diff --git a/README.md b/README.md
index 8568b73497beb741021e241ebbcca2b69877f713..fa8bc2d4aa73dae320d79d6ca5238b21b2dd77df 100644
--- a/README.md
+++ b/README.md
@@ -1,31 +1,31 @@
-# PDB ligand environment component
+# PDB LigandEnv component
-This is a web-component to display ligand structure in 2D along with its interactions. Ligand can be perceived as a set of covalently linked pdb residues (refered to as bound molecule) or a single pdb residue. This depiction can be enriched with a substructure highlight, atom names, and binding site interactions.
+This is a web-component to display ligand structure in 2D along with its interactions. This depiction can be enriched with substructure highlight, atom names, binding site interactions and aggregated protein-ligand interactions.
-## Step after cloning (use local server to see demo pages)
+## Installation
```shell
-npm run install
+npm install
npm run build
npm run start
-
-open any of the *.html pages in the demo directory
```
+To see demo, copy demo directory to build and open any of the html pages.
## Component modes
-* Mode A: Display bound molecule and its interactions
-* Mode B: Display ligand and its interactions
-* Mode C: Display ligand (chemical component) only
+* Mode A: Display ligand and its interactions (Using pdb-id, pdb-res-id and pdb-chain-id)
+* Mode B: Display boundmolecule and its interactions (Using pdb-id and bound-molecule-id)
+* Mode C: Display ligand only (Using pdb-res-name)
+* Mode D: Display ligand and aggregated interactions (Using pdb-res-name and contact-type)
-| Mode A | Mode B | Mode C |
-|:------------------: | :-------: | :-------: |
-| <img src="https://www.ebi.ac.uk/~lpravda/imgs/1cbs_REA_200_A.png"/>| <img src="https://www.ebi.ac.uk/~lpravda/imgs/3d12_bm1.png"/> | <img src="https://www.ebi.ac.uk/pdbe-srv/pdbechem/image/showNew?code=VIA&size=500"/> |
-| [1cbs REA 200 A](https://www.ebi.ac.uk/pdbe/entry/pdb/1cbs/bound/REA) | 3D12 bm1 (`2xGLC-2xBGC-LXZ-NGA-GL0`)| [wwPDB CCD - VIA](https://pdbe.org/chem/VIA)
+| Mode A | Mode B | Mode C | Mode D |
+|:------------------: | :-------: | :-------: | :-------: |
+| <img src="dependencies/REA_A_200.png">| <img src="dependencies/3d12_bm1.png"/> | <img src="https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/ccd/V/VIA/VIA_500.svg"/> | <img src="dependencies/STI_aggregated_interactions.png"> |
+| [1cbs REA 200 A](https://www.ebi.ac.uk/pdbe/entry/pdb/1cbs/bound/REA) | [3D12 bm1 (`2xGLC-2xBGC-LXZ-NGA-GL0`)](https://www.ebi.ac.uk/pdbe/entry/pdb/3d12/branched/4)| [wwPDB CCD - VIA](https://pdbe.org/chem/VIA) | STI |
## How to use it
-The component can be inserted into the pages by two different ways. Either as a `web-component` using html tag, or directly by using javascript as a `plugin`.
+PDB LigandEnv can be inserted into web pages in two different ways. Either as a `web-component` using html tag, or directly by using javascript as a `plugin`.
Interactions data displayed by the component can come from three different environments `Production`, `Development`, `Internal`. If no environment is specified `Production` is used as default..
@@ -53,7 +53,7 @@ A few files needs to be imported in the page before the component is attempted t
charset="utf-8"></script>
<!--PDBe interactions component-->
-<script type="module" src="pdb-ligand-env-component-0.3.0-min.js"></script>
+<script type="module" src="pdb-ligand-env-component-2.0.0-min.js"></script>
```
#### A) Ligand interactions
@@ -68,16 +68,20 @@ A few files needs to be imported in the page before the component is attempted t
<pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1"></pdb-ligand-env>
```
-#### C) Ligand/chemical component
+#### C) Ligand
```html
<pdb-ligand-env pdb-res-name="CLR" zoom-on ></pdb-ligand-env>
```
+#### D) Ligand and aggregated interactions
+```html
+<pdb-ligand-env pdb-res-name="STI", contact-type=["hbond","hydrophobic","vdw"]></pdb-ligand-env>
+```
+
The component contains a number of properties that can be set, in order to change data that are being displayed. First you need to define a component on the page:
```html
-
<pdb-ligand-env id='SIA-component'></pdb-ligand-env>
```
@@ -87,14 +91,15 @@ and then inject data you want to display e.g.:
let chemUrl = `https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/SIA/annotation`;
let interactionsURL = "https://wwwdev.ebi.ac.uk/pdbe/graph-api/pdb/bound_ligand_interactions/4yy1/A/604";
let component = document.getElementById('SIA-component');
-
-const depiction = await (await fetch(chemUrl)).json();
-const interactionsData = await (await fetch(interactionsURL)).json();
-const atomsToHighlight = ['C10', 'C11', 'O10'];
-
-component.depiction = depiction;
-component.ligandHighlight = atomsToHighlight;
-component.interactions = interactionsData;
+(async() => {
+ const depiction = await (await fetch(chemUrl)).json();
+ const interactionsData = await (await fetch(interactionsURL)).json();
+ const atomsToHighlight = ['C10', 'C11', 'O10'];
+
+ component.depiction = depiction;
+ component.ligandHighlight = atomsToHighlight;
+ component.interactions = interactionsData;
+})()
```
### Plugin
@@ -148,6 +153,13 @@ this.display.initLigandInteractions('1cbs', 200, 'A');
// to display chemical component with atom names only
this.display.initLigandDisplay('HEM', true);
+
+// to display aggregated protein-ligand interactions
+this.display.initLigandDisplay('STI').then(() => {
+ this.display.initLigandWeights('STI').then(() => {
+ this.display.showWeights(["hydrophobic"]);
+ })
+})
````
## Parameters
@@ -157,7 +169,8 @@ this.display.initLigandDisplay('HEM', true);
| pdb-id | string | No | PDB id of a protein to retrieve interactions from. `(mode A and B only)` |
| bound-molecule-id | string | No | PDB bound molecule id `(mode A only)` |
| pdb-res-name | string | No | PDB residue name aka: *auth_comp_id* `(mode C only)`
-| pdb-res-id | number | No | PDB residue id aka: *auth_seq_id* `(mode B only)`
+| pdb-res-id | number | No | PDB residue id aka: *auth_seq_id* `(mode B only)` |
+| contact-type | string[] | No | protein-ligand contact_type calculated by pdbe-arpeggio `(mode D only)` |
| pdb-chain-id | string | No | PDB residue chain aka: *auth_asym_id* `(mode B only)`|
| substructure | string[] | No | List of atom names to be highlighted on the ligand structure |
| color | string | No | HEX representation of the color highlight. `(Default: #D3D3D3)` |
diff --git a/demo/demo_aggregated_interaction.html b/demo/demo_aggregated_interaction.html
new file mode 100644
index 0000000000000000000000000000000000000000..02dffae40ef488068947c61e894da9a862c56951
--- /dev/null
+++ b/demo/demo_aggregated_interaction.html
@@ -0,0 +1,33 @@
+<!doctype html>
+<html lang="en">
+
+<head>
+
+ <script src="https://d3js.org/d3.v5.min.js"></script>
+ <!-- CSS style to be used for scene drawing (required for saving SVGs.) -->
+ <link rel="stylesheet" href="http://127.0.0.1:8080/pdb-ligand-env-svg.css" />
+ <!-- UI icons -->
+ <link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css" />
+ <!-- Web component polyfill (only loads what it needs) -->
+ <script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/webcomponents-lite.js" charset="utf-8">
+ </script>
+ <script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js"
+ charset="utf-8"></script>
+ <!--PDBe interactions component-->
+ <script type="module" src="http://127.0.0.1:8080/pdb-ligand-env-component-1.0.0-min.js"></script>
+
+</head>
+
+<body>
+
+ <!--Mode A-->
+ <div style="position: relative; float: left;">
+ <div style="width: 500px; height: 500px; position: relative">
+ <pdb-ligand-env pdb-res-name="STI", contact-type="total"></pdb-ligand-env>
+ </div>
+ </div>
+
+
+</body>
+
+</html>
\ No newline at end of file
diff --git a/dependencies/3d12_bm1.png b/dependencies/3d12_bm1.png
new file mode 100644
index 0000000000000000000000000000000000000000..b1de796a6b71c26506c901a4e9367868dfe81d50
Binary files /dev/null and b/dependencies/3d12_bm1.png differ
diff --git a/dependencies/REA_A_200.png b/dependencies/REA_A_200.png
new file mode 100644
index 0000000000000000000000000000000000000000..110b9035afbdd8eb7cbe5ebefc681119694f230d
Binary files /dev/null and b/dependencies/REA_A_200.png differ
diff --git a/dependencies/STI_aggregated_interactions.png b/dependencies/STI_aggregated_interactions.png
new file mode 100644
index 0000000000000000000000000000000000000000..1c2314c26a373798bf9d14eb6669f7dc649bf4b9
Binary files /dev/null and b/dependencies/STI_aggregated_interactions.png differ
diff --git a/gulpfile.js b/gulpfile.js
index 0808b3af499becd41e7d92f804b198889ce7ac3b..890328f8dfc5816935e855c7a3a7382cb2e73f3a 100644
--- a/gulpfile.js
+++ b/gulpfile.js
@@ -4,6 +4,7 @@ const del = require('del');
const concat = require('gulp-concat');
const header = require('gulp-header');
const minify = require("gulp-minify");
+const cp = require('child_process');
const PACKAGE_ROOT_PATH = process.cwd();
const PKG_JSON = require(path.join(PACKAGE_ROOT_PATH, "package.json"));
@@ -18,7 +19,7 @@ const banner = ['/**',
].join('\n');
const license = ['/**',
- ' * Copyright 2019-2020 Lukas Pravda <lpravda@ebi.ac.uk>',
+ ' * Copyright 2024-2030 Protein Data Bank in Europe <pdbehelp@ebi.ac.uk>',
' * European Bioinformatics Institute (EBI, http://www.ebi.ac.uk/)',
' * European Molecular Biology Laboratory (EMBL, http://www.embl.de/)',
' * Licensed under the Apache License, Version 2.0 (the "License");',
@@ -94,5 +95,11 @@ gulp.task('minifyPlugin', () => {
.pipe(gulp.dest('build/'));
});
+gulp.task('createDoc', function (cb) {
+ cp.exec('./node_modules/.bin/jsdoc -c jsdoc.json', function(err, stdout, stderr){
+ cb(err);
+ })
+});
+
gulp.task('default', gulp.series('clean', 'copyAppCSS', 'concat', 'concatCSS',
- 'copyXML', 'copyIndex', 'copyMapping', 'minifyPlugin'));
\ No newline at end of file
+ 'copyXML', 'copyIndex', 'copyMapping', 'minifyPlugin', 'createDoc'));
\ No newline at end of file
diff --git a/jsdoc.json b/jsdoc.json
new file mode 100644
index 0000000000000000000000000000000000000000..4eff956d9c04a46a61e1237b5aa47d29fb3f9d8b
--- /dev/null
+++ b/jsdoc.json
@@ -0,0 +1,29 @@
+{
+ "tags": {
+ "allowUnknownTags": true
+ },
+ "opts": {
+ "template": "node_modules/better-docs",
+ "destination": "build/docs"
+ },
+ "plugins": [
+ "node_modules/better-docs/typescript",
+ "plugins/markdown"
+ ],
+ "source": {
+ "includePattern": "\\.(jsx|js|ts|tsx)$",
+ "include": ["README.md", "src/component", "src/plugin"]
+ },
+ "templates": {
+ "cleverLinks": false,
+ "monospaceLinks": false,
+ "default": {
+ "outputSourceFiles": true
+ },
+ "path": "ink-docstrap",
+ "theme": "cerulean",
+ "navType": "vertical",
+ "linenums": true,
+ "dateFormat": "MMMM Do YYYY, h:mm:ss a"
+ }
+}
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index fc27827bfff63d56360236e21ee0f840ebdaf96a..b06e4cd56b875a4207b9a01efcbe37267854c921 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -11,11 +11,12 @@
"dependencies": {
"@types/d3": "^5.16.3",
"@types/d3-tip": "^3.5.5",
+ "@types/ws": "^8.5.4",
"d3": "^5.16.0",
"d3-tip": "^0.9.1",
"d3scription": "^1.0.1",
"lit-element": "^2.4.0",
- "typescript": "^4.0.2"
+ "typescript": "^5.3.3"
},
"devDependencies": {
"@babel/core": "^7.12.3",
@@ -23,7 +24,8 @@
"@babel/preset-env": "^7.12.1",
"@babel/runtime": "^7.12.1",
"@webcomponents/webcomponentsjs": "^2.5.0",
- "babel-loader": "^8.1.0",
+ "babel-loader": "^9.1.3",
+ "better-docs": "^2.7.3",
"browser-sync": "^2.26.13",
"camelcase": "^5.0.0",
"clean-webpack-plugin": "^1.0.1",
@@ -35,14 +37,16 @@
"gulp-concat": "^2.6.1",
"gulp-header": "^2.0.9",
"gulp-minify": "^3.1.0",
+ "jsdoc": "^4.0.2",
"live-server": "^1.2.1",
"npm-run-all": "^4.1.3",
"onchange": "^6.1.1",
"style-loader": "^0.23.1",
"ts-node": "^7.0.1",
"url-loader": "^1.1.2",
- "webpack": "^5.2.0",
- "webpack-cli": "^3.3.12"
+ "webpack": "^5.89.0",
+ "webpack-cli": "^5.1.4",
+ "webpack-dev-server": "^4.15.1"
}
},
"node_modules/@babel/code-frame": {
@@ -88,14 +92,18 @@
}
},
"node_modules/@babel/generator": {
- "version": "7.12.1",
- "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.12.1.tgz",
- "integrity": "sha512-DB+6rafIdc9o72Yc3/Ph5h+6hUjeOp66pF0naQBgUFFuPqzQwIlPTm3xZR7YNvduIMtkDIj2t21LSQwnbCrXvg==",
+ "version": "7.23.6",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.6.tgz",
+ "integrity": "sha512-qrSfCYxYQB5owCmGLbl8XRpX1ytXlpueOb0N0UmQwA073KZxejgQTzAmJezxvpwQD9uGtK2shHdi55QT+MbjIw==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.12.1",
- "jsesc": "^2.5.1",
- "source-map": "^0.5.0"
+ "@babel/types": "^7.23.6",
+ "@jridgewell/gen-mapping": "^0.3.2",
+ "@jridgewell/trace-mapping": "^0.3.17",
+ "jsesc": "^2.5.1"
+ },
+ "engines": {
+ "node": ">=6.9.0"
}
},
"node_modules/@babel/helper-annotate-as-pure": {
@@ -311,11 +319,23 @@
"@babel/types": "^7.11.0"
}
},
+ "node_modules/@babel/helper-string-parser": {
+ "version": "7.23.4",
+ "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.23.4.tgz",
+ "integrity": "sha512-803gmbQdqwdf4olxrX4AJyFBV/RTr3rSmOj0rKwesmzlfhYNDEs+/iOcznzpNWlJlIlTJC2QfPFcHB6DlzdVLQ==",
+ "dev": true,
+ "engines": {
+ "node": ">=6.9.0"
+ }
+ },
"node_modules/@babel/helper-validator-identifier": {
- "version": "7.10.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.10.4.tgz",
- "integrity": "sha512-3U9y+43hz7ZM+rzG24Qe2mufW5KhvFg/NhnNph+i9mgCtdTCtMJuI1TMkrIUiK7Ix4PYlRF9I5dhqaLYA/ADXw==",
- "dev": true
+ "version": "7.22.20",
+ "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.20.tgz",
+ "integrity": "sha512-Y4OZ+ytlatR8AI+8KZfKuL5urKp7qey08ha31L8b3BwewJAoJamTzyvxPR/5D+KkdJCGPq/+8TukHBlY10FX9A==",
+ "dev": true,
+ "engines": {
+ "node": ">=6.9.0"
+ }
},
"node_modules/@babel/helper-validator-option": {
"version": "7.12.1",
@@ -358,9 +378,9 @@
}
},
"node_modules/@babel/parser": {
- "version": "7.12.3",
- "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.12.3.tgz",
- "integrity": "sha512-kFsOS0IbsuhO5ojF8Hc8z/8vEIOkylVBrjiZUbLTE3XFe0Qi+uu6HjzQixkFaqr0ZPAMZcBVxEwmsnsLPZ2Xsw==",
+ "version": "7.23.9",
+ "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.23.9.tgz",
+ "integrity": "sha512-9tcKgqKbs3xGJ+NtKF2ndOBBLVwPjl1SHxPQkd36r3Dlirw3xWUeGaTbqr7uGZcTaxkVNwc+03SVP7aCdWrTlA==",
"dev": true,
"bin": {
"parser": "bin/babel-parser.js"
@@ -1064,22 +1084,125 @@
}
},
"node_modules/@babel/types": {
- "version": "7.12.1",
- "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.12.1.tgz",
- "integrity": "sha512-BzSY3NJBKM4kyatSOWh3D/JJ2O3CVzBybHWxtgxnggaxEuaSTTDqeiSb/xk9lrkw2Tbqyivw5ZU4rT+EfznQsA==",
+ "version": "7.23.9",
+ "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.23.9.tgz",
+ "integrity": "sha512-dQjSq/7HaSjRM43FFGnv5keM2HsxpmyV1PfaSVm0nzzjwwTmjOe6J4bC8e3+pTEIgHaHj+1ZlLThRJ2auc/w1Q==",
"dev": true,
"dependencies": {
- "@babel/helper-validator-identifier": "^7.10.4",
- "lodash": "^4.17.19",
+ "@babel/helper-string-parser": "^7.23.4",
+ "@babel/helper-validator-identifier": "^7.22.20",
"to-fast-properties": "^2.0.0"
+ },
+ "engines": {
+ "node": ">=6.9.0"
}
},
+ "node_modules/@bcoe/v8-coverage": {
+ "version": "0.2.3",
+ "resolved": "https://registry.npmjs.org/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz",
+ "integrity": "sha512-0hYQ8SB4Db5zvZB4axdMHGwEaQjkZzFjQiN9LVYvIFB2nSUHW9tYpxWriPrWDASIxiaXax83REcLxuSdnGPZtw==",
+ "dev": true
+ },
"node_modules/@blakeembrey/deque": {
"version": "1.0.5",
"resolved": "https://registry.npmjs.org/@blakeembrey/deque/-/deque-1.0.5.tgz",
"integrity": "sha512-6xnwtvp9DY1EINIKdTfvfeAtCYw4OqBZJhtiqkT3ivjnEfa25VQ3TsKvaFfKm8MyGIEfE95qLe+bNEt3nB0Ylg==",
"dev": true
},
+ "node_modules/@discoveryjs/json-ext": {
+ "version": "0.5.7",
+ "resolved": "https://registry.npmjs.org/@discoveryjs/json-ext/-/json-ext-0.5.7.tgz",
+ "integrity": "sha512-dBVuXR082gk3jsFp7Rd/JI4kytwGHecnCoTtXFb7DB6CNHp4rg5k1bhg0nWdLGLnOV71lmDzGQaLMy8iPLY0pw==",
+ "dev": true,
+ "engines": {
+ "node": ">=10.0.0"
+ }
+ },
+ "node_modules/@istanbuljs/schema": {
+ "version": "0.1.3",
+ "resolved": "https://registry.npmjs.org/@istanbuljs/schema/-/schema-0.1.3.tgz",
+ "integrity": "sha512-ZXRY4jNvVgSVQ8DL3LTcakaAtXwTVUxE81hslsyD2AtoXW/wVob10HkOJ1X/pAlcI7D+2YoZKg5do8G/w6RYgA==",
+ "dev": true,
+ "engines": {
+ "node": ">=8"
+ }
+ },
+ "node_modules/@jridgewell/gen-mapping": {
+ "version": "0.3.3",
+ "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.3.tgz",
+ "integrity": "sha512-HLhSWOLRi875zjjMG/r+Nv0oCW8umGb0BgEhyX3dDX3egwZtB8PqLnjz3yedt8R5StBrzcg4aBpnh8UA9D1BoQ==",
+ "dev": true,
+ "dependencies": {
+ "@jridgewell/set-array": "^1.0.1",
+ "@jridgewell/sourcemap-codec": "^1.4.10",
+ "@jridgewell/trace-mapping": "^0.3.9"
+ },
+ "engines": {
+ "node": ">=6.0.0"
+ }
+ },
+ "node_modules/@jridgewell/resolve-uri": {
+ "version": "3.1.1",
+ "resolved": "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.1.tgz",
+ "integrity": "sha512-dSYZh7HhCDtCKm4QakX0xFpsRDqjjtZf/kjI/v3T3Nwt5r8/qz/M19F9ySyOqU94SXBmeG9ttTul+YnR4LOxFA==",
+ "dev": true,
+ "engines": {
+ "node": ">=6.0.0"
+ }
+ },
+ "node_modules/@jridgewell/set-array": {
+ "version": "1.1.2",
+ "resolved": "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz",
+ "integrity": "sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw==",
+ "dev": true,
+ "engines": {
+ "node": ">=6.0.0"
+ }
+ },
+ "node_modules/@jridgewell/source-map": {
+ "version": "0.3.5",
+ "resolved": "https://registry.npmjs.org/@jridgewell/source-map/-/source-map-0.3.5.tgz",
+ "integrity": "sha512-UTYAUj/wviwdsMfzoSJspJxbkH5o1snzwX0//0ENX1u/55kkZZkcTZP6u9bwKGkv+dkk9at4m1Cpt0uY80kcpQ==",
+ "dev": true,
+ "dependencies": {
+ "@jridgewell/gen-mapping": "^0.3.0",
+ "@jridgewell/trace-mapping": "^0.3.9"
+ }
+ },
+ "node_modules/@jridgewell/sourcemap-codec": {
+ "version": "1.4.15",
+ "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.15.tgz",
+ "integrity": "sha512-eF2rxCRulEKXHTRiDrDy6erMYWqNw4LPdQ8UQA4huuxaQsVeRPFl2oM8oDGxMFhJUWZf9McpLtJasDDZb/Bpeg==",
+ "dev": true
+ },
+ "node_modules/@jridgewell/trace-mapping": {
+ "version": "0.3.21",
+ "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.21.tgz",
+ "integrity": "sha512-SRfKmRe1KvYnxjEMtxEr+J4HIeMX5YBg/qhRHpxEIGjhX1rshcHlnFUE9K0GazhVKWM7B+nARSkV8LuvJdJ5/g==",
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@@ -4409,6 +5481,21 @@
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@@ -4678,6 +5765,20 @@
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"dev": true,
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- "dev": true
- }
+ "clone-deep": "^4.0.1",
+ "flat": "^5.0.2",
+ "wildcard": "^2.0.0"
}
},
+ "webpack-sources": {
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+ "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.3.tgz",
+ "integrity": "sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==",
+ "dev": true
+ },
"websocket-driver": {
- "version": "0.7.0",
- "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.0.tgz",
- "integrity": "sha1-DK+dLXVdk67gSdS90NP+LMoqJOs=",
+ "version": "0.7.4",
+ "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz",
+ "integrity": "sha512-b17KeDIQVjvb0ssuSDF2cYXSg2iztliJ4B9WdsuB6J952qCPKmnVq4DyW5motImXHDC1cBT/1UezrJVsKw5zjg==",
"dev": true,
"requires": {
- "http-parser-js": ">=0.4.0",
+ "http-parser-js": ">=0.5.1",
+ "safe-buffer": ">=5.1.0",
"websocket-extensions": ">=0.1.1"
}
},
@@ -22992,6 +28869,36 @@
"integrity": "sha1-u6Y8qGGUiZT/MHc2CJ47lgJsKk8=",
"dev": true
},
+ "wildcard": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/wildcard/-/wildcard-2.0.1.tgz",
+ "integrity": "sha512-CC1bOL87PIWSBhDcTrdeLo6eGT7mCFtrg0uIJtqJUFyK+eJnzl8A1niH56uu7KMa5XFrtiV+AQuHO3n7DsHnLQ==",
+ "dev": true
+ },
+ "window-size": {
+ "version": "0.1.0",
+ "resolved": "https://registry.npmjs.org/window-size/-/window-size-0.1.0.tgz",
+ "integrity": "sha512-1pTPQDKTdd61ozlKGNCjhNRd+KPmgLSGa3mZTHoOliaGcESD8G1PXhh7c1fgiPjVbNVfgy2Faw4BI8/m0cC8Mg==",
+ "dev": true
+ },
+ "with": {
+ "version": "5.1.1",
+ "resolved": "https://registry.npmjs.org/with/-/with-5.1.1.tgz",
+ "integrity": "sha512-uAnSsFGfSpF6DNhBXStvlZILfHJfJu4eUkfbRGk94kGO1Ta7bg6FwfvoOhhyHAJuFbCw+0xk4uJ3u57jLvlCJg==",
+ "dev": true,
+ "requires": {
+ "acorn": "^3.1.0",
+ "acorn-globals": "^3.0.0"
+ },
+ "dependencies": {
+ "acorn": {
+ "version": "3.3.0",
+ "resolved": "https://registry.npmjs.org/acorn/-/acorn-3.3.0.tgz",
+ "integrity": "sha512-OLUyIIZ7mF5oaAUT1w0TFqQS81q3saT46x8t7ukpPjMNk+nbs4ZHhs7ToV8EWnLYLepjETXd4XaCE4uxkMeqUw==",
+ "dev": true
+ }
+ }
+ },
"wordwrap": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-1.0.0.tgz",
@@ -23072,6 +28979,12 @@
"dev": true,
"requires": {}
},
+ "xmlcreate": {
+ "version": "2.0.4",
+ "resolved": "https://registry.npmjs.org/xmlcreate/-/xmlcreate-2.0.4.tgz",
+ "integrity": "sha512-nquOebG4sngPmGPICTS5EnxqhKbCmz5Ox5hsszI2T6U5qdrJizBc+0ilYSEjTSzU0yZcmvppztXe/5Al5fUwdg==",
+ "dev": true
+ },
"xmlhttprequest": {
"version": "1.8.0",
"resolved": "https://registry.npmjs.org/xmlhttprequest/-/xmlhttprequest-1.8.0.tgz",
@@ -23240,14 +29153,10 @@
}
},
"yargs-parser": {
- "version": "13.1.2",
- "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz",
- "integrity": "sha512-3lbsNRf/j+A4QuSZfDRA7HRSfWrzO0YjqTJd5kjAq37Zep1CEgaYmrH9Q3GwPiB9cHyd1Y1UwggGhJGoxipbzg==",
- "dev": true,
- "requires": {
- "camelcase": "^5.0.0",
- "decamelize": "^1.2.0"
- }
+ "version": "20.2.9",
+ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz",
+ "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==",
+ "dev": true
},
"yeast": {
"version": "0.1.2",
@@ -23260,6 +29169,12 @@
"resolved": "https://registry.npmjs.org/yn/-/yn-2.0.0.tgz",
"integrity": "sha1-5a2ryKz0CPY4X8dklWhMiOavaJo=",
"dev": true
+ },
+ "yocto-queue": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-1.0.0.tgz",
+ "integrity": "sha512-9bnSc/HEW2uRy67wc+T8UwauLuPJVn28jb+GtJY16iiKWyvmYJRXVT4UamsAEGQfPohgr2q4Tq0sQbQlxTfi1g==",
+ "dev": true
}
}
}
diff --git a/package.json b/package.json
index f808e161196fdca400b9e8058042d9c99b9f02dc..882e37f3138c6c55dc1f27583ca1c2759cea8f1c 100644
--- a/package.json
+++ b/package.json
@@ -1,16 +1,17 @@
{
"name": "pdb-ligand-env",
- "version": "1.0.0",
+ "version": "2.0.0",
"description": "",
"main": "app.js",
"dependencies": {
"@types/d3": "^5.16.3",
"@types/d3-tip": "^3.5.5",
+ "@types/ws": "^8.5.4",
"d3": "^5.16.0",
"d3-tip": "^0.9.1",
"d3scription": "^1.0.1",
"lit-element": "^2.4.0",
- "typescript": "^4.0.2"
+ "typescript": "^5.3.3"
},
"devDependencies": {
"@babel/core": "^7.12.3",
@@ -18,7 +19,8 @@
"@babel/preset-env": "^7.12.1",
"@babel/runtime": "^7.12.1",
"@webcomponents/webcomponentsjs": "^2.5.0",
- "babel-loader": "^8.1.0",
+ "babel-loader": "^9.1.3",
+ "better-docs": "^2.7.3",
"browser-sync": "^2.26.13",
"camelcase": "^5.0.0",
"clean-webpack-plugin": "^1.0.1",
@@ -30,14 +32,16 @@
"gulp-concat": "^2.6.1",
"gulp-header": "^2.0.9",
"gulp-minify": "^3.1.0",
+ "jsdoc": "^4.0.2",
"live-server": "^1.2.1",
"npm-run-all": "^4.1.3",
"onchange": "^6.1.1",
"style-loader": "^0.23.1",
"ts-node": "^7.0.1",
"url-loader": "^1.1.2",
- "webpack": "^5.2.0",
- "webpack-cli": "^3.3.12"
+ "webpack": "^5.89.0",
+ "webpack-cli": "^5.1.4",
+ "webpack-dev-server": "^4.15.1"
},
"scripts": {
"tscW": "tsc -w",
diff --git a/src/component/component.js b/src/component/component.js
index 4f54ea025b6c94b53a86ec020a3402bdd54c225c..b7e631dbfeae469603a89d0b1235c33f1c575fcb 100644
--- a/src/component/component.js
+++ b/src/component/component.js
@@ -3,6 +3,14 @@ import { LitElement } from 'lit-element';
import "../styles/pdb-ligand-env.css";
// Extend the LitElement base class
+/**
+ * PDB LigandEnv component to display ligand structure in 2D along with its interactions.
+ * This depiction can be enriched with substructure highlight, atom names, binding site
+ * interactions and aggregated protein-ligand interactions
+ * @component
+ * @example <caption> Basic usage </caption>
+ * <pdb-ligand-env pdb-id="1cbs" pdb-res-id="200" pdb-chain-id="A" environment="development"></pdb-ligand-env>
+ */
class pdbLigandEnv extends LitElement {
//Get properties / attribute values
@@ -13,6 +21,7 @@ class pdbLigandEnv extends LitElement {
entityId: { type: String, attribute: 'entity-id' },
resName: { type: String, attribute: 'pdb-res-name' },
resId: { type: Number, attribute: 'pdb-res-id' },
+ contactType: {type: Array, attribute: 'contact-type', noAccessors: true},
chainId: { type: String, attribute: 'pdb-chain-id' },
substructureHighlight: { type: Array, attribute: 'substructure' },
substructureColor: { type: String, attribute: 'color' },
@@ -22,11 +31,27 @@ class pdbLigandEnv extends LitElement {
};
}
+ // Create custom accessors for contactType
+ set contactType(value) {
+ let prevCType = this._contactType + "";
+ this._contactType = value;
+ if (prevCType.length > 0) {
+ this.renderLigandEnv();
+ }
+ }
+ get contactType() { return this._contactType; }
+
constructor() {
super();
}
async connectedCallback() {
+ this.renderLigandEnv();
+ }
+
+ renderLigandEnv() {
+ this.innerHTML = "";
+
this.highlightSubstructure = [];
let uiParams = new Config.UIParameters();
uiParams.zoom = this.zoomOn;
@@ -47,12 +72,22 @@ class pdbLigandEnv extends LitElement {
this.display.initLigandInteractions(this.pdbId, this.resId, this.chainId);
}
}
- else if (this.resName) {
- this.display.initLigandDisplay(this.resName, names).then(() => this.display.centerScene());
+ else if (this.resName){
+ this.display.initLigandDisplay(this.resName, names).then(() => {
+ if (this.contactType){
+ if(this.display.ligandIntxData === undefined){
+ this.display.initLigandWeights(this.resName).then(() => {
+ this.display.showWeights(this.contactType);
+ })
+ }
+ else {
+ this.display.showWeights(this.contactType);
+ }
+ }
+ })
}
}
-
//#region properties
set depiction(data) {
if (!data) return;
@@ -61,6 +96,10 @@ class pdbLigandEnv extends LitElement {
this.display.centerScene();
}
+ set atomWeights(contactType) {
+ this.display.showWeights(contactType);
+ }
+
set highlightSubstructure(data) {
if (!data || !this.display) {
console.log(`Argument needs to be a non empty array of strings.`);
@@ -78,12 +117,6 @@ class pdbLigandEnv extends LitElement {
this.display.addLigandHighlight(this.substructureHighlight, this.highlightColor);
}
- set contourData(data) {
- if (!data || !this.display || !this.display.depiction !== undefined) return;
-
- this.display.addContours(data);
- }
-
set zoom(data) {
if (this.display !== undefined) this.display.toggleZoom(data);
}
@@ -104,4 +137,4 @@ class pdbLigandEnv extends LitElement {
}
// Register the new element with the browser.
-customElements.define('pdb-ligand-env', pdbLigandEnv);
\ No newline at end of file
+customElements.define('pdb-ligand-env', pdbLigandEnv);
diff --git a/src/plugin/config.ts b/src/plugin/config.ts
index 88292e547807dc1d305c9a554f206c0e1ae7d60c..b0622bcd6f1988216b550cee9a6334e18ed69b3e 100644
--- a/src/plugin/config.ts
+++ b/src/plugin/config.ts
@@ -7,10 +7,16 @@ namespace Config {
export const interactionShowLabelEvent: string = 'PDB.interactions.showLabel';
export const interactionHideLabelEvent: string = 'PDB.interactions.hideLabel';
+ export const LigandShowAtomEvent: string = 'PDB.ligand.showAtom';
+ export const LigandHideAtomEvent: string = 'PDB.ligand.hideAtom';
+
export const molstarClickEvent: string = 'PDB.molstar.click';
export const molstarMouseoverEvent: string = 'PDB.molstar.mouseover';
export const molstarMouseoutEvent: string = 'PDB.molstar.mouseout';
+ export const ligandHeatmapMouseoverEvent: string = 'PDB.ligHeatmap.mouseover';
+ export const ligandHeatmapMouseoutEvent: string = 'PDB.ligHeatmap.mouseout';
+
export const aaTypes = new Map<string, Array<string>>([
['hydrophobic', new Array<string>('A', 'I', 'L', 'M', 'F', 'W', 'V')],
['positive', Array<string>('K', 'R', 'O')],
diff --git a/src/plugin/depiction.ts b/src/plugin/depiction.ts
index 87ecc594318dc12ecdf808595976a99efcd9a3fd..3dd367ed6687b69179d8b1d8e5d9b79632dce2d0 100644
--- a/src/plugin/depiction.ts
+++ b/src/plugin/depiction.ts
@@ -1,36 +1,33 @@
/**
* This class contains all the details which are necessary for redrawing
- * RDKIt style 2D molecule depiction on a client side as well as some
- * other logic which should hopefully help with the initial placement of
+ * RDKit style 2D molecule depiction on a client side as well as some
+ * other logic for initial placement of
* binding partners in the residue-level view.
*
- * @author Lukas Pravda <lpravda@ebi.ac.uk>
* @class Depiction
- * @param {string} ccdId PDB CCD id.
- * @param {Atom[]} atoms List of atoms.
- * @param {Bond[]} bonds Visual representation of bonds.
- * They do not correlate 1:1 with a number of bonds!
- * @param {Vector2D} resolution x,y dimension of the image. Needs to be used
- * for a scene shift, so it is centered.
- */
+ * @param {HTMLElement} parent HTMLElement on which depiction to be displayed.
+ * @param {any} root SVG element for the depiction.
+ * @param {any} data Json annotation of ligand SVG
+ **/
+
class Depiction {
ccdId: string;
atoms: Atom[];
bonds: Bond[];
resolution: Vector2D;
-
+ private parent: HTMLElement;
private root: d3.Selection<SVGGElement, unknown, null, undefined>;
- private structure: d3.Selection<SVGGElement, unknown, null, undefined>;
- private contour: d3.Selection<SVGGElement, unknown, null, undefined>;
private highlight: d3.Selection<SVGGElement, unknown, null, undefined>;
+ public weight: d3.Selection<SVGGElement, unknown, null, undefined>;
+ private structure: d3.Selection<SVGGElement, unknown, null, undefined>;
- constructor(parent: any, data: any) {
- this.root = parent
-
+ constructor(parent: HTMLElement, root: any, data: any) {
+ this.root = root;
+ this.parent = parent;
this.highlight = this.root.append('g').attr('id', 'highlight');
+ this.weight = this.root.append('g').attr('id', 'weight');
this.structure = this.root.append('g').attr('id', 'structure');
- this.contour = this.root.append('g').attr('id', 'contour');
this.ccdId = data.ccd_id;
this.resolution = new Vector2D(data.resolution.x, data.resolution.y);
@@ -53,7 +50,9 @@ class Depiction {
}
this.bonds.push(bond);
+
});
+
}
@@ -62,10 +61,10 @@ class Depiction {
* atom.
*
* Present implementation sorts all the partners based on the atom
- * degree and then gets the one with the lovest degree and places
+ * degree and then gets the one with the lowest degree and places
* the initial residue position along the vector pointing from it.
*
- * @param {string[]} atomNames list of atom names the bound residue
+ * @param {string[]} atomNames array of atom names the bound residue
* has a contact with.
* @returns {Vector2D} Returns an initial placement of the residue in contact.
* @memberof Depiction
@@ -89,6 +88,13 @@ class Depiction {
return new Vector2D(x, y);
}
+
+ /**
+ * Draws ligand structure by appending svg:path
+ * elements corresponding to bonds and atoms with labels
+ * @param {boolean} true if atom names need to be displayed
+ * @memberof Depiction
+ */
public draw(atomNames: boolean = false) {
this.structure.selectAll("*").remove();
@@ -99,6 +105,12 @@ class Depiction {
else this.appendLabels();
}
+ /**
+ * Highlights atoms and bonds connecting them
+ * @param {string[]} atoms array of atom names to higlight
+ * @param {string} color color to be used for higlighting
+ * @memberof Depiction
+ */
public highlightSubgraph(atoms: Array<string>, color: string = undefined) {
if (!this.atoms || !atoms) return;
@@ -125,17 +137,75 @@ class Depiction {
.attr('d', x => `M ${x.bgn.position.x},${x.bgn.position.y} ${x.end.position.x},${x.end.position.y}`)
.attr('style', `fill:none;fill-rule:evenodd;stroke:${color};stroke-width:22px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1`)
}
+
+ /**
+ * Adds circles around atoms corresponding to the value of
+ * their weights.The size, color and number of crcles around
+ * atom indicates the strength of weight. Currently maximum of
+ * three circles are drawn
+ * @param {any} weights objects with atom names and value of weight
+ * @param {string} colorScheme Name of color to be used for circles
+ * @memberof Depiction
+ */
+
+ public addCircles(weights: any, colorScheme: string): void {
+ this.atoms.forEach(x => {
+ x.value = weights.filter(y => y.atom == x.name).map(z => z.value)[0]
- public addContour(data: any) {
- this.contour.selectAll('*').remove();
+ })
+ const data = this.atoms.filter(x => x.value >0);
+ const intxWeights = weights.map(x => x.value);
+ const gradient = new Model.Gradient(intxWeights, colorScheme).getScales();
+ const q1 = d3.quantile(intxWeights, 0.25);
+ const q3 = d3.quantile(intxWeights, 0.75);
+
+ const firstScale = gradient.firstScale;
+ const secondScale = gradient.secondScale;
+ const thirdScale = gradient.thirdScale;
+
+ this.weight.selectAll()
+ .data(data)
+ .enter()
+ .each(function(x: any){
+ if(x.value >= q1){
+ d3.select(this)
+ .append('circle')
+ .attr('cx', x.position.x)
+ .attr('cy', x.position.y)
+ .attr('r', secondScale.radiusScale(x.value))
+ .attr('fill', secondScale.colorScale(x.value))
+ .attr("fill-opacity", "0.5")
+ if(x.value >= q3){
+ d3.select(this)
+ .append('circle')
+ .attr('cx', x.position.x)
+ .attr('cy', x.position.y)
+ .attr('r', thirdScale.radiusScale(x.value))
+ .attr('fill', thirdScale.colorScale(x.value))
+ .attr("fill-opacity", "0.5")
+ }
+ }
+ });
- this.contour.append('div').text(`'contour data goes here: ${data}`);
+ this.weight.selectAll()
+ .data(data)
+ .enter()
+ .append('circle')
+ .attr("cx", x => x.position.x)
+ .attr("cy", x => x.position.y)
+ .attr("r", x => firstScale.radiusScale(x.value))
+ .attr("fill", x=> firstScale.colorScale(x.value))
+ .attr("fill-opacity", "0.5")
+ .on('mouseenter', (x:Atom) => this.atomMouseEnterEventHandler(x, true))
+ .on('mouseleave', () => this.atomMouseLeaveEventHandler(true));
+
}
/**
- * Appends to a given selection the visual representation of bonds as svg:path elements.
- *
+ * Appends to a given selection the visual representation of
+ * bonds as svg:path elements.
* representation of the bond visuals.
+ * @private
* @memberof Depiction
*/
private appendBondVisuals(): void {
@@ -149,7 +219,7 @@ class Depiction {
/**
* Append atom name labels to the visualization.
- *
+ * @private
* @memberof Depiction
*/
private appendAtomNames() {
@@ -167,12 +237,8 @@ class Depiction {
}
/**
- * Append depiction labels to the visualization. Because RDKIt places
- * the labels slightly differently this information needs to be
- * consumed too, because we cannot use just atom position directly.
- * Also there are all sorts of colorful subscripts and superscripts,
- * so it is much easier to use it this way.
- *
+ * Append depiction labels to the visualization.
+ * @private
* @memberof Depiction
*/
private appendLabels() {
@@ -183,7 +249,7 @@ class Depiction {
.data(data)
.enter()
.append('g')
- .attr('filter', 'url(#solid-background)')
+ .attr('filter', 'labels')
.each(function (x: any) {
for (var i = 0; i < x.labels.length; i++) {
d3.select(this)
@@ -196,6 +262,12 @@ class Depiction {
});
}
+ /**
+ * Finds the center of an array of atoms
+ * @param {string} ids atom ids
+ * @return {Vector2D} coordinates of center
+ * @memeberof Depiction
+ */
public getCenter(ids: string[]): Vector2D {
let coords = new Array<Vector2D>();
@@ -214,7 +286,6 @@ class Depiction {
*
*
* @param {Map<string, number>} map
- * @returns
* @memberof Depiction
*/
public sortMap(map: Map<string, number>) {
@@ -232,9 +303,81 @@ class Depiction {
return newMap;
}
+
+ // #region event handlers
+ /**
+ * Mouse enter event handler for circles around atoms
+ * depicting their weights
+ * @public
+ * @param {Atom} atom object
+ * @param {boolean} propagation if event should be triggered on external components
+ * @memebrof Depiction
+ */
+
+ public atomMouseEnterEventHandler(x: Atom, propagation: boolean){
+ this.fireExternalAtomEvent(x, propagation, Config.LigandShowAtomEvent);
+ }
+
+ /**
+ * Mouse leave event handler for circlea round atoms
+ * depicting their weights
+ * @public
+ * @param {boolean} propagation if event should be triggered on external components
+ * @memberof Depiction
+ */
+ public atomMouseLeaveEventHandler(propagation: boolean){
+ this.fireExternalNullEvent(propagation, Config.LigandHideAtomEvent);
+ }
+ // #endregion
+
+ // #region fire events
+ /**
+ * Dispatches custom event to display atom names and
+ * corresponding weights on tooltip on mouse enter
+ * @private
+ * @param {Atom} atom object
+ * @param {string} eventName name of event
+ * @memeberof Depiction
+ */
+ private fireExternalAtomEvent(atom: Atom, propagation:boolean, eventName: string){
+ const e = new CustomEvent(eventName, {
+ bubbles: true,
+ detail: {
+ tooltip: atom.toTooltip(),
+ external: propagation
+ }
+ });
+ this.parent.dispatchEvent(e);
+ }
+
+ /**
+ * Dispatches event to hide tooltip on mouse leave
+ * @private
+ * @param {boolean} propagation if event should be triggered on external components
+ * @param {string} eventName name of event
+ * @memeberof Depiction
+ */
+ private fireExternalNullEvent(propagation:boolean, eventName: string) {
+ const e = new CustomEvent(eventName, {
+ bubbles: true,
+ detail: {
+ external: propagation
+ }
+ });
+
+ this.parent.dispatchEvent(e);
+ }
+
+ // #endregion
+
}
+
+
+
+
+
/**
* Atom from the depiction
*
@@ -247,27 +390,37 @@ class Atom {
name: string;
labels: any;
position: Vector2D;
- connectivity: number
+ connectivity: number;
+ value: number;
constructor(item: any) {
this.name = item.name;
this.labels = item.labels;
this.position = new Vector2D(item.x, item.y);
this.connectivity = 0;
+ this.value = 0;
}
/**
*
*
* @param {Atom} other
- * @returns true if the atoms are equal
+ * @returns {boolean} true if the atoms are equal
* @memberof Atom
*/
- public equals(other: Atom) {
+ public equals(other: Atom): boolean {
if (!(other instanceof Atom)) return false;
return other.name === this.name;
}
+
+ /**
+ * @return {string} name of atom
+ * @memberof Atom
+ */
+ public toTooltip(): string {
+ return `<span>${this.name} | ${this.value}</span>`;
+ }
}
/**
@@ -340,7 +493,6 @@ class Vector2D {
}
}
-
/**
* Represents a bond in a 2D depiction.
*
@@ -356,12 +508,6 @@ class Bond {
coords: string;
style: string;
- /**
- *Creates an instance of the bond.
- * @param {Atom} a
- * @param {Atom} b
- * @memberof Bond
- */
constructor(a: Atom, b: Atom, coords: string, style: string) {
this.bgn = a;
this.end = b;
@@ -389,7 +535,7 @@ class Bond {
* Check whether or not a bond contains the atom.
*
* @param {Atom} other The other side of the bond
- * @returns True if the atom is a part of the bond, false otherwise.
+ * @returns {boolean} True if the atom is a part of the bond, false otherwise.
* @memberof Bond
*/
public containsAtom(other: Atom) {
diff --git a/src/plugin/manager.ts b/src/plugin/manager.ts
index 2a7a07fc62e189a51550f7361a5be33fd61bba8d..62242d4a8175ce465c74f6d8cdf36a44028ffa0a 100644
--- a/src/plugin/manager.ts
+++ b/src/plugin/manager.ts
@@ -1,3 +1,13 @@
+/**
+ * This class contains methods for creating all the visualization
+ * components of the LigandEnv
+ *
+ * @class Visualization
+ * @param {HTMLElement} element HTMLElement to display the visualization
+ * @param {Config.UIParameters} uiParameters UI parameter configurations
+ * @param {string} env environment to fetch data from
+ *
+ */
class Visualization {
// component related
private parent: HTMLElement;
@@ -26,6 +36,7 @@ class Visualization {
private visualsMapper: VisualsMapper;
private interactionsData: any;
+ private ligandIntxData: any;
private selectedResidueHash: string;
private nodeDragged: boolean;
@@ -68,8 +79,11 @@ class Visualization {
if (uiParameters.zoom) this.zoomHandler = this.getZoomHandler();
+ document.addEventListener(Config.ligandHeatmapMouseoverEvent, e => this.ligHeatmapMouseoverEventHandler(e));
+ document.addEventListener(Config.ligandHeatmapMouseoutEvent, () => this.ligHeatmapMouseoutEventHandler());
+
document.addEventListener(Config.molstarClickEvent, e => this.molstarClickEventHandler(e));
- document.addEventListener(Config.molstarMouseoverEvent, e => this.molstarClickEventHandler(e));
+ document.addEventListener(Config.molstarMouseoverEvent, e => this.molstarClickEventHandler(e));
document.addEventListener(Config.molstarMouseoutEvent, () => this.molstarMouseoutEventHandler());
d3.select(this.parent).on('resize', () => this.resize());
@@ -95,7 +109,7 @@ class Visualization {
private molstarClickEventHandler(e: any) {
if (this.fullScreen) return;
- let hash = `${e.eventData.auth_asym_id}${e.eventData.auth_seq_id}${e.eventData.ins_code}`;
+ let hash = `${e.eventData.auth_asym_id}${e.eventData.auth_seq_id}${e.eventData.ins_code}`;
this.nodes?.each((node: Model.InteractionNode, index: number, group: any) => {
this.nodeDim(node, index, group);
@@ -109,6 +123,22 @@ class Visualization {
}
+ private ligHeatmapMouseoverEventHandler(e: any) {
+ if (this.depiction === undefined) return;
+ const atomName = e.detail.name; // CustomEvent
+ const atom = this.depiction.atoms.filter(x => x.value >0 && x.name === atomName);
+ if (atom.length > 0) {
+ this.depiction.atomMouseEnterEventHandler(atom[0], true);
+ } else {
+ this.depiction.atomMouseLeaveEventHandler(false);
+ }
+ }
+
+ private ligHeatmapMouseoutEventHandler() {
+ if (this.depiction === undefined) return;
+ this.depiction.atomMouseLeaveEventHandler(true);
+ }
+
/**
* Handles mouse leave molstar event. Removes interaction node highlight
@@ -260,7 +290,7 @@ class Visualization {
* PDBeChem process.
*
* @param {string} ligandId
- * @returns
+ * @param {boolean} withNames true for displaying atom names
* @memberof Visualization
*/
public async initLigandDisplay(ligandId: string, withNames: boolean = false) {
@@ -272,19 +302,50 @@ class Visualization {
.then(() => this.centerScene());
}
+
+ /**
+ * Download aggregated protein-ligand interactions data.
+ *
+ * @param {string} ligandId
+ * @memberof Visualization
+ */
+
+ public async initLigandWeights(ligandId: string){
+ const weightUrl = `https://raw.githubusercontent.com/roshkjr/Learning-sources/main/${ligandId}_atom_residue_intx.json`
+ return d3.json(weightUrl)
+ .then((d: any) => this.ligandIntxData = d);
+ }
+
/**
* Add depiction to the canvas from external resource.
*
- * @param {*} depiction Content of annotation.json file generated by
+ * @param {any} depiction Content of annotation.json file generated by
* the PDBeChem process.
+ * @param {boolean} withNames true for displaying atom names
* @memberof Visualization
*/
public addDepiction(depiction: any, withNames: boolean) {
- this.depiction = new Depiction(this.depictionRoot, depiction);
+ this.depiction = new Depiction(this.parent, this.depictionRoot, depiction);
this.depiction.draw(withNames);
+
}
+ /**
+ * Adds circles around atoms higlighting the weights of atoms.
+ *
+ * @param {string} contactType
+ * @memberof Visualization
+ */
+ public showWeights(contactType: string[]){
+ if ((this.depiction === undefined) || (this.ligandIntxData) === undefined) return;
+ const atomPropensity= new Model.LigandIntx(this.ligandIntxData, contactType).getAtomIntxPropensity();
+ const colorScheme = "Greens";
+ this.depiction.addCircles(atomPropensity, colorScheme);
+ if(this.zoomHandler !== undefined){
+ this.zoomHandler(this.svg, d3.zoomIdentity)
+ };
+ }
/**
* Show depiction with/without atom names
@@ -312,26 +373,16 @@ class Visualization {
* @memberof Visualization
*/
public addLigandHighlight(highlight: string[], color: string = undefined) {
+ if (!this.depiction) return;
this.depiction.highlightSubgraph(highlight, color);
}
-
- /**
- * Add contours to the ligand structure. The previous contours are
- * going to be removed.
- *
- * @param {*} data
- * @memberof Visualization
- */
- public addContours(data: any) {
- this.depiction.addContour(data);
- }
-
-
+
/**
* Add ligand interactions to the canvas
*
* @param {*} data Data content of the API end point
* /pdb/bound_ligand_interactions
+ * @param {boolean} true if atom names to be displayed
* @memberof Visualization
*/
public addLigandInteractions(data: any, withNames: boolean = false) {
@@ -356,7 +407,7 @@ class Visualization {
/**
* Add bound molecule interactions to the canvas.
*
- * @param {*} data Data content of the API end point
+ * @param {any} data Data content of the API end point
* /pdb/bound_molecule_interactions
* @param {string} bmId Bound molecule id
* @memberof Visualization
@@ -376,6 +427,7 @@ class Visualization {
// #region menu functions
+
/**
* Export scene into an SVG components. It relies on the availability
* of the external CSS for SVG styling. Otherwise it does not work.
@@ -611,6 +663,7 @@ class Visualization {
this.parent.dispatchEvent(e);
}
+
// #endregion fire events
@@ -668,7 +721,6 @@ class Visualization {
* @param {Model.InteractionNode} n Interaction node user clicked to
* @param {number} i index o the interaction node
* @param {*} g group of interaction nodes
- * @returns
* @memberof Visualization
*/
private selectLigand(n: Model.InteractionNode, i: number, g: any) {
@@ -783,7 +835,7 @@ class Visualization {
/**
* Setup display of interactions for bound molecule.
- * * This includes: setup of links, nodes, simulation and subscribing to relevant events.
+ * This includes: setup of links, nodes, simulation and subscribing to relevant events.
* No depiction is required for this step.
*
* @private
diff --git a/src/plugin/model.ts b/src/plugin/model.ts
index 5ee6d58e8b4fde70f9264bdd1050f977c57b5dd2..3df5636f6185a353e68e3eee6eb52deb4a85a2be 100644
--- a/src/plugin/model.ts
+++ b/src/plugin/model.ts
@@ -59,6 +59,8 @@ namespace Model {
/**
* Data model representing a single residue, which is a part of the
* bound molecule. This residue is unique in the entire binding site.
+ * @param {any} data
+ * @param {boolean} isLigand true if the residue is a ligand
*/
export class Residue {
id: string
@@ -496,4 +498,114 @@ namespace Model {
}
}
+ export class LigandIntx{
+ data: any;
+ contactTypes: string[];
+ filteredData: any;
+
+ constructor(data: any, contactTypes:string[]){
+ this.data = data;
+ this.contactTypes = contactTypes;
+ this.filteredData = this.getFilteredData();
+
+ }
+
+ private getAtomResidueObj(x: string[]){
+ return {
+ "atom": x[0],
+ "AA": x[1],
+ "count": x[2]
+ }
+ }
+
+ private getFilteredData(){
+ const filteredData = new Array();
+ for (const contactType in this.data){
+ if (this.contactTypes.includes(contactType)){
+ filteredData.push(...this.data[contactType].map(this.getAtomResidueObj));
+ }
+ }
+ return filteredData
+ }
+
+ public getAtomIntxPropensity(){
+ const atomCount = new Array();
+ this.filteredData.reduce(function(acc, currentValue){
+ if(!acc[currentValue.atom]){
+ acc[currentValue.atom] = {"atom": currentValue.atom, "count": 0};
+ atomCount.push(acc[currentValue.atom]);
+ }
+ acc[currentValue.atom].count += currentValue.count;
+ return acc
+ },{});
+
+ const totalIntx = atomCount.reduce(function(acc, currentValue){
+ acc += currentValue.count;
+ return acc;
+ }, 0)
+
+ const atomPropensity = atomCount.map((x) =>
+ ({"atom": x.atom,
+ "value": (x.count/totalIntx).toFixed(2)
+ })
+ );
+
+ return atomPropensity
+
+ }
+ }
+
+ /**
+ * Data model representing scale of a circles
+ * Stores scale for radius and color
+ */
+ export class Scale{
+ radiusScale: any;
+ colorScale: any;
+
+ constructor(radiusScale:any, colorScale:any){
+ this.radiusScale = radiusScale;
+ this.colorScale = colorScale;
+ }
+
+ }
+
+ /**
+ * Gradient object with three
+ * level scales for circles to highlight
+ * @param {any} weight
+ * @param {string} colorScheme color to be used for generating gradient
+ */
+ export class Gradient {
+ weight: any;
+ colorScheme: string;
+
+ constructor(weight: any, colorScheme:string){
+ this.weight = weight;
+ this.colorScheme = colorScheme;
+ }
+
+ /**
+ * Generates three level scales for the
+ * Gradient object
+ */
+ public getScales(){
+
+ const color = d3[`scheme${this.colorScheme}`][9];
+ const weightMax = Number(d3.max(this.weight));
+ const gradient = {firstScale: new Scale(d3.scaleLinear([0, weightMax], [20, 30]),
+ d3.scaleLinear([0,weightMax], ["#FFFFFF", color[4]])),
+ secondScale: new Scale(d3.scaleLinear([0,weightMax], [10, 20]),
+ d3.scaleLinear([0, weightMax], [color[5], color[7]])),
+ thirdScale: new Scale(d3.scaleLinear([0, weightMax], [2, 10]),
+ d3.scaleLinear([0, weightMax], [color[8], color[9]]))
+
+ };
+
+ return gradient
+
+ }
+
+ }
+
}
\ No newline at end of file
diff --git a/src/plugin/residuefactory.ts b/src/plugin/residuefactory.ts
index af65a1a6b5907e23e5305c911dc38d27c42abc41..6087618a9d980020e66db5ee91a48e0ad0904e7d 100644
--- a/src/plugin/residuefactory.ts
+++ b/src/plugin/residuefactory.ts
@@ -45,7 +45,7 @@ class ResidueProvider {
* Get single letter abbreviation of the ligand.
*
* @param {string} name Name of the chemical compound
- * @returns Single letter abbreviation of the ligand
+ * @returns {string} Single letter abbreviation of the ligand
* @memberof ResidueProvider
*/
public getAminoAcidAbbreviation(name: string): string {
@@ -57,7 +57,6 @@ class ResidueProvider {
* Fetch single letter abbreviations from API if they are not present
*
* @param {string} n
- * @returns
* @memberof ResidueProvider
*/
public downloadAnnotation(r: Model.Residue): void {
diff --git a/src/plugin/resources.ts b/src/plugin/resources.ts
index eeba721813ae9e517e328719e8641936c1ae6937..b5813855481dd242107edb891df6ffa6a98d89da 100644
--- a/src/plugin/resources.ts
+++ b/src/plugin/resources.ts
@@ -128,7 +128,6 @@ namespace Resources {
* @param {string} chainId
* @param {number} resId
* @param {Model.Environment} env
- * @returns
*/
export function ligandInteractionsAPI(pdbId: string, chainId: string, resId: number, env: Model.Environment) {
let url = '';
diff --git a/src/plugin/ui.ts b/src/plugin/ui.ts
index 89f6ff0b02dd82f8598496866f3d07606b0dd9b4..c62cd3debf17577c4df871105687bbc62f4f739c 100644
--- a/src/plugin/ui.ts
+++ b/src/plugin/ui.ts
@@ -114,6 +114,9 @@ let helpBonds = `
// #endregion help
+/**
+ * @class UI
+ */
class UI {
@@ -143,7 +146,6 @@ class UI {
*
* @param {Config.UIParameters} p Object with annotation which
* UI elements should be created.
- * @returns
* @memberof UI
*/
public register(p: Config.UIParameters) {
@@ -263,6 +265,8 @@ class UI {
this.parent.addEventListener(Config.interactionClickEvent, e => this.nodeMouseEnterEventHandler(e));
this.parent.addEventListener(Config.interactionMouseoverEvent, e => this.nodeMouseEnterEventHandler(e));
this.parent.addEventListener(Config.interactionMouseoutEvent, () => this.nodeMouseLeaveEventHandler());
+ this.parent.addEventListener(Config.LigandShowAtomEvent, e => this.nodeMouseEnterEventHandler(e));
+ this.parent.addEventListener(Config.LigandHideAtomEvent, () => this.nodeMouseLeaveEventHandler());
}
if (this.residueLabel !== undefined) {
diff --git a/tsconfig.json b/tsconfig.json
index 2fa5b589702ad83a3eceda9794feb05be9e84cc0..054e1ffa11fc16941cc8949bcc3e01f9562e0645 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -10,7 +10,7 @@
"declaration": true,
"module": "none",
"moduleResolution": "node",
- "out": "build/pdb-ligand-env-plugin.js"
+ "outFile": "build/pdb-ligand-env-plugin.js"
},
"include": ["src/plugin/**/*", ],
"exclude": [