Renamed mol-view mol-canvas3d, moved parameters.ts to mol-util, added mol-plugin

README.md

@@ -17,12 +17,14 @@ The core of Mol* currently consists of these modules:
 - `mol-math` Math related (loosely) algorithms and data structures.
 - `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.
 - `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
-- `mol-model-props` Common "custom properties"
+- `mol-model-props` Common "custom properties".
 - `mol-script` A scriting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
 - `mol-geo` Creating molecular geometries.
-- `mol-gl` A wrapper around WebGL. Uses `mol-geo` to generate geometries.
+- `mol-gl` A lightweight wrapper around WebGL.
+- `mol-canvas3d` A low level 3d view component. Uses `mol-geo` to generate geometries.
+- `mol-state` State representation tree with state saving and automatic updates.
 - `mol-app` Components for builduing UIs.
-- `mol-view` A reference viewer implementation.
+- `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-view3d`.
 - `mol-util` Useful things that do not fit elsewhere.
 
 Moreover, the project contains the imlementation of `servers`, including

package.json

@@ -61,8 +61,9 @@
       "mol-script($|/.*)": "<rootDir>/src/mol-script$1",
       "mol-task($|/.*)": "<rootDir>/src/mol-task$1",
       "mol-state($|/.*)": "<rootDir>/src/mol-state$1",
+      "mol-plugin($|/.*)": "<rootDir>/src/mol-plugin$1",
       "mol-util($|/.*)": "<rootDir>/src/mol-util$1",
-      "mol-view($|/.*)": "<rootDir>/src/mol-view$1"
+      "mol-canvas3d($|/.*)": "<rootDir>/src/mol-canvas3d$1"
     },
     "testRegex": "\\.spec\\.ts$"
   },

src/apps/canvas/app.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import Viewer from 'mol-view/viewer';
+import Viewer from 'mol-canvas3d/viewer';
 import { getCifFromUrl, getModelsFromMmcif, getCifFromFile, getCcp4FromUrl, getVolumeFromCcp4, getCcp4FromFile, getVolumeFromVolcif } from './util';
 import { StructureView } from './structure-view';
 import { BehaviorSubject } from 'rxjs';

src/apps/canvas/assembly-symmetry.ts

@@ -12,7 +12,7 @@ import { Tensor } from 'mol-math/linear-algebra';
 import { addSphere } from 'mol-geo/geometry/mesh/builder/sphere';
 import { addCylinder } from 'mol-geo/geometry/mesh/builder/cylinder';
 import { Shape } from 'mol-model/shape';
-import { ColorTheme } from 'mol-view/theme/color';
+import { ColorTheme } from 'mol-canvas3d/theme/color';
 import { Location } from 'mol-model/location';
 import { StructureElement, Unit, StructureProperties } from 'mol-model/structure';
 

src/apps/canvas/component/representation.tsx

@@ -5,13 +5,13 @@
  */
 
 import * as React from 'react'
-import Viewer from 'mol-view/viewer';
+import Viewer from 'mol-canvas3d/viewer';
 import { App } from '../app';
-import { Params } from 'mol-view/parameter';
+import { Params } from 'mol-util/parameter';
 import { Representation } from 'mol-geo/representation';
 import { ParametersComponent } from 'mol-app/component/parameters';
 import { Progress } from 'mol-task';
-import { ColorTheme } from 'mol-view/theme/color';
+import { ColorTheme } from 'mol-canvas3d/theme/color';
 import { getColorThemeProps } from 'mol-geo/geometry/color-data';
 import { ColorThemeComponent } from 'mol-app/component/color-theme';
 

src/apps/canvas/component/viewport.tsx

@@ -8,7 +8,7 @@ import * as React from 'react'
 import { App } from '../app';
 import { MarkerAction } from 'mol-geo/geometry/marker-data';
 import { EmptyLoci, Loci, areLociEqual } from 'mol-model/loci';
-import { labelFirst } from 'mol-view/label';
+import { labelFirst } from 'mol-canvas3d/label';
 
 interface ViewportProps {
     app: App

src/apps/canvas/structure-view.ts

@@ -11,7 +11,7 @@ import { getStructureFromModel } from './util';
 import { AssemblySymmetry } from 'mol-model-props/rcsb/symmetry';
 import { ShapeRepresentation, ShapeProps } from 'mol-geo/representation/shape';
 import { getAxesShape } from './assembly-symmetry';
-import Viewer from 'mol-view/viewer';
+import Viewer from 'mol-canvas3d/viewer';
 import { CarbohydrateRepresentation } from 'mol-geo/representation/structure/representation/carbohydrate';
 // import { MeshBuilder } from 'mol-geo/mesh/mesh-builder';
 // import { addSphere } from 'mol-geo/mesh/builder/sphere';

src/apps/canvas/volume-view.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import Viewer from 'mol-view/viewer';
+import Viewer from 'mol-canvas3d/viewer';
 import { BehaviorSubject } from 'rxjs';
 import { App } from './app';
 import { Progress } from 'mol-task';

src/mol-app/component/color-theme.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { ColorTheme } from 'mol-view/theme/color';
+import { ColorTheme } from 'mol-canvas3d/theme/color';
 import { Color } from 'mol-util/color';
 
 export interface ColorThemeComponentProps {

src/mol-app/component/parameter/boolean.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { BooleanParam } from 'mol-view/parameter';
+import { BooleanParam } from 'mol-util/parameter';
 
 export interface BooleanParamComponentProps {
     param: BooleanParam

src/mol-app/component/parameter/multi-select.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { MultiSelectParam } from 'mol-view/parameter';
+import { MultiSelectParam } from 'mol-util/parameter';
 
 export interface MultiSelectParamComponentProps<T extends string> {
     param: MultiSelectParam<T>

src/mol-app/component/parameter/number.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { NumberParam } from 'mol-view/parameter';
+import { NumberParam } from 'mol-util/parameter';
 
 export interface NumberParamComponentProps {
     param: NumberParam

src/mol-app/component/parameter/range.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { RangeParam } from 'mol-view/parameter';
+import { RangeParam } from 'mol-util/parameter';
 
 export interface RangeParamComponentProps {
     param: RangeParam

src/mol-app/component/parameter/select.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { SelectParam } from 'mol-view/parameter';
+import { SelectParam } from 'mol-util/parameter';
 
 export interface SelectParamComponentProps<T extends string> {
     param: SelectParam<T>

src/mol-app/component/parameter/text.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { TextParam } from 'mol-view/parameter';
+import { TextParam } from 'mol-util/parameter';
 
 export interface TextParamComponentProps {
     param: TextParam

src/mol-app/component/parameters.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react'
-import { Param, Params } from 'mol-view/parameter';
+import { Param, Params } from 'mol-util/parameter';
 import { BooleanParamComponent } from './parameter/boolean';
 import { NumberParamComponent } from './parameter/number';
 import { RangeParamComponent } from './parameter/range';

src/mol-canvas3d/util.ts

@@ -0,0 +1,18 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+export function resizeCanvas (canvas: HTMLCanvasElement, container: Element) {
+    let w = window.innerWidth
+    let h = window.innerHeight
+    if (container !== document.body) {
+        let bounds = container.getBoundingClientRect()
+        w = bounds.right - bounds.left
+        h = bounds.bottom - bounds.top
+    }
+    canvas.width = window.devicePixelRatio * w
+    canvas.height = window.devicePixelRatio * h
+    Object.assign(canvas.style, { width: `${w}px`, height: `${h}px` })
+}

src/mol-geo/geometry/color-data.ts

@@ -10,7 +10,7 @@ import { Color } from 'mol-util/color';
 import { Vec2, Vec3 } from 'mol-math/linear-algebra';
 import { LocationIterator } from '../util/location-iterator';
 import { NullLocation } from 'mol-model/location';
-import { LocationColor, ColorThemeProps, ColorTheme, ColorThemeName } from 'mol-view/theme/color';
+import { LocationColor, ColorThemeProps, ColorTheme, ColorThemeName } from 'mol-canvas3d/theme/color';
 import { RuntimeContext } from 'mol-task';
 import { getGranularity } from './geometry';
 import { Structure } from 'mol-model/structure';

src/mol-geo/geometry/direct-volume/direct-volume.ts

@@ -7,7 +7,7 @@
 import { RuntimeContext } from 'mol-task'
 import { ValueCell } from 'mol-util'
 import { Sphere3D, Box3D } from 'mol-math/geometry'
-import { paramDefaultValues, RangeParam, SelectParam, TextParam } from 'mol-view/parameter';
+import { paramDefaultValues, RangeParam, SelectParam, TextParam } from 'mol-util/parameter';
 import { DirectVolumeValues } from 'mol-gl/renderable/direct-volume';
 import { Vec3, Mat4 } from 'mol-math/linear-algebra';
 import { Box } from '../../primitive/box';

src/mol-geo/geometry/direct-volume/transfer-function.ts

@@ -18,7 +18,7 @@ export function getControlPointsFromString(s: string): ControlPoint[] {
         return { x: parseFloat(ps[0]), alpha: parseFloat(ps[1]) }
     })
 }
-// TODO move core function to mol-view/color
+// TODO move core function to mol-canvas3d/color
 export function createTransferFunctionTexture(controlPoints: ControlPoint[], texture?: ValueCell<TextureImage<Uint8Array>>): ValueCell<TextureImage<Uint8Array>> {
     const cp = [
         { x: 0, alpha: 0 },

src/mol-geo/geometry/geometry.ts

@@ -10,12 +10,12 @@ import { RenderableState } from 'mol-gl/renderable';
 import { ValueCell } from 'mol-util';
 import { BaseValues } from 'mol-gl/renderable/schema';
 import { Color } from 'mol-util/color';
-import { ColorThemeOptions, ColorThemeName } from 'mol-view/theme/color';
+import { ColorThemeOptions, ColorThemeName } from 'mol-canvas3d/theme/color';
 import { LocationIterator } from '../util/location-iterator';
 import { ColorType } from './color-data';
 import { SizeType } from './size-data';
 import { Lines } from './lines/lines';
-import { paramDefaultValues, RangeParam, BooleanParam, SelectParam, ColorParam, StructureParam, ValueParam } from 'mol-view/parameter'
+import { paramDefaultValues, RangeParam, BooleanParam, SelectParam, ColorParam, StructureParam, ValueParam } from 'mol-util/parameter'
 import { Structure } from 'mol-model/structure';
 import { DirectVolume } from './direct-volume/direct-volume';
 import { Context } from 'mol-gl/webgl/context';

src/mol-geo/geometry/lines/lines.ts

@@ -14,11 +14,11 @@ import { createMarkers } from '../marker-data';
 import { createSizes } from '../size-data';
 import { TransformData } from '../transform-data';
 import { LocationIterator } from '../../util/location-iterator';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { LinesValues } from 'mol-gl/renderable/lines';
 import { Mesh } from '../mesh/mesh';
 import { LinesBuilder } from './lines-builder';
-import { BooleanParam, SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { BooleanParam, SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 /** Wide line */
 export interface Lines {

src/mol-geo/geometry/mesh/mesh.ts

@@ -16,7 +16,7 @@ import { TransformData } from '../transform-data';
 import { LocationIterator } from '../../util/location-iterator';
 import { createColors } from '../color-data';
 import { ChunkedArray } from 'mol-data/util';
-import { BooleanParam, paramDefaultValues } from 'mol-view/parameter';
+import { BooleanParam, paramDefaultValues } from 'mol-util/parameter';
 
 export interface Mesh {
     readonly kind: 'mesh',

src/mol-geo/geometry/points/points.ts

@@ -15,8 +15,8 @@ import { createMarkers } from '../marker-data';
 import { createSizes } from '../size-data';
 import { TransformData } from '../transform-data';
 import { LocationIterator } from '../../util/location-iterator';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
-import { BooleanParam, NumberParam, SelectParam, paramDefaultValues } from 'mol-view/parameter';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
+import { BooleanParam, NumberParam, SelectParam, paramDefaultValues } from 'mol-util/parameter';
 
 /** Point cloud */
 export interface Points {

src/mol-geo/geometry/size-data.ts

@@ -10,7 +10,7 @@ import { TextureImage, createTextureImage } from 'mol-gl/renderable/util';
 import { LocationIterator } from '../util/location-iterator';
 import { Location, NullLocation } from 'mol-model/location';
 import { RuntimeContext } from 'mol-task';
-import { SizeThemeProps, SizeTheme, SizeThemeName } from 'mol-view/theme/size';
+import { SizeThemeProps, SizeTheme, SizeThemeName } from 'mol-canvas3d/theme/size';
 import { getGranularity } from './geometry';
 import { Structure } from 'mol-model/structure';
 

src/mol-geo/representation/index.ts

@@ -9,7 +9,7 @@ import { RenderObject } from 'mol-gl/render-object'
 import { PickingId } from '../geometry/picking';
 import { Loci } from 'mol-model/loci';
 import { MarkerAction } from '../geometry/marker-data';
-import { Params } from 'mol-view/parameter';
+import { Params } from 'mol-util/parameter';
 
 export interface RepresentationProps {}
 

src/mol-geo/representation/shape/index.ts

@@ -11,14 +11,14 @@ import { PickingId } from '../../geometry/picking';
 import { Loci, EmptyLoci, isEveryLoci } from 'mol-model/loci';
 import { MarkerAction, applyMarkerAction } from '../../geometry/marker-data';
 import { ValueCell } from 'mol-util';
-import { ColorThemeName, ColorThemeOptions } from 'mol-view/theme/color';
+import { ColorThemeName, ColorThemeOptions } from 'mol-canvas3d/theme/color';
 import { Shape } from 'mol-model/shape';
 import { LocationIterator } from '../../util/location-iterator';
 import { OrderedSet, Interval } from 'mol-data/int';
 import { createIdentityTransform } from '../../geometry/transform-data';
 import { createRenderableState } from '../../geometry/geometry';
 import { Mesh } from '../../geometry/mesh/mesh';
-import { paramDefaultValues, SelectParam } from 'mol-view/parameter';
+import { paramDefaultValues, SelectParam } from 'mol-util/parameter';
 
 export interface ShapeRepresentation<P extends RepresentationProps = {}> extends Representation<Shape, P> { }
 

src/mol-geo/representation/structure/complex-visual.ts

@@ -19,7 +19,7 @@ import { MarkerAction, applyMarkerAction } from '../../geometry/marker-data';
 import { Interval } from 'mol-data/int';
 import { updateRenderableState, Geometry } from '../../geometry/geometry';
 import { createColors } from '../../geometry/color-data';
-import { MultiSelectParam, paramDefaultValues } from 'mol-view/parameter';
+import { MultiSelectParam, paramDefaultValues } from 'mol-util/parameter';
 import { RenderableValues } from 'mol-gl/renderable/schema';
 import { createSizes } from 'mol-geo/geometry/size-data';
 

src/mol-geo/representation/structure/index.ts

@@ -6,14 +6,14 @@
  */
 
 import { Structure } from 'mol-model/structure';
-import { ColorThemeName, ColorThemeOptions } from 'mol-view/theme/color';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { ColorThemeName, ColorThemeOptions } from 'mol-canvas3d/theme/color';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { Representation, RepresentationProps } from '..';
 import { Geometry } from '../../geometry/geometry';
 import { Mesh } from '../../geometry/mesh/mesh';
 import { Points } from '../../geometry/points/points';
 import { Lines } from '../../geometry/lines/lines';
-import { SelectParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, paramDefaultValues } from 'mol-util/parameter';
 import { DirectVolume } from '../../geometry/direct-volume/direct-volume';
 
 export interface StructureRepresentation<P extends RepresentationProps = {}> extends Representation<Structure, P> { }

src/mol-geo/representation/structure/representation/backbone.ts

@@ -12,7 +12,7 @@ import { Loci } from 'mol-model/loci';
 import { MarkerAction } from '../../../geometry/marker-data';
 import { PolymerBackboneVisual, PolymerBackboneParams } from '../visual/polymer-backbone-cylinder';
 import { getQualityProps } from '../../util';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 
 export const BackboneParams = {
     ...PolymerBackboneParams

src/mol-geo/representation/structure/representation/ball-and-stick.ts

@@ -13,9 +13,9 @@ import { Task } from 'mol-task';
 import { Loci, isEmptyLoci } from 'mol-model/loci';
 import { MarkerAction } from '../../../geometry/marker-data';
 import { InterUnitLinkVisual } from '../visual/inter-unit-link-cylinder';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { getQualityProps } from '../../util';
-import { paramDefaultValues, SelectParam, NumberParam, MultiSelectParam } from 'mol-view/parameter';
+import { paramDefaultValues, SelectParam, NumberParam, MultiSelectParam } from 'mol-util/parameter';
 import { UnitKind, UnitKindOptions } from '../visual/util/common';
 
 export const BallAndStickParams = {

src/mol-geo/representation/structure/representation/carbohydrate.ts

@@ -12,9 +12,9 @@ import { Loci, isEmptyLoci } from 'mol-model/loci';
 import { MarkerAction } from '../../../geometry/marker-data';
 import { CarbohydrateSymbolVisual, CarbohydrateSymbolParams } from '../visual/carbohydrate-symbol-mesh';
 import { CarbohydrateLinkVisual, CarbohydrateLinkParams } from '../visual/carbohydrate-link-cylinder';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { getQualityProps } from '../../util';
-import { paramDefaultValues, SelectParam, NumberParam } from 'mol-view/parameter';
+import { paramDefaultValues, SelectParam, NumberParam } from 'mol-util/parameter';
 
 export const CarbohydrateParams = {
     ...CarbohydrateSymbolParams,

src/mol-geo/representation/structure/representation/cartoon.ts

@@ -13,9 +13,9 @@ import { MarkerAction } from '../../../geometry/marker-data';
 import { PolymerTraceVisual,  PolymerTraceParams } from '../visual/polymer-trace-mesh';
 import { PolymerGapVisual, PolymerGapParams } from '../visual/polymer-gap-cylinder';
 import { NucleotideBlockVisual, NucleotideBlockParams } from '../visual/nucleotide-block-mesh';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { getQualityProps } from '../../util';
-import { paramDefaultValues, SelectParam, NumberParam } from 'mol-view/parameter';
+import { paramDefaultValues, SelectParam, NumberParam } from 'mol-util/parameter';
 // import { PolymerDirectionVisual, DefaultPolymerDirectionProps } from '../visual/polymer-direction-wedge';
 
 export const CartoonParams = {

src/mol-geo/representation/structure/representation/distance-restraint.ts

@@ -11,9 +11,9 @@ import { Task } from 'mol-task';
 import { Loci } from 'mol-model/loci';
 import { MarkerAction } from '../../../geometry/marker-data';
 import { CrossLinkRestraintVisual, CrossLinkRestraintParams } from '../visual/cross-link-restraint-cylinder';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { getQualityProps } from '../../util';
-import { paramDefaultValues, SelectParam, NumberParam } from 'mol-view/parameter';
+import { paramDefaultValues, SelectParam, NumberParam } from 'mol-util/parameter';
 
 export const DistanceRestraintParams = {
     ...CrossLinkRestraintParams,

src/mol-geo/representation/structure/representation/molecular-surface.ts

@@ -14,9 +14,9 @@ import { PickingId } from '../../../geometry/picking';
 import { Task } from 'mol-task';
 import { GaussianWireframeVisual, GaussianWireframeParams } from '../visual/gaussian-surface-wireframe';
 import { getQualityProps } from '../../util';
-import { paramDefaultValues, MultiSelectParam, SelectParam } from 'mol-view/parameter';
+import { paramDefaultValues, MultiSelectParam, SelectParam } from 'mol-util/parameter';
 import { GaussianDensityVolumeParams, GaussianDensityVolumeVisual } from '../visual/gaussian-density-volume';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 
 const VisualOptions = [['surface', 'Surface'], ['wireframe', 'Wireframe'], ['volume', 'Volume']] as [string, string][]
 

src/mol-geo/representation/structure/representation/point.ts

@@ -11,7 +11,7 @@ import { Structure } from 'mol-model/structure';
 import { MarkerAction } from '../../../geometry/marker-data';
 import { Loci } from 'mol-model/loci';
 import { PickingId } from '../../../geometry/picking';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 
 export const PointParams = {
     ...ElementPointParams,

src/mol-geo/representation/structure/representation/spacefill.ts

@@ -12,7 +12,7 @@ import { PickingId } from '../../../geometry/picking';
 import { MarkerAction } from '../../../geometry/marker-data';
 import { Loci } from 'mol-model/loci';
 import { getQualityProps } from '../../util';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 
 export const SpacefillParams = {
     ...ElementSphereParams

src/mol-geo/representation/structure/units-visual.ts

@@ -22,7 +22,7 @@ import { updateRenderableState, Geometry } from '../../geometry/geometry';
 import { createColors } from '../../geometry/color-data';
 import { createSizes } from '../../geometry/size-data';
 import { Lines } from '../../geometry/lines/lines';
-import { MultiSelectParam, paramDefaultValues } from 'mol-view/parameter';
+import { MultiSelectParam, paramDefaultValues } from 'mol-util/parameter';
 import { DirectVolume } from '../../geometry/direct-volume/direct-volume';
 import { RenderableValues } from 'mol-gl/renderable/schema';
 

src/mol-geo/representation/structure/visual/carbohydrate-link-cylinder.ts

@@ -15,11 +15,11 @@ import { LocationIterator } from '../../../util/location-iterator';
 import { createLinkCylinderMesh, LinkCylinderProps, LinkCylinderParams } from './util/link';
 import { OrderedSet, Interval } from 'mol-data/int';
 import { ComplexMeshVisual } from '../complex-visual';
-import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { LinkType } from 'mol-model/structure/model/types';
 import { BitFlags } from 'mol-util';
 import { UnitsMeshParams } from '../units-visual';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 // TODO create seperate visual
 // for (let i = 0, il = carbohydrates.terminalLinks.length; i < il; ++i) {

src/mol-geo/representation/structure/visual/carbohydrate-symbol-mesh.ts

@@ -16,14 +16,14 @@ import { getSaccharideShape, SaccharideShapes } from 'mol-model/structure/struct
 import { LocationIterator } from '../../../util/location-iterator';
 import { OrderedSet, Interval } from 'mol-data/int';
 import { ComplexMeshVisual, ComplexMeshParams } from '../complex-visual';
-import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { addSphere } from '../../../geometry/mesh/builder/sphere';
 import { Box, PerforatedBox } from '../../../primitive/box';
 import { OctagonalPyramid, PerforatedOctagonalPyramid } from '../../../primitive/pyramid';
 import { Star } from '../../../primitive/star';
 import { Octahedron, PerforatedOctahedron } from '../../../primitive/octahedron';
 import { DiamondPrism, PentagonalPrism, HexagonalPrism } from '../../../primitive/prism';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 const t = Mat4.identity()
 const sVec = Vec3.zero()

src/mol-geo/representation/structure/visual/cross-link-restraint-cylinder.ts

@@ -15,10 +15,10 @@ import { Loci, EmptyLoci } from 'mol-model/loci';
 import { ComplexMeshVisual, ComplexMeshParams } from '../complex-visual';
 import { LocationIterator } from '../../../util/location-iterator';
 import { Interval } from 'mol-data/int';
-import { SizeTheme, SizeThemeOptions, SizeThemeName } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeOptions, SizeThemeName } from 'mol-canvas3d/theme/size';
 import { BitFlags } from 'mol-util';
 import { LinkType } from 'mol-model/structure/model/types';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 async function createCrossLinkRestraintCylinderMesh(ctx: RuntimeContext, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
 

src/mol-geo/representation/structure/visual/element-point.ts

@@ -9,11 +9,11 @@ import { RuntimeContext } from 'mol-task'
 import { UnitsVisual, VisualUpdateState } from '..';
 import { getElementLoci, StructureElementIterator, markElement } from './util/element';
 import { Vec3 } from 'mol-math/linear-algebra';
-import { SizeThemeOptions, SizeThemeName } from 'mol-view/theme/size';
+import { SizeThemeOptions, SizeThemeName } from 'mol-canvas3d/theme/size';
 import { UnitsPointsVisual, UnitsPointsParams } from '../units-visual';
 import { Points } from '../../../geometry/points/points';
 import { PointsBuilder } from '../../../geometry/points/points-builder';
-import { SelectParam, NumberParam, BooleanParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, BooleanParam, paramDefaultValues } from 'mol-util/parameter';
 
 export const ElementPointParams = {
     ...UnitsPointsParams,

src/mol-geo/representation/structure/visual/element-sphere.ts

@@ -8,8 +8,8 @@
 import { UnitsVisual, VisualUpdateState } from '..';
 import { createElementSphereMesh, markElement, getElementLoci, StructureElementIterator } from './util/element';
 import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { NumberParam, paramDefaultValues, SelectParam } from 'mol-view/parameter';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { NumberParam, paramDefaultValues, SelectParam } from 'mol-util/parameter';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 
 export const ElementSphereParams = {
     ...UnitsMeshParams,

src/mol-geo/representation/structure/visual/gaussian-density-point.ts

@@ -13,9 +13,9 @@ import { Vec3 } from 'mol-math/linear-algebra';
 import { UnitsPointsVisual, UnitsPointsParams } from '../units-visual';
 import { Points } from '../../../geometry/points/points';
 import { PointsBuilder } from '../../../geometry/points/points-builder';
-import { SizeThemeOptions, SizeThemeName } from 'mol-view/theme/size';
+import { SizeThemeOptions, SizeThemeName } from 'mol-canvas3d/theme/size';
 import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
-import { paramDefaultValues, SelectParam, NumberParam, BooleanParam } from 'mol-view/parameter';
+import { paramDefaultValues, SelectParam, NumberParam, BooleanParam } from 'mol-util/parameter';
 
 export const GaussianDensityPointParams = {
     ...UnitsPointsParams,

src/mol-geo/representation/structure/visual/gaussian-density-volume.ts

@@ -10,7 +10,7 @@ import { RuntimeContext } from 'mol-task'
 import { UnitsDirectVolumeVisual, UnitsDirectVolumeParams } from '../units-visual';
 import { StructureElementIterator, getElementLoci, markElement } from './util/element';
 import { GaussianDensityProps, GaussianDensityParams, computeUnitGaussianDensityTexture } from 'mol-model/structure/structure/unit/gaussian-density';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 import { DirectVolume } from '../../../geometry/direct-volume/direct-volume';
 
 async function createGaussianDensityVolume(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityProps, directVolume?: DirectVolume): Promise<DirectVolume> {

src/mol-geo/representation/structure/visual/gaussian-surface-mesh.ts

@@ -12,7 +12,7 @@ import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
 import { StructureElementIterator, getElementLoci, markElement } from './util/element';
 import { computeMarchingCubesMesh } from '../../../util/marching-cubes/algorithm';
 import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 
 async function createGaussianSurfaceMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityProps, mesh?: Mesh): Promise<Mesh> {
     const { smoothness } = props

src/mol-geo/representation/structure/visual/gaussian-surface-wireframe.ts

@@ -12,8 +12,8 @@ import { StructureElementIterator, getElementLoci, markElement } from './util/el
 import { computeMarchingCubesLines } from '../../../util/marching-cubes/algorithm';
 import { Lines } from '../../../geometry/lines/lines';
 import { GaussianDensityProps, GaussianDensityParams } from 'mol-model/structure/structure/unit/gaussian-density';
-import { paramDefaultValues, SelectParam, NumberParam, BooleanParam } from 'mol-view/parameter';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { paramDefaultValues, SelectParam, NumberParam, BooleanParam } from 'mol-util/parameter';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 
 async function createGaussianWireframe(ctx: RuntimeContext, unit: Unit, structure: Structure, props: GaussianDensityProps, lines?: Lines): Promise<Lines> {
     const { smoothness } = props

src/mol-geo/representation/structure/visual/inter-unit-link-cylinder.ts

@@ -14,9 +14,9 @@ import { Vec3 } from 'mol-math/linear-algebra';
 import { Loci, EmptyLoci } from 'mol-model/loci';
 import { ComplexMeshVisual, ComplexMeshParams } from '../complex-visual';
 import { Interval } from 'mol-data/int';
-import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { BitFlags } from 'mol-util';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 async function createInterUnitLinkCylinderMesh(ctx: RuntimeContext, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
     const links = structure.links

src/mol-geo/representation/structure/visual/intra-unit-link-cylinder.ts

@@ -15,9 +15,9 @@ import { Vec3 } from 'mol-math/linear-algebra';
 import { Loci, EmptyLoci } from 'mol-model/loci';
 import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
 import { Interval } from 'mol-data/int';
-import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { BitFlags } from 'mol-util';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 async function createIntraUnitLinkCylinderMesh(ctx: RuntimeContext, unit: Unit, structure: Structure, props: LinkCylinderProps, mesh?: Mesh) {
     if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh)

src/mol-geo/representation/structure/visual/nucleotide-block-mesh.ts

@@ -17,7 +17,7 @@ import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
 import { addCylinder } from '../../../geometry/mesh/builder/cylinder';
 import { Box } from '../../../primitive/box';
 import { NucleotideLocationIterator, markNucleotideElement, getNucleotideElementLoci } from './util/nucleotide';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 
 const p1 = Vec3.zero()
 const p2 = Vec3.zero()

src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts

@@ -13,11 +13,11 @@ import { PolymerBackboneIterator } from './util/polymer';
 import { getElementLoci, markElement, StructureElementIterator } from './util/element';
 import { Vec3 } from 'mol-math/linear-algebra';
 import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { SizeTheme, SizeThemeOptions, SizeThemeName } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeOptions, SizeThemeName } from 'mol-canvas3d/theme/size';
 import { CylinderProps } from '../../../primitive/cylinder';
 import { OrderedSet } from 'mol-data/int';
 import { addCylinder } from '../../../geometry/mesh/builder/cylinder';
-import { paramDefaultValues, NumberParam, SelectParam } from 'mol-view/parameter';
+import { paramDefaultValues, NumberParam, SelectParam } from 'mol-util/parameter';
 
 export const PolymerBackboneCylinderParams = {
     sizeTheme: SelectParam<SizeThemeName>('Size Theme', '', 'uniform', SizeThemeOptions),

src/mol-geo/representation/structure/visual/polymer-direction-wedge.ts

@@ -13,9 +13,9 @@ import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment,
 import { Vec3, Mat4 } from 'mol-math/linear-algebra';
 import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
 import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { Wedge } from '../../../primitive/wedge';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 const t = Mat4.identity()
 const sVec = Vec3.zero()

src/mol-geo/representation/structure/visual/polymer-gap-cylinder.ts

@@ -12,11 +12,11 @@ import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
 import { PolymerGapIterator, PolymerGapLocationIterator, markPolymerGapElement, getPolymerGapElementLoci } from './util/polymer';
 import { Vec3 } from 'mol-math/linear-algebra';
 import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { SizeTheme, SizeThemeOptions, SizeThemeName } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeOptions, SizeThemeName } from 'mol-canvas3d/theme/size';
 import { CylinderProps } from '../../../primitive/cylinder';
 import { addSphere } from '../../../geometry/mesh/builder/sphere';
 import { addFixedCountDashedCylinder } from '../../../geometry/mesh/builder/cylinder';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 import { LinkCylinderParams } from './util/link';
 
 const segmentCount = 10

src/mol-geo/representation/structure/visual/polymer-trace-mesh.ts

@@ -12,10 +12,10 @@ import { MeshBuilder } from '../../../geometry/mesh/mesh-builder';
 import { PolymerTraceIterator, createCurveSegmentState, interpolateCurveSegment, PolymerLocationIterator, getPolymerElementLoci, markPolymerElement } from './util/polymer';
 import { SecondaryStructureType, isNucleic } from 'mol-model/structure/model/types';
 import { UnitsMeshVisual, UnitsMeshParams } from '../units-visual';
-import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { addSheet } from '../../../geometry/mesh/builder/sheet';
 import { addTube } from '../../../geometry/mesh/builder/tube';
-import { SelectParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 export const PolymerTraceMeshParams = {
     sizeTheme: SelectParam<SizeThemeName>('Size Theme', '', 'physical', SizeThemeOptions),

src/mol-geo/representation/structure/visual/util/element.ts

@@ -13,7 +13,7 @@ import { MeshBuilder } from '../../../../geometry/mesh/mesh-builder';
 import { Loci, EmptyLoci } from 'mol-model/loci';
 import { Interval, OrderedSet } from 'mol-data/int';
 import { PickingId } from '../../../../geometry/picking';
-import { SizeTheme, SizeThemeName } from 'mol-view/theme/size';
+import { SizeTheme, SizeThemeName } from 'mol-canvas3d/theme/size';
 import { LocationIterator } from '../../../../util/location-iterator';
 import { addSphere } from '../../../../geometry/mesh/builder/sphere';
 

src/mol-geo/representation/structure/visual/util/link.ts

@@ -9,12 +9,12 @@ import { RuntimeContext } from 'mol-task';
 import { Mesh } from '../../../../geometry/mesh/mesh';
 import { MeshBuilder } from '../../../../geometry/mesh/mesh-builder';
 import { LinkType } from 'mol-model/structure/model/types';
-import { SizeThemeName, SizeThemeOptions } from 'mol-view/theme/size';
+import { SizeThemeName, SizeThemeOptions } from 'mol-canvas3d/theme/size';
 import { CylinderProps } from '../../../../primitive/cylinder';
 import { LocationIterator } from '../../../../util/location-iterator';
 import { Unit, StructureElement, Structure, Link } from 'mol-model/structure';
 import { addFixedCountDashedCylinder, addCylinder, addDoubleCylinder } from '../../../../geometry/mesh/builder/cylinder';
-import { SelectParam, RangeParam, NumberParam, paramDefaultValues } from 'mol-view/parameter';
+import { SelectParam, RangeParam, NumberParam, paramDefaultValues } from 'mol-util/parameter';
 
 export const LinkCylinderParams = {
     sizeTheme: SelectParam<SizeThemeName>('Size Theme', '', 'uniform', SizeThemeOptions),

src/mol-geo/representation/volume/direct-volume.ts

@@ -12,7 +12,7 @@ import { PickingId } from '../../geometry/picking';
 import { MarkerAction } from '../../geometry/marker-data';
 import { Loci, EmptyLoci } from 'mol-model/loci';
 import { createRenderableState, updateRenderableState, Geometry } from '../../geometry/geometry';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 import { DirectVolume } from '../../geometry/direct-volume/direct-volume';
 import { Vec3, Mat4 } from 'mol-math/linear-algebra';
 import { Box3D } from 'mol-math/geometry';

src/mol-geo/representation/volume/index.ts

@@ -11,7 +11,7 @@ import { PickingId } from '../../geometry/picking';
 import { Loci, EmptyLoci } from 'mol-model/loci';
 import { MarkerAction } from '../../geometry/marker-data';
 import { Geometry } from '../../geometry/geometry';
-import { paramDefaultValues } from 'mol-view/parameter';
+import { paramDefaultValues } from 'mol-util/parameter';
 
 export interface VolumeVisual<P extends RepresentationProps = {}> extends Visual<VolumeData, P> { }
 

src/mol-geo/representation/volume/isosurface-mesh.ts

@@ -18,7 +18,7 @@ import { LocationIterator } from '../../util/location-iterator';
 import { NullLocation } from 'mol-model/location';
 import { createIdentityTransform } from '../../geometry/transform-data';
 import { createRenderableState, updateRenderableState } from '../../geometry/geometry';
-import { paramDefaultValues, RangeParam } from 'mol-view/parameter';
+import { paramDefaultValues, RangeParam } from 'mol-util/parameter';
 import { ValueCell } from 'mol-util';
 
 export async function createVolumeSurface(ctx: RuntimeContext, volume: VolumeData, isoValueAbsolute: number, mesh?: Mesh) {

src/mol-gl/_spec/renderer.spec.ts

@@ -6,7 +6,7 @@
 
 import { createGl } from './gl.shim';
 
-import { PerspectiveCamera } from 'mol-view/camera/perspective';
+import { PerspectiveCamera } from 'mol-canvas3d/camera/perspective';
 import { Vec3, Mat4 } from 'mol-math/linear-algebra';
 import { ValueCell } from 'mol-util';
 

src/mol-gl/renderer.ts

@@ -5,8 +5,8 @@
  */
 
 // import { Vec3, Mat4 } from 'mol-math/linear-algebra'
-import { Viewport } from 'mol-view/camera/util';
-import { Camera } from 'mol-view/camera/base';
+import { Viewport } from 'mol-canvas3d/camera/util';
+import { Camera } from 'mol-canvas3d/camera/base';
 
 import Scene from './scene';
 import { Context, createImageData } from './webgl/context';

src/mol-model/structure/structure/unit/gaussian-density.ts

@@ -5,11 +5,11 @@
  */
 
 import { Unit, StructureElement, ElementIndex } from 'mol-model/structure';
-import { SizeTheme } from 'mol-view/theme/size';
+import { SizeTheme } from 'mol-canvas3d/theme/size';
 import { GaussianDensity } from 'mol-math/geometry/gaussian-density';
 import { Task, RuntimeContext } from 'mol-task';
 import { DensityData } from 'mol-math/geometry';
-import { NumberParam, paramDefaultValues, BooleanParam, ValueParam } from 'mol-view/parameter';
+import { NumberParam, paramDefaultValues, BooleanParam, ValueParam } from 'mol-util/parameter';
 import { Context } from 'mol-gl/webgl/context';
 import { GaussianDensityTexture } from 'mol-math/geometry/gaussian-density/gpu';
 import { Texture } from 'mol-gl/webgl/texture';

src/mol-plugin/index.ts

@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// TODO

src/mol-util/color/scale.ts

@@ -6,7 +6,7 @@
 
 import { Color } from './color'
 import { ColorBrewer } from './tables'
-import { ScaleLegend } from 'mol-view/theme/color';
+import { ScaleLegend } from 'mol-canvas3d/theme/color';
 import { defaults } from 'mol-util';
 
 export interface ColorScale {

src/mol-view/state/context.ts

@@ -1,28 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { BehaviorSubject } from 'rxjs';
-import { UUID } from 'mol-util'
-import { AnyEntity } from './entity';
-import Viewer from '../viewer';
-import { Progress } from 'mol-task';
-
-// TODO
-export type StateTree = {}
-
-export class StateContext {
-    id = UUID.create()
-    change = new BehaviorSubject(0)
-
-    tree: StateTree = {}
-    entities: Set<AnyEntity> = new Set()
-
-    viewer: Viewer
-
-    constructor(readonly log: (p: Progress) => void) {
-
-    }
-}

src/mol-view/state/entity.ts

@@ -1,162 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { readFile, readUrl } from 'mol-util/read'
-import { idFactory } from 'mol-util/id-factory'
-import { StateContext } from './context';
-import { getFileInfo } from 'mol-util/file-info';
-import { CifFile, CifFrame } from 'mol-io/reader/cif';
-import { mmCIF_Database } from 'mol-io/reader/cif/schema/mmcif';
-import { Model, Structure } from 'mol-model/structure';
-import { StructureRepresentation } from 'mol-geo/representation/structure';
-import { SpacefillProps } from 'mol-geo/representation/structure/representation/spacefill';
-import { BallAndStickProps } from 'mol-geo/representation/structure/representation/ball-and-stick';
-import { DistanceRestraintProps } from 'mol-geo/representation/structure/representation/distance-restraint';
-import { CartoonProps } from 'mol-geo/representation/structure/representation/cartoon';
-import { BackboneProps } from 'mol-geo/representation/structure/representation/backbone';
-import { CarbohydrateProps } from 'mol-geo/representation/structure/representation/carbohydrate';
-
-const getNextId = idFactory(1)
-
-export interface StateEntity<T, K extends string> {
-    id: number
-    kind: K
-    value: T
-}
-export namespace StateEntity {
-    export function create<T, K extends string>(ctx: StateContext, kind: K, value: T): StateEntity<T, K> {
-        const entity = { id: getNextId(), kind, value }
-        ctx.entities.add(entity)
-        ctx.change.next(ctx.change.getValue() + 1)
-        return entity
-    }
-}
-
-export type AnyEntity = StateEntity<any, any>
-export type NullEntity = StateEntity<null, 'null'>
-
-export const NullEntity: NullEntity = { id: -1, kind: 'null', value: null }
-export const RootEntity: StateEntity<null, 'root'> = { id: 0, kind: 'root', value: null }
-
-export interface UrlProps {
-    url: string
-    name: string
-    type: string
-    getData: () => Promise<string | Uint8Array>
-}
-
-export type UrlEntity = StateEntity<UrlProps, 'url'>
-export namespace UrlEntity {
-    export function ofUrl(ctx: StateContext, url: string, isBinary?: boolean): UrlEntity {
-        const { name, ext: type, compressed, binary } = getFileInfo(url)
-        return StateEntity.create(ctx, 'url', {
-            url, name, type,
-            getData: () => readUrl(url, isBinary || !!compressed || binary)
-        })
-    }
-}
-
-export interface FileProps {
-    name: string
-    type: string
-    getData: () => Promise<string | Uint8Array>
-}
-
-export type FileEntity = StateEntity<FileProps, 'file'>
-export namespace FileEntity {
-    export function ofFile(ctx: StateContext, file: File, isBinary?: boolean): FileEntity {
-        const { name, ext: type, compressed, binary } = getFileInfo(file)
-        return StateEntity.create(ctx, 'file', {
-            name, type,
-            getData: () => readFile(file, isBinary || !!compressed || binary)
-        })
-    }
-}
-
-export interface DataProps {
-    type: string
-    data: string | Uint8Array
-}
-
-export type DataEntity = StateEntity<DataProps, 'data'>
-export namespace DataEntity {
-    export function ofData<T>(ctx: StateContext, data: string | Uint8Array, type: string): DataEntity {
-        return StateEntity.create(ctx, 'data', {
-            type,
-            data
-        })
-    }
-}
-
-export type CifEntity = StateEntity<CifFile, 'cif'>
-export namespace CifEntity {
-    export function ofCifFile(ctx: StateContext, file: CifFile): CifEntity {
-        return StateEntity.create(ctx, 'cif', file)
-    }
-}
-
-export type MmcifEntity = StateEntity<{ db: mmCIF_Database, frame: CifFrame }, 'mmcif'>
-export namespace MmcifEntity {
-    export function ofMmcifDb(ctx: StateContext, mmCif: { db: mmCIF_Database, frame: CifFrame }): MmcifEntity {
-        return StateEntity.create(ctx, 'mmcif', mmCif)
-    }
-}
-
-export type ModelEntity = StateEntity<ReadonlyArray<Model>, 'model'>
-export namespace ModelEntity {
-    export function ofModels(ctx: StateContext, models: ReadonlyArray<Model>): ModelEntity {
-        return StateEntity.create(ctx, 'model', models)
-    }
-}
-
-export type StructureEntity = StateEntity<Structure, 'structure'>
-export namespace StructureEntity {
-    export function ofStructure(ctx: StateContext, structure: Structure): StructureEntity {
-        return StateEntity.create(ctx, 'structure', structure)
-    }
-}
-
-export type SpacefillEntity = StateEntity<StructureRepresentation<SpacefillProps>, 'spacefill'>
-export namespace SpacefillEntity {
-    export function ofRepr(ctx: StateContext, repr: StructureRepresentation<SpacefillProps>): SpacefillEntity {
-        return StateEntity.create(ctx, 'spacefill', repr)
-    }
-}
-
-export type BallAndStickEntity = StateEntity<StructureRepresentation<BallAndStickProps>, 'ballandstick'>
-export namespace BallAndStickEntity {
-    export function ofRepr(ctx: StateContext, repr: StructureRepresentation<BallAndStickProps>): BallAndStickEntity {
-        return StateEntity.create(ctx, 'ballandstick', repr)
-    }
-}
-
-export type DistanceRestraintEntity = StateEntity<StructureRepresentation<DistanceRestraintProps>, 'distancerestraint'>
-export namespace DistanceRestraintEntity {
-    export function ofRepr(ctx: StateContext, repr: StructureRepresentation<DistanceRestraintProps>): DistanceRestraintEntity {
-        return StateEntity.create(ctx, 'distancerestraint', repr)
-    }
-}
-
-export type BackboneEntity = StateEntity<StructureRepresentation<BackboneProps>, 'backbone'>
-export namespace BackboneEntity {
-    export function ofRepr(ctx: StateContext, repr: StructureRepresentation<BackboneProps>): BackboneEntity {
-        return StateEntity.create(ctx, 'backbone', repr)
-    }
-}
-
-export type CartoonEntity = StateEntity<StructureRepresentation<CartoonProps>, 'cartoon'>
-export namespace CartoonEntity {
-    export function ofRepr(ctx: StateContext, repr: StructureRepresentation<CartoonProps>): CartoonEntity {
-        return StateEntity.create(ctx, 'cartoon', repr)
-    }
-}
-
-export type CarbohydrateEntity = StateEntity<StructureRepresentation<CarbohydrateProps>, 'carbohydrate'>
-export namespace CarbohydrateEntity {
-    export function ofRepr(ctx: StateContext, repr: StructureRepresentation<CarbohydrateProps>): CarbohydrateEntity {
-        return StateEntity.create(ctx, 'carbohydrate', repr)
-    }
-}

src/mol-view/state/transform.ts

@@ -1,274 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import CIF from 'mol-io/reader/cif'
-import { FileEntity, DataEntity, UrlEntity, CifEntity, MmcifEntity, ModelEntity, StructureEntity, SpacefillEntity, AnyEntity, NullEntity, BallAndStickEntity, DistanceRestraintEntity, CartoonEntity, BackboneEntity, CarbohydrateEntity } from './entity';
-import { Model, Structure, Format } from 'mol-model/structure';
-
-import { StateContext } from './context';
-import StructureSymmetry from 'mol-model/structure/structure/symmetry';
-import { SpacefillProps, SpacefillRepresentation } from 'mol-geo/representation/structure/representation/spacefill';
-import { BallAndStickProps, BallAndStickRepresentation } from 'mol-geo/representation/structure/representation/ball-and-stick';
-import { DistanceRestraintRepresentation, DistanceRestraintProps } from 'mol-geo/representation/structure/representation/distance-restraint';
-import { CartoonRepresentation, CartoonProps } from 'mol-geo/representation/structure/representation/cartoon';
-import { BackboneProps, BackboneRepresentation } from 'mol-geo/representation/structure/representation/backbone';
-import { CarbohydrateProps, CarbohydrateRepresentation } from 'mol-geo/representation/structure/representation/carbohydrate';
-
-type transformer<I extends AnyEntity, O extends AnyEntity, P extends {}> = (ctx: StateContext, inputEntity: I, props?: P) => Promise<O>
-
-export interface StateTransform<I extends AnyEntity, O extends AnyEntity, P extends {}> {
-    inputKind: I['kind']
-    outputKind: O['kind']
-    kind: string
-    apply: transformer<I, O, P>
-}
-
-export namespace StateTransform {
-    export function create<I extends AnyEntity, O extends AnyEntity, P extends {}>(inputKind: I['kind'], outputKind: O['kind'], kind: string, transformer: transformer<I, O, P>) {
-        return { inputKind, outputKind, kind, apply: transformer }
-    }
-}
-
-export type AnyTransform = StateTransform<AnyEntity, AnyEntity, {}>
-
-export type UrlToData = StateTransform<UrlEntity, DataEntity, {}>
-export const UrlToData: UrlToData = StateTransform.create('url', 'data', 'url-to-data',
-    async function (ctx: StateContext, urlEntity: UrlEntity) {
-        return DataEntity.ofData(ctx, await urlEntity.value.getData(), urlEntity.value.type)
-    })
-
-export type FileToData = StateTransform<FileEntity, DataEntity, {}>
-export const FileToData: FileToData = StateTransform.create('file', 'data', 'file-to-data',
-    async function (ctx: StateContext, fileEntity: FileEntity) {
-        return DataEntity.ofData(ctx, await fileEntity.value.getData(), fileEntity.value.type)
-    })
-
-export type DataToCif = StateTransform<DataEntity, CifEntity, {}>
-export const DataToCif: DataToCif = StateTransform.create('data', 'cif', 'data-to-cif',
-    async function (ctx: StateContext, dataEntity: DataEntity) {
-        const comp = CIF.parse(dataEntity.value.data)
-        const parsed = await comp.run(ctx.log)
-        if (parsed.isError) throw parsed
-        return CifEntity.ofCifFile(ctx, parsed.result)
-    })
-
-export type CifToMmcif = StateTransform<CifEntity, MmcifEntity, {}>
-export const CifToMmcif: CifToMmcif = StateTransform.create('cif', 'mmcif', 'cif-to-mmcif',
-    async function (ctx: StateContext, cifEntity: CifEntity) {
-        const frame = cifEntity.value.blocks[0];
-        return MmcifEntity.ofMmcifDb(ctx, { frame, db: CIF.schema.mmCIF(frame) })
-    })
-
-export type MmcifToModel = StateTransform<MmcifEntity, ModelEntity, {}>
-export const MmcifToModel: MmcifToModel = StateTransform.create('mmcif', 'model', 'mmcif-to-model',
-    async function (ctx: StateContext, mmcifEntity: MmcifEntity) {
-        const models = await Model.create(Format.mmCIF(mmcifEntity.value.frame, mmcifEntity.value.db)).run(ctx.log)
-        return ModelEntity.ofModels(ctx, models)
-    })
-
-export interface StructureProps {
-    assembly?: string
-}
-
-export type ModelToStructure = StateTransform<ModelEntity, StructureEntity, StructureProps>
-export const ModelToStructure: ModelToStructure = StateTransform.create('model', 'structure', 'model-to-structure',
-    async function (ctx: StateContext, modelEntity: ModelEntity, props: StructureProps = {}) {
-        const model = modelEntity.value[0]
-        const assembly = props.assembly
-        let structure: Structure
-        const assemblies = model.symmetry.assemblies
-        if (assemblies.length) {
-            structure = await StructureSymmetry.buildAssembly(Structure.ofModel(model), assembly || '1').run(ctx.log)
-        } else {
-            structure = Structure.ofModel(model)
-        }
-        return StructureEntity.ofStructure(ctx, structure)
-    })
-
-export type StructureCenter = StateTransform<StructureEntity, NullEntity, {}>
-export const StructureCenter: StructureCenter = StateTransform.create('structure', 'null', 'structure-center',
-    async function (ctx: StateContext, structureEntity: StructureEntity) {
-        ctx.viewer.center(structureEntity.value.boundary.sphere.center)
-        return NullEntity
-    })
-
-export type StructureToSpacefill = StateTransform<StructureEntity, SpacefillEntity, Partial<SpacefillProps>>
-export const StructureToSpacefill: StructureToSpacefill = StateTransform.create('structure', 'spacefill', 'structure-to-spacefill',
-    async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<SpacefillProps> = {}) {
-        const spacefillRepr = SpacefillRepresentation()
-        await spacefillRepr.createOrUpdate(props, structureEntity.value).run(ctx.log)
-        ctx.viewer.add(spacefillRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return SpacefillEntity.ofRepr(ctx, spacefillRepr)
-    })
-
-export type StructureToBallAndStick = StateTransform<StructureEntity, BallAndStickEntity, Partial<BallAndStickProps>>
-export const StructureToBallAndStick: StructureToBallAndStick = StateTransform.create('structure', 'ballandstick', 'structure-to-ballandstick',
-    async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<BallAndStickProps> = {}) {
-        const ballAndStickRepr = BallAndStickRepresentation()
-        await ballAndStickRepr.createOrUpdate(props, structureEntity.value).run(ctx.log)
-        ctx.viewer.add(ballAndStickRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return BallAndStickEntity.ofRepr(ctx, ballAndStickRepr)
-    })
-
-export type StructureToDistanceRestraint = StateTransform<StructureEntity, DistanceRestraintEntity, Partial<DistanceRestraintProps>>
-export const StructureToDistanceRestraint: StructureToDistanceRestraint = StateTransform.create('structure', 'distancerestraint', 'structure-to-distancerestraint',
-    async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<DistanceRestraintProps> = {}) {
-        const distanceRestraintRepr = DistanceRestraintRepresentation()
-        await distanceRestraintRepr.createOrUpdate(props, structureEntity.value).run(ctx.log)
-        ctx.viewer.add(distanceRestraintRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return DistanceRestraintEntity.ofRepr(ctx, distanceRestraintRepr)
-    })
-
-export type StructureToBackbone = StateTransform<StructureEntity, BackboneEntity, Partial<BackboneProps>>
-export const StructureToBackbone: StructureToBackbone = StateTransform.create('structure', 'backbone', 'structure-to-backbone',
-    async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<BackboneProps> = {}) {
-        const backboneRepr = BackboneRepresentation()
-        await backboneRepr.createOrUpdate(props, structureEntity.value).run(ctx.log)
-        ctx.viewer.add(backboneRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return BackboneEntity.ofRepr(ctx, backboneRepr)
-    })
-
-export type StructureToCartoon = StateTransform<StructureEntity, CartoonEntity, Partial<CartoonProps>>
-export const StructureToCartoon: StructureToCartoon = StateTransform.create('structure', 'cartoon', 'structure-to-cartoon',
-    async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<CartoonProps> = {}) {
-        const cartoonRepr = CartoonRepresentation()
-        await cartoonRepr.createOrUpdate(props, structureEntity.value).run(ctx.log)
-        ctx.viewer.add(cartoonRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return CartoonEntity.ofRepr(ctx, cartoonRepr)
-    })
-
-export type StructureToCarbohydrate = StateTransform<StructureEntity, CarbohydrateEntity, Partial<CarbohydrateProps>>
-export const StructureToCarbohydrate: StructureToCarbohydrate = StateTransform.create('structure', 'carbohydrate', 'structure-to-cartoon',
-    async function (ctx: StateContext, structureEntity: StructureEntity, props: Partial<CarbohydrateProps> = {}) {
-        const carbohydrateRepr = CarbohydrateRepresentation()
-        await carbohydrateRepr.createOrUpdate(props, structureEntity.value).run(ctx.log)
-        ctx.viewer.add(carbohydrateRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return CarbohydrateEntity.ofRepr(ctx, carbohydrateRepr)
-    })
-
-export type SpacefillUpdate = StateTransform<SpacefillEntity, NullEntity, Partial<SpacefillProps>>
-export const SpacefillUpdate: SpacefillUpdate = StateTransform.create('spacefill', 'null', 'spacefill-update',
-    async function (ctx: StateContext, spacefillEntity: SpacefillEntity, props: Partial<SpacefillProps> = {}) {
-        const spacefillRepr = spacefillEntity.value
-        await spacefillRepr.createOrUpdate(props).run(ctx.log)
-        ctx.viewer.add(spacefillRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return NullEntity
-    })
-
-export type BallAndStickUpdate = StateTransform<BallAndStickEntity, NullEntity, Partial<BallAndStickProps>>
-export const BallAndStickUpdate: BallAndStickUpdate = StateTransform.create('ballandstick', 'null', 'ballandstick-update',
-    async function (ctx: StateContext, ballAndStickEntity: BallAndStickEntity, props: Partial<BallAndStickProps> = {}) {
-        const ballAndStickRepr = ballAndStickEntity.value
-        await ballAndStickRepr.createOrUpdate(props).run(ctx.log)
-        ctx.viewer.add(ballAndStickRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return NullEntity
-    })
-
-export type DistanceRestraintUpdate = StateTransform<DistanceRestraintEntity, NullEntity, Partial<DistanceRestraintProps>>
-export const DistanceRestraintUpdate: DistanceRestraintUpdate = StateTransform.create('distancerestraint', 'null', 'distancerestraint-update',
-    async function (ctx: StateContext, distanceRestraintEntity: DistanceRestraintEntity, props: Partial<DistanceRestraintProps> = {}) {
-        const distanceRestraintRepr = distanceRestraintEntity.value
-        await distanceRestraintRepr.createOrUpdate(props).run(ctx.log)
-        ctx.viewer.add(distanceRestraintRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return NullEntity
-    })
-
-export type BackboneUpdate = StateTransform<BackboneEntity, NullEntity, Partial<BackboneProps>>
-export const BackboneUpdate: BackboneUpdate = StateTransform.create('backbone', 'null', 'backbone-update',
-    async function (ctx: StateContext, backboneEntity: BackboneEntity, props: Partial<BackboneProps> = {}) {
-        const backboneRepr = backboneEntity.value
-        await backboneRepr.createOrUpdate(props).run(ctx.log)
-        ctx.viewer.add(backboneRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return NullEntity
-    })
-
-export type CartoonUpdate = StateTransform<CartoonEntity, NullEntity, Partial<CartoonProps>>
-export const CartoonUpdate: CartoonUpdate = StateTransform.create('cartoon', 'null', 'cartoon-update',
-    async function (ctx: StateContext, cartoonEntity: CartoonEntity, props: Partial<CartoonProps> = {}) {
-        const cartoonRepr = cartoonEntity.value
-        await cartoonRepr.createOrUpdate(props).run(ctx.log)
-        ctx.viewer.add(cartoonRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return NullEntity
-    })
-
-export type CarbohydrateUpdate = StateTransform<CarbohydrateEntity, NullEntity, Partial<CarbohydrateProps>>
-export const CarbohydrateUpdate: CarbohydrateUpdate = StateTransform.create('carbohydrate', 'null', 'carbohydrate-update',
-    async function (ctx: StateContext, carbohydrateEntity: CarbohydrateEntity, props: Partial<CarbohydrateProps> = {}) {
-        const carbohydrateRepr = carbohydrateEntity.value
-        await carbohydrateRepr.createOrUpdate(props).run(ctx.log)
-        ctx.viewer.add(carbohydrateRepr)
-        ctx.viewer.requestDraw()
-        console.log('stats', ctx.viewer.stats)
-        return NullEntity
-    })
-
-// composed
-
-export type MmcifUrlToModel = StateTransform<UrlEntity, ModelEntity, {}>
-export const MmcifUrlToModel: MmcifUrlToModel = StateTransform.create('url', 'model', 'url-to-model',
-    async function (ctx: StateContext, urlEntity: UrlEntity) {
-        const dataEntity = await UrlToData.apply(ctx, urlEntity)
-        return DataToModel.apply(ctx, dataEntity)
-    })
-
-export type MmcifFileToModel = StateTransform<FileEntity, ModelEntity, {}>
-export const MmcifFileToModel: MmcifFileToModel = StateTransform.create('file', 'model', 'file-to-model',
-    async function (ctx: StateContext, fileEntity: FileEntity) {
-        const dataEntity = await FileToData.apply(ctx, fileEntity)
-        return DataToModel.apply(ctx, dataEntity)
-    })
-
-export type DataToModel = StateTransform<DataEntity, ModelEntity, {}>
-export const DataToModel: DataToModel = StateTransform.create('data', 'model', 'data-to-model',
-    async function getModelFromData(ctx: StateContext, dataEntity: DataEntity) {
-        const cifEntity = await DataToCif.apply(ctx, dataEntity)
-        const mmcifEntity = await CifToMmcif.apply(ctx, cifEntity)
-        return MmcifToModel.apply(ctx, mmcifEntity)
-    })
-
-export type ModelToSpacefill = StateTransform<ModelEntity, SpacefillEntity, Partial<SpacefillProps>>
-export const ModelToSpacefill: ModelToSpacefill = StateTransform.create('model', 'spacefill', 'model-to-spacefill',
-    async function (ctx: StateContext, modelEntity: ModelEntity, props: Partial<SpacefillProps> = {}) {
-        const structureEntity = await ModelToStructure.apply(ctx, modelEntity)
-        // StructureToBond.apply(ctx, structureEntity, props)
-        return StructureToSpacefill.apply(ctx, structureEntity, props)
-    })
-
-export type MmcifUrlToSpacefill = StateTransform<UrlEntity, SpacefillEntity, Partial<SpacefillProps>>
-export const MmcifUrlToSpacefill: MmcifUrlToSpacefill = StateTransform.create('url', 'spacefill', 'url-to-spacefill',
-    async function (ctx: StateContext, urlEntity: UrlEntity, props: Partial<SpacefillProps> = {}) {
-        const modelEntity = await MmcifUrlToModel.apply(ctx, urlEntity)
-        return ModelToSpacefill.apply(ctx, modelEntity, props)
-    })
-
-export type MmcifFileToSpacefill = StateTransform<FileEntity, SpacefillEntity, Partial<SpacefillProps>>
-export const MmcifFileToSpacefill: MmcifFileToSpacefill = StateTransform.create('file', 'spacefill', 'file-to-spacefill',
-    async function (ctx: StateContext, fileEntity: FileEntity, props: Partial<SpacefillProps> = {}) {
-        const modelEntity = await MmcifFileToModel.apply(ctx, fileEntity)
-        return ModelToSpacefill.apply(ctx, modelEntity, props)
-    })

src/mol-view/util.ts

@@ -1,43 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import CIF from 'mol-io/reader/cif'
-import { Progress } from 'mol-task'
-import { VolumeData, parseDensityServerData } from 'mol-model/volume'
-import { DensityServer_Data_Database } from 'mol-io/reader/cif/schema/density-server';
-
-export async function downloadCif(url: string, isBinary: boolean) {
-    const data = await fetch(url);
-    return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
-}
-
-export async function parseCif(data: string|Uint8Array) {
-    const comp = CIF.parse(data)
-    const parsed = await comp.run(Progress.format);
-    if (parsed.isError) throw parsed;
-    return parsed.result
-}
-
-export type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
-
-export async function getVolumeFromEmdId(emdid: string): Promise<Volume> {
-    const cif = await downloadCif(`https://webchem.ncbr.muni.cz/DensityServer/em/emd-${emdid}/cell?detail=4`, true)
-    const data = CIF.schema.densityServer(cif.blocks[1])
-    return { source: data, volume: await parseDensityServerData(data).run() }
-}
-
-export function resizeCanvas (canvas: HTMLCanvasElement, container: Element) {
-    let w = window.innerWidth
-    let h = window.innerHeight
-    if (container !== document.body) {
-        let bounds = container.getBoundingClientRect()
-        w = bounds.right - bounds.left
-        h = bounds.bottom - bounds.top
-    }
-    canvas.width = window.devicePixelRatio * w
-    canvas.height = window.devicePixelRatio * h
-    Object.assign(canvas.style, { width: `${w}px`, height: `${h}px` })
-}

tsconfig.json

@@ -25,9 +25,10 @@
             "mol-ql": ["./mol-ql"],
             "mol-script": ["./mol-script"],
             "mol-state": ["./mol-state", "./mol-state/index.ts"],
+            "mol-plugin": ["./mol-plugin", "./mol-plugin/index.ts"],
             "mol-task": ["./mol-task", "./mol-task/index.ts"],
             "mol-util": ["./mol-util", "./mol-util/index.ts"],
-            "mol-view": ["./mol-view"]
+            "mol-canvas3d": ["./mol-view"]
         }
     },
     "include": [ "**/*" ],