diff --git a/.eslintrc.json b/.eslintrc.json
index c8740de119e38e394988609bade687307a8c8269..34232f64f5623a56bb067ec6d1f047450ecc109d 100644
--- a/.eslintrc.json
+++ b/.eslintrc.json
@@ -54,7 +54,8 @@
"no-multi-spaces": "error",
"block-spacing": "error",
"keyword-spacing": "off",
- "space-before-blocks": "error"
+ "space-before-blocks": "error",
+ "semi-spacing": "error"
},
"overrides": [
{
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 1a52bf384c81e38a291f36a0ad13191c99357ccb..6ddb14b18f8c8eccb57e7eb12cbcb8321b0a2882 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -8,10 +8,10 @@ jobs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- - name: install node v12
+ - name: install node v14
uses: actions/setup-node@v1
with:
- node-version: 12
+ node-version: 14
- name: yarn install
run: yarn install
- name: eslint
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 72472eadf3d1774e01741927b0dff994bdd20795..e2cf63915e19266bc929dede3585e37368c4af4e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,53 @@ All notable changes to this project will be documented in this file, following t
Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
+## [Unreleased]
+
+- Add additional measurement controls: orientation (box, axes, ellipsoid) & plane (best fit)
+- Improve aromatic bond visuals (add ``aromaticScale``, ``aromaticSpacing``, ``aromaticDashCount`` params)
+- [Breaking] Change ``adjustCylinderLength`` default to ``false`` (set to true for focus representation)
+- Fix marker highlight color overriding select color
+
+## [v2.3.5] - 2021-10-19
+
+- Fix sequence viewer for PDB files with COMPND record and multichain entities.
+- Fix index pair bonds order assignment
+
+## [v2.3.4] - 2021-10-12
+
+- Fix pickScale not taken into account in line/point shader
+- Add pixel-scale, pick-scale & pick-padding GET params to Viewer app
+- Fix selecting bonds not adding their atoms in selection manager
+- Add ``preferAtoms`` option to SelectLoci/HighlightLoci behaviors
+- Make the implicit atoms of bond visuals pickable
+ - Add ``preferAtomPixelPadding`` to Canvas3dInteractionHelper
+- Add points & crosses visuals to Line representation
+- Add ``pickPadding`` config option (look around in case target pixel is empty)
+- Add ``multipleBonds`` param to bond visuals with options: off, symmetric, offset
+- Fix ``argparse`` config in servers.
+
+## [v2.3.3] - 2021-10-01
+
+- Fix direct volume shader
+
+## [v2.3.2] - 2021-10-01
+
+- Prefer WebGL1 on iOS devices until WebGL2 support has stabilized.
+
+## [v2.3.1] - 2021-09-28
+
+- Add Charmm saccharide names
+- Treat missing occupancy column as occupancy of 1
+- Fix line shader not accounting for aspect ratio
+- [Breaking] Fix point repr & shader
+ - Was unusable with ``wboit``
+ - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
+ - Set ``pointSizeAttenuation`` to false by default
+ - Set ``sizeTheme`` to ``uniform`` by default
+- Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
+- Add support support for ``chem_comp_bond`` and ``struct_conn`` categories (fixes ModelServer behavior where these categories should have been present)
+- Model and VolumeServer: fix argparse config
+
## [v2.3.0] - 2021-09-06
- Take include/exclude flags into account when displaying aromatic bonds
@@ -111,29 +158,22 @@ Note that since we don't clearly distinguish between a public and private interf
- Fixed Measurements UI labels (#166)
## [v2.0.3] - 2021-04-09
-### Added
-- Support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
-### Changed
+- Add support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
- [Breaking] The ``zip`` function is now asynchronous and expects a ``RuntimeContext``. Also added ``Zip()`` returning a ``Task``.
- [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.
## [v2.0.2] - 2021-03-29
-### Added
-- ``Canvas3D.getRenderObjects``.
-- [WIP] Animate state interpolating, including model trajectories
-### Changed
+- Add ``Canvas3D.getRenderObjects``.
+- [WIP] Animate state interpolating, including model trajectories
- Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
-
-### Fixed
-- VolumeFromDensityServerCif transform label
-
+- Fix VolumeFromDensityServerCif transform label
## [v2.0.1] - 2021-03-23
-### Fixed
-- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
+- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
## [v2.0.0] - 2021-03-23
+
Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.
diff --git a/package-lock.json b/package-lock.json
index a182e4106aefca0f6398e10d764ad3072ddcab85..c5ced1fd9ca1bdff83888b8b2206d48fee639edc 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index c0338722ff1886873e60d13c82fad01e9fc1da23..4d3ffe04fce9d1a53438ac80f304562b6c81e7b9 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "2.3.0",
+ "version": "2.3.5",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
@@ -94,33 +94,33 @@
"@graphql-codegen/typescript": "^2.2.2",
"@graphql-codegen/typescript-graphql-files-modules": "^2.1.0",
"@graphql-codegen/typescript-graphql-request": "^4.1.4",
- "@graphql-codegen/typescript-operations": "^2.1.4",
+ "@graphql-codegen/typescript-operations": "^2.1.6",
"@types/cors": "^2.8.12",
- "@typescript-eslint/eslint-plugin": "^4.31.0",
- "@typescript-eslint/parser": "^4.31.0",
+ "@typescript-eslint/eslint-plugin": "^4.32.0",
+ "@typescript-eslint/parser": "^4.32.0",
"benchmark": "^2.1.4",
- "concurrently": "^6.2.1",
- "cpx2": "^3.0.2",
+ "concurrently": "^6.3.0",
+ "cpx2": "^4.0.0",
"crypto-browserify": "^3.12.0",
- "css-loader": "^6.2.0",
+ "css-loader": "^6.3.0",
"eslint": "^7.32.0",
"extra-watch-webpack-plugin": "^1.0.3",
"file-loader": "^6.2.0",
"fs-extra": "^10.0.0",
- "graphql": "^15.5.3",
- "http-server": "^13.0.1",
- "jest": "^27.1.1",
+ "graphql": "^15.6.0",
+ "http-server": "^13.0.2",
+ "jest": "^27.2.4",
"mini-css-extract-plugin": "^2.3.0",
"node-sass": "^6.0.1",
"path-browserify": "^1.0.1",
"raw-loader": "^4.0.2",
"sass-loader": "^12.1.0",
- "simple-git": "^2.45.1",
+ "simple-git": "^2.46.0",
"stream-browserify": "^3.0.0",
- "style-loader": "^3.2.1",
+ "style-loader": "^3.3.0",
"ts-jest": "^27.0.5",
"typescript": "^4.4.3",
- "webpack": "^5.52.1",
+ "webpack": "^5.56.0",
"webpack-cli": "^4.8.0",
"webpack-version-file-plugin": "^0.4.0"
},
@@ -129,10 +129,10 @@
"@types/benchmark": "^2.1.1",
"@types/compression": "1.7.2",
"@types/express": "^4.17.13",
- "@types/jest": "^27.0.1",
- "@types/node": "^16.9.1",
+ "@types/jest": "^27.0.2",
+ "@types/node": "^16.10.2",
"@types/node-fetch": "^2.5.12",
- "@types/react": "^17.0.20",
+ "@types/react": "^17.0.27",
"@types/react-dom": "^17.0.9",
"@types/swagger-ui-dist": "3.30.1",
"argparse": "^2.0.1",
@@ -146,8 +146,8 @@
"node-fetch": "^2.6.2",
"react": "^17.0.2",
"react-dom": "^17.0.2",
- "rxjs": "^7.3.0",
- "swagger-ui-dist": "^3.52.1",
+ "rxjs": "^7.3.1",
+ "swagger-ui-dist": "^3.52.3",
"tslib": "^2.3.1",
"util.promisify": "^1.1.1",
"xhr2": "^0.2.1"
diff --git a/src/apps/viewer/index.html b/src/apps/viewer/index.html
index 1d9b6ec5ac33d20aebbd2e63c82d77214e5dd12a..40af8122b84c07e39c0c4392580fa905b75b0165 100644
--- a/src/apps/viewer/index.html
+++ b/src/apps/viewer/index.html
@@ -52,12 +52,22 @@
var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
+ var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
+ var pixelScale = getParam('pixel-scale', '[^&]+').trim();
+ var pickScale = getParam('pick-scale', '[^&]+').trim();
+ var pickPadding = getParam('pick-padding', '[^&]+').trim();
var viewer = new molstar.Viewer('app', {
layoutShowControls: !hideControls,
viewportShowExpand: false,
collapseLeftPanel: collapseLeftPanel,
pdbProvider: pdbProvider || 'pdbe',
emdbProvider: emdbProvider || 'pdbe',
+ volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
+ ? 'https://maps.rcsb.org'
+ : 'https://www.ebi.ac.uk/pdbe/densities',
+ pixelScale: parseFloat(pixelScale) || 1,
+ pickScale: parseFloat(pickScale) || 0.25,
+ pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
});
var snapshotId = getParam('snapshot-id', '[^&]+').trim();
diff --git a/src/apps/viewer/index.ts b/src/apps/viewer/index.ts
index 2ffa3624d8e73538b25e234343753eeb491aacd2..84fb6dae83f94e5026e7ee65d860fe2c74ead9ed 100644
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -71,9 +71,11 @@ const DefaultViewerOptions = {
layoutShowLog: true,
layoutShowLeftPanel: true,
collapseLeftPanel: false,
- disableAntialiasing: false,
- pixelScale: 1,
- enableWboit: true,
+ disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
+ pixelScale: PluginConfig.General.PixelScale.defaultValue,
+ pickScale: PluginConfig.General.PickScale.defaultValue,
+ pickPadding: PluginConfig.General.PickPadding.defaultValue,
+ enableWboit: PluginConfig.General.EnableWboit.defaultValue,
viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -130,6 +132,8 @@ export class Viewer {
config: [
[PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
[PluginConfig.General.PixelScale, o.pixelScale],
+ [PluginConfig.General.PickScale, o.pickScale],
+ [PluginConfig.General.PickPadding, o.pickPadding],
[PluginConfig.General.EnableWboit, o.enableWboit],
[PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
[PluginConfig.Viewport.ShowControls, o.viewportShowControls],
diff --git a/src/mol-canvas3d/camera.ts b/src/mol-canvas3d/camera.ts
index 5d1f7a584c02a832aa21cc3008f45bad241dc54a..95074d76a1d1418d90c61ab2c28c8dea20f6df34 100644
--- a/src/mol-canvas3d/camera.ts
+++ b/src/mol-canvas3d/camera.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -27,6 +27,10 @@ interface ICamera {
readonly fogNear: number,
}
+const tmpPos1 = Vec3();
+const tmpPos2 = Vec3();
+const tmpClip = Vec4();
+
class Camera implements ICamera {
readonly view: Mat4 = Mat4.identity();
readonly projection: Mat4 = Mat4.identity();
@@ -155,14 +159,32 @@ class Camera implements ICamera {
}
}
+ /** Transform point into 2D window coordinates. */
project(out: Vec4, point: Vec3) {
return cameraProject(out, point, this.viewport, this.projectionView);
}
- unproject(out: Vec3, point: Vec3) {
+ /**
+ * Transform point from screen space to 3D coordinates.
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
+ */
+ unproject(out: Vec3, point: Vec3 | Vec4) {
return cameraUnproject(out, point, this.viewport, this.inverseProjectionView);
}
+ /** World space pixel size at given `point` */
+ getPixelSize(point: Vec3) {
+ // project -> unproject of `point` does not exactly return the same
+ // to get a sufficiently accurate measure we unproject the original
+ // clip position in addition to the one shifted bey one pixel
+ this.project(tmpClip, point);
+ this.unproject(tmpPos1, tmpClip);
+ tmpClip[0] += 1;
+ this.unproject(tmpPos2, tmpClip);
+ return Vec3.distance(tmpPos1, tmpPos2);
+ }
+
constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(0, 0, 128, 128), props: Partial<{ pixelScale: number }> = {}) {
this.viewport = viewport;
this.pixelScale = props.pixelScale || 1;
@@ -178,7 +200,7 @@ namespace Camera {
/**
* Sets an offseted view in a larger frustum. This is useful for
* - multi-window or multi-monitor/multi-machine setups
- * - jittering the camera position for
+ * - jittering the camera position for sampling
*/
export interface ViewOffset {
enabled: boolean,
diff --git a/src/mol-canvas3d/camera/util.ts b/src/mol-canvas3d/camera/util.ts
index 6e787cbb0595ee654fed8b8ff6f943e700f27663..573d123133eee967a8cbfa0012825f957edcacfb 100644
--- a/src/mol-canvas3d/camera/util.ts
+++ b/src/mol-canvas3d/camera/util.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -55,14 +55,11 @@ namespace Viewport {
//
-const NEAR_RANGE = 0;
-const FAR_RANGE = 1;
-
const tmpVec4 = Vec4();
/** Transform point into 2D window coordinates. */
export function cameraProject(out: Vec4, point: Vec3, viewport: Viewport, projectionView: Mat4) {
- const { x: vX, y: vY, width: vWidth, height: vHeight } = viewport;
+ const { x, y, width, height } = viewport;
// clip space -> NDC -> window coordinates, implicit 1.0 for w component
Vec4.set(tmpVec4, point[0], point[1], point[2], 1.0);
@@ -78,27 +75,28 @@ export function cameraProject(out: Vec4, point: Vec3, viewport: Viewport, projec
tmpVec4[2] /= w;
}
- // transform into window coordinates, set fourth component is (1/clip.w) as in gl_FragCoord.w
- out[0] = vX + vWidth / 2 * tmpVec4[0] + (0 + vWidth / 2);
- out[1] = vY + vHeight / 2 * tmpVec4[1] + (0 + vHeight / 2);
- out[2] = (FAR_RANGE - NEAR_RANGE) / 2 * tmpVec4[2] + (FAR_RANGE + NEAR_RANGE) / 2;
+ // transform into window coordinates, set fourth component to 1 / clip.w as in gl_FragCoord.w
+ out[0] = (tmpVec4[0] + 1) * width * 0.5 + x;
+ out[1] = (1 - tmpVec4[1]) * height * 0.5 + y; // flip Y
+ out[2] = (tmpVec4[2] + 1) * 0.5;
out[3] = w === 0 ? 0 : 1 / w;
return out;
}
/**
* Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
*/
-export function cameraUnproject(out: Vec3, point: Vec3, viewport: Viewport, inverseProjectionView: Mat4) {
- const { x: vX, y: vY, width: vWidth, height: vHeight } = viewport;
+export function cameraUnproject(out: Vec3, point: Vec3 | Vec4, viewport: Viewport, inverseProjectionView: Mat4) {
+ const { x, y, width, height } = viewport;
- const x = point[0] - vX;
- const y = (vHeight - point[1] - 1) - vY;
- const z = point[2];
+ const px = point[0] - x;
+ const py = (height - point[1] - 1) - y;
+ const pz = point[2];
- out[0] = (2 * x) / vWidth - 1;
- out[1] = (2 * y) / vHeight - 1;
- out[2] = 2 * z - 1;
+ out[0] = (2 * px) / width - 1;
+ out[1] = (2 * py) / height - 1;
+ out[2] = 2 * pz - 1;
return Vec3.transformMat4(out, out, inverseProjectionView);
}
\ No newline at end of file
diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index d28751fe5a906c44bcb96e932e14922d43561919..a8a525d6f2e35508dc1c8f85c7e3565e64f24cb4 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -23,7 +23,7 @@ import { Camera } from './camera';
import { ParamDefinition as PD } from '../mol-util/param-definition';
import { DebugHelperParams } from './helper/bounding-sphere-helper';
import { SetUtils } from '../mol-util/set';
-import { Canvas3dInteractionHelper } from './helper/interaction-events';
+import { Canvas3dInteractionHelper, Canvas3dInteractionHelperParams } from './helper/interaction-events';
import { PostprocessingParams } from './passes/postprocessing';
import { MultiSampleHelper, MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
import { PickData } from './passes/pick';
@@ -84,6 +84,7 @@ export const Canvas3DParams = {
marking: PD.Group(MarkingParams),
renderer: PD.Group(RendererParams),
trackball: PD.Group(TrackballControlsParams),
+ interaction: PD.Group(Canvas3dInteractionHelperParams),
debug: PD.Group(DebugHelperParams),
handle: PD.Group(HandleHelperParams),
};
@@ -115,19 +116,23 @@ namespace Canvas3DContext {
preserveDrawingBuffer: true,
pixelScale: 1,
pickScale: 0.25,
- enableWboit: true
+ /** extra pixels to around target to check in case target is empty */
+ pickPadding: 1,
+ enableWboit: true,
+ preferWebGl1: false
};
export type Attribs = typeof DefaultAttribs
export function fromCanvas(canvas: HTMLCanvasElement, attribs: Partial<Attribs> = {}): Canvas3DContext {
const a = { ...DefaultAttribs, ...attribs };
- const { antialias, preserveDrawingBuffer, pixelScale } = a;
+ const { antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
const gl = getGLContext(canvas, {
antialias,
preserveDrawingBuffer,
alpha: true, // the renderer requires an alpha channel
depth: true, // the renderer requires a depth buffer
premultipliedAlpha: true, // the renderer outputs PMA
+ preferWebGl1
});
if (gl === null) throw new Error('Could not create a WebGL rendering context');
@@ -305,8 +310,8 @@ namespace Canvas3D {
const renderer = Renderer.create(webgl, p.renderer);
const helper = new Helper(webgl, scene, p);
- const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height });
- const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera);
+ const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height }, attribs.pickPadding);
+ const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera, p.interaction);
const multiSampleHelper = new MultiSampleHelper(passes.multiSample);
let cameraResetRequested = false;
@@ -642,6 +647,7 @@ namespace Canvas3D {
multiSample: { ...p.multiSample },
renderer: { ...renderer.props },
trackball: { ...controls.props },
+ interaction: { ...interactionHelper.props },
debug: { ...helper.debug.props },
handle: { ...helper.handle.props },
};
@@ -778,6 +784,7 @@ namespace Canvas3D {
if (props.multiSample) Object.assign(p.multiSample, props.multiSample);
if (props.renderer) renderer.setProps(props.renderer);
if (props.trackball) controls.setProps(props.trackball);
+ if (props.interaction) interactionHelper.setProps(props.interaction);
if (props.debug) helper.debug.setProps(props.debug);
if (props.handle) helper.handle.setProps(props.handle);
diff --git a/src/mol-canvas3d/helper/interaction-events.ts b/src/mol-canvas3d/helper/interaction-events.ts
index 9748199ed503f16e890ab915b0e51dde8e5ed6ae..b35b79f697d27fe211eb5eebc5ede7027d43265b 100644
--- a/src/mol-canvas3d/helper/interaction-events.ts
+++ b/src/mol-canvas3d/helper/interaction-events.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,6 +11,8 @@ import { InputObserver, ModifiersKeys, ButtonsType } from '../../mol-util/input/
import { RxEventHelper } from '../../mol-util/rx-event-helper';
import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
import { Camera } from '../camera';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Bond } from '../../mol-model/structure';
type Canvas3D = import('../canvas3d').Canvas3D
type HoverEvent = import('../canvas3d').Canvas3D.HoverEvent
@@ -19,6 +21,17 @@ type ClickEvent = import('../canvas3d').Canvas3D.ClickEvent
const enum InputEvent { Move, Click, Drag }
+const tmpPosA = Vec3();
+const tmpPos = Vec3();
+const tmpNorm = Vec3();
+
+export const Canvas3dInteractionHelperParams = {
+ maxFps: PD.Numeric(30, { min: 10, max: 60, step: 10 }),
+ preferAtomPixelPadding: PD.Numeric(3, { min: 0, max: 20, step: 1 }, { description: 'Number of extra pixels at which to prefer atoms over bonds.' }),
+};
+export type Canvas3dInteractionHelperParams = typeof Canvas3dInteractionHelperParams
+export type Canvas3dInteractionHelperProps = PD.Values<Canvas3dInteractionHelperParams>
+
export class Canvas3dInteractionHelper {
private ev = RxEventHelper.create();
@@ -48,6 +61,12 @@ export class Canvas3dInteractionHelper {
private button: ButtonsType.Flag = ButtonsType.create(0);
private modifiers: ModifiersKeys = ModifiersKeys.None;
+ readonly props: Canvas3dInteractionHelperProps;
+
+ setProps(props: Partial<Canvas3dInteractionHelperProps>) {
+ Object.assign(this.props, props);
+ }
+
private identify(e: InputEvent, t: number) {
const xyChanged = this.startX !== this.endX || this.startY !== this.endY;
@@ -70,7 +89,7 @@ export class Canvas3dInteractionHelper {
}
if (e === InputEvent.Click) {
- const loci = this.getLoci(this.id);
+ const loci = this.getLoci(this.id, this.position);
this.events.click.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
this.prevLoci = loci;
return;
@@ -78,13 +97,13 @@ export class Canvas3dInteractionHelper {
if (!this.inside || this.currentIdentifyT !== t || !xyChanged || this.outsideViewport(this.endX, this.endY)) return;
- const loci = this.getLoci(this.id);
+ const loci = this.getLoci(this.id, this.position);
this.events.hover.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
this.prevLoci = loci;
}
tick(t: number) {
- if (this.inside && t - this.prevT > 1000 / this.maxFps) {
+ if (this.inside && t - this.prevT > 1000 / this.props.maxFps) {
this.prevT = t;
this.currentIdentifyT = t;
this.identify(this.isInteracting ? InputEvent.Drag : InputEvent.Move, t);
@@ -144,11 +163,34 @@ export class Canvas3dInteractionHelper {
);
}
+ private getLoci(pickingId: PickingId | undefined, position: Vec3 | undefined) {
+ const { repr, loci } = this.lociGetter(pickingId);
+ if (position && repr && Bond.isLoci(loci) && loci.bonds.length === 2) {
+ const { aUnit, aIndex } = loci.bonds[0];
+ aUnit.conformation.position(aUnit.elements[aIndex], tmpPosA);
+ Vec3.sub(tmpNorm, this.camera.state.position, this.camera.state.target);
+ Vec3.projectPointOnPlane(tmpPos, position, tmpNorm, tmpPosA);
+ const pixelSize = this.camera.getPixelSize(tmpPos);
+ let radius = repr.theme.size.size(loci.bonds[0]) * (repr.props.sizeFactor ?? 1);
+ if (repr.props.lineSizeAttenuation === false) {
+ // divide by two to get radius
+ radius *= pixelSize / 2;
+ }
+ radius += this.props.preferAtomPixelPadding * pixelSize;
+ if (Vec3.distance(tmpPos, tmpPosA) < radius) {
+ return { repr, loci: Bond.toFirstStructureElementLoci(loci) };
+ }
+ }
+ return { repr, loci };
+ }
+
dispose() {
this.ev.dispose();
}
- constructor(private canvasIdentify: Canvas3D['identify'], private getLoci: Canvas3D['getLoci'], private input: InputObserver, private camera: Camera, private maxFps: number = 30) {
+ constructor(private canvasIdentify: Canvas3D['identify'], private lociGetter: Canvas3D['getLoci'], private input: InputObserver, private camera: Camera, props: Partial<Canvas3dInteractionHelperProps> = {}) {
+ this.props = { ...PD.getDefaultValues(Canvas3dInteractionHelperParams), ...props };
+
input.drag.subscribe(({ x, y, buttons, button, modifiers }) => {
this.isInteracting = true;
// console.log('drag');
diff --git a/src/mol-canvas3d/passes/draw.ts b/src/mol-canvas3d/passes/draw.ts
index 63db5db451b33d91c3d9c299763a0f424acc7743..c3ef689e3d8c061f8a2c69e91e46938ac65e951b 100644
--- a/src/mol-canvas3d/passes/draw.ts
+++ b/src/mol-canvas3d/passes/draw.ts
@@ -362,6 +362,7 @@ export class DrawPass {
render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps, markingProps: MarkingProps) {
renderer.setTransparentBackground(transparentBackground);
renderer.setDrawingBufferSize(this.colorTarget.getWidth(), this.colorTarget.getHeight());
+ renderer.setPixelRatio(this.webgl.pixelRatio);
if (StereoCamera.is(camera)) {
this._render(renderer, camera.left, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps, markingProps);
diff --git a/src/mol-canvas3d/passes/pick.ts b/src/mol-canvas3d/passes/pick.ts
index e89ca205aa57f181676650d4d85e962f9f09b42e..130fe9d80affe760eed23f612d399ed1372b503b 100644
--- a/src/mol-canvas3d/passes/pick.ts
+++ b/src/mol-canvas3d/passes/pick.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -11,6 +11,7 @@ import { WebGLContext } from '../../mol-gl/webgl/context';
import { GraphicsRenderVariant } from '../../mol-gl/webgl/render-item';
import { RenderTarget } from '../../mol-gl/webgl/render-target';
import { Vec3 } from '../../mol-math/linear-algebra';
+import { spiral2d } from '../../mol-math/misc';
import { decodeFloatRGB, unpackRGBAToDepth } from '../../mol-util/float-packing';
import { Camera, ICamera } from '../camera';
import { StereoCamera } from '../camera/stereo';
@@ -88,6 +89,7 @@ export class PickPass {
this.groupPickTarget.bind();
this.renderVariant(renderer, camera, scene, helper, 'pickGroup');
+ // printTexture(this.webgl, this.groupPickTarget.texture, { id: 'group' })
this.depthPickTarget.bind();
this.renderVariant(renderer, camera, scene, helper, 'depth');
@@ -111,6 +113,8 @@ export class PickHelper {
private pickHeight: number
private halfPickWidth: number
+ private spiral: [number, number][]
+
private setupBuffers() {
const bufferSize = this.pickWidth * this.pickHeight * 4;
if (!this.objectBuffer || this.objectBuffer.length !== bufferSize) {
@@ -138,6 +142,8 @@ export class PickHelper {
this.setupBuffers();
}
+
+ this.spiral = spiral2d(Math.round(this.pickScale * this.pickPadding));
}
private syncBuffers() {
@@ -177,6 +183,7 @@ export class PickHelper {
renderer.setTransparentBackground(false);
renderer.setDrawingBufferSize(this.pickPass.objectPickTarget.getWidth(), this.pickPass.objectPickTarget.getHeight());
+ renderer.setPixelRatio(this.pickScale);
if (StereoCamera.is(camera)) {
renderer.setViewport(pickX, pickY, halfPickWidth, pickHeight);
@@ -192,7 +199,7 @@ export class PickHelper {
this.dirty = false;
}
- identify(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
+ private identifyInternal(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
const { webgl, pickScale } = this;
if (webgl.isContextLost) return;
@@ -251,7 +258,14 @@ export class PickHelper {
return { id: { objectId, instanceId, groupId }, position };
}
- constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, private pickPass: PickPass, viewport: Viewport) {
+ identify(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
+ for (const d of this.spiral) {
+ const pickData = this.identifyInternal(x + d[0], y + d[1], camera);
+ if (pickData) return pickData;
+ }
+ }
+
+ constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, private pickPass: PickPass, viewport: Viewport, readonly pickPadding = 1) {
this.setViewport(viewport.x, viewport.y, viewport.width, viewport.height);
}
}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/direct-volume/direct-volume.ts b/src/mol-geo/geometry/direct-volume/direct-volume.ts
index 87bbe53cd7df2a39a10a95febd85056cca5c94f2..c46e32c5d0363e482cefb64d993c30d227848ce7 100644
--- a/src/mol-geo/geometry/direct-volume/direct-volume.ts
+++ b/src/mol-geo/geometry/direct-volume/direct-volume.ts
@@ -9,7 +9,7 @@ import { LocationIterator, PositionLocation } from '../../../mol-geo/util/locati
import { RenderableState } from '../../../mol-gl/renderable';
import { DirectVolumeValues } from '../../../mol-gl/renderable/direct-volume';
import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
-import { Texture } from '../../../mol-gl/webgl/texture';
+import { createNullTexture, Texture } from '../../../mol-gl/webgl/texture';
import { Box3D, Sphere3D } from '../../../mol-math/geometry';
import { Mat4, Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
import { Theme } from '../../../mol-theme/theme';
@@ -129,7 +129,15 @@ export namespace DirectVolume {
}
export function createEmpty(directVolume?: DirectVolume): DirectVolume {
- return {} as DirectVolume; // TODO
+ const bbox = Box3D();
+ const gridDimension = Vec3();
+ const transform = Mat4.identity();
+ const unitToCartn = Mat4.identity();
+ const cellDim = Vec3();
+ const texture = createNullTexture();
+ const stats = Grid.One.stats;
+ const packedGroup = false;
+ return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume);
}
export function createRenderModeParam(stats?: Grid['stats']) {
diff --git a/src/mol-geo/geometry/image/image.ts b/src/mol-geo/geometry/image/image.ts
index 0f34aeff787b93d7e900291fecd77e1de00592df..61447717432b120fb7d10f417ea5e6f08a95ad5e 100644
--- a/src/mol-geo/geometry/image/image.ts
+++ b/src/mol-geo/geometry/image/image.ts
@@ -7,7 +7,7 @@
import { hashFnv32a } from '../../../mol-data/util';
import { LocationIterator } from '../../../mol-geo/util/location-iterator';
import { RenderableState } from '../../../mol-gl/renderable';
-import { calculateTransformBoundingSphere, TextureImage } from '../../../mol-gl/renderable/util';
+import { calculateTransformBoundingSphere, createTextureImage, TextureImage } from '../../../mol-gl/renderable/util';
import { Sphere3D } from '../../../mol-math/geometry';
import { Vec2, Vec4, Vec3 } from '../../../mol-math/linear-algebra';
import { Theme } from '../../../mol-theme/theme';
@@ -113,7 +113,10 @@ namespace Image {
}
export function createEmpty(image?: Image): Image {
- return {} as Image; // TODO
+ const imageTexture = createTextureImage(0, 4, Uint8Array);
+ const corners = image ? image.cornerBuffer.ref.value : new Float32Array(8 * 3);
+ const groupTexture = createTextureImage(0, 4, Uint8Array);
+ return create(imageTexture, corners, groupTexture, image);
}
export const Params = {
diff --git a/src/mol-geo/geometry/lines/lines.ts b/src/mol-geo/geometry/lines/lines.ts
index 4d61a848458e75611ff15a82010f948377a371c2..9809085b67158cd46b91aee50e5ac8b2b84a9de3 100644
--- a/src/mol-geo/geometry/lines/lines.ts
+++ b/src/mol-geo/geometry/lines/lines.ts
@@ -164,7 +164,7 @@ export namespace Lines {
export const Params = {
...BaseGeometry.Params,
- sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }),
+ sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
lineSizeAttenuation: PD.Boolean(false),
};
export type Params = typeof Params
diff --git a/src/mol-geo/geometry/points/points.ts b/src/mol-geo/geometry/points/points.ts
index a3e999d37306db3ad1e92b5e5270a913750153c3..f75a38d84959f69809947c379ba6901444200644 100644
--- a/src/mol-geo/geometry/points/points.ts
+++ b/src/mol-geo/geometry/points/points.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -117,12 +117,19 @@ export namespace Points {
//
+ export const StyleTypes = {
+ 'square': 'Square',
+ 'circle': 'Circle',
+ 'fuzzy': 'Fuzzy',
+ };
+ export type StyleTypes = keyof typeof StyleTypes;
+ export const StyleTypeNames = Object.keys(StyleTypes) as StyleTypes[];
+
export const Params = {
...BaseGeometry.Params,
- sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }),
+ sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
pointSizeAttenuation: PD.Boolean(false),
- pointFilledCircle: PD.Boolean(false),
- pointEdgeBleach: PD.Numeric(0.2, { min: 0, max: 1, step: 0.05 }),
+ pointStyle: PD.Select('square', PD.objectToOptions(StyleTypes)),
};
export type Params = typeof Params
@@ -189,8 +196,7 @@ export namespace Points {
...BaseGeometry.createValues(props, counts),
uSizeFactor: ValueCell.create(props.sizeFactor),
dPointSizeAttenuation: ValueCell.create(props.pointSizeAttenuation),
- dPointFilledCircle: ValueCell.create(props.pointFilledCircle),
- uPointEdgeBleach: ValueCell.create(props.pointEdgeBleach),
+ dPointStyle: ValueCell.create(props.pointStyle),
};
}
@@ -204,8 +210,7 @@ export namespace Points {
BaseGeometry.updateValues(values, props);
ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor);
ValueCell.updateIfChanged(values.dPointSizeAttenuation, props.pointSizeAttenuation);
- ValueCell.updateIfChanged(values.dPointFilledCircle, props.pointFilledCircle);
- ValueCell.updateIfChanged(values.uPointEdgeBleach, props.pointEdgeBleach);
+ ValueCell.updateIfChanged(values.dPointStyle, props.pointStyle);
}
function updateBoundingSphere(values: PointsValues, points: Points) {
@@ -229,10 +234,7 @@ export namespace Points {
function updateRenderableState(state: RenderableState, props: PD.Values<Params>) {
BaseGeometry.updateRenderableState(state, props);
- state.opaque = state.opaque && (
- !props.pointFilledCircle ||
- (props.pointFilledCircle && props.pointEdgeBleach === 0)
- );
+ state.opaque = state.opaque && props.pointStyle !== 'fuzzy';
state.writeDepth = state.opaque;
}
}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/texture-mesh/texture-mesh.ts b/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
index 47bbecb2829076c3a7d24f15963ce5b338b7ef9b..f8df9d171ce3ad2daeffaac5588200a895944ed0 100644
--- a/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
+++ b/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
@@ -19,7 +19,7 @@ import { createEmptyOverpaint } from '../overpaint-data';
import { createEmptyTransparency } from '../transparency-data';
import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
-import { Texture } from '../../../mol-gl/webgl/texture';
+import { createNullTexture, Texture } from '../../../mol-gl/webgl/texture';
import { Vec2, Vec4 } from '../../../mol-math/linear-algebra';
import { createEmptyClipping } from '../clipping-data';
import { NullLocation } from '../../../mol-model/location';
@@ -97,7 +97,11 @@ export namespace TextureMesh {
}
export function createEmpty(textureMesh?: TextureMesh): TextureMesh {
- return {} as TextureMesh; // TODO
+ const vt = textureMesh ? textureMesh.vertexTexture.ref.value : createNullTexture();
+ const gt = textureMesh ? textureMesh.groupTexture.ref.value : createNullTexture();
+ const nt = textureMesh ? textureMesh.normalTexture.ref.value : createNullTexture();
+ const bs = textureMesh ? textureMesh.boundingSphere : Sphere3D();
+ return create(0, 0, vt, gt, nt, bs, textureMesh);
}
export const Params = {
diff --git a/src/mol-gl/_spec/renderer.spec.ts b/src/mol-gl/_spec/renderer.spec.ts
index 0c2a9ea4fbb1190c0f49664505017011de0190b6..c07e61bc5a9d490ba34cae3e20a6f04188af0ee1 100644
--- a/src/mol-gl/_spec/renderer.spec.ts
+++ b/src/mol-gl/_spec/renderer.spec.ts
@@ -85,8 +85,7 @@ function createPoints() {
uSizeFactor: ValueCell.create(1),
dPointSizeAttenuation: ValueCell.create(true),
- dPointFilledCircle: ValueCell.create(false),
- uPointEdgeBleach: ValueCell.create(0.5),
+ dPointStyle: ValueCell.create('square'),
};
const state: RenderableState = {
disposed: false,
diff --git a/src/mol-gl/renderable/points.ts b/src/mol-gl/renderable/points.ts
index 315d6de4b0c7e8bad628b1855060e3d65d52f2b9..ec815261b18e2c668cb8049365dba004e0be70dc 100644
--- a/src/mol-gl/renderable/points.ts
+++ b/src/mol-gl/renderable/points.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -7,9 +7,10 @@
import { Renderable, RenderableState, createRenderable } from '../renderable';
import { WebGLContext } from '../webgl/context';
import { createGraphicsRenderItem } from '../webgl/render-item';
-import { GlobalUniformSchema, BaseSchema, AttributeSpec, UniformSpec, DefineSpec, Values, InternalSchema, SizeSchema, InternalValues, GlobalTextureSchema } from './schema';
+import { GlobalUniformSchema, BaseSchema, AttributeSpec, DefineSpec, Values, InternalSchema, SizeSchema, InternalValues, GlobalTextureSchema } from './schema';
import { PointsShaderCode } from '../shader-code';
import { ValueCell } from '../../mol-util';
+import { Points } from '../../mol-geo/geometry/points/points';
export const PointsSchema = {
...BaseSchema,
@@ -17,8 +18,7 @@ export const PointsSchema = {
aGroup: AttributeSpec('float32', 1, 0),
aPosition: AttributeSpec('float32', 3, 0),
dPointSizeAttenuation: DefineSpec('boolean'),
- dPointFilledCircle: DefineSpec('boolean'),
- uPointEdgeBleach: UniformSpec('f'),
+ dPointStyle: DefineSpec('string', Points.StyleTypeNames),
};
export type PointsSchema = typeof PointsSchema
export type PointsValues = Values<PointsSchema>
diff --git a/src/mol-gl/renderable/schema.ts b/src/mol-gl/renderable/schema.ts
index e9b486a936b8c272dab33c352f867f0cd0443b71..2b2bf6a5e851d851af275a76bf60f3aceaba76b1 100644
--- a/src/mol-gl/renderable/schema.ts
+++ b/src/mol-gl/renderable/schema.ts
@@ -121,7 +121,6 @@ export const GlobalUniformSchema = {
uIsOrtho: UniformSpec('f'),
uPixelRatio: UniformSpec('f'),
- uViewportHeight: UniformSpec('f'),
uViewport: UniformSpec('v4'),
uViewOffset: UniformSpec('v2'),
uDrawingBufferSize: UniformSpec('v2'),
@@ -162,6 +161,7 @@ export const GlobalUniformSchema = {
uSelectColor: UniformSpec('v3'),
uHighlightStrength: UniformSpec('f'),
uSelectStrength: UniformSpec('f'),
+ uMarkerPriority: UniformSpec('i'),
uXrayEdgeFalloff: UniformSpec('f'),
diff --git a/src/mol-gl/renderer.ts b/src/mol-gl/renderer.ts
index 82991710f04d66d8519a509f990074ef374a939e..0cdb2112fa1e4a7b8e4a63cb127e333d97fd73e5 100644
--- a/src/mol-gl/renderer.ts
+++ b/src/mol-gl/renderer.ts
@@ -62,6 +62,7 @@ interface Renderer {
setViewport: (x: number, y: number, width: number, height: number) => void
setTransparentBackground: (value: boolean) => void
setDrawingBufferSize: (width: number, height: number) => void
+ setPixelRatio: (value: number) => void
dispose: () => void
}
@@ -80,6 +81,7 @@ export const RendererParams = {
selectColor: PD.Color(Color.fromNormalizedRgb(0.2, 1.0, 0.1)),
highlightStrength: PD.Numeric(0.7, { min: 0.0, max: 1.0, step: 0.1 }),
selectStrength: PD.Numeric(0.7, { min: 0.0, max: 1.0, step: 0.1 }),
+ markerPriority: PD.Select(1, [[1, 'Highlight'], [2, 'Select']]),
xrayEdgeFalloff: PD.Numeric(1, { min: 0.0, max: 3.0, step: 0.1 }),
@@ -233,7 +235,6 @@ namespace Renderer {
uViewOffset: ValueCell.create(viewOffset),
uPixelRatio: ValueCell.create(ctx.pixelRatio),
- uViewportHeight: ValueCell.create(viewport.height),
uViewport: ValueCell.create(Viewport.toVec4(Vec4(), viewport)),
uDrawingBufferSize: ValueCell.create(drawingBufferSize),
@@ -274,6 +275,7 @@ namespace Renderer {
uSelectColor: ValueCell.create(Color.toVec3Normalized(Vec3(), p.selectColor)),
uHighlightStrength: ValueCell.create(p.highlightStrength),
uSelectStrength: ValueCell.create(p.selectStrength),
+ uMarkerPriority: ValueCell.create(p.markerPriority),
uXrayEdgeFalloff: ValueCell.create(p.xrayEdgeFalloff),
};
@@ -571,7 +573,7 @@ namespace Renderer {
// TODO: simplify, handle in renderable.state???
// uAlpha is updated in "render" so we need to recompute it here
const alpha = clamp(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
- if (alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dRenderMode?.ref.value !== 'volume' && !r.values.dPointFilledCircle?.ref.value && !r.values.dXrayShaded?.ref.value) {
+ if (alpha === 1 && r.values.transparencyAverage.ref.value !== 1 && r.values.dRenderMode?.ref.value !== 'volume' && r.values.dPointStyle?.ref.value !== 'fuzzy' && !r.values.dXrayShaded?.ref.value) {
renderObject(r, 'colorWboit');
}
}
@@ -587,7 +589,7 @@ namespace Renderer {
// TODO: simplify, handle in renderable.state???
// uAlpha is updated in "render" so we need to recompute it here
const alpha = clamp(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
- if (alpha < 1 || r.values.transparencyAverage.ref.value > 0 || r.values.dRenderMode?.ref.value === 'volume' || r.values.dPointFilledCircle?.ref.value || !!r.values.uBackgroundColor || r.values.dXrayShaded?.ref.value) {
+ if (alpha < 1 || r.values.transparencyAverage.ref.value > 0 || r.values.dRenderMode?.ref.value === 'volume' || r.values.dPointStyle?.ref.value === 'fuzzy' || !!r.values.uBackgroundColor || r.values.dXrayShaded?.ref.value) {
renderObject(r, 'colorWboit');
}
}
@@ -670,6 +672,10 @@ namespace Renderer {
p.selectStrength = props.selectStrength;
ValueCell.update(globalUniforms.uSelectStrength, p.selectStrength);
}
+ if (props.markerPriority !== undefined && props.markerPriority !== p.markerPriority) {
+ p.markerPriority = props.markerPriority;
+ ValueCell.update(globalUniforms.uMarkerPriority, p.markerPriority);
+ }
if (props.xrayEdgeFalloff !== undefined && props.xrayEdgeFalloff !== p.xrayEdgeFalloff) {
p.xrayEdgeFalloff = props.xrayEdgeFalloff;
@@ -700,7 +706,6 @@ namespace Renderer {
gl.scissor(x, y, width, height);
if (x !== viewport.x || y !== viewport.y || width !== viewport.width || height !== viewport.height) {
Viewport.set(viewport, x, y, width, height);
- ValueCell.update(globalUniforms.uViewportHeight, height);
ValueCell.update(globalUniforms.uViewport, Vec4.set(globalUniforms.uViewport.ref.value, x, y, width, height));
}
},
@@ -712,6 +717,9 @@ namespace Renderer {
ValueCell.update(globalUniforms.uDrawingBufferSize, Vec2.set(drawingBufferSize, width, height));
}
},
+ setPixelRatio: (value: number) => {
+ ValueCell.update(globalUniforms.uPixelRatio, value);
+ },
props: p,
get stats(): RendererStats {
diff --git a/src/mol-gl/shader/chunks/apply-marker-color.glsl.ts b/src/mol-gl/shader/chunks/apply-marker-color.glsl.ts
index 9b888c7493cab936e2fddc26a84258b3efe49482..6f09848c28ae456bf73cf2d39b8895e63fa46c43 100644
--- a/src/mol-gl/shader/chunks/apply-marker-color.glsl.ts
+++ b/src/mol-gl/shader/chunks/apply-marker-color.glsl.ts
@@ -1,6 +1,6 @@
export const apply_marker_color = `
-if (marker > 0.1) {
- if (intMod(marker, 2.0) > 0.1) {
+if (marker > 0.0) {
+ if ((uMarkerPriority == 1 && marker != 2.0) || (uMarkerPriority != 1 && marker == 1.0)) {
gl_FragColor.rgb = mix(gl_FragColor.rgb, uHighlightColor, uHighlightStrength);
gl_FragColor.a = max(gl_FragColor.a, uHighlightStrength * 0.002); // for direct-volume rendering
} else {
diff --git a/src/mol-gl/shader/chunks/assign-material-color.glsl.ts b/src/mol-gl/shader/chunks/assign-material-color.glsl.ts
index c147051ec483c6b642b3d0a3af4c4ad224b9634d..9d550b8f14277d2fd128601971edcc78cf9d9136 100644
--- a/src/mol-gl/shader/chunks/assign-material-color.glsl.ts
+++ b/src/mol-gl/shader/chunks/assign-material-color.glsl.ts
@@ -3,9 +3,8 @@ export const assign_material_color = `
#if defined(dMarkerType_uniform)
float marker = uMarker;
#elif defined(dMarkerType_groupInstance)
- float marker = vMarker;
+ float marker = floor(vMarker * 255.0 + 0.5); // rounding required to work on some cards on win
#endif
- marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win
#endif
#if defined(dRenderVariant_color)
diff --git a/src/mol-gl/shader/chunks/common-frag-params.glsl.ts b/src/mol-gl/shader/chunks/common-frag-params.glsl.ts
index e3aac5f0e61d0a1740385f21a90a9beaabc95a2e..e062b9e02b4af74910b4af29c06123eb51fed4c1 100644
--- a/src/mol-gl/shader/chunks/common-frag-params.glsl.ts
+++ b/src/mol-gl/shader/chunks/common-frag-params.glsl.ts
@@ -23,6 +23,7 @@ uniform vec3 uHighlightColor;
uniform vec3 uSelectColor;
uniform float uHighlightStrength;
uniform float uSelectStrength;
+uniform int uMarkerPriority;
#if defined(dMarkerType_uniform)
uniform float uMarker;
diff --git a/src/mol-gl/shader/direct-volume.frag.ts b/src/mol-gl/shader/direct-volume.frag.ts
index 6611631063258c21475ccd630f82e8304c33f409..e6fc9d32471a93a0a8dcc115f17dd373edf4093d 100644
--- a/src/mol-gl/shader/direct-volume.frag.ts
+++ b/src/mol-gl/shader/direct-volume.frag.ts
@@ -55,6 +55,7 @@ uniform vec3 uHighlightColor;
uniform vec3 uSelectColor;
uniform float uHighlightStrength;
uniform float uSelectStrength;
+uniform int uMarkerPriority;
#if defined(dMarkerType_uniform)
uniform float uMarker;
diff --git a/src/mol-gl/shader/lines.vert.ts b/src/mol-gl/shader/lines.vert.ts
index b39198d888020593ba1c9b79b80c3541088532ae..6a8c6c5e2e1c04278adeeef486702299a048c9a7 100644
--- a/src/mol-gl/shader/lines.vert.ts
+++ b/src/mol-gl/shader/lines.vert.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*
@@ -18,7 +18,7 @@ precision highp int;
#include common_clip
uniform float uPixelRatio;
-uniform float uViewportHeight;
+uniform vec4 uViewport;
attribute mat4 aTransform;
attribute float aInstance;
@@ -39,6 +39,8 @@ void trimSegment(const in vec4 start, inout vec4 end) {
}
void main(){
+ float aspect = uViewport.z / uViewport.w;
+
#include assign_group
#include assign_color_varying
#include assign_marker_varying
@@ -83,15 +85,15 @@ void main(){
vec2 dir = ndcEnd - ndcStart;
// account for clip-space aspect ratio
- dir.x *= uPixelRatio;
+ dir.x *= aspect;
dir = normalize(dir);
// perpendicular to dir
vec2 offset = vec2(dir.y, - dir.x);
// undo aspect ratio adjustment
- dir.x /= uPixelRatio;
- offset.x /= uPixelRatio;
+ dir.x /= aspect;
+ offset.x /= aspect;
// sign flip
if (aMapping.x < 0.0) offset *= -1.0;
@@ -99,16 +101,17 @@ void main(){
// calculate linewidth
float linewidth;
#ifdef dLineSizeAttenuation
- linewidth = size * uPixelRatio * ((uViewportHeight / 2.0) / -start.z) * 5.0;
+ linewidth = size * uPixelRatio * ((uViewport.w / 2.0) / -start.z) * 5.0;
#else
linewidth = size * uPixelRatio;
#endif
+ linewidth = max(1.0, linewidth);
// adjust for linewidth
offset *= linewidth;
// adjust for clip-space to screen-space conversion
- offset /= uViewportHeight;
+ offset /= uViewport.w;
// select end
vec4 clip = (aMapping.y < 0.5) ? clipStart : clipEnd;
diff --git a/src/mol-gl/shader/points.frag.ts b/src/mol-gl/shader/points.frag.ts
index c18506882ebd89581df63f96a0474c9fa28718f8..0d52802e2b016c3dcdec83863ab2ce6180eb0448 100644
--- a/src/mol-gl/shader/points.frag.ts
+++ b/src/mol-gl/shader/points.frag.ts
@@ -13,10 +13,6 @@ precision highp int;
#include color_frag_params
#include common_clip
-#ifdef dPointFilledCircle
- uniform float uPointEdgeBleach;
-#endif
-
const vec2 center = vec2(0.5);
const float radius = 0.5;
@@ -27,6 +23,15 @@ void main(){
bool interior = false;
#include assign_material_color
+ #if defined(dPointStyle_circle)
+ float dist = distance(gl_PointCoord, center);
+ if (dist > radius) discard;
+ #elif defined(dPointStyle_fuzzy)
+ float dist = distance(gl_PointCoord, center);
+ float fuzzyAlpha = 1.0 - smoothstep(0.0, radius, dist);
+ if (fuzzyAlpha < 0.0001) discard;
+ #endif
+
#if defined(dRenderVariant_pick)
#include check_picking_alpha
gl_FragColor = material;
@@ -37,11 +42,8 @@ void main(){
#elif defined(dRenderVariant_color)
gl_FragColor = material;
- #ifdef dPointFilledCircle
- float dist = distance(gl_PointCoord, center);
- float alpha = 1.0 - smoothstep(radius - uPointEdgeBleach, radius, dist);
- if (alpha < 0.0001) discard;
- gl_FragColor.a *= alpha;
+ #if defined(dPointStyle_fuzzy)
+ gl_FragColor.a *= fuzzyAlpha;
#endif
#include apply_marker_color
diff --git a/src/mol-gl/shader/points.vert.ts b/src/mol-gl/shader/points.vert.ts
index db206d1c9aa0aa9416385734707f199f962658b1..0efca334f6532e87ec7fcdcc128aafbc8651eebe 100644
--- a/src/mol-gl/shader/points.vert.ts
+++ b/src/mol-gl/shader/points.vert.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -16,7 +16,7 @@ precision highp int;
#include common_clip
uniform float uPixelRatio;
-uniform float uViewportHeight;
+uniform vec4 uViewport;
attribute vec3 aPosition;
attribute mat4 aTransform;
@@ -32,10 +32,11 @@ void main(){
#include assign_size
#ifdef dPointSizeAttenuation
- gl_PointSize = size * uPixelRatio * ((uViewportHeight / 2.0) / -mvPosition.z) * 5.0;
+ gl_PointSize = size * uPixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 5.0;
#else
gl_PointSize = size * uPixelRatio;
#endif
+ gl_PointSize = max(1.0, gl_PointSize);
gl_Position = uProjection * mvPosition;
diff --git a/src/mol-gl/shader/text.vert.ts b/src/mol-gl/shader/text.vert.ts
index 18b2c256b9a38948caf8082f12f8f2cbae48e94b..38779f2d02ca3c4d2f96932f74bf0406614ab4d0 100644
--- a/src/mol-gl/shader/text.vert.ts
+++ b/src/mol-gl/shader/text.vert.ts
@@ -31,7 +31,7 @@ uniform float uOffsetZ;
// uniform bool ortho;
uniform float uPixelRatio;
-uniform float uViewportHeight;
+uniform vec4 uViewport;
varying vec2 vTexCoord;
@@ -60,9 +60,9 @@ void main(void){
// TODO
// #ifdef FIXED_SIZE
// if (ortho) {
- // scale /= pixelRatio * ((uViewportHeight / 2.0) / -uCameraPosition.z) * 0.1;
+ // scale /= pixelRatio * ((uViewport.w / 2.0) / -uCameraPosition.z) * 0.1;
// } else {
- // scale /= pixelRatio * ((uViewportHeight / 2.0) / -mvPosition.z) * 0.1;
+ // scale /= pixelRatio * ((uViewport.w / 2.0) / -mvPosition.z) * 0.1;
// }
// #endif
diff --git a/src/mol-gl/webgl/context.ts b/src/mol-gl/webgl/context.ts
index 7f255febaeee485d10adbcb2dfad07ddcec33b3a..5ce242b2aa25b81dfebe4beb48376d0a3ac582c5 100644
--- a/src/mol-gl/webgl/context.ts
+++ b/src/mol-gl/webgl/context.ts
@@ -18,7 +18,7 @@ import { now } from '../../mol-util/now';
import { Texture, TextureFilter } from './texture';
import { ComputeRenderable } from '../renderable';
-export function getGLContext(canvas: HTMLCanvasElement, attribs?: WebGLContextAttributes): GLRenderingContext | null {
+export function getGLContext(canvas: HTMLCanvasElement, attribs?: WebGLContextAttributes & { preferWebGl1?: boolean }): GLRenderingContext | null {
function get(id: 'webgl' | 'experimental-webgl' | 'webgl2') {
try {
return canvas.getContext(id, attribs) as GLRenderingContext | null;
@@ -26,7 +26,7 @@ export function getGLContext(canvas: HTMLCanvasElement, attribs?: WebGLContextAt
return null;
}
}
- const gl = get('webgl2') || get('webgl') || get('experimental-webgl');
+ const gl = (attribs?.preferWebGl1 ? null : get('webgl2')) || get('webgl') || get('experimental-webgl');
if (isDebugMode) console.log(`isWebgl2: ${isWebGL2(gl)}`);
return gl;
}
diff --git a/src/mol-io/reader/common/text/column/token.ts b/src/mol-io/reader/common/text/column/token.ts
index b07d20a881152e2566a3e3c7469cb0f50b5dd660..8560c80ecb6968d00d9679ebeebde7384c17fa31 100644
--- a/src/mol-io/reader/common/text/column/token.ts
+++ b/src/mol-io/reader/common/text/column/token.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Column, ColumnHelpers } from '../../../../../mol-data/db';
@@ -50,4 +51,12 @@ export function areValuesEqualProvider(tokens: Tokens) {
}
return true;
};
+}
+
+export function areTokensEmpty(tokens: Tokens) {
+ const { count, indices } = tokens;
+ for (let i = 0; i < count; ++i) {
+ if (indices[2 * i] !== indices[2 * i + 1]) return false;
+ }
+ return true;
}
\ No newline at end of file
diff --git a/src/mol-math/geometry/primitives/axes3d.ts b/src/mol-math/geometry/primitives/axes3d.ts
index bb70f70ef48dcb5af3a4883bf6b62e9762790c04..5db8ae4f5cd692322ebc7dcf7b58572334549f38 100644
--- a/src/mol-math/geometry/primitives/axes3d.ts
+++ b/src/mol-math/geometry/primitives/axes3d.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -48,7 +48,7 @@ namespace Axes3D {
return out;
}
- const tmpTransformMat3 = Mat3.zero();
+ const tmpTransformMat3 = Mat3();
/** Transform axes with a Mat4 */
export function transform(out: Axes3D, a: Axes3D, m: Mat4): Axes3D {
Vec3.transformMat4(out.origin, a.origin, m);
@@ -58,6 +58,13 @@ namespace Axes3D {
Vec3.transformMat3(out.dirC, a.dirC, n);
return out;
}
+
+ export function scale(out: Axes3D, a: Axes3D, scale: number): Axes3D {
+ Vec3.scale(out.dirA, a.dirA, scale);
+ Vec3.scale(out.dirB, a.dirB, scale);
+ Vec3.scale(out.dirC, a.dirC, scale);
+ return out;
+ }
}
export { Axes3D };
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d/vec3.ts b/src/mol-math/linear-algebra/3d/vec3.ts
index c65a310db89b8fb7c98f5d19906df9f2a5589ea7..c0bf8b04f94f8fbcac6d791041609aae78211347 100644
--- a/src/mol-math/linear-algebra/3d/vec3.ts
+++ b/src/mol-math/linear-algebra/3d/vec3.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -540,9 +540,17 @@ namespace Vec3 {
/** Project `point` onto `vector` starting from `origin` */
export function projectPointOnVector(out: Vec3, point: Vec3, vector: Vec3, origin: Vec3) {
- sub(out, copy(out, point), origin);
+ sub(out, point, origin);
const scalar = dot(vector, out) / squaredMagnitude(vector);
- return add(out, scale(out, copy(out, vector), scalar), origin);
+ return add(out, scale(out, vector, scalar), origin);
+ }
+
+ const tmpProjectPlane = zero();
+ /** Project `point` onto `plane` defined by `normal` starting from `origin` */
+ export function projectPointOnPlane(out: Vec3, point: Vec3, normal: Vec3, origin: Vec3) {
+ normalize(tmpProjectPlane, normal);
+ sub(out, point, origin);
+ return sub(out, point, scale(tmpProjectPlane, tmpProjectPlane, dot(out, tmpProjectPlane)));
}
export function projectOnVector(out: Vec3, p: Vec3, vector: Vec3) {
diff --git a/src/mol-math/linear-algebra/tensor.ts b/src/mol-math/linear-algebra/tensor.ts
index 94a6df386d7d1fb1ae28582efb1f240e942e29a2..f28143270888831464486009c7a7ba5ade3b892e 100644
--- a/src/mol-math/linear-algebra/tensor.ts
+++ b/src/mol-math/linear-algebra/tensor.ts
@@ -109,7 +109,10 @@ export namespace Tensor {
set: (t, d, x) => t[d] = x,
add: (t, d, x) => t[d] += x,
dataOffset: (d) => d,
- getCoords: (o, c) => { c[0] = o; return c as number[]; }
+ getCoords: (o, c) => {
+ c[0] = o;
+ return c as number[];
+ }
};
case 2: {
// column major
@@ -120,7 +123,11 @@ export namespace Tensor {
set: (t, i, j, x) => t[j * rows + i] = x,
add: (t, i, j, x) => t[j * rows + i] += x,
dataOffset: (i, j) => j * rows + i,
- getCoords: (o, c) => { c[0] = o % rows; c[1] = Math.floor(o / rows) ; return c as number[]; }
+ getCoords: (o, c) => {
+ c[0] = o % rows;
+ c[1] = Math.floor(o / rows);
+ return c as number[];
+ }
};
}
if (ao[0] === 1 && ao[1] === 0) {
@@ -130,7 +137,11 @@ export namespace Tensor {
set: (t, i, j, x) => t[i * cols + j] = x,
add: (t, i, j, x) => t[i * cols + j] += x,
dataOffset: (i, j) => i * cols + j,
- getCoords: (o, c) => { c[0] = Math.floor(o / cols); c[1] = o % cols; return c as number[]; }
+ getCoords: (o, c) => {
+ c[0] = Math.floor(o / cols);
+ c[1] = o % cols;
+ return c as number[];
+ }
};
}
throw new Error('bad axis order');
diff --git a/src/mol-math/misc.ts b/src/mol-math/misc.ts
index 235baa8a53d672a2136e76df813193000b64c1e0..05afcf7f225d9a53ec90906813f7259ddbb388ff 100644
--- a/src/mol-math/misc.ts
+++ b/src/mol-math/misc.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -37,4 +37,28 @@ export function absMax(...values: number[]) {
/** Length of an arc with angle in radians */
export function arcLength(angle: number, radius: number) {
return angle * radius;
+}
+
+/** Create an outward spiral of given `radius` on a 2d grid */
+export function spiral2d(radius: number) {
+ let x = 0;
+ let y = 0;
+ const delta = [0, -1];
+ const size = radius * 2 + 1;
+ const halfSize = size / 2;
+ const out: [number, number][] = [];
+
+ for (let i = Math.pow(size, 2); i > 0; --i) {
+ if ((-halfSize < x && x <= halfSize) && (-halfSize < y && y <= halfSize)) {
+ out.push([x, y]);
+ }
+
+ if (x === y || (x < 0 && x === -y) || (x > 0 && x === 1 - y)) {
+ [delta[0], delta[1]] = [-delta[1], delta[0]]; // change direction
+ }
+
+ x += delta[0];
+ y += delta[1];
+ }
+ return out;
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/basic/atomic.ts b/src/mol-model-formats/structure/basic/atomic.ts
index 250bca12f4559df4fdb0bb485d898aa03e05d24f..10ad709b99e408c000add90f88bac8f6e612ed56 100644
--- a/src/mol-model-formats/structure/basic/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -100,7 +100,7 @@ function getConformation(atom_site: AtomSite): AtomicConformation {
return {
id: UUID.create22(),
atomId: atom_site.id,
- occupancy: atom_site.occupancy,
+ occupancy: atom_site.occupancy.isDefined ? atom_site.occupancy : Column.ofConst(1, atom_site._rowCount, Column.Schema.float),
B_iso_or_equiv: atom_site.B_iso_or_equiv,
xyzDefined: atom_site.Cartn_x.isDefined && atom_site.Cartn_y.isDefined && atom_site.Cartn_z.isDefined,
x: atom_site.Cartn_x.toArray({ array: Float32Array }),
diff --git a/src/mol-model-formats/structure/pdb/atom-site.ts b/src/mol-model-formats/structure/pdb/atom-site.ts
index 94aa82e7110f4b448cce2be92801c8b6ba86e52d..7fcc6389101767f11bcf71164ecfaff54a2ba2b1 100644
--- a/src/mol-model-formats/structure/pdb/atom-site.ts
+++ b/src/mol-model-formats/structure/pdb/atom-site.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,6 +10,7 @@ import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
import { TokenBuilder, Tokenizer } from '../../../mol-io/reader/common/text/tokenizer';
import { guessElementSymbolTokens } from '../util';
import { Column } from '../../../mol-data/db';
+import { areTokensEmpty } from '../../../mol-io/reader/common/text/column/token';
type AtomSiteTemplate = typeof getAtomSiteTemplate extends (...args: any) => infer T ? T : never
export function getAtomSiteTemplate(data: string, count: number) {
@@ -63,7 +64,7 @@ export function getAtomSite(sites: AtomSiteTemplate): { [K in keyof mmCIF_Schema
label_seq_id: CifField.ofUndefined(sites.index, Column.Schema.int),
label_entity_id: CifField.ofStrings(sites.label_entity_id),
- occupancy: CifField.ofTokens(sites.occupancy),
+ occupancy: areTokensEmpty(sites.occupancy) ? CifField.ofUndefined(sites.index, Column.Schema.float) : CifField.ofTokens(sites.occupancy),
type_symbol: CifField.ofTokens(sites.type_symbol),
pdbx_PDB_ins_code: CifField.ofTokens(sites.pdbx_PDB_ins_code),
diff --git a/src/mol-model-formats/structure/pdb/entity.ts b/src/mol-model-formats/structure/pdb/entity.ts
index b40f9b2e2cd6808d34d9993ee0afb6d00461596b..9276a0c851c8a830df298f9c6642e211365295eb 100644
--- a/src/mol-model-formats/structure/pdb/entity.ts
+++ b/src/mol-model-formats/structure/pdb/entity.ts
@@ -25,7 +25,7 @@ export function parseCmpnd(lines: Tokens, lineStart: number, lineEnd: number) {
let currentSpec: Spec | undefined;
let currentCompound: EntityCompound = { chains: [], description: '' };
- const Compounds: EntityCompound[] = [];
+ const compounds: EntityCompound[] = [];
for (let i = lineStart; i < lineEnd; i++) {
const line = getLine(i);
@@ -55,7 +55,7 @@ export function parseCmpnd(lines: Tokens, lineStart: number, lineEnd: number) {
chains: [],
description: ''
};
- Compounds.push(currentCompound);
+ compounds.push(currentCompound);
} else if (currentSpec === 'MOLECULE') {
if (currentCompound.description) currentCompound.description += ' ';
currentCompound.description += value;
@@ -64,7 +64,31 @@ export function parseCmpnd(lines: Tokens, lineStart: number, lineEnd: number) {
}
}
- return Compounds;
+ // Define a seprate entity for each chain
+ // --------------------------------------
+ //
+ // This is a workaround for how sequences are currently determined for PDB files.
+ //
+ // The current approach infers the "observed sequence" from the atomic hierarchy.
+ // However, for example for PDB ID 3HHR, this approach fails, since chains B and C
+ // belong to the same entity but contain different observed sequence, which causes display
+ // errors in the sequence viewer (since the sequences are determined "per entity").
+ //
+ // A better approach could be to parse SEQRES categories and use it to construct
+ // entity_poly_seq category. However, this would require constructing label_seq_id (with gaps)
+ // from RES ID pdb column (auth_seq_id), which isn't a trivial exercise.
+ //
+ // (properly formatted) mmCIF structures do not exhibit this issue.
+ const singletons: EntityCompound[] = [];
+ for (const comp of compounds) {
+ for (const chain of comp.chains) {
+ singletons.push({
+ description: comp.description,
+ chains: [chain]
+ });
+ }
+ }
+ return singletons;
}
export function parseHetnam(lines: Tokens, lineStart: number, lineEnd: number) {
diff --git a/src/mol-model-formats/structure/pdb/secondary-structure.ts b/src/mol-model-formats/structure/pdb/secondary-structure.ts
index d6c6e60e11caf9f8d2a2985e563ee76d3c467aa9..626a201bd917ee58939eedd26e49efce69fc9fa9 100644
--- a/src/mol-model-formats/structure/pdb/secondary-structure.ts
+++ b/src/mol-model-formats/structure/pdb/secondary-structure.ts
@@ -102,7 +102,7 @@ export function parseHelix(lines: Tokens, lineStart: number, lineEnd: number): C
const beg_auth_comp_id = CifField.ofStrings(helices.map(h => h.initResName));
const end_auth_asym_id = CifField.ofStrings(helices.map(h => h.endChainID));
- const end_auth_comp_id = CifField.ofStrings(helices.map(h => h.endResName));;
+ const end_auth_comp_id = CifField.ofStrings(helices.map(h => h.endResName));
const struct_conf: CifCategory.Fields<mmCIF_Schema['struct_conf']> = {
beg_label_asym_id: beg_auth_asym_id,
diff --git a/src/mol-model-props/computed/helix-orientation/helix-orientation.ts b/src/mol-model-props/computed/helix-orientation/helix-orientation.ts
index 5f83a2ce64f7244a7495596b329458270a68946e..512531204bc7ff861993f0bc10f6e6dcafa31a0a 100644
--- a/src/mol-model-props/computed/helix-orientation/helix-orientation.ts
+++ b/src/mol-model-props/computed/helix-orientation/helix-orientation.ts
@@ -127,7 +127,8 @@ export function calcHelixOrientation(model: Model): HelixOrientation {
Vec3.fromArray(v2, centers, e3 - 6);
Vec3.normalize(axis, Vec3.sub(axis, v1, v2));
const eI = traceElementIndex[e];
- Vec3.set(a1, x[eI], y[eI], z[eI]);Vec3.copy(vt, a1);
+ Vec3.set(a1, x[eI], y[eI], z[eI]);
+ Vec3.copy(vt, a1);
Vec3.projectPointOnVector(vt, vt, axis, v1);
Vec3.toArray(vt, centers, e3);
}
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index 64d264efdb40ca2370b4e1f30554f0a8db7ee245..a85152bc8fcfa6dab7b9a062adb8c25ad29736fa 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -283,8 +283,8 @@ namespace Loci {
* Converts structure related loci to StructureElement.Loci and applies
* granularity if given
*/
- export function normalize(loci: Loci, granularity?: Granularity) {
- if (granularity !== 'element' && Bond.isLoci(loci)) {
+ export function normalize(loci: Loci, granularity?: Granularity, alwaysConvertBonds = false) {
+ if ((granularity !== 'element' || alwaysConvertBonds) && Bond.isLoci(loci)) {
// convert Bond.Loci to a StructureElement.Loci so granularity can be applied
loci = Bond.toStructureElementLoci(loci);
}
diff --git a/src/mol-model/structure/export/categories/misc.ts b/src/mol-model/structure/export/categories/misc.ts
index 31887e0d6864f09315fa4fcce6aa6edcfd50a077..a74772ede2aa31ffc63b6a4107124663052528ce 100644
--- a/src/mol-model/structure/export/categories/misc.ts
+++ b/src/mol-model/structure/export/categories/misc.ts
@@ -22,6 +22,18 @@ export const _chem_comp: CifCategory<CifExportContext> = {
}
};
+export const _chem_comp_bond: CifCategory<CifExportContext> = {
+ name: 'chem_comp_bond',
+ instance({ firstModel, structures, cache }) {
+ const chem_comp_bond = getModelMmCifCategory(structures[0].model, 'chem_comp_bond');
+ if (!chem_comp_bond) return CifCategory.Empty;
+ const { comp_id } = chem_comp_bond;
+ const names = cache.uniqueResidueNames || (cache.uniqueResidueNames = getUniqueResidueNamesFromStructures(structures));
+ const indices = Column.indicesOf(comp_id, id => names.has(id));
+ return CifCategory.ofTable(chem_comp_bond, indices);
+ }
+};
+
export const _pdbx_chem_comp_identifier: CifCategory<CifExportContext> = {
name: 'pdbx_chem_comp_identifier',
instance({ firstModel, structures, cache }) {
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 6615a4f87199336ab5497743a33ce49afd7c62e4..eb806f24670562536e68c523d15052a1043a9eb8 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -11,7 +11,7 @@ import { Structure } from '../structure';
import { _atom_site } from './categories/atom_site';
import CifCategory = CifWriter.Category
import { _struct_conf, _struct_sheet_range } from './categories/secondary-structure';
-import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
+import { _chem_comp, _chem_comp_bond, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './categories/misc';
import { Model } from '../model';
import { getUniqueEntityIndicesFromStructures, copy_mmCif_category, copy_source_mmCifCategory } from './categories/utils';
import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
@@ -81,9 +81,12 @@ const Categories = [
copy_mmCif_category('pdbx_entity_branch_link'),
copy_mmCif_category('pdbx_branch_scheme'),
+ // Struct conn
+ copy_mmCif_category('struct_conn'),
+
// Misc
- // TODO: filter for actual present residues?
_chem_comp,
+ _chem_comp_bond,
_pdbx_chem_comp_identifier,
copy_mmCif_category('atom_sites'),
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index 6517d7c7ab756f6355292c957b31bf2b850f40c4..dc8a1c449c8ea5aa14e7fe1742d20d553c6cf5e9 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -309,14 +309,48 @@ const UnknownSaccharideNames = [
'PUF', 'GDA', '9WJ', // via updated CCD
];
+/**
+ * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
+ */
+const CharmmSaccharideNames: { [k: string]: string[] } = {
+ Glc: ['AGLC', 'BGLC'],
+ GlcNAc: ['AGLCNA', 'BGLCNA', 'BGLCN0'],
+ GlcA: ['AGLCA', 'BGLCA', 'BGLCA0'],
+ Man: ['AMAN', 'BMAN'],
+ Rha: ['ARHM', 'BRHM'],
+ Ara: ['AARB', 'BARB'],
+ Gal: ['AGAL', 'BGAL'],
+ GalNAc: ['AGALNA', 'BGALNA'],
+ Gul: ['AGUL', 'BGUL'],
+ Alt: ['AALT', 'BALT'],
+ All: ['AALL', 'BALL'],
+ Tal: ['ATAL', 'BTAL'],
+ Ido: ['AIDO', 'BIDO'],
+ IdoA: ['AIDOA', 'BIDOA'],
+ Fuc: ['AFUC', 'BFUC'],
+ Lyx: ['ALYF', 'BLYF'],
+ Xyl: ['AXYL', 'BXYL', 'AXYF', 'BXYF'],
+ Rib: ['ARIB', 'BRIB'],
+ Fru: ['AFRU', 'BFRU'],
+ Neu5Ac: ['ANE5AC', 'BNE5AC'],
+};
+
export const SaccharideCompIdMap = (function () {
const map = new Map<string, SaccharideComponent>();
for (let i = 0, il = Monosaccharides.length; i < il; ++i) {
const saccharide = Monosaccharides[i];
- const names = CommonSaccharideNames[saccharide.abbr];
- if (names) {
- for (let j = 0, jl = names.length; j < jl; ++j) {
- map.set(names[j], saccharide);
+
+ const common = CommonSaccharideNames[saccharide.abbr];
+ if (common) {
+ for (let j = 0, jl = common.length; j < jl; ++j) {
+ map.set(common[j], saccharide);
+ }
+ }
+
+ const charmm = CharmmSaccharideNames[saccharide.abbr];
+ if (charmm) {
+ for (let j = 0, jl = charmm.length; j < jl; ++j) {
+ map.set(charmm[j], saccharide);
}
}
}
diff --git a/src/mol-model/structure/structure/element/loci.ts b/src/mol-model/structure/structure/element/loci.ts
index 617f869a57916cf5402bb8bd18409376ee0111a2..53c2780c60f4191ab4300bb880b507b9ee490370 100644
--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/src/mol-model/structure/structure/element/loci.ts
@@ -582,6 +582,20 @@ export namespace Loci {
return PrincipalAxes.ofPositions(positions);
}
+ export function getPrincipalAxesMany(locis: Loci[]): PrincipalAxes {
+ let elementCount = 0;
+ locis.forEach(l => {
+ elementCount += size(l);
+ });
+ const positions = new Float32Array(3 * elementCount);
+ let offset = 0;
+ locis.forEach(l => {
+ toPositionsArray(l, positions, offset);
+ offset += size(l) * 3;
+ });
+ return PrincipalAxes.ofPositions(positions);
+ }
+
function sourceIndex(unit: Unit, element: ElementIndex) {
return Unit.isAtomic(unit)
? unit.model.atomicHierarchy.atomSourceIndex.value(element)
diff --git a/src/mol-model/structure/structure/unit.ts b/src/mol-model/structure/structure/unit.ts
index c68322ec210bc4674c196888f0596ebdff4780f1..62a2ec7cf35d25612abaf47062cb22832d68bca5 100644
--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.ts
@@ -369,7 +369,7 @@ namespace Unit {
readonly props: CoarseProperties;
getChild(elements: StructureElement.Set): Unit {
- if (elements.length === this.elements.length) return this as any as Unit /** lets call this an ugly temporary hack */;
+ if (elements.length === this.elements.length) return this as any as Unit; // lets call this an ugly temporary hack
return createCoarse(this.id, this.invariantId, this.chainGroupId, this.traits, this.model, this.kind, elements, this.conformation, CoarseProperties());
}
@@ -465,7 +465,7 @@ namespace Unit {
export class Gaussians extends Coarse<Kind.Gaussians, CoarseGaussianConformation> { }
function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, chainGroupId: number, traits: Traits, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties): K extends Kind.Spheres ? Spheres : Gaussians {
- return new Coarse(id, invariantId, chainGroupId, traits, model, kind, elements, conformation, props) as any /** lets call this an ugly temporary hack */;
+ return new Coarse(id, invariantId, chainGroupId, traits, model, kind, elements, conformation, props) as any; // lets call this an ugly temporary hack
}
export function areSameChainOperatorGroup(a: Unit, b: Unit) {
diff --git a/src/mol-model/structure/structure/unit/bonds.ts b/src/mol-model/structure/structure/unit/bonds.ts
index e00ee03148b64183cff7dc8d94f6c9af68a967ff..20f562397f43989f92f78ea1347a77ae26027c1e 100644
--- a/src/mol-model/structure/structure/unit/bonds.ts
+++ b/src/mol-model/structure/structure/unit/bonds.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -8,7 +8,7 @@
import { Unit, StructureElement } from '../../structure';
import { Structure } from '../structure';
import { BondType } from '../../model/types';
-import { SortedArray, Iterator } from '../../../../mol-data/int';
+import { SortedArray, Iterator, OrderedSet } from '../../../../mol-data/int';
import { CentroidHelper } from '../../../../mol-math/geometry/centroid-helper';
import { Sphere3D } from '../../../../mol-math/geometry';
@@ -132,6 +132,11 @@ namespace Bond {
return StructureElement.Loci(loci.structure, elements);
}
+ export function toFirstStructureElementLoci(loci: Loci): StructureElement.Loci {
+ const { aUnit, aIndex } = loci.bonds[0];
+ return StructureElement.Loci(loci.structure, [{ unit: aUnit, indices: OrderedSet.ofSingleton(aIndex) }]);
+ }
+
export function getType(structure: Structure, location: Location<Unit.Atomic>): BondType {
if (location.aUnit === location.bUnit) {
const bonds = location.aUnit.bonds;
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index 427bf7378901e3e50d3b2d9aa1b05cb271263959..9a77f179656b166a9dfdfc4a7465714ffc2522a3 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -79,7 +79,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
if ((d !== -1 && equalEps(dist, d, 0.5)) || dist < maxDistance) {
atomA[atomA.length] = _aI;
atomB[atomB.length] = _bI;
- orders[order.length] = order[i];
+ orders[orders.length] = order[i];
flags[flags.length] = flag[i];
}
}
@@ -133,7 +133,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
const p = partnerA.atomIndex === aI ? partnerB : partnerA;
const _bI = SortedArray.indexOf(unit.elements, p.atomIndex) as StructureElement.UnitIndex;
- if (_bI < 0) continue;
+ if (_bI < 0 || atoms[_bI] < aI) continue;
atomA[atomA.length] = _aI;
atomB[atomB.length] = _bI;
diff --git a/src/mol-plugin-state/manager/interactivity.ts b/src/mol-plugin-state/manager/interactivity.ts
index 947014640573c2f8f97bec9775256822592167c3..8805432230c49f0046ac8d8f24c5c98d08646775 100644
--- a/src/mol-plugin-state/manager/interactivity.ts
+++ b/src/mol-plugin-state/manager/interactivity.ts
@@ -101,10 +101,10 @@ namespace InteractivityManager {
// TODO clear, then re-apply remaining providers
}
- protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity = true) {
+ protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity: boolean, alwaysConvertBonds = false) {
const { loci, repr } = reprLoci;
const granularity = applyGranularity ? this.props.granularity : undefined;
- return { loci: Loci.normalize(loci, granularity), repr };
+ return { loci: Loci.normalize(loci, granularity, alwaysConvertBonds), repr };
}
protected mark(current: Representation.Loci, action: MarkerAction, noRender = false) {
@@ -187,7 +187,8 @@ namespace InteractivityManager {
toggle(current: Representation.Loci, applyGranularity = true) {
if (Loci.isEmpty(current.loci)) return;
- const normalized = this.normalizedLoci(current, applyGranularity);
+ const normalized = this.normalizedLoci(current, applyGranularity, true);
+
if (StructureElement.Loci.is(normalized.loci)) {
this.toggleSel(normalized);
} else {
@@ -198,7 +199,7 @@ namespace InteractivityManager {
toggleExtend(current: Representation.Loci, applyGranularity = true) {
if (Loci.isEmpty(current.loci)) return;
- const normalized = this.normalizedLoci(current, applyGranularity);
+ const normalized = this.normalizedLoci(current, applyGranularity, true);
if (StructureElement.Loci.is(normalized.loci)) {
const loci = this.sel.tryGetRange(normalized.loci) || normalized.loci;
this.toggleSel({ loci, repr: normalized.repr });
@@ -206,7 +207,7 @@ namespace InteractivityManager {
}
select(current: Representation.Loci, applyGranularity = true) {
- const normalized = this.normalizedLoci(current, applyGranularity);
+ const normalized = this.normalizedLoci(current, applyGranularity, true);
if (StructureElement.Loci.is(normalized.loci)) {
this.sel.modify('add', normalized.loci);
}
@@ -214,7 +215,7 @@ namespace InteractivityManager {
}
selectJoin(current: Representation.Loci, applyGranularity = true) {
- const normalized = this.normalizedLoci(current, applyGranularity);
+ const normalized = this.normalizedLoci(current, applyGranularity, true);
if (StructureElement.Loci.is(normalized.loci)) {
this.sel.modify('intersect', normalized.loci);
}
@@ -222,7 +223,7 @@ namespace InteractivityManager {
}
selectOnly(current: Representation.Loci, applyGranularity = true) {
- const normalized = this.normalizedLoci(current, applyGranularity);
+ const normalized = this.normalizedLoci(current, applyGranularity, true);
if (StructureElement.Loci.is(normalized.loci)) {
// only deselect for the structure of the given loci
this.deselect({ loci: Structure.toStructureElementLoci(normalized.loci.structure), repr: normalized.repr }, false);
@@ -232,7 +233,7 @@ namespace InteractivityManager {
}
deselect(current: Representation.Loci, applyGranularity = true) {
- const normalized = this.normalizedLoci(current, applyGranularity);
+ const normalized = this.normalizedLoci(current, applyGranularity, true);
if (StructureElement.Loci.is(normalized.loci)) {
this.sel.modify('remove', normalized.loci);
}
@@ -255,8 +256,9 @@ namespace InteractivityManager {
// do a full deselect/select for the current structure so visuals that are
// marked with granularity unequal to 'element' and join/intersect operations
// are handled properly
- super.mark({ loci: Structure.Loci(loci.structure) }, MarkerAction.Deselect, true);
- super.mark({ loci: this.sel.getLoci(loci.structure) }, MarkerAction.Select);
+ const selLoci = this.sel.getLoci(loci.structure);
+ super.mark({ loci: Structure.Loci(loci.structure) }, MarkerAction.Deselect, !Loci.isEmpty(selLoci));
+ super.mark({ loci: selLoci }, MarkerAction.Select);
} else {
super.mark(current, action);
}
diff --git a/src/mol-plugin-state/manager/structure/measurement.ts b/src/mol-plugin-state/manager/structure/measurement.ts
index 4907eb3e7edf84d536604126b5811b722e8265ec..bbd3f14226a471b5c3bfb4c1c8cc8bd8ddffce0a 100644
--- a/src/mol-plugin-state/manager/structure/measurement.ts
+++ b/src/mol-plugin-state/manager/structure/measurement.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { StructureElement } from '../../../mol-model/structure';
@@ -15,6 +16,7 @@ import { StatefulPluginComponent } from '../../component';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { MeasurementRepresentationCommonTextParams, LociLabelTextParams } from '../../../mol-repr/shape/loci/common';
import { LineParams } from '../../../mol-repr/structure/representation/line';
+import { Expression } from '../../../mol-script/language/expression';
export { StructureMeasurementManager };
@@ -35,6 +37,7 @@ export interface StructureMeasurementManagerState {
angles: StructureMeasurementCell[],
dihedrals: StructureMeasurementCell[],
orientations: StructureMeasurementCell[],
+ planes: StructureMeasurementCell[],
options: StructureMeasurementOptions
}
@@ -222,19 +225,25 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true } });
}
- async addOrientation(a: StructureElement.Loci) {
- const cellA = this.plugin.helpers.substructureParent.get(a.structure);
+ async addOrientation(locis: StructureElement.Loci[]) {
+ const selections: { key: string, ref: string, groupId?: string, expression: Expression }[] = [];
+ const dependsOn: string[] = [];
- if (!cellA) return;
+ for (let i = 0, il = locis.length; i < il; ++i) {
+ const l = locis[i];
+ const cell = this.plugin.helpers.substructureParent.get(l.structure);
+ if (!cell) continue;
- const dependsOn = [cellA.transform.ref];
+ arraySetAdd(dependsOn, cell.transform.ref);
+ selections.push({ key: `l${i}`, ref: cell.transform.ref, expression: StructureElement.Loci.toExpression(l) });
+ }
+
+ if (selections.length === 0) return;
const update = this.getGroup();
update
.apply(StateTransforms.Model.MultiStructureSelectionFromExpression, {
- selections: [
- { key: 'a', ref: cellA.transform.ref, expression: StructureElement.Loci.toExpression(a) },
- ],
+ selections,
isTransitive: true,
label: 'Orientation'
}, { dependsOn })
@@ -244,6 +253,34 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true } });
}
+ async addPlane(locis: StructureElement.Loci[]) {
+ const selections: { key: string, ref: string, groupId?: string, expression: Expression }[] = [];
+ const dependsOn: string[] = [];
+
+ for (let i = 0, il = locis.length; i < il; ++i) {
+ const l = locis[i];
+ const cell = this.plugin.helpers.substructureParent.get(l.structure);
+ if (!cell) continue;
+
+ arraySetAdd(dependsOn, cell.transform.ref);
+ selections.push({ key: `l${i}`, ref: cell.transform.ref, expression: StructureElement.Loci.toExpression(l) });
+ }
+
+ if (selections.length === 0) return;
+
+ const update = this.getGroup();
+ update
+ .apply(StateTransforms.Model.MultiStructureSelectionFromExpression, {
+ selections,
+ isTransitive: true,
+ label: 'Plane'
+ }, { dependsOn })
+ .apply(StateTransforms.Representation.StructureSelectionsPlane3D);
+
+ const state = this.plugin.state.data;
+ await PluginCommands.State.Update(this.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+ }
+
private _empty: any[] = [];
private getTransforms<T extends StateTransformer<A, B, any>, A extends PluginStateObject.Molecule.Structure.Selections, B extends StateObject>(transformer: T) {
const state = this.plugin.state.data;
@@ -259,13 +296,14 @@ class StructureMeasurementManager extends StatefulPluginComponent<StructureMeasu
distances: this.getTransforms(StateTransforms.Representation.StructureSelectionsDistance3D),
angles: this.getTransforms(StateTransforms.Representation.StructureSelectionsAngle3D),
dihedrals: this.getTransforms(StateTransforms.Representation.StructureSelectionsDihedral3D),
- orientations: this.getTransforms(StateTransforms.Representation.StructureSelectionsOrientation3D)
+ orientations: this.getTransforms(StateTransforms.Representation.StructureSelectionsOrientation3D),
+ planes: this.getTransforms(StateTransforms.Representation.StructureSelectionsPlane3D),
});
if (updated) this.stateUpdated();
}
constructor(private plugin: PluginContext) {
- super({ labels: [], distances: [], angles: [], dihedrals: [], orientations: [], options: DefaultStructureMeasurementOptions });
+ super({ labels: [], distances: [], angles: [], dihedrals: [], orientations: [], planes: [], options: DefaultStructureMeasurementOptions });
plugin.state.data.events.changed.subscribe(e => {
if (e.inTransaction || plugin.behaviors.state.isAnimating.value) return;
diff --git a/src/mol-plugin-state/manager/structure/selection.ts b/src/mol-plugin-state/manager/structure/selection.ts
index a8e99b6d0f709cda0a278e8871ab4c72d5e7d531..c043a9e614cde87c2312401549f90828ff847b96 100644
--- a/src/mol-plugin-state/manager/structure/selection.ts
+++ b/src/mol-plugin-state/manager/structure/selection.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -22,6 +22,7 @@ import { PluginStateObject as PSO } from '../../objects';
import { UUID } from '../../../mol-util';
import { StructureRef } from './hierarchy-state';
import { Boundary } from '../../../mol-math/geometry/boundary';
+import { iterableToArray } from '../../../mol-data/util';
interface StructureSelectionManagerState {
entries: Map<string, SelectionEntry>,
@@ -405,14 +406,8 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
}
getPrincipalAxes(): PrincipalAxes {
- const elementCount = this.elementCount();
- const positions = new Float32Array(3 * elementCount);
- let offset = 0;
- this.entries.forEach(v => {
- StructureElement.Loci.toPositionsArray(v.selection, positions, offset);
- offset += StructureElement.Loci.size(v.selection) * 3;
- });
- return PrincipalAxes.ofPositions(positions);
+ const values = iterableToArray(this.entries.values());
+ return StructureElement.Loci.getPrincipalAxesMany(values.map(v => v.selection));
}
modify(modifier: StructureSelectionModifier, loci: Loci) {
diff --git a/src/mol-plugin-state/transforms/helpers.ts b/src/mol-plugin-state/transforms/helpers.ts
index 55ca620ae5581c1021a46947a0f2b66a63d44f60..9bdd857bd67f5149b7b4f7cb029a676fbc5437d6 100644
--- a/src/mol-plugin-state/transforms/helpers.ts
+++ b/src/mol-plugin-state/transforms/helpers.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -10,6 +10,7 @@ import { LabelData } from '../../mol-repr/shape/loci/label';
import { OrientationData } from '../../mol-repr/shape/loci/orientation';
import { AngleData } from '../../mol-repr/shape/loci/angle';
import { DihedralData } from '../../mol-repr/shape/loci/dihedral';
+import { PlaneData } from '../../mol-repr/shape/loci/plane';
export function getDistanceDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): DistanceData {
const lociA = s[0].loci;
@@ -38,6 +39,9 @@ export function getLabelDataFromStructureSelections(s: ReadonlyArray<PluginState
}
export function getOrientationDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): OrientationData {
- const loci = s[0].loci;
- return { locis: [loci] };
+ return { locis: s.map(v => v.loci) };
+}
+
+export function getPlaneDataFromStructureSelections(s: ReadonlyArray<PluginStateObject.Molecule.Structure.SelectionEntry>): PlaneData {
+ return { locis: s.map(v => v.loci) };
}
\ No newline at end of file
diff --git a/src/mol-plugin-state/transforms/model.ts b/src/mol-plugin-state/transforms/model.ts
index 204f783e5ddafc3a2af4a14f613d02c37e029101..ea75c491b015fd1f6967dd0b3ac20f1d473d5ee1 100644
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -645,7 +645,8 @@ const MultiStructureSelectionFromExpression = PluginStateTransform.BuiltIn({
totalSize += StructureElement.Loci.size(loci.loci);
continue;
- } if (entry.expression !== sel.expression) {
+ }
+ if (entry.expression !== sel.expression) {
recreate = true;
} else {
// TODO: properly support "transitive" queries. For that Structure.areUnitAndIndicesEqual needs to be fixed;
diff --git a/src/mol-plugin-state/transforms/representation.ts b/src/mol-plugin-state/transforms/representation.ts
index 6c1d37b0fd74453bf47878dca70639d0ddc91756..1b257422f4ad930792ac663b4daf07dd5b4d7197 100644
--- a/src/mol-plugin-state/transforms/representation.ts
+++ b/src/mol-plugin-state/transforms/representation.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -28,7 +28,7 @@ import { BaseGeometry } from '../../mol-geo/geometry/base';
import { Script } from '../../mol-script/script';
import { UnitcellParams, UnitcellRepresentation, getUnitcellData } from '../../mol-repr/shape/model/unitcell';
import { DistanceParams, DistanceRepresentation } from '../../mol-repr/shape/loci/distance';
-import { getDistanceDataFromStructureSelections, getLabelDataFromStructureSelections, getOrientationDataFromStructureSelections, getAngleDataFromStructureSelections, getDihedralDataFromStructureSelections } from './helpers';
+import { getDistanceDataFromStructureSelections, getLabelDataFromStructureSelections, getOrientationDataFromStructureSelections, getAngleDataFromStructureSelections, getDihedralDataFromStructureSelections, getPlaneDataFromStructureSelections } from './helpers';
import { LabelParams, LabelRepresentation } from '../../mol-repr/shape/loci/label';
import { OrientationRepresentation, OrientationParams } from '../../mol-repr/shape/loci/orientation';
import { AngleParams, AngleRepresentation } from '../../mol-repr/shape/loci/angle';
@@ -40,6 +40,7 @@ import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
import { getBoxMesh } from './shape';
import { Shape } from '../../mol-model/shape';
import { Box3D } from '../../mol-math/geometry';
+import { PlaneParams, PlaneRepresentation } from '../../mol-repr/shape/loci/plane';
export { StructureRepresentation3D };
export { ExplodeStructureRepresentation3D };
@@ -986,4 +987,37 @@ const StructureSelectionsOrientation3D = PluginStateTransform.BuiltIn({
return StateTransformer.UpdateResult.Updated;
});
},
+});
+
+export { StructureSelectionsPlane3D };
+type StructureSelectionsPlane3D = typeof StructureSelectionsPlane3D
+const StructureSelectionsPlane3D = PluginStateTransform.BuiltIn({
+ name: 'structure-selections-plane-3d',
+ display: '3D Plane',
+ from: SO.Molecule.Structure.Selections,
+ to: SO.Shape.Representation3D,
+ params: () => ({
+ ...PlaneParams,
+ })
+})({
+ canAutoUpdate({ oldParams, newParams }) {
+ return true;
+ },
+ apply({ a, params }, plugin: PluginContext) {
+ return Task.create('Structure Plane', async ctx => {
+ const data = getPlaneDataFromStructureSelections(a.data);
+ const repr = PlaneRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => PlaneParams);
+ await repr.createOrUpdate(params, data).runInContext(ctx);
+ return new SO.Shape.Representation3D({ repr, sourceData: data }, { label: `Plane` });
+ });
+ },
+ update({ a, b, oldParams, newParams }, plugin: PluginContext) {
+ return Task.create('Structure Plane', async ctx => {
+ const props = { ...b.data.repr.props, ...newParams };
+ const data = getPlaneDataFromStructureSelections(a.data);
+ await b.data.repr.createOrUpdate(props, data).runInContext(ctx);
+ b.data.sourceData = data;
+ return StateTransformer.UpdateResult.Updated;
+ });
+ },
});
\ No newline at end of file
diff --git a/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx b/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
index 46e7e8788322fb17a7903ad29893ed3c3014bfea..968068d2b19af01f43c727df22a60a8c180729b6 100644
--- a/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
+++ b/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
@@ -207,7 +207,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
const updatedPoint = this.unNormalizePoint(Vec2.create(this.updatedX, this.updatedY));
const points = this.state.points.filter((_, i) => i !== selected[0]);
- points.push(updatedPoint);;
+ points.push(updatedPoint);
points.sort((a, b) => {
if (a[0] === b[0]) {
if (a[0] === 0) {
@@ -372,7 +372,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
const data = points;
const size = data.length;
- for (let i = 0; i < size - 1;i++) {
+ for (let i = 0; i < size - 1; i++) {
const x1 = data[i][0];
const y1 = data[i][1];
const x2 = data[i + 1][0];
diff --git a/src/mol-plugin-ui/sequence/sequence.tsx b/src/mol-plugin-ui/sequence/sequence.tsx
index c7bda2a661b723364c886d4c331bb4213055f9c2..bea9c49754924dc736f196a689dc6834f5fe8767 100644
--- a/src/mol-plugin-ui/sequence/sequence.tsx
+++ b/src/mol-plugin-ui/sequence/sequence.tsx
@@ -153,7 +153,11 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
private getBackgroundColor(marker: number) {
// TODO: make marker color configurable
if (typeof marker === 'undefined') console.error('unexpected marker value');
- return marker === 0 ? '' : marker % 2 === 0 ? 'rgb(51, 255, 25)' /* selected */ : 'rgb(255, 102, 153)' /* highlighted */;
+ return marker === 0
+ ? ''
+ : marker % 2 === 0
+ ? 'rgb(51, 255, 25)' // selected
+ : 'rgb(255, 102, 153)'; // highlighted
}
private getResidueClass(seqIdx: number, label: string) {
diff --git a/src/mol-plugin-ui/structure/measurements.tsx b/src/mol-plugin-ui/structure/measurements.tsx
index b1cdfb2a33ae1bfa5b289a29e7f79959bd4b36cd..29763a3cfe262d53a12b4a2ecbfbf8b833caf3f1 100644
--- a/src/mol-plugin-ui/structure/measurements.tsx
+++ b/src/mol-plugin-ui/structure/measurements.tsx
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -15,7 +15,8 @@ import { AngleData } from '../../mol-repr/shape/loci/angle';
import { DihedralData } from '../../mol-repr/shape/loci/dihedral';
import { DistanceData } from '../../mol-repr/shape/loci/distance';
import { LabelData } from '../../mol-repr/shape/loci/label';
-import { angleLabel, dihedralLabel, distanceLabel, lociLabel } from '../../mol-theme/label';
+import { OrientationData } from '../../mol-repr/shape/loci/orientation';
+import { angleLabel, dihedralLabel, distanceLabel, lociLabel, structureElementLociLabelMany } from '../../mol-theme/label';
import { FiniteArray } from '../../mol-util/type-helpers';
import { CollapsableControls, PurePluginUIComponent } from '../base';
import { ActionMenu } from '../controls/action-menu';
@@ -67,6 +68,8 @@ export class MeasurementList extends PurePluginUIComponent {
{this.renderGroup(measurements.distances, 'Distances')}
{this.renderGroup(measurements.angles, 'Angles')}
{this.renderGroup(measurements.dihedrals, 'Dihedrals')}
+ {this.renderGroup(measurements.orientations, 'Orientations')}
+ {this.renderGroup(measurements.planes, 'Planes')}
</div>;
}
}
@@ -108,13 +111,31 @@ export class MeasurementControls extends PurePluginUIComponent<{}, { isBusy: boo
this.plugin.managers.structure.measurement.addLabel(loci[0].loci);
}
+ addOrientation = () => {
+ const locis: StructureElement.Loci[] = [];
+ this.plugin.managers.structure.selection.entries.forEach(v => {
+ locis.push(v.selection);
+ });
+ this.plugin.managers.structure.measurement.addOrientation(locis);
+ }
+
+ addPlane = () => {
+ const locis: StructureElement.Loci[] = [];
+ this.plugin.managers.structure.selection.entries.forEach(v => {
+ locis.push(v.selection);
+ });
+ this.plugin.managers.structure.measurement.addPlane(locis);
+ }
+
get actions(): ActionMenu.Items {
const history = this.selection.additionsHistory;
const ret: ActionMenu.Item[] = [
- { kind: 'item', label: `Label ${history.length === 0 ? ' (1 selection required)' : ' (1st selection)'}`, value: this.addLabel, disabled: history.length === 0 },
- { kind: 'item', label: `Distance ${history.length < 2 ? ' (2 selections required)' : ' (top 2 selections)'}`, value: this.measureDistance, disabled: history.length < 2 },
- { kind: 'item', label: `Angle ${history.length < 3 ? ' (3 selections required)' : ' (top 3 selections)'}`, value: this.measureAngle, disabled: history.length < 3 },
- { kind: 'item', label: `Dihedral ${history.length < 4 ? ' (4 selections required)' : ' (top 4 selections)'}`, value: this.measureDihedral, disabled: history.length < 4 },
+ { kind: 'item', label: `Label ${history.length === 0 ? ' (1 selection item required)' : ' (1st selection item)'}`, value: this.addLabel, disabled: history.length === 0 },
+ { kind: 'item', label: `Distance ${history.length < 2 ? ' (2 selection items required)' : ' (top 2 selection items)'}`, value: this.measureDistance, disabled: history.length < 2 },
+ { kind: 'item', label: `Angle ${history.length < 3 ? ' (3 selection items required)' : ' (top 3 items)'}`, value: this.measureAngle, disabled: history.length < 3 },
+ { kind: 'item', label: `Dihedral ${history.length < 4 ? ' (4 selection items required)' : ' (top 4 selection items)'}`, value: this.measureDihedral, disabled: history.length < 4 },
+ { kind: 'item', label: `Orientation ${history.length === 0 ? ' (selection required)' : ' (current selection)'}`, value: this.addOrientation, disabled: history.length === 0 },
+ { kind: 'item', label: `Plane ${history.length === 0 ? ' (selection required)' : ' (current selection)'}`, value: this.addPlane, disabled: history.length === 0 },
];
return ret;
}
@@ -219,7 +240,7 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
}
get selections() {
- return this.props.cell.obj?.data.sourceData as Partial<DistanceData & AngleData & DihedralData & LabelData> | undefined;
+ return this.props.cell.obj?.data.sourceData as Partial<DistanceData & AngleData & DihedralData & LabelData & OrientationData> | undefined;
}
delete = () => {
@@ -266,6 +287,7 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
if (selections.pairs) return selections.pairs[0].loci;
if (selections.triples) return selections.triples[0].loci;
if (selections.quads) return selections.quads[0].loci;
+ if (selections.locis) return selections.locis;
return [];
}
@@ -277,6 +299,7 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
if (selections.pairs) return distanceLabel(selections.pairs[0], { condensed: true, unitLabel: this.plugin.managers.structure.measurement.state.options.distanceUnitLabel });
if (selections.triples) return angleLabel(selections.triples[0], { condensed: true });
if (selections.quads) return dihedralLabel(selections.quads[0], { condensed: true });
+ if (selections.locis) return structureElementLociLabelMany(selections.locis, { countsOnly: true });
return '<empty>';
}
diff --git a/src/mol-plugin/behavior/dynamic/representation.ts b/src/mol-plugin/behavior/dynamic/representation.ts
index 45928cbe516f9a34ea5d0fb950053c131850f3cf..a561ae846bf9be8815987038e3ce131086c6ae28 100644
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/src/mol-plugin/behavior/dynamic/representation.ts
@@ -16,7 +16,7 @@ import { ButtonsType, ModifiersKeys } from '../../../mol-util/input/input-observ
import { Binding } from '../../../mol-util/binding';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { EmptyLoci, Loci } from '../../../mol-model/loci';
-import { Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
+import { Bond, Structure, StructureElement, StructureProperties } from '../../../mol-model/structure';
import { arrayMax } from '../../../mol-util/array';
import { Representation } from '../../../mol-repr/representation';
import { LociLabel } from '../../../mol-plugin-state/manager/loci-label';
@@ -34,6 +34,7 @@ const DefaultHighlightLociBindings = {
const HighlightLociParams = {
bindings: PD.Value(DefaultHighlightLociBindings, { isHidden: true }),
ignore: PD.Value<Loci['kind'][]>([], { isHidden: true }),
+ preferAtoms: PD.Boolean(false, { description: 'Always prefer atoms over bonds' }),
mark: PD.Boolean(true)
};
type HighlightLociProps = PD.Values<typeof HighlightLociParams>
@@ -46,10 +47,17 @@ export const HighlightLoci = PluginBehavior.create({
if (!this.ctx.canvas3d || !this.params.mark) return;
this.ctx.canvas3d.mark(interactionLoci, action, noRender);
}
+ private getLoci(loci: Loci) {
+ return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
+ ? Bond.toFirstStructureElementLoci(loci)
+ : loci;
+ }
register() {
this.subscribeObservable(this.ctx.behaviors.interaction.hover, ({ current, buttons, modifiers }) => {
if (!this.ctx.canvas3d || this.ctx.isBusy) return;
- if (this.params.ignore?.indexOf(current.loci.kind) >= 0) {
+
+ const loci = this.getLoci(current.loci);
+ if (this.params.ignore?.indexOf(loci.kind) >= 0) {
this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EmptyLoci });
return;
}
@@ -58,13 +66,13 @@ export const HighlightLoci = PluginBehavior.create({
if (Binding.match(this.params.bindings.hoverHighlightOnly, buttons, modifiers)) {
// remove repr to highlight loci everywhere on hover
- this.ctx.managers.interactivity.lociHighlights.highlightOnly({ loci: current.loci });
+ this.ctx.managers.interactivity.lociHighlights.highlightOnly({ loci });
matched = true;
}
if (Binding.match(this.params.bindings.hoverHighlightOnlyExtend, buttons, modifiers)) {
// remove repr to highlight loci everywhere on hover
- this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend({ loci: current.loci });
+ this.ctx.managers.interactivity.lociHighlights.highlightOnlyExtend({ loci });
matched = true;
}
@@ -95,6 +103,7 @@ const DefaultSelectLociBindings = {
const SelectLociParams = {
bindings: PD.Value(DefaultSelectLociBindings, { isHidden: true }),
ignore: PD.Value<Loci['kind'][]>([], { isHidden: true }),
+ preferAtoms: PD.Boolean(false, { description: 'Always prefer atoms over bonds' }),
mark: PD.Boolean(true)
};
type SelectLociProps = PD.Values<typeof SelectLociParams>
@@ -108,6 +117,11 @@ export const SelectLoci = PluginBehavior.create({
if (!this.ctx.canvas3d || !this.params.mark) return;
this.ctx.canvas3d.mark({ loci: reprLoci.loci }, action, noRender);
}
+ private getLoci(loci: Loci) {
+ return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
+ ? Bond.toFirstStructureElementLoci(loci)
+ : loci;
+ }
private applySelectMark(ref: string, clear?: boolean) {
const cell = this.ctx.state.data.cells.get(ref);
if (cell && SO.isRepresentation3D(cell.obj)) {
@@ -123,10 +137,10 @@ export const SelectLoci = PluginBehavior.create({
}
}
register() {
- const lociIsEmpty = (current: Representation.Loci) => Loci.isEmpty(current.loci);
- const lociIsNotEmpty = (current: Representation.Loci) => !Loci.isEmpty(current.loci);
+ const lociIsEmpty = (loci: Loci) => Loci.isEmpty(loci);
+ const lociIsNotEmpty = (loci: Loci) => !Loci.isEmpty(loci);
- const actions: [keyof typeof DefaultSelectLociBindings, (current: Representation.Loci) => void, ((current: Representation.Loci) => boolean) | undefined][] = [
+ const actions: [keyof typeof DefaultSelectLociBindings, (current: Representation.Loci) => void, ((current: Loci) => boolean) | undefined][] = [
['clickSelect', current => this.ctx.managers.interactivity.lociSelects.select(current), lociIsNotEmpty],
['clickToggle', current => this.ctx.managers.interactivity.lociSelects.toggle(current), lociIsNotEmpty],
['clickToggleExtend', current => this.ctx.managers.interactivity.lociSelects.toggleExtend(current), lociIsNotEmpty],
@@ -145,12 +159,14 @@ export const SelectLoci = PluginBehavior.create({
this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
if (!this.ctx.canvas3d || this.ctx.isBusy || !this.ctx.selectionMode) return;
- if (this.params.ignore?.indexOf(current.loci.kind) >= 0) return;
+
+ const loci = this.getLoci(current.loci);
+ if (this.params.ignore?.indexOf(loci.kind) >= 0) return;
// only trigger the 1st action that matches
for (const [binding, action, condition] of actions) {
- if (Binding.match(this.params.bindings[binding], button, modifiers) && (!condition || condition(current))) {
- action(current);
+ if (Binding.match(this.params.bindings[binding], button, modifiers) && (!condition || condition(loci))) {
+ action({ repr: current.repr, loci });
break;
}
}
diff --git a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
index 43ad81abd070d9b3d51ec70d004b6bc6ce6ff664..fbd8fa87c570f069641eacf95c3e36b46badd536 100644
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
@@ -25,7 +25,7 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
targetParams: PD.Group(reprParams, {
label: 'Target',
- customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51 } })
+ customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51, adjustCylinderLength: true } })
}),
surroundingsParams: PD.Group(reprParams, {
label: 'Surroundings',
diff --git a/src/mol-plugin/config.ts b/src/mol-plugin/config.ts
index 2144de4e0b7b4c78e6765fbab56807e48f0b6745..bfd3b5aa3d996ca7844abc339c29c6d90a293402 100644
--- a/src/mol-plugin/config.ts
+++ b/src/mol-plugin/config.ts
@@ -19,6 +19,16 @@ export class PluginConfigItem<T = any> {
function item<T>(key: string, defaultValue?: T) { return new PluginConfigItem(key, defaultValue); }
+
+// adapted from https://stackoverflow.com/questions/9038625/detect-if-device-is-ios
+function is_iOS() {
+ if (typeof navigator === 'undefined' || typeof window === 'undefined') return false;
+ const isIOS = /iPad|iPhone|iPod/.test(navigator.userAgent);
+ const isAppleDevice = navigator.userAgent.includes('Macintosh');
+ const isTouchScreen = navigator.maxTouchPoints >= 4; // true for iOS 13 (and hopefully beyond)
+ return !(window as any).MSStream && (isIOS || (isAppleDevice && isTouchScreen));
+}
+
export const PluginConfig = {
item,
General: {
@@ -27,7 +37,11 @@ export const PluginConfig = {
DisablePreserveDrawingBuffer: item('plugin-config.disable-preserve-drawing-buffer', false),
PixelScale: item('plugin-config.pixel-scale', 1),
PickScale: item('plugin-config.pick-scale', 0.25),
+ PickPadding: item('plugin-config.pick-padding', 3),
EnableWboit: item('plugin-config.enable-wboit', true),
+ // as of Oct 1 2021, WebGL 2 doesn't work on iOS 15.
+ // TODO: check back in a few weeks to see if it was fixed
+ PreferWebGl1: item('plugin-config.prefer-webgl1', is_iOS()),
},
State: {
DefaultServer: item('plugin-state.server', 'https://webchem.ncbr.muni.cz/molstar-state'),
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index f08217e64b4caa412eb3af40e6bdb3b4c4089a11..76542ab04fb46674bdbb0404c2ccd55a0368ffad 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -196,8 +196,11 @@ export class PluginContext {
const preserveDrawingBuffer = !(this.config.get(PluginConfig.General.DisablePreserveDrawingBuffer) ?? false);
const pixelScale = this.config.get(PluginConfig.General.PixelScale) || 1;
const pickScale = this.config.get(PluginConfig.General.PickScale) || 0.25;
+ const pickPadding = this.config.get(PluginConfig.General.PickPadding) ?? 1;
const enableWboit = this.config.get(PluginConfig.General.EnableWboit) || false;
- (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, { antialias, preserveDrawingBuffer, pixelScale, pickScale, enableWboit });
+ const preferWebGl1 = this.config.get(PluginConfig.General.PreferWebGl1) || false;
+ (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, { antialias, preserveDrawingBuffer, pixelScale, pickScale, enableWboit, preferWebGl1 });
+ (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, { antialias, preserveDrawingBuffer, pixelScale, pickScale, pickPadding, enableWboit });
}
(this.canvas3d as Canvas3D) = Canvas3D.create(this.canvas3dContext!);
this.canvas3dInit.next(true);
diff --git a/src/mol-repr/representation.ts b/src/mol-repr/representation.ts
index bad2eb42e7e851310c44f6df16845529f58f688e..9be1c63371d7150c4294aa2b4a32acb56e2514dd 100644
--- a/src/mol-repr/representation.ts
+++ b/src/mol-repr/representation.ts
@@ -65,12 +65,16 @@ export namespace RepresentationProvider {
export type AnyRepresentationProvider = RepresentationProvider<any, {}, Representation.State>
-const EmptyRepresentationProvider = {
+export const EmptyRepresentationProvider: RepresentationProvider = {
+ name: '',
label: '',
description: '',
factory: () => Representation.Empty,
getParams: () => ({}),
- defaultValues: {}
+ defaultValues: {},
+ defaultColorTheme: ColorTheme.EmptyProvider,
+ defaultSizeTheme: SizeTheme.EmptyProvider,
+ isApplicable: () => true
};
function getTypes(list: { name: string, provider: RepresentationProvider<any, any, any> }[]) {
@@ -114,7 +118,7 @@ export class RepresentationRegistry<D, S extends Representation.State> {
}
get<P extends PD.Params>(name: string): RepresentationProvider<D, P, S> {
- return this._map.get(name) || EmptyRepresentationProvider as unknown as RepresentationProvider<D, P, S>;
+ return this._map.get(name) || EmptyRepresentationProvider;
}
get list() {
@@ -226,7 +230,7 @@ namespace Representation {
let version = 0;
const updated = new Subject<number>();
const currentState = stateBuilder.create();
- const currentTheme = Theme.createEmpty();
+ let currentTheme = Theme.createEmpty();
let currentParams: P;
let currentProps: PD.Values<P>;
@@ -314,6 +318,7 @@ namespace Representation {
}
},
setTheme: (theme: Theme) => {
+ currentTheme = theme;
for (let i = 0, il = reprList.length; i < il; ++i) {
reprList[i].setTheme(theme);
}
diff --git a/src/mol-repr/shape/loci/orientation.ts b/src/mol-repr/shape/loci/orientation.ts
index 4a5b120ec8acf1b73722a4c90d56db084290672a..451aff38efdfbee738e3dd54ec5db5f38ef8946c 100644
--- a/src/mol-repr/shape/loci/orientation.ts
+++ b/src/mol-repr/shape/loci/orientation.ts
@@ -1,10 +1,9 @@
/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { Loci } from '../../../mol-model/loci';
import { RuntimeContext } from '../../../mol-task';
import { ParamDefinition as PD } from '../../../mol-util/param-definition';
import { ColorNames } from '../../../mol-util/color/names';
@@ -13,21 +12,23 @@ import { Representation, RepresentationParamsGetter, RepresentationContext } fro
import { Shape } from '../../../mol-model/shape';
import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
-import { lociLabel } from '../../../mol-theme/label';
+import { structureElementLociLabelMany } from '../../../mol-theme/label';
import { addAxes } from '../../../mol-geo/geometry/mesh/builder/axes';
import { addOrientedBox } from '../../../mol-geo/geometry/mesh/builder/box';
import { addEllipsoid } from '../../../mol-geo/geometry/mesh/builder/ellipsoid';
import { Axes3D } from '../../../mol-math/geometry';
import { Vec3 } from '../../../mol-math/linear-algebra';
import { MarkerActions } from '../../../mol-util/marker-action';
+import { StructureElement } from '../../../mol-model/structure';
export interface OrientationData {
- locis: Loci[]
+ locis: StructureElement.Loci[]
}
const SharedParams = {
color: PD.Color(ColorNames.orange),
- scale: PD.Numeric(2, { min: 0.1, max: 10, step: 0.1 })
+ scaleFactor: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
+ radiusScale: PD.Numeric(2, { min: 0.1, max: 10, step: 0.1 })
};
const AxesParams = {
@@ -57,97 +58,84 @@ const OrientationVisuals = {
export const OrientationParams = {
...AxesParams,
...BoxParams,
+ ...EllipsoidParams,
visuals: PD.MultiSelect(['box'], PD.objectToOptions(OrientationVisuals)),
- color: PD.Color(ColorNames.orange),
- scale: PD.Numeric(2, { min: 0.1, max: 5, step: 0.1 })
};
export type OrientationParams = typeof OrientationParams
export type OrientationProps = PD.Values<OrientationParams>
//
-function orientationLabel(loci: Loci) {
- const label = lociLabel(loci, { countsOnly: true });
+function getAxesName(locis: StructureElement.Loci[]) {
+ const label = structureElementLociLabelMany(locis, { countsOnly: true });
return `Principal Axes of ${label}`;
}
-function getOrientationName(data: OrientationData) {
- return data.locis.length === 1 ? orientationLabel(data.locis[0]) : `${data.locis.length} Orientations`;
-}
-
-//
-
function buildAxesMesh(data: OrientationData, props: OrientationProps, mesh?: Mesh): Mesh {
const state = MeshBuilder.createState(256, 128, mesh);
- for (let i = 0, il = data.locis.length; i < il; ++i) {
- const principalAxes = Loci.getPrincipalAxes(data.locis[i]);
- if (principalAxes) {
- state.currentGroup = i;
- addAxes(state, principalAxes.momentsAxes, props.scale, 2, 20);
- }
- }
+ const principalAxes = StructureElement.Loci.getPrincipalAxesMany(data.locis);
+ Axes3D.scale(principalAxes.momentsAxes, principalAxes.momentsAxes, props.scaleFactor);
+
+ state.currentGroup = 0;
+ addAxes(state, principalAxes.momentsAxes, props.radiusScale, 2, 20);
return MeshBuilder.getMesh(state);
}
function getAxesShape(ctx: RuntimeContext, data: OrientationData, props: OrientationProps, shape?: Shape<Mesh>) {
const mesh = buildAxesMesh(data, props, shape && shape.geometry);
- const name = getOrientationName(data);
- const getLabel = function (groupId: number) {
- return orientationLabel(data.locis[groupId]);
- };
- return Shape.create(name, data, mesh, () => props.color, () => 1, getLabel);
+ const name = getAxesName(data.locis);
+ return Shape.create(name, data, mesh, () => props.color, () => 1, () => name);
}
//
+function getBoxName(locis: StructureElement.Loci[]) {
+ const label = structureElementLociLabelMany(locis, { countsOnly: true });
+ return `Oriented Box of ${label}`;
+}
+
function buildBoxMesh(data: OrientationData, props: OrientationProps, mesh?: Mesh): Mesh {
const state = MeshBuilder.createState(256, 128, mesh);
- for (let i = 0, il = data.locis.length; i < il; ++i) {
- const principalAxes = Loci.getPrincipalAxes(data.locis[i]);
- if (principalAxes) {
- state.currentGroup = i;
- addOrientedBox(state, principalAxes.boxAxes, props.scale, 2, 20);
- }
- }
+ const principalAxes = StructureElement.Loci.getPrincipalAxesMany(data.locis);
+ Axes3D.scale(principalAxes.boxAxes, principalAxes.boxAxes, props.scaleFactor);
+
+ state.currentGroup = 0;
+ addOrientedBox(state, principalAxes.boxAxes, props.radiusScale, 2, 20);
return MeshBuilder.getMesh(state);
}
function getBoxShape(ctx: RuntimeContext, data: OrientationData, props: OrientationProps, shape?: Shape<Mesh>) {
const mesh = buildBoxMesh(data, props, shape && shape.geometry);
- const name = getOrientationName(data);
- const getLabel = function (groupId: number) {
- return orientationLabel(data.locis[groupId]);
- };
- return Shape.create(name, data, mesh, () => props.color, () => 1, getLabel);
+ const name = getBoxName(data.locis);
+ return Shape.create(name, data, mesh, () => props.color, () => 1, () => name);
}
//
+function getEllipsoidName(locis: StructureElement.Loci[]) {
+ const label = structureElementLociLabelMany(locis, { countsOnly: true });
+ return `Oriented Ellipsoid of ${label}`;
+}
+
function buildEllipsoidMesh(data: OrientationData, props: OrientationProps, mesh?: Mesh): Mesh {
const state = MeshBuilder.createState(256, 128, mesh);
- for (let i = 0, il = data.locis.length; i < il; ++i) {
- const principalAxes = Loci.getPrincipalAxes(data.locis[i]);
- if (principalAxes) {
- const axes = principalAxes.boxAxes;
- const { origin, dirA, dirB } = axes;
- const size = Axes3D.size(Vec3(), axes);
- Vec3.scale(size, size, 0.5);
- const radiusScale = Vec3.create(size[2], size[1], size[0]);
-
- state.currentGroup = i;
- addEllipsoid(state, origin, dirA, dirB, radiusScale, 2);
- }
- }
+ const principalAxes = StructureElement.Loci.getPrincipalAxesMany(data.locis);
+
+ const axes = principalAxes.boxAxes;
+ const { origin, dirA, dirB } = axes;
+ const size = Axes3D.size(Vec3(), axes);
+ Vec3.scale(size, size, 0.5 * props.scaleFactor);
+ const radiusScale = Vec3.create(size[2], size[1], size[0]);
+
+ state.currentGroup = 0;
+ addEllipsoid(state, origin, dirA, dirB, radiusScale, 2);
return MeshBuilder.getMesh(state);
}
function getEllipsoidShape(ctx: RuntimeContext, data: OrientationData, props: OrientationProps, shape?: Shape<Mesh>) {
const mesh = buildEllipsoidMesh(data, props, shape && shape.geometry);
- const name = getOrientationName(data);
- const getLabel = function (groupId: number) {
- return orientationLabel(data.locis[groupId]);
- };
- return Shape.create(name, data, mesh, () => props.color, () => 1, getLabel);
+ const name = getEllipsoidName(data.locis);
+ return Shape.create(name, data, mesh, () => props.color, () => 1, () => name);
}
//
diff --git a/src/mol-repr/shape/loci/plane.ts b/src/mol-repr/shape/loci/plane.ts
new file mode 100644
index 0000000000000000000000000000000000000000..719f3ae19611accf74fde85089eb347c7ff14d2d
--- /dev/null
+++ b/src/mol-repr/shape/loci/plane.ts
@@ -0,0 +1,84 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { RuntimeContext } from '../../../mol-task';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { ColorNames } from '../../../mol-util/color/names';
+import { ShapeRepresentation } from '../representation';
+import { Representation, RepresentationParamsGetter, RepresentationContext } from '../../representation';
+import { Shape } from '../../../mol-model/shape';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { structureElementLociLabelMany } from '../../../mol-theme/label';
+import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { MarkerActions } from '../../../mol-util/marker-action';
+import { Plane } from '../../../mol-geo/primitive/plane';
+import { StructureElement } from '../../../mol-model/structure';
+import { Axes3D } from '../../../mol-math/geometry';
+
+export interface PlaneData {
+ locis: StructureElement.Loci[]
+}
+
+const _PlaneParams = {
+ ...Mesh.Params,
+ color: PD.Color(ColorNames.orange),
+ scaleFactor: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }),
+};
+type _PlaneParams = typeof _PlaneParams
+
+const PlaneVisuals = {
+ 'plane': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<PlaneData, _PlaneParams>) => ShapeRepresentation(getPlaneShape, Mesh.Utils),
+};
+
+export const PlaneParams = {
+ ..._PlaneParams,
+ visuals: PD.MultiSelect(['plane'], PD.objectToOptions(PlaneVisuals)),
+};
+export type PlaneParams = typeof PlaneParams
+export type PlaneProps = PD.Values<PlaneParams>
+
+//
+
+function getPlaneName(locis: StructureElement.Loci[]) {
+ const label = structureElementLociLabelMany(locis, { countsOnly: true });
+ return `Best Fit Plane of ${label}`;
+}
+
+const tmpMat = Mat4();
+const tmpV = Vec3();
+function buildPlaneMesh(data: PlaneData, props: PlaneProps, mesh?: Mesh): Mesh {
+ const state = MeshBuilder.createState(256, 128, mesh);
+ const principalAxes = StructureElement.Loci.getPrincipalAxesMany(data.locis);
+ const axes = principalAxes.boxAxes;
+ const plane = Plane();
+
+ Vec3.add(tmpV, axes.origin, axes.dirC);
+ Mat4.targetTo(tmpMat, tmpV, axes.origin, axes.dirB);
+ Mat4.scale(tmpMat, tmpMat, Axes3D.size(tmpV, axes));
+ Mat4.scaleUniformly(tmpMat, tmpMat, props.scaleFactor);
+ Mat4.setTranslation(tmpMat, axes.origin);
+
+ state.currentGroup = 0;
+ MeshBuilder.addPrimitive(state, tmpMat, plane);
+ MeshBuilder.addPrimitiveFlipped(state, tmpMat, plane);
+ return MeshBuilder.getMesh(state);
+}
+
+function getPlaneShape(ctx: RuntimeContext, data: PlaneData, props: PlaneProps, shape?: Shape<Mesh>) {
+ const mesh = buildPlaneMesh(data, props, shape && shape.geometry);
+ const name = getPlaneName(data.locis);
+ return Shape.create(name, data, mesh, () => props.color, () => 1, () => name);
+}
+
+//
+
+export type PlaneRepresentation = Representation<PlaneData, PlaneParams>
+export function PlaneRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<PlaneData, PlaneParams>): PlaneRepresentation {
+ const repr = Representation.createMulti('Plane', ctx, getParams, Representation.StateBuilder, PlaneVisuals as unknown as Representation.Def<PlaneData, PlaneParams>);
+ repr.setState({ markerActions: MarkerActions.Highlighting });
+ return repr;
+}
\ No newline at end of file
diff --git a/src/mol-repr/structure/representation/line.ts b/src/mol-repr/structure/representation/line.ts
index 2f9c5c5d6e03c692f5069e94f82a2db80f4cd797..c0936561151e29bc9222e7ac2c755c058d9344c7 100644
--- a/src/mol-repr/structure/representation/line.ts
+++ b/src/mol-repr/structure/representation/line.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -14,23 +14,32 @@ import { Representation, RepresentationParamsGetter, RepresentationContext } fro
import { ThemeRegistryContext } from '../../../mol-theme/theme';
import { Structure } from '../../../mol-model/structure';
import { getUnitKindsParam } from '../params';
+import { ElementPointParams, ElementPointVisual } from '../visual/element-point';
+import { ElementCrossParams, ElementCrossVisual } from '../visual/element-cross';
const LineVisuals = {
'intra-bond': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, IntraUnitBondLineParams>) => UnitsRepresentation('Intra-unit bond line', ctx, getParams, IntraUnitBondLineVisual),
'inter-bond': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, InterUnitBondLineParams>) => ComplexRepresentation('Inter-unit bond line', ctx, getParams, InterUnitBondLineVisual),
+ 'element-point': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ElementPointParams>) => UnitsRepresentation('Points', ctx, getParams, ElementPointVisual),
+ 'element-cross': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ElementCrossParams>) => UnitsRepresentation('Crosses', ctx, getParams, ElementCrossVisual),
};
export const LineParams = {
...IntraUnitBondLineParams,
...InterUnitBondLineParams,
+ ...ElementPointParams,
+ ...ElementCrossParams,
+ multipleBonds: PD.Select('offset', PD.arrayToOptions(['off', 'symmetric', 'offset'] as const)),
includeParent: PD.Boolean(false),
- sizeFactor: PD.Numeric(1.5, { min: 0.01, max: 10, step: 0.01 }),
+ sizeFactor: PD.Numeric(3, { min: 0.01, max: 10, step: 0.01 }),
unitKinds: getUnitKindsParam(['atomic']),
- visuals: PD.MultiSelect(['intra-bond', 'inter-bond'], PD.objectToOptions(LineVisuals))
+ visuals: PD.MultiSelect(['intra-bond', 'inter-bond', 'element-point', 'element-cross'], PD.objectToOptions(LineVisuals))
};
export type LineParams = typeof LineParams
export function getLineParams(ctx: ThemeRegistryContext, structure: Structure) {
- return PD.clone(LineParams);
+ const params = PD.clone(LineParams);
+ params.pointStyle.defaultValue = 'circle';
+ return params;
}
export type LineRepresentation = StructureRepresentation<LineParams>
@@ -41,7 +50,7 @@ export function LineRepresentation(ctx: RepresentationContext, getParams: Repres
export const LineRepresentationProvider = StructureRepresentationProvider({
name: 'line',
label: 'Line',
- description: 'Displays bonds as lines.',
+ description: 'Displays bonds as lines and atoms as points or croses.',
factory: LineRepresentation,
getParams: getLineParams,
defaultValues: PD.getDefaultValues(LineParams),
diff --git a/src/mol-repr/structure/representation/point.ts b/src/mol-repr/structure/representation/point.ts
index 019d61ca955a7ca1934dc58bebd06cfa797621bd..0bcddfe18913d220af265f931f988ca057117d70 100644
--- a/src/mol-repr/structure/representation/point.ts
+++ b/src/mol-repr/structure/representation/point.ts
@@ -32,11 +32,11 @@ export function PointRepresentation(ctx: RepresentationContext, getParams: Repre
export const PointRepresentationProvider = StructureRepresentationProvider({
name: 'point',
label: 'Point',
- description: 'Displays elements (atoms, coarse spheres) as spheres.',
+ description: 'Displays elements (atoms, coarse spheres) as points.',
factory: PointRepresentation,
getParams: getPointParams,
defaultValues: PD.getDefaultValues(PointParams),
defaultColorTheme: { name: 'element-symbol' },
- defaultSizeTheme: { name: 'physical' },
+ defaultSizeTheme: { name: 'uniform' },
isApplicable: (structure: Structure) => structure.elementCount > 0
});
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
index d9bf85548561a1fb6fcef6264f84f6d843c7fbf6..5385bac813dbc3f0b461d149c8d9d3a116de447f 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
@@ -40,7 +40,10 @@ function getInterUnitBondCylinderBuilderProps(structure: Structure, theme: Theme
const bonds = structure.interUnitBonds;
const { edgeCount, edges } = bonds;
- const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds } = props;
+ const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds, multipleBonds } = props;
+
+ const mbOff = multipleBonds === 'off';
+ const mbSymmetric = multipleBonds === 'symmetric';
const delta = Vec3();
@@ -136,14 +139,16 @@ function getInterUnitBondCylinderBuilderProps(structure: Structure, theme: Theme
// show metallic coordinations and hydrogen bonds with dashed cylinders
return LinkStyle.Dashed;
} else if (o === 3) {
- return LinkStyle.Triple;
+ return mbOff ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Triple :
+ LinkStyle.OffsetTriple;
} else if (aromaticBonds && BondType.is(f, BondType.Flag.Aromatic)) {
return LinkStyle.Aromatic;
- } else if (o === 2) {
- return LinkStyle.Double;
}
- return LinkStyle.Solid;
+ return (o !== 2 || mbOff) ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Double :
+ LinkStyle.OffsetDouble;
},
radius: (edgeIndex: number) => {
return radius(edgeIndex) * sizeAspectRatio;
@@ -210,13 +215,17 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
newProps.stubCap !== currentProps.stubCap ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
- newProps.adjustCylinderLength !== currentProps.adjustCylinderLength
+ newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
+ newProps.multipleBonds !== currentProps.multipleBonds
);
if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
@@ -248,13 +257,17 @@ export function InterUnitBondCylinderMeshVisual(materialId: number): ComplexVisu
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
newProps.stubCap !== currentProps.stubCap ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
- newProps.adjustCylinderLength !== currentProps.adjustCylinderLength
+ newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
+ newProps.multipleBonds !== currentProps.multipleBonds
);
if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-line.ts b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
index 5578b8011c44b6f38eeaab7e443296a8ba4aa5c2..1fb4b9784d8fe7cfbb7a56fa27a9243d96ab69f0 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
@@ -32,10 +32,14 @@ function setRefPosition(pos: Vec3, structure: Structure, unit: Unit.Atomic, inde
function createInterUnitBondLines(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<InterUnitBondLineParams>, lines?: Lines) {
const bonds = structure.interUnitBonds;
const { edgeCount, edges } = bonds;
- const { sizeFactor, aromaticBonds } = props;
if (!edgeCount) return Lines.createEmpty(lines);
+ const { sizeFactor, aromaticBonds, multipleBonds } = props;
+
+ const mbOff = multipleBonds === 'off';
+ const mbSymmetric = multipleBonds === 'symmetric';
+
const ref = Vec3();
const loc = StructureElement.Location.create();
@@ -74,14 +78,16 @@ function createInterUnitBondLines(ctx: VisualContext, structure: Structure, them
// show metallic coordinations and hydrogen bonds with dashed cylinders
return LinkStyle.Dashed;
} else if (o === 3) {
- return LinkStyle.Triple;
+ return mbOff ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Triple :
+ LinkStyle.OffsetTriple;
} else if (aromaticBonds && BondType.is(f, BondType.Flag.Aromatic)) {
return LinkStyle.Aromatic;
- } else if (o === 2) {
- return LinkStyle.Double;
}
- return LinkStyle.Solid;
+ return (o !== 2 || mbOff) ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Double :
+ LinkStyle.OffsetDouble;
},
radius: (edgeIndex: number) => {
const b = edges[edgeIndex];
@@ -125,10 +131,12 @@ export function InterUnitBondLineVisual(materialId: number): ComplexVisual<Inter
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
- !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes)
+ !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
+ newProps.multipleBonds !== currentProps.multipleBonds
);
if (newStructure.interUnitBonds !== currentStructure.interUnitBonds) {
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index a53098c30270d139fd18420af02261c418162b76..abd5d82a7282c0f403faec6fbb92597030c134f5 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -33,7 +33,10 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
const bonds = unit.bonds;
const { edgeCount, a, b, edgeProps, offset } = bonds;
const { order: _order, flags: _flags } = edgeProps;
- const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds, includeTypes, excludeTypes } = props;
+ const { sizeFactor, sizeAspectRatio, adjustCylinderLength, aromaticBonds, includeTypes, excludeTypes, multipleBonds } = props;
+
+ const mbOff = multipleBonds === 'off';
+ const mbSymmetric = multipleBonds === 'symmetric';
const include = BondType.fromNames(includeTypes);
const exclude = BondType.fromNames(excludeTypes);
@@ -130,7 +133,9 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
// show metallic coordinations and hydrogen bonds with dashed cylinders
return LinkStyle.Dashed;
} else if (o === 3) {
- return LinkStyle.Triple;
+ return mbOff ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Triple :
+ LinkStyle.OffsetTriple;
} else if (aromaticBonds) {
const aI = a[edgeIndex], bI = b[edgeIndex];
const aR = elementAromaticRingIndices.get(aI);
@@ -146,7 +151,9 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
}
}
- return o === 2 ? LinkStyle.Double : LinkStyle.Solid;
+ return (o !== 2 || mbOff) ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Double :
+ LinkStyle.OffsetDouble;
},
radius: (edgeIndex: number) => {
return radius(edgeIndex) * sizeAspectRatio;
@@ -221,6 +228,9 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
@@ -228,7 +238,8 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
- newProps.aromaticBonds !== currentProps.aromaticBonds
+ newProps.aromaticBonds !== currentProps.aromaticBonds ||
+ newProps.multipleBonds !== currentProps.multipleBonds
);
const newUnit = newStructureGroup.group.units[0];
@@ -264,6 +275,9 @@ export function IntraUnitBondCylinderMeshVisual(materialId: number): UnitsVisual
newProps.linkSpacing !== currentProps.linkSpacing ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
newProps.linkCap !== currentProps.linkCap ||
+ newProps.aromaticScale !== currentProps.aromaticScale ||
+ newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.dashScale !== currentProps.dashScale ||
newProps.dashCap !== currentProps.dashCap ||
@@ -271,7 +285,8 @@ export function IntraUnitBondCylinderMeshVisual(materialId: number): UnitsVisual
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
newProps.adjustCylinderLength !== currentProps.adjustCylinderLength ||
- newProps.aromaticBonds !== currentProps.aromaticBonds
+ newProps.aromaticBonds !== currentProps.aromaticBonds ||
+ newProps.multipleBonds !== currentProps.multipleBonds
);
const newUnit = newStructureGroup.group.units[0];
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-line.ts b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
index 49e9c1bb2f72988f3846401463b5626615de13ec..1ad1fa45f7bbbad9eda44e63e311bd0e995925a4 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
@@ -39,7 +39,10 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
if (!edgeCount) return Lines.createEmpty(lines);
const { order: _order, flags: _flags } = edgeProps;
- const { sizeFactor, aromaticBonds, includeTypes, excludeTypes } = props;
+ const { sizeFactor, aromaticBonds, includeTypes, excludeTypes, multipleBonds } = props;
+
+ const mbOff = multipleBonds === 'off';
+ const mbSymmetric = multipleBonds === 'symmetric';
const include = BondType.fromNames(includeTypes);
const exclude = BondType.fromNames(excludeTypes);
@@ -91,7 +94,9 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
// show metallic coordinations and hydrogen bonds with dashed cylinders
return LinkStyle.Dashed;
} else if (o === 3) {
- return LinkStyle.Triple;
+ return mbOff ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Triple :
+ LinkStyle.OffsetTriple;
} else if (aromaticBonds) {
const aI = a[edgeIndex], bI = b[edgeIndex];
const aR = elementAromaticRingIndices.get(aI);
@@ -107,7 +112,9 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
}
}
- return o === 2 ? LinkStyle.Double : LinkStyle.Solid;
+ return (o !== 2 || mbOff) ? LinkStyle.Solid :
+ mbSymmetric ? LinkStyle.Double :
+ LinkStyle.OffsetDouble;
},
radius: (edgeIndex: number) => {
location.element = elements[a[edgeIndex]];
@@ -146,11 +153,13 @@ export function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUn
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.linkScale !== currentProps.linkScale ||
newProps.linkSpacing !== currentProps.linkSpacing ||
+ newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
newProps.dashCount !== currentProps.dashCount ||
newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
!arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
!arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
- newProps.aromaticBonds !== currentProps.aromaticBonds
+ newProps.aromaticBonds !== currentProps.aromaticBonds ||
+ newProps.multipleBonds !== currentProps.multipleBonds
);
const newUnit = newStructureGroup.group.units[0];
diff --git a/src/mol-repr/structure/visual/element-cross.ts b/src/mol-repr/structure/visual/element-cross.ts
new file mode 100644
index 0000000000000000000000000000000000000000..557a970feedadcd0090fc661e273dc0d7647df62
--- /dev/null
+++ b/src/mol-repr/structure/visual/element-cross.ts
@@ -0,0 +1,94 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsVisual, UnitsLinesParams, UnitsLinesVisual } from '../units-visual';
+import { VisualContext } from '../../visual';
+import { Unit, Structure, StructureElement } from '../../../mol-model/structure';
+import { Theme } from '../../../mol-theme/theme';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { ElementIterator, getElementLoci, eachElement, makeElementIgnoreTest } from './util/element';
+import { VisualUpdateState } from '../../util';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { Lines } from '../../../mol-geo/geometry/lines/lines';
+import { LinesBuilder } from '../../../mol-geo/geometry/lines/lines-builder';
+import { bondCount } from '../../../mol-model-props/computed/chemistry/util';
+
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3scaleAndAdd = Vec3.scaleAndAdd;
+const v3unitX = Vec3.unitX;
+const v3unitY = Vec3.unitY;
+const v3unitZ = Vec3.unitZ;
+
+export const ElementCrossParams = {
+ ...UnitsLinesParams,
+ lineSizeAttenuation: PD.Boolean(false),
+ ignoreHydrogens: PD.Boolean(false),
+ traceOnly: PD.Boolean(false),
+ crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'] as const)),
+ crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }),
+};
+export type ElementCrossParams = typeof ElementCrossParams
+
+export function createElementCross(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ElementCrossParams>, lines: Lines) {
+ const { child } = structure;
+ if (child && !child.unitMap.get(unit.id)) return Lines.createEmpty(lines);
+
+ const elements = unit.elements;
+ const n = elements.length;
+ const builder = LinesBuilder.create(n, n / 10, lines);
+
+ const p = Vec3();
+ const s = Vec3();
+ const e = Vec3();
+
+ const pos = unit.conformation.invariantPosition;
+ const ignore = makeElementIgnoreTest(structure, unit, props);
+
+ const r = props.crossSize / 2;
+ const lone = props.crosses === 'lone';
+
+ for (let i = 0 as StructureElement.UnitIndex; i < n; ++i) {
+ if (ignore && ignore(elements[i])) continue;
+ if (lone && Unit.isAtomic(unit) && bondCount(structure, unit, i) !== 0) continue;
+
+ pos(elements[i], p);
+ v3scaleAndAdd(s, p, v3unitX, r);
+ v3scaleAndAdd(e, p, v3unitX, -r);
+ builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
+ v3scaleAndAdd(s, p, v3unitY, r);
+ v3scaleAndAdd(e, p, v3unitY, -r);
+ builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
+ v3scaleAndAdd(s, p, v3unitZ, r);
+ v3scaleAndAdd(e, p, v3unitZ, -r);
+ builder.add(s[0], s[1], s[2], e[0], e[1], e[2], i);
+ }
+
+ const l = builder.getLines();
+
+ const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+ l.setBoundingSphere(sphere);
+
+ return l;
+}
+
+export function ElementCrossVisual(materialId: number): UnitsVisual<ElementCrossParams> {
+ return UnitsLinesVisual<ElementCrossParams>({
+ defaultProps: PD.getDefaultValues(ElementCrossParams),
+ createGeometry: createElementCross,
+ createLocationIterator: ElementIterator.fromGroup,
+ getLoci: getElementLoci,
+ eachLocation: eachElement,
+ setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementCrossParams>, currentProps: PD.Values<ElementCrossParams>) => {
+ state.createGeometry = (
+ newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+ newProps.traceOnly !== currentProps.traceOnly ||
+ newProps.crosses !== currentProps.crosses ||
+ newProps.crossSize !== currentProps.crossSize
+ );
+ }
+ }, materialId);
+}
\ No newline at end of file
diff --git a/src/mol-repr/structure/visual/element-point.ts b/src/mol-repr/structure/visual/element-point.ts
index 5ccea9224332e198f413b13140f957f60d8e5fbc..3f41e74ff0f114c0a6efee414248c67b32e31021 100644
--- a/src/mol-repr/structure/visual/element-point.ts
+++ b/src/mol-repr/structure/visual/element-point.ts
@@ -18,7 +18,7 @@ import { Sphere3D } from '../../../mol-math/geometry';
export const ElementPointParams = {
...UnitsPointsParams,
- pointSizeAttenuation: PD.Boolean(true),
+ pointSizeAttenuation: PD.Boolean(false),
ignoreHydrogens: PD.Boolean(false),
traceOnly: PD.Boolean(false),
};
diff --git a/src/mol-repr/structure/visual/util/bond.ts b/src/mol-repr/structure/visual/util/bond.ts
index 5e2ddafd6c006f47817c606fddc93b0c0d35646b..d2fb94a7769d27880135d6008e0c46c724ae1ef4 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -20,6 +20,7 @@ export const BondParams = {
excludeTypes: PD.MultiSelect([] as BondType.Names[], PD.objectToOptions(BondType.Names)),
ignoreHydrogens: PD.Boolean(false),
aromaticBonds: PD.Boolean(false, { description: 'Display aromatic bonds with dashes' }),
+ multipleBonds: PD.Select('symmetric', PD.arrayToOptions(['off', 'symmetric', 'offset'] as const)),
};
export const DefaultBondProps = PD.getDefaultValues(BondParams);
export type BondProps = typeof DefaultBondProps
@@ -27,7 +28,7 @@ export type BondProps = typeof DefaultBondProps
export const BondCylinderParams = {
...LinkCylinderParams,
...BondParams,
- adjustCylinderLength: PD.Boolean(true, { description: 'Shorten cylinders to reduce overlap with spheres.' })
+ adjustCylinderLength: PD.Boolean(false, { description: 'Shorten cylinders to reduce overlap with spheres. Useful for for transparent bonds. Not working well with aromatic bonds.' })
};
export const DefaultBondCylinderProps = PD.getDefaultValues(BondCylinderParams);
export type BondCylinderProps = typeof DefaultBondCylinderProps
diff --git a/src/mol-repr/structure/visual/util/link.ts b/src/mol-repr/structure/visual/util/link.ts
index 34752801b2bd219933552315cf5b03fedcf16933..c62aea5d0a496badcf2924404c35ce6153cf9c3f 100644
--- a/src/mol-repr/structure/visual/util/link.ts
+++ b/src/mol-repr/structure/visual/util/link.ts
@@ -21,6 +21,9 @@ export const LinkCylinderParams = {
linkScale: PD.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
linkSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
linkCap: PD.Boolean(false),
+ aromaticScale: PD.Numeric(0.3, { min: 0, max: 1, step: 0.01 }),
+ aromaticSpacing: PD.Numeric(1.5, { min: 0, max: 3, step: 0.01 }),
+ aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
dashScale: PD.Numeric(0.8, { min: 0, max: 2, step: 0.1 }),
dashCap: PD.Boolean(true),
@@ -33,6 +36,7 @@ export type LinkCylinderProps = typeof DefaultLinkCylinderProps
export const LinkLineParams = {
linkScale: PD.Numeric(0.5, { min: 0, max: 1, step: 0.1 }),
linkSpacing: PD.Numeric(0.1, { min: 0, max: 2, step: 0.01 }),
+ aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
};
export const DefaultLinkLineProps = PD.getDefaultValues(LinkLineParams);
@@ -83,10 +87,12 @@ export const enum LinkStyle {
Solid = 0,
Dashed = 1,
Double = 2,
- Triple = 3,
- Disk = 4,
- Aromatic = 5,
- MirroredAromatic = 6,
+ OffsetDouble = 3,
+ Triple = 4,
+ OffsetTriple = 5,
+ Disk = 6,
+ Aromatic = 7,
+ MirroredAromatic = 8,
}
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
@@ -105,7 +111,7 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
if (!linkCount) return Mesh.createEmpty(mesh);
- const { linkScale, linkSpacing, radialSegments, linkCap, dashCount, dashScale, dashCap, stubCap } = props;
+ const { linkScale, linkSpacing, radialSegments, linkCap, aromaticScale, aromaticSpacing, aromaticDashCount, dashCount, dashScale, dashCap, stubCap } = props;
const vertexCountEstimate = radialSegments * 2 * linkCount * 2;
const builderState = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
@@ -128,14 +134,15 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
position(va, vb, edgeIndex);
v3sub(tmpV12, vb, va);
+ const dirFlag = v3dot(tmpV12, up) > 0;
const linkRadius = radius(edgeIndex);
const linkStyle = style ? style(edgeIndex) : LinkStyle.Solid;
const linkStub = stubCap && (stub ? stub(edgeIndex) : false);
- const [topCap, bottomCap] = (v3dot(tmpV12, up) > 0) ? [linkStub, linkCap] : [linkCap, linkStub];
+ const [topCap, bottomCap] = dirFlag ? [linkStub, linkCap] : [linkCap, linkStub];
builderState.currentGroup = edgeIndex;
- const aromaticOffsetFactor = 4.5;
+ const aromaticSegmentCount = aromaticDashCount + 1;
if (linkStyle === LinkStyle.Solid) {
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
@@ -148,9 +155,9 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
addFixedCountDashedCylinder(builderState, va, vb, 0.5, segmentCount, cylinderProps);
- } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
- const order = linkStyle === LinkStyle.Double ? 2 :
- linkStyle === LinkStyle.Triple ? 3 : 1.5;
+ } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+ const order = (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble) ? 2 :
+ (linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple) ? 3 : 1.5;
const multiRadius = linkRadius * (linkScale / (0.5 * order));
const absOffset = (linkRadius - multiRadius) * linkSpacing;
@@ -163,18 +170,49 @@ export function createLinkCylinderMesh(ctx: VisualContext, linkBuilder: LinkBuil
cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
addCylinder(builderState, va, vb, 0.5, cylinderProps);
- cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * linkScale;
+ const aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
+
+ v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
+ v3add(va, va, tmpV12);
+ v3sub(vb, vb, tmpV12);
+
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * aromaticScale;
cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+ v3setMagnitude(vShift, vShift, aromaticOffset);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
- addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+ addFixedCountDashedCylinder(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
if (linkStyle === LinkStyle.MirroredAromatic) {
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+ v3setMagnitude(vShift, vShift, aromaticOffset * 2);
+ v3add(va, va, vShift);
+ v3add(vb, vb, vShift);
+ addFixedCountDashedCylinder(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
+ }
+ } else if (linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.OffsetTriple) {
+ const multipleOffset = linkRadius + multiRadius + linkScale * linkRadius * linkSpacing;
+ v3setMagnitude(vShift, vShift, multipleOffset);
+
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
+ addCylinder(builderState, va, vb, 0.5, cylinderProps);
+
+ v3scale(tmpV12, tmpV12, linkSpacing * linkScale * 0.2);
+ v3add(va, va, tmpV12);
+ v3sub(vb, vb, tmpV12);
+
+ cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
+ cylinderProps.topCap = dirFlag ? linkStub : dashCap;
+ cylinderProps.bottomCap = dirFlag ? dashCap : linkStub;
+ v3setMagnitude(vShift, vShift, multipleOffset);
+ v3sub(va, va, vShift);
+ v3sub(vb, vb, vShift);
+ addCylinder(builderState, va, vb, 0.5, cylinderProps);
+
+ if (order === 3) {
+ v3setMagnitude(vShift, vShift, multipleOffset * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
- addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+ addCylinder(builderState, va, vb, 0.5, cylinderProps);
}
} else {
v3setMagnitude(vShift, vShift, absOffset);
@@ -208,7 +246,7 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
if (!linkCount) return Cylinders.createEmpty(cylinders);
- const { linkScale, linkSpacing, linkCap, dashCount, dashScale, dashCap, stubCap } = props;
+ const { linkScale, linkSpacing, linkCap, aromaticScale, aromaticSpacing, aromaticDashCount, dashCount, dashScale, dashCap, stubCap } = props;
const cylindersCountEstimate = linkCount * 2;
const builder = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
@@ -222,9 +260,8 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
const segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
const lengthScale = 0.5 - (0.5 / 2 / segmentCount);
- const aromaticSegmentCount = 3;
+ const aromaticSegmentCount = aromaticDashCount + 1;
const aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
- const aromaticOffsetFactor = 4.5;
for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
if (ignore && ignore(edgeIndex)) continue;
@@ -242,9 +279,9 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
v3sub(vb, vb, tmpV12);
builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
- } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
- const order = linkStyle === LinkStyle.Double ? 2 :
- linkStyle === LinkStyle.Triple ? 3 : 1.5;
+ } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+ const order = (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble) ? 2 :
+ (linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple) ? 3 : 1.5;
const multiScale = linkScale / (0.5 * order);
const absOffset = (linkRadius - multiScale * linkRadius) * linkSpacing;
@@ -254,24 +291,40 @@ export function createLinkCylinderImpostors(ctx: VisualContext, linkBuilder: Lin
if (linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+ const aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
+
v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
v3sub(vb, vb, tmpV12);
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+ v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
+ v3add(va, va, tmpV12);
+
+ v3setMagnitude(vShift, vShift, aromaticOffset);
v3sub(va, va, vShift);
v3sub(vb, vb, vShift);
- builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+ builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
if (linkStyle === LinkStyle.MirroredAromatic) {
- v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+ v3setMagnitude(vShift, vShift, aromaticOffset * 2);
v3add(va, va, vShift);
v3add(vb, vb, vShift);
- builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+ builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
}
+ } else if (linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.OffsetTriple) {
+ const multipleOffset = linkRadius + multiScale * linkRadius + linkScale * linkRadius * linkSpacing;
+ v3setMagnitude(vShift, vShift, multipleOffset);
+
+ builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+
+ v3setMagnitude(tmpV12, v3sub(tmpV12, va, vb), linkRadius / 1.5);
+ v3sub(va, va, tmpV12);
+
+ if (order === 3) builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
+ builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, dashCap, linkStub, edgeIndex);
} else {
v3setMagnitude(vShift, vShift, absOffset);
- if (order === 3) builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, false, edgeIndex);
+ if (order === 3) builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, linkStub, edgeIndex);
builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
}
@@ -296,7 +349,7 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
if (!linkCount) return Lines.createEmpty(lines);
- const { linkScale, linkSpacing, dashCount } = props;
+ const { linkScale, linkSpacing, aromaticDashCount, dashCount } = props;
const linesCountEstimate = linkCount * 2;
const builder = LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
@@ -310,9 +363,10 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
const segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
const lengthScale = 0.5 - (0.5 / 2 / segmentCount);
- const aromaticSegmentCount = 3;
+ const aromaticSegmentCount = aromaticDashCount + 1;
const aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
const aromaticOffsetFactor = 4.5;
+ const multipleOffsetFactor = 3;
for (let edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
if (ignore && ignore(edgeIndex)) continue;
@@ -328,9 +382,9 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
v3sub(vb, vb, tmpV12);
builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
- } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
- const order = linkStyle === LinkStyle.Double ? 2 :
- linkStyle === LinkStyle.Triple ? 3 : 1.5;
+ } else if (linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple || linkStyle === LinkStyle.Aromatic || linkStyle === LinkStyle.MirroredAromatic) {
+ const order = linkStyle === LinkStyle.Double || linkStyle === LinkStyle.OffsetDouble ? 2 :
+ linkStyle === LinkStyle.Triple || linkStyle === LinkStyle.OffsetTriple ? 3 : 1.5;
const multiRadius = 1 * (linkScale / (0.5 * order));
const absOffset = (1 - multiRadius) * linkSpacing;
@@ -354,8 +408,18 @@ export function createLinkLines(ctx: VisualContext, linkBuilder: LinkBuilderProp
v3add(vb, vb, vShift);
builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
}
+ } else if (linkStyle === LinkStyle.OffsetDouble || linkStyle === LinkStyle.OffsetTriple) {
+ v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
+
+ builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
+
+ v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale);
+ v3sub(va, va, tmpV12);
+
+ if (order === 3) builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], edgeIndex);
+ builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], edgeIndex);
} else {
- v3setMagnitude(vShift, vShift, absOffset);
+ v3setMagnitude(vShift, vShift, absOffset * 1.5);
if (order === 3) builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], edgeIndex);
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index 73c123a859f98f572151db59980b1841fd6500cf..d43df4dd7e87a0d2904d8afb271e9f0303849d2f 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -92,6 +92,14 @@ export function structureElementStatsLabel(stats: StructureElement.Stats, option
return o.htmlStyling ? label : stripTags(label);
}
+export function structureElementLociLabelMany(locis: StructureElement.Loci[], options: Partial<LabelOptions> = {}): string {
+ const stats = StructureElement.Stats.create();
+ for (const l of locis) {
+ StructureElement.Stats.add(stats, stats, StructureElement.Stats.ofLoci(l));
+ }
+ return structureElementStatsLabel(stats, options);
+}
+
function _structureElementStatsLabel(stats: StructureElement.Stats, countsOnly = false, hidePrefix = false, condensed = false, reverse = false): string {
const { structureCount, chainCount, residueCount, conformationCount, elementCount } = stats;
diff --git a/src/mol-util/marker-action.ts b/src/mol-util/marker-action.ts
index 53bcd5e4fadca982ce45040684d6c0847e0d680f..324b625b6a313fa368026c68150e3f68a3b31a54 100644
--- a/src/mol-util/marker-action.ts
+++ b/src/mol-util/marker-action.ts
@@ -68,11 +68,19 @@ export function applyMarkerAction(array: Uint8Array, set: OrderedSet, action: Ma
if (Interval.is(set)) {
const start = Interval.start(set);
const end = Interval.end(set);
- const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
-
const viewStart = (start + 3) >> 2;
const viewEnd = viewStart + ((end - 4 * viewStart) >> 2);
+ if (viewEnd <= viewStart) {
+ // avoid edge cases with overlapping front/end intervals
+ for (let i = start; i < end; ++i) {
+ applyMarkerActionAtPosition(array, i, action);
+ }
+ return true;
+ }
+
+ const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+
const frontStart = start;
const frontEnd = Math.min(4 * viewStart, end);
const backStart = Math.max(start, 4 * viewEnd);
diff --git a/src/mol-util/zip/bin.ts b/src/mol-util/zip/bin.ts
index 1b3d2a1a4feffe2be4fa128fc7342ff184691f06..fae13877ad1b1226aea461d673e90d2ae4f335fe 100644
--- a/src/mol-util/zip/bin.ts
+++ b/src/mol-util/zip/bin.ts
@@ -92,7 +92,7 @@ export function sizeUTF8(str: string) {
for (let ci = 0; ci < strl; ci++) {
const code = str.charCodeAt(ci);
if ((code & (0xffffffff - (1 << 7) + 1)) === 0) {
- i++ ;
+ i++;
} else if ((code & (0xffffffff - (1 << 11) + 1)) === 0) {
i += 2;
} else if ((code & (0xffffffff - (1 << 16) + 1)) === 0) {
diff --git a/src/servers/model/CHANGELOG.md b/src/servers/model/CHANGELOG.md
index db7e0e2f24be611e661b46e0825a1be4da63c134..3835d9dbc948cf2f6dca77c6fdb1a6640c0c82ea 100644
--- a/src/servers/model/CHANGELOG.md
+++ b/src/servers/model/CHANGELOG.md
@@ -1,3 +1,6 @@
+# 0.9.8
+* fix support for chem_comp_bond and struct_conn categories
+
# 0.9.7
* add Surrounding Ligands query
diff --git a/src/servers/model/config.ts b/src/servers/model/config.ts
index 0cfd9d6b42edfd409a408707d0aef441728715e5..5fa1823a046593b2cbeaa08b125b6412fdd05685 100644
--- a/src/servers/model/config.ts
+++ b/src/servers/model/config.ts
@@ -229,10 +229,10 @@ function addJsonConfigArgs(parser: argparse.ArgumentParser) {
'JSON config file path',
'If a property is not specified, cmd line param/OS variable/default value are used.'
].join('\n'),
- required: false
+ required: false,
});
- parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
- parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
+ parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, action: 'store_true' });
+ parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, action: 'store_true' });
}
function setConfig(config: ModelServerConfig) {
@@ -271,7 +271,7 @@ function parseConfigArguments() {
export function configureServer() {
const config = parseConfigArguments();
- if (config.cfgTemplate !== null) {
+ if (!!config.cfgTemplate) {
console.log(JSON.stringify(ModelServerConfigTemplate, null, 2));
process.exit(0);
}
@@ -284,7 +284,7 @@ export function configureServer() {
setConfig(cfg);
}
- if (config.printCfg !== null) {
+ if (!!config.printCfg) {
console.log(JSON.stringify(ModelServerConfig, null, 2));
process.exit(0);
}
diff --git a/src/servers/model/version.ts b/src/servers/model/version.ts
index 48ad2176e31bbd3cf37859acef4438aafe90dee4..84aac74f66131719349de17f4ccbafbfd9b1459b 100644
--- a/src/servers/model/version.ts
+++ b/src/servers/model/version.ts
@@ -1,7 +1,7 @@
/**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
-export const VERSION = '0.9.7';
\ No newline at end of file
+export const VERSION = '0.9.8';
\ No newline at end of file
diff --git a/src/servers/volume/config.ts b/src/servers/volume/config.ts
index 53d247d7205284c441f20ba1eef93fa728c6f69c..cc51934c1acc0275d88c3bb37b1e846b8e91e7d1 100644
--- a/src/servers/volume/config.ts
+++ b/src/servers/volume/config.ts
@@ -89,10 +89,10 @@ function addJsonConfigArgs(parser: argparse.ArgumentParser) {
'JSON config file path',
'If a property is not specified, cmd line param/OS variable/default value are used.'
].join('\n'),
- required: false
+ required: false,
});
- parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, nargs: 0 });
- parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, nargs: 0 });
+ parser.add_argument('--printCfg', { help: 'Print current config for validation and exit.', required: false, action: 'store_true' });
+ parser.add_argument('--cfgTemplate', { help: 'Prints default JSON config template to be modified and exits.', required: false, action: 'store_true' });
}
export interface ServerJsonConfig {
@@ -165,7 +165,7 @@ export function configureServer() {
addLimitsArgs(parser);
const config = parser.parse_args() as FullServerConfig & ServerJsonConfig;
- if (config.cfgTemplate !== null) {
+ if (!!config.cfgTemplate) {
console.log(JSON.stringify(ServerConfigTemplate, null, 2));
process.exit(0);
}
@@ -178,7 +178,7 @@ export function configureServer() {
setConfig(cfg);
}
- if (config.printCfg !== null) {
+ if (config.printCfg) {
console.log(JSON.stringify({ ...ServerConfig, ...LimitsConfig }, null, 2));
process.exit(0);
}
@@ -197,7 +197,7 @@ export function configureLocal() {
description: VOLUME_SERVER_HEADER
});
parser.add_argument('--jobs', { help: `Path to a JSON file with job specification.`, required: false });
- parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });;
+ parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });
addJsonConfigArgs(parser);
addLimitsArgs(parser);