2.0.0-dev.3

- if it has not changed much

.eslintrc.json

@@ -3,60 +3,21 @@
         "browser": true,
         "node": true
     },
-    "parser": "@typescript-eslint/parser",
     "parserOptions": {
-        "project": ["tsconfig.json", "tsconfig.servers.json"],
-        "sourceType": "module"
+        "ecmaVersion": 2018,
+        "sourceType": "module",
+        "ecmaFeatures": {
+            "impliedStrict": true
+        }
     },
-    "plugins": [
-        "@typescript-eslint"
-    ],
     "rules": {
-        "@typescript-eslint/ban-types": "warn",
-        "@typescript-eslint/class-name-casing": "off",
         "indent": "off",
-        "@typescript-eslint/indent": [
-            "error",
-            4
-        ],
-        "@typescript-eslint/member-delimiter-style": [
-            "off",
-            {
-                "multiline": {
-                    "delimiter": "none",
-                    "requireLast": true
-                },
-                "singleline": {
-                    "delimiter": "semi",
-                    "requireLast": false
-                }
-            }
-        ],
-        "@typescript-eslint/prefer-namespace-keyword": "warn",
-        "@typescript-eslint/quotes": [
-            "error",
-            "single",
-            {
-                "avoidEscape": true,
-                "allowTemplateLiterals": true
-            }
-        ],
-        "@typescript-eslint/semi": [
-            "off",
-            null
-        ],
-        "@typescript-eslint/type-annotation-spacing": "error",
         "arrow-parens": [
             "off",
             "as-needed"
         ],
         "brace-style": "off",
-        "@typescript-eslint/brace-style": [
-            "error",
-            "1tbs", { "allowSingleLine": true }
-        ],
         "comma-spacing": "off",
-        "@typescript-eslint/comma-spacing": "error",
         "space-infix-ops": "error",
         "comma-dangle": "off",
         "eqeqeq": [
@@ -70,6 +31,66 @@
         "no-unsafe-finally": "warn",
         "no-var": "error",
         "spaced-comment": "error",
-        "semi": "warn"
-    }
+        "semi": "warn",
+        "no-restricted-syntax": [
+            "error",
+            {
+                "selector": "ExportDefaultDeclaration",
+                "message": "Default exports are not allowed"
+            }
+        ]
+    },
+    "overrides": [
+        {
+            "files": ["**/*.ts", "**/*.tsx"],
+            "parser": "@typescript-eslint/parser",
+            "parserOptions": {
+                "project": ["tsconfig.json", "tsconfig.commonjs.json"],
+                "sourceType": "module"
+            },
+            "plugins": [
+                "@typescript-eslint"
+            ],
+            "rules": {
+                "@typescript-eslint/ban-types": "off",
+                "@typescript-eslint/class-name-casing": "off",
+                "@typescript-eslint/indent": [
+                    "error",
+                    4
+                ],
+                "@typescript-eslint/member-delimiter-style": [
+                    "off",
+                    {
+                        "multiline": {
+                            "delimiter": "none",
+                            "requireLast": true
+                        },
+                        "singleline": {
+                            "delimiter": "semi",
+                            "requireLast": false
+                        }
+                    }
+                ],
+                "@typescript-eslint/prefer-namespace-keyword": "warn",
+                "@typescript-eslint/quotes": [
+                    "error",
+                    "single",
+                    {
+                        "avoidEscape": true,
+                        "allowTemplateLiterals": true
+                    }
+                ],
+                "@typescript-eslint/semi": [
+                    "off",
+                    null
+                ],
+                "@typescript-eslint/type-annotation-spacing": "error",
+                "@typescript-eslint/brace-style": [
+                    "error",
+                    "1tbs", { "allowSingleLine": true }
+                ],
+                "@typescript-eslint/comma-spacing": "error"
+            }
+        }
+    ]
 }

.gitignore

@@ -5,6 +5,7 @@ node_modules/
 debug.log
 npm-debug.log
 tsconfig.tsbuildinfo
+tsconfig.commonjs.tsbuildinfo
 
 *.sublime-workspace
 .idea

.npmignore

@@ -1 +1 @@
-tsconfig.servers.buildinfo
+tsconfig.commonjs.buildinfo

.travis.yml

@@ -14,6 +14,5 @@ before_install:
 node_js:
   - "12"
   - "10"
-  - "8"
 before_script:
   - export DISPLAY=:99.0; sh -e /etc/init.d/xvfb start

README.md

@@ -41,7 +41,7 @@ Moreover, the project contains the implementation of `servers`, including
 - `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
 - `servers/plugin-state` A basic server to store Mol* Plugin states.
 
-The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `apps` (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+The project also contains performance tests (`perf-tests`), `examples`, and basic proof of concept `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
 
 ## Previous Work
 This project builds on experience from previous solutions:
@@ -90,19 +90,28 @@ and navigate to `build/viewer`
 ### Code generation
 **CIF schemas**
 
-    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
-    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
-    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
-    node ./lib/apps/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
+
+**Lipid names**
+
+    node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
+
+**Ion names**
+
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
+
 
 **GraphQL schemas**
 
-    ./node_modules/.bin/graphql-codegen -c ./src/extensions/rcsb/graphql/codegen.yml
+    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
 
 ### Other scripts
 **Create chem comp bond table**
 
-    node --max-old-space-size=4096 lib/apps/chem-comp-bond/create-table.js build/data/ccb.bcif -b
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
 
 **Test model server**
 
@@ -120,7 +129,7 @@ To see all available commands, use ``node lib/servers/model/preprocess -h``.
 
 Or
 
-    node ./lib/apps/cif2bcif
+    node lib/commonjs/cli/cif2bcif
 
 ## Development
 
@@ -168,3 +177,4 @@ Funding sources include but are not limited to:
 * [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
 * [PDBe, EMBL-EBI](https://pdbe.org)
 * [CEITEC](https://www.ceitec.eu/)
+* [EntosAI](https://www.entos.ai) (``alpha-orbitals`` extension)

docs/interesting-pdb-entries.md

@@ -0,0 +1,28 @@
+* Cyclic polymers (1sfi, 6dny, 1HVZ)
+* B-DNA (1bna)
+* Missing carbonyl oxygen (1gfl)
+* Mono-saccharides with alt locs (1B5F)
+* Microheterogeneity
+    * Protein (1EJG, 3NIR)
+    * DNA (3VOK)
+* PNA: peptide nucleic acid (5eme, 1xj9)
+* Peptide derived residues
+    * GFP chromophores (5Z6Y)
+* Nucleotides that don’t have a parent base set, i.e. detect purine/pyrimidine from geometry (THX in 1AUL, OMC in e.g. 5D3G)
+* Bases with modified ring atoms
+    * DZ has C1 instead of N1 (e.g. 6I4N)
+    * DP has N5 instead of C5 and C7 instead of N7 (e.g. 6I4N)
+* Beta & Gamma peptides (e.g. 1GAC, 6PQF)
+* Mixed (heterogeneous) all-atom/trace-only RNA model (1JGQ)
+* Polymers with residues with missing trace atoms (e.g. 2QFJ)
+* Modified RNA bases (1y26, 5L4O)
+* Discontinuous chains, i.e. gaps in the sequence (3sn6)
+* Lots of sheets (1cbs)
+* DNA (2np2, 1d66)
+* C-alpha only (2rcj)
+* Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6SW3)
+* Close backbone atoms but not linked (e.g. 4HIV)
+* Non-standard residues
+    * Protein (1BRR, 5Z6Y)
+    * DNA (5D3G)
+* Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)

docs/model-server/readme.md

@@ -24,7 +24,7 @@ npm run build-tsc
 and run the server by 
 
 ```
-node lib/servers/model/server/server
+node lib/commonjs/servers/model/server/server
 ```
 
 ## From NPM
@@ -54,12 +54,12 @@ Sometimes nodejs might run into problems with memory. This is usually resolved b
 
 ## Preprocessor
 
-The preprocessor application allows to add custom data to CIF files and/or convert CIF to BinaryCIF. ``node lib/servers/servers/model/preprocess`` or ``model-server-preprocess`` binary from the NPM package.
+The preprocessor application allows to add custom data to CIF files and/or convert CIF to BinaryCIF. ``node lib/commonjs/servers/model/preprocess`` or ``model-server-preprocess`` binary from the NPM package.
 
 
 ## Local Mode
 
-The server can be run in local/file based mode using ``node lib/servers/servers/model/query`` (``model-server-query`` binary from the NPM package).
+The server can be run in local/file based mode using ``node lib/commonjs/servers/model/query`` (``model-server-query`` binary from the NPM package).
 
 Custom Properties
 =================

docs/volume-server/README.md

@@ -28,7 +28,7 @@ npm run build-tsc
 and run the server by 
 
 ```
-node lib/servers/servers/volume/server
+node lib/commonjs/servers/volume/server
 ```
 
 ## From NPM
@@ -60,11 +60,11 @@ Sometimes nodejs might run into problems with memory. This is usually resolved b
 ## Preparing the Data
 
 For the server to work, CCP4/MAP (models 0, 1, 2 are supported) input data need to be converted into a custom block format. 
-To achieve this, use the ``pack`` application (``node lib/servers/servers/volume/pack`` or ``volume-server-pack`` binary from the NPM package).
+To achieve this, use the ``pack`` application (``node lib/commonjs/servers/volume/pack`` or ``volume-server-pack`` binary from the NPM package).
 
 ## Local Mode
 
-The program  ``lib/servers/servers/volume/pack`` (``volume-server-query`` in NPM package) can be used to query the data without running a http server.
+The program  ``lib/commonjs/servers/volume/pack`` (``volume-server-query`` in NPM package) can be used to query the data without running a http server.
 
 ## Navigating the Source Code
 

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.1-dev.5",
+  "version": "2.0.0-dev.3",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -11,12 +11,12 @@
     "url": "https://github.com/molstar/molstar/issues"
   },
   "scripts": {
-    "lint": "eslint ./**/*.{ts,tsx}",
-    "lint-fix": "eslint ./**/*.{ts,tsx} --fix",
+    "lint": "eslint .",
+    "lint-fix": "eslint . --fix",
     "test": "npm run lint && jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
-    "build-tsc": "tsc --incremental && tsc --build tsconfig.servers.json --incremental",
+    "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",
     "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
     "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
     "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
@@ -24,16 +24,16 @@
     "watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
     "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
     "watch-tsc": "tsc --watch --incremental",
-    "watch-servers": "tsc --build tsconfig.servers.json --watch --incremental",
+    "watch-servers": "tsc --build tsconfig.commonjs.json --watch --incremental",
     "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
     "watch-webpack": "webpack -w --mode development --display minimal",
     "watch-webpack-viewer": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.js",
     "watch-webpack-viewer-debug": "webpack -w --mode development --display errors-only --info-verbosity verbose --config ./webpack.config.viewer.debug.js",
-    "serve": "http-server -p 1338",
-    "model-server": "node lib/servers/servers/model/server.js",
-    "model-server-watch": "nodemon --watch lib lib/servers/servers/model/server.js",
-    "volume-server-test": "node lib/servers/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
-    "plugin-state": "node lib/servers/servers/plugin-state/index.js",
+    "serve": "http-server -p 1338 -g",
+    "model-server": "node lib/commonjs/servers/model/server.js",
+    "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
+    "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
+    "plugin-state": "node lib/commonjs/servers/plugin-state/index.js --working-folder ./build/state --port 1339",
     "preversion": "npm run test",
     "version": "npm run build",
     "postversion": "git push && git push --tags"
@@ -43,14 +43,14 @@
     "build/viewer/"
   ],
   "bin": {
-    "cif2bcif": "lib/apps/cif2bcif/index.js",
-    "cifschema": "lib/apps/cifschema/index.js",
-    "model-server": "lib/servers/servers/model/server.js",
-    "model-server-query": "lib/servers/servers/model/query.js",
-    "model-server-preprocess": "lib/servers/servers/model/preprocess.js",
-    "volume-server": "lib/servers/servers/volume/server.js",
-    "volume-server-query": "lib/servers/servers/volume/query.js",
-    "volume-server-pack": "lib/servers/servers/volume/pack.js"
+    "cif2bcif": "lib/commonjs/cli/cif2bcif/index.js",
+    "cifschema": "lib/commonjs/cli/cifschema/index.js",
+    "model-server": "lib/commonjs/servers/model/server.js",
+    "model-server-query": "lib/commonjs/servers/model/query.js",
+    "model-server-preprocess": "lib/commonjs/servers/model/preprocess.js",
+    "volume-server": "lib/commonjs/servers/volume/server.js",
+    "volume-server-query": "lib/commonjs/servers/volume/query.js",
+    "volume-server-pack": "lib/commonjs/servers/volume/pack.js"
   },
   "nodemonConfig": {
     "ignoreRoot": [
@@ -80,67 +80,71 @@
     "Alexander Rose <alexander.rose@weirdbyte.de>",
     "David Sehnal <david.sehnal@gmail.com>",
     "Sebastian Bittrich <sebastian.bittrich@rcsb.org>",
-    "Ludovic Autin <autin@scripps.edu>"
+    "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
+    "Ludovic Autin <autin@scripps.edu>",
+    "Michal Malý <michal.maly@ibt.cas.cz>",
+    "Jiří Černý <jiri.cerny@ibt.cas.cz>"
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^1.13.5",
-    "@graphql-codegen/cli": "^1.13.5",
-    "@graphql-codegen/time": "^1.13.5",
-    "@graphql-codegen/typescript": "^1.13.5",
-    "@graphql-codegen/typescript-graphql-files-modules": "^1.13.5",
-    "@graphql-codegen/typescript-graphql-request": "^1.13.5",
-    "@graphql-codegen/typescript-operations": "^1.13.5",
-    "@types/cors": "^2.8.6",
-    "@typescript-eslint/eslint-plugin": "^2.32.0",
-    "@typescript-eslint/parser": "^2.32.0",
+    "@graphql-codegen/add": "^2.0.2",
+    "@graphql-codegen/cli": "^1.19.4",
+    "@graphql-codegen/time": "^2.0.2",
+    "@graphql-codegen/typescript": "^1.19.0",
+    "@graphql-codegen/typescript-graphql-files-modules": "^1.18.1",
+    "@graphql-codegen/typescript-graphql-request": "^2.0.3",
+    "@graphql-codegen/typescript-operations": "^1.17.12",
+    "@types/cors": "^2.8.8",
+    "@typescript-eslint/eslint-plugin": "^4.9.1",
+    "@typescript-eslint/parser": "^4.9.1",
     "benchmark": "^2.1.4",
-    "concurrently": "^5.2.0",
-    "cpx2": "^2.0.0",
-    "css-loader": "^3.5.3",
-    "eslint": "^7.0.0",
+    "concurrently": "^5.3.0",
+    "cpx2": "^3.0.0",
+    "css-loader": "^5.0.1",
+    "eslint": "^7.15.0",
     "extra-watch-webpack-plugin": "^1.0.3",
-    "file-loader": "^6.0.0",
-    "fs-extra": "^9.0.0",
-    "graphql": "^15.0.0",
+    "file-loader": "^6.2.0",
+    "fs-extra": "^9.0.1",
+    "graphql": "^15.4.0",
     "http-server": "^0.12.3",
-    "jest": "^26.0.1",
-    "mini-css-extract-plugin": "^0.9.0",
-    "node-sass": "^4.14.1",
-    "raw-loader": "^4.0.1",
-    "sass-loader": "^8.0.2",
-    "simple-git": "^2.4.0",
-    "style-loader": "^1.2.1",
-    "ts-jest": "^25.5.1",
-    "typescript": "^3.8.3",
-    "webpack": "^4.43.0",
-    "webpack-cli": "^3.3.11",
+    "jest": "^26.6.3",
+    "mini-css-extract-plugin": "^1.3.2",
+    "node-sass": "^5.0.0",
+    "raw-loader": "^4.0.2",
+    "sass-loader": "^10.1.0",
+    "simple-git": "^2.25.0",
+    "style-loader": "^2.0.0",
+    "ts-jest": "^26.4.4",
+    "typescript": "^4.1.2",
+    "webpack": "^4.44.1",
+    "webpack-cli": "^3.3.12",
     "webpack-version-file-plugin": "^0.4.0"
   },
   "dependencies": {
     "@types/argparse": "^1.0.38",
-    "@types/benchmark": "^1.0.31",
+    "@types/benchmark": "^2.1.0",
     "@types/compression": "1.7.0",
-    "@types/express": "^4.17.6",
-    "@types/jest": "^25.2.1",
-    "@types/node": "^13.13.5",
+    "@types/express": "^4.17.9",
+    "@types/jest": "^26.0.18",
+    "@types/node": "^14.14.11",
     "@types/node-fetch": "^2.5.7",
-    "@types/react": "^16.9.35",
-    "@types/react-dom": "^16.9.8",
-    "@types/swagger-ui-dist": "3.0.5",
+    "@types/react": "^17.0.0",
+    "@types/react-dom": "^17.0.0",
+    "@types/swagger-ui-dist": "3.30.0",
     "argparse": "^1.0.10",
     "body-parser": "^1.19.0",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
     "express": "^4.17.1",
-    "immer": "^6.0.5",
+    "h264-mp4-encoder": "^1.0.12",
+    "immer": "^8.0.0",
     "immutable": "^3.8.2",
-    "node-fetch": "^2.6.0",
-    "react": "^16.13.1",
-    "react-dom": "^16.13.1",
-    "rxjs": "^6.5.5",
-    "swagger-ui-dist": "^3.25.2",
-    "tslib": "^1.11.2",
+    "node-fetch": "^2.6.1",
+    "react": "^17.0.1",
+    "react-dom": "^17.0.1",
+    "rxjs": "^6.6.3",
+    "swagger-ui-dist": "^3.37.2",
+    "tslib": "^2.0.3",
     "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }

scripts/deploy.js

@@ -4,40 +4,40 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-const git = require('simple-git')
-const path = require('path')
-const fs = require("fs")
-const fse = require("fs-extra")
+const git = require('simple-git');
+const path = require('path');
+const fs = require("fs");
+const fse = require("fs-extra");
 
-const remoteUrl = "https://github.com/molstar/molstar.github.io.git"
-const buildDir = path.resolve(__dirname, '../build/')
-const deployDir = path.resolve(buildDir, 'deploy/')
-const localPath = path.resolve(deployDir, 'molstar.github.io/')
+const remoteUrl = "https://github.com/molstar/molstar.github.io.git";
+const buildDir = path.resolve(__dirname, '../build/');
+const deployDir = path.resolve(buildDir, 'deploy/');
+const localPath = path.resolve(deployDir, 'molstar.github.io/');
 
 function log(command, stdout, stderr) {
     if (command) {
-        console.log('\n###', command)
-        stdout.pipe(process.stdout)
-        stderr.pipe(process.stderr)
+        console.log('\n###', command);
+        stdout.pipe(process.stdout);
+        stderr.pipe(process.stderr);
     }
 }
 
 function copyViewer() {
-    console.log('\n###', 'copy viewer files')
-    const viewerBuildPath = path.resolve(buildDir, '../build/viewer/')
-    const viewerDeployPath = path.resolve(localPath, 'viewer/')
-    fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true })
+    console.log('\n###', 'copy viewer files');
+    const viewerBuildPath = path.resolve(buildDir, '../build/viewer/');
+    const viewerDeployPath = path.resolve(localPath, 'viewer/');
+    fse.copySync(viewerBuildPath, viewerDeployPath, { overwrite: true });
 }
 
 if (!fs.existsSync(localPath)) {
-    console.log('\n###', 'create localPath')
-    fs.mkdirSync(localPath, { recursive: true })
+    console.log('\n###', 'create localPath');
+    fs.mkdirSync(localPath, { recursive: true });
 }
 
 process.chdir(localPath);
 
 if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
-    console.log('\n###', 'clone repository')
+    console.log('\n###', 'clone repository');
     git()
         .outputHandler(log)
         .clone(remoteUrl, localPath)
@@ -45,9 +45,9 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .exec(copyViewer)
         .add(['-A'])
         .commit('updated viewer')
-        .push()
+        .push();
 } else {
-    console.log('\n###', 'update repository')
+    console.log('\n###', 'update repository');
     git()
         .outputHandler(log)
         .fetch(['--all'])
@@ -55,5 +55,5 @@ if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
         .exec(copyViewer)
         .add(['-A'])
         .commit('updated viewer')
-        .push()
+        .push();
 }

src/apps/docking-viewer/index.html

@@ -0,0 +1,37 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Docking Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            var viewer = new DockingViewer('app', [0x33DD22, 0x1133EE], true);
+
+            function getParam(name, regex) {
+                var r = new RegExp(name + '=' + '(' + regex + ')[&]?', 'i');
+                return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
+            }
+            var pdbqt = getParam('pdbqt', '[^&]+').trim();
+            var mol2 = getParam('mol2', '[^&]+').trim();
+
+            viewer.loadStructuresFromUrlsAndMerge([
+                { url: pdbqt, format: 'pdbqt' },
+                { url: mol2, format: 'mol2' }
+            ]);
+        </script>
+    </body>
+</html>

src/apps/docking-viewer/index.ts

@@ -0,0 +1,213 @@
+/**
+ * Copyright (c) 2018-2020 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 '../../mol-util/polyfill';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import './index.html';
+import { PluginContext } from '../../mol-plugin/context';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginSpec } from '../../mol-plugin/spec';
+import { PluginConfig } from '../../mol-plugin/config';
+import { ObjectKeys } from '../../mol-util/type-helpers';
+import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { Structure } from '../../mol-model/structure';
+import { PluginStateTransform, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Task } from '../../mol-task';
+import { StateObject } from '../../mol-state';
+import { ViewportComponent, StructurePreset, ShowButtons } from './viewport';
+import { PluginBehaviors } from '../../mol-plugin/behavior';
+import { ColorNames } from '../../mol-util/color/names';
+import { Color } from '../../mol-util/color';
+
+require('mol-plugin-ui/skin/light.scss');
+
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setProductionMode, setDebugMode } from '../../mol-util/debug';
+
+const DefaultViewerOptions = {
+    extensions: ObjectKeys({}),
+    layoutIsExpanded: true,
+    layoutShowControls: true,
+    layoutShowRemoteState: true,
+    layoutControlsDisplay: 'reactive' as PluginLayoutControlsDisplay,
+    layoutShowSequence: true,
+    layoutShowLog: true,
+    layoutShowLeftPanel: true,
+
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
+    viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
+    viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
+    pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
+    volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
+    emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
+};
+
+class Viewer {
+    plugin: PluginContext
+
+    constructor(elementOrId: string | HTMLElement, colors = [Color(0x992211), Color(0xDDDDDD)], showButtons = true) {
+        const o = { ...DefaultViewerOptions, ...{
+            layoutIsExpanded: false,
+            layoutShowControls: false,
+            layoutShowRemoteState: false,
+            layoutShowSequence: true,
+            layoutShowLog: false,
+            layoutShowLeftPanel: true,
+
+            viewportShowExpand: true,
+            viewportShowControls: false,
+            viewportShowSettings: false,
+            viewportShowSelectionMode: false,
+            viewportShowAnimation: false,
+        } };
+        const defaultSpec = DefaultPluginSpec();
+
+        const spec: PluginSpec = {
+            actions: [...defaultSpec.actions],
+            behaviors: [
+                PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci, { mark: false }),
+                PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
+                PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
+
+                PluginSpec.Behavior(PluginBehaviors.CustomProps.StructureInfo),
+                PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
+                PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
+            ],
+            animations: [...defaultSpec.animations || []],
+            customParamEditors: defaultSpec.customParamEditors,
+            layout: {
+                initial: {
+                    isExpanded: o.layoutIsExpanded,
+                    showControls: o.layoutShowControls,
+                    controlsDisplay: o.layoutControlsDisplay,
+                },
+                controls: {
+                    ...defaultSpec.layout && defaultSpec.layout.controls,
+                    top: o.layoutShowSequence ? undefined : 'none',
+                    bottom: o.layoutShowLog ? undefined : 'none',
+                    left: o.layoutShowLeftPanel ? undefined : 'none',
+                }
+            },
+            components: {
+                ...defaultSpec.components,
+                remoteState: o.layoutShowRemoteState ? 'default' : 'none',
+                viewport: {
+                    view: ViewportComponent
+                }
+            },
+            config: [
+                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
+                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                [PluginConfig.State.DefaultServer, o.pluginStateServer],
+                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider],
+                [ShowButtons, showButtons]
+            ]
+        };
+
+        const element = typeof elementOrId === 'string'
+            ? document.getElementById(elementOrId)
+            : elementOrId;
+        if (!element) throw new Error(`Could not get element with id '${elementOrId}'`);
+        this.plugin = createPlugin(element, spec);
+
+        (this.plugin.customState as any) = {
+            colorPalette: {
+                name: 'colors',
+                params: { list: { colors } }
+            }
+        };
+
+        this.plugin.behaviors.canvas3d.initialized.subscribe(v => {
+            if (v) {
+                PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
+                    renderer: {
+                        ...this.plugin.canvas3d!.props.renderer,
+                        backgroundColor: ColorNames.white,
+                    },
+                    camera: {
+                        ...this.plugin.canvas3d!.props.camera,
+                        helper: { axes: { name: 'off', params: {} } }
+                    }
+                } });
+            }
+        });
+    }
+
+    async loadStructuresFromUrlsAndMerge(sources: { url: string, format: BuiltInTrajectoryFormat, isBinary?: boolean }[]) {
+        const structures: { ref: string }[] = [];
+        for (const { url, format, isBinary } of sources) {
+            const data = await this.plugin.builders.data.download({ url, isBinary });
+            const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
+            const model = await this.plugin.builders.structure.createModel(trajectory);
+            const modelProperties = await this.plugin.builders.structure.insertModelProperties(model);
+            const structure = await this.plugin.builders.structure.createStructure(modelProperties || model);
+            const structureProperties = await this.plugin.builders.structure.insertStructureProperties(structure);
+
+            structures.push({ ref: structureProperties?.ref || structure.ref });
+        }
+
+        // remove current structuresfrom hierarchy as they will be merged
+        // TODO only works with using loadStructuresFromUrlsAndMerge once
+        //      need some more API metho to work with the hierarchy
+        this.plugin.managers.structure.hierarchy.updateCurrent(this.plugin.managers.structure.hierarchy.current.structures, 'remove');
+
+        const dependsOn = structures.map(({ ref }) => ref);
+        const data = this.plugin.state.data.build().toRoot().apply(MergeStructures, { structures }, { dependsOn });
+        const structure = await data.commit();
+        const structureProperties = await this.plugin.builders.structure.insertStructureProperties(structure);
+        this.plugin.behaviors.canvas3d.initialized.subscribe(async v => {
+            await this.plugin.builders.structure.representation.applyPreset(structureProperties || structure, StructurePreset);
+        });
+    }
+}
+
+type MergeStructures = typeof MergeStructures
+const MergeStructures = PluginStateTransform.BuiltIn({
+    name: 'merge-structures',
+    display: { name: 'Merge Structures', description: 'Merge Structure' },
+    from: PSO.Root,
+    to: PSO.Molecule.Structure,
+    params: {
+        structures: PD.ObjectList({
+            ref: PD.Text('')
+        }, ({ ref }) => ref, { isHidden: true })
+    }
+})({
+    apply({ params, dependencies }) {
+        return Task.create('Merge Structures', async ctx => {
+            if (params.structures.length === 0) return StateObject.Null;
+
+            const first = dependencies![params.structures[0].ref].data as Structure;
+            const builder = Structure.Builder({ masterModel: first.models[0] });
+            for (const { ref } of params.structures) {
+                const s = dependencies![ref].data as Structure;
+                for (const unit of s.units) {
+                    // TODO invariantId
+                    builder.addUnit(unit.kind, unit.model, unit.conformation.operator, unit.elements, unit.traits);
+                }
+            }
+
+            const structure = builder.getStructure();
+            return new PSO.Molecule.Structure(structure, { label: 'Merged Structure' });
+        });
+    }
+});
+
+(window as any).DockingViewer = Viewer;
+export { Viewer as DockingViewer };

src/apps/docking-viewer/viewport.tsx

@@ -0,0 +1,276 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as React from 'react';
+import { PluginUIComponent } from '../../mol-plugin-ui/base';
+import { Viewport, ViewportControls } from '../../mol-plugin-ui/viewport';
+import { BackgroundTaskProgress } from '../../mol-plugin-ui/task';
+import { LociLabels } from '../../mol-plugin-ui/controls';
+import { Toasts } from '../../mol-plugin-ui/toast';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { StructureRepresentationPresetProvider, presetStaticComponent } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { StateObjectRef } from '../../mol-state';
+import { StructureSelectionQueries, StructureSelectionQuery } from '../../mol-plugin-state/helpers/structure-selection-query';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { InteractionsRepresentationProvider } from '../../mol-model-props/computed/representations/interactions';
+import { InteractionTypeColorThemeProvider } from '../../mol-model-props/computed/themes/interaction-type';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import { StructureRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
+import { Color } from '../../mol-util/color';
+import { PluginConfig } from '../../mol-plugin/config';
+
+function shinyStyle(plugin: PluginContext) {
+    return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
+        renderer: {
+            ...plugin.canvas3d!.props.renderer,
+            style: { name: 'plastic', params: {} },
+        },
+        postprocessing: {
+            ...plugin.canvas3d!.props.postprocessing,
+            occlusion: { name: 'off', params: {} },
+            outline: { name: 'off', params: {} }
+        }
+    } });
+}
+
+function occlusionStyle(plugin: PluginContext) {
+    return PluginCommands.Canvas3D.SetSettings(plugin, { settings: {
+        renderer: {
+            ...plugin.canvas3d!.props.renderer,
+            style: { name: 'flat', params: {} }
+        },
+        postprocessing: {
+            ...plugin.canvas3d!.props.postprocessing,
+            occlusion: { name: 'on', params: {
+                samples: 64,
+                radius: 8,
+                bias: 1.0,
+                blurKernelSize: 13
+            } },
+            outline: { name: 'on', params: {
+                scale: 1.0,
+                threshold: 0.33
+            } }
+        }
+    } });
+}
+
+const ligandPlusSurroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of Ligand plus Ligand itself', MS.struct.modifier.union([
+    MS.struct.modifier.includeSurroundings({
+        0: StructureSelectionQueries.ligand.expression,
+        radius: 5,
+        'as-whole-residues': true
+    })
+]));
+
+const ligandSurroundings = StructureSelectionQuery('Surrounding Residues (5 \u212B) of Ligand', MS.struct.modifier.union([
+    MS.struct.modifier.exceptBy({
+        0: ligandPlusSurroundings.expression,
+        by: StructureSelectionQueries.ligand.expression
+    })
+]));
+
+const PresetParams = {
+    ...StructureRepresentationPresetProvider.CommonParams,
+};
+
+
+
+export const StructurePreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure',
+    display: { name: 'Structure' },
+    params: () => PresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        if (!structureCell) return {};
+
+        const components = {
+            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
+            polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
+        };
+
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+        const representations = {
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.35 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'cartoon', typeParams: { ...typeParams }, color: 'chain-id', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
+        };
+
+        await update.commit({ revertOnError: true });
+        await shinyStyle(plugin);
+        plugin.managers.interactivity.setProps({ granularity: 'residue' });
+
+        return { components, representations };
+    }
+});
+
+export const IllustrativePreset = StructureRepresentationPresetProvider({
+    id: 'preset-illustrative',
+    display: { name: 'Illustrative' },
+    params: () => PresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        if (!structureCell) return {};
+
+        const components = {
+            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
+            polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
+        };
+
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+        const representations = {
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'spacefill', typeParams: { ...typeParams }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'spacefill', typeParams: { ...typeParams }, color: 'illustrative', colorParams: { palette: (plugin.customState as any).colorPalette } }, { tag: 'polymer' }),
+        };
+
+        await update.commit({ revertOnError: true });
+        await occlusionStyle(plugin);
+        plugin.managers.interactivity.setProps({ granularity: 'residue' });
+
+        return { components, representations };
+    }
+});
+
+const SurfacePreset = StructureRepresentationPresetProvider({
+    id: 'preset-surface',
+    display: { name: 'Surface' },
+    params: () => PresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        const components = {
+            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
+            polymer: await presetStaticComponent(plugin, structureCell, 'polymer'),
+        };
+
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+        const representations = {
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            polymer: builder.buildRepresentation(update, components.polymer, { type: 'molecular-surface', typeParams: { ...typeParams, quality: 'custom', resolution: 0.5, doubleSided: true }, color: 'partial-charge' }, { tag: 'polymer' }),
+        };
+
+        await update.commit({ revertOnError: true });
+        await shinyStyle(plugin);
+        plugin.managers.interactivity.setProps({ granularity: 'residue' });
+
+        return { components, representations };
+    }
+});
+
+const PocketPreset = StructureRepresentationPresetProvider({
+    id: 'preset-pocket',
+    display: { name: 'Pocket' },
+    params: () => PresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        const components = {
+            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
+            surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
+        };
+
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+        const representations = {
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.26 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            surroundings: builder.buildRepresentation(update, components.surroundings, { type: 'molecular-surface', typeParams: { ...typeParams, includeParent: true, quality: 'custom', resolution: 0.2, doubleSided: true }, color: 'partial-charge' }, { tag: 'surroundings' }),
+        };
+
+        await update.commit({ revertOnError: true });
+        await shinyStyle(plugin);
+        plugin.managers.interactivity.setProps({ granularity: 'element' });
+
+        return { components, representations };
+    }
+});
+
+const InteractionsPreset = StructureRepresentationPresetProvider({
+    id: 'preset-interactions',
+    display: { name: 'Interactions' },
+    params: () => PresetParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        const components = {
+            ligand: await presetStaticComponent(plugin, structureCell, 'ligand'),
+            surroundings: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandSurroundings, `surroundings`),
+            interactions: await plugin.builders.structure.tryCreateComponentFromSelection(structureCell, ligandPlusSurroundings, `interactions`)
+        };
+
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+        const representations = {
+            ligand: builder.buildRepresentation(update, components.ligand, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.3 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ligand' }),
+            ballAndStick: builder.buildRepresentation(update, components.surroundings, { type: 'ball-and-stick', typeParams: { ...typeParams, sizeFactor: 0.1, sizeAspectRatio: 1 }, color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ball-and-stick' }),
+            interactions: builder.buildRepresentation(update, components.interactions, { type: InteractionsRepresentationProvider, typeParams: { ...typeParams }, color: InteractionTypeColorThemeProvider }, { tag: 'interactions' }),
+            label: builder.buildRepresentation(update, components.surroundings, { type: 'label', typeParams: { ...typeParams, background: false, borderWidth: 0.1 }, color: 'uniform', colorParams: { value: Color(0x000000) } }, { tag: 'label' }),
+        };
+
+        await update.commit({ revertOnError: true });
+        await shinyStyle(plugin);
+        plugin.managers.interactivity.setProps({ granularity: 'element' });
+
+        return { components, representations };
+    }
+});
+
+export const ShowButtons = PluginConfig.item('showButtons', true);
+
+export class ViewportComponent extends PluginUIComponent {
+    async _set(structures: readonly StructureRef[], preset: StructureRepresentationPresetProvider) {
+        await this.plugin.managers.structure.component.clear(structures);
+        await this.plugin.managers.structure.component.applyPreset(structures, preset);
+    }
+
+    set = async (preset: StructureRepresentationPresetProvider) => {
+        await this._set(this.plugin.managers.structure.hierarchy.selection.structures, preset);
+    }
+
+    structurePreset = () => this.set(StructurePreset);
+    illustrativePreset = () => this.set(IllustrativePreset);
+    surfacePreset = () => this.set(SurfacePreset);
+    pocketPreset = () => this.set(PocketPreset);
+    interactionsPreset = () => this.set(InteractionsPreset);
+
+    get showButtons () {
+        return this.plugin.config.get(ShowButtons);
+    }
+
+    render() {
+        const VPControls = this.plugin.spec.components?.viewport?.controls || ViewportControls;
+
+        return <>
+            <Viewport />
+            {this.showButtons && <div className='msp-viewport-top-left-controls'>
+                <div style={{ marginBottom: '4px' }}>
+                    <Button onClick={this.structurePreset} >Structure</Button>
+                </div>
+                <div style={{ marginBottom: '4px' }}>
+                    <Button onClick={this.illustrativePreset}>Illustrative</Button>
+                </div>
+                <div style={{ marginBottom: '4px' }}>
+                    <Button onClick={this.surfacePreset}>Surface</Button>
+                </div>
+                {/* <div style={{ marginBottom: '4px' }}>
+                    <Button onClick={this.pocketPreset}>Pocket</Button>
+                </div> */}
+                <div style={{ marginBottom: '4px' }}>
+                    <Button onClick={this.interactionsPreset}>Interactions</Button>
+                </div>
+            </div>}
+            <VPControls />
+            <BackgroundTaskProgress />
+            <div className='msp-highlight-toast-wrapper'>
+                <LociLabels />
+                <Toasts />
+            </div>
+        </>;
+    }
+}

src/apps/viewer/embedded.html

@@ -36,28 +36,8 @@
                 emdbProvider: 'rcsb',
             });
             viewer.loadPdb('7bv2');
-            viewer.loadEmdb('EMD-30210');
-
-            // TODO add Volume.customProperty and load suggested isoValue via custom property
-            var sub = viewer.plugin.managers.volume.hierarchy.behaviors.selection.subscribe(function (value) {
-                if (value.volume?.representations[0]) {
-                    var ref = value.volume.representations[0].cell;
-                    var tree = viewer.plugin.state.data.build().to(ref).update({
-                        type: {
-                            name: 'isosurface',
-                            params: {
-                                isoValue: {
-                                    kind: 'relative',
-                                    relativeValue: 6
-                                }
-                            }
-                        },
-                        colorTheme: ref.transform.params?.colorTheme
-                    });
-                    viewer.plugin.runTask(viewer.plugin.state.data.updateTree(tree));
-                    if (typeof sub !== 'undefined') sub.unsubscribe();
-                }
-            });
+            viewer.loadEmdb('EMD-30210', { detail: 6 });
+            // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
         </script>
     </body>
 </html>

src/apps/viewer/index.html

@@ -46,12 +46,18 @@
             }
 
             var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
-            if (debugMode) molstar.setDebugMode(debugMode);
+            if (debugMode) molstar.setDebugMode(debugMode, debugMode);
 
+            var disableAntialiasing = getParam('disable-antialiasing', '[^&]+').trim() === '1';
+            var pixelScale = parseFloat(getParam('pixel-scale', '[^&]+').trim() || '1');
+            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
             var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
             var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
             var viewer = new molstar.Viewer('app', {
+                disableAntialiasing: disableAntialiasing,
+                pixelScale: pixelScale,
+                enableWboit: !disableWboit,
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
                 pdbProvider: pdbProvider || 'pdbe',

src/apps/viewer/index.ts

@@ -6,7 +6,8 @@
  */
 
 import '../../mol-util/polyfill';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import './index.html';
 import './embedded.html';
 import './favicon.ico';
@@ -24,20 +25,41 @@ import { PluginState } from '../../mol-plugin/state';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
+import { ANVILMembraneOrientation } from '../../extensions/anvil/behavior';
+import { DnatcoConfalPyramids } from '../../extensions/dnatco';
+import { G3DFormat, G3dProvider } from '../../extensions/g3d/format';
+import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
+import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
+import { Color } from '../../mol-util/color';
+import { StateObjectSelector } from '../../mol-state';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { Mp4Export } from '../../extensions/mp4-export';
+import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 
 require('mol-plugin-ui/skin/light.scss');
 
 export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
 export { setProductionMode, setDebugMode } from '../../mol-util/debug';
 
+const CustomFormats = [
+    ['g3d', G3dProvider] as const
+];
+
 const Extensions = {
     'cellpack': PluginSpec.Behavior(CellPack),
+    'dnatco-confal-pyramids': PluginSpec.Behavior(DnatcoConfalPyramids),
     'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
     'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
-    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport)
+    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
+    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
+    'g3d': PluginSpec.Behavior(G3DFormat),
+    'mp4-export': PluginSpec.Behavior(Mp4Export)
 };
 
 const DefaultViewerOptions = {
+    customFormats: CustomFormats as [string, DataFormatProvider][],
     extensions: ObjectKeys(Extensions),
     layoutIsExpanded: true,
     layoutShowControls: true,
@@ -46,12 +68,18 @@ const DefaultViewerOptions = {
     layoutShowSequence: true,
     layoutShowLog: true,
     layoutShowLeftPanel: true,
+    disableAntialiasing: false,
+    pixelScale: 1,
+    enableWboit: true,
 
     viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
     viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
     viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
     pluginStateServer: PluginConfig.State.DefaultServer.defaultValue,
     volumeStreamingServer: PluginConfig.VolumeStreaming.DefaultServer.defaultValue,
+    volumeStreamingDisabled: !PluginConfig.VolumeStreaming.Enabled.defaultValue,
     pdbProvider: PluginConfig.Download.DefaultPdbProvider.defaultValue,
     emdbProvider: PluginConfig.Download.DefaultEmdbProvider.defaultValue,
 };
@@ -62,15 +90,17 @@ export class Viewer {
 
     constructor(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
         const o = { ...DefaultViewerOptions, ...options };
+        const defaultSpec = DefaultPluginSpec();
 
         const spec: PluginSpec = {
-            actions: [...DefaultPluginSpec.actions],
+            actions: [...defaultSpec.actions],
             behaviors: [
-                ...DefaultPluginSpec.behaviors,
+                ...defaultSpec.behaviors,
                 ...o.extensions.map(e => Extensions[e]),
             ],
-            animations: [...DefaultPluginSpec.animations || []],
-            customParamEditors: DefaultPluginSpec.customParamEditors,
+            animations: [...defaultSpec.animations || []],
+            customParamEditors: defaultSpec.customParamEditors,
+            customFormats: o?.customFormats,
             layout: {
                 initial: {
                     isExpanded: o.layoutIsExpanded,
@@ -78,23 +108,29 @@ export class Viewer {
                     controlsDisplay: o.layoutControlsDisplay,
                 },
                 controls: {
-                    ...DefaultPluginSpec.layout && DefaultPluginSpec.layout.controls,
+                    ...defaultSpec.layout && defaultSpec.layout.controls,
                     top: o.layoutShowSequence ? undefined : 'none',
                     bottom: o.layoutShowLog ? undefined : 'none',
                     left: o.layoutShowLeftPanel ? undefined : 'none',
                 }
             },
             components: {
-                ...DefaultPluginSpec.components,
+                ...defaultSpec.components,
                 remoteState: o.layoutShowRemoteState ? 'default' : 'none',
             },
             config: [
+                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
+                [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.EnableWboit, o.enableWboit],
                 [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
                 [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
                 [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
                 [PluginConfig.State.DefaultServer, o.pluginStateServer],
                 [PluginConfig.State.CurrentServer, o.pluginStateServer],
                 [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.VolumeStreaming.Enabled, !o.volumeStreamingDisabled],
                 [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
                 [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
             ]
@@ -116,7 +152,7 @@ export class Viewer {
         return PluginCommands.State.Snapshots.OpenUrl(this.plugin, { url, type });
     }
 
-    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false) {
+    loadStructureFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
         const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
@@ -125,19 +161,28 @@ export class Viewer {
                     url: Asset.Url(url),
                     format: format as any,
                     isBinary,
-                    options: params.source.params.options,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
                 }
             }
         }));
     }
 
+    async loadAllModelsOrAssemblyFromUrl(url: string, format: BuiltInTrajectoryFormat = 'mmcif', isBinary = false, options?: LoadStructureOptions) {
+        const plugin = this.plugin;
+
+        const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
+
+        await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', { useDefaultIfSingleModel: true, representationPresetParams: options?.representationParams });
+    }
+
     async loadStructureFromData(data: string | number[], format: BuiltInTrajectoryFormat, options?: { dataLabel?: string }) {
         const _data = await this.plugin.builders.data.rawData({ data, label: options?.dataLabel });
         const trajectory = await this.plugin.builders.structure.parseTrajectory(_data, format);
         await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default');
     }
 
-    loadPdb(pdb: string) {
+    loadPdb(pdb: string, options?: LoadStructureOptions) {
         const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
@@ -151,7 +196,7 @@ export class Viewer {
                             params: PdbDownloadProvider[provider].defaultValue as any
                         }
                     },
-                    options: params.source.params.options,
+                    options: { ...params.source.params.options, representationParams: options?.representationParams as any },
                 }
             }
         }));
@@ -173,7 +218,7 @@ export class Viewer {
         }));
     }
 
-    loadEmdb(emdb: string) {
+    loadEmdb(emdb: string, options?: { detail?: number }) {
         const provider = this.plugin.config.get(PluginConfig.Download.DefaultEmdbProvider)!;
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
             source: {
@@ -183,9 +228,52 @@ export class Viewer {
                         id: emdb,
                         server: provider,
                     },
-                    detail: 3,
+                    detail: options?.detail ?? 3,
                 }
             }
         }));
     }
+
+    async loadVolumeFromUrl(url: string, format: BuildInVolumeFormat, isBinary: boolean, isovalues: VolumeIsovalueInfo[], entryId?: string) {
+        const plugin = this.plugin;
+
+        if (!plugin.dataFormats.get(format)) {
+            throw new Error(`Unknown density format: ${format}`);
+        }
+
+        return plugin.dataTransaction(async () => {
+            const data = await plugin.builders.data.download({ url, isBinary, label: entryId }, { state: { isGhost: true } });
+
+            const parsed = await plugin.dataFormats.get(format)!.parse(plugin, data, { entryId });
+            const volume = (parsed.volume || parsed.volumes[0]) as StateObjectSelector<PluginStateObject.Volume.Data>;
+            if (!volume?.isOk) throw new Error('Failed to parse any volume.');
+
+            const repr = plugin.build().to(volume);
+            for (const iso of isovalues) {
+                repr.apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, volume.data!, {
+                    type: 'isosurface',
+                    typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ?  { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                    color: 'uniform',
+                    colorParams: { value: iso.color }
+                }));
+            }
+
+            await repr.commit();
+        });
+    }
+
+    handleResize() {
+        this.plugin.layout.events.updated.next();
+    }
+}
+
+export interface LoadStructureOptions {
+    representationParams?: StructureRepresentationPresetProvider.CommonParams
+}
+
+export interface VolumeIsovalueInfo {
+    type: 'absolute' | 'relative',
+    value: number,
+    color: Color,
+    alpha?: number
 }

src/cli/chem-comp-dict/create-ions.ts

@@ -0,0 +1,73 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Josh McMenemy <josh.mcmenemy@gmail.com>
+ */
+
+import * as argparse from 'argparse';
+import * as path from 'path';
+import util from 'util';
+import fs from 'fs';
+require('util.promisify').shim();
+const writeFile = util.promisify(fs.writeFile);
+
+import { DatabaseCollection } from '../../mol-data/db';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+import { ensureDataAvailable, readCCD } from './util';
+
+function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
+    const ionNames: string[] = [];
+    for (const k in ccd) {
+        const {chem_comp} = ccd[k];
+        if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
+            ionNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra ions that don't have ION in their name
+    ionNames.push('NCO', 'OHX');
+    return ionNames;
+}
+
+function writeIonNamesFile(filePath: string, ionNames: string[]) {
+    const output = `/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/chem-comp-dict/create-table cli
+ */
+
+export const IonNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+    writeFile(filePath, output);
+}
+
+async function run(out: string, forceDownload = false) {
+    await ensureDataAvailable(forceDownload);
+    const ccd = await readCCD();
+    const ionNames = extractIonNames(ccd);
+    if (!fs.existsSync(path.dirname(out))) {
+        fs.mkdirSync(path.dirname(out));
+    }
+    writeIonNamesFile(out, ionNames);
+}
+
+const parser = new argparse.ArgumentParser({
+    addHelp: true,
+    description: 'Extract and save IonNames from CCD.'
+});
+parser.addArgument('out', {
+    help: 'Generated file output path.'
+});
+parser.addArgument([ '--forceDownload', '-f' ], {
+    action: 'storeTrue',
+    help: 'Force download of CCD and PVCD.'
+});
+interface Args {
+    out: string,
+    forceDownload?: boolean,
+}
+const args: Args = parser.parseArgs();
+
+run(args.out, args.forceDownload);

src/cli/chem-comp-dict/create-table.ts

@@ -1,5 +1,6 @@
+#!/usr/bin/env node
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -8,69 +9,16 @@ import * as argparse from 'argparse';
 import * as util from 'util';
 import * as path from 'path';
 import * as fs from 'fs';
-import * as zlib from 'zlib';
-import fetch from 'node-fetch';
 require('util.promisify').shim();
-const readFile = util.promisify(fs.readFile);
 const writeFile = util.promisify(fs.writeFile);
 
-import { Progress } from '../../mol-task';
 import { Database, Table, DatabaseCollection } from '../../mol-data/db';
-import { CIF } from '../../mol-io/reader/cif';
-import { CifWriter } from '../../mol-io/writer/cif';
 import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
 import { SetUtils } from '../../mol-util/set';
 import { DefaultMap } from '../../mol-util/map';
 import { mmCIF_chemCompBond_schema } from '../../mol-io/reader/cif/schema/mmcif-extras';
-
-export async function ensureAvailable(path: string, url: string) {
-    if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
-        console.log(`downloading ${url}...`);
-        const data = await fetch(url);
-        if (!fs.existsSync(DATA_DIR)) {
-            fs.mkdirSync(DATA_DIR);
-        }
-        if (url.endsWith('.gz')) {
-            await writeFile(path, zlib.gunzipSync(await data.buffer()));
-        } else {
-            await writeFile(path, await data.text());
-        }
-        console.log(`done downloading ${url}`);
-    }
-}
-
-export async function ensureDataAvailable() {
-    await ensureAvailable(CCD_PATH, CCD_URL);
-    await ensureAvailable(PVCD_PATH, PVCD_URL);
-}
-
-export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
-    const parsed = await parseCif(await readFile(path, 'utf8'));
-    return CIF.toDatabaseCollection(schema, parsed.result);
-}
-
-export async function readCCD() {
-    return readFileAsCollection(CCD_PATH, CCD_Schema);
-}
-
-export async function readPVCD() {
-    return readFileAsCollection(PVCD_PATH, CCD_Schema);
-}
-
-async function parseCif(data: string | Uint8Array) {
-    const comp = CIF.parse(data);
-    console.time('parse cif');
-    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
-    console.timeEnd('parse cif');
-    if (parsed.isError) throw parsed;
-    return parsed;
-}
-
-export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
-    const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
-    CifWriter.Encoder.writeDatabase(encoder, name, database);
-    return encoder.getData();
-}
+import { ccd_chemCompAtom_schema } from '../../mol-io/reader/cif/schema/ccd-extras';
+import { ensureDataAvailable, getEncodedCif, readCCD, readPVCD } from './util';
 
 type CCB = Table<CCD_Schema['chem_comp_bond']>
 type CCA = Table<CCD_Schema['chem_comp_atom']>
@@ -79,6 +27,10 @@ function ccbKey(compId: string, atomId1: string, atomId2: string) {
     return atomId1 < atomId2 ? `${compId}:${atomId1}-${atomId2}` : `${compId}:${atomId2}-${atomId1}`;
 }
 
+function ccaKey(compId: string, atomId: string) {
+    return `${compId}:${atomId}`;
+}
+
 function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
     for (let i = 0, il = ccb._rowCount; i < il; ++i) {
         set.add(ccbKey(ccb.comp_id.value(i), ccb.atom_id_1.value(i), ccb.atom_id_2.value(i)));
@@ -88,7 +40,7 @@ function addChemCompBondToSet(set: Set<string>, ccb: CCB) {
 
 function addChemCompAtomToSet(set: Set<string>, cca: CCA) {
     for (let i = 0, il = cca._rowCount; i < il; ++i) {
-        set.add(cca.atom_id.value(i));
+        set.add(ccaKey(cca.comp_id.value(i), cca.atom_id.value(i)));
     }
     return set;
 }
@@ -134,11 +86,32 @@ function checkAddingBondsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
     }
 }
 
-async function createBonds() {
-    await ensureDataAvailable();
-    const ccd = await readCCD();
-    const pvcd = await readPVCD();
+function checkAddingAtomsFromPVCD(pvcd: DatabaseCollection<CCD_Schema>) {
+    const ccaSetByParent = DefaultMap<string, Set<string>>(() => new Set());
 
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_atom } = pvcd[k];
+        if (chem_comp_atom._rowCount) {
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
+            if (parentIds.length === 0) {
+                const set = ccaSetByParent.getDefault(chem_comp.id.value(0));
+                addChemCompAtomToSet(set, chem_comp_atom);
+            } else {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    const parentId = parentIds[i];
+                    const set = ccaSetByParent.getDefault(parentId);
+                    addChemCompAtomToSet(set, chem_comp_atom);
+                }
+            }
+        }
+    }
+}
+
+async function createBonds(
+    ccd: DatabaseCollection<CCD_Schema>,
+    pvcd: DatabaseCollection<CCD_Schema>,
+    atomsRequested: boolean
+) {
     const ccbSet = new Set<string>();
 
     const comp_id: string[] = [];
@@ -199,31 +172,97 @@ async function createBonds() {
     });
 
     const bondDatabase =  Database.ofTables(
-        TABLE_NAME,
+        CCB_TABLE_NAME,
         { chem_comp_bond: mmCIF_chemCompBond_schema },
         { chem_comp_bond: bondTable }
     );
 
-    return bondDatabase;
+    return { bonds: bondDatabase, atoms: atomsRequested ? createAtoms(ccd, pvcd) : void 0 };
 }
 
-async function run(out: string, binary = false) {
-    const bonds = await createBonds();
+function createAtoms(ccd: DatabaseCollection<CCD_Schema>, pvcd: DatabaseCollection<CCD_Schema>) {
+    const ccaSet = new Set<string>();
 
-    const cif = getEncodedCif(TABLE_NAME, bonds, binary);
+    const comp_id: string[] = [];
+    const atom_id: string[] = [];
+    const charge: number[] = [];
+    const pdbx_stereo_config: typeof CCD_Schema.chem_comp_atom['pdbx_stereo_config']['T'][] = [];
+
+    function addAtoms(compId: string, cca: CCA) {
+        for (let i = 0, il = cca._rowCount; i < il; ++i) {
+            const atomId = cca.atom_id.value(i);
+            const k = ccaKey(compId, atomId);
+            if (!ccaSet.has(k)) {
+                atom_id.push(atomId);
+                comp_id.push(compId);
+                charge.push(cca.charge.value(i));
+                pdbx_stereo_config.push(cca.pdbx_stereo_config.value(i));
+                ccaSet.add(k);
+            }
+        }
+    }
+
+    // check adding atoms from PVCD
+    checkAddingAtomsFromPVCD(pvcd);
+
+    // add atoms from PVCD
+    for (const k in pvcd) {
+        const { chem_comp, chem_comp_atom } = pvcd[k];
+        if (chem_comp_atom._rowCount) {
+            const parentIds = chem_comp.mon_nstd_parent_comp_id.value(0);
+            if (parentIds.length === 0) {
+                addAtoms(chem_comp.id.value(0), chem_comp_atom);
+            } else {
+                for (let i = 0, il = parentIds.length; i < il; ++i) {
+                    addAtoms(parentIds[i], chem_comp_atom);
+                }
+            }
+        }
+    }
+
+    // add atoms from CCD
+    for (const k in ccd) {
+        const { chem_comp, chem_comp_atom } = ccd[k];
+        if (chem_comp_atom._rowCount) {
+            addAtoms(chem_comp.id.value(0), chem_comp_atom);
+        }
+    }
+
+    const atomTable = Table.ofArrays(ccd_chemCompAtom_schema, {
+        comp_id, atom_id, charge, pdbx_stereo_config
+    });
+
+    return Database.ofTables(
+        CCA_TABLE_NAME,
+        { chem_comp_atom: ccd_chemCompAtom_schema },
+        { chem_comp_atom: atomTable }
+    );
+}
+
+async function run(out: string, binary = false, forceDownload = false, ccaOut?: string) {
+    await ensureDataAvailable(forceDownload);
+    const ccd = await readCCD();
+    const pvcd = await readPVCD();
+
+    const { bonds, atoms } = await createBonds(ccd, pvcd, !!ccaOut);
+
+    const ccbCif = getEncodedCif(CCB_TABLE_NAME, bonds, binary);
     if (!fs.existsSync(path.dirname(out))) {
         fs.mkdirSync(path.dirname(out));
     }
-    writeFile(out, cif);
+    writeFile(out, ccbCif);
+
+    if (!!ccaOut) {
+        const ccaCif = getEncodedCif(CCA_TABLE_NAME, atoms, binary);
+        if (!fs.existsSync(path.dirname(ccaOut))) {
+            fs.mkdirSync(path.dirname(ccaOut));
+        }
+        writeFile(ccaOut, ccaCif);
+    }
 }
 
-const TABLE_NAME = 'CHEM_COMP_BONDS';
-
-const DATA_DIR = path.join(__dirname, '..', '..', '..', 'build/data');
-const CCD_PATH = path.join(DATA_DIR, 'components.cif');
-const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
-const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
-const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';
+const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
+const CCA_TABLE_NAME = 'CHEM_COMP_ATOMS';
 
 const parser = new argparse.ArgumentParser({
     addHelp: true,
@@ -240,13 +279,16 @@ parser.addArgument([ '--binary', '-b' ], {
     action: 'storeTrue',
     help: 'Output as BinaryCIF.'
 });
+parser.addArgument(['--ccaOut', '-a'], {
+    help: 'Optional generated file output path for chem_comp_atom data.',
+    required: false
+});
 interface Args {
-    out: string
-    forceDownload?: boolean
-    binary?: boolean
+    out: string,
+    forceDownload?: boolean,
+    binary?: boolean,
+    ccaOut?: string
 }
 const args: Args = parser.parseArgs();
 
-const FORCE_DOWNLOAD = args.forceDownload;
-
-run(args.out, args.binary);
+run(args.out, args.binary, args.forceDownload, args.ccaOut);

src/cli/chem-comp-dict/util.ts

@@ -0,0 +1,75 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as util from 'util';
+import * as path from 'path';
+import * as fs from 'fs';
+import * as zlib from 'zlib';
+import fetch from 'node-fetch';
+require('util.promisify').shim();
+const readFile = util.promisify(fs.readFile);
+const writeFile = util.promisify(fs.writeFile);
+
+import { Progress } from '../../mol-task';
+import { Database } from '../../mol-data/db';
+import { CIF } from '../../mol-io/reader/cif';
+import { CifWriter } from '../../mol-io/writer/cif';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+
+export async function ensureAvailable(path: string, url: string, forceDownload = false) {
+    if (forceDownload || !fs.existsSync(path)) {
+        console.log(`downloading ${url}...`);
+        const data = await fetch(url);
+        if (!fs.existsSync(DATA_DIR)) {
+            fs.mkdirSync(DATA_DIR);
+        }
+        if (url.endsWith('.gz')) {
+            await writeFile(path, zlib.gunzipSync(await data.buffer()));
+        } else {
+            await writeFile(path, await data.text());
+        }
+        console.log(`done downloading ${url}`);
+    }
+}
+
+export async function ensureDataAvailable(forceDownload = false) {
+    await ensureAvailable(CCD_PATH, CCD_URL, forceDownload);
+    await ensureAvailable(PVCD_PATH, PVCD_URL, forceDownload);
+}
+
+export async function readFileAsCollection<S extends Database.Schema>(path: string, schema: S) {
+    const parsed = await parseCif(await readFile(path, 'utf8'));
+    return CIF.toDatabaseCollection(schema, parsed.result);
+}
+
+export async function readCCD() {
+    return readFileAsCollection(CCD_PATH, CCD_Schema);
+}
+
+export async function readPVCD() {
+    return readFileAsCollection(PVCD_PATH, CCD_Schema);
+}
+
+async function parseCif(data: string | Uint8Array) {
+    const comp = CIF.parse(data);
+    console.time('parse cif');
+    const parsed = await comp.run(p => console.log(Progress.format(p)), 250);
+    console.timeEnd('parse cif');
+    if (parsed.isError) throw parsed;
+    return parsed;
+}
+
+export function getEncodedCif(name: string, database: Database<Database.Schema>, binary = false) {
+    const encoder = CifWriter.createEncoder({ binary, encoderName: 'mol*' });
+    CifWriter.Encoder.writeDatabase(encoder, name, database);
+    return encoder.getData();
+}
+
+const DATA_DIR = path.join(__dirname, '..', '..', '..', '..', 'build/data');
+const CCD_PATH = path.join(DATA_DIR, 'components.cif');
+const PVCD_PATH = path.join(DATA_DIR, 'aa-variants-v1.cif');
+const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif';
+const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif';

src/cli/cif2bcif/converter.ts

@@ -70,7 +70,7 @@ function classify(name: string, field: CifField): CifWriter.Field {
     }
 }
 
-export default function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
+export function convert(path: string, asText = false, hints?: EncodingStrategyHint[], filter?: string) {
     return Task.create<Uint8Array>('BinaryCIF', async ctx => {
         const encodingProvider: BinaryEncodingProvider = hints
             ? CifWriter.createEncodingProviderFromJsonConfig(hints)

src/cli/cif2bcif/index.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
@@ -9,7 +10,7 @@ import * as argparse from 'argparse';
 import * as util from 'util';
 import * as fs from 'fs';
 import * as zlib from 'zlib';
-import convert from './converter';
+import { convert } from './converter';
 
 require('util.promisify').shim();
 

src/cli/cifschema/index.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
@@ -11,7 +12,7 @@ import fetch from 'node-fetch';
 
 import { parseCsv } from '../../mol-io/reader/csv/parser';
 import { CifFrame, CifBlock } from '../../mol-io/reader/cif';
-import parseText from '../../mol-io/reader/cif/text/parser';
+import { parseCifText } from '../../mol-io/reader/cif/text/parser';
 import { generateSchema } from './util/cif-dic';
 import { generate } from './util/generate';
 import { Filter, Database } from './util/schema';
@@ -27,19 +28,19 @@ function getDicNamespace(block: CifBlock) {
 
 async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
     await ensureMmcifDicAvailable();
-    const mmcifDic = await parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
+    const mmcifDic = await parseCifText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')).run();
     if (mmcifDic.isError) throw mmcifDic;
 
     await ensureIhmDicAvailable();
-    const ihmDic = await parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
+    const ihmDic = await parseCifText(fs.readFileSync(IHM_DIC_PATH, 'utf8')).run();
     if (ihmDic.isError) throw ihmDic;
 
     await ensureCarbBranchDicAvailable();
-    const carbBranchDic = await parseText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
+    const carbBranchDic = await parseCifText(fs.readFileSync(CARB_BRANCH_DIC_PATH, 'utf8')).run();
     if (carbBranchDic.isError) throw carbBranchDic;
 
     await ensureCarbCompDicAvailable();
-    const carbCompDic = await parseText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
+    const carbCompDic = await parseCifText(fs.readFileSync(CARB_COMP_DIC_PATH, 'utf8')).run();
     if (carbCompDic.isError) throw carbCompDic;
 
     const mmcifDicVersion = getDicVersion(mmcifDic.result.blocks[0]);
@@ -55,7 +56,7 @@ async function runGenerateSchemaMmcif(name: string, fieldNamesPath: string, type
 
 async function runGenerateSchemaCifCore(name: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
     await ensureCifCoreDicAvailable();
-    const cifCoreDic = await parseText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
+    const cifCoreDic = await parseCifText(fs.readFileSync(CIF_CORE_DIC_PATH, 'utf8')).run();
     if (cifCoreDic.isError) throw cifCoreDic;
 
     const cifCoreDicVersion = getDicVersion(cifCoreDic.result.blocks[0]);
@@ -79,7 +80,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
                 if (!file) continue;
                 if (imports.has(file)) continue;
 
-                const dic = await parseText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
+                const dic = await parseCifText(fs.readFileSync(path.join(baseDir, file), 'utf8')).run();
                 if (dic.isError) throw dic;
 
                 imports.set(file, [...dic.result.blocks[0].saveFrames]);
@@ -91,7 +92,7 @@ async function resolveImports(frames: CifFrame[], baseDir: string): Promise<Map<
 }
 
 async function runGenerateSchemaDic(name: string, dicPath: string, fieldNamesPath: string, typescript = false, out: string, moldbImportPath: string, addAliases: boolean) {
-    const dic = await parseText(fs.readFileSync(dicPath, 'utf8')).run();
+    const dic = await parseCifText(fs.readFileSync(dicPath, 'utf8')).run();
     if (dic.isError) throw dic;
 
     const dicVersion = getDicVersion(dic.result.blocks[0]);
@@ -159,7 +160,7 @@ async function ensureDicAvailable(dicPath: string, dicUrl: string) {
     }
 }
 
-const DIC_DIR = path.resolve(__dirname, '../../../build/dics/');
+const DIC_DIR = path.resolve(__dirname, '../../../../build/dics/');
 const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`;
 const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic';
 const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`;
@@ -237,22 +238,22 @@ switch (args.preset) {
     case 'mmCIF':
         args.name = 'mmCIF';
         args.dic = 'mmCIF';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/mmcif-field-names.csv');
+        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/mmcif-field-names.csv');
         break;
     case 'CCD':
         args.name = 'CCD';
         args.dic = 'mmCIF';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/ccd-field-names.csv');
+        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/ccd-field-names.csv');
         break;
     case 'BIRD':
         args.name = 'BIRD';
         args.dic = 'mmCIF';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/bird-field-names.csv');
+        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/bird-field-names.csv');
         break;
     case 'CifCore':
         args.name = 'CifCore';
         args.dic = 'CifCore';
-        args.fieldNamesPath = path.resolve(__dirname, '../../../data/cif-field-names/cif-core-field-names.csv');
+        args.fieldNamesPath = path.resolve(__dirname, '../../../../data/cif-field-names/cif-core-field-names.csv');
         break;
 }
 

src/cli/cifschema/util/generate.ts

@@ -17,15 +17,15 @@ function header (name: string, info: string, moldataImportPath: string) {
  * @author molstar/ciftools package
  */
 
-import { Database, Column } from '${moldataImportPath}/db'
+import { Database, Column } from '${moldataImportPath}/db';
 
-import Schema = Column.Schema`;
+import Schema = Column.Schema;`;
 }
 
 function footer (name: string) {
     return `
 export type ${name}_Schema = typeof ${name}_Schema;
-export interface ${name}_Database extends Database<${name}_Schema> {}`;
+export interface ${name}_Database extends Database<${name}_Schema> {};`;
 }
 
 function getTypeShorthands(schema: Database, fields?: Filter) {
@@ -122,7 +122,7 @@ export function generate (name: string, info: string, schema: Database, fields:
         });
         codeLines.push('    },');
     });
-    codeLines.push('}');
+    codeLines.push('};');
 
     if (addAliases) {
         codeLines.push('');
@@ -144,7 +144,7 @@ export function generate (name: string, info: string, schema: Database, fields:
             });
             codeLines.push('    ],');
         });
-        codeLines.push('}');
+        codeLines.push('};');
     }
 
     return `${header(name, info, moldataImportPath)}\n\n${getTypeShorthands(schema, fields)}\n\n${codeLines.join('\n')}\n${footer(name)}`;

src/cli/lipid-params/index.ts

@@ -0,0 +1,93 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as fs from 'fs';
+import * as path from 'path';
+import fetch from 'node-fetch';
+import { UniqueArray } from '../../mol-data/generic';
+
+const LIPIDS_DIR = path.resolve(__dirname, '../../../../build/lipids/');
+
+const MARTINI_LIPIDS_PATH = path.resolve(LIPIDS_DIR, 'martini_lipids.itp');
+const MARTINI_LIPIDS_URL = 'http://www.cgmartini.nl/images/parameters/lipids/Collections/martini_v2.0_lipids_all_201506.itp';
+
+async function ensureAvailable(path: string, url: string) {
+    if (FORCE_DOWNLOAD || !fs.existsSync(path)) {
+        const name = url.substr(url.lastIndexOf('/') + 1);
+        console.log(`downloading ${name}...`);
+        const data = await fetch(url);
+        if (!fs.existsSync(LIPIDS_DIR)) {
+            fs.mkdirSync(LIPIDS_DIR);
+        }
+        fs.writeFileSync(path, await data.text());
+        console.log(`done downloading ${name}`);
+    }
+}
+
+async function ensureLipidsAvailable() { await ensureAvailable(MARTINI_LIPIDS_PATH, MARTINI_LIPIDS_URL); }
+
+const extraLipids = ['DMPC'];
+
+async function run(out: string) {
+    await ensureLipidsAvailable();
+    const lipidsItpStr = fs.readFileSync(MARTINI_LIPIDS_PATH, 'utf8');
+
+    const lipids = UniqueArray.create<string>();
+    const reLipid = /\[moleculetype\]\n; molname      nrexcl\n +([a-zA-Z]{3,5})/g;
+    let m: RegExpExecArray | null;
+
+    while ((m = reLipid.exec(lipidsItpStr)) !== null) {
+        const v = m[0].substr(m[0].lastIndexOf(' ') + 1);
+        UniqueArray.add(lipids, v, v);
+    }
+
+    for (const v of extraLipids) {
+        UniqueArray.add(lipids, v, v);
+    }
+
+    const lipidNames = JSON.stringify(lipids.array);
+
+    if (out) {
+        const output = `/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
+ *
+ * @author molstar/lipid-params cli
+ */
+
+export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+        fs.writeFileSync(out, output);
+    } else {
+        console.log(lipidNames);
+    }
+}
+
+const parser = new argparse.ArgumentParser({
+    addHelp: true,
+    description: 'Create lipid params (from martini lipids itp)'
+});
+parser.addArgument([ '--out', '-o' ], {
+    help: 'Generated lipid params output path, if not given printed to stdout'
+});
+parser.addArgument([ '--forceDownload', '-f' ], {
+    action: 'storeTrue',
+    help: 'Force download of martini lipids itp'
+});
+interface Args {
+    out: string
+    forceDownload: boolean
+}
+const args: Args = parser.parseArgs();
+
+const FORCE_DOWNLOAD = args.forceDownload;
+
+run(args.out || '').catch(e => {
+    console.error(e);
+});

src/cli/state-docs/index.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

src/cli/state-docs/pd-to-md.ts

@@ -26,6 +26,8 @@ function paramInfo(param: PD.Any, offset: number): string {
         case 'file': return `JavaScript File Handle`;
         case 'file-list': return `JavaScript FileList Handle`;
         case 'select': return `One of ${oToS(param.options)}`;
+        case 'value-ref': return `Reference to a runtime defined value.`;
+        case 'data-ref': return `Reference to a computed data value.`;
         case 'text': return 'String';
         case 'interval': return `Interval [min, max]`;
         case 'group': return `Object with:\n${getParams(param.params, offset + 2)}`;

src/cli/structure-info/model.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
@@ -9,7 +10,7 @@ import * as argparse from 'argparse';
 require('util.promisify').shim();
 
 import { CifFrame } from '../../mol-io/reader/cif';
-import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing } from '../../mol-model/structure';
+import { Model, Structure, StructureElement, Unit, StructureProperties, UnitRing, Trajectory } from '../../mol-model/structure';
 // import { Run, Progress } from '../../mol-task'
 import { OrderedSet } from '../../mol-data/int';
 import { openCif, downloadCif } from './helpers';
@@ -18,6 +19,7 @@ import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
 import { Sequence } from '../../mol-model/sequence';
 import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { Task } from '../../mol-task';
 
 
 async function downloadFromPdb(pdb: string) {
@@ -33,20 +35,22 @@ export async function readCifFile(path: string) {
 
 export function atomLabel(model: Model, aI: number) {
     const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
-    const { label_atom_id } = atoms;
-    const { label_comp_id, label_seq_id } = residues;
+    const { label_atom_id, label_comp_id } = atoms;
+    const { label_seq_id } = residues;
     const { label_asym_id } = chains;
     const rI = residueAtomSegments.index[aI];
     const cI = chainAtomSegments.index[aI];
-    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`;
+    return `${label_asym_id.value(cI)} ${label_comp_id.value(aI)} ${label_seq_id.value(rI)} ${label_atom_id.value(aI)}`;
 }
 
 export function residueLabel(model: Model, rI: number) {
-    const { residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
-    const { label_comp_id, label_seq_id } = residues;
+    const { atoms, residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy;
+    const { label_comp_id } = atoms;
+    const { label_seq_id } = residues;
     const { label_asym_id } = chains;
-    const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]];
-    return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`;
+    const aI = residueAtomSegments.offsets[rI];
+    const cI = chainAtomSegments.index[aI];
+    return `${label_asym_id.value(cI)} ${label_comp_id.value(aI)} ${label_seq_id.value(rI)}`;
 }
 
 export function printSecStructure(model: Model) {
@@ -95,15 +99,17 @@ export function printBonds(structure: Structure, showIntra: boolean, showInter:
         for (const unit of structure.units) {
             if (!Unit.isAtomic(unit)) continue;
 
-            for (const pairBonds of bonds.getConnectedUnits(unit)) {
+            for (const pairBonds of bonds.getConnectedUnits(unit.id)) {
                 if (!pairBonds.areUnitsOrdered || pairBonds.edgeCount === 0) continue;
 
-                const { unitA, unitB } = pairBonds;
-                console.log(`${pairBonds.unitA.id} - ${pairBonds.unitB.id}: ${pairBonds.edgeCount} bond(s)`);
+                const { unitA, unitB, edgeCount } = pairBonds;
+                const uA = structure.unitMap.get(unitA);
+                const uB = structure.unitMap.get(unitB);
+                console.log(`${unitA} - ${unitB}: ${edgeCount} bond(s)`);
 
                 for (const aI of pairBonds.connectedIndices) {
                     for (const bond of pairBonds.getEdges(aI)) {
-                        console.log(`${atomLabel(unitA.model, unitA.elements[aI])} -- ${atomLabel(unitB.model, unitB.elements[bond.indexB])}`);
+                        console.log(`${atomLabel(uA.model, uA.elements[aI])} -- ${atomLabel(uB.model, uB.elements[bond.indexB])}`);
                     }
                 }
             }
@@ -180,10 +186,11 @@ export function printSymmetryInfo(model: Model) {
     console.log(`NCS operators: ${symmetry.ncsOperators && symmetry.ncsOperators.map(a => a.name).join(', ')}`);
 }
 
-export function printModelStats(models: ReadonlyArray<Model>) {
+export async function printModelStats(models: Trajectory) {
     console.log('\nModels\n=============');
 
-    for (const m of models) {
+    for (let i = 0; i < models.frameCount; i++) {
+        const m = await Task.resolveInContext(models.getFrameAtIndex(i));
         if (m.coarseHierarchy.isDefined) {
             console.log(`${m.label} ${m.modelNum}: ${m.atomicHierarchy.atoms._rowCount} atom(s), ${m.coarseHierarchy.spheres.count} sphere(s), ${m.coarseHierarchy.gaussians.count} gaussian(s)`);
         } else {
@@ -195,7 +202,7 @@ export function printModelStats(models: ReadonlyArray<Model>) {
 
 export async function getModelsAndStructure(frame: CifFrame) {
     const models = await trajectoryFromMmCIF(frame).run();
-    const structure = Structure.ofModel(models[0]);
+    const structure = Structure.ofModel(models.representative);
     return { models, structure };
 }
 
@@ -203,13 +210,13 @@ async function run(frame: CifFrame, args: Args) {
     const { models, structure } = await getModelsAndStructure(frame);
 
     if (args.models) printModelStats(models);
-    if (args.seq) printSequence(models[0]);
+    if (args.seq) printSequence(models.representative);
     if (args.units) printUnits(structure);
-    if (args.sym) printSymmetryInfo(models[0]);
+    if (args.sym) printSymmetryInfo(models.representative);
     if (args.rings) printRings(structure);
     if (args.intraBonds) printBonds(structure, true, false);
     if (args.interBonds) printBonds(structure, false, true);
-    if (args.sec) printSecStructure(models[0]);
+    if (args.sec) printSecStructure(models.representative);
 }
 
 async function runDL(pdb: string, args: Args) {

src/cli/structure-info/volume.ts

@@ -1,3 +1,4 @@
+#!/usr/bin/env node
 /**
  * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *

src/examples/alpha-orbitals/controls.tsx

@@ -0,0 +1,25 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as React from 'react';
+import * as ReactDOM from 'react-dom';
+import { AlphaOrbitalsExample } from '.';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
+import { PluginContextContainer } from '../../mol-plugin-ui/plugin';
+
+export function mountControls(orbitals: AlphaOrbitalsExample, parent: Element) {
+    ReactDOM.render(<PluginContextContainer plugin={orbitals.plugin}>
+        <Controls orbitals={orbitals} />
+    </PluginContextContainer>, parent);
+}
+
+function Controls({ orbitals }: { orbitals: AlphaOrbitalsExample }) {
+    const params = useBehavior(orbitals.params);
+    const values = useBehavior(orbitals.state);
+
+    return <ParameterControls params={params as any} values={values} onChangeValues={(vs: any) => orbitals.state.next(vs)} />;
+}

src/examples/alpha-orbitals/index.html

@@ -0,0 +1,37 @@
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <title>Mol* Alpha Orbitals Example</title>
+        <style>
+            * {
+                margin: 0;
+                padding: 0;
+                box-sizing: border-box;
+            }
+            #app {
+                position: absolute;
+                left: 0;
+                top: 0;
+                bottom: 0;
+                right: 0;
+            }
+            #controls {
+                position: absolute;
+                left: 8px;
+                top: 8px;
+                width: 300px;
+            }            
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+        <script type="text/javascript" src="./index.js"></script>
+    </head>
+    <body>
+        <div id="app"></div>
+        <div id='controls'></div>
+        <script>
+            AlphaOrbitalsExample.init('app')
+        </script>
+    </body>
+</html>

src/examples/alpha-orbitals/index.ts

@@ -0,0 +1,213 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { SphericalBasisOrder } from '../../extensions/alpha-orbitals/spherical-functions';
+import { BasisAndOrbitals, CreateOrbitalDensityVolume, CreateOrbitalRepresentation3D, CreateOrbitalVolume, StaticBasisAndOrbitals } from '../../extensions/alpha-orbitals/transforms';
+import { createPluginAsync } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { PluginStateObject } from '../../mol-plugin-state/objects';
+import { PluginConfig } from '../../mol-plugin/config';
+import { PluginContext } from '../../mol-plugin/context';
+import { StateObjectSelector, StateTransformer } from '../../mol-state';
+import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition } from '../../mol-util/param-definition';
+import { mountControls } from './controls';
+import { DemoMoleculeSDF, DemoOrbitals } from './example-data';
+import { BehaviorSubject } from 'rxjs';
+import { debounceTime, skip } from 'rxjs/operators';
+import './index.html';
+import { Basis, AlphaOrbital } from '../../extensions/alpha-orbitals/data-model';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
+require('mol-plugin-ui/skin/light.scss');
+
+interface DemoInput {
+    moleculeSdf: string,
+    basis: Basis,
+    order: SphericalBasisOrder,
+    orbitals: AlphaOrbital[]
+}
+
+interface Params {
+    show: { name: 'orbital', params: { index: number } } | { name: 'density', params: {} },
+    isoValue: number,
+    gpuSurface: boolean
+}
+
+type Selectors = {
+    type: 'orbital',
+    volume: StateObjectSelector<PluginStateObject.Volume.Data, typeof CreateOrbitalVolume>,
+    positive: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
+    negative: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
+} | {
+    type: 'density',
+    volume: StateObjectSelector<PluginStateObject.Volume.Data, typeof CreateOrbitalDensityVolume>,
+    positive: StateObjectSelector<PluginStateObject.Volume.Representation3D, typeof CreateOrbitalRepresentation3D>
+}
+
+export class AlphaOrbitalsExample {
+    plugin: PluginContext;
+
+    async init(target: string | HTMLElement) {
+        this.plugin = await createPluginAsync(typeof target === 'string' ? document.getElementById(target)! : target, {
+            ...DefaultPluginSpec(),
+            layout: {
+                initial: {
+                    isExpanded: false,
+                    showControls: false
+                },
+                controls: { left: 'none', right: 'none', top: 'none', bottom: 'none' },
+            },
+            config: [
+                [PluginConfig.Viewport.ShowExpand, false],
+                [PluginConfig.Viewport.ShowControls, false],
+                [PluginConfig.Viewport.ShowSelectionMode, false],
+                [PluginConfig.Viewport.ShowAnimation, false],
+            ]
+        });
+
+        this.plugin.managers.interactivity.setProps({ granularity: 'element' });
+
+        if (!canComputeGrid3dOnGPU(this.plugin.canvas3d?.webgl)) {
+            PluginCommands.Toast.Show(this.plugin, {
+                title: 'Error',
+                message: `Browser/device does not support required WebGL extension (OES_texture_float).`
+            });
+            return;
+        }
+
+        this.load({
+            moleculeSdf: DemoMoleculeSDF,
+            ...DemoOrbitals
+        });
+
+        mountControls(this, document.getElementById('controls')!);
+    }
+
+    readonly params = new BehaviorSubject<ParamDefinition.For<Params>>({} as any);
+    readonly state = new BehaviorSubject<Params>({ show: { name: 'orbital', params: { index: 32 } }, isoValue: 1, gpuSurface: false });
+
+    private selectors?: Selectors = void 0;
+    private basis?: StateObjectSelector<BasisAndOrbitals> = void 0;
+
+    private currentParams: Params = { ...this.state.value };
+
+    private clearVolume() {
+        if (!this.selectors) return;
+        const v = this.selectors.volume;
+        this.selectors = void 0;
+        return this.plugin.build().delete(v).commit();
+    }
+
+    private async syncVolume() {
+        if (!this.basis?.isOk) return;
+
+        const state = this.state.value;
+
+        if (state.show.name !== this.selectors?.type) {
+            await this.clearVolume();
+        }
+
+        const update = this.plugin.build();
+        if (state.show.name === 'orbital') {
+            if (!this.selectors) {
+                const volume = update
+                    .to(this.basis)
+                    .apply(CreateOrbitalVolume, { index: state.show.params.index });
+
+                const positive = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('positive', ColorNames.blue)).selector;
+                const negative = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('negative', ColorNames.red)).selector;
+
+                this.selectors = { type: 'orbital', volume: volume.selector, positive, negative };
+            } else {
+                const index = state.show.params.index;
+                update.to(this.selectors.volume).update(CreateOrbitalVolume, () => ({ index }));
+            }
+        } else {
+            if (!this.selectors) {
+                const volume = update
+                    .to(this.basis)
+                    .apply(CreateOrbitalDensityVolume);
+                const positive = volume.apply(CreateOrbitalRepresentation3D, this.volumeParams('positive', ColorNames.blue)).selector;
+                this.selectors = { type: 'density', volume: volume.selector, positive };
+            }
+        }
+
+        await update.commit();
+
+        if (this.currentParams.gpuSurface !== this.state.value.gpuSurface) {
+            await this.setIsovalue();
+        }
+
+        this.currentParams = this.state.value;
+    }
+
+    private setIsovalue() {
+        if (!this.selectors) return;
+
+        this.currentParams = this.state.value;
+        const update = this.plugin.build();
+        update.to(this.selectors.positive).update(this.volumeParams('positive', ColorNames.blue));
+        if (this.selectors?.type === 'orbital') {
+            update.to(this.selectors.negative).update(this.volumeParams('negative', ColorNames.red));
+        }
+        return update.commit();
+    }
+
+    private volumeParams(kind: 'positive' | 'negative', color: Color): StateTransformer.Params<typeof CreateOrbitalRepresentation3D> {
+        return {
+            alpha: 0.85,
+            color,
+            directVolume: this.state.value.gpuSurface,
+            kind,
+            relativeIsovalue: this.state.value.isoValue,
+            pickable: false,
+            xrayShaded: true
+        };
+    }
+
+    async load(input: DemoInput) {
+        await this.plugin.clear();
+
+        const data = await this.plugin.builders.data.rawData({ data: input.moleculeSdf }, { state: { isGhost: true } });
+        const trajectory = await this.plugin.builders.structure.parseTrajectory(data, 'mol');
+        const model = await this.plugin.builders.structure.createModel(trajectory);
+        const structure = await this.plugin.builders.structure.createStructure(model);
+
+        const all = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'all');
+        if (all) await this.plugin.builders.structure.representation.addRepresentation(all, { type: 'ball-and-stick', color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } });
+
+
+        this.basis = await this.plugin.build().toRoot()
+            .apply(StaticBasisAndOrbitals, { basis: input.basis, order: input.order, orbitals: input.orbitals })
+            .commit();
+
+        await this.syncVolume();
+
+        this.params.next({
+            show: ParamDefinition.MappedStatic('orbital', {
+                'orbital': ParamDefinition.Group({
+                    index: ParamDefinition.Numeric(32, { min: 0, max: input.orbitals.length - 1 }, { immediateUpdate: true, isEssential: true }),
+                }),
+                'density': ParamDefinition.EmptyGroup()
+            }, { cycle: true }),
+            isoValue: ParamDefinition.Numeric(this.currentParams.isoValue, { min: 0.5, max: 3, step: 0.1 }, { immediateUpdate: true, isEssential: false }),
+            gpuSurface: ParamDefinition.Boolean(this.currentParams.gpuSurface, { isHidden: true })
+        });
+
+        this.state.pipe(skip(1), debounceTime(1000 / 24)).subscribe(async params => {
+            if (params.show.name !== this.currentParams.show.name
+                || (params.show.name === 'orbital' && this.currentParams.show.name === 'orbital' && params.show.params.index !== this.currentParams.show.params.index)) {
+                this.syncVolume();
+            } else if (params.isoValue !== this.currentParams.isoValue || params.gpuSurface !== this.currentParams.gpuSurface) {
+                this.setIsovalue();
+            }
+        });
+    }
+}
+
+(window as any).AlphaOrbitalsExample = new AlphaOrbitalsExample();

src/examples/basic-wrapper/index.html

@@ -86,7 +86,7 @@
 
             // adjust this number to make the animation faster or slower
             // requires to "restart" the animation if changed
-            BasicMolStarWrapper.animate.modelIndex.maxFPS = 30;
+            BasicMolStarWrapper.animate.modelIndex.targetFps = 30;
 
             addControl('Play To End', () => BasicMolStarWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => BasicMolStarWrapper.animate.modelIndex.onceBackward());

src/examples/basic-wrapper/index.ts

@@ -6,10 +6,10 @@
 
 import { EmptyLoci } from '../../mol-model/loci';
 import { StructureSelection } from '../../mol-model/structure';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
-import { PluginStateObject } from '../../mol-plugin-state/objects';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
 import { Script } from '../../mol-script/script';
@@ -29,7 +29,7 @@ class BasicWrapper {
 
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
+            ...DefaultPluginSpec(),
             layout: {
                 initial: {
                     isExpanded: false,
@@ -83,13 +83,17 @@ class BasicWrapper {
         if (!this.plugin.canvas3d.props.trackball.spin) PluginCommands.Camera.Reset(this.plugin, {});
     }
 
+    private animateModelIndexTargetFps() {
+        return Math.max(1, this.animate.modelIndex.targetFps | 0);
+    }
+
     animate = {
         modelIndex: {
-            maxFPS: 8,
-            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
-            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
-            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
-            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
+            targetFps: 8,
+            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
+            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
+            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
+            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: {} } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
     }
@@ -113,8 +117,10 @@ class BasicWrapper {
 
     interactivity = {
         highlightOn: () => {
+            const data = this.plugin.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data;
+            if (!data) return;
+
             const seq_id = 7;
-            const data = (this.plugin.state.data.select('asm')[0].obj as PluginStateObject.Molecule.Structure).data;
             const sel = Script.getStructureSelection(Q => Q.struct.generator.atomGroups({
                 'residue-test': Q.core.rel.eq([Q.struct.atomProperty.macromolecular.label_seq_id(), seq_id]),
                 'group-by': Q.struct.atomProperty.macromolecular.residueKey()

src/examples/basic-wrapper/superposition.ts

@@ -10,7 +10,7 @@ import { superpose } from '../../mol-model/structure/structure/util/superpositio
 import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import Expression from '../../mol-script/language/expression';
+import { Expression } from '../../mol-script/language/expression';
 import { compile } from '../../mol-script/runtime/query/compiler';
 import { StateObjectRef } from '../../mol-state';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';

src/examples/domain-annotation-server/mapping.ts

@@ -9,7 +9,7 @@ import { CifWriter } from '../../mol-io/writer/cif';
 import * as S from './schemas';
 // import { getCategoryInstanceProvider } from './utils'
 
-export default function create(allData: any) {
+export function createMapping(allData: any) {
     const mols = Object.keys(allData);
     const enc = CifWriter.createEncoder();
     enc.startDataBlock(mols[0]);

src/examples/domain-annotation-server/server.ts

@@ -6,7 +6,7 @@
 
 import express from 'express';
 import fetch from 'node-fetch';
-import createMapping from './mapping';
+import { createMapping } from './mapping';
 
 async function getMappings(id: string) {
     const data = await fetch(`https://www.ebi.ac.uk/pdbe/api/mappings/${id}`);

src/examples/domain-annotation-server/test.ts

@@ -5,7 +5,7 @@
  */
 
 import fetch from 'node-fetch';
-import createMapping from './mapping';
+import { createMapping } from './mapping';
 
 (async function () {
     const data = await fetch('https://www.ebi.ac.uk/pdbe/api/mappings/1tqn?pretty=true');

src/examples/lighting/index.html

@@ -12,18 +12,18 @@
             }
             #app {
                 position: absolute;
-                left: 160px;
-                top: 100px;
-                width: 600px;
-                height: 600px;
-                border: 1px solid #ccc;
+                width: 100%;
+                height: 100%;
             }
 
             #controls {
                 position: absolute;
                 width: 150px;
-                top: 100px;
-                left: 780px;
+                bottom: 100px;
+                right: 50px;
+                z-index: 10;
+                font-family: sans-serif;
+                font-size: smaller;
             }
 
             #controls > button {
@@ -46,13 +46,13 @@
         <div id="app"></div>
         <script>
             LightingDemo.init('app')
-            LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' })
+            LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3)
 
             addHeader('Example PDB IDs');
-            addControl('1M07', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1M07.cif', assemblyId: '1' }));
-            addControl('6HY0', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6HY0.cif', assemblyId: '1' }));
-            addControl('6QVK', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/6QVK.cif', assemblyId: '1' }));
-            addControl('1RB8', () => LightingDemo.load({ url: 'https://files.rcsb.org/download/1RB8.cif', assemblyId: '1' }));
+            addControl('4KTC', () => LightingDemo.load({ url: 'https://models.rcsb.org/4KTC.bcif', assemblyId: '1' }, 5, 1.3));
+            addControl('5FJ5', () => LightingDemo.load({ url: 'https://models.rcsb.org/5FJ5.bcif', assemblyId: '1' }, 8, 1.8));
+            addControl('1UPN', () => LightingDemo.load({ url: 'https://models.rcsb.org/1UPN.bcif', assemblyId: '1' }, 7, 1.6));
+            addControl('1RB8', () => LightingDemo.load({ url: 'https://models.rcsb.org/1RB8.bcif', assemblyId: '1' }, 6, 1.3));
 
             addSeparator()
 

src/examples/lighting/index.ts

@@ -5,7 +5,8 @@
  */
 
 import { Canvas3DProps } from '../../mol-canvas3d/canvas3d';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
@@ -24,12 +25,11 @@ const Canvas3DPresets = {
             mode: 'temporal' as Canvas3DProps['multiSample']['mode']
         },
         postprocessing: {
-            occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
-            outline: { name: 'on', params: { scale: 1, threshold: 0.8 } }
+            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+            outline: { name: 'on', params: { scale: 1, threshold: 0.1 } }
         },
         renderer: {
-            ambientIntensity: 1,
-            lightIntensity: 0,
+            style: { name: 'flat', params: {} }
         }
     },
     occlusion: <Preset> {
@@ -37,12 +37,11 @@ const Canvas3DPresets = {
             mode: 'temporal' as Canvas3DProps['multiSample']['mode']
         },
         postprocessing: {
-            occlusion: { name: 'on', params: { bias: 0.8, kernelSize: 6, radius: 64 } },
+            occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
             outline: { name: 'off', params: { } }
         },
         renderer: {
-            ambientIntensity: 0.4,
-            lightIntensity: 0.6,
+            style: { name: 'matte', params: {} }
         }
     },
     standard: <Preset> {
@@ -54,20 +53,24 @@ const Canvas3DPresets = {
             outline: { name: 'off', params: { } }
         },
         renderer: {
-            ambientIntensity: 0.4,
-            lightIntensity: 0.6,
+            style: { name: 'matte', params: {} }
         }
     }
 };
 
+
 type Canvas3DPreset = keyof typeof Canvas3DPresets
 
 class LightingDemo {
     plugin: PluginContext;
 
+    private radius = 5;
+    private bias = 1.1;
+    private preset: Canvas3DPreset = 'illustrative';
+
     init(target: string | HTMLElement) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
+            ...DefaultPluginSpec(),
             layout: {
                 initial: {
                     isExpanded: false,
@@ -82,6 +85,10 @@ class LightingDemo {
 
     setPreset(preset: Canvas3DPreset) {
         const props = Canvas3DPresets[preset];
+        if (props.postprocessing.occlusion?.name === 'on') {
+            props.postprocessing.occlusion.params.radius = this.radius;
+            props.postprocessing.occlusion.params.bias = this.bias;
+        }
         PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: {
             ...props,
             multiSample: {
@@ -99,7 +106,7 @@ class LightingDemo {
         }});
     }
 
-    async load({ url, format = 'mmcif', isBinary = false, assemblyId = '' }: LoadParams) {
+    async load({ url, format = 'mmcif', isBinary = true, assemblyId = '' }: LoadParams, radius: number, bias: number) {
         await this.plugin.clear();
 
         const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
@@ -111,7 +118,11 @@ class LightingDemo {
         if (polymer) await this.plugin.builders.structure.representation.addRepresentation(polymer, { type: 'spacefill', color: 'illustrative' });
 
         const ligand = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'ligand');
-        if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick' });
+        if (ligand) await this.plugin.builders.structure.representation.addRepresentation(ligand, { type: 'ball-and-stick', color: 'element-symbol', colorParams: { carbonColor: { name: 'element-symbol', params: {} } } });
+
+        this.radius = radius;
+        this.bias = bias;
+        this.setPreset(this.preset);
     }
 }
 

src/examples/proteopedia-wrapper/helpers.ts

@@ -58,7 +58,7 @@ export namespace ModelInfo {
             const entityType = model.entities.data.type.value(eI);
             if (entityType !== 'non-polymer' && entityType !== 'branched') continue;
 
-            const comp_id = model.atomicHierarchy.residues.label_comp_id.value(rI);
+            const comp_id = model.atomicHierarchy.atoms.label_comp_id.value(residueOffsets[rI]);
 
             let lig = hetMap.get(comp_id);
             if (!lig) {

src/examples/proteopedia-wrapper/index.html

@@ -147,7 +147,7 @@
 
             // adjust this number to make the animation faster or slower
             // requires to "restart" the animation if changed
-            PluginWrapper.animate.modelIndex.maxFPS = 30;
+            PluginWrapper.animate.modelIndex.targetFps = 30;
 
             addControl('Play To End', () => PluginWrapper.animate.modelIndex.onceForward());
             addControl('Play To Start', () => PluginWrapper.animate.modelIndex.onceBackward());

src/examples/proteopedia-wrapper/index.ts

@@ -6,8 +6,9 @@
 
 import * as ReactDOM from 'react-dom';
 import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
-import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
+import { createPlugin } from '../../mol-plugin';
+import { DefaultPluginSpec } from '../../mol-plugin/spec';
+import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in/model-index';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
 import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
@@ -46,7 +47,7 @@ class MolStarProteopediaWrapper {
         customColorList?: number[]
     }) {
         this.plugin = createPlugin(typeof target === 'string' ? document.getElementById(target)! : target, {
-            ...DefaultPluginSpec,
+            ...DefaultPluginSpec(),
             animations: [
                 AnimateModelIndex
             ],
@@ -271,13 +272,17 @@ class MolStarProteopediaWrapper {
         resetPosition: () => PluginCommands.Camera.Reset(this.plugin, { })
     }
 
+    private animateModelIndexTargetFps() {
+        return Math.max(1, this.animate.modelIndex.targetFps | 0);
+    }
+
     animate = {
         modelIndex: {
-            maxFPS: 8,
-            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'forward' } } }); },
-            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'once', params: { direction: 'backward' } } }); },
-            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'palindrome', params: {} } }); },
-            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { maxFPS: Math.max(0.5, this.animate.modelIndex.maxFPS | 0), mode: { name: 'loop', params: {} } }); },
+            targetFps: 8,
+            onceForward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'forward' } } }); },
+            onceBackward: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'once', params: { direction: 'backward' } } }); },
+            palindrome: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'palindrome', params: {} } }); },
+            loop: () => { this.plugin.managers.animation.play(AnimateModelIndex, { duration: { name: 'computed', params: { targetFps: this.animateModelIndexTargetFps() } }, mode: { name: 'loop', params: {} } }); },
             stop: () => this.plugin.managers.animation.stop()
         }
     }
@@ -403,7 +408,7 @@ class MolStarProteopediaWrapper {
         },
         download: async (type: 'molj' | 'molx' = 'molj', params?: PluginState.SnapshotParams) => {
             const data = await this.plugin.managers.snapshot.serialize({ type, params });
-            download(data, `mol-star_state_${(name || getFormattedTime())}.${type}`);
+            download(data, `mol-star_state_${getFormattedTime()}.${type}`);
         },
         fetch: async (url: string, type: 'molj' | 'molx' = 'molj') => {
             try {

src/extensions/alpha-orbitals/_spec/collocation.spec.ts

@@ -0,0 +1,214 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Box3D } from '../../../mol-math/geometry';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../../mol-task';
+import { sphericalCollocation } from '../collocation';
+import { Basis, CubeGridInfo } from '../data-model';
+
+describe('alpha-orbitals-cubes', () => {
+    it('water', async () => {
+        const grid: CubeGridInfo = {
+            params: {
+                basis: _testBasis,
+                cutoffThreshold: 0,
+                sphericalOrder: 'cca-reverse',
+                boxExpand: 0,
+                gridSpacing: []
+            },
+            box: Box3D.create(Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1)),
+            delta: Vec3.create(2, 2, 2),
+            dimensions: Vec3.create(2, 2, 2),
+            npoints: 8,
+            size: Vec3.create(2, 2, 2)
+        };
+
+        const matrix = await sphericalCollocation(grid, {
+            energy: 0,
+            occupancy: 0,
+            alpha: [-2.2623991420609075e-16, 0.6360205395000592, 0.6672122399886391, -0.3876927909355508, -1.6780131293332933e-16, 2.844782862661151e-16, 4.977960694176068e-19, -2.3945919908996803e-16]
+        }, RuntimeContext.Synchronous);
+
+        const expected = [-0.1451730622877498, 0.06479453956039086, -0.2777738736440713, -0.057116584776260436, 0.05929916178822645, 0.2742903371231049, -0.07221698722165386, 0.15389180241391376];
+
+        expect(matrix.length).toBe(expected.length);
+
+        for (let i = 0; i < matrix.length; i++) {
+            expect(Math.abs(matrix[i] - expected[i]) < 1e-6).toBe(true);
+        }
+    });
+});
+
+const _testBasis: Basis = {
+    'atoms': [
+        {
+            'center': [
+                0.025886090588624934,
+                0.019164790004065606,
+                -0.013539970104105408
+            ] as Vec3,
+            'shells': [
+                {
+                    'angularMomentum': [0],
+                    'coefficients': [
+                        [
+                            -0.004151277818987536,
+                            -0.02067024147993795,
+                            -0.05150303336984537,
+                            0.33462711739899537,
+                            0.5621061300983125,
+                            0.17129946969948573
+                        ]
+                    ],
+                    'exponents': [
+                        152.28769660788095,
+                        27.928015215973073,
+                        7.848374792384515,
+                        1.1223350202705642,
+                        0.5093846587907856,
+                        0.24292266532510307
+                    ]
+                },
+                {
+                    'angularMomentum': [1],
+                    'coefficients': [
+                        [
+                            0.007924233646294425,
+                            0.051441048251911314,
+                            0.18984000600705359,
+                            0.4049863191150474,
+                            0.40123628611490797,
+                            0.1051855189039082
+                        ]
+                    ],
+                    'exponents': [
+                        27.203421487167727,
+                        7.09409912597673,
+                        2.5383362605345954,
+                        1.0610730767843852,
+                        0.4851948916410433,
+                        0.22938302550642545
+                    ]
+                }
+            ]
+        },
+        {
+            'center': [
+                0.5082729578468134,
+                1.6880351220025265,
+                0.4963443067810461
+            ] as Vec3,
+            'shells': [
+                {
+                    'angularMomentum': [0],
+                    'coefficients': [
+                        [
+                            0.009163596280542963,
+                            0.04936149294292479,
+                            0.16853830490998634,
+                            0.37056279972195677,
+                            0.4164915298246781,
+                            0.13033408410772263
+                        ]
+                    ],
+                    'exponents': [
+                        33.710073211949485,
+                        6.180705022740464,
+                        1.7291385346152253,
+                        0.5940057549921978,
+                        0.2306698170449518,
+                        0.09500256906284119
+                    ]
+                },
+                {
+                    'angularMomentum': [0],
+                    'coefficients': [
+                        [
+                            -0.32279868167000036,
+                            3.209629817295221,
+                            2.4672629224617935,
+                            -0.048487066612842224,
+                            -0.2611850111200143,
+                            -0.8917817597810863,
+                            -1.9607480081275706,
+                            -2.203769342520311,
+                            -0.6896328935259993
+                        ]
+                    ],
+                    'exponents': [
+                        10.256286070314905,
+                        0.6227965325875392,
+                        0.2391007667853915,
+                        33.710073211949485,
+                        6.180705022740464,
+                        1.7291385346152253,
+                        0.5940057549921978,
+                        0.2306698170449518,
+                        0.09500256906284119
+                    ]
+                }
+            ]
+        },
+        {
+            'center': [
+                1.1367367844436005,
+                -0.47018519422670163,
+                -1.356802622574504
+            ] as Vec3,
+            'shells': [
+                {
+                    'angularMomentum': [0],
+                    'coefficients': [
+                        [
+                            0.009163596280542963,
+                            0.04936149294292479,
+                            0.16853830490998634,
+                            0.37056279972195677,
+                            0.4164915298246781,
+                            0.13033408410772263
+                        ]
+                    ],
+                    'exponents': [
+                        33.710073211949485,
+                        6.180705022740464,
+                        1.7291385346152253,
+                        0.5940057549921978,
+                        0.2306698170449518,
+                        0.09500256906284119
+                    ]
+                },
+                {
+                    'angularMomentum': [0],
+                    'coefficients': [
+                        [
+                            -0.32279868167000036,
+                            3.209629817295221,
+                            2.4672629224617935,
+                            -0.048487066612842224,
+                            -0.2611850111200143,
+                            -0.8917817597810863,
+                            -1.9607480081275706,
+                            -2.203769342520311,
+                            -0.6896328935259993
+                        ]
+                    ],
+                    'exponents': [
+                        10.256286070314905,
+                        0.6227965325875392,
+                        0.2391007667853915,
+                        33.710073211949485,
+                        6.180705022740464,
+                        1.7291385346152253,
+                        0.5940057549921978,
+                        0.2306698170449518,
+                        0.09500256906284119
+                    ]
+                }
+            ]
+        }
+    ]
+};

src/extensions/alpha-orbitals/collocation.ts

@@ -0,0 +1,162 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Inspired by https://github.com/dgasmith/gau2grid.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../mol-task';
+import { arrayMin } from '../../mol-util/array';
+import { AlphaOrbital, CubeGridInfo } from './data-model';
+import { normalizeBasicOrder, SphericalFunctions } from './spherical-functions';
+
+export async function sphericalCollocation(
+    grid: CubeGridInfo,
+    orbital: AlphaOrbital,
+    taskCtx: RuntimeContext
+) {
+    const { basis, sphericalOrder, cutoffThreshold } = grid.params;
+    let baseCount = 0;
+
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            for (const L of shell.angularMomentum) {
+                if (L > 4) {
+                    // TODO: will L > 4 be required? Would need to precompute more functions in that case.
+                    throw new Error('Angular momentum L > 4 not supported.');
+                }
+
+                baseCount += 2 * L + 1;
+            }
+        }
+    }
+
+    const matrix = new Float32Array(grid.npoints);
+
+    let baseIndex = 0;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            let amIndex = 0;
+            for (const L of shell.angularMomentum) {
+                const alpha = normalizeBasicOrder(
+                    L,
+                    orbital.alpha.slice(baseIndex, baseIndex + 2 * L + 1),
+                    sphericalOrder
+                );
+                baseIndex += 2 * L + 1;
+
+                collocationBasis(
+                    matrix,
+                    grid,
+                    L,
+                    shell.coefficients[amIndex++],
+                    shell.exponents,
+                    atom.center,
+                    cutoffThreshold,
+                    alpha
+                );
+
+                if (taskCtx.shouldUpdate) {
+                    await taskCtx.update({
+                        message: 'Computing...',
+                        current: baseIndex,
+                        max: baseCount,
+                        isIndeterminate: false,
+                    });
+                }
+            }
+        }
+    }
+
+    return matrix;
+}
+
+function collocationBasis(
+    matrix: Float32Array,
+    grid: CubeGridInfo,
+    L: number,
+    coefficients: number[],
+    exponents: number[],
+    center: Vec3,
+    cutoffThreshold: number,
+    alpha: number[]
+) {
+    const ncoeff = exponents.length;
+    const sphericalFunc = SphericalFunctions[L];
+
+    const cx = center[0],
+        cy = center[1],
+        cz = center[2];
+    const ny = grid.dimensions[1],
+        nz = grid.dimensions[2];
+    const gdx = grid.delta[0],
+        gdy = grid.delta[1],
+        gdz = grid.delta[2];
+    const sx = grid.box.min[0],
+        sy = grid.box.min[1],
+        sz = grid.box.min[2];
+
+    const cutoffRadius =
+        cutoffThreshold > 0
+            ? Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(exponents))
+            : 10000;
+    const cutoffSquared = cutoffRadius * cutoffRadius;
+
+    const radiusBox = getRadiusBox(grid, center, cutoffRadius);
+    const iMin = radiusBox[0][0],
+        jMin = radiusBox[0][1],
+        kMin = radiusBox[0][2];
+    const iMax = radiusBox[1][0],
+        jMax = radiusBox[1][1],
+        kMax = radiusBox[1][2];
+
+    for (let i = iMin; i <= iMax; i++) {
+        const x = sx + gdx * i - cx;
+        const oX = i * ny * nz;
+
+        for (let j = jMin; j <= jMax; j++) {
+            const y = sy + gdy * j - cy;
+            const oY = oX + j * nz;
+            for (let k = kMin; k <= kMax; k++) {
+                const z = sz + gdz * k - cz;
+                const R2 = x * x + y * y + z * z;
+
+                if (R2 > cutoffSquared) {
+                    continue;
+                }
+
+                let gaussianSum = 0;
+                for (let c = 0; c < ncoeff; c++) {
+                    gaussianSum +=
+                        coefficients[c] * Math.exp(-exponents[c] * R2);
+                }
+
+                const sphericalSum = L === 0 ? alpha[0] : sphericalFunc(alpha, x, y, z);
+
+
+                matrix[k + oY] += gaussianSum * sphericalSum;
+            }
+        }
+    }
+}
+
+function getRadiusBox(grid: CubeGridInfo, center: Vec3, radius: number) {
+    const r = Vec3.create(radius, radius, radius);
+    const min = Vec3.scaleAndAdd(Vec3(), center, r, -1);
+    const max = Vec3.add(Vec3(), center, r);
+
+    Vec3.sub(min, min, grid.box.min);
+    Vec3.sub(max, max, grid.box.min);
+
+    Vec3.div(min, min, grid.delta);
+    Vec3.floor(min, min);
+    Vec3.max(min, min, Vec3());
+
+    Vec3.div(max, max, grid.delta);
+    Vec3.ceil(max, max);
+    Vec3.min(max, max, Vec3.subScalar(Vec3(), grid.dimensions, 1));
+
+    return [min, max];
+}

src/extensions/alpha-orbitals/data-model.ts

@@ -0,0 +1,131 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Mat4, Tensor, Vec3 } from '../../mol-math/linear-algebra';
+import { Grid } from '../../mol-model/volume';
+import { SphericalBasisOrder } from './spherical-functions';
+import { Box3D, RegularGrid3d } from '../../mol-math/geometry';
+import { arrayMin, arrayMax, arrayRms, arrayMean } from '../../mol-util/array';
+
+// Note: generally contracted gaussians are currently not supported.
+export interface SphericalElectronShell {
+    exponents: number[];
+    angularMomentum: number[];
+    // number[] for each angular momentum
+    coefficients: number[][];
+}
+
+export interface Basis {
+    atoms: {
+        // in Bohr units!
+        center: Vec3;
+        shells: SphericalElectronShell[];
+    }[];
+}
+
+export interface AlphaOrbital {
+    energy: number;
+    occupancy: number;
+    alpha: number[];
+}
+
+export interface CubeGridComputationParams {
+    basis: Basis;
+    /**
+     * for each electron shell compute a cutoff radius as
+     *    const cutoffRadius = Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(exponents));
+     */
+    cutoffThreshold: number;
+    sphericalOrder: SphericalBasisOrder;
+    boxExpand: number;
+    gridSpacing: number | [atomCountThreshold: number, spacing: number][];
+    doNotComputeIsovalues?: boolean;
+}
+
+export interface CubeGridInfo {
+    params: CubeGridComputationParams;
+    dimensions: Vec3;
+    box: Box3D;
+    size: Vec3;
+    npoints: number;
+    delta: Vec3;
+}
+
+export interface CubeGrid {
+    grid: Grid;
+    isovalues?: { negative?: number; positive?: number };
+}
+
+export function initCubeGrid(params: CubeGridComputationParams): CubeGridInfo {
+    const geometry = params.basis.atoms.map(a => a.center);
+    const { gridSpacing: spacing, boxExpand: expand } = params;
+
+    const count = geometry.length;
+    const box = Box3D.expand(
+        Box3D(),
+        Box3D.fromVec3Array(Box3D(), geometry),
+        Vec3.create(expand, expand, expand)
+    );
+    const size = Box3D.size(Vec3(), box);
+
+    const spacingThresholds =
+        typeof spacing === 'number' ? [[0, spacing]] : [...spacing];
+    spacingThresholds.sort((a, b) => b[0] - a[0]);
+
+    let s = 0.4;
+    for (let i = 0; i <= spacingThresholds.length; i++) {
+        s = spacingThresholds[i][1];
+        if (spacingThresholds[i][0] <= count) break;
+    }
+
+    const dimensions = Vec3.ceil(Vec3(), Vec3.scale(Vec3(), size, 1 / s));
+
+    return {
+        params,
+        box,
+        dimensions,
+        size,
+        npoints: dimensions[0] * dimensions[1] * dimensions[2],
+        delta: Vec3.div(Vec3(), size, Vec3.subScalar(Vec3(), dimensions, 1)),
+    };
+}
+
+const BohrToAngstromFactor = 0.529177210859;
+
+export function createGrid(gridInfo: RegularGrid3d, values: Float32Array, axisOrder: number[]) {
+    const boxSize = Box3D.size(Vec3(), gridInfo.box);
+    const boxOrigin = Vec3.clone(gridInfo.box.min);
+
+    Vec3.scale(boxSize, boxSize, BohrToAngstromFactor);
+    Vec3.scale(boxOrigin, boxOrigin, BohrToAngstromFactor);
+
+    const scale = Mat4.fromScaling(
+        Mat4(),
+        Vec3.div(
+            Vec3(),
+            boxSize,
+            Vec3.sub(Vec3(), gridInfo.dimensions, Vec3.create(1, 1, 1))
+        )
+    );
+    const translate = Mat4.fromTranslation(Mat4(), boxOrigin);
+    const matrix = Mat4.mul(Mat4(), translate, scale);
+
+    const grid: Grid = {
+        transform: { kind: 'matrix', matrix },
+        cells: Tensor.create(
+            Tensor.Space(gridInfo.dimensions, axisOrder, Float32Array),
+            (values as any) as Tensor.Data
+        ),
+        stats: {
+            min: arrayMin(values),
+            max: arrayMax(values),
+            mean: arrayMean(values),
+            sigma: arrayRms(values),
+        },
+    };
+
+    return grid;
+}

src/extensions/alpha-orbitals/density.ts

@@ -0,0 +1,124 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { sortArray } from '../../mol-data/util';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Task } from '../../mol-task';
+import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
+import { gpuComputeAlphaOrbitalsDensityGridValues } from './gpu/compute';
+
+export function createSphericalCollocationDensityGrid(
+    params: CubeGridComputationParams, orbitals: AlphaOrbital[], webgl?: WebGLContext
+): Task<CubeGrid> {
+    return Task.create('Spherical Collocation Grid', async (ctx) => {
+        const cubeGrid = initCubeGrid(params);
+
+        let matrix: Float32Array;
+        if (canComputeGrid3dOnGPU(webgl)) {
+            // console.time('gpu');
+            matrix = await gpuComputeAlphaOrbitalsDensityGridValues(ctx, webgl!, cubeGrid, orbitals);
+            // console.timeEnd('gpu');
+        } else {
+            throw new Error('Missing OES_texture_float WebGL extension.');
+        }
+
+        const grid = createGrid(cubeGrid, matrix, [0, 1, 2]);
+        let isovalues: { negative?: number, positive?: number } | undefined;
+
+        if (!params.doNotComputeIsovalues) {
+            isovalues = computeDensityIsocontourValues(matrix, 0.85);
+        }
+
+        return { grid, isovalues };
+    });
+}
+
+export function computeDensityIsocontourValues(input: Float32Array, cumulativeThreshold: number) {
+    let weightSum = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = Math.abs(v);
+        weightSum += w;
+    }
+    const avgWeight = weightSum / input.length;
+    let minWeight = 3 * avgWeight;
+
+    // do not try to identify isovalues for degenerate data
+    // e.g. all values are almost same
+    if (Math.abs(avgWeight - input[0] * input[0]) < 1e-5) {
+        return { negative: void 0, positive: void 0 };
+    }
+
+    let size = 0;
+    while (true) {
+        let csum = 0;
+        size = 0;
+        for (let i = 0, _i = input.length; i < _i; i++) {
+            const v = input[i];
+            const w = Math.abs(v);
+            if (w >= minWeight) {
+                csum += w;
+                size++;
+            }
+        }
+
+        if (csum / weightSum > cumulativeThreshold) {
+            break;
+        }
+
+        minWeight -= avgWeight;
+    }
+
+    const values = new Float32Array(size);
+    const weights = new Float32Array(size);
+    const indices = new Int32Array(size);
+
+    let o = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = Math.abs(v);
+        if (w >= minWeight) {
+            values[o] = v;
+            weights[o] = w;
+            indices[o] = o;
+            o++;
+        }
+    }
+
+    sortArray(
+        indices,
+        (indices, i, j) => weights[indices[j]] - weights[indices[i]]
+    );
+
+    let cweight = 0,
+        cutoffIndex = 0;
+    for (let i = 0; i < size; i++) {
+        cweight += weights[indices[i]];
+
+        if (cweight / weightSum >= cumulativeThreshold) {
+            cutoffIndex = i;
+            break;
+        }
+    }
+
+    let positive = Number.POSITIVE_INFINITY,
+        negative = Number.NEGATIVE_INFINITY;
+
+    for (let i = 0; i < cutoffIndex; i++) {
+        const v = values[indices[i]];
+        if (v > 0) {
+            if (v < positive) positive = v;
+        } else if (v < 0) {
+            if (v > negative) negative = v;
+        }
+    }
+
+    return {
+        negative: negative !== Number.NEGATIVE_INFINITY ? negative : void 0,
+        positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
+    };
+}

src/extensions/alpha-orbitals/gpu/compute.ts

@@ -0,0 +1,170 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { createGrid3dComputeRenderable } from '../../../mol-gl/compute/grid3d';
+import { TextureSpec, UnboxedValues, UniformSpec } from '../../../mol-gl/renderable/schema';
+import { WebGLContext } from '../../../mol-gl/webgl/context';
+import { RuntimeContext } from '../../../mol-task';
+import { ValueCell } from '../../../mol-util';
+import { arrayMin } from '../../../mol-util/array';
+import { AlphaOrbital, Basis, CubeGridInfo } from '../data-model';
+import { normalizeBasicOrder, SphericalBasisOrder } from '../spherical-functions';
+import { MAIN, UTILS } from './shader.frag';
+
+const Schema = {
+    tCenters: TextureSpec('image-float32', 'rgba', 'float', 'nearest'),
+    tInfo: TextureSpec('image-float32', 'rgba', 'float', 'nearest'),
+    tCoeff: TextureSpec('image-float32', 'rgb', 'float', 'nearest'),
+    tAlpha: TextureSpec('image-float32', 'alpha', 'float', 'nearest'),
+    uNCenters: UniformSpec('i'),
+    uNAlpha: UniformSpec('i'),
+    uNCoeff: UniformSpec('i'),
+    uMaxCoeffs: UniformSpec('i'),
+};
+
+const Orbitals = createGrid3dComputeRenderable({
+    schema: Schema,
+    loopBounds: ['uNCenters', 'uMaxCoeffs'],
+    mainCode: MAIN,
+    utilCode: UTILS,
+    returnCode: 'v',
+    values(params: { grid: CubeGridInfo, orbital: AlphaOrbital }) {
+        return createTextureData(params.grid, params.orbital);
+    }
+});
+
+const Density = createGrid3dComputeRenderable({
+    schema: {
+        ...Schema,
+        uOccupancy: UniformSpec('f'),
+    },
+    loopBounds: ['uNCenters', 'uMaxCoeffs'],
+    mainCode: MAIN,
+    utilCode: UTILS,
+    returnCode: 'current + uOccupancy * v * v',
+    values(params: { grid: CubeGridInfo, orbitals: AlphaOrbital[] }) {
+        return {
+            ...createTextureData(params.grid, params.orbitals[0]),
+            uOccupancy: 0
+        };
+    },
+    cumulative: {
+        states(params: { grid: CubeGridInfo, orbitals: AlphaOrbital[] }) {
+            return params.orbitals.filter(o => o.occupancy !== 0);
+        },
+        update({ grid }, state: AlphaOrbital, values) {
+            const alpha = getNormalizedAlpha(grid.params.basis, state.alpha, grid.params.sphericalOrder);
+            ValueCell.updateIfChanged(values.uOccupancy, state.occupancy);
+            ValueCell.update(values.tAlpha, { width: alpha.length, height: 1, array: alpha });
+        }
+    }
+});
+
+export function gpuComputeAlphaOrbitalsGridValues(ctx: RuntimeContext, webgl: WebGLContext, grid: CubeGridInfo, orbital: AlphaOrbital) {
+    return Orbitals(ctx, webgl, grid, { grid, orbital });
+}
+
+export function gpuComputeAlphaOrbitalsDensityGridValues(ctx: RuntimeContext, webgl: WebGLContext, grid: CubeGridInfo, orbitals: AlphaOrbital[]) {
+    return Density(ctx, webgl, grid, { grid, orbitals });
+}
+
+function getNormalizedAlpha(basis: Basis, alphaOrbitals: number[], sphericalOrder: SphericalBasisOrder) {
+    const alpha = new Float32Array(alphaOrbitals.length);
+
+    let aO = 0;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            for (const L of shell.angularMomentum) {
+                const a0 = normalizeBasicOrder(L, alphaOrbitals.slice(aO, aO + 2 * L + 1), sphericalOrder);
+                for (let i = 0; i < a0.length; i++) alpha[aO + i] = a0[i];
+                aO += 2 * L + 1;
+            }
+        }
+    }
+
+    return alpha;
+}
+
+function createTextureData(grid: CubeGridInfo, orbital: AlphaOrbital): UnboxedValues<typeof Schema> {
+    const { basis, sphericalOrder, cutoffThreshold } = grid.params;
+
+    let centerCount = 0;
+    let baseCount = 0;
+    let coeffCount = 0;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+            for (const L of shell.angularMomentum) {
+                if (L > 4) {
+                    // TODO: will L > 4 be required? Would need to precompute more functions in that case.
+                    throw new Error('Angular momentum L > 4 not supported.');
+                }
+
+                centerCount++;
+                baseCount += 2 * L + 1;
+                coeffCount += shell.exponents.length;
+            }
+        }
+    }
+
+    const centers = new Float32Array(4 * centerCount);
+    // L, alpha_offset, coeff_offset_start, coeff_offset_end
+    const info = new Float32Array(4 * centerCount);
+    const alpha = new Float32Array(baseCount);
+    const coeff = new Float32Array(3 * coeffCount);
+
+    let maxCoeffs = 0;
+    let cO = 0, aO = 0, coeffO = 0;
+    for (const atom of basis.atoms) {
+        for (const shell of atom.shells) {
+
+            let amIndex = 0;
+            for (const L of shell.angularMomentum) {
+                const a0 = normalizeBasicOrder(L, orbital.alpha.slice(aO, aO + 2 * L + 1), sphericalOrder);
+
+                const cutoffRadius = cutoffThreshold > 0
+                    ? Math.sqrt(-Math.log(cutoffThreshold) / arrayMin(shell.exponents))
+                    : 10000;
+
+                centers[4 * cO + 0] = atom.center[0];
+                centers[4 * cO + 1] = atom.center[1];
+                centers[4 * cO + 2] = atom.center[2];
+                centers[4 * cO + 3] = cutoffRadius * cutoffRadius;
+
+                info[4 * cO + 0] = L;
+                info[4 * cO + 1] = aO;
+                info[4 * cO + 2] = coeffO;
+                info[4 * cO + 3] = coeffO + shell.exponents.length;
+
+                for (let i = 0; i < a0.length; i++) alpha[aO + i] = a0[i];
+
+                const c0 = shell.coefficients[amIndex++];
+                for (let i = 0; i < shell.exponents.length; i++) {
+                    coeff[3 * (coeffO + i) + 0] = c0[i];
+                    coeff[3 * (coeffO + i) + 1] = shell.exponents[i];
+                }
+
+                if (c0.length > maxCoeffs) {
+                    maxCoeffs = c0.length;
+                }
+
+                cO++;
+                aO += 2 * L + 1;
+                coeffO += shell.exponents.length;
+            }
+        }
+    }
+
+    return {
+        uNCenters: centerCount,
+        uNAlpha: baseCount,
+        uNCoeff: coeffCount,
+        uMaxCoeffs: maxCoeffs,
+        tCenters: { width: centerCount, height: 1, array: centers },
+        tInfo: { width: centerCount, height: 1, array: info },
+        tCoeff: { width: coeffCount, height: 1, array: coeff },
+        tAlpha: { width: baseCount, height: 1, array: alpha },
+    };
+}

src/extensions/alpha-orbitals/gpu/shader.frag.ts

@@ -0,0 +1,145 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export const UTILS = `
+float L1(vec3 p, float a0, float a1, float a2) {
+    return a0 * p.z + a1 * p.x + a2 * p.y;
+}
+
+float L2(vec3 p, float a0, float a1, float a2, float a3, float a4) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    return (
+        a0 * (-0.5 * xx - 0.5 * yy + zz) +
+        a1 * (1.7320508075688772 * x * z) +
+        a2 * (1.7320508075688772 * y * z) +
+        a3 * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
+        a4 * (1.7320508075688772 * x * y)
+    );
+}
+
+float L3(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    return (
+        a0 * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
+        a1 * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
+        a2 * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
+        a3 * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
+        a4 * (3.872983346207417 * x * y * z) +
+        a5 * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
+        a6 * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
+    );
+}
+
+float L4(vec3 p, float a0, float a1, float a2, float a3, float a4, float a5, float a6, float a7, float a8) {
+    float x = p.x, y = p.y, z = p.z;
+    float xx = x * x, yy = y * y, zz = z * z;
+    float xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    float xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
+    return (
+        a0 * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
+        a1 * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
+        a2 * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
+        a3 * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
+        a4 * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
+        a5 * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
+        a6 * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
+        a7 * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
+        a8 * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
+    );
+}
+
+float alpha(float offset, float f) {
+    #ifdef WEBGL1
+        // in webgl1, the value is in the alpha channel!
+        return texture2D(tAlpha, vec2(offset * f, 0.5)).a;
+    #else
+        return texture2D(tAlpha, vec2(offset * f, 0.5)).x;
+    #endif
+}
+
+float Y(int L, vec3 X, float aO, float fA) {
+    if (L == 0) {
+        return alpha(aO, fA);
+    } else if (L == 1) {
+        return L1(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA)
+        );
+    } else if (L == 2) {
+        return L2(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA)
+        );
+    } else if (L == 3) {
+        return L3(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
+            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA)
+        );
+    } else if (L == 4) {
+        return L4(X,
+            alpha(aO, fA), alpha(aO + 1.0, fA), alpha(aO + 2.0, fA), alpha(aO + 3.0, fA), alpha(aO + 4.0, fA),
+            alpha(aO + 5.0, fA), alpha(aO + 6.0, fA), alpha(aO + 7.0, fA), alpha(aO + 8.0, fA)
+        );
+    }
+    // TODO: do we need L > 4?
+    return 0.0;
+}
+
+#ifndef WEBGL1
+    float R(float R2, int start, int end, float fCoeff) {
+        float gauss = 0.0;
+        for (int i = start; i < end; i++) {
+            vec2 c = texture2D(tCoeff, vec2(float(i) * fCoeff, 0.5)).xy;
+            gauss += c.x * exp(-c.y * R2);
+        }
+        return gauss;
+    }
+#else
+    float R(float R2, int start, int end, float fCoeff) {
+        float gauss = 0.0;
+        int o = start;
+        for (int i = 0; i < uMaxCoeffs; i++) {
+            if (o >= end) break;
+
+            vec2 c = texture2D(tCoeff, vec2(float(o) * fCoeff, 0.5)).xy;
+            gauss += c.x * exp(-c.y * R2);
+            o++;
+        }
+        return gauss;
+    }
+#endif
+`;
+
+export const MAIN = `
+    float fCenter = 1.0 / float(uNCenters - 1);
+    float fCoeff = 1.0 / float(uNCoeff - 1);
+    float fA = 1.0 / float(uNAlpha - 1);
+
+    float v = 0.0;
+
+    for (int i = 0; i < uNCenters; i++) {
+        vec2 cCoord = vec2(float(i) * fCenter, 0.5);
+
+        vec4 center = texture2D(tCenters, cCoord);
+        vec3 X = xyz - center.xyz;
+        float R2 = dot(X, X);
+
+        // center.w is squared cutoff radius
+        if (R2 > center.w) {
+            continue;
+        }
+
+        vec4 info = texture2D(tInfo, cCoord);
+
+        int L = int(info.x);
+        float aO = info.y;
+        int coeffStart = int(info.z);
+        int coeffEnd = int(info.w);
+
+        v += R(R2, coeffStart, coeffEnd, fCoeff) * Y(L, X, aO, fA);
+    }
+`;

src/extensions/alpha-orbitals/orbitals.ts

@@ -0,0 +1,131 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Inspired by https://github.com/dgasmith/gau2grid.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { sortArray } from '../../mol-data/util';
+import { canComputeGrid3dOnGPU } from '../../mol-gl/compute/grid3d';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Task } from '../../mol-task';
+import { sphericalCollocation } from './collocation';
+import { AlphaOrbital, createGrid, CubeGrid, CubeGridComputationParams, initCubeGrid } from './data-model';
+import { gpuComputeAlphaOrbitalsGridValues } from './gpu/compute';
+
+// setDebugMode(true);
+
+export function createSphericalCollocationGrid(
+    params: CubeGridComputationParams, orbital: AlphaOrbital, webgl?: WebGLContext
+): Task<CubeGrid> {
+    return Task.create('Spherical Collocation Grid', async (ctx) => {
+        const cubeGrid = initCubeGrid(params);
+
+        let matrix: Float32Array;
+        if (canComputeGrid3dOnGPU(webgl)) {
+            // console.time('gpu');
+            matrix = await gpuComputeAlphaOrbitalsGridValues(ctx, webgl!, cubeGrid, orbital);
+            // console.timeEnd('gpu');
+        } else {
+            // console.time('cpu');
+            matrix = await sphericalCollocation(cubeGrid, orbital, ctx);
+            // console.timeEnd('cpu');
+        }
+
+        const grid = createGrid(cubeGrid, matrix, [0, 1, 2]);
+        let isovalues: { negative?: number, positive?: number } | undefined;
+
+        if (!params.doNotComputeIsovalues) {
+            isovalues = computeOrbitalIsocontourValues(matrix, 0.85);
+        }
+
+        return { grid, isovalues };
+    });
+}
+
+export function computeOrbitalIsocontourValues(input: Float32Array, cumulativeThreshold: number) {
+    let weightSum = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = v * v;
+        weightSum += w;
+    }
+    const avgWeight = weightSum / input.length;
+    let minWeight = 3 * avgWeight;
+
+    // do not try to identify isovalues for degenerate data
+    // e.g. all values are almost same
+    if (Math.abs(avgWeight - input[0] * input[0]) < 1e-5) {
+        return { negative: void 0, positive: void 0 };
+    }
+
+    let size = 0;
+    while (true) {
+        let csum = 0;
+        size = 0;
+        for (let i = 0, _i = input.length; i < _i; i++) {
+            const v = input[i];
+            const w = v * v;
+            if (w >= minWeight) {
+                csum += w;
+                size++;
+            }
+        }
+
+        if (csum / weightSum > cumulativeThreshold) {
+            break;
+        }
+
+        minWeight -= avgWeight;
+    }
+
+    const values = new Float32Array(size);
+    const weights = new Float32Array(size);
+    const indices = new Int32Array(size);
+
+    let o = 0;
+    for (let i = 0, _i = input.length; i < _i; i++) {
+        const v = input[i];
+        const w = v * v;
+        if (w >= minWeight) {
+            values[o] = v;
+            weights[o] = w;
+            indices[o] = o;
+            o++;
+        }
+    }
+
+    sortArray(
+        indices,
+        (indices, i, j) => weights[indices[j]] - weights[indices[i]]
+    );
+
+    let cweight = 0,
+        cutoffIndex = 0;
+    for (let i = 0; i < size; i++) {
+        cweight += weights[indices[i]];
+
+        if (cweight / weightSum >= cumulativeThreshold) {
+            cutoffIndex = i;
+            break;
+        }
+    }
+
+    let positive = Number.POSITIVE_INFINITY,
+        negative = Number.NEGATIVE_INFINITY;
+
+    for (let i = 0; i < cutoffIndex; i++) {
+        const v = values[indices[i]];
+        if (v > 0) {
+            if (v < positive) positive = v;
+        } else if (v < 0) {
+            if (v > negative) negative = v;
+        }
+    }
+
+    return {
+        negative: negative !== Number.NEGATIVE_INFINITY ? negative : void 0,
+        positive: positive !== Number.POSITIVE_INFINITY ? positive : void 0,
+    };
+}

src/extensions/alpha-orbitals/spherical-functions.ts

@@ -0,0 +1,93 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Inspired by https://github.com/dgasmith/gau2grid.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+// gaussian:
+//     R_0, R^+_1, R^-_1, ..., R^+_l, R^-_l
+// cca:
+//     R^-_(l), R^-_(l-1), ..., R_0, ..., R^+_(l-1), R^+_l
+// cca-reverse:
+//     R^+_(l), R^+_(l-1), ..., R_0, ..., R^-_(l-1), R^-_l
+export type SphericalBasisOrder = 'gaussian' | 'cca' | 'cca-reverse';
+
+export function normalizeBasicOrder(
+    L: number,
+    alpha: number[],
+    order: SphericalBasisOrder
+) {
+    if (order === 'gaussian' || L === 0) return alpha;
+
+    const ret: number[] = [alpha[L]];
+    for (let l = 0; l < L; l++) {
+        const a = alpha[L - l - 1],
+            b = alpha[L + l + 1];
+        if (order === 'cca') ret.push(b, a);
+        else ret.push(a, b);
+    }
+    return ret;
+}
+
+export type SphericalFunc = (
+    alpha: number[],
+    x: number,
+    y: number,
+    z: number
+) => number;
+
+export const SphericalFunctions: SphericalFunc[] = [L0, L1, L2, L3, L4];
+
+// L_i functions were auto-generated.
+
+function L0(alpha: number[], x: number, y: number, z: number) {
+    return alpha[0];
+}
+
+function L1(alpha: number[], x: number, y: number, z: number) {
+    return alpha[0] * z + alpha[1] * x + alpha[2] * y;
+}
+
+function L2(alpha: number[], x: number, y: number, z: number) {
+    const xx = x * x, yy = y * y, zz = z * z;
+    return (
+        alpha[0] * (-0.5 * xx - 0.5 * yy + zz) +
+        alpha[1] * (1.7320508075688772 * x * z) +
+        alpha[2] * (1.7320508075688772 * y * z) +
+        alpha[3] * (0.8660254037844386 * xx - 0.8660254037844386 * yy) +
+        alpha[4] * (1.7320508075688772 * x * y)
+    );
+}
+
+function L3(alpha: number[], x: number, y: number, z: number) {
+    const xx = x * x, yy = y * y, zz = z * z;
+    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    return (
+        alpha[0] * (-1.5 * xx * z - 1.5 * yy * z + zzz) +
+        alpha[1] * (-0.6123724356957945 * xxx - 0.6123724356957945 * x * yy + 2.449489742783178 * x * zz) +
+        alpha[2] * (-0.6123724356957945 * xx * y - 0.6123724356957945 * yyy + 2.449489742783178 * y * zz) +
+        alpha[3] * (1.9364916731037085 * xx * z - 1.9364916731037085 * yy * z) +
+        alpha[4] * (3.872983346207417 * x * y * z) +
+        alpha[5] * (0.7905694150420949 * xxx - 2.3717082451262845 * x * yy) +
+        alpha[6] * (2.3717082451262845 * xx * y - 0.7905694150420949 * yyy)
+    );
+}
+
+function L4(alpha: number[], x: number, y: number, z: number) {
+    const xx = x * x, yy = y * y, zz = z * z;
+    const xxx = xx * x, yyy = yy * y, zzz = zz * z;
+    const xxxx = xxx * x, yyyy = yyy * y, zzzz = zzz * z;
+    return (
+        alpha[0] * (0.375 * xxxx + 0.75 * xx * yy + 0.375 * yyyy - 3.0 * xx * zz - 3.0 * yy * zz + zzzz) +
+        alpha[1] * (-2.3717082451262845 * xxx * z - 2.3717082451262845 * x * yy * z + 3.1622776601683795 * x * zzz) +
+        alpha[2] * (-2.3717082451262845 * xx * y * z - 2.3717082451262845 * yyy * z + 3.1622776601683795 * y * zzz) +
+        alpha[3] * (-0.5590169943749475 * xxxx + 0.5590169943749475 * yyyy + 3.3541019662496847 * xx * zz - 3.3541019662496847 * yy * zz) +
+        alpha[4] * (-1.118033988749895 * xxx * y - 1.118033988749895 * x * yyy + 6.708203932499369 * x * y * zz) +
+        alpha[5] * (2.091650066335189 * xxx * z + -6.274950199005566 * x * yy * z) +
+        alpha[6] * (6.274950199005566 * xx * y * z + -2.091650066335189 * yyy * z) +
+        alpha[7] * (0.739509972887452 * xxxx - 4.437059837324712 * xx * yy + 0.739509972887452 * yyyy) +
+        alpha[8] * (2.958039891549808 * xxx * y + -2.958039891549808 * x * yyy)
+    );
+}

src/extensions/alpha-orbitals/transforms.ts

@@ -0,0 +1,236 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
+import { createSphericalCollocationGrid } from './orbitals';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Task } from '../../mol-task';
+import { CustomProperties } from '../../mol-model/custom-property';
+import { SphericalBasisOrder } from './spherical-functions';
+import { Volume } from '../../mol-model/volume';
+import { PluginContext } from '../../mol-plugin/context';
+import { ColorNames } from '../../mol-util/color/names';
+import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
+import { StateTransformer } from '../../mol-state';
+import { Theme } from '../../mol-theme/theme';
+import { VolumeRepresentation3DHelpers } from '../../mol-plugin-state/transforms/representation';
+import { AlphaOrbital, Basis, CubeGrid } from './data-model';
+import { createSphericalCollocationDensityGrid } from './density';
+import { Tensor } from '../../mol-math/linear-algebra';
+
+export class BasisAndOrbitals extends PluginStateObject.Create<{ basis: Basis, order: SphericalBasisOrder, orbitals: AlphaOrbital[] }>({ name: 'Basis', typeClass: 'Object' }) { }
+
+export const StaticBasisAndOrbitals = PluginStateTransform.BuiltIn({
+    name: 'static-basis-and-orbitals',
+    display: 'Basis and Orbitals',
+    from: PluginStateObject.Root,
+    to: BasisAndOrbitals,
+    params: {
+        label: PD.Text('Orbital Data', { isHidden: true }),
+        basis: PD.Value<Basis>(void 0 as any, { isHidden: true }),
+        order: PD.Text<SphericalBasisOrder>('gaussian' as SphericalBasisOrder, { isHidden: true }),
+        orbitals: PD.Value<AlphaOrbital[]>([], { isHidden: true })
+    },
+})({
+    apply({ params }) {
+        return new BasisAndOrbitals({ basis: params.basis, order: params.order, orbitals: params.orbitals }, { label: params.label });
+    }
+});
+
+const CreateOrbitalVolumeParamBase = {
+    cutoffThreshold: PD.Numeric(0.0015, { min: 0, max: 0.1, step: 0.0001 }),
+    boxExpand: PD.Numeric(4.5, { min: 0, max: 7, step: 0.1 }),
+    gridSpacing: PD.ObjectList({ atomCount: PD.Numeric(0), spacing: PD.Numeric(0.35, { min: 0.1, max: 2, step: 0.01 }) }, e => `Atoms ${e.atomCount}: ${e.spacing}`, {
+        defaultValue: [
+            { atomCount: 55, spacing: 0.5 },
+            { atomCount: 40, spacing: 0.45 },
+            { atomCount: 25, spacing: 0.4 },
+            { atomCount: 0, spacing: 0.35 },
+        ]
+    }),
+    clampValues: PD.MappedStatic('off', {
+        off: PD.EmptyGroup(),
+        on: PD.Group({
+            sigma: PD.Numeric(8, { min: 1, max: 20 }, { description: 'Clamp values to range [sigma * negIsoValue, sigma * posIsoValue].' })
+        })
+    })
+};
+
+function clampData(matrix: Tensor.Data, min: number, max: number) {
+    for (let i = 0, _i = matrix.length; i < _i; i++) {
+        const v = matrix[i];
+        if (v < min) matrix[i] = min;
+        else if (v > max) matrix[i] = max;
+    }
+}
+
+function clampGrid(data: CubeGrid, v: number) {
+    const grid = data.grid;
+    const min = (data.isovalues?.negative ?? data.grid.stats.min) * v;
+    const max = (data.isovalues?.positive ?? data.grid.stats.max) * v;
+
+    // clamp values for better direct volume resolution
+    // current implementation uses Byte array for values
+    // if this is not enough, update mol* to use float
+    // textures instead
+    if (grid.stats.min < min || grid.stats.max > max) {
+        clampData(data.grid.cells.data, min, max);
+        if (grid.stats.min < min) {
+            (grid.stats.min as number) = min;
+        }
+        if (grid.stats.max > max) {
+            (grid.stats.max as number) = max;
+        }
+    }
+}
+
+export const CreateOrbitalVolume = PluginStateTransform.BuiltIn({
+    name: 'create-orbital-volume',
+    display: 'Orbital Volume',
+    from: BasisAndOrbitals,
+    to: PluginStateObject.Volume.Data,
+    params: (a) => {
+        if (!a) {
+            return { index: PD.Numeric(0), ...CreateOrbitalVolumeParamBase };
+        }
+
+        return {
+            index: PD.Select(0, a.data.orbitals.map((o, i) => [i, `[${i + 1}] ${o.energy.toFixed(4)}`])),
+            ...CreateOrbitalVolumeParamBase
+        };
+    }
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Orbital Volume', async ctx => {
+            const data = await createSphericalCollocationGrid({
+                basis: a.data.basis,
+                cutoffThreshold: params.cutoffThreshold,
+                sphericalOrder: a.data.order,
+                boxExpand: params.boxExpand,
+                gridSpacing: params.gridSpacing.map(e => [e.atomCount, e.spacing] as [number, number])
+            }, a.data.orbitals[params.index], plugin.canvas3d?.webgl).runInContext(ctx);
+            const volume: Volume = {
+                grid: data.grid,
+                sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },
+                customProperties: new CustomProperties(),
+                _propertyData: Object.create(null),
+            };
+
+            if (params.clampValues?.name === 'on') {
+                clampGrid(data, params.clampValues?.params?.sigma ?? 8);
+            }
+
+            return new PluginStateObject.Volume.Data(volume, { label: 'Orbital Volume' });
+        });
+    }
+});
+
+export const CreateOrbitalDensityVolume = PluginStateTransform.BuiltIn({
+    name: 'create-orbital-density-volume',
+    display: 'Orbital Density Volume',
+    from: BasisAndOrbitals,
+    to: PluginStateObject.Volume.Data,
+    params: CreateOrbitalVolumeParamBase
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Orbital Volume', async ctx => {
+            const data = await createSphericalCollocationDensityGrid({
+                basis: a.data.basis,
+                cutoffThreshold: params.cutoffThreshold,
+                sphericalOrder: a.data.order,
+                boxExpand: params.boxExpand,
+                gridSpacing: params.gridSpacing.map(e => [e.atomCount, e.spacing] as [number, number])
+            }, a.data.orbitals, plugin.canvas3d?.webgl).runInContext(ctx);
+            const volume: Volume = {
+                grid: data.grid,
+                sourceData: { name: 'custom grid', kind: 'alpha-orbitals', data },
+                customProperties: new CustomProperties(),
+                _propertyData: Object.create(null),
+            };
+
+            if (params.clampValues?.name === 'on') {
+                clampGrid(data, params.clampValues?.params?.sigma ?? 8);
+            }
+
+            return new PluginStateObject.Volume.Data(volume, { label: 'Orbital Volume' });
+        });
+    }
+});
+
+export const CreateOrbitalRepresentation3D = PluginStateTransform.BuiltIn({
+    name: 'create-orbital-representation-3d',
+    display: 'Orbital Representation 3D',
+    from: PluginStateObject.Volume.Data,
+    to: PluginStateObject.Volume.Representation3D,
+    params: {
+        directVolume: PD.Boolean(false),
+        relativeIsovalue: PD.Numeric(1, { min: 0.01, max: 5, step: 0.01 }),
+        kind: PD.Select<'positive' | 'negative'>('positive', [['positive', 'Positive'], ['negative', 'Negative']]),
+        color: PD.Color(ColorNames.blue),
+        alpha: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+        xrayShaded: PD.Boolean(false),
+        pickable: PD.Boolean(true)
+    }
+})({
+    canAutoUpdate() {
+        return true;
+    },
+    apply({ a, params: srcParams }, plugin: PluginContext) {
+        return Task.create('Orbitals Representation 3D', async ctx => {
+            const params = volumeParams(plugin, a, srcParams);
+
+            const propertyCtx = { runtime: ctx, assetManager: plugin.managers.asset };
+            const provider = plugin.representation.volume.registry.get(params.type.name);
+            if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
+            const props = params.type.params || {};
+            const repr = provider.factory({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.volume.themes }, provider.getParams);
+            repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, params));
+            await repr.createOrUpdate(props, a.data).runInContext(ctx);
+            repr.setState({ pickable: srcParams.pickable });
+            return new PluginStateObject.Volume.Representation3D({ repr, source: a }, { label: provider.label, description: VolumeRepresentation3DHelpers.getDescription(props) });
+        });
+    },
+    update({ a, b, newParams: srcParams }, plugin: PluginContext) {
+        return Task.create('Orbitals Representation 3D', async ctx => {
+            const newParams = volumeParams(plugin, a, srcParams);
+
+            const props = { ...b.data.repr.props, ...newParams.type.params };
+            b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
+            await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            b.data.repr.setState({ pickable: srcParams.pickable });
+            b.description = VolumeRepresentation3DHelpers.getDescription(props);
+            return StateTransformer.UpdateResult.Updated;
+        });
+    }
+});
+
+function volumeParams(plugin: PluginContext, volume: PluginStateObject.Volume.Data, params: StateTransformer.Params<typeof CreateOrbitalRepresentation3D>) {
+    if (volume.data.sourceData.kind !== 'alpha-orbitals') throw new Error('Invalid data source kind.');
+
+    const { isovalues } = volume.data.sourceData.data as CubeGrid;
+    if (!isovalues) throw new Error('Isovalues are not computed.');
+
+    const value = isovalues[params.kind];
+
+    return createVolumeRepresentationParams(plugin, volume.data, params.directVolume ? {
+        type: 'direct-volume',
+        typeParams: {
+            alpha: params.alpha,
+            renderMode: {
+                name: 'isosurface',
+                params: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, singleLayer: false }
+            },
+            xrayShaded: params.xrayShaded
+        },
+        color: 'uniform',
+        colorParams: { value: params.color }
+    } : {
+        type: 'isosurface',
+        typeParams: { isoValue: { kind: 'absolute', absoluteValue: (value ?? 1000) * params.relativeIsovalue }, alpha: params.alpha, xrayShaded: params.xrayShaded },
+        color: 'uniform',
+        colorParams: { value: params.color }
+    });
+}

src/extensions/anvil/algorithm.ts

@@ -0,0 +1,370 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Structure, StructureElement, StructureProperties } from '../../mol-model/structure';
+import { Task, RuntimeContext } from '../../mol-task';
+import { CentroidHelper } from '../../mol-math/geometry/centroid-helper';
+import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { getElementMoleculeType } from '../../mol-model/structure/util';
+import { MoleculeType } from '../../mol-model/structure/model/types';
+import { AccessibleSurfaceArea } from '../../mol-model-props/computed/accessible-surface-area/shrake-rupley';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { MembraneOrientation } from './prop';
+
+interface ANVILContext {
+    structure: Structure,
+
+    numberOfSpherePoints: number,
+    stepSize: number,
+    minThickness: number,
+    maxThickness: number,
+    asaCutoff: number,
+
+    offsets: ArrayLike<number>,
+    exposed: ArrayLike<boolean>,
+    centroid: Vec3,
+    extent: number
+};
+
+export const ANVILParams = {
+    numberOfSpherePoints: PD.Numeric(120, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),
+    stepSize: PD.Numeric(1, { min: 0.25, max: 4, step: 0.25 }, { description: 'Thickness of membrane slices that will be tested' }),
+    minThickness: PD.Numeric(20, { min: 10, max: 30, step: 1}, { description: 'Minimum membrane thickness used during refinement' }),
+    maxThickness: PD.Numeric(40, { min: 30, max: 50, step: 1}, { description: 'Maximum membrane thickness used during refinement' }),
+    asaCutoff: PD.Numeric(40, { min: 10, max: 100, step: 1 }, { description: 'Absolute ASA cutoff above which residues will be considered' })
+};
+export type ANVILParams = typeof ANVILParams
+export type ANVILProps = PD.Values<ANVILParams>
+
+/**
+ * Implements:
+ * Membrane positioning for high- and low-resolution protein structures through a binary classification approach
+ * Guillaume Postic, Yassine Ghouzam, Vincent Guiraud, and Jean-Christophe Gelly
+ * Protein Engineering, Design & Selection, 2015, 1–5
+ * doi: 10.1093/protein/gzv063
+ */
+export function computeANVIL(structure: Structure, props: ANVILProps) {
+    return Task.create('Compute Membrane Orientation', async runtime => {
+        return await calculate(runtime, structure, props);
+    });
+}
+
+
+const centroidHelper = new CentroidHelper();
+function initialize(structure: Structure, props: ANVILProps): ANVILContext {
+    const l = StructureElement.Location.create(structure);
+    const { label_atom_id, x, y, z } = StructureProperties.atom;
+    const elementCount = structure.polymerResidueCount;
+    centroidHelper.reset();
+
+    let offsets = new Int32Array(elementCount);
+    let exposed = new Array<boolean>(elementCount);
+
+    const accessibleSurfaceArea = structure && AccessibleSurfaceAreaProvider.get(structure);
+    const asa = accessibleSurfaceArea.value!;
+
+    const vec = Vec3();
+    let m = 0;
+    for (let i = 0, il = structure.units.length; i < il; ++i) {
+        const unit = structure.units[i];
+        const { elements } = unit;
+        l.unit = unit;
+
+        for (let j = 0, jl = elements.length; j < jl; ++j) {
+            const eI = elements[j];
+            l.element = eI;
+
+            // consider only amino acids
+            if (getElementMoleculeType(unit, eI) !== MoleculeType.Protein) {
+                continue;
+            }
+
+            // only CA is considered for downstream operations
+            if (label_atom_id(l) !== 'CA') {
+                continue;
+            }
+
+            // while iterating use first pass to compute centroid
+            Vec3.set(vec, x(l), y(l), z(l));
+            centroidHelper.includeStep(vec);
+
+            // keep track of offsets and exposed state to reuse
+            offsets[m] = structure.serialMapping.getSerialIndex(l.unit, l.element);
+            exposed[m] = AccessibleSurfaceArea.getValue(l, asa) > props.asaCutoff;
+
+            m++;
+        }
+    }
+
+    // omit potentially empty tail1
+    offsets = offsets.slice(0, m);
+    exposed = exposed.slice(0, m);
+
+    // calculate centroid and extent
+    centroidHelper.finishedIncludeStep();
+    const centroid = centroidHelper.center;
+    for (let k = 0, kl = offsets.length; k < kl; k++) {
+        setLocation(l, structure, offsets[k]);
+        Vec3.set(vec, x(l), y(l), z(l));
+        centroidHelper.radiusStep(vec);
+    }
+    const extent = 1.2 * Math.sqrt(centroidHelper.radiusSq);
+
+    return {
+        ...props,
+        structure: structure,
+
+        offsets: offsets,
+        exposed: exposed,
+        centroid: centroid,
+        extent: extent
+    };
+}
+
+export async function calculate(runtime: RuntimeContext, structure: Structure, params: ANVILProps): Promise<MembraneOrientation> {
+    const { label_comp_id } = StructureProperties.atom;
+
+    const ctx = initialize(structure, params);
+    const initialHphobHphil = HphobHphil.filtered(ctx, label_comp_id);
+
+    const initialMembrane = findMembrane(ctx, generateSpherePoints(ctx, ctx.numberOfSpherePoints), initialHphobHphil, label_comp_id);
+    const alternativeMembrane = findMembrane(ctx, findProximateAxes(ctx, initialMembrane), initialHphobHphil, label_comp_id);
+
+    const membrane = initialMembrane.qmax! > alternativeMembrane.qmax! ? initialMembrane : alternativeMembrane;
+
+    return {
+        planePoint1: membrane.planePoint1,
+        planePoint2: membrane.planePoint2,
+        normalVector: membrane.normalVector!,
+        radius: ctx.extent,
+        centroid: ctx.centroid
+    };
+}
+
+interface MembraneCandidate {
+    planePoint1: Vec3,
+    planePoint2: Vec3,
+    stats: HphobHphil,
+    normalVector?: Vec3,
+    spherePoint?: Vec3,
+    qmax?: number
+}
+
+namespace MembraneCandidate {
+    export function initial(c1: Vec3, c2: Vec3, stats: HphobHphil): MembraneCandidate {
+        return {
+            planePoint1: c1,
+            planePoint2: c2,
+            stats: stats
+        };
+    }
+
+    export function scored(spherePoint: Vec3, c1: Vec3, c2: Vec3, stats: HphobHphil, qmax: number, centroid: Vec3): MembraneCandidate {
+        const diam_vect = Vec3();
+        Vec3.sub(diam_vect, centroid, spherePoint);
+        return {
+            planePoint1: c1,
+            planePoint2: c2,
+            stats: stats,
+            normalVector: diam_vect,
+            spherePoint: spherePoint,
+            qmax: qmax
+        };
+    }
+}
+
+function findMembrane(ctx: ANVILContext, spherePoints: Vec3[], initialStats: HphobHphil, label_comp_id: StructureElement.Property<string>): MembraneCandidate {
+    const { centroid, stepSize, minThickness, maxThickness } = ctx;
+    // best performing membrane
+    let membrane: MembraneCandidate;
+    // score of the best performing membrane
+    let qmax = 0;
+
+    // construct slices of thickness 1.0 along the axis connecting the centroid and the spherePoint
+    const diam = Vec3();
+    for (let i = 0, il = spherePoints.length; i < il; i++) {
+        const spherePoint = spherePoints[i];
+        Vec3.sub(diam, centroid, spherePoint);
+        Vec3.scale(diam, diam, 2);
+        const diamNorm = Vec3.magnitude(diam);
+        const qvartemp = [];
+
+        for (let i = 0, il = diamNorm - stepSize; i < il; i += stepSize) {
+            const c1 = Vec3();
+            const c2 = Vec3();
+            Vec3.scaleAndAdd(c1, spherePoint, diam, i / diamNorm);
+            Vec3.scaleAndAdd(c2, spherePoint, diam, (i + stepSize) / diamNorm);
+
+            // evaluate how well this membrane slice embeddeds the peculiar residues
+            const stats = HphobHphil.filtered(ctx, label_comp_id, (testPoint: Vec3) => isInMembranePlane(testPoint, diam, c1, c2));
+            qvartemp.push(MembraneCandidate.initial(c1, c2, stats));
+        }
+
+        let jmax = (minThickness / stepSize) - 1;
+
+        for (let width = 0, widthl = maxThickness; width < widthl;) {
+            const imax = qvartemp.length - 1 - jmax;
+
+            for (let i = 0, il = imax; i < il; i++) {
+                const c1 = qvartemp[i].planePoint1;
+                const c2 = qvartemp[i + jmax].planePoint2;
+
+                let hphob = 0;
+                let hphil = 0;
+                let total = 0;
+                for (let j = 0; j < jmax; j++) {
+                    const ij = qvartemp[i + j];
+                    if (j === 0 || j === jmax - 1) {
+                        hphob += 0.5 * ij.stats.hphob;
+                        hphil += 0.5 * ij.stats.hphil;
+                    } else {
+                        hphob += ij.stats.hphob;
+                        hphil += ij.stats.hphil;
+                    }
+                    total += ij.stats.total;
+                }
+
+                const stats = HphobHphil.of(hphob, hphil, total);
+
+                if (hphob !== 0) {
+                    const qvaltest = qValue(stats, initialStats);
+                    if (qvaltest > qmax) {
+                        qmax = qvaltest;
+                        membrane = MembraneCandidate.scored(spherePoint, c1, c2, HphobHphil.of(hphob, hphil, total), qmax, centroid);
+                    }
+                }
+            }
+            jmax++;
+            width = (jmax + 1) * stepSize;
+        }
+    }
+
+    return membrane!;
+}
+
+function qValue(currentStats: HphobHphil, initialStats: HphobHphil): number {
+    if(initialStats.hphob < 1) {
+        initialStats.hphob = 0.1;
+    }
+
+    if(initialStats.hphil < 1) {
+        initialStats.hphil += 1;
+    }
+
+    const part_tot = currentStats.hphob + currentStats.hphil;
+    return (currentStats.hphob * (initialStats.hphil - currentStats.hphil) - currentStats.hphil * (initialStats.hphob - currentStats.hphob)) /
+            Math.sqrt(part_tot * initialStats.hphob * initialStats.hphil * (initialStats.hphob + initialStats.hphil - part_tot));
+}
+
+export function isInMembranePlane(testPoint: Vec3, normalVector: Vec3, planePoint1: Vec3, planePoint2: Vec3): boolean {
+    const d1 = -Vec3.dot(normalVector, planePoint1);
+    const d2 = -Vec3.dot(normalVector, planePoint2);
+    const d = -Vec3.dot(normalVector, testPoint);
+    return d > Math.min(d1, d2) && d < Math.max(d1, d2);
+}
+
+// generates a defined number of points on a sphere with radius = extent around the specified centroid
+function generateSpherePoints(ctx: ANVILContext, numberOfSpherePoints: number): Vec3[] {
+    const { centroid, extent } = ctx;
+    const points = [];
+    let oldPhi = 0, h, theta, phi;
+    for(let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) {
+        h = -1 + 2 * (k - 1) / (numberOfSpherePoints - 1);
+        theta = Math.acos(h);
+        phi = (k === 1 || k === numberOfSpherePoints) ? 0 : (oldPhi + 3.6 / Math.sqrt(numberOfSpherePoints * (1 - h * h))) % (2 * Math.PI);
+
+        const point = Vec3.create(
+            extent * Math.sin(phi) * Math.sin(theta) + centroid[0],
+            extent * Math.cos(theta) + centroid[1],
+            extent * Math.cos(phi) * Math.sin(theta) + centroid[2]
+        );
+        points[k - 1] = point;
+        oldPhi = phi;
+    }
+
+    return points;
+}
+
+// generates sphere points close to that of the initial membrane
+function findProximateAxes(ctx: ANVILContext, membrane: MembraneCandidate): Vec3[] {
+    const { numberOfSpherePoints, extent } = ctx;
+    const points = generateSpherePoints(ctx, 30000);
+    let j = 4;
+    let sphere_pts2: Vec3[] = [];
+    while (sphere_pts2.length < numberOfSpherePoints) {
+        const d = 2 * extent / numberOfSpherePoints + j;
+        const dsq = d * d;
+        sphere_pts2 = [];
+        for (let i = 0, il = points.length; i < il; i++) {
+            if (Vec3.squaredDistance(points[i], membrane.spherePoint!) < dsq) {
+                sphere_pts2.push(points[i]);
+            }
+        }
+        j += 0.2;
+    }
+    return sphere_pts2;
+}
+
+interface HphobHphil {
+    hphob: number,
+    hphil: number,
+    total: number
+}
+
+namespace HphobHphil {
+    export function of(hphob: number, hphil: number, total?: number) {
+        return {
+            hphob: hphob,
+            hphil: hphil,
+            total: !!total ? total : hphob + hphil
+        };
+    }
+
+    const testPoint = Vec3();
+    export function filtered(ctx: ANVILContext, label_comp_id: StructureElement.Property<string>, filter?: (test: Vec3) => boolean): HphobHphil {
+        const { offsets, exposed, structure } = ctx;
+        const l = StructureElement.Location.create(structure);
+        const { x, y, z } = StructureProperties.atom;
+        let hphob = 0;
+        let hphil = 0;
+        for (let k = 0, kl = offsets.length; k < kl; k++) {
+            // ignore buried residues
+            if (!exposed[k]) {
+                continue;
+            }
+
+            setLocation(l, structure, offsets[k]);
+            Vec3.set(testPoint, x(l), y(l), z(l));
+
+            // testPoints have to be in putative membrane layer
+            if (filter && !filter(testPoint)) {
+                continue;
+            }
+
+            if (isHydrophobic(label_comp_id(l))) {
+                hphob++;
+            } else {
+                hphil++;
+            }
+        }
+        return of(hphob, hphil);
+    }
+}
+
+// ANVIL-specific (not general) definition of membrane-favoring amino acids
+const HYDROPHOBIC_AMINO_ACIDS = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'THR', 'VAL']);
+export function isHydrophobic(label_comp_id: string): boolean {
+    return HYDROPHOBIC_AMINO_ACIDS.has(label_comp_id);
+}
+
+function setLocation(l: StructureElement.Location, structure: Structure, serialIndex: number) {
+    l.structure = structure;
+    l.unit = structure.units[structure.serialMapping.unitIndices[serialIndex]];
+    l.element = structure.serialMapping.elementIndices[serialIndex];
+    return l;
+}

src/extensions/anvil/behavior.ts

@@ -0,0 +1,174 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { MembraneOrientationProvider, MembraneOrientation } from './prop';
+import { StateObjectRef, StateTransformer, StateTransform } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { PluginBehavior } from '../../mol-plugin/behavior';
+import { MembraneOrientationRepresentationProvider, MembraneOrientationParams, MembraneOrientationRepresentation } from './representation';
+import { HydrophobicityColorThemeProvider } from '../../mol-theme/color/hydrophobicity';
+import { PluginStateObject, PluginStateTransform } from '../../mol-plugin-state/objects';
+import { PluginContext } from '../../mol-plugin/context';
+import { DefaultQueryRuntimeTable } from '../../mol-script/runtime/query/compiler';
+import { StructureSelectionQuery, StructureSelectionCategory } from '../../mol-plugin-state/helpers/structure-selection-query';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { GenericRepresentationRef } from '../../mol-plugin-state/manager/structure/hierarchy-state';
+
+const Tag = MembraneOrientation.Tag;
+
+export const ANVILMembraneOrientation = PluginBehavior.create<{ autoAttach: boolean }>({
+    name: 'anvil-membrane-orientation-prop',
+    category: 'custom-props',
+    display: {
+        name: 'Membrane Orientation',
+        description: 'Data calculated with ANVIL algorithm.'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean }> {
+        private provider = MembraneOrientationProvider
+
+        register(): void {
+            DefaultQueryRuntimeTable.addCustomProp(this.provider.descriptor);
+
+            this.ctx.customStructureProperties.register(this.provider, this.params.autoAttach);
+
+            this.ctx.representation.structure.registry.add(MembraneOrientationRepresentationProvider);
+            this.ctx.query.structure.registry.add(isTransmembrane);
+
+            this.ctx.genericRepresentationControls.set(Tag.Representation, selection => {
+                const refs: GenericRepresentationRef[] = [];
+                selection.structures.forEach(structure => {
+                    const memRepr = structure.genericRepresentations?.filter(r => r.cell.transform.transformer.id === MembraneOrientation3D.id)[0];
+                    if (memRepr) refs.push(memRepr);
+                });
+                return [refs, 'Membrane Orientation'];
+            });
+            this.ctx.builders.structure.representation.registerPreset(MembraneOrientationPreset);
+        }
+
+        update(p: { autoAttach: boolean }) {
+            let updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+
+        unregister() {
+            DefaultQueryRuntimeTable.removeCustomProp(this.provider.descriptor);
+
+            this.ctx.customStructureProperties.unregister(this.provider.descriptor.name);
+
+            this.ctx.representation.structure.registry.remove(MembraneOrientationRepresentationProvider);
+            this.ctx.query.structure.registry.remove(isTransmembrane);
+
+            this.ctx.genericRepresentationControls.delete(Tag.Representation);
+            this.ctx.builders.structure.representation.unregisterPreset(MembraneOrientationPreset);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(false)
+    })
+});
+
+//
+
+export const isTransmembrane = StructureSelectionQuery('Residues Embedded in Membrane', MS.struct.modifier.union([
+    MS.struct.modifier.wholeResidues([
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'atom-test': MembraneOrientation.symbols.isTransmembrane.symbol(),
+            })
+        ])
+    ])
+]), {
+    description: 'Select residues that are embedded between the membrane layers.',
+    category: StructureSelectionCategory.Residue,
+    ensureCustomProperties: (ctx, structure) => {
+        return MembraneOrientationProvider.attach(ctx, structure);
+    }
+});
+
+//
+
+export { MembraneOrientation3D };
+
+type MembraneOrientation3D = typeof MembraneOrientation3D
+const MembraneOrientation3D = PluginStateTransform.BuiltIn({
+    name: 'membrane-orientation-3d',
+    display: {
+        name: 'Membrane Orientation',
+        description: 'Membrane Orientation planes and rims. Data calculated with ANVIL algorithm.'
+    },
+    from: PluginStateObject.Molecule.Structure,
+    to: PluginStateObject.Shape.Representation3D,
+    params: (a) => {
+        return {
+            ...MembraneOrientationParams,
+        };
+    }
+})({
+    canAutoUpdate({ oldParams, newParams }) {
+        return true;
+    },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Membrane Orientation', async ctx => {
+            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            const repr = MembraneOrientationRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => MembraneOrientationParams);
+            await repr.createOrUpdate(params, a.data).runInContext(ctx);
+            return new PluginStateObject.Shape.Representation3D({ repr, source: a }, { label: 'Membrane Orientation' });
+        });
+    },
+    update({ a, b, newParams }, plugin: PluginContext) {
+        return Task.create('Membrane Orientation', async ctx => {
+            await MembraneOrientationProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, a.data);
+            const props = { ...b.data.repr.props, ...newParams };
+            await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
+            return StateTransformer.UpdateResult.Updated;
+        });
+    },
+    isApplicable(a) {
+        return MembraneOrientationProvider.isApplicable(a.data);
+    }
+});
+
+export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
+    id: 'preset-membrane-orientation',
+    display: {
+        name: 'Membrane Orientation', group: 'Annotation',
+        description: 'Shows orientation of membrane layers. Data calculated with ANVIL algorithm.' // TODO add ' or obtained via RCSB PDB'
+    },
+    isApplicable(a) {
+        return MembraneOrientationProvider.isApplicable(a.data);
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const structure  = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
+
+        if (!MembraneOrientationProvider.get(structure).value) {
+            await plugin.runTask(Task.create('Membrane Orientation', async runtime => {
+                await MembraneOrientationProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure);
+            }));
+        }
+
+        const membraneOrientation = await tryCreateMembraneOrientation(plugin, structureCell);
+        const colorTheme = HydrophobicityColorThemeProvider.name as any;
+        const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
+
+        return { components: preset.components, representations: { ...preset.representations, membraneOrientation } };
+    }
+});
+
+export function tryCreateMembraneOrientation(plugin: PluginContext, structure: StateObjectRef<PluginStateObject.Molecule.Structure>, params?: StateTransformer.Params<MembraneOrientation3D>, initialState?: Partial<StateTransform.State>) {
+    const state = plugin.state.data;
+    const membraneOrientation = state.build().to(structure)
+        .applyOrUpdateTagged('membrane-orientation-3d', MembraneOrientation3D, params, { state: initialState });
+    return membraneOrientation.commit({ revertOnError: true });
+}

src/extensions/anvil/prop.ts

@@ -0,0 +1,82 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Structure, StructureProperties, Unit } from '../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
+import { ANVILParams, ANVILProps, computeANVIL, isInMembranePlane } from './algorithm';
+import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
+import { CustomProperty } from '../../mol-model-props/common/custom-property';
+import { AccessibleSurfaceAreaProvider } from '../../mol-model-props/computed/accessible-surface-area';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
+import { CustomPropSymbol } from '../../mol-script/language/symbol';
+import { Type } from '../../mol-script/language/type';
+
+export const MembraneOrientationParams = {
+    ...ANVILParams
+};
+export type MembraneOrientationParams = typeof MembraneOrientationParams
+export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
+
+export { MembraneOrientation };
+
+interface MembraneOrientation {
+    // point in membrane boundary
+    readonly planePoint1: Vec3,
+    // point in opposite side of membrane boundary
+    readonly planePoint2: Vec3,
+    // normal vector of membrane layer
+    readonly normalVector: Vec3,
+    // the radius of the membrane layer
+    readonly radius: number,
+    readonly centroid: Vec3
+}
+
+namespace MembraneOrientation {
+    export enum Tag {
+        Representation = 'membrane-orientation-3d'
+    }
+
+    const pos = Vec3();
+    export const symbols = {
+        isTransmembrane: QuerySymbolRuntime.Dynamic(CustomPropSymbol('computed', 'membrane-orientation.is-transmembrane', Type.Bool),
+            ctx => {
+                const { unit, structure } = ctx.element;
+                const { x, y, z } = StructureProperties.atom;
+                if (!Unit.isAtomic(unit)) return 0;
+                const membraneOrientation = MembraneOrientationProvider.get(structure).value;
+                if (!membraneOrientation) return 0;
+                Vec3.set(pos, x(ctx.element), y(ctx.element), z(ctx.element));
+                const { normalVector, planePoint1, planePoint2 } = membraneOrientation!;
+                return isInMembranePlane(pos, normalVector, planePoint1, planePoint2);
+            })
+    };
+}
+
+export const MembraneOrientationProvider: CustomStructureProperty.Provider<MembraneOrientationParams, MembraneOrientation> = CustomStructureProperty.createProvider({
+    label: 'Membrane Orientation',
+    descriptor: CustomPropertyDescriptor({
+        name: 'anvil_computed_membrane_orientation',
+        symbols: MembraneOrientation.symbols,
+        // TODO `cifExport`
+    }),
+    type: 'root',
+    defaultParams: MembraneOrientationParams,
+    getParams: (data: Structure) => MembraneOrientationParams,
+    isApplicable: (data: Structure) => true,
+    obtain: async (ctx: CustomProperty.Context, data: Structure, props: Partial<MembraneOrientationProps>) => {
+        const p = { ...PD.getDefaultValues(MembraneOrientationParams), ...props };
+        return { value: await computeAnvil(ctx, data, p) };
+    }
+});
+
+async function computeAnvil(ctx: CustomProperty.Context, data: Structure, props: Partial<ANVILProps>): Promise<MembraneOrientation> {
+    await AccessibleSurfaceAreaProvider.attach(ctx, data);
+    const p = { ...PD.getDefaultValues(ANVILParams), ...props };
+    return await computeANVIL(data, p).runInContext(ctx.runtime);
+}

src/extensions/anvil/representation.ts

@@ -0,0 +1,156 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
+ */
+
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
+import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../mol-repr/representation';
+import { Structure } from '../../mol-model/structure';
+import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
+import { StructureRepresentationProvider, StructureRepresentation, StructureRepresentationStateBuilder } from '../../mol-repr/structure/representation';
+import { MembraneOrientation } from './prop';
+import { ThemeRegistryContext } from '../../mol-theme/theme';
+import { ShapeRepresentation } from '../../mol-repr/shape/representation';
+import { Shape } from '../../mol-model/shape';
+import { RuntimeContext } from '../../mol-task';
+import { Lines } from '../../mol-geo/geometry/lines/lines';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { LinesBuilder } from '../../mol-geo/geometry/lines/lines-builder';
+import { Circle } from '../../mol-geo/primitive/circle';
+import { transformPrimitive } from '../../mol-geo/primitive/primitive';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+import { MembraneOrientationProvider } from './prop';
+import { MarkerActions } from '../../mol-util/marker-action';
+import { lociLabel } from '../../mol-theme/label';
+import { ColorNames } from '../../mol-util/color/names';
+import { CustomProperty } from '../../mol-model-props/common/custom-property';
+
+const SharedParams = {
+    color: PD.Color(ColorNames.lightgrey),
+    radiusFactor: PD.Numeric(0.8333, { min: 0.1, max: 3.0, step: 0.01 }, { description: 'Scale the radius of the membrane layer' })
+};
+
+const BilayerSpheresParams = {
+    ...Spheres.Params,
+    ...SharedParams,
+    sphereSize: PD.Numeric(1, { min: 0.1, max: 10, step: 0.1 }, { description: 'Size of spheres that represent membrane planes' }),
+    density: PD.Numeric(1, { min: 0.25, max: 10, step: 0.25 }, { description: 'Distance between spheres'})
+};
+export type BilayerSpheresParams = typeof BilayerSpheresParams
+export type BilayerSpheresProps = PD.Values<BilayerSpheresParams>
+
+const BilayerPlanesParams = {
+    ...Mesh.Params,
+    ...SharedParams,
+    sectorOpacity: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }),
+};
+export type BilayerPlanesParams = typeof BilayerPlanesParams
+export type BilayerPlanesProps = PD.Values<BilayerPlanesParams>
+
+const BilayerRimsParams = {
+    ...Lines.Params,
+    ...SharedParams,
+    lineSizeAttenuation: PD.Boolean(true),
+    linesSize: PD.Numeric(0.3, { min: 0.01, max: 50, step: 0.01 }),
+    dashedLines: PD.Boolean(true),
+};
+export type BilayerRimsParams = typeof BilayerRimsParams
+export type BilayerRimsProps = PD.Values<BilayerRimsParams>
+
+const MembraneOrientationVisuals = {
+    'bilayer-planes': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneOrientation, BilayerPlanesParams>) => ShapeRepresentation(getBilayerPlanes, Mesh.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }), modifyProps: p => ({ ...p, alpha: p.sectorOpacity, ignoreLight: true, doubleSided: false }) }),
+    'bilayer-rims': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneOrientation, BilayerRimsParams>) => ShapeRepresentation(getBilayerRims, Lines.Utils, { modifyState: s => ({ ...s, markerActions: MarkerActions.Highlighting }) })
+};
+
+export const MembraneOrientationParams = {
+    ...BilayerSpheresParams,
+    ...BilayerPlanesParams,
+    ...BilayerRimsParams,
+    visuals: PD.MultiSelect(['bilayer-planes', 'bilayer-rims'], PD.objectToOptions(MembraneOrientationVisuals)),
+};
+export type MembraneOrientationParams = typeof MembraneOrientationParams
+export type MembraneOrientationProps = PD.Values<MembraneOrientationParams>
+
+export function getMembraneOrientationParams(ctx: ThemeRegistryContext, structure: Structure) {
+    return PD.clone(MembraneOrientationParams);
+}
+
+export type MembraneOrientationRepresentation = StructureRepresentation<MembraneOrientationParams>
+export function MembraneOrientationRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MembraneOrientationParams>): MembraneOrientationRepresentation {
+    return Representation.createMulti('Membrane Orientation', ctx, getParams, StructureRepresentationStateBuilder, MembraneOrientationVisuals as unknown as Representation.Def<Structure, MembraneOrientationParams>);
+}
+
+export const MembraneOrientationRepresentationProvider = StructureRepresentationProvider({
+    name: 'membrane-orientation',
+    label: 'Membrane Orientation',
+    description: 'Displays a grid of points representing membrane layers.',
+    factory: MembraneOrientationRepresentation,
+    getParams: getMembraneOrientationParams,
+    defaultValues: PD.getDefaultValues(MembraneOrientationParams),
+    defaultColorTheme: { name: 'shape-group' },
+    defaultSizeTheme: { name: 'shape-group' },
+    isApplicable: (structure: Structure) => structure.elementCount > 0,
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, structure: Structure) => MembraneOrientationProvider.attach(ctx, structure, void 0, true),
+        detach: (data) => MembraneOrientationProvider.ref(data, false)
+    }
+});
+
+function membraneLabel(data: Structure) {
+    return `${lociLabel(Structure.Loci(data))} | Membrane Orientation`;
+}
+
+function getBilayerRims(ctx: RuntimeContext, data: Structure, props: BilayerRimsProps, shape?: Shape<Lines>): Shape<Lines> {
+    const { planePoint1: p1, planePoint2: p2, centroid, normalVector: normal, radius } = MembraneOrientationProvider.get(data).value!;
+    const scaledRadius = props.radiusFactor * radius;
+    const builder = LinesBuilder.create(128, 64, shape?.geometry);
+    getLayerCircle(builder, p1, centroid, normal, scaledRadius, props);
+    getLayerCircle(builder, p2, centroid, normal, scaledRadius, props);
+    return Shape.create('Bilayer rims', data, builder.getLines(), () => props.color, () => props.linesSize, () => membraneLabel(data));
+}
+
+function getLayerCircle(builder: LinesBuilder, p: Vec3, centroid: Vec3, normal: Vec3, radius: number, props: BilayerRimsProps, shape?: Shape<Lines>) {
+    const circle = getCircle(p, centroid, normal, radius);
+    const { indices, vertices } = circle;
+    for (let j = 0, jl = indices.length; j < jl; j += 3) {
+        if (props.dashedLines && j % 2 === 1) continue; // draw every other segment to get dashes
+        const start = indices[j] * 3;
+        const end = indices[j + 1] * 3;
+        const startX = vertices[start];
+        const startY = vertices[start + 1];
+        const startZ = vertices[start + 2];
+        const endX = vertices[end];
+        const endY = vertices[end + 1];
+        const endZ = vertices[end + 2];
+        builder.add(startX, startY, startZ, endX, endY, endZ, 0);
+    }
+}
+
+const tmpMat = Mat4();
+function getCircle(p: Vec3, centroid: Vec3, normal: Vec3, radius: number) {
+    Mat4.targetTo(tmpMat, p, centroid, normal);
+    Mat4.setTranslation(tmpMat, p);
+    Mat4.mul(tmpMat, tmpMat, Mat4.rotX90);
+
+    const circle = Circle({ radius, segments: 64 });
+    return transformPrimitive(circle, tmpMat);
+}
+
+function getBilayerPlanes(ctx: RuntimeContext, data: Structure, props: BilayerPlanesProps, shape?: Shape<Mesh>): Shape<Mesh> {
+    const { planePoint1: p1, planePoint2: p2, centroid, normalVector: normal, radius } = MembraneOrientationProvider.get(data).value!;
+    const state = MeshBuilder.createState(128, 64, shape && shape.geometry);
+    const scaledRadius = props.radiusFactor * radius;
+    getLayerPlane(state, p1, centroid, normal, scaledRadius);
+    getLayerPlane(state, p2, centroid, normal, scaledRadius);
+    return Shape.create('Bilayer planes', data, MeshBuilder.getMesh(state), () => props.color, () => 1, () => membraneLabel(data));
+}
+
+function getLayerPlane(state: MeshBuilder.State, p: Vec3, centroid: Vec3, normal: Vec3, radius: number) {
+    const circle = getCircle(p, centroid, normal, radius);
+    state.currentGroup = 0;
+    MeshBuilder.addPrimitive(state, Mat4.id, circle);
+    MeshBuilder.addPrimitiveFlipped(state, Mat4.id, circle);
+}

src/extensions/cellpack/color/generate.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>
  */
@@ -10,7 +10,7 @@ import { Color } from '../../../mol-util/color';
 import { getPalette } from '../../../mol-util/color/palette';
 import { ColorTheme, LocationColor } from '../../../mol-theme/color';
 import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
-import { StructureElement, Bond } from '../../../mol-model/structure';
+import { StructureElement, Bond, Model } from '../../../mol-model/structure';
 import { Location } from '../../../mol-model/location';
 import { CellPackInfoProvider } from '../property';
 import { distinctColors } from '../../../mol-util/color/distinct';
@@ -40,28 +40,27 @@ export function CellPackGenerateColorTheme(ctx: ThemeDataContext, props: PD.Valu
         const { models } = ctx.structure.root;
 
         let size = 0;
-        for (const m of models) size = Math.max(size, m.trajectoryInfo.size);
+        for (const m of models) size = Math.max(size, Model.TrajectoryInfo.get(m).size);
 
         const palette = getPalette(size, { palette: {
             name: 'generate',
             params: {
                 hue, chroma: [30, 80], luminance: [15, 85],
-                clusteringStepCount: 50, minSampleCount: 800, maxCount: 75,
-                minLabel: 'Min', maxLabel: 'Max', valueLabel: (i: number) => `${i + 1}`,
+                clusteringStepCount: 50, minSampleCount: 800, maxCount: 75
             }
-        }});
+        }}, { minLabel: 'Min', maxLabel: 'Max' });
         legend = palette.legend;
         const modelColor = new Map<number, Color>();
         for (let i = 0, il = models.length; i < il; ++i) {
-            const idx = models[i].trajectoryInfo.index;
-            modelColor.set(models[i].trajectoryInfo.index, palette.color(idx));
+            const idx = Model.TrajectoryInfo.get(models[i]).index;
+            modelColor.set(Model.TrajectoryInfo.get(models[i]).index, palette.color(idx));
         }
 
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location)) {
-                return modelColor.get(location.unit.model.trajectoryInfo.index)!;
+                return modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!;
             } else if (Bond.isLocation(location)) {
-                return modelColor.get(location.aUnit.model.trajectoryInfo.index)!;
+                return modelColor.get(Model.TrajectoryInfo.get(location.aUnit.model).index)!;
             }
             return DefaultColor;
         };
@@ -89,7 +88,6 @@ export const CellPackGenerateColorThemeProvider: ColorTheme.Provider<CellPackGen
     isApplicable: (ctx: ThemeDataContext) => {
         return (
             !!ctx.structure && ctx.structure.elementCount > 0 &&
-            ctx.structure.models[0].trajectoryInfo.size > 1 &&
             !!CellPackInfoProvider.get(ctx.structure).value
         );
     }

src/extensions/cellpack/color/provided.ts

@@ -9,7 +9,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Color } from '../../../mol-util/color';
 import { ColorTheme, LocationColor } from '../../../mol-theme/color';
 import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
-import { StructureElement } from '../../../mol-model/structure';
+import { StructureElement, Model, Bond } from '../../../mol-model/structure';
 import { Location } from '../../../mol-model/location';
 import { CellPackInfoProvider } from '../property';
 
@@ -32,14 +32,17 @@ export function CellPackProvidedColorTheme(ctx: ThemeDataContext, props: PD.Valu
         const { models } = ctx.structure.root;
         const modelColor = new Map<number, Color>();
         for (let i = 0, il = models.length; i < il; ++i) {
-            const idx = models[i].trajectoryInfo.index;
-            modelColor.set(models[i].trajectoryInfo.index, info.colors[idx]);
+            const idx = Model.TrajectoryInfo.get(models[i]).index;
+            modelColor.set(Model.TrajectoryInfo.get(models[i]).index, info.colors[idx]);
         }
 
         color = (location: Location): Color => {
-            return StructureElement.Location.is(location)
-                ? modelColor.get(location.unit.model.trajectoryInfo.index)!
-                : DefaultColor;
+            if (StructureElement.Location.is(location)) {
+                return modelColor.get(Model.TrajectoryInfo.get(location.unit.model).index)!;
+            } else if (Bond.isLocation(location)) {
+                return modelColor.get(Model.TrajectoryInfo.get(location.aUnit.model).index)!;
+            }
+            return DefaultColor;
         };
     } else {
         color = () => DefaultColor;
@@ -65,7 +68,7 @@ export const CellPackProvidedColorThemeProvider: ColorTheme.Provider<CellPackPro
     isApplicable: (ctx: ThemeDataContext) => {
         return (
             !!ctx.structure && ctx.structure.elementCount > 0 &&
-            ctx.structure.models[0].trajectoryInfo.size > 1 &&
+            Model.TrajectoryInfo.get(ctx.structure.models[0]).size > 1 &&
             !!CellPackInfoProvider.get(ctx.structure).value?.colors
         );
     }

src/extensions/cellpack/model.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>
  */
@@ -10,7 +10,7 @@ import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Ingredient, IngredientSource, CellPacking } from './data';
 import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean, getFromOPM } from './util';
-import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../mol-model/structure';
+import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit, Trajectory } from '../../mol-model/structure';
 import { trajectoryFromMmCIF, MmcifFormat } from '../../mol-model-formats/structure/mmcif';
 import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
 import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
@@ -36,8 +36,8 @@ function getCellPackModelUrl(fileName: string, baseUrl: string) {
 }
 
 class TrajectoryCache {
-    private map = new Map<string, Model.Trajectory>();
-    set(id: string, trajectory: Model.Trajectory) { this.map.set(id, trajectory); }
+    private map = new Map<string, Trajectory>();
+    set(id: string, trajectory: Trajectory) { this.map.set(id, trajectory); }
     get(id: string) { return this.map.get(id); }
 }
 
@@ -94,9 +94,9 @@ async function getModel(plugin: PluginContext, id: string, ingredient: Ingredien
                 trajectory = await plugin.runTask(trajectoryFromMmCIF(data.mmcif));
             }
         }
-        trajCache.set(id, trajectory);
+        trajCache.set(id, trajectory!);
     }
-    const model = trajectory[modelIndex];
+    const model = await plugin.resolveTask(trajectory?.getFrameAtIndex(modelIndex)!);
     return { model, assets };
 }
 
@@ -303,7 +303,7 @@ async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredi
     const curveModelTask = Task.create('Curve Model', async ctx => {
         const format = MmcifFormat.fromFrame(cif);
         const models = await createModels(format.data.db, format, ctx);
-        return models[0];
+        return models.representative;
     });
 
     const curveModel = await plugin.runTask(curveModelTask);
@@ -396,25 +396,27 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
         }
 
         if (ctx.shouldUpdate) await ctx.update(`${name} - units`);
-        const builder = Structure.Builder({ label: name });
+        const units: Unit[] = [];
         let offsetInvariantId = 0;
+        let offsetChainGroupId = 0;
         for (const s of structures) {
             if (ctx.shouldUpdate) await ctx.update(`${s.label}`);
             let maxInvariantId = 0;
+            let maxChainGroupId = 0;
             for (const u of s.units) {
                 const invariantId = u.invariantId + offsetInvariantId;
+                const chainGroupId = u.chainGroupId + offsetChainGroupId;
                 if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
-                builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
+                units.push(Unit.create(units.length, invariantId, chainGroupId, u.traits, u.kind, u.model, u.conformation.operator, u.elements, u.props));
             }
             offsetInvariantId += maxInvariantId + 1;
+            offsetChainGroupId += maxChainGroupId + 1;
         }
 
         if (ctx.shouldUpdate) await ctx.update(`${name} - structure`);
-        const structure = builder.getStructure();
+        const structure = new Structure(units);
         for( let i = 0, il = structure.models.length; i < il; ++i) {
-            const { trajectoryInfo } = structure.models[i];
-            trajectoryInfo.size = il;
-            trajectoryInfo.index = i;
+            Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
         }
         return { structure, assets, colors: skipColors ? undefined : colors };
     });
@@ -444,9 +446,9 @@ async function handleHivRna(plugin: PluginContext, packings: CellPacking[], base
 
 async function loadMembrane(plugin: PluginContext, name: string, state: State, params: LoadCellPackModelParams) {
     let file: Asset.File | undefined = undefined;
-    if (params.ingredients.files !== null) {
+    if (params.ingredients !== null) {
         const fileName = `${name}.bcif`;
-        for (const f of params.ingredients.files) {
+        for (const f of params.ingredients) {
             if (fileName === f.name) {
                 file = f;
                 break;
@@ -455,7 +457,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
         if (!file){
             // check for cif directly
             const cifileName = `${name}.cif`;
-            for (const f of params.ingredients.files) {
+            for (const f of params.ingredients) {
                 if (cifileName === f.name) {
                     file = f;
                     break;
@@ -490,7 +492,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
 }
 
 async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
-    const ingredientFiles = params.ingredients.files || [];
+    const ingredientFiles = params.ingredients || [];
 
     let cellPackJson: StateBuilder.To<PSO.Format.Json, StateTransformer<PSO.Data.String, PSO.Format.Json>>;
     if (params.source.name === 'id') {
@@ -565,9 +567,7 @@ const LoadCellPackModelParams = {
     }, { options: [['id', 'Id'], ['file', 'File']] }),
     baseUrl: PD.Text(DefaultCellPackBaseUrl),
     membrane: PD.Boolean(true),
-    ingredients : PD.Group({
-        files: PD.FileList({ accept: '.cif,.bcif,.pdb' })
-    }, { isExpanded: true }),
+    ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredients' }),
     preset: PD.Group({
         traceOnly: PD.Boolean(false),
         representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation']))

src/extensions/cellpack/state.ts

@@ -13,7 +13,7 @@ import { IngredientFiles } from './util';
 import { Asset } from '../../mol-util/assets';
 import { PluginContext } from '../../mol-plugin/context';
 import { CellPackInfoProvider } from './property';
-import { Structure, StructureSymmetry, Unit } from '../../mol-model/structure';
+import { Structure, StructureSymmetry, Unit, Model } from '../../mol-model/structure';
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 
 export const DefaultCellPackBaseUrl = 'https://mesoscope.scripps.edu/data/cellPACK_data/cellPACK_database_1.1.0/';
@@ -125,7 +125,7 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
                     const s = await StructureSymmetry.buildAssembly(initial_structure, a.id).runInContext(ctx);
                     structures.push(s);
                 }
-                const builder = Structure.Builder({ label: name });
+                const builder = Structure.Builder();
                 let offsetInvariantId = 0;
                 for (const s of structures) {
                     let maxInvariantId = 0;
@@ -138,9 +138,7 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
                 }
                 structure = builder.getStructure();
                 for( let i = 0, il = structure.models.length; i < il; ++i) {
-                    const { trajectoryInfo } = structure.models[i];
-                    trajectoryInfo.size = il;
-                    trajectoryInfo.index = i;
+                    Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
                 }
             }
             return new PSO.Molecule.Structure(structure, { label: a.label, description: `${a.description}` });
@@ -150,55 +148,3 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
         b?.data.customPropertyDescriptors.dispose();
     }
 });
-
-// export { GetAllAssamblyinOneStructure };
-// type GetAllAssamblyinOneStructure = typeof GetAllAssamblyinOneStructure
-// const GetAllAssamblyinOneStructure = PluginStateTransform.BuiltIn({
-//     name: 'get assambly from structure',
-//     display: { name: 'get assambly from structure' },
-//     isDecorator: true,
-//     from: PSO.Molecule.Structure,
-//     to: PSO.Molecule.Structure,
-//     params(a) {
-//         return { };
-//     }
-// })({
-//     apply({ a, params }) {
-//         return Task.create('Build Structure Assemblies', async ctx => {
-//             // TODO: optimze
-//             // TODO: think of ways how to fast-track changes to this for animations
-//             const initial_structure = a.data;
-//             const structures: Structure[] = [];
-//             let structure: Structure = initial_structure;
-//             // the list of asambly *?
-//             const symmetry = ModelSymmetry.Provider.get(initial_structure.model);
-//             if (symmetry){
-//                 if (symmetry.assemblies.length !== 0) {
-//                     for (const a of symmetry.assemblies) {
-//                         const s = await StructureSymmetry.buildAssembly(initial_structure, a.id!).runInContext(ctx);
-//                         structures.push(s);
-//                     }
-//                     const builder = Structure.Builder({ label: name });
-//                     let offsetInvariantId = 0;
-//                     for (const s of structures) {
-//                         let maxInvariantId = 0;
-//                         for (const u of s.units) {
-//                             const invariantId = u.invariantId + offsetInvariantId;
-//                             if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
-//                             builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
-//                         }
-//                         offsetInvariantId += maxInvariantId + 1;
-//                     }
-//                     structure = builder.getStructure();
-//                     for( let i = 0, il = structure.models.length; i < il; ++i) {
-//                         const { trajectoryInfo } = structure.models[i];
-//                         trajectoryInfo.size = il;
-//                         trajectoryInfo.index = i;
-//                     }
-//                 }
-//             }
-//             return new PSO.Molecule.Structure(structure, { label: a.label, description: `${a.description}` });
-//         });
-//     }
-// });
-

src/extensions/dnatco/README.md

@@ -0,0 +1,10 @@
+## DNATCO Extensions
+
+### Confal Pyramids
+
+The Confal Pyramids extensions displays tetrahedron-like pyramids. These pyramids are a simple visual representation of nucleotide conformer classes that can be assigned to individual steps in nucleic acid structures.
+
+For more information, see:
+* [Černý et al., Nucleic Acids Research, 44, W284 (2016)](http://dx.doi.org/10.1093/nar/gkw381)
+* [Schneider et al., Acta Cryst D, 74, 52-64 (2018)](http://dx.doi.org/10.1107/S2059798318000050)
+* [Schneider et al., Genes, 8(10), 278, (2017)](http://dx.doi.org/10.3390/genes8100278)

src/extensions/dnatco/confal-pyramids/behavior.ts

@@ -0,0 +1,103 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { ConfalPyramidsColorThemeProvider } from './color';
+import { ConfalPyramids, ConfalPyramidsProvider } from './property';
+import { ConfalPyramidsRepresentationProvider } from './representation';
+import { Loci } from '../../../mol-model/loci';
+import { PluginBehavior } from '../../../mol-plugin/behavior/behavior';
+import { StructureRepresentationPresetProvider, PresetStructureRepresentations } from '../../../mol-plugin-state/builder/structure/representation-preset';
+import { StateObjectRef } from '../../../mol-state';
+import { Task } from '../../../mol-task';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+
+export const DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider({
+    id: 'preset-structure-representation-confal-pyramids',
+    display: {
+        name: 'Confal Pyramids', group: 'Annotation',
+        description: 'Schematic depiction of conformer class and confal value.',
+    },
+    isApplicable(a) {
+        return a.data.models.length >= 1 && a.data.models.some(m => ConfalPyramids.isApplicable(m));
+    },
+    params: () => StructureRepresentationPresetProvider.CommonParams,
+    async apply(ref, params, plugin) {
+        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
+        const model = structureCell?.obj?.data.model;
+        if (!structureCell || !model) return {};
+
+        await plugin.runTask(Task.create('Confal Pyramids', async runtime => {
+            await ConfalPyramidsProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+        }));
+
+        const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params }, plugin);
+
+        const pyramids = await plugin.builders.structure.tryCreateComponentStatic(structureCell, 'nucleic', { label: 'Confal Pyramids' });
+        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, params);
+
+        let pyramidsRepr;
+        if (representations)
+            pyramidsRepr = builder.buildRepresentation(update, pyramids,  { type: ConfalPyramidsRepresentationProvider, typeParams, color: ConfalPyramidsColorThemeProvider }, { tag: 'confal-pyramdis' } );
+
+        await update.commit({ revertOnError: true });
+        return  { components: { ...components, pyramids }, representations: { ...representations, pyramidsRepr } };
+    }
+});
+
+export const DnatcoConfalPyramids = PluginBehavior.create<{ autoAttach: boolean, showToolTip: boolean }>({
+    name: 'dnatco-confal-pyramids-prop',
+    category: 'custom-props',
+    display: {
+        name: 'Confal Pyramids',
+        description: 'Schematic depiction of conformer class and confal value.',
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showToolTip: boolean }> {
+
+        private provider = ConfalPyramidsProvider;
+
+        private labelConfalPyramids = {
+            label: (loci: Loci): string | undefined => {
+                if (!this.params.showToolTip) return void 0;
+
+                /* TODO: Implement this */
+                return void 0;
+            }
+        }
+
+        register(): void {
+            this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
+            this.ctx.managers.lociLabels.addProvider(this.labelConfalPyramids);
+
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(ConfalPyramidsColorThemeProvider);
+            this.ctx.representation.structure.registry.add(ConfalPyramidsRepresentationProvider);
+
+            this.ctx.builders.structure.representation.registerPreset(DnatcoConfalPyramidsPreset);
+        }
+
+        update(p: { autoAttach: boolean, showToolTip: boolean }) {
+            const updated = this.params.autoAttach !== p.autoAttach;
+            this.params.autoAttach = p.autoAttach;
+            this.params.showToolTip = p.showToolTip;
+            this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
+            return updated;
+        }
+
+        unregister() {
+            this.ctx.customModelProperties.unregister(ConfalPyramidsProvider.descriptor.name);
+            this.ctx.managers.lociLabels.removeProvider(this.labelConfalPyramids);
+
+            this.ctx.representation.structure.registry.remove(ConfalPyramidsRepresentationProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(ConfalPyramidsColorThemeProvider);
+
+            this.ctx.builders.structure.representation.unregisterPreset(DnatcoConfalPyramidsPreset);
+        }
+    },
+    params: () => ({
+        autoAttach: PD.Boolean(true),
+        showToolTip: PD.Boolean(true)
+    })
+});

src/extensions/dnatco/confal-pyramids/color.ts

@@ -0,0 +1,186 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { ConfalPyramids, ConfalPyramidsProvider } from './property';
+import { ConfalPyramidsTypes as CPT } from './types';
+import { Location } from '../../../mol-model/location';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { ColorTheme } from '../../../mol-theme/color';
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { Color } from '../../../mol-util/color';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { TableLegend } from '../../../mol-util/legend';
+import { iterableToArray } from '../../../mol-data/util';
+
+const DefaultColor = Color(0xCCCCCC);
+const Description = 'Assigns colors to confal pyramids';
+const ErrorColor = Color(0xFFA10A);
+
+type ConformerClasses = 'A' | 'B' | 'BII' | 'miB' | 'Z' | 'IC' | 'OPN' | 'SYN' | 'N';
+
+const ColorMapping: ReadonlyMap<ConformerClasses, Color> = new Map([
+    ['A', Color(0xFFC1C1)],
+    ['B', Color(0xC8CFFF)],
+    ['BII', Color(0x0059DA)],
+    ['miB', Color(0x3BE8FB)],
+    ['Z',  Color(0x01F60E)],
+    ['IC', Color(0xFA5CFB)],
+    ['OPN', Color(0xE90000)],
+    ['SYN', Color(0xFFFF01)],
+    ['N', Color(0xF2F2F2)],
+]);
+
+const NtCToClasses: ReadonlyMap<string, [ConformerClasses, ConformerClasses]> = new Map([
+    ['NANT', ['N', 'N']],
+    ['AA00', ['A', 'A']],
+    ['AA02', ['A', 'A']],
+    ['AA03', ['A', 'A']],
+    ['AA04', ['A', 'A']],
+    ['AA08', ['A', 'A']],
+    ['AA09', ['A', 'A']],
+    ['AA01', ['A', 'A']],
+    ['AA05', ['A', 'A']],
+    ['AA06', ['A', 'A']],
+    ['AA10', ['A', 'A']],
+    ['AA11', ['A', 'A']],
+    ['AA07', ['A', 'A']],
+    ['AA12', ['A', 'A']],
+    ['AA13', ['A', 'A']],
+    ['AB01', ['A', 'B']],
+    ['AB02', ['A', 'B']],
+    ['AB03', ['A', 'B']],
+    ['AB04', ['A', 'B']],
+    ['AB05', ['A', 'B']],
+    ['BA01', ['B', 'A']],
+    ['BA05', ['B', 'A']],
+    ['BA09', ['B', 'A']],
+    ['BA08', ['BII', 'A']],
+    ['BA10', ['B', 'A']],
+    ['BA13', ['BII', 'A']],
+    ['BA16', ['BII', 'A']],
+    ['BA17', ['BII', 'A']],
+    ['BB00', ['B', 'B']],
+    ['BB01', ['B', 'B']],
+    ['BB17', ['B', 'B']],
+    ['BB02', ['B', 'B']],
+    ['BB03', ['B', 'B']],
+    ['BB11', ['B', 'B']],
+    ['BB16', ['B', 'B']],
+    ['BB04', ['B', 'BII']],
+    ['BB05', ['B', 'BII']],
+    ['BB07', ['BII', 'BII']],
+    ['BB08', ['BII', 'BII']],
+    ['BB10', ['miB', 'miB']],
+    ['BB12', ['miB', 'miB']],
+    ['BB13', ['miB', 'miB']],
+    ['BB14', ['miB', 'miB']],
+    ['BB15', ['miB', 'miB']],
+    ['BB20', ['miB', 'miB']],
+    ['IC01', ['IC', 'IC']],
+    ['IC02', ['IC', 'IC']],
+    ['IC03', ['IC', 'IC']],
+    ['IC04', ['IC', 'IC']],
+    ['IC05', ['IC', 'IC']],
+    ['IC06', ['IC', 'IC']],
+    ['IC07', ['IC', 'IC']],
+    ['OP01', ['OPN', 'OPN']],
+    ['OP02', ['OPN', 'OPN']],
+    ['OP03', ['OPN', 'OPN']],
+    ['OP04', ['OPN', 'OPN']],
+    ['OP05', ['OPN', 'OPN']],
+    ['OP06', ['OPN', 'OPN']],
+    ['OP07', ['OPN', 'OPN']],
+    ['OP08', ['OPN', 'OPN']],
+    ['OP09', ['OPN', 'OPN']],
+    ['OP10', ['OPN', 'OPN']],
+    ['OP11', ['OPN', 'OPN']],
+    ['OP12', ['OPN', 'OPN']],
+    ['OP13', ['OPN', 'OPN']],
+    ['OP14', ['OPN', 'OPN']],
+    ['OP15', ['OPN', 'OPN']],
+    ['OP16', ['OPN', 'OPN']],
+    ['OP17', ['OPN', 'OPN']],
+    ['OP18', ['OPN', 'OPN']],
+    ['OP19', ['OPN', 'OPN']],
+    ['OP20', ['OPN', 'OPN']],
+    ['OP21', ['OPN', 'OPN']],
+    ['OP22', ['OPN', 'OPN']],
+    ['OP23', ['OPN', 'OPN']],
+    ['OP24', ['OPN', 'OPN']],
+    ['OP25', ['OPN', 'OPN']],
+    ['OP26', ['OPN', 'OPN']],
+    ['OP27', ['OPN', 'OPN']],
+    ['OP28', ['OPN', 'OPN']],
+    ['OP29', ['OPN', 'OPN']],
+    ['OP30', ['OPN', 'OPN']],
+    ['OP31', ['OPN', 'OPN']],
+    ['OPS1', ['OPN', 'OPN']],
+    ['OP1S', ['OPN', 'SYN']],
+    ['AAS1', ['SYN', 'A']],
+    ['AB1S', ['A', 'SYN']],
+    ['AB2S', ['A', 'SYN']],
+    ['BB1S', ['B', 'SYN']],
+    ['BB2S', ['B', 'SYN']],
+    ['BBS1', ['SYN', 'B']],
+    ['ZZ01', ['Z', 'Z']],
+    ['ZZ02', ['Z', 'Z']],
+    ['ZZ1S', ['Z', 'SYN']],
+    ['ZZ2S', ['Z', 'SYN']],
+    ['ZZS1', ['SYN', 'Z']],
+    ['ZZS2', ['SYN', 'Z']],
+]);
+
+function getConformerColor(ntc: string, useLower: boolean): Color {
+    const item = NtCToClasses.get(ntc);
+    if (!item) return ErrorColor;
+    return ColorMapping.get(useLower ? item[1] : item[0]) ?? ErrorColor;
+}
+
+export const ConfalPyramidsColorThemeParams = {};
+export type ConfalPyramidsColorThemeParams = typeof ConfalPyramidsColorThemeParams
+export function getConfalPyramidsColorThemeParams(ctx: ThemeDataContext) {
+    return ConfalPyramidsColorThemeParams; // TODO return copy
+}
+
+export function ConfalPyramidsColorTheme(ctx: ThemeDataContext, props: PD.Values<ConfalPyramidsColorThemeParams>): ColorTheme<ConfalPyramidsColorThemeParams> {
+    function color(location: Location, isSecondary: boolean): Color {
+        if (CPT.isLocation(location)) {
+            const { pyramid, isLower } = location.data;
+            return getConformerColor(pyramid.NtC, isLower);
+        }
+
+        return DefaultColor;
+    }
+
+    return {
+        factory: ConfalPyramidsColorTheme,
+        granularity: 'group',
+        color,
+        props,
+        description: Description,
+        legend: TableLegend(iterableToArray(ColorMapping.entries()).map(([conformer, color]) => {
+            return [conformer, color] as [string, Color];
+        }).concat([
+            [ 'Error', ErrorColor ],
+            [ 'Unknown', DefaultColor ]
+        ]))
+    };
+}
+
+export const ConfalPyramidsColorThemeProvider: ColorTheme.Provider<ConfalPyramidsColorThemeParams, 'confal-pyramids'> = {
+    name: 'confal-pyramids',
+    label: 'Confal Pyramids',
+    category: ColorTheme.Category.Residue,
+    factory: ConfalPyramidsColorTheme,
+    getParams: getConfalPyramidsColorThemeParams,
+    defaultValues: PD.getDefaultValues(ConfalPyramidsColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure && ctx.structure.models.some(m => ConfalPyramids.isApplicable(m)),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, data: ThemeDataContext) => data.structure ? ConfalPyramidsProvider.attach(ctx, data.structure.models[0], void 0, true) : Promise.resolve(),
+        detach: (data) => data.structure && data.structure.models[0].customProperties.reference(ConfalPyramidsProvider.descriptor, false)
+    }
+};

src/extensions/dnatco/confal-pyramids/property.ts

@@ -0,0 +1,172 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { ConfalPyramidsTypes as CPT } from './types';
+import { Column, Table } from '../../../mol-data/db';
+import { toTable } from '../../../mol-io/reader/cif/schema';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
+import { Model } from '../../../mol-model/structure';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
+import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
+
+export type ConfalPyramids = PropertyWrapper<CPT.PyramidsData | undefined >;
+
+export namespace ConfalPyramids {
+    export const Schema = {
+        ndb_struct_ntc_step: {
+            id: Column.Schema.int,
+            name: Column.Schema.str,
+            PDB_model_number: Column.Schema.int,
+            label_entity_id_1: Column.Schema.int,
+            label_asym_id_1: Column.Schema.str,
+            label_seq_id_1: Column.Schema.int,
+            label_comp_id_1: Column.Schema.str,
+            label_alt_id_1: Column.Schema.str,
+            label_entity_id_2: Column.Schema.int,
+            label_asym_id_2: Column.Schema.str,
+            label_seq_id_2: Column.Schema.int,
+            label_comp_id_2: Column.Schema.str,
+            label_alt_id_2: Column.Schema.str,
+            auth_asym_id_1: Column.Schema.str,
+            auth_seq_id_1: Column.Schema.int,
+            auth_asym_id_2: Column.Schema.str,
+            auth_seq_id_2: Column.Schema.int,
+            PDB_ins_code_1: Column.Schema.str,
+            PDB_ins_code_2: Column.Schema.str,
+        },
+        ndb_struct_ntc_step_summary: {
+            step_id: Column.Schema.int,
+            assigned_CANA: Column.Schema.str,
+            assigned_NtC: Column.Schema.str,
+            confal_score: Column.Schema.int,
+            euclidean_distance_NtC_ideal: Column.Schema.float,
+            cartesian_rmsd_closest_NtC_representative: Column.Schema.float,
+            closest_CANA: Column.Schema.str,
+            closest_NtC: Column.Schema.str,
+            closest_step_golden: Column.Schema.str
+        }
+    };
+    export type Schema = typeof Schema;
+
+    export async function fromCif(ctx: CustomProperty.Context, model: Model, props: ConfalPyramidsProps): Promise<CustomProperty.Data<ConfalPyramids>> {
+        const info = PropertyWrapper.createInfo();
+        const data = getCifData(model);
+        if (data === undefined) return { value: { info, data: undefined } };
+
+        const fromCif = createPyramidsFromCif(model, data.steps, data.stepsSummary);
+        return { value: { info, data: fromCif } };
+    }
+
+    function getCifData(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) throw new Error('Data format must be mmCIF');
+        if (!hasNdbStructNtcCategories(model)) return undefined;
+        return {
+            steps: toTable(Schema.ndb_struct_ntc_step, model.sourceData.data.frame.categories.ndb_struct_ntc_step),
+            stepsSummary: toTable(Schema.ndb_struct_ntc_step_summary, model.sourceData.data.frame.categories.ndb_struct_ntc_step_summary)
+        };
+    }
+
+    function hasNdbStructNtcCategories(model: Model): boolean {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+        const names = (model.sourceData).data.frame.categoryNames;
+        return names.includes('ndb_struct_ntc_step') && names.includes('ndb_struct_ntc_step_summary');
+    }
+
+    export function isApplicable(model?: Model): boolean {
+        return !!model && hasNdbStructNtcCategories(model);
+    }
+}
+
+export const ConfalPyramidsParams = {};
+export type ConfalPyramidsParams = typeof ConfalPyramidsParams;
+export type ConfalPyramidsProps = PD.Values<ConfalPyramidsParams>;
+
+export const ConfalPyramidsProvider: CustomModelProperty.Provider<ConfalPyramidsParams, ConfalPyramids> = CustomModelProperty.createProvider({
+    label: 'Confal Pyramids',
+    descriptor: CustomPropertyDescriptor({
+        name: 'confal_pyramids',
+    }),
+    type: 'static',
+    defaultParams: ConfalPyramidsParams,
+    getParams: (data: Model) => ConfalPyramidsParams,
+    isApplicable: (data: Model) => ConfalPyramids.isApplicable(data),
+    obtain: async (ctx: CustomProperty.Context, data: Model, props: Partial<ConfalPyramidsProps>) => {
+        const p = { ...PD.getDefaultValues(ConfalPyramidsParams), ...props };
+        return ConfalPyramids.fromCif(ctx, data, p);
+    }
+});
+
+type StepsSummaryTable = Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step_summary>;
+
+function createPyramidsFromCif(model: Model,
+    steps: Table<typeof ConfalPyramids.Schema.ndb_struct_ntc_step>,
+    stepsSummary: StepsSummaryTable): CPT.PyramidsData {
+    const pyramids = new Array<CPT.Pyramid>();
+    const names = new Map<string, number>();
+    const locations = new Array<CPT.Location>();
+    let hasMultipleModels = false;
+
+    const {
+        id, PDB_model_number, name,
+        auth_asym_id_1, auth_seq_id_1, label_comp_id_1, label_alt_id_1, PDB_ins_code_1,
+        auth_asym_id_2, auth_seq_id_2, label_comp_id_2, label_alt_id_2, PDB_ins_code_2,
+        _rowCount } = steps;
+
+    if (_rowCount !== stepsSummary._rowCount) throw new Error('Inconsistent mmCIF data');
+
+    for (let i = 0; i < _rowCount; i++) {
+        const model_num = PDB_model_number.value(i);
+        if (model_num !== model.modelNum) {
+            hasMultipleModels = true;
+            continue; // We are only interested in data for the current model
+        }
+
+        const { _NtC, _confal_score } = getNtCAndConfalScore(id.value(i), i, stepsSummary);
+
+        const pyramid = {
+            PDB_model_number: model_num,
+            name: name.value(i),
+            auth_asym_id_1: auth_asym_id_1.value(i),
+            auth_seq_id_1: auth_seq_id_1.value(i),
+            label_comp_id_1: label_comp_id_1.value(i),
+            label_alt_id_1: label_alt_id_1.value(i),
+            PDB_ins_code_1: PDB_ins_code_1.value(i),
+            auth_asym_id_2: auth_asym_id_2.value(i),
+            auth_seq_id_2: auth_seq_id_2.value(i),
+            label_comp_id_2: label_comp_id_2.value(i),
+            label_alt_id_2: label_alt_id_2.value(i),
+            PDB_ins_code_2: PDB_ins_code_2.value(i),
+            confal_score: _confal_score,
+            NtC: _NtC
+        };
+
+        pyramids.push(pyramid);
+        names.set(pyramid.name, pyramids.length - 1);
+
+        locations.push(CPT.Location(pyramid, false));
+        locations.push(CPT.Location(pyramid, true));
+    }
+
+    return { pyramids, names, locations, hasMultipleModels };
+}
+
+function getNtCAndConfalScore(id: number, i: number, stepsSummary: StepsSummaryTable) {
+    const { step_id, confal_score, assigned_NtC } = stepsSummary;
+
+    // Assume that step_ids in ntc_step_summary are in the same order as steps in ntc_step
+    for (let j = i; j < stepsSummary._rowCount; j++) {
+        if (id === step_id.value(j)) return { _NtC: assigned_NtC.value(j), _confal_score: confal_score.value(j) };
+    }
+    // Safety net for cases where the previous assumption is not met
+    for (let j = 0; j < i; j++) {
+        if (id === step_id.value(j)) return { _NtC: assigned_NtC.value(j), _confal_score: confal_score.value(j) };
+    }
+    throw new Error('Inconsistent mmCIF data');
+}

src/extensions/dnatco/confal-pyramids/representation.ts

@@ -0,0 +1,186 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { ConfalPyramids, ConfalPyramidsProvider } from './property';
+import { ConfalPyramidsUtil } from './util';
+import { ConfalPyramidsTypes as CPT } from './types';
+import { Interval } from '../../../mol-data/int';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { PickingId } from '../../../mol-geo/geometry/picking';
+import { PrimitiveBuilder } from '../../../mol-geo/primitive/primitive';
+import { LocationIterator } from '../../../mol-geo/util/location-iterator';
+import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { EmptyLoci, Loci } from '../../../mol-model/loci';
+import { Structure, StructureProperties, Unit } from '../../../mol-model/structure';
+import { CustomProperty } from '../../../mol-model-props/common/custom-property';
+import { Representation, RepresentationContext, RepresentationParamsGetter } from '../../../mol-repr/representation';
+import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder, UnitsRepresentation } from '../../../mol-repr/structure/representation';
+import { StructureGroup, UnitsMeshParams, UnitsMeshVisual, UnitsVisual } from '../../../mol-repr/structure/units-visual';
+import { VisualUpdateState } from '../../../mol-repr/util';
+import { VisualContext } from '../../../mol-repr/visual';
+import { getAltResidueLociFromId } from '../../../mol-repr/structure/visual/util/common';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Theme, ThemeRegistryContext } from '../../../mol-theme/theme';
+import { NullLocation } from '../../../mol-model/location';
+
+const t = Mat4.identity();
+const w = Vec3.zero();
+const mp = Vec3.zero();
+
+function calcMidpoint(mp: Vec3, v: Vec3, w: Vec3) {
+    Vec3.sub(mp, v, w);
+    Vec3.scale(mp, mp, 0.5);
+    Vec3.add(mp, mp, w);
+}
+
+function shiftVertex(vec: Vec3, ref: Vec3, scale: number) {
+    Vec3.sub(w, vec, ref);
+    Vec3.scale(w, w, scale);
+    Vec3.add(vec, vec, w);
+}
+
+const ConfalPyramidsMeshParams = {
+    ...UnitsMeshParams
+};
+type ConfalPyramidsMeshParams = typeof ConfalPyramidsMeshParams;
+
+function createConfalPyramidsIterator(structureGroup: StructureGroup): LocationIterator {
+    const { structure, group } = structureGroup;
+    const instanceCount = group.units.length;
+
+    const prop = ConfalPyramidsProvider.get(structure.model).value;
+    if (prop === undefined || prop.data === undefined) {
+        return LocationIterator(0, 1, 1, () => NullLocation);
+    }
+
+    const { locations } = prop.data;
+
+    const getLocation = (groupIndex: number, instanceIndex: number) => {
+        if (locations.length <= groupIndex) return NullLocation;
+        return locations[groupIndex];
+    };
+    return LocationIterator(locations.length, instanceCount, 1, getLocation);
+}
+
+function createConfalPyramidsMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<ConfalPyramidsMeshParams>, mesh?: Mesh) {
+    if (!Unit.isAtomic(unit)) return Mesh.createEmpty(mesh);
+
+    const prop = ConfalPyramidsProvider.get(structure.model).value;
+    if (prop === undefined || prop.data === undefined) return Mesh.createEmpty(mesh);
+
+    const { pyramids } = prop.data;
+    if (pyramids.length === 0) return Mesh.createEmpty(mesh);
+
+    const mb = MeshBuilder.createState(512, 512, mesh);
+
+    const handler = (pyramid: CPT.Pyramid, first: ConfalPyramidsUtil.FirstResidueAtoms, second: ConfalPyramidsUtil.SecondResidueAtoms, firsLocIndex: number, secondLocIndex: number) => {
+        if (firsLocIndex === -1 || secondLocIndex === -1)
+            throw new Error('Invalid location index');
+
+        const scale = (pyramid.confal_score - 20.0) / 100.0;
+        const O3 = first.O3.pos;
+        const OP1 = second.OP1.pos; const OP2 = second.OP2.pos; const O5 = second.O5.pos; const P = second.P.pos;
+
+        shiftVertex(O3, P, scale);
+        shiftVertex(OP1, P, scale);
+        shiftVertex(OP2, P, scale);
+        shiftVertex(O5, P, scale);
+        calcMidpoint(mp, O3, O5);
+
+        mb.currentGroup = firsLocIndex;
+        let pb = PrimitiveBuilder(3);
+        /* Upper part (for first residue in step) */
+        pb.add(O3, OP1, OP2);
+        pb.add(O3, mp, OP1);
+        pb.add(O3, OP2, mp);
+        MeshBuilder.addPrimitive(mb, t, pb.getPrimitive());
+
+        /* Lower part (for second residue in step */
+        mb.currentGroup = secondLocIndex;
+        pb = PrimitiveBuilder(3);
+        pb.add(mp, O5, OP1);
+        pb.add(mp, OP2, O5);
+        pb.add(O5, OP2, OP1);
+        MeshBuilder.addPrimitive(mb, t, pb.getPrimitive());
+    };
+
+    const walker = new ConfalPyramidsUtil.UnitWalker(structure, unit, handler);
+    walker.walk();
+
+    return MeshBuilder.getMesh(mb);
+}
+
+function getConfalPyramidLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number) {
+    const { groupId, objectId, instanceId } = pickingId;
+    if (objectId !== id) return EmptyLoci;
+
+    const { structure } = structureGroup;
+
+    const unit = structureGroup.group.units[instanceId];
+    if (!Unit.isAtomic(unit)) return EmptyLoci;
+
+    const prop = ConfalPyramidsProvider.get(structure.model).value;
+    if (prop === undefined || prop.data === undefined) return EmptyLoci;
+
+    const { locations } = prop.data;
+
+    if (locations.length <= groupId) return EmptyLoci;
+    const altId = StructureProperties.atom.label_alt_id(CPT.toElementLocation(locations[groupId]));
+    const rI = unit.residueIndex[locations[groupId].element.element];
+
+    return getAltResidueLociFromId(structure, unit, rI, altId);
+}
+
+function eachConfalPyramid(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
+    return false; // TODO: Implement me
+}
+
+function ConfalPyramidsVisual(materialId: number): UnitsVisual<ConfalPyramidsMeshParams> {
+    return UnitsMeshVisual<ConfalPyramidsMeshParams>({
+        defaultProps: PD.getDefaultValues(ConfalPyramidsMeshParams),
+        createGeometry: createConfalPyramidsMesh,
+        createLocationIterator: createConfalPyramidsIterator,
+        getLoci: getConfalPyramidLoci,
+        eachLocation: eachConfalPyramid,
+        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ConfalPyramidsMeshParams>, currentProps: PD.Values<ConfalPyramidsMeshParams>) => {
+        }
+    }, materialId);
+}
+const ConfalPyramidsVisuals = {
+    'confal-pyramids-symbol': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, UnitsMeshParams>) => UnitsRepresentation('Confal Pyramids Symbol Mesh', ctx, getParams, ConfalPyramidsVisual),
+};
+
+export const ConfalPyramidsParams = {
+    ...UnitsMeshParams
+};
+export type ConfalPyramidsParams = typeof ConfalPyramidsParams;
+export function getConfalPyramidsParams(ctx: ThemeRegistryContext, structure: Structure) {
+    return PD.clone(ConfalPyramidsParams);
+}
+
+export type ConfalPyramidsRepresentation = StructureRepresentation<ConfalPyramidsParams>;
+export function ConfalPyramidsRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, ConfalPyramidsParams>): ConfalPyramidsRepresentation {
+    const repr = Representation.createMulti('Confal Pyramids', ctx, getParams, StructureRepresentationStateBuilder, ConfalPyramidsVisuals as unknown as Representation.Def<Structure, ConfalPyramidsParams>);
+    return repr;
+}
+
+export const ConfalPyramidsRepresentationProvider = StructureRepresentationProvider({
+    name: 'confal-pyramids',
+    label: 'Confal Pyramids',
+    description: 'Displays schematic depiction of conformer classes and confal values',
+    factory: ConfalPyramidsRepresentation,
+    getParams: getConfalPyramidsParams,
+    defaultValues: PD.getDefaultValues(ConfalPyramidsParams),
+    defaultColorTheme: { name: 'confal-pyramids' },
+    defaultSizeTheme: { name: 'uniform' },
+    isApplicable: (structure: Structure) => structure.models.some(m => ConfalPyramids.isApplicable(m)),
+    ensureCustomProperties: {
+        attach: (ctx: CustomProperty.Context, structure: Structure) => ConfalPyramidsProvider.attach(ctx, structure.model, void 0, true),
+        detach: (data) => ConfalPyramidsProvider.ref(data.model, false),
+    }
+});

src/extensions/dnatco/confal-pyramids/types.ts

@@ -0,0 +1,60 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { DataLocation } from '../../../mol-model/location';
+import { ElementIndex, Structure, StructureElement, Unit } from '../../../mol-model/structure';
+
+export namespace ConfalPyramidsTypes {
+    export type Pyramid = {
+        PDB_model_number: number,
+        name: string,
+        auth_asym_id_1: string,
+        auth_seq_id_1: number,
+        label_comp_id_1: string,
+        label_alt_id_1: string,
+        PDB_ins_code_1: string,
+        auth_asym_id_2: string,
+        auth_seq_id_2: number,
+        label_comp_id_2: string,
+        label_alt_id_2: string,
+        PDB_ins_code_2: string,
+        confal_score: number,
+        NtC: string
+    }
+
+    export interface PyramidsData {
+        pyramids: Array<Pyramid>,
+        names: Map<string, number>,
+        locations: Array<Location>,
+        hasMultipleModels: boolean
+    }
+
+    export interface LocationData {
+        readonly pyramid: Pyramid
+        readonly isLower: boolean;
+    }
+
+    export interface Element {
+        structure: Structure;
+        unit: Unit.Atomic;
+        element: ElementIndex;
+    }
+
+    export interface Location extends DataLocation<LocationData, Element> {}
+
+    export function Location(pyramid: Pyramid, isLower: boolean, structure?: Structure, unit?: Unit.Atomic, element?: ElementIndex) {
+        return DataLocation('pyramid', { pyramid, isLower }, { structure: structure as any, unit: unit as any, element: element as any });
+    }
+
+    export function isLocation(x: any): x is Location {
+        return !!x && x.kind === 'data-location' && x.tag === 'pyramid';
+    }
+
+    export function toElementLocation(location: Location) {
+        return StructureElement.Location.create(location.element.structure, location.element.unit, location.element.element);
+    }
+}

src/extensions/dnatco/confal-pyramids/util.ts

@@ -0,0 +1,299 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+import { ConfalPyramidsProvider } from './property';
+import { ConfalPyramidsTypes as CPT } from './types';
+import { OrderedSet, Segmentation } from '../../../mol-data/int';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { ChainIndex, ElementIndex, ResidueIndex, Structure, StructureElement, StructureProperties, Unit } from '../../../mol-model/structure';
+
+export namespace ConfalPyramidsUtil {
+    type Residue = Segmentation.Segment<ResidueIndex>;
+
+    export type AtomInfo = {
+        pos: Vec3,
+        index: ElementIndex,
+        fakeAltId: string,
+    };
+
+    export type FirstResidueAtoms = {
+        O3: AtomInfo,
+    };
+
+    export type SecondResidueAtoms = {
+        OP1: AtomInfo,
+        OP2: AtomInfo,
+        O5: AtomInfo,
+        P: AtomInfo,
+    };
+
+    type ResidueInfo = {
+        PDB_model_num: number,
+        asym_id: string,
+        auth_asym_id: string,
+        seq_id: number,
+        auth_seq_id: number,
+        comp_id: string,
+        alt_id: string,
+        ins_code: string,
+    };
+
+    export type Handler = (pyramid: CPT.Pyramid, first: FirstResidueAtoms, second: SecondResidueAtoms, firstLocIndex: number, secondLocIndex: number) => void;
+
+    function residueInfoFromLocation(loc: StructureElement.Location): ResidueInfo {
+        return {
+            PDB_model_num: StructureProperties.unit.model_num(loc),
+            asym_id: StructureProperties.chain.label_asym_id(loc),
+            auth_asym_id: StructureProperties.chain.auth_asym_id(loc),
+            seq_id: StructureProperties.residue.label_seq_id(loc),
+            auth_seq_id: StructureProperties.residue.auth_seq_id(loc),
+            comp_id: StructureProperties.atom.label_comp_id(loc),
+            alt_id: StructureProperties.atom.label_alt_id(loc),
+            ins_code: StructureProperties.residue.pdbx_PDB_ins_code(loc)
+        };
+    }
+
+    export function hasMultipleModels(unit: Unit.Atomic): boolean {
+        const prop = ConfalPyramidsProvider.get(unit.model).value;
+        if (prop === undefined || prop.data === undefined) throw new Error('No custom properties data');
+        return prop.data.hasMultipleModels;
+    }
+
+    function getPossibleAltIdsIndices(eIFirst: ElementIndex, eILast: ElementIndex, structure: Structure, unit: Unit.Atomic): string[] {
+        const loc = StructureElement.Location.create(structure, unit, -1 as ElementIndex);
+
+        const uIFirst = OrderedSet.indexOf(unit.elements, eIFirst);
+        const uILast = OrderedSet.indexOf(unit.elements, eILast);
+
+        const possibleAltIds: string[] = [];
+        for (let uI = uIFirst; uI <= uILast; uI++) {
+            loc.element = unit.elements[uI];
+            const altId = StructureProperties.atom.label_alt_id(loc);
+            if (altId !== '' && !possibleAltIds.includes(altId)) possibleAltIds.push(altId);
+        }
+
+        return possibleAltIds;
+    }
+
+    function getPossibleAltIdsResidue(residue: Residue, structure: Structure, unit: Unit.Atomic): string[] {
+        return getPossibleAltIdsIndices(unit.elements[residue.start], unit.elements[residue.end - 1], structure, unit);
+    }
+
+    class Utility {
+        protected getPyramidByName(name: string): { pyramid: CPT.Pyramid | undefined, index: number } {
+            const index = this.data.names.get(name);
+            if (index === undefined) return { pyramid: undefined, index: -1 };
+
+            return { pyramid: this.data.pyramids[index], index };
+        }
+
+        protected stepToName(entry_id: string, modelNum: number, locFirst: StructureElement.Location, locSecond: StructureElement.Location, fakeAltId_1: string, fakeAltId_2: string) {
+            const first = residueInfoFromLocation(locFirst);
+            const second = residueInfoFromLocation(locSecond);
+            const model_id = this.hasMultipleModels ? `-m${modelNum}` : '';
+            const alt_id_1 =  fakeAltId_1 !== '' ? `.${fakeAltId_1}` : (first.alt_id.length ? `.${first.alt_id}` : '');
+            const alt_id_2 = fakeAltId_2 !== '' ? `.${fakeAltId_2}` : (second.alt_id.length ? `.${second.alt_id}` : '');
+            const ins_code_1 = first.ins_code.length ? `.${first.ins_code}` : '';
+            const ins_code_2 = second.ins_code.length ? `.${second.ins_code}` : '';
+
+            return `${entry_id}${model_id}_${first.auth_asym_id}_${first.comp_id}${alt_id_1}_${first.auth_seq_id}${ins_code_1}_${second.comp_id}${alt_id_2}_${second.auth_seq_id}${ins_code_2}`;
+        }
+
+        constructor(unit: Unit.Atomic) {
+            const prop = ConfalPyramidsProvider.get(unit.model).value;
+            if (prop === undefined || prop.data === undefined) throw new Error('No custom properties data');
+
+            this.data = prop.data;
+            this.hasMultipleModels = hasMultipleModels(unit);
+
+            this.entryId = unit.model.entryId.toLowerCase();
+            this.modelNum = unit.model.modelNum;
+        }
+
+        protected readonly data: CPT.PyramidsData
+        protected readonly hasMultipleModels: boolean;
+        protected readonly entryId: string;
+        protected readonly modelNum: number;
+    }
+
+    export class UnitWalker extends Utility {
+        private getAtomIndices(names: string[], residue: Residue): ElementIndex[] {
+            let rI = residue.start;
+            const rILast = residue.end - 1;
+            const indices: ElementIndex[] = [];
+
+            for (; rI !== rILast; rI++) {
+                const eI = this.unit.elements[rI];
+                const loc = StructureElement.Location.create(this.structure, this.unit, eI);
+                const thisName = StructureProperties.atom.label_atom_id(loc);
+                if (names.includes(thisName)) indices.push(eI);
+            }
+
+            if (indices.length === 0)
+                throw new Error(`Element ${name} not found on residue ${residue.index}`);
+
+            return indices;
+        }
+
+        private getAtomPositions(indices: ElementIndex[]): Vec3[] {
+            const pos = this.unit.conformation.invariantPosition;
+            const positions: Vec3[] = [];
+
+            for (const eI of indices) {
+                const v = Vec3.zero();
+                pos(eI, v);
+                positions.push(v);
+            }
+
+            return positions;
+        }
+
+        private handleStep(firstAtoms: FirstResidueAtoms[], secondAtoms: SecondResidueAtoms[]) {
+            const modelNum = this.hasMultipleModels ? this.modelNum : -1;
+            let ok = false;
+
+            const firstLoc = StructureElement.Location.create(this.structure, this.unit, -1 as ElementIndex);
+            const secondLoc = StructureElement.Location.create(this.structure, this.unit, -1 as ElementIndex);
+            for (let i = 0; i < firstAtoms.length; i++) {
+                const first = firstAtoms[i];
+                for (let j = 0; j < secondAtoms.length; j++) {
+                    const second = secondAtoms[j];
+                    firstLoc.element = first.O3.index;
+                    secondLoc.element = second.OP1.index;
+
+                    const name = this.stepToName(this.entryId, modelNum, firstLoc, secondLoc, first.O3.fakeAltId, second.OP1.fakeAltId);
+                    const { pyramid, index } = this.getPyramidByName(name);
+                    if (pyramid !== undefined) {
+                        const setLoc = (loc: CPT.Location, eI: ElementIndex) => {
+                            loc.element.structure = this.structure;
+                            loc.element.unit = this.unit;
+                            loc.element.element = eI;
+                        };
+
+                        const locIndex = index * 2;
+                        setLoc(this.data.locations[locIndex], firstLoc.element);
+                        setLoc(this.data.locations[locIndex + 1], secondLoc.element);
+                        this.handler(pyramid, first, second, locIndex, locIndex + 1);
+                        ok = true;
+                    }
+                }
+            }
+
+            if (!ok) throw new Error('Bogus step');
+        }
+
+        private processFirstResidue(residue: Residue, possibleAltIds: string[]) {
+            const indO3 = this.getAtomIndices(['O3\'', 'O3*'], residue);
+            const posO3 = this.getAtomPositions(indO3);
+
+            const altPos: FirstResidueAtoms[] = [
+                { O3: { pos: posO3[0], index: indO3[0], fakeAltId: '' } }
+            ];
+
+            for (let i = 1; i < indO3.length; i++) {
+                altPos.push({ O3: { pos: posO3[i], index: indO3[i], fakeAltId: '' } });
+            }
+
+            if (altPos.length === 1 && possibleAltIds.length > 1) {
+                /* We have some alternate positions on the residue but O3 does not have any - fake them */
+                altPos[0].O3.fakeAltId = possibleAltIds[0];
+
+                for (let i = 1; i < possibleAltIds.length; i++)
+                    altPos.push({ O3: { pos: posO3[0], index: indO3[0], fakeAltId: possibleAltIds[i] } });
+            }
+
+            return altPos;
+        }
+
+        private processSecondResidue(residue: Residue, possibleAltIds: string[]) {
+            const indOP1 = this.getAtomIndices(['OP1'], residue);
+            const indOP2 = this.getAtomIndices(['OP2'], residue);
+            const indO5 = this.getAtomIndices(['O5\'', 'O5*'], residue);
+            const indP = this.getAtomIndices(['P'], residue);
+
+            const posOP1 = this.getAtomPositions(indOP1);
+            const posOP2 = this.getAtomPositions(indOP2);
+            const posO5 = this.getAtomPositions(indO5);
+            const posP = this.getAtomPositions(indP);
+
+            const infoOP1: AtomInfo[] = [];
+            /* We use OP1 as "pivotal" atom. There is no specific reason
+             * to pick OP1, it is as good a choice as any other atom
+             */
+            if (indOP1.length === 1 && possibleAltIds.length > 1) {
+                /* No altIds on OP1, fake them */
+                for (const altId of possibleAltIds)
+                    infoOP1.push({ pos: posOP1[0], index: indOP1[0], fakeAltId: altId });
+            } else {
+                for (let i = 0; i < indOP1.length; i++)
+                    infoOP1.push({ pos: posOP1[i], index: indOP1[i], fakeAltId: '' });
+            }
+
+            const mkInfo = (i: number, indices: ElementIndex[], positions: Vec3[], altId: string) => {
+                if (i >= indices.length) {
+                    const last = indices.length - 1;
+                    return { pos: positions[last], index: indices[last], fakeAltId: altId };
+                }
+
+                return { pos: positions[i], index: indices[i], fakeAltId: altId };
+            };
+
+            const altPos: SecondResidueAtoms[] = [];
+            for (let i = 0; i < infoOP1.length; i++) {
+                const altId = infoOP1[i].fakeAltId;
+
+                const OP2 = mkInfo(i, indOP2, posOP2, altId);
+                const O5 = mkInfo(i, indO5, posO5, altId);
+                const P = mkInfo(i, indP, posP, altId);
+
+                altPos.push({ OP1: infoOP1[i], OP2, O5, P });
+            }
+
+            return altPos;
+        }
+
+        private step(residue: Residue): { firstAtoms: FirstResidueAtoms[], secondAtoms: SecondResidueAtoms[] } {
+            const firstPossibleAltIds = getPossibleAltIdsResidue(residue, this.structure, this.unit);
+            const firstAtoms = this.processFirstResidue(residue, firstPossibleAltIds);
+
+            residue = this.residueIt.move();
+
+            const secondPossibleAltIds = getPossibleAltIdsResidue(residue, this.structure, this.unit);
+            const secondAtoms = this.processSecondResidue(residue, secondPossibleAltIds);
+
+            return { firstAtoms, secondAtoms };
+        }
+
+        walk() {
+            while (this.chainIt.hasNext) {
+                this.residueIt.setSegment(this.chainIt.move());
+
+                let residue = this.residueIt.move();
+                while (this.residueIt.hasNext) {
+                    try {
+                        const { firstAtoms, secondAtoms } = this.step(residue);
+
+                        this.handleStep(firstAtoms, secondAtoms);
+                    } catch (error) {
+                        /* Skip and move along */
+                        residue = this.residueIt.move();
+                    }
+                }
+            }
+        }
+
+        constructor(private structure: Structure, private unit: Unit.Atomic, private handler: Handler) {
+            super(unit);
+
+            this.chainIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, unit.elements);
+            this.residueIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
+        }
+
+        private chainIt: Segmentation.SegmentIterator<ChainIndex>;
+        private residueIt: Segmentation.SegmentIterator<ResidueIndex>;
+    }
+}

src/extensions/dnatco/index.ts

@@ -0,0 +1,8 @@
+/**
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Michal Malý <michal.maly@ibt.cas.cz>
+ * @author Jiří Černý <jiri.cerny@ibt.cas.cz>
+ */
+
+export { DnatcoConfalPyramids } from './confal-pyramids/behavior';

src/extensions/g3d/data.ts

@@ -0,0 +1,66 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { decodeMsgPack } from '../../mol-io/common/msgpack/decode';
+import { PluginContext } from '../../mol-plugin/context';
+import { Task } from '../../mol-task';
+import { inflate } from '../../mol-util/zip/zip';
+
+export interface G3dHeader {
+    magic: 'G3D',
+    version: number,
+    genome: string,
+    name: string,
+    offsets: { [resolution: string]: { offset: number, size: number } },
+    resolutions: number[]
+}
+
+export type G3dDataBlock = {
+    header: G3dHeader,
+    resolution: number,
+    data: {
+        [haplotype: string]: {
+            [ch: string]: {
+                start: number[]
+                x: number[],
+                y: number[],
+                z: number[],
+            }
+        }
+    }
+}
+
+const HEADER_SIZE = 64000;
+
+export async function getG3dHeader(ctx: PluginContext, urlOrData: string | Uint8Array): Promise<G3dHeader> {
+    const data: Uint8Array = await getRawData(ctx, urlOrData, { offset: 0, size: HEADER_SIZE });
+    let last = data.length - 1;
+    for (; last >= 0; last--) {
+        if (data[last] !== 0) break;
+    }
+    const header = decodeMsgPack(data.slice(0, last + 1));
+    return header;
+}
+
+export async function getG3dDataBlock(ctx: PluginContext, header: G3dHeader, urlOrData: string | Uint8Array, resolution: number): Promise<G3dDataBlock> {
+    if (!header.offsets[resolution]) throw new Error(`Resolution ${resolution} not available.`);
+    const data = await getRawData(ctx, urlOrData, header.offsets[resolution]);
+    const unzipped = await ctx.runTask(Task.create('Unzip', ctx => inflate(ctx, data)));
+
+    return {
+        header,
+        resolution,
+        data: decodeMsgPack(unzipped)
+    };
+}
+
+async function getRawData(ctx: PluginContext, urlOrData: string | Uint8Array, range: { offset: number, size: number }) {
+    if (typeof urlOrData === 'string') {
+        return await ctx.runTask(ctx.fetch({ url: urlOrData, headers: [['Range', `bytes=${range.offset}-${range.offset + range.size - 1}`]], type: 'binary' }));
+    } else {
+        return urlOrData.slice(range.offset, range.offset + range.size);
+    }
+}

src/extensions/g3d/format.ts

@@ -0,0 +1,173 @@
+/**
+ * Copyright (c) 2020 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 { Trajectory } from '../../mol-model/structure';
+import { TrajectoryFormatCategory, TrajectoryFormatProvider } from '../../mol-plugin-state/formats/trajectory';
+import { PluginStateObject as SO, PluginStateTransform } from '../../mol-plugin-state/objects';
+import { PluginBehavior } from '../../mol-plugin/behavior';
+import { PluginContext } from '../../mol-plugin/context';
+import { DefaultQueryRuntimeTable } from '../../mol-script/runtime/query/base';
+import { StateAction, StateObjectRef } from '../../mol-state';
+import { Task } from '../../mol-task';
+import { ParamDefinition } from '../../mol-util/param-definition';
+import { G3dHeader, getG3dDataBlock, getG3dHeader } from './data';
+import { g3dHaplotypeQuery, G3dLabelProvider, trajectoryFromG3D, G3dSymbols, G3dInfoDataProperty } from './model';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
+import { stringToWords } from '../../mol-util/string';
+import { objectForEach } from '../../mol-util/object';
+
+export const G3dProvider: TrajectoryFormatProvider = {
+    label: 'G3D',
+    description: 'G3D',
+    category: TrajectoryFormatCategory,
+    binaryExtensions: ['g3d'],
+    parse: async (plugin, data) => {
+        const trajectory = await plugin.state.data.build()
+            .to(data)
+            .apply(G3DHeaderFromFile, {}, { state: { isGhost: true } })
+            .apply(G3DTrajectory)
+            .commit();
+
+        return { trajectory };
+    },
+    visuals: defaultStructure
+};
+
+async function defaultStructure(plugin: PluginContext, data: { trajectory: StateObjectRef<SO.Molecule.Trajectory> }) {
+    const builder = plugin.builders.structure;
+    const model = await builder.createModel(data.trajectory);
+
+    if (!model) return;
+    const structure = await builder.createStructure(model);
+
+    const info = G3dInfoDataProperty.get(model.data!);
+    if (!info) return;
+
+    const components = plugin.build().to(structure);
+
+    const repr = createStructureRepresentationParams(plugin, void 0, {
+        type: 'cartoon',
+        color: 'polymer-index',
+        size: 'uniform',
+        sizeParams: { value: 0.25 }
+    });
+
+    for (const h of info.haplotypes) {
+        components
+            .apply(StateTransforms.Model.StructureSelectionFromExpression, { expression: g3dHaplotypeQuery(h), label: stringToWords(h) })
+            .apply(StateTransforms.Representation.StructureRepresentation3D, repr);
+    }
+
+    await components.commit();
+}
+
+export class G3dHeaderObject extends SO.Create<{
+    header: G3dHeader,
+    urlOrData: Uint8Array | string,
+    cache: { [resolution: number]: Trajectory | undefined }
+}>({ name: 'G3D Header', typeClass: 'Data' }) { }
+
+export type G3DHeaderFromFile = typeof G3DHeaderFromFile
+export const G3DHeaderFromFile = PluginStateTransform.BuiltIn({
+    name: 'g3d-header-from-file',
+    display: { name: 'G3D Header', description: 'Parse G3D Header' },
+    from: SO.Data.Binary,
+    to: G3dHeaderObject
+})({
+    apply({ a }, plugin: PluginContext) {
+        return Task.create('Parse G3D', async () => {
+            const header = await getG3dHeader(plugin, a.data);
+            return new G3dHeaderObject({ header, urlOrData: a.data, cache: { } }, { label: header.name, description: header.genome });
+        });
+    }
+});
+
+export type G3DHeaderFromUrl = typeof G3DHeaderFromUrl
+export const G3DHeaderFromUrl = PluginStateTransform.BuiltIn({
+    name: 'g3d-header-from-url',
+    display: { name: 'G3D Header', description: 'Parse G3D Header' },
+    params: { url: ParamDefinition.Text('') },
+    from: SO.Root,
+    to: G3dHeaderObject
+})({
+    apply({ params }, plugin: PluginContext) {
+        return Task.create('Parse G3D', async () => {
+            const header = await getG3dHeader(plugin, params.url);
+            return new G3dHeaderObject({ header, urlOrData: params.url, cache: { } }, { label: header.name, description: header.genome });
+        });
+    }
+});
+
+export type G3DTrajectory = typeof G3DHeaderFromUrl
+export const G3DTrajectory = PluginStateTransform.BuiltIn({
+    name: 'g3d-trajecotry',
+    display: { name: 'G3D Trajectory', description: 'Create G3D Trajectory' },
+    params: a => {
+        if (!a) return { resolution: ParamDefinition.Numeric(200000) };
+        const rs = a.data.header.resolutions;
+        return {
+            resolution: ParamDefinition.Select(rs[rs.length - 1], rs.map(r => [r, '' + r] as const))
+        };
+    },
+    from: G3dHeaderObject,
+    to: SO.Molecule.Trajectory
+})({
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('G3D Trajectory', async ctx => {
+            if (a.data.cache[params.resolution]) {
+                return new SO.Molecule.Trajectory(a.data.cache[params.resolution]!, { label: a.label, description: a.description });
+            }
+            const data = await getG3dDataBlock(plugin, a.data.header, a.data.urlOrData, params.resolution);
+            const traj = await trajectoryFromG3D(data).runInContext(ctx);
+            a.data.cache[params.resolution] = traj;
+            return new SO.Molecule.Trajectory(traj, { label: a.label, description: a.description });
+        });
+    }
+});
+
+export const LoadG3D = StateAction.build({
+    display: { name: 'Load Genome 3D (G3D)', description: 'Load G3D file from the specified URL.' },
+    from: SO.Root,
+    params: { url: ParamDefinition.Text('') }
+})(({ params, state }, ctx: PluginContext) => Task.create('Genome3D', taskCtx => {
+    return state.transaction(async () => {
+        if (params.url.trim().length === 0) {
+            throw new Error('Specify URL');
+        }
+
+        ctx.behaviors.layout.leftPanelTabName.next('data');
+
+        const trajectory = await state.build().toRoot()
+            .apply(G3DHeaderFromUrl, { url: params.url })
+            .apply(G3DTrajectory)
+            .commit();
+
+        await defaultStructure(ctx, { trajectory });
+    }).runInContext(taskCtx);
+}));
+
+export const G3DFormat = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'g3d',
+    category: 'misc',
+    display: {
+        name: 'G3D',
+        description: 'G3D Format Support'
+    },
+    ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
+        register() {
+            this.ctx.state.data.actions.add(LoadG3D);
+            objectForEach(G3dSymbols, s => DefaultQueryRuntimeTable.addSymbol(s));
+            this.ctx.managers.lociLabels.addProvider(G3dLabelProvider);
+        }
+        unregister() {
+            this.ctx.state.data.actions.remove(LoadG3D);
+            objectForEach(G3dSymbols, s => DefaultQueryRuntimeTable.removeSymbol(s));
+            this.ctx.managers.lociLabels.removeProvider(G3dLabelProvider);
+        }
+    }
+});

src/extensions/g3d/model.ts

@@ -0,0 +1,245 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { OrderedSet } from '../../mol-data/int';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { createModels } from '../../mol-model-formats/structure/basic/parser';
+import { BasicSchema, createBasic } from '../../mol-model-formats/structure/basic/schema';
+import { EntityBuilder } from '../../mol-model-formats/structure/common/entity';
+import { Loci } from '../../mol-model/loci';
+import { Trajectory, Unit } from '../../mol-model/structure';
+import { MoleculeType } from '../../mol-model/structure/model/types';
+import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { CustomPropSymbol } from '../../mol-script/language/symbol';
+import { Type } from '../../mol-script/language/type';
+import { QuerySymbolRuntime } from '../../mol-script/runtime/query/base';
+import { RuntimeContext, Task } from '../../mol-task';
+import { objectForEach } from '../../mol-util/object';
+import { G3dDataBlock } from './data';
+import { FormatPropertyProvider } from '../../mol-model-formats/structure/common/property';
+
+interface NormalizedData {
+    entity_id: string[],
+    chromosome: string[],
+    seq_id_begin: Int32Array,
+    seq_id_end: Int32Array,
+    start: Int32Array,
+    x: Float32Array,
+    y: Float32Array,
+    z: Float32Array,
+    r: Float32Array,
+    haplotype: string[]
+}
+
+function getColumns(block: G3dDataBlock) {
+    const { data } = block;
+    let size = 0;
+
+    objectForEach(data, h => objectForEach(h, g => size += g.start.length));
+
+    const normalized: NormalizedData = {
+        entity_id: new Array(size),
+        chromosome: new Array(size),
+        seq_id_begin: new Int32Array(size),
+        seq_id_end: new Int32Array(size),
+        start: new Int32Array(size),
+        x: new Float32Array(size),
+        y: new Float32Array(size),
+        z: new Float32Array(size),
+        r: new Float32Array(size),
+        haplotype: new Array(size)
+    };
+
+    const p = [Vec3(), Vec3(), Vec3()];
+
+    let o = 0;
+    objectForEach(data, (hs, h) => {
+        objectForEach(hs, (chs, ch) => {
+            const entity_id = `${ch}-${h}`;
+            const l =  chs.start.length;
+            if (l === 0) return;
+
+            let x = chs.x[0];
+            let y = chs.y[0];
+            let z = chs.z[0];
+
+            Vec3.set(p[0], x, y, z);
+            Vec3.set(p[2], x, y, z);
+
+            for (let i = 0; i < l; i++) {
+                normalized.entity_id[o] = entity_id;
+                normalized.chromosome[o] = ch;
+                normalized.start[o] = chs.start[i];
+                normalized.seq_id_begin[o] = o;
+                normalized.seq_id_end[o] = o;
+
+                x = chs.x[i];
+                y = chs.y[i];
+                z = chs.z[i];
+
+                Vec3.set(p[1], x, y, z);
+                if (i + 1 < l) Vec3.set(p[2], chs.x[i + 1], chs.y[i + 1], chs.z[i + 1]);
+                else Vec3.set(p[2], x, y, z);
+
+                normalized.x[o] = x;
+                normalized.y[o] = y;
+                normalized.z[o] = z;
+                normalized.r[o] = 2 / 3 * Math.min(Vec3.distance(p[0], p[1]), Vec3.distance(p[1], p[2]));
+                normalized.haplotype[o] = h;
+
+                const _p = p[0];
+                p[0] = p[1];
+                p[1] = _p;
+                o++;
+            }
+
+            if (l === 1) {
+                normalized.r[o - 1] = 1;
+            }
+        });
+    });
+
+    return normalized;
+}
+
+async function getTraj(ctx: RuntimeContext, data: G3dDataBlock) {
+    const normalized = getColumns(data);
+
+    const rowCount = normalized.seq_id_begin.length;
+    const entityIds = new Array<string>(rowCount);
+    const entityBuilder = new EntityBuilder();
+
+    const eName = { customName: '' };
+    for (let i = 0; i < rowCount; ++i) {
+        const e = normalized.entity_id[i];
+        eName.customName = e;
+        const entityId = entityBuilder.getEntityId(e, MoleculeType.DNA, e, eName);
+        entityIds[i] = entityId;
+    }
+
+    const ihm_sphere_obj_site = Table.ofPartialColumns(BasicSchema.ihm_sphere_obj_site, {
+        id: Column.range(0, rowCount),
+        entity_id: Column.ofStringArray(entityIds),
+        seq_id_begin: Column.ofIntArray(normalized.seq_id_begin),
+        seq_id_end: Column.ofIntArray(normalized.seq_id_end),
+        asym_id: Column.ofStringArray(normalized.chromosome),
+
+        Cartn_x: Column.ofFloatArray(normalized.x),
+        Cartn_y: Column.ofFloatArray(normalized.y),
+        Cartn_z: Column.ofFloatArray(normalized.z),
+
+        object_radius: Column.ofFloatArray(normalized.r),
+        rmsf: Column.ofConst(0, rowCount, Column.Schema.float),
+        model_id: Column.ofConst(1, rowCount, Column.Schema.int),
+    }, rowCount);
+
+    const basic = createBasic({
+        entity: entityBuilder.getEntityTable(),
+        ihm_model_list: Table.ofPartialColumns(BasicSchema.ihm_model_list, {
+            model_id: Column.ofIntArray([1]),
+            model_name: Column.ofStringArray(['G3D Model']),
+        }, 1),
+        ihm_sphere_obj_site
+    });
+
+    const models = await createModels(basic, { kind: 'g3d', name: 'G3D', data }, ctx);
+
+    G3dInfoDataProperty.set(models.representative, {
+        haplotypes: Object.keys(data.data),
+        haplotype: normalized.haplotype,
+        resolution: data.resolution,
+        start: normalized.start,
+        chroms: normalized.chromosome,
+    });
+
+    return models;
+}
+
+export function trajectoryFromG3D(data: G3dDataBlock): Task<Trajectory> {
+    return Task.create('Parse G3D', async ctx => {
+        return getTraj(ctx, data);
+    });
+}
+
+export const G3dSymbols = {
+    haplotype: QuerySymbolRuntime.Dynamic(CustomPropSymbol('g3d', 'haplotype', Type.Str),
+        ctx => {
+            if (Unit.isAtomic(ctx.element.unit)) return '';
+            const info = (G3dInfoDataProperty as any).get(ctx.element.unit.model);
+            if (!info) return '';
+            const seqId = ctx.element.unit.model.coarseHierarchy.spheres.seq_id_begin.value(ctx.element.element);
+            return info.haplotype[seqId] || '';
+        }
+    ),
+    chromosome: QuerySymbolRuntime.Dynamic(CustomPropSymbol('g3d', 'chromosome', Type.Str),
+        ctx => {
+            if (Unit.isAtomic(ctx.element.unit)) return '';
+            const { asym_id } = ctx.element.unit.model.coarseHierarchy.spheres;
+            return asym_id.value(ctx.element.element) || '';
+        }
+    ),
+    region: QuerySymbolRuntime.Dynamic(CustomPropSymbol('g3d', 'region', Type.Num),
+        ctx => {
+            if (Unit.isAtomic(ctx.element.unit)) return '';
+            const info = (G3dInfoDataProperty as any).get(ctx.element.unit.model);
+            if (!info) return 0;
+            const seqId = ctx.element.unit.model.coarseHierarchy.spheres.seq_id_begin.value(ctx.element.element);
+            return info.start[seqId] || 0;
+        }
+    )
+};
+
+export const G3dInfoDataProperty = FormatPropertyProvider.create<G3dInfoData>({ name: 'g3d_info' });
+
+export function g3dHaplotypeQuery(haplotype: string) {
+    return MS.struct.generator.atomGroups({
+        'chain-test': MS.core.rel.eq([G3dSymbols.haplotype.symbol(), haplotype]),
+    });
+}
+
+export function g3dChromosomeQuery(chr: string) {
+    return MS.struct.generator.atomGroups({
+        'chain-test': MS.core.logic.and([
+            MS.core.rel.eq([MS.ammp('objectPrimitive'), 'sphere']),
+            MS.core.rel.eq([G3dSymbols.chromosome.symbol(), chr])
+        ])
+    });
+}
+
+export function g3dRegionQuery(chr: string, start: number, end: number) {
+    return MS.struct.generator.atomGroups({
+        'chain-test': MS.core.logic.and([
+            MS.core.rel.eq([MS.ammp('objectPrimitive'), 'sphere']),
+            MS.core.rel.eq([G3dSymbols.chromosome.symbol(), chr])
+        ]),
+        'residue-test': MS.core.rel.inRange([G3dSymbols.region.symbol(), start, end])
+    });
+}
+
+export interface G3dInfoData {
+    haplotypes: string[],
+    haplotype: string[],
+    start: Int32Array,
+    resolution: number,
+    chroms: string[]
+};
+
+export const G3dLabelProvider: LociLabelProvider = {
+    label: (e: Loci): string | undefined => {
+        if (e.kind !== 'element-loci' || Loci.isEmpty(e)) return;
+
+        const first = e.elements[0];
+        if (e.elements.length !== 1 || Unit.isAtomic(first.unit)) return;
+        const info = G3dInfoDataProperty.get(first.unit.model);
+        if (!info) return;
+
+        const eI = first.unit.elements[OrderedSet.getAt(first.indices, 0)];
+        const seqId = first.unit.model.coarseHierarchy.spheres.seq_id_begin.value(eI);
+        return `<b>Start:</b> ${info.start[seqId]} <small>| resolution ${info.resolution}<small>`;
+    }
+};

src/extensions/mp4-export/controls.ts

@@ -0,0 +1,144 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { debounceTime } from 'rxjs/operators';
+import { PluginStateAnimation } from '../../mol-plugin-state/animation/model';
+import { PluginComponent } from '../../mol-plugin-state/component';
+import { PluginContext } from '../../mol-plugin/context';
+import { Task } from '../../mol-task';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { encodeMp4Animation } from './encoder';
+
+export interface Mp4AnimationInfo {
+    width: number,
+    height: number
+}
+
+export const Mp4AnimationParams = {
+    quantization: PD.Numeric(18, { min: 10, max: 51 }, { description: 'Lower is better, but slower.' })
+};
+
+export class Mp4Controls extends PluginComponent {
+    private currentNames = new Set<string>();
+    private animations: PluginStateAnimation[] = [];
+
+    readonly behaviors = {
+        animations: this.ev.behavior<PD.Params>({ }),
+        current: this.ev.behavior<{ anim: PluginStateAnimation, params: PD.Params, values: any } | undefined>(void 0),
+        canApply: this.ev.behavior<PluginStateAnimation.CanApply>({ canApply: false }),
+        info: this.ev.behavior<Mp4AnimationInfo>({ width: 0, height: 0 }),
+        params: this.ev.behavior<PD.Values<typeof Mp4AnimationParams>>(PD.getDefaultValues(Mp4AnimationParams))
+    }
+
+    setCurrent(name?: string) {
+        const anim = this.animations.find(a => a.name === name);
+        if (!anim) {
+            this.behaviors.current.next(anim);
+            return;
+        }
+
+        const params = anim.params(this.plugin) as PD.Params;
+        const values = PD.getDefaultValues(params);
+
+        this.behaviors.current.next({ anim, params, values });
+        this.behaviors.canApply.next(anim.canApply?.(this.plugin) ?? { canApply: true });
+    }
+
+    setCurrentParams(values: any) {
+        this.behaviors.current.next({ ...this.behaviors.current.value!, values });
+    }
+
+    get current() {
+        return this.behaviors.current.value;
+    }
+
+    render() {
+        const task = Task.create('Export Animation', async ctx => {
+            try {
+                const resolution = this.plugin.helpers.viewportScreenshot?.getSizeAndViewport()!;
+                const anim = this.current!;
+                const movie = await encodeMp4Animation(this.plugin, ctx, {
+                    animation: {
+                        definition: anim.anim,
+                        params: anim.values,
+                    },
+                    ...resolution,
+                    quantizationParameter: this.behaviors.params.value.quantization,
+                    pass: this.plugin.helpers.viewportScreenshot?.imagePass!,
+                });
+
+                const filename = anim.anim.display.name.toLowerCase().replace(/\s/g, '-').replace(/[^a-z0-9_\-]/g, '');
+                return { movie, filename: `${this.plugin.helpers.viewportScreenshot?.getFilename('')}_${filename}.mp4` };
+            } catch (e) {
+                this.plugin.log.error('' + e);
+                throw e;
+            }
+        });
+
+        return this.plugin.runTask(task, { useOverlay: true });
+    }
+
+    private get manager() {
+        return this.plugin.managers.animation;
+    }
+
+    private syncInfo() {
+        const helper = this.plugin.helpers.viewportScreenshot;
+        const size = helper?.getSizeAndViewport();
+        if (!size) return;
+
+        this.behaviors.info.next({ width: size.viewport.width, height: size.viewport.height });
+    }
+
+    private sync() {
+        const animations = this.manager.animations.filter(a => a.isExportable);
+
+        const hasAll = animations.every(a => this.currentNames.has(a.name));
+        if (hasAll && this.currentNames.size === animations.length) {
+            return;
+        }
+
+        const params = {
+            current: PD.Select(animations[0]?.name,
+                animations.map(a => [a.name, a.display.name] as [string, string]),
+                { label: 'Animation' })
+        };
+
+        const current = this.behaviors.current.value;
+        const hasCurrent = !!animations.find(a => a.name === current?.anim.name);
+
+        this.animations = animations;
+        if (!hasCurrent) {
+            this.setCurrent(animations[0]?.name);
+        }
+        this.behaviors.animations.next(params);
+    }
+
+    private init() {
+        this.subscribe(this.plugin.managers.animation.events.updated.pipe(debounceTime(16)), () => {
+            this.sync();
+        });
+
+        this.subscribe(this.plugin.canvas3d?.resized!, () => this.syncInfo());
+        this.subscribe(this.plugin.helpers.viewportScreenshot?.events.previewed!, () => this.syncInfo());
+
+        this.subscribe(this.plugin.behaviors.state.isBusy, b => {
+            const anim = this.current;
+            if (!b && anim) {
+                this.behaviors.canApply.next(anim.anim.canApply?.(this.plugin) ?? { canApply: true });
+            }
+        });
+
+        this.sync();
+        this.syncInfo();
+    }
+
+    constructor(private plugin: PluginContext) {
+        super();
+
+        this.init();
+    }
+}

src/extensions/mp4-export/encoder.ts

@@ -0,0 +1,105 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as HME from 'h264-mp4-encoder';
+import { Viewport } from '../../mol-canvas3d/camera/util';
+import { ImagePass } from '../../mol-canvas3d/passes/image';
+import { PluginStateAnimation } from '../../mol-plugin-state/animation/model';
+import { PluginContext } from '../../mol-plugin/context';
+import { RuntimeContext } from '../../mol-task';
+import { Color } from '../../mol-util/color';
+
+export interface Mp4EncoderParams<A extends PluginStateAnimation = PluginStateAnimation> {
+    pass: ImagePass,
+    customBackground?: Color,
+    animation: PluginStateAnimation.Instance<A>,
+    width: number,
+    height: number,
+    viewport: Viewport,
+    /** default is 30 */
+    fps?: number,
+    /** Number from 10 (best quality, slowest) to 51 (worst, fastest) */
+    quantizationParameter?: number
+}
+
+export async function encodeMp4Animation<A extends PluginStateAnimation>(plugin: PluginContext, ctx: RuntimeContext, params: Mp4EncoderParams<A>) {
+    await ctx.update({ message: 'Initializing...', isIndeterminate: true });
+
+    validateViewport(params);
+    const durationMs = PluginStateAnimation.getDuration(plugin, params.animation);
+    if (durationMs === void 0) {
+        throw new Error('The animation does not have the duration specified.');
+    }
+
+    const encoder = await HME.createH264MP4Encoder();
+
+    const { width, height } = params;
+    let vw = params.viewport.width, vh = params.viewport.height;
+
+    // dimensions must be a multiple of 2
+    if (vw % 2 !== 0) vw -= 1;
+    if (vh % 2 !== 0) vh -= 1;
+
+    const normalizedViewport: Viewport = { ...params.viewport, width: vw, height: vh };
+
+    encoder.width = vw;
+    encoder.height = vh;
+    if (params.quantizationParameter) encoder.quantizationParameter = params.quantizationParameter;
+    if (params.fps) encoder.frameRate = params.fps;
+    encoder.initialize();
+
+    const loop = plugin.animationLoop;
+    const canvasProps = plugin.canvas3d?.props;
+    const wasAnimating = loop.isAnimating;
+    let stoppedAnimation = true, finalized = false;
+
+    try {
+        loop.stop();
+        loop.resetTime(0);
+
+        if (params.customBackground !== void 0) {
+            plugin.canvas3d?.setProps({ renderer: { backgroundColor: params.customBackground }, transparentBackground: false }, true);
+        }
+
+        const fps = encoder.frameRate;
+        const N = Math.ceil(durationMs / 1000 * fps);
+        const dt = durationMs / N;
+
+        await ctx.update({ message: 'Rendering...', isIndeterminate: false, current: 0, max: N + 1 });
+
+        await plugin.managers.animation.play(params.animation.definition, params.animation.params);
+        stoppedAnimation = false;
+        for (let i = 0; i <= N; i++) {
+            await loop.tick(i * dt, { isSynchronous: true, manualDraw: true });
+
+            const image = params.pass.getImageData(width, height, normalizedViewport);
+            encoder.addFrameRgba(image.data);
+
+            if (ctx.shouldUpdate) {
+                await ctx.update({ current: i + 1 });
+            }
+        }
+        await ctx.update({ message: 'Applying finishing touches...', isIndeterminate: true });
+        await plugin.managers.animation.stop();
+        stoppedAnimation = true;
+        encoder.finalize();
+        finalized = true;
+        return encoder.FS.readFile(encoder.outputFilename);
+    } finally {
+        if (finalized) encoder.delete();
+        if (params.customBackground !== void 0) {
+            plugin.canvas3d?.setProps({ renderer: { backgroundColor: canvasProps?.renderer!.backgroundColor }, transparentBackground: canvasProps?.transparentBackground });
+        }
+        if (!stoppedAnimation) await plugin.managers.animation.stop();
+        if (wasAnimating) loop.start();
+    }
+}
+
+function validateViewport(params: Mp4EncoderParams) {
+    if (params.viewport.x + params.viewport.width > params.width || params.viewport.y + params.viewport.height > params.height) {
+        throw new Error('Viewport exceeds the canvas dimensions.');
+    }
+}

src/extensions/mp4-export/index.ts

@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { Mp4EncoderUI } from './ui';
+
+export const Mp4Export = PluginBehavior.create<{ }>({
+    name: 'extension-mp4-export',
+    category: 'misc',
+    display: {
+        name: 'MP4 Animation Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{ }> {
+        register(): void {
+            this.ctx.customStructureControls.set('mp4-export', Mp4EncoderUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customStructureControls.delete('mp4-export');
+        }
+    },
+    params: () => ({ })
+});

src/extensions/mp4-export/ui.tsx

@@ -0,0 +1,123 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import React from 'react';
+import { merge } from 'rxjs';
+import { debounceTime } from 'rxjs/operators';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { CameraOutlinedSvg, GetAppSvg, Icon, SubscriptionsOutlinedSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { download } from '../../mol-util/download';
+import { Mp4AnimationParams, Mp4Controls } from './controls';
+
+interface State {
+    busy?: boolean,
+    data?: { movie: Uint8Array, filename: string };
+}
+
+export class Mp4EncoderUI extends CollapsableControls<{}, State> {
+    private _controls: Mp4Controls | undefined;
+
+    get controls() {
+        return this._controls || (this._controls = new Mp4Controls(this.plugin));
+    }
+
+    protected defaultState(): State & CollapsableState {
+        return {
+            header: 'Export Animation',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: SubscriptionsOutlinedSvg }
+        };
+    }
+
+    private downloadControls() {
+        return <>
+            <div className='msp-control-offset msp-help-text'>
+                <div className='msp-help-description' style={{ textAlign: 'center' }}>
+                    Rendering successful!
+                </div>
+            </div>
+            <Button icon={GetAppSvg} onClick={this.save} style={{ marginTop: 1 }}>Save Animation</Button>
+            <Button onClick={() => this.setState({ data: void 0 })} style={{ marginTop: 6 }}>Clear</Button>
+        </>;
+    }
+
+    protected renderControls(): JSX.Element | null {
+        if (this.state.data) {
+            return this.downloadControls();
+        }
+
+        const ctrl = this.controls;
+        const current = ctrl.behaviors.current.value;
+        const info = ctrl.behaviors.info.value;
+        const canApply = ctrl.behaviors.canApply.value;
+        return <>
+            <ParameterControls
+                params={ctrl.behaviors.animations.value}
+                values={{ current: current?.anim.name }}
+                onChangeValues={xs => ctrl.setCurrent(xs.current)}
+                isDisabled={this.state.busy}
+            />
+            {current && <ParameterControls
+                params={current.params}
+                values={current.values}
+                onChangeValues={xs => ctrl.setCurrentParams(xs)}
+                isDisabled={this.state.busy}
+            />}
+            <div className='msp-control-offset msp-help-text'>
+                <div className='msp-help-description' style={{ textAlign: 'center' }}>
+                    Resolution: {info.width}x{info.height}<br />
+                    Adjust in viewport using <Icon svg={CameraOutlinedSvg} inline />
+                </div>
+            </div>
+            <ParameterControls
+                params={Mp4AnimationParams}
+                values={ctrl.behaviors.params.value}
+                onChangeValues={xs => ctrl.behaviors.params.next(xs)}
+                isDisabled={this.state.busy}
+            />
+            <Button onClick={this.generate} style={{ marginTop: 1 }}
+                disabled={this.state.busy || !canApply.canApply}
+                commit={canApply.canApply ? 'on' : 'off'}>
+                {canApply.canApply ? 'Render' : canApply.reason ?? 'Invalid params/state'}
+            </Button>
+        </>;
+    }
+
+    componentDidMount() {
+        const merged = merge(
+            this.controls.behaviors.animations,
+            this.controls.behaviors.current,
+            this.controls.behaviors.canApply,
+            this.controls.behaviors.info,
+            this.controls.behaviors.params
+        );
+
+        this.subscribe(merged.pipe(debounceTime(10)), () => {
+            if (!this.state.isCollapsed) this.forceUpdate();
+        });
+    }
+
+    componentWillUnmount() {
+        this._controls?.dispose();
+        this._controls = void 0;
+    }
+
+    save = () => {
+        download(new Blob([this.state.data!.movie]), this.state.data!.filename);
+    }
+
+    generate = async () => {
+        try {
+            this.setState({ busy: true });
+            const data = await this.controls.render();
+            this.setState({ busy: false, data });
+        } catch {
+            this.setState({ busy: false });
+        }
+    }
+}

src/extensions/pdbe/structure-quality-report/color.ts

@@ -6,7 +6,7 @@
 
 import { StructureQualityReport, StructureQualityReportProvider } from './prop';
 import { Location } from '../../../mol-model/location';
-import { StructureElement } from '../../../mol-model/structure';
+import { Bond, StructureElement } from '../../../mol-model/structure';
 import { ColorTheme, LocationColor } from '../../../mol-theme/color';
 import { ThemeDataContext } from '../../../mol-theme/theme';
 import { Color } from '../../../mol-util/color';
@@ -46,11 +46,16 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
 
     if (ctx.structure && !ctx.structure.isEmpty && ctx.structure.models[0].customProperties.has(StructureQualityReportProvider.descriptor)) {
         const getIssues = StructureQualityReport.getIssues;
+        const l = StructureElement.Location.create(ctx.structure);
 
         if (props.type.name === 'issue-count') {
             color = (location: Location) => {
                 if (StructureElement.Location.is(location)) {
                     return ValidationColors[Math.min(3, getIssues(location).length) + 1];
+                } else if (Bond.isLocation(location)) {
+                    l.unit = location.aUnit;
+                    l.element = location.aUnit.elements[location.aIndex];
+                    return ValidationColors[Math.min(3, getIssues(l).length) + 1];
                 }
                 return ValidationColors[0];
             };
@@ -59,6 +64,10 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
             color = (location: Location) => {
                 if (StructureElement.Location.is(location) && getIssues(location).indexOf(issue) >= 0) {
                     return ValidationColors[4];
+                } else if (Bond.isLocation(location)) {
+                    l.unit = location.aUnit;
+                    l.element = location.aUnit.elements[location.aIndex];
+                    return ValidationColors[Math.min(3, getIssues(l).length) + 1];
                 }
                 return ValidationColors[0];
             };

src/extensions/pdbe/structure-quality-report/prop.ts

@@ -13,7 +13,7 @@ import { Model, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-m
 import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
 import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
-import Type from '../../../mol-script/language/type';
+import { Type } from '../../../mol-script/language/type';
 import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { arraySetAdd } from '../../../mol-util/array';

src/extensions/rcsb/assembly-symmetry/behavior.ts

@@ -181,8 +181,8 @@ export const AssemblySymmetryPreset = StructureRepresentationPresetProvider({
         }
 
         const assemblySymmetry = await tryCreateAssemblySymmetry(plugin, structureCell);
-        const globalThemeName = assemblySymmetry.isOk ? Tag.Cluster as any : undefined;
-        const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName }, plugin);
+        const colorTheme = assemblySymmetry.isOk ? Tag.Cluster as any : undefined;
+        const preset = await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
 
         return { components: preset.components, representations: { ...preset.representations, assemblySymmetry } };
     }

src/extensions/rcsb/assembly-symmetry/color.ts

@@ -9,7 +9,7 @@ import { ColorTheme, LocationColor } from '../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { AssemblySymmetryProvider, AssemblySymmetry } from './prop';
 import { Color } from '../../../mol-util/color';
-import { Unit, StructureElement, StructureProperties } from '../../../mol-model/structure';
+import { Unit, StructureElement, StructureProperties, Bond } from '../../../mol-model/structure';
 import { Location } from '../../../mol-model/location';
 import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
 import { getPalette, getPaletteParams } from '../../../mol-util/color/palette';
@@ -50,6 +50,8 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
     const clusters = assemblySymmetry?.value?.clusters;
 
     if (clusters?.length && ctx.structure) {
+        const l = StructureElement.Location.create(ctx.structure);
+
         const clusterByMember = new Map<string, number>();
         for (let i = 0, il = clusters.length; i < il; ++i) {
             const { members } = clusters[i]!;
@@ -67,12 +69,20 @@ export function AssemblySymmetryClusterColorTheme(ctx: ThemeDataContext, props:
         legend = palette.legend;
 
         const _emptyList: any[] = [];
+        const getColor = (location: StructureElement.Location) => {
+            const { assembly } = location.unit.conformation.operator;
+            const asymId = getAsymId(location.unit)(location);
+            const cluster = clusterByMember.get(clusterMemberKey(asymId, assembly?.operList || _emptyList));
+            return cluster !== undefined ? palette.color(cluster) : DefaultColor;
+        };
+
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location)) {
-                const { assembly } = location.unit.conformation.operator;
-                const asymId = getAsymId(location.unit)(location);
-                const cluster = clusterByMember.get(clusterMemberKey(asymId, assembly?.operList || _emptyList));
-                return cluster !== undefined ? palette.color(cluster) : DefaultColor;
+                return getColor(location);
+            } else if (Bond.isLocation(location)) {
+                l.unit = location.aUnit;
+                l.element = location.aUnit.elements[location.aIndex];
+                return getColor(l);
             }
             return DefaultColor;
         };

src/extensions/rcsb/assembly-symmetry/prop.ts

@@ -5,7 +5,7 @@
  */
 
 import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphql/types';
-import query from '../graphql/symmetry.gql';
+import { symmetry_gql } from '../graphql/symmetry.gql';
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
@@ -66,7 +66,7 @@ export namespace AssemblySymmetry {
             assembly_id: structure.units[0].conformation.operator.assembly?.id || '',
             entry_id: structure.units[0].model.entryId
         };
-        const result = await client.request(ctx.runtime, query, variables);
+        const result = await client.request(ctx.runtime, symmetry_gql, variables);
         let value: AssemblySymmetryDataValue = [];
 
         if (!result.data.assembly?.rcsb_struct_symmetry) {

src/extensions/rcsb/graphql/symmetry.gql.ts

@@ -1,4 +1,4 @@
-export default /* GraphQL */ `
+export const symmetry_gql = /* GraphQL */ `
 query AssemblySymmetry($assembly_id: String!, $entry_id: String!) {
     assembly(assembly_id: $assembly_id, entry_id: $entry_id) {
         rcsb_struct_symmetry {

src/extensions/rcsb/validation-report/behavior.ts

@@ -309,15 +309,15 @@ export const ValidationReportGeometryQualityPreset = StructureRepresentationPres
     params: () => StructureRepresentationPresetProvider.CommonParams,
     async apply(ref, params, plugin) {
         const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const model = structureCell?.obj?.data.model;
-        if (!structureCell || !model) return {};
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
 
         await plugin.runTask(Task.create('Validation Report', async runtime => {
-            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure.models[0]);
         }));
 
         const colorTheme = GeometryQualityColorThemeProvider.name as any;
-        const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin);
+        const { components, representations } = await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
 
         const clashes = await plugin.builders.structure.tryCreateComponentFromExpression(structureCell, hasClash.expression, 'clashes', { label: 'Clashes' });
 
@@ -329,6 +329,7 @@ export const ValidationReportGeometryQualityPreset = StructureRepresentationPres
         }
 
         await update.commit({ revertOnError: true });
+
         return { components: { ...components, clashes }, representations: { ...representations, clashesBallAndStick, clashesRepr } };
     }
 });
@@ -345,15 +346,15 @@ export const ValidationReportDensityFitPreset = StructureRepresentationPresetPro
     params: () => StructureRepresentationPresetProvider.CommonParams,
     async apply(ref, params, plugin) {
         const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const model = structureCell?.obj?.data.model;
-        if (!structureCell || !model) return {};
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
 
         await plugin.runTask(Task.create('Validation Report', async runtime => {
-            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure.models[0]);
         }));
 
         const colorTheme = DensityFitColorThemeProvider.name as any;
-        return await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin);
+        return await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
     }
 });
 
@@ -369,14 +370,14 @@ export const ValidationReportRandomCoilIndexPreset = StructureRepresentationPres
     params: () => StructureRepresentationPresetProvider.CommonParams,
     async apply(ref, params, plugin) {
         const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const model = structureCell?.obj?.data.model;
-        if (!structureCell || !model) return {};
+        const structure = structureCell?.obj?.data;
+        if (!structureCell || !structure) return {};
 
         await plugin.runTask(Task.create('Validation Report', async runtime => {
-            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, model);
+            await ValidationReportProvider.attach({ runtime, assetManager: plugin.managers.asset }, structure.models[0]);
         }));
 
         const colorTheme = RandomCoilIndexColorThemeProvider.name as any;
-        return await PresetStructureRepresentations.auto.apply(ref, { ...params, globalThemeName: colorTheme }, plugin);
+        return await PresetStructureRepresentations.auto.apply(ref, { ...params, theme: { globalName: colorTheme, focus: { name: colorTheme } } }, plugin);
     }
 });

src/extensions/rcsb/validation-report/color/density-fit.ts

@@ -8,7 +8,7 @@ import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Color, ColorScale } from '../../../../mol-util/color';
-import { StructureElement, Model } from '../../../../mol-model/structure';
+import { StructureElement, Model, ElementIndex, Bond } from '../../../../mol-model/structure';
 import { Location } from '../../../../mol-model/location';
 import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
 import { ValidationReportProvider, ValidationReport } from '../prop';
@@ -37,13 +37,19 @@ export function DensityFitColorTheme(ctx: ThemeDataContext, props: {}): ColorThe
     if (validationReport?.value && model) {
         const { rsrz, rscc } = validationReport.value;
         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+        const getColor = (element: ElementIndex) => {
+            const rsrzValue = rsrz.get(residueIndex[element]);
+            if (rsrzValue !== undefined) return scaleRsrz.color(rsrzValue);
+            const rsccValue = rscc.get(residueIndex[element]);
+            if (rsccValue !== undefined) return scaleRscc.color(rsccValue);
+            return DefaultColor;
+        };
+
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location) && location.unit.model === model) {
-                const rsrzValue = rsrz.get(residueIndex[location.element]);
-                if (rsrzValue !== undefined) return scaleRsrz.color(rsrzValue);
-                const rsccValue = rscc.get(residueIndex[location.element]);
-                if (rsccValue !== undefined) return scaleRscc.color(rsccValue);
-                return DefaultColor;
+                return getColor(location.element);
+            } else if (Bond.isLocation(location) && location.aUnit.model === model) {
+                return getColor(location.aUnit.elements[location.aIndex]);
             }
             return DefaultColor;
         };

src/extensions/rcsb/validation-report/color/geometry-quality.ts

@@ -8,7 +8,7 @@ import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Color } from '../../../../mol-util/color';
-import { StructureElement } from '../../../../mol-model/structure';
+import { Bond, ElementIndex, StructureElement } from '../../../../mol-model/structure';
 import { Location } from '../../../../mol-model/location';
 import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
 import { ValidationReportProvider, ValidationReport } from '../prop';
@@ -32,7 +32,7 @@ const ColorLegend = TableLegend([
 ]);
 
 export function getGeometricQualityColorThemeParams(ctx: ThemeDataContext) {
-    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]).value;
+    const validationReport = !!ctx.structure && ctx.structure.models.length > 0 && ValidationReportProvider.get(ctx.structure.models[0]).value;
     const options: [string, string][] = [];
     if (validationReport) {
         const kinds = new Set<string>();
@@ -48,7 +48,7 @@ export type GeometricQualityColorThemeParams = ReturnType<typeof getGeometricQua
 export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Values<GeometricQualityColorThemeParams>): ColorTheme<GeometricQualityColorThemeParams> {
     let color: LocationColor = () => DefaultColor;
 
-    const validationReport = ctx.structure && ValidationReportProvider.get(ctx.structure.models[0]);
+    const validationReport = !!ctx.structure && ctx.structure.models.length > 0 ? ValidationReportProvider.get(ctx.structure.models[0]) : void 0;
     const contextHash = validationReport?.version;
 
     const value = validationReport?.value;
@@ -59,31 +59,35 @@ export function GeometryQualityColorTheme(ctx: ThemeDataContext, props: PD.Value
         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
         const { polymerType } = model.atomicHierarchy.derived.residue;
         const ignore = new Set(props.ignore);
+        const getColor = (element: ElementIndex) => {
+            const rI = residueIndex[element];
+
+            const value = geometryIssues.get(rI);
+            if (value === undefined) return DefaultColor;
+
+            let count = SetUtils.differenceSize(value, ignore);
+
+            if (count > 0 && polymerType[rI] === PolymerType.NA) {
+                count = 0;
+                if (!ignore.has('clash') && clashes.getVertexEdgeCount(element) > 0) count += 1;
+                if (!ignore.has('mog-bond-outlier') && bondOutliers.index.has(element)) count += 1;
+                if (!ignore.has('mog-angle-outlier') && angleOutliers.index.has(element)) count += 1;
+            }
+
+            switch (count) {
+                case undefined: return DefaultColor;
+                case 0: return NoIssuesColor;
+                case 1: return OneIssueColor;
+                case 2: return TwoIssuesColor;
+                default: return ThreeOrMoreIssuesColor;
+            }
+        };
 
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location) && location.unit.model === model) {
-                const { element } = location;
-                const rI = residueIndex[element];
-
-                const value = geometryIssues.get(rI);
-                if (value === undefined) return DefaultColor;
-
-                let count = SetUtils.differenceSize(value, ignore);
-
-                if (count > 0 && polymerType[rI] === PolymerType.NA) {
-                    count = 0;
-                    if (!ignore.has('clash') && clashes.getVertexEdgeCount(element) > 0) count += 1;
-                    if (!ignore.has('mog-bond-outlier') && bondOutliers.index.has(element)) count += 1;
-                    if (!ignore.has('mog-angle-outlier') && angleOutliers.index.has(element)) count += 1;
-                }
-
-                switch (count) {
-                    case undefined: return DefaultColor;
-                    case 0: return NoIssuesColor;
-                    case 1: return OneIssueColor;
-                    case 2: return TwoIssuesColor;
-                    default: return ThreeOrMoreIssuesColor;
-                }
+                return getColor(location.element);
+            } else if (Bond.isLocation(location) && location.aUnit.model === model) {
+                return getColor(location.aUnit.elements[location.aIndex]);
             }
             return DefaultColor;
         };

src/extensions/rcsb/validation-report/color/random-coil-index.ts

@@ -8,7 +8,7 @@ import { ThemeDataContext } from '../../../../mol-theme/theme';
 import { ColorTheme, LocationColor } from '../../../../mol-theme/color';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Color, ColorScale } from '../../../../mol-util/color';
-import { StructureElement, Model } from '../../../../mol-model/structure';
+import { StructureElement, Model, ElementIndex, Bond } from '../../../../mol-model/structure';
 import { Location } from '../../../../mol-model/location';
 import { CustomProperty } from '../../../../mol-model-props/common/custom-property';
 import { ValidationReportProvider, ValidationReport } from '../prop';
@@ -31,10 +31,16 @@ export function RandomCoilIndexColorTheme(ctx: ThemeDataContext, props: {}): Col
 
     if (rci && model) {
         const residueIndex = model.atomicHierarchy.residueAtomSegments.index;
+        const getColor = (element: ElementIndex) => {
+            const value = rci.get(residueIndex[element]);
+            return value === undefined ? DefaultColor : scale.color(value);
+        };
+
         color = (location: Location): Color => {
             if (StructureElement.Location.is(location) && location.unit.model === model) {
-                const value = rci.get(residueIndex[location.element]);
-                return value === undefined ? DefaultColor : scale.color(value);
+                return getColor(location.element);
+            } else if (Bond.isLocation(location) && location.aUnit.model === model) {
+                return getColor(location.aUnit.elements[location.aIndex]);
             }
             return DefaultColor;
         };

src/extensions/rcsb/validation-report/prop.ts

@@ -19,7 +19,7 @@ import { equalEps } from '../../../mol-math/linear-algebra/3d/common';
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
-import Type from '../../../mol-script/language/type';
+import { Type } from '../../../mol-script/language/type';
 import { Asset } from '../../../mol-util/assets';
 import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
@@ -187,7 +187,7 @@ type InterUnitClashesProps = {
 }
 
 export type IntraUnitClashes = IntAdjacencyGraph<UnitIndex, IntraUnitClashesProps>
-export type InterUnitClashes = InterUnitGraph<Unit.Atomic, UnitIndex, InterUnitClashesProps>
+export type InterUnitClashes = InterUnitGraph<number, UnitIndex, InterUnitClashesProps>
 
 export interface Clashes {
     readonly interUnit: InterUnitClashes
@@ -195,7 +195,7 @@ export interface Clashes {
 }
 
 function createInterUnitClashes(structure: Structure, clashes: ValidationReport['clashes']) {
-    const builder = new InterUnitGraph.Builder<Unit.Atomic, UnitIndex, InterUnitClashesProps>();
+    const builder = new InterUnitGraph.Builder<number, UnitIndex, InterUnitClashesProps>();
     const { a, b, edgeProps: { id, magnitude, distance } } = clashes;
 
     const pA = Vec3(), pB = Vec3();
@@ -204,7 +204,7 @@ function createInterUnitClashes(structure: Structure, clashes: ValidationReport[
         const elementsA = unitA.elements;
         const elementsB = unitB.elements;
 
-        builder.startUnitPair(unitA as Unit.Atomic, unitB as Unit.Atomic);
+        builder.startUnitPair(unitA.id, unitB.id);
 
         for (let i = 0, il = clashes.edgeCount * 2; i < il; ++i) {
             // TODO create lookup

src/extensions/rcsb/validation-report/representation.ts

@@ -15,7 +15,7 @@ import { Interval } from '../../../mol-data/int';
 import { RepresentationContext, RepresentationParamsGetter, Representation } from '../../../mol-repr/representation';
 import { UnitsRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider, ComplexRepresentation } from '../../../mol-repr/structure/representation';
 import { VisualContext } from '../../../mol-repr/visual';
-import { createLinkCylinderMesh, LinkCylinderParams, LinkCylinderStyle } from '../../../mol-repr/structure/visual/util/link';
+import { createLinkCylinderMesh, LinkCylinderParams, LinkStyle } from '../../../mol-repr/structure/visual/util/link';
 import { UnitsMeshParams, UnitsVisual, UnitsMeshVisual, StructureGroup } from '../../../mol-repr/structure/units-visual';
 import { VisualUpdateState } from '../../../mol-repr/util';
 import { LocationIterator } from '../../../mol-geo/util/location-iterator';
@@ -50,7 +50,7 @@ function createIntraUnitClashCylinderMesh(ctx: VisualContext, unit: Unit, struct
             pos(elements[a[edgeIndex]], posA);
             pos(elements[b[edgeIndex]], posB);
         },
-        style: (edgeIndex: number) => LinkCylinderStyle.Disk,
+        style: (edgeIndex: number) => LinkStyle.Disk,
         radius: (edgeIndex: number) => magnitude[edgeIndex] * sizeFactor,
     };
 
@@ -143,7 +143,7 @@ function createIntraClashIterator(structureGroup: StructureGroup): LocationItera
         location.element = unit.elements[a[groupIndex]];
         return location;
     };
-    return LocationIterator(groupCount, instanceCount, getLocation);
+    return LocationIterator(groupCount, instanceCount, 1, getLocation);
 }
 
 //
@@ -159,11 +159,12 @@ function createInterUnitClashCylinderMesh(ctx: VisualContext, structure: Structu
         linkCount: edgeCount,
         position: (posA: Vec3, posB: Vec3, edgeIndex: number) => {
             const b = edges[edgeIndex];
-            const uA = b.unitA, uB = b.unitB;
+            const uA = structure.unitMap.get(b.unitA);
+            const uB = structure.unitMap.get(b.unitB);
             uA.conformation.position(uA.elements[b.indexA], posA);
             uB.conformation.position(uB.elements[b.indexB], posB);
         },
-        style: (edgeIndex: number) => LinkCylinderStyle.Disk,
+        style: (edgeIndex: number) => LinkStyle.Disk,
         radius: (edgeIndex: number) => edges[edgeIndex].props.magnitude * sizeFactor
     };
 
@@ -197,11 +198,13 @@ export function InterUnitClashVisual(materialId: number): ComplexVisual<InterUni
     }, materialId);
 }
 
-function getInterClashBoundingSphere(clashes: InterUnitClashes, elements: number[], boundingSphere: Sphere3D) {
+function getInterClashBoundingSphere(structure: Structure, clashes: InterUnitClashes, elements: number[], boundingSphere: Sphere3D) {
     return CentroidHelper.fromPairProvider(elements.length, (i, pA, pB) => {
         const c = clashes.edges[elements[i]];
-        c.unitA.conformation.position(c.unitA.elements[c.indexA], pA);
-        c.unitB.conformation.position(c.unitB.elements[c.indexB], pB);
+        const uA = structure.unitMap.get(c.unitA);
+        const uB = structure.unitMap.get(c.unitB);
+        uA.conformation.position(uA.elements[c.indexA], pA);
+        uB.conformation.position(uB.elements[c.indexB], pB);
     }, boundingSphere);
 }
 
@@ -209,18 +212,20 @@ function getInterClashLabel(structure: Structure, clashes: InterUnitClashes, ele
     const idx = elements[0];
     if (idx === undefined) return '';
     const c = clashes.edges[idx];
+    const uA = structure.unitMap.get(c.unitA);
+    const uB = structure.unitMap.get(c.unitB);
     const mag = c.props.magnitude.toFixed(2);
     const dist = c.props.distance.toFixed(2);
 
     return [
         `Clash id: ${c.props.id} | Magnitude: ${mag} \u212B | Distance: ${dist} \u212B`,
-        bondLabel(Bond.Location(structure, c.unitA, c.indexA, structure, c.unitB, c.indexB))
+        bondLabel(Bond.Location(structure, uA, c.indexA, structure, uB, c.indexB))
     ].join('</br>');
 }
 
 function InterClashLoci(structure: Structure, clashes: InterUnitClashes, elements: number[]) {
     return DataLoci('inter-clashes', clashes, elements,
-        (boundingSphere: Sphere3D) =>  getInterClashBoundingSphere(clashes, elements, boundingSphere),
+        (boundingSphere: Sphere3D) =>  getInterClashBoundingSphere(structure, clashes, elements, boundingSphere),
         () => getInterClashLabel(structure, clashes, elements));
 }
 
@@ -246,11 +251,11 @@ function createInterClashIterator(structure: Structure): LocationIterator {
     const location = StructureElement.Location.create(structure);
     const getLocation = (groupIndex: number) => {
         const clash = clashes.edges[groupIndex];
-        location.unit = clash.unitA;
-        location.element = clash.unitA.elements[clash.indexA];
+        location.unit = structure.unitMap.get(clash.unitA);
+        location.element = location.unit.elements[clash.indexA];
         return location;
     };
-    return LocationIterator(groupCount, instanceCount, getLocation, true);
+    return LocationIterator(groupCount, instanceCount, 1, getLocation, true);
 }
 
 //

src/mol-canvas3d/camera.ts

@@ -10,22 +10,37 @@ import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
 
-export { Camera };
+export { ICamera, Camera };
 
-class Camera {
+interface ICamera {
+    readonly viewport: Viewport,
+    readonly view: Mat4,
+    readonly projection: Mat4,
+    readonly projectionView: Mat4,
+    readonly inverseProjectionView: Mat4,
+    readonly state: Readonly<Camera.Snapshot>,
+    readonly viewOffset: Camera.ViewOffset,
+    readonly far: number,
+    readonly near: number,
+    readonly fogFar: number,
+    readonly fogNear: number,
+}
+
+class Camera implements ICamera {
     readonly view: Mat4 = Mat4.identity();
     readonly projection: Mat4 = Mat4.identity();
     readonly projectionView: Mat4 = Mat4.identity();
     readonly inverseProjectionView: Mat4 = Mat4.identity();
 
+    private pixelScale: number
+    get pixelRatio () {
+        const dpr = (typeof window !== 'undefined') ? window.devicePixelRatio : 1;
+        return dpr * this.pixelScale;
+    }
+
     readonly viewport: Viewport;
     readonly state: Readonly<Camera.Snapshot> = Camera.createDefaultSnapshot();
-    readonly viewOffset: Camera.ViewOffset = {
-        enabled: false,
-        fullWidth: 1, fullHeight: 1,
-        offsetX: 0, offsetY: 0,
-        width: 1, height: 1
-    }
+    readonly viewOffset = Camera.ViewOffset();
 
     near = 1
     far = 10000
@@ -52,6 +67,10 @@ class Camera {
 
     update() {
         const snapshot = this.state as Camera.Snapshot;
+        if (snapshot.radiusMax === 0) {
+            return false;
+        }
+
         const height = 2 * Math.tan(snapshot.fov / 2) * Vec3.distance(snapshot.position, snapshot.target);
         this.zoom = this.viewport.height / height;
 
@@ -86,12 +105,7 @@ class Camera {
     }
 
     getTargetDistance(radius: number) {
-        const r = Math.max(radius, 0.01);
-        const { fov } = this.state;
-        const { width, height } = this.viewport;
-        const aspect = width / height;
-        const aspectFactor = (height < width ? 1 : aspect);
-        return Math.abs((r / aspectFactor) / Math.sin(fov / 2));
+        return Camera.targetDistance(radius, this.state.fov, this.viewport.width, this.viewport.height);
     }
 
     getFocus(target: Vec3, radius: number, up?: Vec3, dir?: Vec3): Partial<Camera.Snapshot> {
@@ -126,8 +140,9 @@ class Camera {
         return cameraUnproject(out, point, this.viewport, this.inverseProjectionView);
     }
 
-    constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(-1, -1, 1, 1)) {
+    constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(0, 0, 128, 128), props: Partial<{ pixelScale: number }> = {}) {
         this.viewport = viewport;
+        this.pixelScale = props.pixelScale || 1;
         Camera.copySnapshot(this.state, state);
     }
 }
@@ -150,6 +165,15 @@ namespace Camera {
         height: number
     }
 
+    export function ViewOffset(): ViewOffset {
+        return {
+            enabled: false,
+            fullWidth: 1, fullHeight: 1,
+            offsetX: 0, offsetY: 0,
+            width: 1, height: 1
+        };
+    }
+
     export function setViewOffset(out: ViewOffset, fullWidth: number, fullHeight: number, offsetX: number, offsetY: number, width: number, height: number) {
         out.fullWidth = fullWidth;
         out.fullHeight = fullHeight;
@@ -159,6 +183,23 @@ namespace Camera {
         out.height = height;
     }
 
+    export function copyViewOffset(out: ViewOffset, view: ViewOffset) {
+        out.enabled = view.enabled;
+        out.fullWidth = view.fullWidth;
+        out.fullHeight = view.fullHeight;
+        out.offsetX = view.offsetX;
+        out.offsetY = view.offsetY;
+        out.width = view.width;
+        out.height = view.height;
+    }
+
+    export function targetDistance(radius: number, fov: number, width: number, height: number) {
+        const r = Math.max(radius, 0.01);
+        const aspect = width / height;
+        const aspectFactor = (height < width ? 1 : aspect);
+        return Math.abs((r / aspectFactor) / Math.sin(fov / 2));
+    }
+
     export function createDefaultSnapshot(): Snapshot {
         return {
             mode: 'perspective',
@@ -168,8 +209,8 @@ namespace Camera {
             up: Vec3.create(0, 1, 0),
             target: Vec3.create(0, 0, 0),
 
-            radius: 10,
-            radiusMax: 10,
+            radius: 0,
+            radiusMax: 0,
             fog: 50,
             clipFar: true
         };
@@ -211,10 +252,10 @@ namespace Camera {
 function updateOrtho(camera: Camera) {
     const { viewport, zoom, near, far, viewOffset } = camera;
 
-    const fullLeft = -(viewport.width - viewport.x) / 2;
-    const fullRight = (viewport.width - viewport.x) / 2;
-    const fullTop = (viewport.height - viewport.y) / 2;
-    const fullBottom = -(viewport.height - viewport.y) / 2;
+    const fullLeft = -viewport.width / 2;
+    const fullRight = viewport.width / 2;
+    const fullTop = viewport.height / 2;
+    const fullBottom = -viewport.height / 2;
 
     const dx = (fullRight - fullLeft) / (2 * zoom);
     const dy = (fullTop - fullBottom) / (2 * zoom);
@@ -278,12 +319,12 @@ function updateClip(camera: Camera) {
     let far = cameraDistance + normalizedFar;
 
     const fogNearFactor = -(50 - fog) / 50;
-    let fogNear = cameraDistance - (normalizedFar * fogNearFactor);
-    let fogFar = far;
+    const fogNear = cameraDistance - (normalizedFar * fogNearFactor);
+    const fogFar = far;
 
     if (mode === 'perspective') {
         // set at least to 5 to avoid slow sphere impostor rendering
-        near = Math.max(5, near);
+        near = Math.max(Math.min(radiusMax, 5), near);
         far = Math.max(5, far);
     } else {
         near = Math.max(0, near);
@@ -296,7 +337,7 @@ function updateClip(camera: Camera) {
     }
 
     camera.near = near;
-    camera.far = far;
+    camera.far = 2 * far; // avoid precision issues distingushing far objects from background
     camera.fogNear = fogNear;
     camera.fogFar = fogFar;
 }

src/mol-canvas3d/camera/stereo.ts

@@ -0,0 +1,141 @@
+/**
+ * Copyright (c) 2020 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>
+ *
+ * Adapted from three.js, The MIT License, Copyright © 2010-2020 three.js authors
+ */
+
+import { Mat4 } from '../../mol-math/linear-algebra';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Camera, ICamera } from '../camera';
+import { Viewport } from './util';
+
+export const StereoCameraParams = {
+    eyeSeparation: PD.Numeric(0.064, { min: 0.01, max: 0.5, step: 0.001 }),
+    focus: PD.Numeric(10, { min: 1, max: 100, step: 0.01 }),
+};
+export const DefaultStereoCameraProps = PD.getDefaultValues(StereoCameraParams);
+export type StereoCameraProps = PD.Values<typeof StereoCameraParams>
+
+export { StereoCamera };
+
+class StereoCamera {
+    readonly left: ICamera = new EyeCamera();
+    readonly right: ICamera = new EyeCamera();
+
+    get viewport() {
+        return this.parent.viewport;
+    }
+
+    get viewOffset() {
+        return this.parent.viewOffset;
+    }
+
+    private props: StereoCameraProps
+
+    constructor(private parent: Camera, props: Partial<StereoCameraProps> = {}) {
+        this.props = { ...DefaultStereoCameraProps, ...props };
+    }
+
+    setProps(props: Partial<StereoCameraProps>) {
+        Object.assign(this.props, props);
+    }
+
+    update() {
+        this.parent.update();
+        update(this.parent, this.props, this.left as EyeCamera, this.right as EyeCamera);
+    }
+}
+
+namespace StereoCamera {
+    export function is(camera: Camera | StereoCamera): camera is StereoCamera {
+        return 'left' in camera && 'right' in camera;
+    }
+}
+
+class EyeCamera implements ICamera {
+    viewport = Viewport.create(0, 0, 0, 0);
+    view = Mat4();
+    projection = Mat4();
+    projectionView = Mat4();
+    inverseProjectionView = Mat4();
+    state: Readonly<Camera.Snapshot> = Camera.createDefaultSnapshot();
+    viewOffset: Readonly<Camera.ViewOffset> = Camera.ViewOffset();
+    far: number = 0;
+    near: number = 0;
+    fogFar: number = 0;
+    fogNear: number = 0;
+}
+
+const eyeLeft = Mat4.identity(), eyeRight = Mat4.identity();
+
+function update(camera: Camera, props: StereoCameraProps, left: EyeCamera, right: EyeCamera) {
+    // Copy the states
+
+    Viewport.copy(left.viewport, camera.viewport);
+    Mat4.copy(left.view, camera.view);
+    Mat4.copy(left.projection, camera.projection);
+    Camera.copySnapshot(left.state, camera.state);
+    Camera.copyViewOffset(left.viewOffset, camera.viewOffset);
+    left.far = camera.far;
+    left.near = camera.near;
+    left.fogFar = camera.fogFar;
+    left.fogNear = camera.fogNear;
+
+    Viewport.copy(right.viewport, camera.viewport);
+    Mat4.copy(right.view, camera.view);
+    Mat4.copy(right.projection, camera.projection);
+    Camera.copySnapshot(right.state, camera.state);
+    Camera.copyViewOffset(right.viewOffset, camera.viewOffset);
+    right.far = camera.far;
+    right.near = camera.near;
+    right.fogFar = camera.fogFar;
+    right.fogNear = camera.fogNear;
+
+    // update the view offsets
+
+    const w = Math.floor(camera.viewport.width / 2);
+    const aspect = w / camera.viewport.height;
+
+    left.viewport.width = w;
+    right.viewport.x += w;
+    right.viewport.width -= w;
+
+    // update the projection and view matrices
+
+    const eyeSepHalf = props.eyeSeparation / 2;
+    const eyeSepOnProjection = eyeSepHalf * camera.near / props.focus;
+    const ymax = camera.near * Math.tan(camera.state.fov * 0.5);
+    let xmin, xmax;
+
+    // translate xOffset
+
+    eyeLeft[12] = -eyeSepHalf;
+    eyeRight[12] = eyeSepHalf;
+
+    // for left eye
+
+    xmin = -ymax * aspect + eyeSepOnProjection;
+    xmax = ymax * aspect + eyeSepOnProjection;
+
+    left.projection[0] = 2 * camera.near / (xmax - xmin);
+    left.projection[8] = (xmax + xmin) / (xmax - xmin);
+
+    Mat4.mul(left.view, left.view, eyeLeft);
+    Mat4.mul(left.projectionView, left.projection, left.view);
+    Mat4.invert(left.inverseProjectionView, left.projectionView);
+
+    // for right eye
+
+    xmin = -ymax * aspect - eyeSepOnProjection;
+    xmax = ymax * aspect - eyeSepOnProjection;
+
+    right.projection[0] = 2 * camera.near / (xmax - xmin);
+    right.projection[8] = (xmax + xmin) / (xmax - xmin);
+
+    Mat4.mul(right.view, right.view, eyeRight);
+    Mat4.mul(right.projectionView, right.projection, right.view);
+    Mat4.invert(right.inverseProjectionView, right.projectionView);
+}

src/mol-canvas3d/canvas3d.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>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -7,45 +7,51 @@
 
 import { BehaviorSubject, Subscription } from 'rxjs';
 import { now } from '../mol-util/now';
-import { Vec3 } from '../mol-math/linear-algebra';
-import InputObserver, { ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
-import Renderer, { RendererStats, RendererParams } from '../mol-gl/renderer';
+import { Vec3, Vec2 } from '../mol-math/linear-algebra';
+import { InputObserver, ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
+import { Renderer, RendererStats, RendererParams } from '../mol-gl/renderer';
 import { GraphicsRenderObject } from '../mol-gl/render-object';
 import { TrackballControls, TrackballControlsParams } from './controls/trackball';
 import { Viewport } from './camera/util';
 import { createContext, WebGLContext, getGLContext } from '../mol-gl/webgl/context';
 import { Representation } from '../mol-repr/representation';
-import Scene from '../mol-gl/scene';
-import { GraphicsRenderVariant } from '../mol-gl/webgl/render-item';
+import { Scene } from '../mol-gl/scene';
 import { PickingId } from '../mol-geo/geometry/picking';
 import { MarkerAction } from '../mol-util/marker-action';
 import { Loci, EmptyLoci, isEmptyLoci } from '../mol-model/loci';
 import { Camera } from './camera';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
-import { BoundingSphereHelper, DebugHelperParams } from './helper/bounding-sphere-helper';
+import { DebugHelperParams } from './helper/bounding-sphere-helper';
 import { SetUtils } from '../mol-util/set';
 import { Canvas3dInteractionHelper } from './helper/interaction-events';
-import { PostprocessingParams, PostprocessingPass } from './passes/postprocessing';
-import { MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
-import { PixelData } from '../mol-util/image';
-import { readTexture } from '../mol-gl/compute/util';
-import { DrawPass } from './passes/draw';
-import { PickPass } from './passes/pick';
+import { PostprocessingParams } from './passes/postprocessing';
+import { MultiSampleHelper, MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
+import { PickData } from './passes/pick';
+import { PickHelper } from './passes/pick';
 import { ImagePass, ImageProps } from './passes/image';
 import { Sphere3D } from '../mol-math/geometry';
 import { isDebugMode } from '../mol-util/debug';
 import { CameraHelperParams } from './helper/camera-helper';
 import { produce } from 'immer';
-import { HandleHelper, HandleHelperParams } from './helper/handle-helper';
+import { HandleHelperParams } from './helper/handle-helper';
+import { StereoCamera, StereoCameraParams } from './camera/stereo';
+import { Helper } from './helper/helper';
+import { Passes } from './passes/passes';
+import { shallowEqual } from '../mol-util';
 
 export const Canvas3DParams = {
     camera: PD.Group({
-        mode: PD.Select('perspective', [['perspective', 'Perspective'], ['orthographic', 'Orthographic']] as const, { label: 'Camera' }),
-        helper: PD.Group(CameraHelperParams, { isFlat: true })
+        mode: PD.Select('perspective', PD.arrayToOptions(['perspective', 'orthographic'] as const), { label: 'Camera' }),
+        helper: PD.Group(CameraHelperParams, { isFlat: true }),
+        stereo: PD.MappedStatic('off', {
+            on: PD.Group(StereoCameraParams),
+            off: PD.Group({})
+        }, { cycle: true, hideIf: p => p?.mode !== 'perspective' }),
+        manualReset: PD.Boolean(false, { isHidden: true }),
     }, { pivot: 'mode' }),
     cameraFog: PD.MappedStatic('on', {
         on: PD.Group({
-            intensity: PD.Numeric(50, { min: 1, max: 100, step: 1 }),
+            intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
         }),
         off: PD.Group({})
     }, { cycle: true, description: 'Show fog in the distance' }),
@@ -53,6 +59,15 @@ export const Canvas3DParams = {
         radius: PD.Numeric(100, { min: 0, max: 99, step: 1 }, { label: 'Clipping', description: 'How much of the scene to show.' }),
         far: PD.Boolean(true, { description: 'Hide scene in the distance' }),
     }, { pivot: 'radius' }),
+    viewport: PD.MappedStatic('canvas', {
+        canvas: PD.Group({}),
+        custom: PD.Group({
+            x: PD.Numeric(0),
+            y: PD.Numeric(0),
+            width: PD.Numeric(128),
+            height: PD.Numeric(128)
+        })
+    }),
 
     cameraResetDurationMs: PD.Numeric(250, { min: 0, max: 1000, step: 1 }, { description: 'The time it takes to reset the camera.' }),
     transparentBackground: PD.Boolean(false),
@@ -66,70 +81,57 @@ export const Canvas3DParams = {
 };
 export const DefaultCanvas3DParams = PD.getDefaultValues(Canvas3DParams);
 export type Canvas3DProps = PD.Values<typeof Canvas3DParams>
-
-export { Canvas3D };
-
-interface Canvas3D {
-    readonly webgl: WebGLContext,
-
-    add(repr: Representation.Any): void
-    remove(repr: Representation.Any): void
-    /**
-     * This function must be called if animate() is not set up so that add/remove actions take place.
-     */
-    commit(isSynchronous?: boolean): void
-    update(repr?: Representation.Any, keepBoundingSphere?: boolean): void
-    clear(): void
-    syncVisibility(): void
-
-    requestDraw(force?: boolean): void
-    animate(): void
-    identify(x: number, y: number): PickingId | undefined
-    mark(loci: Representation.Loci, action: MarkerAction): void
-    getLoci(pickingId: PickingId): Representation.Loci
-
-    readonly didDraw: BehaviorSubject<now.Timestamp>
-    readonly reprCount: BehaviorSubject<number>
-
-    handleResize(): void
-    /** Focuses camera on scene's bounding sphere, centered and zoomed. */
-    requestCameraReset(options?: { durationMs?: number, snapshot?: Partial<Camera.Snapshot> }): void
-    readonly camera: Camera
-    readonly boundingSphere: Readonly<Sphere3D>
-    getPixelData(variant: GraphicsRenderVariant): PixelData
-    setProps(props: Partial<Canvas3DProps> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void)): void
-    getImagePass(props: Partial<ImageProps>): ImagePass
-
-    /** Returns a copy of the current Canvas3D instance props */
-    readonly props: Readonly<Canvas3DProps>
-    readonly input: InputObserver
-    readonly stats: RendererStats
-    readonly interaction: Canvas3dInteractionHelper['events']
-
-    dispose(): void
+export type PartialCanvas3DProps = {
+    [K in keyof Canvas3DProps]?: Canvas3DProps[K] extends { name: string, params: any } ? Canvas3DProps[K] : Partial<Canvas3DProps[K]>
 }
 
-const requestAnimationFrame = typeof window !== 'undefined' ? window.requestAnimationFrame : (f: (time: number) => void) => setImmediate(()=>f(Date.now()));
+export { Canvas3DContext };
 
-namespace Canvas3D {
-    export interface HoverEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys }
-    export interface ClickEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys }
+/** Can be used to create multiple Canvas3D objects */
+interface Canvas3DContext {
+    readonly canvas: HTMLCanvasElement
+    readonly webgl: WebGLContext
+    readonly input: InputObserver
+    readonly passes: Passes
+    readonly attribs: Readonly<Canvas3DContext.Attribs>
+    readonly contextLost: BehaviorSubject<now.Timestamp>
+    readonly contextRestored: BehaviorSubject<now.Timestamp>
+    dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => void
+}
 
-    export function fromCanvas(canvas: HTMLCanvasElement, props: Partial<Canvas3DProps> = {}) {
+namespace Canvas3DContext {
+    const DefaultAttribs = {
+        /** true by default to avoid issues with Safari (Jan 2021) */
+        antialias: true,
+        /** true to support multiple Canvas3D objects with a single context */
+        preserveDrawingBuffer: true,
+        pixelScale: 1,
+        pickScale: 0.25,
+        enableWboit: true
+    };
+    export type Attribs = typeof DefaultAttribs
+
+    export function fromCanvas(canvas: HTMLCanvasElement, attribs: Partial<Attribs> = {}): Canvas3DContext {
+        const a = { ...DefaultAttribs, ...attribs };
+        const { antialias, preserveDrawingBuffer, pixelScale } = a;
         const gl = getGLContext(canvas, {
-            alpha: true,
-            antialias: true,
-            depth: true,
-            preserveDrawingBuffer: true,
-            premultipliedAlpha: false,
+            antialias,
+            preserveDrawingBuffer,
+            alpha: true, // the renderer requires an alpha channel
+            depth: true, // the renderer requires a depth buffer
+            premultipliedAlpha: true, // the renderer outputs PMA
         });
         if (gl === null) throw new Error('Could not create a WebGL rendering context');
-        const input = InputObserver.fromElement(canvas);
-        const webgl = createContext(gl);
+
+        const input = InputObserver.fromElement(canvas, { pixelScale });
+        const webgl = createContext(gl, { pixelScale });
+        const passes = new Passes(webgl, attribs);
 
         if (isDebugMode) {
             const loseContextExt = gl.getExtension('WEBGL_lose_context');
             if (loseContextExt) {
+                // Hold down shift+ctrl+alt and press any mouse button to call `loseContext`.
+                // After 1 second `restoreContext` will be called.
                 canvas.addEventListener('mousedown', e => {
                     if (webgl.isContextLost) return;
                     if (!e.shiftKey || !e.ctrlKey || !e.altKey) return;
@@ -148,35 +150,130 @@ namespace Canvas3D {
 
         // https://www.khronos.org/webgl/wiki/HandlingContextLost
 
-        canvas.addEventListener('webglcontextlost', e => {
+        const contextLost = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
+
+        const handleWebglContextLost = (e: Event) => {
             webgl.setContextLost();
             e.preventDefault();
             if (isDebugMode) console.log('context lost');
-        }, false);
+            contextLost.next(now());
+        };
 
-        canvas.addEventListener('webglcontextrestored', () => {
+        const handlewWebglContextRestored = () => {
             if (!webgl.isContextLost) return;
-            webgl.handleContextRestored();
+            webgl.handleContextRestored(() => {
+                passes.draw.reset();
+            });
             if (isDebugMode) console.log('context restored');
-        }, false);
+        };
 
-        return Canvas3D.create(webgl, input, props);
+        canvas.addEventListener('webglcontextlost', handleWebglContextLost, false);
+        canvas.addEventListener('webglcontextrestored', handlewWebglContextRestored, false);
+
+        return {
+            canvas,
+            webgl,
+            input,
+            passes,
+            attribs: a,
+            contextLost,
+            contextRestored: webgl.contextRestored,
+            dispose: (options?: Partial<{ doNotForceWebGLContextLoss: boolean }>) => {
+                input.dispose();
+
+                canvas.removeEventListener('webglcontextlost', handleWebglContextLost, false);
+                canvas.removeEventListener('webglcontextrestored', handlewWebglContextRestored, false);
+                webgl.destroy(options);
+            }
+        };
     }
+}
 
-    export function create(webgl: WebGLContext, input: InputObserver, props: Partial<Canvas3DProps> = {}): Canvas3D {
-        const p = { ...DefaultCanvas3DParams, ...props };
+export { Canvas3D };
+
+interface Canvas3D {
+    readonly webgl: WebGLContext,
+
+    add(repr: Representation.Any): void
+    remove(repr: Representation.Any): void
+    /**
+     * This function must be called if animate() is not set up so that add/remove actions take place.
+     */
+    commit(isSynchronous?: boolean): void
+    /**
+     * Funcion for external "animation" control
+     * Calls commit.
+     */
+    tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean }): void
+    update(repr?: Representation.Any, keepBoundingSphere?: boolean): void
+    clear(): void
+    syncVisibility(): void
+
+    requestDraw(force?: boolean): void
+
+    /** Reset the timers, used by "animate" */
+    resetTime(t: number): void
+    animate(): void
+    pause(): void
+    identify(x: number, y: number): PickData | undefined
+    mark(loci: Representation.Loci, action: MarkerAction): void
+    getLoci(pickingId: PickingId | undefined): Representation.Loci
+
+    notifyDidDraw: boolean,
+    readonly didDraw: BehaviorSubject<now.Timestamp>
+    readonly commited: BehaviorSubject<now.Timestamp>
+    readonly reprCount: BehaviorSubject<number>
+    readonly resized: BehaviorSubject<any>
+
+    handleResize(): void
+    /** performs handleResize on the next animation frame */
+    requestResize(): void
+    /** Focuses camera on scene's bounding sphere, centered and zoomed. */
+    requestCameraReset(options?: { durationMs?: number, snapshot?: Partial<Camera.Snapshot> }): void
+    readonly camera: Camera
+    readonly boundingSphere: Readonly<Sphere3D>
+    setProps(props: PartialCanvas3DProps | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void), doNotRequestDraw?: boolean /* = false */): void
+    getImagePass(props: Partial<ImageProps>): ImagePass
+
+    /** Returns a copy of the current Canvas3D instance props */
+    readonly props: Readonly<Canvas3DProps>
+    readonly input: InputObserver
+    readonly stats: RendererStats
+    readonly interaction: Canvas3dInteractionHelper['events']
+
+    dispose(): void
+}
+
+const requestAnimationFrame = typeof window !== 'undefined'
+    ? window.requestAnimationFrame
+    : (f: (time: number) => void) => setImmediate(() => f(Date.now())) as unknown as number;
+const cancelAnimationFrame = typeof window !== 'undefined'
+    ? window.cancelAnimationFrame
+    : (handle: number) => clearImmediate(handle as unknown as NodeJS.Immediate);
+
+namespace Canvas3D {
+    export interface HoverEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, page?: Vec2, position?: Vec3 }
+    export interface DragEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, pageStart: Vec2, pageEnd: Vec2 }
+    export interface ClickEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, page?: Vec2, position?: Vec3 }
+
+    export function create({ webgl, input, passes, attribs }: Canvas3DContext, props: Partial<Canvas3DProps> = {}): Canvas3D {
+        const p: Canvas3DProps = { ...DefaultCanvas3DParams, ...props };
 
         const reprRenderObjects = new Map<Representation.Any, Set<GraphicsRenderObject>>();
         const reprUpdatedSubscriptions = new Map<Representation.Any, Subscription>();
         const reprCount = new BehaviorSubject(0);
 
-        const startTime = now();
+        let startTime = now();
         const didDraw = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
+        const commited = new BehaviorSubject<now.Timestamp>(0 as now.Timestamp);
 
         const { gl, contextRestored } = webgl;
 
-        let width = gl.drawingBufferWidth;
-        let height = gl.drawingBufferHeight;
+        let x = 0;
+        let y = 0;
+        let width = 128;
+        let height = 128;
+        updateViewport();
 
         const scene = Scene.create(webgl);
 
@@ -185,40 +282,41 @@ namespace Canvas3D {
             mode: p.camera.mode,
             fog: p.cameraFog.name === 'on' ? p.cameraFog.params.intensity : 0,
             clipFar: p.cameraClipping.far
-        });
+        }, { x, y, width, height }, { pixelScale: attribs.pixelScale });
+        const stereoCamera = new StereoCamera(camera, p.camera.stereo.params);
 
         const controls = TrackballControls.create(input, camera, p.trackball);
         const renderer = Renderer.create(webgl, p.renderer);
-        const debugHelper = new BoundingSphereHelper(webgl, scene, p.debug);
-        const handleHelper = new HandleHelper(webgl, p.handle);
-        const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input);
+        const helper = new Helper(webgl, scene, p);
 
-        const drawPass = new DrawPass(webgl, renderer, scene, camera, debugHelper, handleHelper, {
-            cameraHelper: p.camera.helper
-        });
-        const pickPass = new PickPass(webgl, renderer, scene, camera, handleHelper, 0.5);
-        const postprocessing = new PostprocessingPass(webgl, camera, drawPass, p.postprocessing);
-        const multiSample = new MultiSamplePass(webgl, camera, drawPass, postprocessing, p.multiSample);
+        const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height });
+        const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera);
+        const multiSampleHelper = new MultiSampleHelper(passes.multiSample);
 
         let drawPending = false;
         let cameraResetRequested = false;
         let nextCameraResetDuration: number | undefined = void 0;
         let nextCameraResetSnapshot: Partial<Camera.Snapshot> | undefined = void 0;
+        let resizeRequested = false;
 
-        function getLoci(pickingId: PickingId) {
+        let notifyDidDraw = true;
+
+        function getLoci(pickingId: PickingId | undefined) {
             let loci: Loci = EmptyLoci;
             let repr: Representation.Any = Representation.Empty;
-            loci = handleHelper.getLoci(pickingId);
-            reprRenderObjects.forEach((_, _repr) => {
-                const _loci = _repr.getLoci(pickingId);
-                if (!isEmptyLoci(_loci)) {
-                    if (!isEmptyLoci(loci)) {
-                        console.warn('found another loci, this should not happen');
+            if (pickingId) {
+                loci = helper.handle.getLoci(pickingId);
+                reprRenderObjects.forEach((_, _repr) => {
+                    const _loci = _repr.getLoci(pickingId);
+                    if (!isEmptyLoci(_loci)) {
+                        if (!isEmptyLoci(loci)) {
+                            console.warn('found another loci, this should not happen');
+                        }
+                        loci = _loci;
+                        repr = _repr;
                     }
-                    loci = _loci;
-                    repr = _repr;
-                }
-            });
+                });
+            }
             return { loci, repr };
         }
 
@@ -228,36 +326,50 @@ namespace Canvas3D {
             if (repr) {
                 changed = repr.mark(loci, action);
             } else {
-                changed = handleHelper.mark(loci, action);
+                changed = helper.handle.mark(loci, action);
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
             if (changed) {
                 scene.update(void 0, true);
-                handleHelper.scene.update(void 0, true);
-                const prevPickDirty = pickPass.pickDirty;
+                helper.handle.scene.update(void 0, true);
+                const prevPickDirty = pickHelper.dirty;
                 draw(true);
-                pickPass.pickDirty = prevPickDirty; // marking does not change picking buffers
+                pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
             }
         }
 
         function render(force: boolean) {
             if (webgl.isContextLost) return false;
 
+            let resized = false;
+            if (resizeRequested) {
+                handleResize(false);
+                resizeRequested = false;
+                resized = true;
+            }
+
+            if (x > gl.drawingBufferWidth || x + width < 0 ||
+                y > gl.drawingBufferHeight || y + height < 0
+            ) return false;
+
             let didRender = false;
             controls.update(currentTime);
-            Viewport.set(camera.viewport, 0, 0, width, height);
             const cameraChanged = camera.update();
-            multiSample.update(force || cameraChanged, currentTime);
+            const multiSampleChanged = multiSampleHelper.update(force || cameraChanged, p.multiSample);
 
-            if (force || cameraChanged || multiSample.enabled) {
-                renderer.setViewport(0, 0, width, height);
-                if (multiSample.enabled) {
-                    multiSample.render(true, p.transparentBackground);
-                } else {
-                    drawPass.render(!postprocessing.enabled, p.transparentBackground);
-                    if (postprocessing.enabled) postprocessing.render(true);
+            if (resized || force || cameraChanged || multiSampleChanged) {
+                let cam: Camera | StereoCamera = camera;
+                if (p.camera.stereo.name === 'on') {
+                    stereoCamera.update();
+                    cam = stereoCamera;
                 }
-                pickPass.pickDirty = true;
+
+                if (MultiSamplePass.isEnabled(p.multiSample)) {
+                    multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
+                } else {
+                    passes.draw.render(renderer, cam, scene, helper, true, p.transparentBackground, p.postprocessing);
+                }
+                pickHelper.dirty = true;
                 didRender = true;
             }
 
@@ -265,10 +377,11 @@ namespace Canvas3D {
         }
 
         let forceNextDraw = false;
+        let forceDrawAfterAllCommited = false;
         let currentTime = 0;
 
         function draw(force?: boolean) {
-            if (render(!!force || forceNextDraw)) {
+            if (render(!!force || forceNextDraw) && notifyDidDraw) {
                 didDraw.next(now() - startTime as now.Timestamp);
             }
             forceNextDraw = false;
@@ -281,26 +394,60 @@ namespace Canvas3D {
             forceNextDraw = !!force;
         }
 
-        function animate() {
-            currentTime = now();
-            commit();
+        let animationFrameHandle = 0;
+
+        function tick(t: now.Timestamp, options?: { isSynchronous?: boolean, manualDraw?: boolean }) {
+            currentTime = t;
+            commit(options?.isSynchronous);
             camera.transition.tick(currentTime);
 
+            if (options?.manualDraw) {
+                return;
+            }
+
             draw(false);
             if (!camera.transition.inTransition && !webgl.isContextLost) {
                 interactionHelper.tick(currentTime);
             }
-            requestAnimationFrame(animate);
         }
 
-        function identify(x: number, y: number): PickingId | undefined {
-            return webgl.isContextLost ? undefined : pickPass.identify(x, y);
+        function _animate() {
+            tick(now());
+            animationFrameHandle = requestAnimationFrame(_animate);
+        }
+
+        function resetTime(t: now.Timestamp) {
+            startTime = t;
+            controls.start(t);
+        }
+
+        function animate() {
+            controls.start(now());
+            if (animationFrameHandle === 0) _animate();
+        }
+
+        function pause() {
+            cancelAnimationFrame(animationFrameHandle);
+            animationFrameHandle = 0;
+        }
+
+        function identify(x: number, y: number): PickData | undefined {
+            const cam = p.camera.stereo.name === 'on' ? stereoCamera : camera;
+            return webgl.isContextLost ? undefined : pickHelper.identify(x, y, cam);
         }
 
         function commit(isSynchronous: boolean = false) {
             const allCommited = commitScene(isSynchronous);
             // Only reset the camera after the full scene has been commited.
-            if (allCommited) resolveCameraReset();
+            if (allCommited) {
+                resolveCameraReset();
+                if (forceDrawAfterAllCommited) {
+                    if (helper.debug.isEnabled) helper.debug.update();
+                    draw(true);
+                    forceDrawAfterAllCommited = false;
+                }
+                commited.next(now());
+            }
         }
 
         function resolveCameraReset() {
@@ -311,7 +458,7 @@ namespace Canvas3D {
                 const duration = nextCameraResetDuration === undefined ? p.cameraResetDurationMs : nextCameraResetDuration;
                 const focus = camera.getFocus(center, radius);
                 const snapshot = nextCameraResetSnapshot ? { ...focus, ...nextCameraResetSnapshot } : focus;
-                camera.setState(snapshot, duration);
+                camera.setState({ ...snapshot, radiusMax: scene.boundingSphere.radius }, duration);
             }
 
             nextCameraResetDuration = void 0;
@@ -338,7 +485,8 @@ namespace Canvas3D {
                 const b = r.values.boundingSphere.ref.value;
                 if (!b.radius) continue;
 
-                if (!Sphere3D.includes(oldBoundingSphereVisible, b)) return true;
+                const cameraDist = Vec3.distance(cameraSphere.center, b.center);
+                if ((cameraDist > cameraSphere.radius || cameraDist > b.radius || b.radius > camera.state.radiusMax) && !Sphere3D.includes(oldBoundingSphereVisible, b)) return true;
                 if (Sphere3D.overlaps(cameraSphere, b)) cameraSphereOverlapsNone = false;
             }
 
@@ -354,8 +502,8 @@ namespace Canvas3D {
 
             if (!scene.commit(isSynchronous ? void 0 : sceneCommitTimeoutMs)) return false;
 
-            if (debugHelper.isEnabled) debugHelper.update();
-            if (reprCount.value === 0 || shouldResetCamera()) {
+            if (helper.debug.isEnabled) helper.debug.update();
+            if (!p.camera.manualReset && (reprCount.value === 0 || shouldResetCamera())) {
                 cameraResetRequested = true;
             }
             if (oldBoundingSphereVisible.radius === 0) nextCameraResetDuration = 0;
@@ -372,7 +520,16 @@ namespace Canvas3D {
                 drawCount: r.values.drawCount.ref.value,
                 instanceCount: r.values.instanceCount.ref.value,
                 materialId: r.materialId,
+                renderItemId: r.id,
             })));
+            console.log(webgl.stats);
+
+            const { texture, attribute, elements } = webgl.resources.getByteCounts();
+            console.log({
+                texture: `${(texture / 1024 / 1024).toFixed(3)} MiB`,
+                attribute: `${(attribute / 1024 / 1024).toFixed(3)} MiB`,
+                elements: `${(elements / 1024 / 1024).toFixed(3)} MiB`,
+            });
         }
 
         function add(repr: Representation.Any) {
@@ -393,6 +550,7 @@ namespace Canvas3D {
             reprRenderObjects.set(repr, newRO);
 
             scene.update(repr.renderObjects, false);
+            forceDrawAfterAllCommited = true;
             if (isDebugMode) consoleStats();
         }
 
@@ -403,7 +561,7 @@ namespace Canvas3D {
             if (renderObjects) {
                 renderObjects.forEach(o => scene.remove(o));
                 reprRenderObjects.delete(repr);
-                scene.update(repr.renderObjects, false, true);
+                forceDrawAfterAllCommited = true;
                 if (isDebugMode) consoleStats();
             }
         }
@@ -432,7 +590,9 @@ namespace Canvas3D {
             return {
                 camera: {
                     mode: camera.state.mode,
-                    helper: { ...drawPass.props.cameraHelper }
+                    helper: { ...helper.camera.props },
+                    stereo: { ...p.camera.stereo },
+                    manualReset: !!p.camera.manualReset
                 },
                 cameraFog: camera.state.fog > 0
                     ? { name: 'on' as const, params: { intensity: camera.state.fog } }
@@ -440,23 +600,36 @@ namespace Canvas3D {
                 cameraClipping: { far: camera.state.clipFar, radius },
                 cameraResetDurationMs: p.cameraResetDurationMs,
                 transparentBackground: p.transparentBackground,
+                viewport: p.viewport,
 
-                postprocessing: { ...postprocessing.props },
-                multiSample: { ...multiSample.props },
+                postprocessing: { ...p.postprocessing },
+                multiSample: { ...p.multiSample },
                 renderer: { ...renderer.props },
                 trackball: { ...controls.props },
-                debug: { ...debugHelper.props },
-                handle: { ...handleHelper.props },
+                debug: { ...helper.debug.props },
+                handle: { ...helper.handle.props },
             };
         }
 
-        handleResize();
-
         const contextRestoredSub = contextRestored.subscribe(() => {
-            pickPass.pickDirty = true;
+            pickHelper.dirty = true;
+            draw(true);
+            // Unclear why, but in Chrome with wboit enabled the first `draw` only clears
+            // the drawingBuffer. Note that in Firefox the drawingBuffer is preserved after
+            // context loss so it is unclear if it behaves the same.
             draw(true);
         });
 
+        const resized = new BehaviorSubject<any>(0);
+
+        function handleResize(draw = true) {
+            passes.updateSize();
+            updateViewport();
+            syncViewport();
+            if (draw) requestDraw(true);
+            resized.next(+new Date());
+        }
+
         return {
             webgl,
 
@@ -470,13 +643,14 @@ namespace Canvas3D {
                 } else {
                     scene.update(void 0, !!keepSphere);
                 }
+                forceDrawAfterAllCommited = true;
             },
             clear: () => {
                 reprUpdatedSubscriptions.forEach(v => v.unsubscribe());
                 reprUpdatedSubscriptions.clear();
                 reprRenderObjects.clear();
                 scene.clear();
-                debugHelper.clear();
+                helper.debug.clear();
                 requestDraw(true);
                 reprCount.next(reprRenderObjects.size);
             },
@@ -487,18 +661,24 @@ namespace Canvas3D {
                 }
 
                 if (scene.syncVisibility()) {
-                    if (debugHelper.isEnabled) debugHelper.update();
+                    if (helper.debug.isEnabled) helper.debug.update();
                 }
+                requestDraw(true);
             },
 
-            // draw,
             requestDraw,
+            tick,
             animate,
+            resetTime,
+            pause,
             identify,
             mark,
             getLoci,
 
             handleResize,
+            requestResize: () => {
+                resizeRequested = true;
+            },
             requestCameraReset: options => {
                 nextCameraResetDuration = options?.durationMs;
                 nextCameraResetSnapshot = options?.snapshot;
@@ -506,19 +686,14 @@ namespace Canvas3D {
             },
             camera,
             boundingSphere: scene.boundingSphere,
-            getPixelData: (variant: GraphicsRenderVariant) => {
-                switch (variant) {
-                    case 'color': return webgl.getDrawingBufferPixelData();
-                    case 'pickObject': return pickPass.objectPickTarget.getPixelData();
-                    case 'pickInstance': return pickPass.instancePickTarget.getPixelData();
-                    case 'pickGroup': return pickPass.groupPickTarget.getPixelData();
-                    case 'depth': return readTexture(webgl, drawPass.depthTexture) as PixelData;
-                }
-            },
+            get notifyDidDraw() { return notifyDidDraw; },
+            set notifyDidDraw(v: boolean) { notifyDidDraw = v; },
             didDraw,
+            commited,
             reprCount,
-            setProps: (properties) => {
-                const props: Partial<Canvas3DProps> = typeof properties === 'function'
+            resized,
+            setProps: (properties, doNotRequestDraw = false) => {
+                const props: PartialCanvas3DProps = typeof properties === 'function'
                     ? produce(getProps(), properties)
                     : properties;
 
@@ -526,7 +701,7 @@ namespace Canvas3D {
                 if (props.camera && props.camera.mode !== undefined && props.camera.mode !== camera.state.mode) {
                     cameraState.mode = props.camera.mode;
                 }
-                if (props.cameraFog !== undefined) {
+                if (props.cameraFog !== undefined && props.cameraFog.params) {
                     const newFog = props.cameraFog.name === 'on' ? props.cameraFog.params.intensity : 0;
                     if (newFog !== camera.state.fog) cameraState.fog = newFog;
                 }
@@ -544,47 +719,43 @@ namespace Canvas3D {
                 }
                 if (Object.keys(cameraState).length > 0) camera.setState(cameraState);
 
-                if (props.camera?.helper) drawPass.setProps({ cameraHelper: props.camera.helper });
+                if (props.camera?.helper) helper.camera.setProps(props.camera.helper);
+                if (props.camera?.manualReset !== undefined) p.camera.manualReset = props.camera.manualReset;
+                if (props.camera?.stereo !== undefined) Object.assign(p.camera.stereo, props.camera.stereo);
                 if (props.cameraResetDurationMs !== undefined) p.cameraResetDurationMs = props.cameraResetDurationMs;
                 if (props.transparentBackground !== undefined) p.transparentBackground = props.transparentBackground;
+                if (props.viewport !== undefined) {
+                    const doNotUpdate = p.viewport === props.viewport ||
+                        (p.viewport.name === props.viewport.name && shallowEqual(p.viewport.params, props.viewport.params));
 
-                if (props.postprocessing) postprocessing.setProps(props.postprocessing);
-                if (props.multiSample) multiSample.setProps(props.multiSample);
+                    if (!doNotUpdate) {
+                        p.viewport = props.viewport;
+                        updateViewport();
+                        syncViewport();
+                    }
+                }
+
+                if (props.postprocessing) Object.assign(p.postprocessing, props.postprocessing);
+                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.debug) debugHelper.setProps(props.debug);
-                if (props.handle) handleHelper.setProps(props.handle);
+                if (props.debug) helper.debug.setProps(props.debug);
+                if (props.handle) helper.handle.setProps(props.handle);
 
-                requestDraw(true);
+                if (cameraState.mode === 'orthographic') {
+                    p.camera.stereo.name = 'off';
+                }
+
+                if (!doNotRequestDraw) {
+                    requestDraw(true);
+                }
             },
             getImagePass: (props: Partial<ImageProps> = {}) => {
-                return new ImagePass(webgl, renderer, scene, camera, debugHelper, handleHelper, props);
+                return new ImagePass(webgl, renderer, scene, camera, helper, passes.draw.wboitEnabled, props);
             },
 
             get props() {
-                const radius = scene.boundingSphere.radius > 0
-                    ? 100 - Math.round((camera.transition.target.radius / scene.boundingSphere.radius) * 100)
-                    : 0;
-
-                return {
-                    camera: {
-                        mode: camera.state.mode,
-                        helper: { ...drawPass.props.cameraHelper }
-                    },
-                    cameraFog: camera.state.fog > 0
-                        ? { name: 'on' as const, params: { intensity: camera.state.fog } }
-                        : { name: 'off' as const, params: {} },
-                    cameraClipping: { far: camera.state.clipFar, radius },
-                    cameraResetDurationMs: p.cameraResetDurationMs,
-                    transparentBackground: p.transparentBackground,
-
-                    postprocessing: { ...postprocessing.props },
-                    multiSample: { ...multiSample.props },
-                    renderer: { ...renderer.props },
-                    trackball: { ...controls.props },
-                    debug: { ...debugHelper.props },
-                    handle: { ...handleHelper.props },
-                };
+                return getProps();
             },
             get input() {
                 return input;
@@ -599,28 +770,32 @@ namespace Canvas3D {
                 contextRestoredSub.unsubscribe();
 
                 scene.clear();
-                debugHelper.clear();
-                input.dispose();
+                helper.debug.clear();
                 controls.dispose();
                 renderer.dispose();
                 interactionHelper.dispose();
             }
         };
 
-        function handleResize() {
-            width = gl.drawingBufferWidth;
-            height = gl.drawingBufferHeight;
+        function updateViewport() {
+            if (p.viewport.name === 'canvas') {
+                x = 0;
+                y = 0;
+                width = gl.drawingBufferWidth;
+                height = gl.drawingBufferHeight;
+            } else {
+                x = p.viewport.params.x * webgl.pixelRatio;
+                y = p.viewport.params.y * webgl.pixelRatio;
+                width = p.viewport.params.width * webgl.pixelRatio;
+                height = p.viewport.params.height * webgl.pixelRatio;
+            }
+        }
 
-            renderer.setViewport(0, 0, width, height);
-            Viewport.set(camera.viewport, 0, 0, width, height);
-            Viewport.set(controls.viewport, 0, 0, width, height);
-
-            drawPass.setSize(width, height);
-            pickPass.setSize(width, height);
-            postprocessing.setSize(width, height);
-            multiSample.setSize(width, height);
-
-            requestDraw(true);
+        function syncViewport() {
+            pickHelper.setViewport(x, y, width, height);
+            renderer.setViewport(x, y, width, height);
+            Viewport.set(camera.viewport, x, y, width, height);
+            Viewport.set(controls.viewport, x, y, width, height);
         }
     }
 }

src/mol-canvas3d/controls/object.ts

@@ -0,0 +1,58 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
+import { Camera } from '../camera';
+import { Viewport } from '../camera/util';
+
+export namespace ObjectControls {
+    function mouseOnScreen(out: Vec2, page: Vec2, viewport: Viewport) {
+        return Vec2.set(
+            out,
+            (page[0] - viewport.x) / viewport.width,
+            (page[1] - viewport.y) / viewport.height
+        );
+    }
+
+    const panMouseChange = Vec2();
+    const panObjUp = Vec3();
+    const panOffset = Vec3();
+    const eye = Vec3();
+    const panStart = Vec2();
+    const panEnd = Vec2();
+
+    const target = Vec3();
+
+    /**
+     * Get vector for movement in camera projection plane:
+     * `pageStart` and `pageEnd` are 2d window coordinates;
+     * `ref` defines the plane depth, if not given `camera.target` is used
+     */
+    export function panDirection(out: Vec3, pageStart: Vec2, pageEnd: Vec2, camera: Camera, ref?: Vec3) {
+        mouseOnScreen(panStart, pageStart, camera.viewport);
+        mouseOnScreen(panEnd, pageEnd, camera.viewport);
+        Vec2.sub(panMouseChange, Vec2.copy(panMouseChange, panEnd), panStart);
+        Vec3.sub(eye, camera.position, camera.target);
+
+        if (!ref || camera.state.mode === 'orthographic') Vec3.copy(target, camera.target);
+        else Vec3.projectPointOnVector(target, ref, eye, camera.position);
+
+        const dist = Vec3.distance(camera.position, target);
+        const height = 2 * Math.tan(camera.state.fov / 2) * dist;
+        const zoom = camera.viewport.height / height;
+
+        panMouseChange[0] *= (1 / zoom) * camera.viewport.width * camera.pixelRatio;
+        panMouseChange[1] *= (1 / zoom) * camera.viewport.height * camera.pixelRatio;
+
+        Vec3.cross(panOffset, Vec3.copy(panOffset, eye), camera.up);
+        Vec3.setMagnitude(panOffset, panOffset, panMouseChange[0]);
+
+        Vec3.setMagnitude(panObjUp, camera.up, panMouseChange[1]);
+        Vec3.add(panOffset, panOffset, panObjUp);
+
+        return Vec3.negate(out, panOffset);
+    }
+}

src/mol-canvas3d/controls/trackball.ts

@@ -10,7 +10,7 @@
 
 import { Quat, Vec2, Vec3, EPSILON } from '../../mol-math/linear-algebra';
 import { Viewport } from '../camera/util';
-import InputObserver, { DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
+import { InputObserver, DragInput, WheelInput, PinchInput, ButtonsType, ModifiersKeys } from '../../mol-util/input/input-observer';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Camera } from '../camera';
 import { absMax } from '../../mol-math/misc';
@@ -36,9 +36,9 @@ export const DefaultTrackballBindings = {
 export const TrackballControlsParams = {
     noScroll: PD.Boolean(true, { isHidden: true }),
 
-    rotateSpeed: PD.Numeric(3.0, { min: 0.1, max: 10, step: 0.1 }),
-    zoomSpeed: PD.Numeric(6.0, { min: 0.1, max: 10, step: 0.1 }),
-    panSpeed: PD.Numeric(0.8, { min: 0.1, max: 5, step: 0.1 }),
+    rotateSpeed: PD.Numeric(5.0, { min: 1, max: 10, step: 1 }),
+    zoomSpeed: PD.Numeric(7.0, { min: 1, max: 15, step: 1 }),
+    panSpeed: PD.Numeric(1.0, { min: 0.1, max: 5, step: 0.1 }),
 
     spin: PD.Boolean(false, { description: 'Spin the 3D scene around the x-axis in view space' }),
     spinSpeed: PD.Numeric(1, { min: -20, max: 20, step: 1 }),
@@ -60,6 +60,7 @@ interface TrackballControls {
     readonly props: Readonly<TrackballControlsProps>
     setProps: (props: Partial<TrackballControlsProps>) => void
 
+    start: (t: number) => void
     update: (t: number) => void
     reset: () => void
     dispose: () => void
@@ -68,7 +69,7 @@ namespace TrackballControls {
     export function create(input: InputObserver, camera: Camera, props: Partial<TrackballControlsProps> = {}): TrackballControls {
         const p = { ...PD.getDefaultValues(TrackballControlsParams), ...props };
 
-        const viewport = Viewport();
+        const viewport = Viewport.clone(camera.viewport);
 
         let disposed = false;
 
@@ -137,7 +138,8 @@ namespace TrackballControls {
             const dy = _rotCurr[1] - _rotPrev[1];
             Vec3.set(rotMoveDir, dx, dy, 0);
 
-            const angle = Vec3.magnitude(rotMoveDir) * p.rotateSpeed;
+            const aspectRatio = input.width / input.height;
+            const angle = Vec3.magnitude(rotMoveDir) * p.rotateSpeed * input.pixelRatio * aspectRatio;
 
             if (angle) {
                 Vec3.sub(_eye, camera.position, camera.target);
@@ -227,7 +229,9 @@ namespace TrackballControls {
             Vec2.sub(panMouseChange, Vec2.copy(panMouseChange, _panEnd), _panStart);
 
             if (Vec2.squaredMagnitude(panMouseChange)) {
-                Vec2.scale(panMouseChange, panMouseChange, Vec3.magnitude(_eye) * p.panSpeed);
+                const factor = input.pixelRatio * p.panSpeed;
+                panMouseChange[0] *= (1 / camera.zoom) * camera.viewport.width * factor;
+                panMouseChange[1] *= (1 / camera.zoom) * camera.viewport.height * factor;
 
                 Vec3.cross(panOffset, Vec3.copy(panOffset, _eye), camera.up);
                 Vec3.setMagnitude(panOffset, panOffset, panMouseChange[0]);
@@ -269,11 +273,22 @@ namespace TrackballControls {
             }
         }
 
+        function outsideViewport(x: number, y: number) {
+            x *= input.pixelRatio;
+            y *= input.pixelRatio;
+            return (
+                x > viewport.x + viewport.width ||
+                input.height - y > viewport.y + viewport.height ||
+                x < viewport.x ||
+                input.height - y < viewport.y
+            );
+        }
+
         let lastUpdated = -1;
         /** Update the object's position, direction and up vectors */
         function update(t: number) {
             if (lastUpdated === t) return;
-            if (p.spin) spin(t - lastUpdated);
+            if (p.spin && lastUpdated > 0) spin(t - lastUpdated);
 
             Vec3.sub(_eye, camera.position, camera.target);
 
@@ -305,7 +320,12 @@ namespace TrackballControls {
 
         // listeners
 
-        function onDrag({ pageX, pageY, buttons, modifiers, isStart }: DragInput) {
+        function onDrag({ x, y, pageX, pageY, buttons, modifiers, isStart }: DragInput) {
+            const isOutside = outsideViewport(x, y);
+
+            if (isStart && isOutside) return;
+            if (!isStart && !_isInteracting) return;
+
             _isInteracting = true;
 
             const dragRotate = Binding.match(p.bindings.dragRotate, buttons, modifiers);
@@ -356,7 +376,9 @@ namespace TrackballControls {
             _isInteracting = false;
         }
 
-        function onWheel({ dx, dy, dz, buttons, modifiers }: WheelInput) {
+        function onWheel({ x, y, dx, dy, dz, buttons, modifiers }: WheelInput) {
+            if (outsideViewport(x, y)) return;
+
             const delta = absMax(dx, dy, dz);
             if (Binding.match(p.bindings.scrollZoom, buttons, modifiers)) {
                 _zoomEnd[1] += delta * 0.0001;
@@ -385,13 +407,17 @@ namespace TrackballControls {
 
         const _spinSpeed = Vec2.create(0.005, 0);
         function spin(deltaT: number) {
+            if (p.spinSpeed === 0) return;
+
             const frameSpeed = (p.spinSpeed || 0) / 1000;
             _spinSpeed[0] = 60 * Math.min(Math.abs(deltaT), 1000 / 8) / 1000 * frameSpeed;
             if (!_isInteracting) Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
         }
 
-        // force an update at start
-        update(0);
+        function start(t: number) {
+            lastUpdated = -1;
+            update(t);
+        }
 
         return {
             viewport,
@@ -401,6 +427,7 @@ namespace TrackballControls {
                 Object.assign(p, props);
             },
 
+            start,
             update,
             reset,
             dispose

src/mol-canvas3d/helper/bounding-sphere-helper.ts

@@ -9,7 +9,7 @@ import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
 import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
 import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import Scene from '../../mol-gl/scene';
+import { Scene } from '../../mol-gl/scene';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Sphere3D } from '../../mol-math/geometry';
 import { Color } from '../../mol-util/color';
@@ -67,6 +67,7 @@ export class BoundingSphereHelper {
                 uInstanceCount: ro.values.uInstanceCount,
                 instanceCount: ro.values.instanceCount,
                 aInstance: ro.values.aInstance,
+                hasReflection: ro.values.hasReflection,
             });
             if (newInstanceData) this.instancesData.set(ro, newInstanceData);
         });
@@ -131,7 +132,7 @@ function updateBoundingSphereData(scene: Scene, boundingSphere: Sphere3D, data:
         const mesh = createBoundingSphereMesh(boundingSphere, data && data.mesh);
         const renderObject = data ? data.renderObject : createBoundingSphereRenderObject(mesh, color, materialId, transform);
         if (data) {
-            ValueCell.update(renderObject.values.drawCount, Geometry.getDrawCount(mesh));
+            ValueCell.updateIfChanged(renderObject.values.drawCount, Geometry.getDrawCount(mesh));
         } else {
             scene.add(renderObject);
         }
@@ -159,5 +160,5 @@ const instanceMaterialId = getNextMaterialId();
 
 function createBoundingSphereRenderObject(mesh: Mesh, color: Color, materialId: number, transform?: TransformData) {
     const values = Mesh.Utils.createValuesSimple(mesh, { alpha: 0.1, doubleSided: false }, color, 1, transform);
-    return createRenderObject('mesh', values, { visible: true, alphaFactor: 1, pickable: false, opaque: false, writeDepth: false }, materialId);
+    return createRenderObject('mesh', values, { disposed: false, visible: true, alphaFactor: 1, pickable: false, colorOnly: false, opaque: false, writeDepth: false, noClip: false }, materialId);
 }

src/mol-canvas3d/helper/camera-helper.ts

@@ -5,8 +5,8 @@
  */
 
 import { WebGLContext } from '../../mol-gl/webgl/context';
-import Scene from '../../mol-gl/scene';
-import { Camera } from '../camera';
+import { Scene } from '../../mol-gl/scene';
+import { Camera, ICamera } from '../camera';
 import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
@@ -15,7 +15,6 @@ import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
 import { ColorNames } from '../../mol-util/color/names';
 import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
 import { Viewport } from '../camera/util';
-import { ValueCell } from '../../mol-util';
 import { Sphere3D } from '../../mol-math/geometry';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import produce from 'immer';
@@ -71,6 +70,7 @@ export class CameraHelper {
                     this.scene.clear();
                     const params = { ...props.axes.params, scale: props.axes.params.scale * this.webgl.pixelRatio };
                     this.renderObject = createAxesRenderObject(params);
+                    this.renderObject.state.noClip = true;
                     this.scene.add(this.renderObject);
                     this.scene.commit();
 
@@ -87,43 +87,47 @@ export class CameraHelper {
         return this.props.axes.name === 'on';
     }
 
-    update(camera: Camera) {
+    update(camera: ICamera) {
         if (!this.renderObject) return;
 
-        updateCamera(this.camera, camera.viewport);
-
-        const m = this.renderObject.values.aTransform.ref.value as unknown as Mat4;
-        Mat4.extractRotation(m, camera.view);
+        updateCamera(this.camera, camera.viewport, camera.viewOffset);
+        Mat4.extractRotation(this.scene.view, camera.view);
 
         const r = this.renderObject.values.boundingSphere.ref.value.radius;
-        Mat4.setTranslation(m, Vec3.create(
+        Mat4.setTranslation(this.scene.view, Vec3.create(
             -camera.viewport.width / 2 + r,
             -camera.viewport.height / 2 + r,
             0
         ));
-
-        ValueCell.update(this.renderObject.values.aTransform, this.renderObject.values.aTransform.ref.value);
-        this.scene.update([this.renderObject], true);
     }
 }
 
-function updateCamera(camera: Camera, viewport: Viewport) {
+function updateCamera(camera: Camera, viewport: Viewport, viewOffset: Camera.ViewOffset) {
     const { near, far } = camera;
 
-    const fullLeft = -(viewport.width - viewport.x) / 2;
-    const fullRight = (viewport.width - viewport.x) / 2;
-    const fullTop = (viewport.height - viewport.y) / 2;
-    const fullBottom = -(viewport.height - viewport.y) / 2;
+    const fullLeft = -viewport.width / 2;
+    const fullRight = viewport.width / 2;
+    const fullTop = viewport.height / 2;
+    const fullBottom = -viewport.height / 2;
 
     const dx = (fullRight - fullLeft) / 2;
     const dy = (fullTop - fullBottom) / 2;
     const cx = (fullRight + fullLeft) / 2;
     const cy = (fullTop + fullBottom) / 2;
 
-    const left = cx - dx;
-    const right = cx + dx;
-    const top = cy + dy;
-    const bottom = cy - dy;
+    let left = cx - dx;
+    let right = cx + dx;
+    let top = cy + dy;
+    let bottom = cy - dy;
+
+    if (viewOffset.enabled) {
+        const scaleW = (fullRight - fullLeft) / viewOffset.width;
+        const scaleH = (fullTop - fullBottom) / viewOffset.height;
+        left += scaleW * viewOffset.offsetX;
+        right = left + scaleW * viewOffset.width;
+        top -= scaleH * viewOffset.offsetY;
+        bottom = top - scaleH * viewOffset.height;
+    }
 
     Mat4.ortho(camera.projection, left, right, top, bottom, near, far);
 }