature change.
-    - ``loadVolumeFromUrl(url, format, isBinary, isovalues, entryId)`` => ``loadVolumeFromUrl({ url, format, isBinary }, isovalues, { entryId, isLazy })``
-- Add ``TextureMesh`` support to ``geo-export`` extension.
-
-## [v2.0.4] - 2021-04-20
-
-- [WIP] Mesh export extension
-- ``Structure.eachAtomicHierarchyElement`` (#161)
-- Fixed reading multi-line values in SDF format
-- Fixed Measurements UI labels (#166)
-
-## [v2.0.3] - 2021-04-09
-
-- Add support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
-- [Breaking] The ``zip`` function is now asynchronous and expects a ``RuntimeContext``. Also added ``Zip()`` returning a ``Task``.
-- [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.
-
-## [v2.0.2] - 2021-03-29
-
-- Add ``Canvas3D.getRenderObjects``.
-- [WIP] Animate state interpolating, including model trajectories
-- Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
-- Fix VolumeFromDensityServerCif transform label
-
-## [v2.0.1] - 2021-03-23
-
-- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
-
-## [v2.0.0] - 2021-03-23
-
-Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.

package/lib/commonjs/mol-repr/structure/visual/util/color.d.ts

@@ -1,24 +0,0 @@
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { MeshValues } from '../../../../mol-gl/renderable/mesh';
-import { TextureMeshValues } from '../../../../mol-gl/renderable/texture-mesh';
-import { WebGLContext } from '../../../../mol-gl/webgl/context';
-import { Texture } from '../../../../mol-gl/webgl/texture';
-import { Theme } from '../../../../mol-theme/theme';
-import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-export declare const ColorSmoothingParams: {
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
-        resolutionFactor: number;
-        sampleStride: number;
-    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
-};
-export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
-export declare function getColorSmoothingProps(props: PD.Values<ColorSmoothingParams>, theme: Theme, resolution?: number): {
-    resolution: number;
-    stride: number;
-} | undefined;
-export declare function applyMeshColorSmoothing(values: MeshValues, resolution: number, stride: number, webgl?: WebGLContext, colorTexture?: Texture): void;
-export declare function applyTextureMeshColorSmoothing(values: TextureMeshValues, resolution: number, stride: number, webgl: WebGLContext, colorTexture?: Texture): void;

package/lib/commonjs/mol-repr/structure/visual/util/color.js

@@ -1,100 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.applyTextureMeshColorSmoothing = exports.applyMeshColorSmoothing = exports.getColorSmoothingProps = exports.ColorSmoothingParams = void 0;
-var color_smoothing_1 = require("../../../../mol-geo/geometry/mesh/color-smoothing");
-var color_smoothing_2 = require("../../../../mol-geo/geometry/texture-mesh/color-smoothing");
-var interpolate_1 = require("../../../../mol-math/interpolate");
-var mol_util_1 = require("../../../../mol-util");
-var param_definition_1 = require("../../../../mol-util/param-definition");
-exports.ColorSmoothingParams = {
-    smoothColors: param_definition_1.ParamDefinition.MappedStatic('auto', {
-        auto: param_definition_1.ParamDefinition.Group({}),
-        on: param_definition_1.ParamDefinition.Group({
-            resolutionFactor: param_definition_1.ParamDefinition.Numeric(2, { min: 0.5, max: 6, step: 0.1 }),
-            sampleStride: param_definition_1.ParamDefinition.Numeric(3, { min: 1, max: 12, step: 1 }),
-        }),
-        off: param_definition_1.ParamDefinition.Group({})
-    }),
-};
-function getColorSmoothingProps(props, theme, resolution) {
-    if ((props.smoothColors.name === 'on' || (props.smoothColors.name === 'auto' && theme.color.preferSmoothing)) && resolution && resolution < 3) {
-        var stride = 3;
-        if (props.smoothColors.name === 'on') {
-            resolution *= props.smoothColors.params.resolutionFactor;
-            stride = props.smoothColors.params.sampleStride;
-        }
-        else {
-            // https://graphtoy.com/?f1(x,t)=(2-smoothstep(0,1.1,x))*x&coords=0.7,0.6,1.8
-            resolution *= 2 - (0, interpolate_1.smoothstep)(0, 1.1, resolution);
-            resolution = Math.max(0.5, resolution);
-            if (resolution > 1.2)
-                stride = 2;
-        }
-        return { resolution: resolution, stride: stride };
-    }
-    ;
-}
-exports.getColorSmoothingProps = getColorSmoothingProps;
-function isSupportedColorType(x) {
-    return x === 'group' || x === 'groupInstance';
-}
-function applyMeshColorSmoothing(values, resolution, stride, webgl, colorTexture) {
-    if (!isSupportedColorType(values.dColorType.ref.value))
-        return;
-    var smoothingData = (0, color_smoothing_1.calcMeshColorSmoothing)({
-        vertexCount: values.uVertexCount.ref.value,
-        instanceCount: values.uInstanceCount.ref.value,
-        groupCount: values.uGroupCount.ref.value,
-        transformBuffer: values.aTransform.ref.value,
-        instanceBuffer: values.aInstance.ref.value,
-        positionBuffer: values.aPosition.ref.value,
-        groupBuffer: values.aGroup.ref.value,
-        colorData: values.tColor.ref.value,
-        colorType: values.dColorType.ref.value,
-        boundingSphere: values.boundingSphere.ref.value,
-        invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
-    }, resolution, stride, webgl, colorTexture);
-    if (smoothingData.kind === 'volume') {
-        mol_util_1.ValueCell.updateIfChanged(values.dColorType, smoothingData.type);
-        mol_util_1.ValueCell.update(values.tColorGrid, smoothingData.texture);
-        mol_util_1.ValueCell.update(values.uColorTexDim, smoothingData.gridTexDim);
-        mol_util_1.ValueCell.update(values.uColorGridDim, smoothingData.gridDim);
-        mol_util_1.ValueCell.update(values.uColorGridTransform, smoothingData.gridTransform);
-    }
-    else if (smoothingData.kind === 'vertex') {
-        mol_util_1.ValueCell.updateIfChanged(values.dColorType, smoothingData.type);
-        mol_util_1.ValueCell.update(values.tColor, smoothingData.texture);
-        mol_util_1.ValueCell.update(values.uColorTexDim, smoothingData.texDim);
-    }
-}
-exports.applyMeshColorSmoothing = applyMeshColorSmoothing;
-function applyTextureMeshColorSmoothing(values, resolution, stride, webgl, colorTexture) {
-    if (!isSupportedColorType(values.dColorType.ref.value))
-        return;
-    stride *= 3; // triple because TextureMesh is never indexed (no elements buffer)
-    var smoothingData = (0, color_smoothing_2.calcTextureMeshColorSmoothing)({
-        vertexCount: values.uVertexCount.ref.value,
-        instanceCount: values.uInstanceCount.ref.value,
-        groupCount: values.uGroupCount.ref.value,
-        transformBuffer: values.aTransform.ref.value,
-        instanceBuffer: values.aInstance.ref.value,
-        positionTexture: values.tPosition.ref.value,
-        groupTexture: values.tGroup.ref.value,
-        colorData: values.tColor.ref.value,
-        colorType: values.dColorType.ref.value,
-        boundingSphere: values.boundingSphere.ref.value,
-        invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
-    }, resolution, stride, webgl, colorTexture);
-    mol_util_1.ValueCell.updateIfChanged(values.dColorType, smoothingData.type);
-    mol_util_1.ValueCell.update(values.tColorGrid, smoothingData.texture);
-    mol_util_1.ValueCell.update(values.uColorTexDim, smoothingData.gridTexDim);
-    mol_util_1.ValueCell.update(values.uColorGridDim, smoothingData.gridDim);
-    mol_util_1.ValueCell.update(values.uColorGridTransform, smoothingData.gridTransform);
-}
-exports.applyTextureMeshColorSmoothing = applyTextureMeshColorSmoothing;
-//# sourceMappingURL=color.js.map

package/lib/commonjs/mol-repr/structure/visual/util/color.js.map

@@ -1 +0,0 @@
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package/lib/mol-gl/_spec/shader.spec.js

@@ -1,2 +0,0 @@
-"use strict";
-//# sourceMappingURL=shader.spec.js.map

package/lib/mol-gl/_spec/shader.spec.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"shader.spec.js","sourceRoot":"","sources":["../../../src/mol-gl/_spec/shader.spec.ts"],"names":[],"mappings":""}

package/lib/mol-repr/structure/visual/orientation-axes-mesh.d.ts

@@ -1,35 +0,0 @@
-/**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { UnitsVisual } from '../units-visual';
-import { VisualContext } from '../../visual';
-import { Unit, Structure } from '../../../mol-model/structure';
-import { Theme } from '../../../mol-theme/theme';
-import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
-export declare const OrientationAxesMeshParams: {
-    sizeFactor: PD.Numeric;
-    axesScale: PD.Numeric;
-    radialSegments: PD.Numeric;
-    detail: PD.Numeric;
-    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
-    includeParent: PD.BooleanParam;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
-    ignoreLight: PD.BooleanParam;
-    xrayShaded: PD.BooleanParam;
-    alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
-};
-export declare type OrientationAxesMeshParams = typeof OrientationAxesMeshParams;
-export declare function OrientationAxesMeshVisual(materialId: number): UnitsVisual<OrientationAxesMeshParams>;
-export interface OrientationAxesMeshProps {
-    detail: number;
-    radialSegments: number;
-    sizeFactor: number;
-    axesScale: number;
-}
-export declare function createOrientationAxesMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: OrientationAxesMeshProps, mesh?: Mesh): Mesh;

package/lib/mol-repr/structure/visual/orientation-axes-mesh.js

@@ -1,43 +0,0 @@
-/**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { __assign } from "tslib";
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { UnitsMeshParams, UnitsMeshVisual } from '../units-visual';
-import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
-import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
-import { addAxes } from '../../../mol-geo/geometry/mesh/builder/axes';
-import { Sphere3D } from '../../../mol-math/geometry';
-import { BaseGeometry } from '../../../mol-geo/geometry/base';
-import { eachUnit, getUnitLoci, isUnitApplicable, UnitIterator } from './util/orientation';
-export var OrientationAxesMeshParams = __assign(__assign({}, UnitsMeshParams), { sizeFactor: PD.Numeric(1, { min: 0, max: 2, step: 0.1 }), axesScale: PD.Numeric(1, { min: 0, max: 20, step: 0.1 }), radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo) });
-export function OrientationAxesMeshVisual(materialId) {
-    return UnitsMeshVisual({
-        defaultProps: PD.getDefaultValues(OrientationAxesMeshParams),
-        createGeometry: createOrientationAxesMesh,
-        createLocationIterator: UnitIterator,
-        getLoci: getUnitLoci,
-        eachLocation: eachUnit,
-        setUpdateState: function (state, newProps, currentProps) {
-            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
-                newProps.detail !== currentProps.detail);
-        }
-    }, materialId);
-}
-export function createOrientationAxesMesh(ctx, unit, structure, theme, props, mesh) {
-    if (!isUnitApplicable(unit))
-        return Mesh.createEmpty(mesh);
-    var detail = props.detail, sizeFactor = props.sizeFactor, radialSegments = props.radialSegments, axesScale = props.axesScale;
-    var vertexCount = 256;
-    var builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
-    var axes = unit.principalAxes.momentsAxes;
-    builderState.currentGroup = 0;
-    addAxes(builderState, axes, axesScale, detail, radialSegments);
-    var m = MeshBuilder.getMesh(builderState);
-    var sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
-    return m;
-}
-//# sourceMappingURL=orientation-axes-mesh.js.map

package/lib/mol-repr/structure/visual/orientation-axes-mesh.js.map

@@ -1 +0,0 @@
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package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh copy.d.ts

@@ -1,31 +0,0 @@
-/**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { UnitsVisual } from '../../../mol-repr/structure/units-visual';
-import { VisualContext } from '../../../mol-repr/visual';
-import { Unit, Structure } from '../../../mol-model/structure';
-import { Theme } from '../../../mol-theme/theme';
-import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
-export declare const OrientationEllipsoidMeshParams: {
-    sizeFactor: PD.Numeric;
-    detail: PD.Numeric;
-    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
-    includeParent: PD.BooleanParam;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
-    ignoreLight: PD.BooleanParam;
-    xrayShaded: PD.BooleanParam;
-    alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
-};
-export declare type OrientationEllipsoidMeshParams = typeof OrientationEllipsoidMeshParams;
-export declare function OrientationEllipsoidMeshVisual(materialId: number): UnitsVisual<OrientationEllipsoidMeshParams>;
-export interface OrientationEllipsoidMeshProps {
-    detail: number;
-    sizeFactor: number;
-}
-export declare function createOrientationEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: OrientationEllipsoidMeshProps, mesh?: Mesh): Mesh;

package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh copy.js

@@ -1,48 +0,0 @@
-/**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { __assign } from "tslib";
-import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { UnitsMeshParams, UnitsMeshVisual } from '../../../mol-repr/structure/units-visual';
-import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
-import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
-import { Vec3 } from '../../../mol-math/linear-algebra';
-import { addEllipsoid } from '../../../mol-geo/geometry/mesh/builder/ellipsoid';
-import { Axes3D, Sphere3D } from '../../../mol-math/geometry';
-import { BaseGeometry } from '../../../mol-geo/geometry/base';
-import { eachUnit, getUnitLoci, isUnitApplicable, UnitIterator } from './util/orientation';
-export var OrientationEllipsoidMeshParams = __assign(__assign({}, UnitsMeshParams), { sizeFactor: PD.Numeric(1, { min: 0, max: 2, step: 0.1 }), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo) });
-export function OrientationEllipsoidMeshVisual(materialId) {
-    return UnitsMeshVisual({
-        defaultProps: PD.getDefaultValues(OrientationEllipsoidMeshParams),
-        createGeometry: createOrientationEllipsoidMesh,
-        createLocationIterator: UnitIterator,
-        getLoci: getUnitLoci,
-        eachLocation: eachUnit,
-        setUpdateState: function (state, newProps, currentProps) {
-            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
-                newProps.detail !== currentProps.detail);
-        }
-    }, materialId);
-}
-export function createOrientationEllipsoidMesh(ctx, unit, structure, theme, props, mesh) {
-    if (!isUnitApplicable(unit))
-        return Mesh.createEmpty(mesh);
-    var detail = props.detail, sizeFactor = props.sizeFactor;
-    var vertexCount = 256;
-    var builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
-    var axes = unit.principalAxes.boxAxes;
-    var origin = axes.origin, dirA = axes.dirA, dirB = axes.dirB;
-    var size = Axes3D.size(Vec3(), axes);
-    Vec3.scale(size, size, sizeFactor / 2);
-    var radiusScale = Vec3.create(size[2], size[1], size[0]);
-    builderState.currentGroup = 0;
-    addEllipsoid(builderState, origin, dirA, dirB, radiusScale, detail + 1);
-    var m = MeshBuilder.getMesh(builderState);
-    var sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
-    m.setBoundingSphere(sphere);
-    return m;
-}
-//# sourceMappingURL=orientation-ellipsoid-mesh%20copy.js.map

package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh copy.js.map

@@ -1 +0,0 @@
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package/lib/mol-repr/structure/visual/util/color.d.ts

@@ -1,24 +0,0 @@
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { MeshValues } from '../../../../mol-gl/renderable/mesh';
-import { TextureMeshValues } from '../../../../mol-gl/renderable/texture-mesh';
-import { WebGLContext } from '../../../../mol-gl/webgl/context';
-import { Texture } from '../../../../mol-gl/webgl/texture';
-import { Theme } from '../../../../mol-theme/theme';
-import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-export declare const ColorSmoothingParams: {
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
-        resolutionFactor: number;
-        sampleStride: number;
-    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
-};
-export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
-export declare function getColorSmoothingProps(props: PD.Values<ColorSmoothingParams>, theme: Theme, resolution?: number): {
-    resolution: number;
-    stride: number;
-} | undefined;
-export declare function applyMeshColorSmoothing(values: MeshValues, resolution: number, stride: number, webgl?: WebGLContext, colorTexture?: Texture): void;
-export declare function applyTextureMeshColorSmoothing(values: TextureMeshValues, resolution: number, stride: number, webgl: WebGLContext, colorTexture?: Texture): void;