tweak cube clamp param

CHANGELOG.md

@@ -6,6 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+- Make `PluginContext.initContainer` checkered canvas background optional
+
 ## [v3.23.0] - 2022-10-19
 
 - Add `PluginContext.initContainer/mount/unmount` methods; these should make it easier to reuse a plugin context with both custom and built-in UI

src/cli/cifschema/util/cif-dic.ts

@@ -71,6 +71,7 @@ export function getFieldType(type: string, description: string, values?: string[
         case 'ec-type':
         case 'ucode-alphanum-csv':
         case 'id_list':
+        case 'entity_id_list':
             return ListCol('str', ',', description);
         case 'id_list_spc':
             return ListCol('str', ' ', description);

src/mol-gl/shader/chunks/apply-light-color.glsl.ts

@@ -57,7 +57,7 @@ export const apply_light_color = `
     RE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);
 
     vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;
-    outgoingLight = clamp(outgoingLight, 0.0, 1.0); // prevents black artifacts on specular highlight with transparent background
+    outgoingLight = clamp(outgoingLight, 0.01, 0.99); // prevents black artifacts on specular highlight with transparent background
 
     gl_FragColor = vec4(outgoingLight, color.a);
 #endif

src/mol-io/reader/cif/schema/bird.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.360, IHM 1.17, MA 1.4.2.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.362, IHM 1.17, MA 1.4.3.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/ccd.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.360, IHM 1.17, MA 1.4.2.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.362, IHM 1.17, MA 1.4.3.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.360, IHM 1.17, MA 1.4.2.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.362, IHM 1.17, MA 1.4.3.
  *
  * @author molstar/ciftools package
  */

src/mol-model-formats/volume/cube.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { CubeFile } from '../../mol-io/reader/cube/parser';
@@ -11,8 +12,9 @@ import { Task } from '../../mol-task';
 import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
 import { ModelFormat } from '../format';
 import { CustomProperties } from '../../mol-model/custom-property';
+import { clamp } from '../../mol-math/interpolate';
 
-export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string, entryId?: string }): Task<Volume> {
+export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string, entryId?: string, clamp?: { min: number, max: number } }): Task<Volume> {
     return Task.create<Volume>('Create Volume', async () => {
         const { header, values: sourceValues } = source;
         const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
@@ -24,6 +26,7 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
             // get every nth value from the source values
             const [h, k, l] = header.dim;
             const nth = (params?.dataIndex || 0) + 1;
+            const { min, max } = params?.clamp || { min: -Infinity, max: Infinity };
 
             let o = 0, s = 0;
 
@@ -31,7 +34,7 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
             for (let u = 0; u < h; u++) {
                 for (let v = 0; v < k; v++) {
                     for (let w = 0; w < l; w++) {
-                        values[o++] = sourceValues[s];
+                        values[o++] = clamp(sourceValues[s], min, max);
                         s += nth;
                     }
                 }

src/mol-plugin-state/transforms/volume.ts

@@ -88,12 +88,24 @@ const VolumeFromCube = PluginStateTransform.BuiltIn({
         return {
             dataIndex,
             entryId: PD.Text(''),
+            clamp: PD.MappedStatic('off', {
+                'off': PD.EmptyGroup(),
+                'on': PD.Group({
+                    min: PD.Numeric(-1024),
+                    max: PD.Numeric(1024),
+                })
+            }, { cycle: true })
         };
     }
 })({
     apply({ a, params }) {
         return Task.create('Create volume from Cube', async ctx => {
-            const volume = await volumeFromCube(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
+            const volume = await volumeFromCube(a.data, {
+                dataIndex: params.dataIndex,
+                label: a.data.name || a.label,
+                entryId: params.entryId,
+                clamp: params.clamp.name === 'on' ? params.clamp.params : undefined,
+            }).runInContext(ctx);
             const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.dim[0]}\u00D7${a.data.header.dim[1]}\u00D7${a.data.header.dim[2]}` };
             return new SO.Volume.Data(volume, props);
         });

src/mol-plugin-ui/viewport/canvas.tsx

@@ -38,7 +38,7 @@ export class ViewportCanvas extends PluginUIComponent<ViewportCanvasParams, View
     };
 
     componentDidMount() {
-        if (!this.container.current || !this.plugin.mount(this.container.current!)) {
+        if (!this.container.current || !this.plugin.mount(this.container.current!, { checkeredCanvasBackground: true })) {
             this.setState({ noWebGl: true });
             return;
         }

src/mol-plugin/context.ts

@@ -193,7 +193,7 @@ export class PluginContext {
      */
     readonly customState: unknown = Object.create(null);
 
-    initContainer(canvas3dContext?: Canvas3DContext) {
+    initContainer(options?: { canvas3dContext?: Canvas3DContext, checkeredCanvasBackground?: boolean }) {
         if (this.canvasContainer) return true;
 
         const container = document.createElement('div');
@@ -209,27 +209,33 @@ export class PluginContext {
             '-webkit-touch-callout': 'none',
             'touch-action': 'manipulation',
         });
-        let canvas = canvas3dContext?.canvas;
+        let canvas = options?.canvas3dContext?.canvas;
         if (!canvas) {
             canvas = document.createElement('canvas');
-            Object.assign(canvas.style, {
-                'background-image': 'linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey), linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey)',
-                'background-size': '60px 60px',
-                'background-position': '0 0, 30px 30px'
-            });
+            if (options?.checkeredCanvasBackground) {
+                Object.assign(canvas.style, {
+                    'background-image': 'linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey), linear-gradient(45deg, lightgrey 25%, transparent 25%, transparent 75%, lightgrey 75%, lightgrey)',
+                    'background-size': '60px 60px',
+                    'background-position': '0 0, 30px 30px'
+                });
+            }
             container.appendChild(canvas);
         }
-        if (!this.initViewer(canvas, container, canvas3dContext)) {
+        if (!this.initViewer(canvas, container, options?.canvas3dContext)) {
             return false;
         }
         this.canvasContainer = container;
         return true;
     }
 
-    mount(target: HTMLElement) {
+    /**
+     * Mount the plugin into the target element (assumes the target has "relative"-like positioninig).
+     * If initContainer wasn't called separately before, initOptions will be passed to it.
+     */
+    mount(target: HTMLElement, initOptions?: { canvas3dContext?: Canvas3DContext, checkeredCanvasBackground?: boolean }) {
         if (this.disposed) throw new Error('Cannot mount a disposed context');
 
-        if (!this.initContainer()) return false;
+        if (!this.initContainer(initOptions)) return false;
 
         if (this.canvasContainer!.parentElement !== target) {
             this.canvasContainer!.parentElement?.removeChild(this.canvasContainer!);