diff --git a/doc/usage/interaction-controls.md b/doc/usage/interaction-controls.md index 12551a609..f0a860cfc 100644 --- a/doc/usage/interaction-controls.md +++ b/doc/usage/interaction-controls.md @@ -81,7 +81,6 @@ Note that the [MouseControls](../class/src/controls/mouse-controls.js~MouseContr stage.signals.clicked.add(function (pickingProxy) {...}); ``` - ### Hovered Basis usage: @@ -151,6 +150,12 @@ The default controls are as follows: - `drag-ctrl-left` rotate hovered component - `clickPick-middle` auto view picked component element - `hoverPick` show tooltip for hovered component element +- `clickPick-shift-left` de/select an atom +- `doubleClick-shift-left` clear selected atoms +- `drag-shift-left` move selected atoms + + +Four presets are available: "default", "pymol", "coot", and "astexviewer". ### Observer diff --git a/package-lock.json b/package-lock.json index ea007bfcb..d058bc2eb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -5,23 +5,144 @@ "requires": true, 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"p-finally": "^1.0.0", "signal-exit": "^3.0.0", "strip-eof": "^1.0.0" + }, + "dependencies": { + "cross-spawn": { + "version": "6.0.5", + "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-6.0.5.tgz", + "integrity": "sha512-eTVLrBSt7fjbDygz805pMnstIs2VTBNkRm0qxZd+M7A5XDdxVRWO5MxGBXZhjY4cqLYLdtrGqRf8mBPmzwSpWQ==", + "dev": true, + "requires": { + "nice-try": "^1.0.4", + "path-key": "^2.0.1", + "semver": "^5.5.0", + "shebang-command": "^1.2.0", + "which": "^1.2.9" + } + } } }, "exit": { @@ -2498,17 +3982,17 @@ } }, "expect": { - "version": "23.4.0", - "resolved": "https://registry.npmjs.org/expect/-/expect-23.4.0.tgz", - "integrity": "sha1-baTsyZwUcSU+cogziYOtHrrbYMM=", + "version": "24.8.0", + "resolved": "https://registry.npmjs.org/expect/-/expect-24.8.0.tgz", + "integrity": "sha512-/zYvP8iMDrzaaxHVa724eJBCKqSHmO0FA7EDkBiRHxg6OipmMn1fN+C8T9L9K8yr7UONkOifu6+LLH+z76CnaA==", "dev": true, "requires": { + "@jest/types": "^24.8.0", "ansi-styles": "^3.2.0", - "jest-diff": 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"sha512-z8H8/diyk76B7q5wg+Ud0+CqzcAF3mBBI/bA5ne5zrRUUIvNkJY//D3BqyH571KuAC4Nr7Rw7CjWX4r0y9DvNg==", + "version": "1.2.9", + "resolved": "https://registry.npmjs.org/fsevents/-/fsevents-1.2.9.tgz", + "integrity": "sha512-oeyj2H3EjjonWcFjD5NvZNE9Rqe4UW+nQBU2HNeKw0koVLEFIhtyETyAakeAM3de7Z/SW5kcA+fZUait9EApnw==", "dev": true, "optional": true, "requires": { - "nan": "^2.9.2", - "node-pre-gyp": "^0.10.0" + "nan": "^2.12.1", + "node-pre-gyp": "^0.12.0" }, "dependencies": { "abbrev": { @@ -2794,7 +4274,8 @@ "ansi-regex": { "version": "2.1.1", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "aproba": { "version": "1.2.0", @@ -2803,7 +4284,7 @@ "optional": true }, "are-we-there-yet": { - "version": "1.1.4", + "version": "1.1.5", "bundled": true, "dev": true, "optional": true, @@ -2815,19 +4296,21 @@ "balanced-match": { "version": "1.0.0", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "brace-expansion": { "version": "1.1.11", "bundled": true, "dev": true, + "optional": true, "requires": { "balanced-match": "^1.0.0", "concat-map": "0.0.1" } }, "chownr": { - "version": "1.0.1", + "version": "1.1.1", "bundled": true, "dev": true, "optional": true @@ -2835,17 +4318,20 @@ "code-point-at": { "version": "1.1.0", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "concat-map": { "version": "0.0.1", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "console-control-strings": { "version": "1.1.0", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "core-util-is": { "version": "1.0.2", @@ -2854,16 +4340,16 @@ "optional": true }, "debug": { - "version": "2.6.9", + "version": "4.1.1", "bundled": true, "dev": true, "optional": true, "requires": { - "ms": "2.0.0" + "ms": "^2.1.1" } }, "deep-extend": { - "version": "0.5.1", + "version": "0.6.0", "bundled": true, "dev": true, "optional": true @@ -2912,7 +4398,7 @@ } }, "glob": { - "version": "7.1.2", + "version": "7.1.3", "bundled": true, "dev": true, "optional": true, @@ -2932,12 +4418,12 @@ "optional": true }, "iconv-lite": { - "version": "0.4.21", + "version": "0.4.24", "bundled": true, "dev": true, "optional": true, "requires": { - "safer-buffer": "^2.1.0" + "safer-buffer": ">= 2.1.2 < 3" } }, "ignore-walk": { @@ -2962,7 +4448,8 @@ "inherits": { "version": "2.0.3", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "ini": { "version": "1.3.5", @@ -2974,6 +4461,7 @@ "version": "1.0.0", "bundled": true, "dev": true, + "optional": true, "requires": { "number-is-nan": "^1.0.0" } @@ -2988,6 +4476,7 @@ "version": "3.0.4", "bundled": true, "dev": true, + "optional": true, "requires": { "brace-expansion": "^1.1.7" } @@ -2995,19 +4484,21 @@ "minimist": { "version": "0.0.8", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "minipass": { - "version": "2.2.4", + "version": "2.3.5", "bundled": true, "dev": true, + "optional": true, "requires": { - "safe-buffer": "^5.1.1", + "safe-buffer": "^5.1.2", "yallist": "^3.0.0" } }, "minizlib": { - "version": "1.1.0", + "version": "1.2.1", "bundled": true, "dev": true, "optional": true, @@ -3019,40 +4510,48 @@ "version": "0.5.1", "bundled": true, "dev": true, + "optional": true, "requires": { "minimist": "0.0.8" } }, "ms": { - "version": "2.0.0", + "version": "2.1.1", "bundled": true, "dev": true, "optional": true }, + "nan": { + "version": "2.13.2", + "resolved": "https://registry.npmjs.org/nan/-/nan-2.13.2.tgz", + "integrity": "sha512-TghvYc72wlMGMVMluVo9WRJc0mB8KxxF/gZ4YYFy7V2ZQX9l7rgbPg7vjS9mt6U5HXODVFVI2bOduCzwOMv/lw==", + "dev": true, + "optional": true + }, "needle": { - "version": "2.2.0", + "version": "2.3.0", "bundled": true, "dev": true, "optional": true, "requires": { - "debug": "^2.1.2", + "debug": "^4.1.0", "iconv-lite": "^0.4.4", "sax": "^1.2.4" } }, "node-pre-gyp": { - "version": "0.10.0", + "version": "0.12.0", "bundled": true, "dev": true, "optional": true, "requires": { "detect-libc": "^1.0.2", "mkdirp": "^0.5.1", - "needle": "^2.2.0", + "needle": "^2.2.1", "nopt": "^4.0.1", "npm-packlist": "^1.1.6", "npmlog": "^4.0.2", - "rc": "^1.1.7", + "rc": "^1.2.7", "rimraf": "^2.6.1", "semver": "^5.3.0", "tar": "^4" @@ -3069,13 +4568,13 @@ } }, "npm-bundled": { - "version": "1.0.3", + "version": "1.0.6", "bundled": true, "dev": true, "optional": true }, "npm-packlist": { - "version": "1.1.10", + "version": "1.4.1", "bundled": true, "dev": true, "optional": true, @@ -3099,7 +4598,8 @@ "number-is-nan": { "version": "1.0.1", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "object-assign": { "version": "4.1.1", @@ -3111,6 +4611,7 @@ "version": "1.4.0", "bundled": true, "dev": true, + "optional": true, "requires": { "wrappy": "1" } @@ -3150,12 +4651,12 @@ "optional": true }, "rc": { - "version": "1.2.7", + "version": "1.2.8", "bundled": true, "dev": true, "optional": true, "requires": { - "deep-extend": "^0.5.1", + "deep-extend": "^0.6.0", "ini": "~1.3.0", "minimist": "^1.2.0", "strip-json-comments": "~2.0.1" @@ -3185,18 +4686,19 @@ } }, "rimraf": { - "version": "2.6.2", + "version": "2.6.3", "bundled": true, "dev": true, "optional": true, "requires": { - "glob": "^7.0.5" + "glob": "^7.1.3" } }, "safe-buffer": { - "version": "5.1.1", + "version": "5.1.2", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "safer-buffer": { "version": "2.1.2", @@ -3211,7 +4713,7 @@ "optional": true }, "semver": { - "version": "5.5.0", + "version": "5.7.0", "bundled": true, "dev": true, "optional": true @@ -3232,6 +4734,7 @@ "version": "1.0.2", "bundled": true, "dev": true, + "optional": true, "requires": { "code-point-at": "^1.0.0", "is-fullwidth-code-point": "^1.0.0", @@ -3251,6 +4754,7 @@ "version": "3.0.1", "bundled": true, "dev": true, + "optional": true, "requires": { "ansi-regex": "^2.0.0" } @@ -3262,17 +4766,17 @@ "optional": true }, "tar": { - "version": "4.4.1", + "version": "4.4.8", "bundled": true, "dev": true, "optional": true, "requires": { - "chownr": "^1.0.1", + "chownr": "^1.1.1", "fs-minipass": "^1.2.5", - "minipass": "^2.2.4", - "minizlib": "^1.1.0", + "minipass": "^2.3.4", + "minizlib": "^1.1.1", "mkdirp": "^0.5.0", - "safe-buffer": "^5.1.1", + "safe-buffer": "^5.1.2", "yallist": "^3.0.2" } }, @@ -3283,23 +4787,25 @@ "optional": true }, "wide-align": { - "version": "1.1.2", + "version": "1.1.3", "bundled": true, "dev": true, "optional": true, "requires": { - "string-width": "^1.0.2" + "string-width": "^1.0.2 || 2" } }, "wrappy": { "version": "1.0.2", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "yallist": { - "version": "3.0.2", + "version": "3.0.3", "bundled": true, - "dev": true + "dev": true, + "optional": true } } }, @@ -3334,10 +4840,13 @@ "dev": true }, "get-stream": { - "version": "3.0.0", - "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-3.0.0.tgz", - "integrity": "sha1-jpQ9E1jcN1VQVOy+LtsFqhdO3hQ=", - "dev": true + "version": "4.1.0", + "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-4.1.0.tgz", + "integrity": "sha512-GMat4EJ5161kIy2HevLlr4luNjBgvmj413KaQA7jt4V8B4RDsfpHk7WQ9GVqfYyyx8OS/L66Kox+rJRNklLK7w==", + "dev": true, + "requires": { + "pump": "^3.0.0" + } }, "get-value": { "version": "2.0.6", @@ -3435,91 +4944,22 @@ "dev": true }, "handlebars": { - "version": "4.0.11", - "resolved": "https://registry.npmjs.org/handlebars/-/handlebars-4.0.11.tgz", - "integrity": "sha1-Ywo13+ApS8KB7a5v/F0yn8eYLcw=", + "version": "4.1.2", + "resolved": "https://registry.npmjs.org/handlebars/-/handlebars-4.1.2.tgz", + "integrity": "sha512-nvfrjqvt9xQ8Z/w0ijewdD/vvWDTOweBUm96NTr66Wfvo1mJenBLwcYmPs3TIBP5ruzYGD7Hx/DaM9RmhroGPw==", "dev": true, "requires": { - "async": "^1.4.0", + "neo-async": "^2.6.0", "optimist": "^0.6.1", - "source-map": "^0.4.4", - "uglify-js": "^2.6" + "source-map": "^0.6.1", + "uglify-js": "^3.1.4" }, "dependencies": { - "async": { - "version": "1.5.2", - "resolved": 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"https://registry.npmjs.org/yargs-parser/-/yargs-parser-11.1.1.tgz", + "integrity": "sha512-C6kB/WJDiaxONLJQnF8ccx9SEeoTTLek8RVbaOIsrAUS8VrBEXfmeSnCZxygc+XC2sNMBIwOOnfcxiynjHsVSQ==", "dev": true, "requires": { - "camelcase": "^4.1.0" + "camelcase": "^5.0.0", + "decamelize": "^1.2.0" } } } diff --git a/package.json b/package.json index 58a4d7991..34d0a5ab3 100644 --- a/package.json +++ b/package.json @@ -73,10 +73,10 @@ "chai": "^4.1.1", "chroma-js": "^1.3.7", "cpx": "^1.5.0", - "eslint": "^5.3.0", + "eslint": "^5.16.0", "eslint-plugin-import": "^2.13.0", "eslint-plugin-react": "^7.10.0", - "jest": "^23.4.2", + "jest": "^24.8.0", "mocha": "^5.2.0", "promise-polyfill": "^8.0.0", "rollup": "^0.63.5", @@ -93,7 +93,7 @@ "standard": "^11.0.1", "three": "^0.95.0", "ts-jest": "^23.1.3", - "typedoc": "^0.11.1", + "typedoc": "^0.14.2", "typescript": "^3.0.1", "uglify-js": "^3.4.6" }, diff --git a/src/component/representation-element.ts b/src/component/representation-element.ts index 915200c39..38f400a49 100644 --- a/src/component/representation-element.ts +++ b/src/component/representation-element.ts @@ -154,6 +154,19 @@ class RepresentationElement extends Element { return this } + /** + * Set selected atoms via indices + * @param {number[]} indices array of selected atom indices + * @return {RepresentationElement} this object + */ + setSelectedAtomIndices (indices: number[]) { + if (indices) { + return this.setSelection('@'+indices.join()) + } else { + return this.setSelection('none') + } + } + /** * Set representation parameters * @param {RepresentationParameters} params - parameter object diff --git a/src/component/structure-component.ts b/src/component/structure-component.ts index f581c0a19..d6a374afe 100644 --- a/src/component/structure-component.ts +++ b/src/component/structure-component.ts @@ -6,7 +6,7 @@ import { Signal } from 'signals' -import { ComponentRegistry, MeasurementDefaultParams } from '../globals' +import { ComponentRegistry, MeasurementDefaultParams, SelectionDefaultParams } from '../globals' import { defaults, /*deepEqual, */createRingBuffer, RingBuffer, createSimpleDict, SimpleDict } from '../utils' @@ -25,11 +25,12 @@ import Stage from '../stage/stage' import StructureRepresentation from '../representation/structure-representation' import AtomProxy from '../proxy/atom-proxy' import { Vector3, Box3 } from 'three'; +import { createToggleSet, ToggleSet } from '../utils/toggle-set'; export type StructureRepresentationType = ( 'angle'|'axes'|'backbone'|'ball+stick'|'base'|'cartoon'|'contact'|'dihedral'| 'distance'|'helixorient'|'hyperball'|'label'|'licorice'|'line'|'surface'| - 'ribbon'|'rocket'|'rope'|'spacefill'|'trace'|'tube'|'unitcell' + 'ribbon'|'rocket'|'rope'|'selected'|'spacefill'|'trace'|'tube'|'unitcell' ) export const StructureComponentDefaultParameters = Object.assign({ @@ -66,11 +67,13 @@ class StructureComponent extends Component { pickBuffer: RingBuffer pickDict: SimpleDict lastPick?: number + selectedAtomIndices: ToggleSet spacefillRepresentation: RepresentationElement distanceRepresentation: RepresentationElement angleRepresentation: RepresentationElement dihedralRepresentation: RepresentationElement + selectedRepresentation: RepresentationElement measureRepresentations: RepresentationCollection @@ -89,6 +92,7 @@ class StructureComponent extends Component { this.pickBuffer = createRingBuffer(4) this.pickDict = createSimpleDict() + this.selectedAtomIndices = createToggleSet() this.spacefillRepresentation = this.addRepresentation('spacefill', { sele: 'none', @@ -108,6 +112,15 @@ class StructureComponent extends Component { 'dihedral', MeasurementDefaultParams, true ) + this.selectedRepresentation = this.addRepresentation('spacefill', { + sele: 'none', + color: SelectionDefaultParams.color, + opacity: 0.4, + disablePicking: true, + radiusType: 'data' + }, true) + + this.measureRepresentations = new RepresentationCollection([ this.spacefillRepresentation, this.distanceRepresentation, @@ -173,14 +186,15 @@ class StructureComponent extends Component { * @param {String} value - assembly name * @return {undefined} */ - setDefaultAssembly (value:string) { - // filter out non-exsisting assemblies + setDefaultAssembly (value: string) { + // filter out non-existing assemblies if (this.structure.biomolDict[value] === undefined) value = '' // only set default assembly when changed if (this.parameters.defaultAssembly !== value) { const reprParams = { defaultAssembly: value } this.reprList.forEach(repr => repr.setParameters(reprParams)) this.measureRepresentations.setParameters(reprParams) + this.selectedRepresentation.setParameters(reprParams) this.parameters.defaultAssembly = value this.signals.defaultAssemblyChanged.dispatch(value) } @@ -196,6 +210,7 @@ class StructureComponent extends Component { repr.build() }) this.measureRepresentations.build() + this.selectedRepresentation.build() } /** @@ -211,6 +226,7 @@ class StructureComponent extends Component { updateRepresentations (what: any) { super.updateRepresentations(what) this.measureRepresentations.update(what) + this.selectedRepresentation.update(what) } addRepresentation (type: StructureRepresentationType, params: { [k: string]: any } = {}, hidden = false) { @@ -258,6 +274,7 @@ class StructureComponent extends Component { this.trajList.length = 0 this.structure.dispose() this.measureRepresentations.dispose() + this.selectedRepresentation.dispose() super.dispose() } @@ -431,6 +448,41 @@ class StructureComponent extends Component { } this.measureBuild() } + + selectedPick (atoms: AtomProxy[]) { + let atomIndices: number[] = [] + atoms.forEach(function (x) { + atomIndices.push(x.index) + }) + this.selectedPickIndices(atomIndices) + } + + selectedPickIndices (atomIndices: number[]) { + this.selectedAtomIndices.toggleAny(atomIndices) + this.selectedUpdate() + } + + setSelectedIndices (atomIndices: number[]) { + this.selectedAtomIndices.clear() + for (var i = 0; i < atomIndices.length; i++) { + this.selectedAtomIndices.add(atomIndices[i]) + } + this.selectedUpdate() + } + + + selectedUpdate () { + const pickData = this.selectedAtomIndices.list + const radiusData: { [k: number]: number } = {} + pickData.forEach(ai => { + const r = Math.max(0.1, this.getMaxRepresentationRadius(ai)) + radiusData[ai] = r * (2.3 - smoothstep(0.1, 2, r)) + }) + this.selectedRepresentation.setSelection( + pickData.length ? ('@' + pickData.join(',')) : 'none' + ) + this.selectedRepresentation.setParameters({ radiusData }) + } } export const enum MeasurementFlags { diff --git a/src/controls/mouse-actions.ts b/src/controls/mouse-actions.ts index 4c155ddd8..c0365010d 100644 --- a/src/controls/mouse-actions.ts +++ b/src/controls/mouse-actions.ts @@ -176,6 +176,29 @@ class MouseActions { stage.trackballControls.rotateComponent(dx, dy) } + /** + * Move picked component based on mouse coordinate changes + * @param {Stage} stage + * @param {Number} dx - amount to move in x direction + * @param {Number} dy - amount to move in y direction + * @return {undefined} + */ + static moveComponentDrag (stage: Stage, dx: number, dy: number) { + stage.trackballControls.translateAtoms(dx, dy) + } + + /** + * Rotate picked component based on mouse coordinate changes. + * Doesn't work very well; not implemented in mouse presets. + * @param {Stage} stage + * @param {Number} dx - amount to move in x direction + * @param {Number} dy - amount to move in y direction + * @return {undefined} + */ + static rotateSelectionDrag (stage: Stage, dx: number, dy: number) { + stage.trackballControls.rotateAtoms(dx, dy) + } + /** * Move picked element to the center of the screen * @param {Stage} stage - the stage @@ -217,6 +240,27 @@ class MouseActions { stage.measureClear() } } + + /** + * Add pick + * @param {Stage} stage - the stage + * @param {PickingProxy} pickingProxy - the picking data object + * @return {undefined} + */ + static selectPick (stage: Stage, pickingProxy: PickingProxy) { + if (pickingProxy && (pickingProxy.atom || pickingProxy.bond)) { + const atoms = [pickingProxy.atom.index] || [pickingProxy.bond.atom1.index, pickingProxy.bond.atom2.index] + const sc = pickingProxy.component as StructureComponent + sc.selectedPickIndices(atoms) + } + } + + static clearSelect (stage: Stage) { + stage.eachComponent(function (sc: StructureComponent) { + sc.selectedAtomIndices.clear() + sc.selectedUpdate() + }, "structure") + } } type MouseActionPreset = [ string, MouseActionCallback ][] @@ -231,11 +275,14 @@ export const MouseActionPresets = { [ 'drag-right', MouseActions.panDrag ], [ 'drag-ctrl-left', MouseActions.panDrag ], [ 'drag-ctrl-right', MouseActions.zRotateDrag ], + [ 'drag-shift-right', MouseActions.moveComponentDrag ], [ 'drag-shift-left', MouseActions.zoomDrag ], [ 'drag-middle', MouseActions.zoomFocusDrag ], [ 'drag-ctrl-shift-right', MouseActions.panComponentDrag ], [ 'drag-ctrl-shift-left', MouseActions.rotateComponentDrag ], + [ 'clickPick-shift-left', MouseActions.selectPick ], + [ 'doubleClick-shift-left', MouseActions.clearSelect ], [ 'clickPick-right', MouseActions.measurePick ], [ 'clickPick-ctrl-left', MouseActions.measurePick ], diff --git a/src/controls/trackball-controls.ts b/src/controls/trackball-controls.ts index 3b7f02852..2763a7744 100644 --- a/src/controls/trackball-controls.ts +++ b/src/controls/trackball-controls.ts @@ -13,6 +13,7 @@ import Viewer from '../viewer/viewer' import ViewerControls from './viewer-controls' import AtomProxy from '../proxy/atom-proxy'; import Component from '../component/component'; +import StructureComponent from '../component/structure-component'; const tmpRotateXMatrix = new Matrix4() const tmpRotateYMatrix = new Matrix4() @@ -118,6 +119,45 @@ class TrackballControls { this.component.updateRepresentations({ 'position': true }) } + private _translateAtom (panMatrix: Matrix4, atom: AtomProxy, x: number, y: number) { + let _tmpAtomVector = new Vector3(); + let _tmpPanVector = new Vector3(); + atom.positionToVector3(_tmpAtomVector) + _tmpAtomVector.add(this.viewer.translationGroup.position) + _tmpAtomVector.applyMatrix4(this.viewer.rotationGroup.matrix) + + let scaleFactor = this.controls.getCanvasScaleFactor(_tmpAtomVector.z) + _tmpPanVector.set(x, y, 0) + _tmpPanVector.multiplyScalar(this.panSpeed * scaleFactor) + _tmpPanVector.applyMatrix4(panMatrix) + + + atom.positionAdd(_tmpPanVector) + } + + private _translateComponent (comp: StructureComponent, x: number, y: number) { + + let _tmpPanMatrix = new Matrix4(); + _tmpPanMatrix.extractRotation(comp.transform) + _tmpPanMatrix.premultiply(this.viewer.rotationGroup.matrix) + _tmpPanMatrix.getInverse(_tmpPanMatrix) + + for (var j = 0; j < comp.selectedAtomIndices.list.length; j++) { + let i = comp.selectedAtomIndices.list[j] + let atom = comp.structure.getAtomProxy(i) + this._translateAtom(_tmpPanMatrix, atom, x, y) + } + + comp.updateRepresentations({'position': true}) + } + + translateAtoms (x: number, y: number) { + let comps = this.stage.structureComponents + for (var i = 0; i < comps.length; i++) { + this._translateComponent(comps[i], x, y) + } + } + rotate (x: number, y: number) { const [ dx, dy ] = this._getRotateXY(x, y) @@ -153,6 +193,51 @@ class TrackballControls { this.component.quaternion.premultiply(tmpRotateQuaternion) this.component.updateMatrix() } + + _rotateAtoms (comp: StructureComponent, x: number, y: number) { + // TODO + // Fix rotation + const [ dx, dy ] = this._getRotateXY(x, y) + + let rot: Matrix4 = this.viewer.rotationGroup.matrix + let rotInv: Matrix4 = this.viewer.rotationGroup.matrix + rotInv.getInverse(rotInv) + + tmpRotateMatrix.extractRotation(comp.transform) + tmpRotateMatrix.premultiply(rot) + tmpRotateMatrix.getInverse(tmpRotateMatrix) + tmpRotateVector.set(1, 0, 0) + tmpRotateVector.applyMatrix4(tmpRotateMatrix) + tmpRotateXMatrix.makeRotationAxis(tmpRotateVector, dy) + tmpRotateVector.set(0, 1, 0) + tmpRotateVector.applyMatrix4(tmpRotateMatrix) + tmpRotateYMatrix.makeRotationAxis(tmpRotateVector, dx) + tmpRotateXMatrix.multiply(tmpRotateYMatrix) + tmpRotateQuaternion.setFromRotationMatrix(tmpRotateXMatrix) + + for (var j = 0; j < comp.selectedAtomIndices.list.length; j++) { + let i = comp.selectedAtomIndices.list[j] + let atom = comp.structure.getAtomProxy(i) + let _tmpAtomVector = new Vector3(); + atom.positionToVector3(_tmpAtomVector) + + _tmpAtomVector.add(this.viewer.translationGroup.position) + _tmpAtomVector.applyMatrix4(rot) + _tmpAtomVector.applyQuaternion(tmpRotateQuaternion) + _tmpAtomVector.applyMatrix4(rotInv) + _tmpAtomVector.sub(this.viewer.translationGroup.position) + atom.positionFromVector3(_tmpAtomVector) + } + + comp.updateRepresentations({'position': true}) + } + + rotateAtoms (x: number, y: number) { + let comps = this.stage.structureComponents + for (var i = 0; i < comps.length; i++) { + this._rotateAtoms(comps[i], x, y) + } + } } export default TrackballControls diff --git a/src/globals.ts b/src/globals.ts index a31a62cc9..69b94d11f 100644 --- a/src/globals.ts +++ b/src/globals.ts @@ -75,10 +75,25 @@ export let MeasurementDefaultParams = { arcVisible: true, planeVisible: false } + +export let SelectionDefaultParams = { + color: 'white', + lineOpacity: 0.8, + linewidth: 5.0, + opacity: 0.6, + + labelUnit: 'angstrom', + arcVisible: true, + planeVisible: false +} export function setMeasurementDefaultParams (params = {}) { Object.assign(MeasurementDefaultParams, params) } +export function setSelectionDefaultParams (params = {}) { + Object.assign(SelectionDefaultParams, params) +} + export let Debug = boolean(getQuery('debug')) export function setDebug (value: boolean) { Debug = value diff --git a/src/ngl.ts b/src/ngl.ts index 98a2e78be..e75b3a468 100644 --- a/src/ngl.ts +++ b/src/ngl.ts @@ -15,6 +15,7 @@ import _Promise from 'promise-polyfill' export { Debug, setDebug, MeasurementDefaultParams, setMeasurementDefaultParams, + SelectionDefaultParams, setSelectionDefaultParams, ScriptExtensions, ColormakerRegistry, DatasourceRegistry, DecompressorRegistry, ParserRegistry, RepresentationRegistry, diff --git a/src/proxy/bond-proxy.ts b/src/proxy/bond-proxy.ts index e380d9194..d1471f822 100644 --- a/src/proxy/bond-proxy.ts +++ b/src/proxy/bond-proxy.ts @@ -53,6 +53,13 @@ class BondProxy { return this.structure.getAtomProxy(this.atomIndex2) } + /** + * @type {[AtomProxy, AtomProxy]} + */ + get atoms () { + return [this.atom1, this.atom2] + } + /** * @type {Integer} */ diff --git a/src/stage/stage.ts b/src/stage/stage.ts index 57741a1ce..b45f79ed2 100644 --- a/src/stage/stage.ts +++ b/src/stage/stage.ts @@ -899,6 +899,29 @@ class Stage { this.eachComponent((sc: StructureComponent) => sc.measureUpdate(), 'structure') } + selectedUpdate() { + this.eachComponent((sc: StructureComponent) => sc.selectedUpdate(), 'structure') + } + + get selectedProxies() { + let proxies: AtomProxy[] = []; + this.eachComponent(function (sc: StructureComponent) { + sc.selectedAtomIndices.list.forEach(function (i) { + let ap = sc.structure.getAtomProxy(i) + proxies.push(ap) + }) + }, "structure") + return proxies + } + + get structureComponents() { + let comps: StructureComponent[] = []; + this.eachComponent(function (sc: StructureComponent) { + comps.push(sc) + }, "structure") + return comps + } + /** * Cleanup when disposing of a stage object */ diff --git a/src/utils/toggle-set.ts b/src/utils/toggle-set.ts new file mode 100644 index 000000000..8b64a635f --- /dev/null +++ b/src/utils/toggle-set.ts @@ -0,0 +1,71 @@ +/** + * @file toggle-set + * @author Lily Wang + * @private + */ + +export interface ToggleSet { + has: (value: T) => boolean + add: (value: T) => void + del: (value: T) => void + toggle: (value: T) => void + toggleAny: (value: T[]) => void + count: number + list: T[] + clear: () => void +} + +export function createToggleSet(): ToggleSet { + const list: T[] = [] + + return { + has: function (value: T) { return list.indexOf(value) !== -1 }, + add: function (value: T) { + if (list.indexOf(value) === -1) { + list.push(value) + } + }, + del: function (value: T) { + if (list.indexOf(value) !== -1) { + list.splice(list.indexOf(value), 1) + } + }, + toggle: function (value: T) { + if (this.has(value)) { + this.del(value) + } else { + this.add(value) + } + }, + toggleAny: function (values: T[]) { + let addAll = false; + for (var i = 0; i < values.length; i++) { + if (!list.includes(values[i])) { + addAll = true; + } + } + + if (addAll) { + for (var i = 0; i < values.length; i++) { + let value = values[i] + if (!list.includes(value)) { + list.push(value) + } + } + } else { + for (var i = 0; i < values.length; i++) { + let value = values[i] + if (list.indexOf(value) !== -1) { + list.splice(list.indexOf(value), 1) + } + } + } + + }, + get count() { return list.length }, + get list() { return list }, + clear: function () { + list.splice(0) + } + } +} \ No newline at end of file