Merge branch 'master' of https://github.com/molstar/molstar into pick-atom

CHANGELOG.md

@@ -6,6 +6,24 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+- Fix pickScale not taken into account in line/point shader
+- Add pixel-scale & pick-scale 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 visual to Line representation
+
+## [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
@@ -14,14 +32,9 @@ Note that since we don't clearly distinguish between a public and private interf
     - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
     - Set ``pointSizeAttenuation`` to false by default
     - Set ``sizeTheme`` to ``uniform`` by default
-- Fix pickScale not taken into account in line/point shader
-- Add pixel-scale & pick-scale 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 ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
-- Add points visual to Line representation
+- 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
 

package-lock.json

@@ -1,12 +1,11 @@
 {
   "name": "molstar",
-  "version": "2.3.0",
+  "version": "2.3.3",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
-      "name": "molstar",
-      "version": "2.3.0",
+      "version": "2.3.3",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.10",
@@ -4314,6 +4313,7 @@
       "dependencies": {
         "anymatch": "~3.1.2",
         "braces": "~3.0.2",
+        "fsevents": "~2.3.2",
         "glob-parent": "~5.1.2",
         "is-binary-path": "~2.1.0",
         "is-glob": "~4.0.1",
@@ -5627,7 +5627,8 @@
         "esprima": "^4.0.1",
         "estraverse": "^5.2.0",
         "esutils": "^2.0.2",
-        "optionator": "^0.8.1"
+        "optionator": "^0.8.1",
+        "source-map": "~0.6.1"
       },
       "bin": {
         "escodegen": "bin/escodegen.js",
@@ -8250,6 +8251,7 @@
         "@types/node": "*",
         "anymatch": "^3.0.3",
         "fb-watchman": "^2.0.0",
+        "fsevents": "^2.3.2",
         "graceful-fs": "^4.2.4",
         "jest-regex-util": "^27.0.6",
         "jest-serializer": "^27.0.6",
@@ -8917,6 +8919,7 @@
       "integrity": "sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ==",
       "dev": true,
       "dependencies": {
+        "graceful-fs": "^4.1.6",
         "universalify": "^2.0.0"
       },
       "optionalDependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "2.3.0",
+  "version": "2.3.3",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/mol-canvas3d/canvas3d.ts

@@ -116,19 +116,21 @@ namespace Canvas3DContext {
         preserveDrawingBuffer: true,
         pixelScale: 1,
         pickScale: 0.25,
-        enableWboit: true
+        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');
 

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;

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;
 }

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 }) {

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'),
 

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: {
@@ -28,6 +38,9 @@ export const PluginConfig = {
         PixelScale: item('plugin-config.pixel-scale', 1),
         PickScale: item('plugin-config.pick-scale', 0.25),
         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'),

src/mol-plugin/context.ts

@@ -197,7 +197,8 @@ export class PluginContext {
                 const pixelScale = this.config.get(PluginConfig.General.PixelScale) || 1;
                 const pickScale = this.config.get(PluginConfig.General.PickScale) || 0.25;
                 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.canvas3d as Canvas3D) = Canvas3D.create(this.canvas3dContext!);
             this.canvas3dInit.next(true);

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
 

src/servers/model/config.ts

@@ -229,10 +229,11 @@ 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,
+        action: 'store_true'
     });
-    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 +272,7 @@ 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 +285,7 @@ export function configureServer() {
             setConfig(cfg);
         }
 
-        if (config.printCfg !== null) {
+        if (!!config.printCfg) {
             console.log(JSON.stringify(ModelServerConfig, null, 2));
             process.exit(0);
         }

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';
+export const VERSION = '0.9.8';

src/servers/volume/config.ts

@@ -89,10 +89,11 @@ 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,
+        action: 'store_true'
     });
-    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 +166,7 @@ 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 +179,7 @@ export function configureServer() {
             setConfig(cfg);
         }
 
-        if (config.printCfg !== null) {
+        if (config.printCfg) {
             console.log(JSON.stringify({ ...ServerConfig, ...LimitsConfig }, null, 2));
             process.exit(0);
         }