diff --git a/.gitignore b/.gitignore
index eca9dd3b7e8f7d95939544640a51468fc64a9397..517220d6014ddfdc95de08f4cb6afb4b8aa9b943 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,5 +2,4 @@
.mypy_cache
node_modules
-build/*.js*
-build/app*
\ No newline at end of file
+build/*
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index cb692041d37da9237189d49ab50775bf939a6e94..652aa5894bf8ae6dff67d48c176059600c1ae6fd 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,9 +2,7 @@ image: node:latest
before_script:
- npm install
- - npm install --save-dev webpack
- - node_modules/.bin/webpack --mode=production
- - node_modules/.bin/tsc
+ - npm run build
pages:
script:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9cc32c9aa6ae718e8fbda93591a8e0ce7c0a5874..5a8572c285d581cc3fd684470b6f3224759cf357 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,16 @@
-# RELEASE 0.1 - 28 January 2019
+## RELEASE 0.2 - 24 February 2020
+
+Component rembranded to `pdb-ligand-env`
+
+### Features
+
+* A lot of bug fixes and under the hood improvements
+
+## RELEASE 0.1 - 28 January 2019
First release for public testing.
-## Features
+### Features
* Bound molecule interactions view
* Residue-level interactions view
diff --git a/README.md b/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..4d3be49506ef5e08cb623a521f986e5750c8ca8c
--- /dev/null
+++ b/README.md
@@ -0,0 +1,153 @@
+# PDB ligand environment 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 and binding site interactions.
+
+## Step after cloning (use local server to see demo pages)
+
+```shell
+npm run-script build
+cp demo/demo* build/ (this copies demo_component.html and demo_plugin.html to build folder)
+cd build
+python3 -m http.server
+```
+
+## 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 | 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)
+
+## 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`.
+
+### Web-component
+
+A few files needs to be imported in the page before the component is attempted to be loaded:
+
+```html
+
+<!-- D3 -->
+<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="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="pdb-ligand-env-component-0.2.0-min.js"></script>
+```
+
+#### A) Ligand interactions
+
+```html
+<pdb-ligand-env pdb-id="1cbs" pdb-res-id="200" pdb-chain-id="A"></pdb-ligand-env>
+```
+
+#### B) Bound molecule interactions
+
+```html
+<pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1"></pdb-ligand-env>
+```
+
+#### C) Ligand/chemical component
+
+```html
+<pdb-ligand-env pdb-res-name="CLR" zoom-on ></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>
+```
+
+and then inject data you want to display e.g.:
+
+```javascript
+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;
+```
+
+### Plugin
+
+The component can be also added to DOM directly from JavaScript. There are some requirements
+
+```html
+
+<!-- D3 -->
+<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="pdb-ligand-env-svg.css" />
+
+<!-- UI icons -->
+<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css" />
+
+<!--PDB ligand environment plugin-->
+<script src="pdb-ligand-env-plugin-min.js"></script>
+<link rel="stylesheet" href="pdb-ligand-env.css" />
+
+```
+
+and then the component can be instantiated as simply as:
+
+```javascript
+let component = document.getElementById('SIA-component');
+let uiParams = {
+ reinitialize: true, // allow reinitialize option in the component menu
+ zoom: true, // allow scene zoom
+ fullScreen: true, // allow allow full screen option in the component menu
+ downloadImage: true, // allow image download from the component menu
+ downloadData: true, // allow interactions data download from compoment menu
+ center: true, // allow scene centering option from the component menu
+ help: false, // allow help option from the component menu
+ residueLabel: true, // show residue label
+ tooltip: true // show residue tooltip on mouse hover
+};
+
+this.display = new Visualization(this, uiParams);
+
+// to display bound molecule interactions
+this.display.initBoundMoleculeInteractions('3d12', 'bm1');
+// to display ligand interactions
+this.display.initLigandInteractions('1cbs', 200, 'A');
+
+// to display chemical component only
+this.display.initLigandDisplay('HEM');
+````
+
+## Parameters
+
+| Parametr | Type | Required | Description |
+|-------------------- | --------- | -------- | ------- |
+| 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-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)` |
+| zoom-on | boolean | No | Allow zoom functionality on the component level. |
diff --git a/build/pdbe-interactions-svgstyles.css b/build/pdbe-interactions-svgstyles.css
deleted file mode 100644
index 4a397dce79a1aaa9b0f3c7e88a34513ee9b05bba..0000000000000000000000000000000000000000
--- a/build/pdbe-interactions-svgstyles.css
+++ /dev/null
@@ -1,148 +0,0 @@
-.svg-shadow-node {
- stroke-width: 0;
- fill: white;
-}
-
-.svg-shadow-bond {
- stroke-width: 15px;
- stroke: transparent;
-}
-
-.svg-bond {
- fill: none;
- fill-rule: evenodd;
- stroke-linecap: butt;
- stroke-linejoin: miter;
- stroke-opacity: 1;
-}
-
-.svg-bond-ligand {
- stroke-width: 4px;
- stroke: black;
-}
-
-.svg-bond-electrostatic {
- stroke-width: 3px;
- stroke-dasharray: 10 10;
- stroke: #3F26BF;
-}
-
-.svg-bond-stacking {
- stroke-width: 3px;
- stroke: green;
-}
-
-.svg-bond-atom-pi {
- stroke-width: 3px;
- stroke: green;
-}
-
-.svg-bond-amide {
- stroke-width: 3px;
- stroke: green;
-}
-
-.svg-bond-vdw {
- stroke-width: 3px;
- stroke-dasharray: 10 10;
- stroke: #9B7653;
-}
-
-.svg-bond-hydrophobic {
- stroke-width: 0px;
-}
-
-.svg-bond-aromatic {
- stroke-width: 4px;
- stroke-dasharray: 1 10;
- stroke: #AD4379;
-}
-
-.svg-bond-metal {
- stroke-width: 4px;
- stroke: #008080;
-}
-
-.svg-bond-clashes {
- stroke-width: 3px;
- stroke: #FF5050;
-}
-
-.svg-bond-covalent {
- stroke-width: 3px;
- stroke: black;
-}
-
-.svg-bond-other {
- stroke-width: 1px;
- stroke: black;
-}
-
-.svg-node circle {
- stroke-width: 3px;
-}
-
-.svg-node text {
- cursor: inherit;
- font-family: Arial, Helvetica, sans-serif;
- stroke: black !important;
- fill: black !important;
-}
-
-.svg-node text tspan:first-child {
- cursor: inherit;
- font-weight: 100;
- font-size: 0.75em;
-}
-
-.svg-node text tspan:nth-child(2) {
- cursor: inherit;
- font-weight: lighter;
- font-size: 0.55em;
-}
-
-.svg-ligand-res {
- stroke: black;
- fill: white;
-}
-
-.svg-water-res {
- stroke: #A9A9A9;
- fill: #00BFFF;
-}
-
-.svg-cystein-res {
- stroke: #A9A9A9;
- fill: yellow;
-}
-
-.svg-positive-res {
- stroke: #A9A9A9;
- fill: #007FFF;
-}
-
-.svg-negative-res {
- stroke: #A9A9A9;
- fill: #FF4500;
-}
-
-.svg-polar-res {
- stroke: #A9A9A9;
- fill: #9DC183;
-}
-
-.svg-aromatic-res {
- stroke: #A9A9A9;
- fill: #FFA2FF;
-}
-
-.svg-aliphatic-res {
- stroke: #A9A9A9;
- fill: #808080;
-}
-
-.svg-others-res {
- stroke: #A9A9A9;
- fill: #C0C0C0;
-
-}
\ No newline at end of file
diff --git a/demo/demo_component.html b/demo/demo_component.html
new file mode 100644
index 0000000000000000000000000000000000000000..9957b578aa270e3a6b0ec816b2062765c9323a0a
--- /dev/null
+++ b/demo/demo_component.html
@@ -0,0 +1,45 @@
+<!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="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="pdb-ligand-env-component-0.2.0-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-id="1cbs" pdb-res-id="200" pdb-chain-id="A"></pdb-ligand-env>
+ </div>
+ </div>
+
+ <!--Mode B-->
+ <div style="position: relative; float: left;">
+ <div style="width: 500px; height: 500px; position: relative">
+ <pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1"></pdb-ligand-env>
+ </div>
+ </div>
+
+ <!--Mode C-->
+ <div style="position: relative; float: left;">
+ <div style="width: 500px; height: 500px; position: relative">
+ <pdb-ligand-env pdb-res-name="CLR" zoom-on></pdb-ligand-env>
+ </div>
+ </div>
+
+ </body>
+
+</html>
\ No newline at end of file
diff --git a/demo/demo_plugin.html b/demo/demo_plugin.html
new file mode 100644
index 0000000000000000000000000000000000000000..23621872cd42193df387f55dbe9925f2d302a06c
--- /dev/null
+++ b/demo/demo_plugin.html
@@ -0,0 +1,65 @@
+<!doctype html>
+<html lang="en">
+ <head>
+
+ <link rel="stylesheet" href="pdb-ligand-env.css" />
+
+ <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="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 plugin-->
+ <script src="pdb-ligand-env-plugin-min.js"></script>
+
+ <!--Initialize Visualization-->
+ <script>
+ document.addEventListener("DOMContentLoaded", function (event) {
+ //<!--Mode A-->
+ var eleLigInteraction = document.getElementById('ligand-interaction');
+ this.lidisplay = new Visualization(eleLigInteraction, undefined);
+ this.lidisplay.initLigandInteractions('1cbs', 200, 'A');
+
+ //<!--Mode B-->
+ var eleBoundInteraction = document.getElementById('boundmolecule-interaction');
+ this.bmdisplay = new Visualization(eleBoundInteraction, undefined);
+ this.bmdisplay.initBoundMoleculeInteractions('3d12', 'bm1');
+
+ //<!--Mode C-->
+ var eleChemComp = document.getElementById('chem-comp');
+ this.ccdisplay = new Visualization(eleChemComp, undefined);
+ this.ccdisplay.initLigandDisplay('HEM');
+ });
+ </script>
+
+ </head>
+ <body>
+ <!--Mode A-->
+ <div style="position: relative; float: left;">
+ <div style="width: 600px; height: 600px; position: relative">
+ <div id='ligand-interaction'></div>
+ </div>
+ </div>
+
+ <!--Mode B-->
+ <div style="position: relative; float: left;">
+ <div style="width: 600px; height: 600px; position: relative">
+ <div id='boundmolecule-interaction'></div>
+ </div>
+
+ <!--Mode C-->
+ <div style="position: relative; float: left;">
+ <div style="width: 600px; height: 600px; position: relative">
+ <div id='chem-comp'></div>
+ </div>
+ </div>
+
+ </body>
+
+</html>
\ No newline at end of file
diff --git a/build/het_mapping.json b/dependencies/het_mapping.json
similarity index 100%
rename from build/het_mapping.json
rename to dependencies/het_mapping.json
diff --git a/build/index.html b/dependencies/index.html
similarity index 77%
rename from build/index.html
rename to dependencies/index.html
index b919569c7ae0ebb3570b49a3a0079a8d98aee6e8..99eaf8058a6e205198a283f95a9aa730875f0194 100644
--- a/build/index.html
+++ b/dependencies/index.html
@@ -3,8 +3,7 @@
<script src="https://d3js.org/d3.v5.min.js"></script>
<script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
<!--testing purposes only-->
-<link rel="stylesheet" href="pdbe-interactions-styles.css" />
-<link rel="stylesheet" href="pdbe-interactions-svgstyles.css" />
+<link rel="stylesheet" href="pdb-ligand-env-svg.css" />
<link rel="stylesheet" href="https://ebi.emblstatic.net/web_guidelines/EBI-Icon-fonts/v1.3/fonts.css" />
<!-- MOL* -->
@@ -12,8 +11,6 @@
href="https://wwwdev.ebi.ac.uk/pdbe/pdb-component-library/v1.0/css/molstar-light-0.0.1.css">
<script src="https://wwwdev.ebi.ac.uk/pdbe/pdb-component-library/v1.0/js/molstar-0.0.1.js"></script>
-<script src="app.js"></script>
-
<!-- Web component polyfill (only loads what it needs) -->
<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/webcomponents-lite.js" charset="utf-8">
</script>
@@ -21,16 +18,17 @@
<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js"
charset="utf-8"></script>
-<script type="module" src="component.js"></script>
+<script type="module" src="pdb-ligand-env-component-0.2.0-min.js"></script>
<script>
var renderBmInteractions = function (id, bmId) {
- var int = `<pdb-interactions pdb-id="${id}" bound-molecule-id="${bmId}"></pdb-interactions>`
+ var int =
+ `<pdb-ligand-env style="border: 1px solid black" pdb-id="${id}" bound-molecule-id="${bmId}"></pdb-ligand-env>`
document.getElementById('rt').innerHTML = int;
};
var renderLigandInteractions = function (id, chain, resId) {
var int =
- `<pdb-interactions pdb-id="${id}" pdb-chain-id="${chain}" pdb-res-id="${resId}"></pdb-interactions>`
+ `<pdb-ligand-env style="border: 1px solid black" pdb-id="${id}" pdb-chain-id="${chain}" pdb-res-id="${resId}" zoom-on></pdb-ligand-env>`
document.getElementById('rt').innerHTML = int;
};
@@ -71,8 +69,6 @@
query: "https://wwwdev.ebi.ac.uk/pdbe/coordinates/1cbs/ligandInteraction?&authAsymId=$A&authSeqNumber=$200&radius=5&dataSource=hydrogens"
};
}
- console.log('Perceived parameters:');
- console.log(params);
if (params.bmid === undefined) {
renderLigandInteractions(params.pdbid, params.chain, params.resid);
@@ -94,7 +90,11 @@
showPDBeLogo: false,
assemblyId: 'preferred', //'deposited'
// selectInteraction: false,
- ligandView: {auth_asym_Id: params.chain, auth_seq_id: params.resid, hydrogens: true},
+ ligandView: {
+ auth_asym_Id: params.chain,
+ auth_seq_id: params.resid,
+ hydrogens: true
+ },
backgroundColour: '0xFFFFFF',
//customColorList: [0xff0000, 0x0000ff],
//representationStyle: representationStyle//,
@@ -112,25 +112,30 @@
<body>
<div style="position: relative; float: left;">
- <div id="rt" style="width: 500px; height: 500px; border: 1px solid black; position: relative">
+ <div id="rt" style="width: 500px; height: 500px; position: relative">
</div>
</div>
<div style="position: relative; float: left;">
<div id='3dViewer' style="position:relative; width: 500px;height: 500px;"></div>
</div>
- <!-- <div style="position: relative; float: left;">
- <div id="rt" style="width: 500px; height: 500px; border: 1px solid black; position: relative">
- <pdb-interactions pdb-id="3d11" bound-molecule-id="bm1"></pdb-interactions>
- </div> -->
+ <div style="position: relative; float: left;">
+ <div id="rt 1" style="width: 500px; height: 500px; position: relative">
+ <pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1" zoom-on></pdb-ligand-env>
+ </div>
+ </div>
+ <div style="position: relative; float: left;">
+ <div id="rt 1" style="width: 500px; height: 500px; position: relative">
+ <pdb-ligand-env pdb-id="2aw3" bound-molecule-id="bm1" zoom-on></pdb-ligand-env>
+ </div>
</div>
<!--
Further use in the app for bound molecule interactions:
- <pdb-interactions pdb-id="3d12" bound-molecule-id="bm1"></pdb-interactions>
+ <pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1"></pdb-ligand-env>
for ligand interactions:
- <pdb-interactions pdb-id="3d12" pdb-chain-id="A" pdb-res-id="200"></pdb-interactions>
+ <pdb-ligand-env pdb-id="3d12" pdb-chain-id="A" pdb-res-id="200"></pdb-ligand-env>
-->
<script>
diff --git a/build/visuals.xml b/dependencies/pdb-snfg-visuals.xml
similarity index 52%
rename from build/visuals.xml
rename to dependencies/pdb-snfg-visuals.xml
index 1984d5560f21fed5e75a480f230ce1280f10a6ee..e1bd990bb0ba83abd5d310f24b77da95ea3c9457 100644
--- a/build/visuals.xml
+++ b/dependencies/pdb-snfg-visuals.xml
@@ -2,298 +2,298 @@
<glycans>
<!--Hexose-->
<g name="Glc">
- <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#0090bc;fill-opacity:1" r="25" />
+ <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#0090bc;fill-opacity:1" r="30" />
</g>
<g name="Man">
- <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#00a651;fill-opacity:1" r="25" />
+ <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#00a651;fill-opacity:1" r="30" />
</g>
<g name="Gal">
- <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#ffd400;fill-opacity:1" r="25" />
+ <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#ffd400;fill-opacity:1" r="30" />
</g>
<g name="Gul">
- <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#f47920;fill-opacity:1" r="25" />
+ <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#f47920;fill-opacity:1" r="30" />
</g>
<g name="Alt">
- <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#f69ea1;fill-opacity:1" r="25" />
+ <circle style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#f69ea1;fill-opacity:1" r="30" />
</g>
<g name="All">
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+ <g name="Psi" transform="translate(-30,-30)">
+ <polygon points="30,0 60,22 52,60 8,60 0,22" style="stroke:black;stroke-width:3;fill-rule:nonzero;fill:#f69ea1;fill-opacity:1" />
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diff --git a/gulpfile.js b/gulpfile.js
new file mode 100644
index 0000000000000000000000000000000000000000..83ea7951a492013b2dba53e793dde53ff36bdf4c
--- /dev/null
+++ b/gulpfile.js
@@ -0,0 +1,92 @@
+const gulp = require('gulp');
+const path = require('path');
+const del = require('del');
+const concat = require('gulp-concat');
+const header = require('gulp-header');
+const minify = require("gulp-minify");
+
+const PACKAGE_ROOT_PATH = process.cwd();
+const PKG_JSON = require(path.join(PACKAGE_ROOT_PATH, "package.json"));
+
+const banner = ['/**',
+ ` * ${PKG_JSON.name}`,
+ ` * @version ${PKG_JSON.version}`,
+ ' * @link https://gitlab.ebi.ac.uk/pdbe/web-components/ligand-env',
+ ' * @license Apache 2.0',
+ ' */',
+ ''
+].join('\n');
+
+const license = ['/**',
+ ' * Copyright 2019-2020 Lukas Pravda <lpravda@ebi.ac.uk>',
+ ' * European Bioinformatics Institute (EBI, http://www.ebi.ac.uk/)',
+ ' * European Molecular Biology Laboratory (EMBL, http://www.embl.de/)',
+ ' * Licensed under the Apache License, Version 2.0 (the "License");',
+ ' * you may not use this file except in compliance with the License.',
+ ' * You may obtain a copy of the License at ',
+ ' * http://www.apache.org/licenses/LICENSE-2.0',
+ ' * ',
+ ' * Unless required by applicable law or agreed to in writing, software',
+ ' * distributed under the License is distributed on an "AS IS" BASIS, ',
+ ' * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.',
+ ' * See the License for the specific language governing permissions and ',
+ ' * limitations under the License.',
+ ' */',
+ ''
+].join('\n');
+
+
+gulp.task('clean', function () {
+ return del([`build/${PKG_JSON.name}-component-${PKG_JSON.version}.js`, '!build']);
+});
+
+gulp.task('concatCSS', () => {
+ return gulp.src(['src/styles/pdb-ligand-env-svg.css'])
+ .pipe(concat(`${PKG_JSON.name}-svg.css`))
+ .pipe(header(license, {}))
+ .pipe(header(banner, {}))
+ .pipe(gulp.dest('build/'));
+});
+
+gulp.task('copyIndex', () => {
+ return gulp.src(['dependencies/index.html'])
+ .pipe(concat(`index.html`))
+ .pipe(gulp.dest('build/'));
+});
+
+gulp.task('copyMapping', () => {
+ return gulp.src(['dependencies/het_mapping.json'])
+ .pipe(concat(`het_mapping.json`))
+ .pipe(gulp.dest('build/'));
+});
+
+gulp.task('copyXML', () => {
+ return gulp.src(['dependencies/pdb-snfg-visuals.xml'])
+ .pipe(concat(`pdb-snfg-visuals.xml`))
+ .pipe(gulp.dest('build/'));
+});
+
+gulp.task('concat', () => {
+ return gulp.src([`build/${PKG_JSON.name}-plugin.js`, `build/${PKG_JSON.name}-component-init.js`])
+ .pipe(concat(`${PKG_JSON.name}-component-${PKG_JSON.version}.js`))
+ .pipe(header(license, {}))
+ .pipe(header(banner, {}))
+ .pipe(minify({
+ noSource: true
+ }))
+ .pipe(gulp.dest('build/'));
+});
+
+gulp.task('minifyPlugin', () => {
+ return gulp.src([`build/${PKG_JSON.name}-plugin.js`])
+ .pipe(concat(`${PKG_JSON.name}-plugin.js`))
+ .pipe(header(license, {}))
+ .pipe(header(banner, {}))
+ .pipe(minify({
+ noSource: true
+ }))
+ .pipe(gulp.dest('build/'));
+});
+
+gulp.task('default', gulp.series('clean', 'concat', 'concatCSS',
+ 'copyXML', 'copyIndex', 'copyMapping', 'minifyPlugin'));
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index 639c1631a773074226c5f0fe77c3fdceaa6afd39..cc0981366d691aaaea4a6d14f7a08f693231775c 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,260 +1,294 @@
{
- "name": "interactions",
- "version": "1.0.0",
+ "name": "pdb-ligand-env",
+ "version": "0.2.0",
"lockfileVersion": 1,
"requires": true,
"dependencies": {
"@babel/code-frame": {
- "version": "7.0.0",
- "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.0.0.tgz",
- "integrity": "sha512-OfC2uemaknXr87bdLUkWog7nYuliM9Ij5HUcajsVcMCpQrcLmtxRbVFTIqmcSkSeYRBFBRxs2FiUqFJDLdiebA==",
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.8.3.tgz",
+ "integrity": "sha512-a9gxpmdXtZEInkCSHUJDLHZVBgb1QS0jhss4cPP93EW7s+uC5bikET2twEF3KV+7rDblJcmNvTR7VJejqd2C2g==",
+ "dev": true,
+ "requires": {
+ "@babel/highlight": "^7.8.3"
+ }
+ },
+ "@babel/compat-data": {
+ "version": "7.8.1",
+ "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.8.1.tgz",
+ "integrity": "sha512-Z+6ZOXvyOWYxJ50BwxzdhRnRsGST8Y3jaZgxYig575lTjVSs3KtJnmESwZegg6e2Dn0td1eDhoWlp1wI4BTCPw==",
"dev": true,
"requires": {
- "@babel/highlight": "^7.0.0"
+ "browserslist": "^4.8.2",
+ "invariant": "^2.2.4",
+ "semver": "^5.5.0"
}
},
"@babel/core": {
- "version": "7.4.5",
- "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.4.5.tgz",
- "integrity": "sha512-OvjIh6aqXtlsA8ujtGKfC7LYWksYSX8yQcM8Ay3LuvVeQ63lcOKgoZWVqcpFwkd29aYU9rVx7jxhfhiEDV9MZA==",
- "dev": true,
- "requires": {
- "@babel/code-frame": "^7.0.0",
- "@babel/generator": "^7.4.4",
- "@babel/helpers": "^7.4.4",
- "@babel/parser": "^7.4.5",
- "@babel/template": "^7.4.4",
- "@babel/traverse": "^7.4.5",
- "@babel/types": "^7.4.4",
- "convert-source-map": "^1.1.0",
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.8.3.tgz",
+ "integrity": "sha512-4XFkf8AwyrEG7Ziu3L2L0Cv+WyY47Tcsp70JFmpftbAA1K7YL/sgE9jh9HyNj08Y/U50ItUchpN0w6HxAoX1rA==",
+ "dev": true,
+ "requires": {
+ "@babel/code-frame": "^7.8.3",
+ "@babel/generator": "^7.8.3",
+ "@babel/helpers": "^7.8.3",
+ "@babel/parser": "^7.8.3",
+ "@babel/template": "^7.8.3",
+ "@babel/traverse": "^7.8.3",
+ "@babel/types": "^7.8.3",
+ "convert-source-map": "^1.7.0",
"debug": "^4.1.0",
+ "gensync": "^1.0.0-beta.1",
"json5": "^2.1.0",
- "lodash": "^4.17.11",
+ "lodash": "^4.17.13",
"resolve": "^1.3.2",
"semver": "^5.4.1",
"source-map": "^0.5.0"
}
},
"@babel/generator": {
- "version": "7.4.4",
- "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.4.4.tgz",
- "integrity": "sha512-53UOLK6TVNqKxf7RUh8NE851EHRxOOeVXKbK2bivdb+iziMyk03Sr4eaE9OELCbyZAAafAKPDwF2TPUES5QbxQ==",
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.8.3.tgz",
+ "integrity": "sha512-WjoPk8hRpDRqqzRpvaR8/gDUPkrnOOeuT2m8cNICJtZH6mwaCo3v0OKMI7Y6SM1pBtyijnLtAL0HDi41pf41ug==",
"dev": true,
"requires": {
- "@babel/types": "^7.4.4",
+ "@babel/types": "^7.8.3",
"jsesc": "^2.5.1",
- "lodash": "^4.17.11",
- "source-map": "^0.5.0",
- "trim-right": "^1.0.1"
+ "lodash": "^4.17.13",
+ "source-map": "^0.5.0"
}
},
"@babel/helper-annotate-as-pure": {
- "version": "7.0.0",
- "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.0.0.tgz",
- "integrity": "sha512-3UYcJUj9kvSLbLbUIfQTqzcy5VX7GRZ/CCDrnOaZorFFM01aXp1+GJwuFGV4NDDoAS+mOUyHcO6UD/RfqOks3Q==",
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.8.3.tgz",
+ "integrity": "sha512-6o+mJrZBxOoEX77Ezv9zwW7WV8DdluouRKNY/IR5u/YTMuKHgugHOzYWlYvYLpLA9nPsQCAAASpCIbjI9Mv+Uw==",
"dev": true,
"requires": {
- "@babel/types": "^7.0.0"
+ "@babel/types": "^7.8.3"
}
},
"@babel/helper-builder-binary-assignment-operator-visitor": {
- "version": "7.1.0",
- "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.1.0.tgz",
- "integrity": "sha512-qNSR4jrmJ8M1VMM9tibvyRAHXQs2PmaksQF7c1CGJNipfe3D8p+wgNwgso/P2A2r2mdgBWAXljNWR0QRZAMW8w==",
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.8.3.tgz",
+ "integrity": "sha512-5eFOm2SyFPK4Rh3XMMRDjN7lBH0orh3ss0g3rTYZnBQ+r6YPj7lgDyCvPphynHvUrobJmeMignBr6Acw9mAPlw==",
"dev": true,
"requires": {
- "@babel/helper-explode-assignable-expression": "^7.1.0",
- "@babel/types": "^7.0.0"
+ "@babel/helper-explode-assignable-expression": "^7.8.3",
+ "@babel/types": "^7.8.3"
}
},
"@babel/helper-call-delegate": {
- "version": "7.4.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-call-delegate/-/helper-call-delegate-7.4.4.tgz",
- "integrity": "sha512-l79boDFJ8S1c5hvQvG+rc+wHw6IuH7YldmRKsYtpbawsxURu/paVy57FZMomGK22/JckepaikOkY0MoAmdyOlQ==",
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-call-delegate/-/helper-call-delegate-7.8.3.tgz",
+ "integrity": "sha512-6Q05px0Eb+N4/GTyKPPvnkig7Lylw+QzihMpws9iiZQv7ZImf84ZsZpQH7QoWN4n4tm81SnSzPgHw2qtO0Zf3A==",
+ "dev": true,
+ "requires": {
+ "@babel/helper-hoist-variables": "^7.8.3",
+ "@babel/traverse": "^7.8.3",
+ "@babel/types": "^7.8.3"
+ }
+ },
+ "@babel/helper-compilation-targets": {
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.8.3.tgz",
+ "integrity": "sha512-JLylPCsFjhLN+6uBSSh3iYdxKdeO9MNmoY96PE/99d8kyBFaXLORtAVhqN6iHa+wtPeqxKLghDOZry0+Aiw9Tw==",
+ "dev": true,
+ "requires": {
+ "@babel/compat-data": "^7.8.1",
+ "browserslist": "^4.8.2",
+ "invariant": "^2.2.4",
+ "levenary": "^1.1.0",
+ "semver": "^5.5.0"
+ }
+ },
+ "@babel/helper-create-regexp-features-plugin": {
+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.8.3.tgz",
+ "integrity": "sha512-Gcsm1OHCUr9o9TcJln57xhWHtdXbA2pgQ58S0Lxlks0WMGNXuki4+GLfX0p+L2ZkINUGZvfkz8rzoqJQSthI+Q==",
"dev": true,
"requires": {
- "@babel/helper-hoist-variables": "^7.4.4",
- "@babel/traverse": "^7.4.4",
- "@babel/types": "^7.4.4"
+ "@babel/helper-regex": "^7.8.3",
+ "regexpu-core": "^4.6.0"
}
},
"@babel/helper-define-map": {
- "version": "7.4.4",
- "resolved": "https://registry.npmjs.org/@babel/helper-define-map/-/helper-define-map-7.4.4.tgz",
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+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-define-map/-/helper-define-map-7.8.3.tgz",
+ "integrity": "sha512-PoeBYtxoZGtct3md6xZOCWPcKuMuk3IHhgxsRRNtnNShebf4C8YonTSblsK4tvDbm+eJAw2HAPOfCr+Q/YRG/g==",
"dev": true,
"requires": {
- "@babel/helper-function-name": "^7.1.0",
- "@babel/types": "^7.4.4",
- "lodash": "^4.17.11"
+ "@babel/helper-function-name": "^7.8.3",
+ "@babel/types": "^7.8.3",
+ "lodash": "^4.17.13"
}
},
"@babel/helper-explode-assignable-expression": {
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- "resolved": "https://registry.npmjs.org/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.1.0.tgz",
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+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.8.3.tgz",
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"dev": true,
"requires": {
- "@babel/traverse": "^7.1.0",
- "@babel/types": "^7.0.0"
+ "@babel/traverse": "^7.8.3",
+ "@babel/types": "^7.8.3"
}
},
"@babel/helper-function-name": {
- "version": "7.1.0",
- "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.1.0.tgz",
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+ "version": "7.8.3",
+ "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.8.3.tgz",
+ "integrity": "sha512-BCxgX1BC2hD/oBlIFUgOCQDOPV8nSINxCwM3o93xP4P9Fq6aV5sgv2cOOITDMtCfQ+3PvHp3l689XZvAM9QyOA==",
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"requires": {
- "@babel/helper-get-function-arity": "^7.0.0",
- "@babel/template": "^7.1.0",
- "@babel/types": "^7.0.0"
+ "@babel/helper-get-function-arity": "^7.8.3",
+ "@babel/template": "^7.8.3",
+ "@babel/types": "^7.8.3"
}
},
"@babel/helper-get-function-arity": {
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+ "resolved": "https://registry.npmjs.org/remove-bom-stream/-/remove-bom-stream-1.2.0.tgz",
+ "integrity": "sha1-BfGlk/FuQuH7kOv1nejlaVJflSM=",
+ "dev": true,
+ "requires": {
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+ "safe-buffer": "^5.1.0",
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+ "resolved": "https://registry.npmjs.org/replace-ext/-/replace-ext-1.0.0.tgz",
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+ "resolved": "https://registry.npmjs.org/replace-homedir/-/replace-homedir-1.0.0.tgz",
+ "integrity": "sha1-6H9tUTuSjd6AgmDBK+f+xv9ueYw=",
+ "dev": true,
+ "requires": {
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+ "is-absolute": "^1.0.0",
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@@ -7089,6 +8625,15 @@
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+ "resolved": "https://registry.npmjs.org/resolve-options/-/resolve-options-1.1.0.tgz",
+ "integrity": "sha1-MrueOcBtZzONyTeMDW1gdFZq0TE=",
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"dev": true
},
+ "reusify": {
+ "version": "1.0.4",
+ "resolved": "https://registry.npmjs.org/reusify/-/reusify-1.0.4.tgz",
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+ },
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"resolved": "https://registry.npmjs.org/rimraf/-/rimraf-2.6.3.tgz",
@@ -7166,6 +8717,12 @@
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+ "resolved": "https://registry.npmjs.org/run-parallel/-/run-parallel-1.1.9.tgz",
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+ "dev": true
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"dev": true
},
+ "semver-greatest-satisfied-range": {
+ "version": "1.1.0",
+ "resolved": "https://registry.npmjs.org/semver-greatest-satisfied-range/-/semver-greatest-satisfied-range-1.1.0.tgz",
+ "integrity": "sha1-E+jCZYq5aRywzXEJMkAoDTb3els=",
+ "dev": true,
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@@ -7473,6 +9039,12 @@
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+ "resolved": "https://registry.npmjs.org/slash/-/slash-3.0.0.tgz",
+ "integrity": "sha512-g9Q1haeby36OSStwb4ntCGGGaKsaVSjQ68fBxoQcutl5fS1vuY18H3wSt3jFyFtrkx+Kz0V1G85A4MyAdDMi2Q==",
+ "dev": true
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"resolved": "https://registry.npmjs.org/slice-ansi/-/slice-ansi-1.0.0.tgz",
@@ -7828,6 +9400,12 @@
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},
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+ "version": "1.0.1",
+ "resolved": "https://registry.npmjs.org/sparkles/-/sparkles-1.0.1.tgz",
+ "integrity": "sha512-dSO0DDYUahUt/0/pD/Is3VIm5TGJjludZ0HVymmhYF6eNA53PVLhnUk0znSYbH8IYBuJdCE+1luR22jNLMaQdw==",
+ "dev": true
+ },
"spdx-correct": {
"version": "3.1.0",
"resolved": "https://registry.npmjs.org/spdx-correct/-/spdx-correct-3.1.0.tgz",
@@ -7893,6 +9471,12 @@
"figgy-pudding": "^3.5.1"
}
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+ "resolved": "https://registry.npmjs.org/stack-trace/-/stack-trace-0.0.10.tgz",
+ "integrity": "sha1-VHxws0fo0ytOEI6hoqFZ5f3eGcA=",
+ "dev": true
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@@ -7949,6 +9533,12 @@
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}
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+ "resolved": "https://registry.npmjs.org/stream-exhaust/-/stream-exhaust-1.0.2.tgz",
+ "integrity": "sha512-b/qaq/GlBK5xaq1yrK9/zFcyRSTNxmcZwFLGSTG0mXgZl/4Z6GgiyYOXOvY7N3eEvFRAG1bkDRz5EPGSvPYQlw==",
+ "dev": true
+ },
"stream-http": {
"version": "2.8.3",
"resolved": "https://registry.npmjs.org/stream-http/-/stream-http-2.8.3.tgz",
@@ -8058,6 +9648,16 @@
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}
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+ "version": "1.5.0",
+ "resolved": "https://registry.npmjs.org/sver-compat/-/sver-compat-1.5.0.tgz",
+ "integrity": "sha1-PPh9/rTQe0o/FIJ7wYaz/QxkXNg=",
+ "dev": true,
+ "requires": {
+ "es6-iterator": "^2.0.1",
+ "es6-symbol": "^3.1.1"
+ }
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"symbol-observable": {
"version": "1.0.1",
"resolved": "https://registry.npmjs.org/symbol-observable/-/symbol-observable-1.0.1.tgz",
@@ -8250,6 +9850,22 @@
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}
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+ "through2-filter": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/through2-filter/-/through2-filter-3.0.0.tgz",
+ "integrity": "sha512-jaRjI2WxN3W1V8/FMZ9HKIBXixtiqs3SQSX4/YGIiP3gL6djW48VoZq9tDqeCWs3MT8YY5wb/zli8VW8snY1CA==",
+ "dev": true,
+ "requires": {
+ "through2": "~2.0.0",
+ "xtend": "~4.0.0"
+ }
+ },
+ "time-stamp": {
+ "version": "1.1.0",
+ "resolved": "https://registry.npmjs.org/time-stamp/-/time-stamp-1.1.0.tgz",
+ "integrity": "sha1-dkpaEa9QVhkhsTPztE5hhofg9cM=",
+ "dev": true
+ },
"timers-browserify": {
"version": "2.0.11",
"resolved": "https://registry.npmjs.org/timers-browserify/-/timers-browserify-2.0.11.tgz",
@@ -8268,6 +9884,16 @@
"os-tmpdir": "~1.0.2"
}
},
+ "to-absolute-glob": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/to-absolute-glob/-/to-absolute-glob-2.0.2.tgz",
+ "integrity": "sha1-GGX0PZ50sIItufFFt4z/fQ98hJs=",
+ "dev": true,
+ "requires": {
+ "is-absolute": "^1.0.0",
+ "is-negated-glob": "^1.0.0"
+ }
+ },
"to-array": {
"version": "0.1.4",
"resolved": "https://registry.npmjs.org/to-array/-/to-array-0.1.4.tgz",
@@ -8328,16 +9954,25 @@
"repeat-string": "^1.6.1"
}
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+ "to-through": {
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/to-through/-/to-through-2.0.0.tgz",
+ "integrity": "sha1-/JKtq6ByZHvAtn1rA2ZKoZUJOvY=",
+ "dev": true,
+ "requires": {
+ "through2": "^2.0.3"
+ }
+ },
"toidentifier": {
"version": "1.0.0",
"resolved": "https://registry.npmjs.org/toidentifier/-/toidentifier-1.0.0.tgz",
"integrity": "sha512-yaOH/Pk/VEhBWWTlhI+qXxDFXlejDGcQipMlyxda9nthulaxLZUNcUqFxokp0vcYnvteJln5FNQDRrxj3YcbVw==",
"dev": true
},
- "trim-right": {
- "version": "1.0.1",
- "resolved": "https://registry.npmjs.org/trim-right/-/trim-right-1.0.1.tgz",
- "integrity": "sha1-yy4SAwZ+DI3h9hQJS5/kVwTqYAM=",
+ "tree-kill": {
+ "version": "1.2.2",
+ "resolved": "https://registry.npmjs.org/tree-kill/-/tree-kill-1.2.2.tgz",
+ "integrity": "sha512-L0Orpi8qGpRG//Nd+H90vFB+3iHnue1zSSGmNOOCh1GLJ7rUKVwV2HvijphGQS2UmhUZewS9VgvxYIdgr+fG1A==",
"dev": true
},
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@@ -8368,6 +10003,12 @@
"integrity": "sha1-oVe6QC2iTpv5V/mqadUk7tQpAaY=",
"dev": true
},
+ "type": {
+ "version": "1.2.0",
+ "resolved": "https://registry.npmjs.org/type/-/type-1.2.0.tgz",
+ "integrity": "sha512-+5nt5AAniqsCnu2cEQQdpzCAh33kVx8n0VoFidKpB1dVVLAN/F+bgVOqOJqOnEnrhp222clB5p3vUlD+1QAnfg==",
+ "dev": true
+ },
"type-check": {
"version": "0.3.2",
"resolved": "https://registry.npmjs.org/type-check/-/type-check-0.3.2.tgz",
@@ -8384,9 +10025,9 @@
"dev": true
},
"typescript": {
- "version": "3.5.1",
- "resolved": "https://registry.npmjs.org/typescript/-/typescript-3.5.1.tgz",
- "integrity": "sha512-64HkdiRv1yYZsSe4xC1WVgamNigVYjlssIoaH2HcZF0+ijsk5YK2g0G34w9wJkze8+5ow4STd22AynfO6ZYYLw=="
+ "version": "3.7.4",
+ "resolved": "https://registry.npmjs.org/typescript/-/typescript-3.7.4.tgz",
+ "integrity": "sha512-A25xv5XCtarLwXpcDNZzCGvW2D1S3/bACratYBx2sax8PefsFhlYmkQicKHvpYflFS8if4zne5zT5kpJ7pzuvw=="
},
"ua-parser-js": {
"version": "0.7.17",
@@ -8400,6 +10041,35 @@
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"dev": true
},
+ "unc-path-regex": {
+ "version": "0.1.2",
+ "resolved": "https://registry.npmjs.org/unc-path-regex/-/unc-path-regex-0.1.2.tgz",
+ "integrity": "sha1-5z3T17DXxe2G+6xrCufYxqadUPo=",
+ "dev": true
+ },
+ "undertaker": {
+ "version": "1.2.1",
+ "resolved": "https://registry.npmjs.org/undertaker/-/undertaker-1.2.1.tgz",
+ "integrity": "sha512-71WxIzDkgYk9ZS+spIB8iZXchFhAdEo2YU8xYqBYJ39DIUIqziK78ftm26eecoIY49X0J2MLhG4hr18Yp6/CMA==",
+ "dev": true,
+ "requires": {
+ "arr-flatten": "^1.0.1",
+ "arr-map": "^2.0.0",
+ "bach": "^1.0.0",
+ "collection-map": "^1.0.0",
+ "es6-weak-map": "^2.0.1",
+ "last-run": "^1.1.0",
+ "object.defaults": "^1.0.0",
+ "object.reduce": "^1.0.0",
+ "undertaker-registry": "^1.0.0"
+ }
+ },
+ "undertaker-registry": {
+ "version": "1.0.1",
+ "resolved": "https://registry.npmjs.org/undertaker-registry/-/undertaker-registry-1.0.1.tgz",
+ "integrity": "sha1-XkvaMI5KiirlhPm5pDWaSZglzFA=",
+ "dev": true
+ },
"unicode-canonical-property-names-ecmascript": {
"version": "1.0.4",
"resolved": "https://registry.npmjs.org/unicode-canonical-property-names-ecmascript/-/unicode-canonical-property-names-ecmascript-1.0.4.tgz",
@@ -8464,6 +10134,16 @@
"imurmurhash": "^0.1.4"
}
},
+ "unique-stream": {
+ "version": "2.3.1",
+ "resolved": "https://registry.npmjs.org/unique-stream/-/unique-stream-2.3.1.tgz",
+ "integrity": "sha512-2nY4TnBE70yoxHkDli7DMazpWiP7xMdCYqU2nBRO0UB+ZpEkGsSija7MvmvnZFUeC+mrgiUfcHSr3LmRFIg4+A==",
+ "dev": true,
+ "requires": {
+ "json-stable-stringify-without-jsonify": "^1.0.1",
+ "through2-filter": "^3.0.0"
+ }
+ },
"universalify": {
"version": "0.1.2",
"resolved": "https://registry.npmjs.org/universalify/-/universalify-0.1.2.tgz",
@@ -8625,6 +10305,15 @@
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"dev": true
},
+ "v8flags": {
+ "version": "3.1.3",
+ "resolved": "https://registry.npmjs.org/v8flags/-/v8flags-3.1.3.tgz",
+ "integrity": "sha512-amh9CCg3ZxkzQ48Mhcb8iX7xpAfYJgePHxWMQCBWECpOSqJUXgY26ncA61UTV0BkPqfhcy6mzwCIoP4ygxpW8w==",
+ "dev": true,
+ "requires": {
+ "homedir-polyfill": "^1.0.1"
+ }
+ },
"validate-npm-package-license": {
"version": "3.0.4",
"resolved": "https://registry.npmjs.org/validate-npm-package-license/-/validate-npm-package-license-3.0.4.tgz",
@@ -8635,12 +10324,83 @@
"spdx-expression-parse": "^3.0.0"
}
},
+ "value-or-function": {
+ "version": "3.0.0",
+ "resolved": "https://registry.npmjs.org/value-or-function/-/value-or-function-3.0.0.tgz",
+ "integrity": "sha1-HCQ6ULWVwb5Up1S/7OhWO5/42BM=",
+ "dev": true
+ },
"vary": {
"version": "1.1.2",
"resolved": "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz",
"integrity": "sha1-IpnwLG3tMNSllhsLn3RSShj2NPw=",
"dev": true
},
+ "vinyl": {
+ "version": "2.2.0",
+ "resolved": "https://registry.npmjs.org/vinyl/-/vinyl-2.2.0.tgz",
+ "integrity": "sha512-MBH+yP0kC/GQ5GwBqrTPTzEfiiLjta7hTtvQtbxBgTeSXsmKQRQecjibMbxIXzVT3Y9KJK+drOz1/k+vsu8Nkg==",
+ "dev": true,
+ "requires": {
+ "clone": "^2.1.1",
+ "clone-buffer": "^1.0.0",
+ "clone-stats": "^1.0.0",
+ "cloneable-readable": "^1.0.0",
+ "remove-trailing-separator": "^1.0.1",
+ "replace-ext": "^1.0.0"
+ }
+ },
+ "vinyl-fs": {
+ "version": "3.0.3",
+ "resolved": "https://registry.npmjs.org/vinyl-fs/-/vinyl-fs-3.0.3.tgz",
+ "integrity": "sha512-vIu34EkyNyJxmP0jscNzWBSygh7VWhqun6RmqVfXePrOwi9lhvRs//dOaGOTRUQr4tx7/zd26Tk5WeSVZitgng==",
+ "dev": true,
+ "requires": {
+ "fs-mkdirp-stream": "^1.0.0",
+ "glob-stream": "^6.1.0",
+ "graceful-fs": "^4.0.0",
+ "is-valid-glob": "^1.0.0",
+ "lazystream": "^1.0.0",
+ "lead": "^1.0.0",
+ "object.assign": "^4.0.4",
+ "pumpify": "^1.3.5",
+ "readable-stream": "^2.3.3",
+ "remove-bom-buffer": "^3.0.0",
+ "remove-bom-stream": "^1.2.0",
+ "resolve-options": "^1.1.0",
+ "through2": "^2.0.0",
+ "to-through": "^2.0.0",
+ "value-or-function": "^3.0.0",
+ "vinyl": "^2.0.0",
+ "vinyl-sourcemap": "^1.1.0"
+ }
+ },
+ "vinyl-sourcemap": {
+ "version": "1.1.0",
+ "resolved": "https://registry.npmjs.org/vinyl-sourcemap/-/vinyl-sourcemap-1.1.0.tgz",
+ "integrity": "sha1-kqgAWTo4cDqM2xHYswCtS+Y7PhY=",
+ "dev": true,
+ "requires": {
+ "append-buffer": "^1.0.2",
+ "convert-source-map": "^1.5.0",
+ "graceful-fs": "^4.1.6",
+ "normalize-path": "^2.1.1",
+ "now-and-later": "^2.0.0",
+ "remove-bom-buffer": "^3.0.0",
+ "vinyl": "^2.0.0"
+ },
+ "dependencies": {
+ "normalize-path": {
+ "version": "2.1.1",
+ "resolved": "https://registry.npmjs.org/normalize-path/-/normalize-path-2.1.1.tgz",
+ "integrity": "sha1-GrKLVW4Zg2Oowab35vogE3/mrtk=",
+ "dev": true,
+ "requires": {
+ "remove-trailing-separator": "^1.0.1"
+ }
+ }
+ }
+ },
"vm-browserify": {
"version": "1.1.2",
"resolved": "https://registry.npmjs.org/vm-browserify/-/vm-browserify-1.1.2.tgz",
diff --git a/package.json b/package.json
index eedd3718e484fd6c29fc63349285f40c2c78b6ac..fb953c66bfe3608eda769636b4d0178b825f573c 100644
--- a/package.json
+++ b/package.json
@@ -1,32 +1,38 @@
{
- "name": "interactions",
- "version": "1.0.0",
+ "name": "pdb-ligand-env",
+ "version": "0.2.0",
"description": "",
"main": "app.js",
"dependencies": {
"@types/d3": "^5.0.1",
"@types/d3-tip": "^3.5.5",
- "d3": "^5.7.0",
+ "d3": "^5.15.0",
"d3-tip": "^0.9.1",
"d3scription": "^1.0.1",
- "lit-element": "^2.1.0",
- "typescript": "^3.1.6"
+ "lit-element": "^2.2.1",
+ "typescript": "^3.7.4"
},
"devDependencies": {
- "@babel/core": "^7.3.3",
- "@babel/plugin-transform-runtime": "^7.2.0",
- "@babel/preset-env": "^7.3.1",
- "@babel/runtime": "^7.3.1",
- "@webcomponents/webcomponentsjs": "^2.1.3",
+ "@babel/core": "^7.8.3",
+ "@babel/plugin-transform-runtime": "^7.8.3",
+ "@babel/preset-env": "^7.8.3",
+ "@babel/runtime": "^7.8.3",
+ "@webcomponents/webcomponentsjs": "^2.4.1",
"babel-loader": "^8.0.5",
"browser-sync": "^2.26.7",
"camelcase": "^5.0.0",
"clean-webpack-plugin": "^1.0.1",
"css-loader": "^2.1.0",
+ "del": "^5.1.0",
"eslint": "^4.12.0",
"file-loader": "^3.0.1",
+ "gulp": "^4.0.2",
+ "gulp-concat": "^2.6.1",
+ "gulp-header": "^2.0.9",
+ "gulp-minify": "^3.1.0",
"live-server": "^1.2.1",
"npm-run-all": "^4.1.3",
+ "onchange": "^6.1.0",
"style-loader": "^0.23.1",
"ts-node": "^7.0.1",
"url-loader": "^1.1.2",
@@ -34,12 +40,12 @@
"webpack-cli": "^3.3.10"
},
"scripts": {
- "tsc:w": "tsc -w",
- "prestart": "tsc",
- "serve": "live-server build --watch=src/**/*.html,src/bundle.js,src/**/*.css",
- "start": "npm-run-all --parallel serve tsc:w",
- "webpack": "webpack",
- "buildComponent": "webpack --mode=development"
+ "tscW": "tsc -w",
+ "serve": "live-server build --watch=build",
+ "start": "npm-run-all --parallel watch serve",
+ "build": "tsc && webpack --mode=development && gulp",
+ "watch": "onchange 'src/**/*' -- npm run build",
+ "buildProduction": "tsc && webpack --mode=production && gulp"
},
"author": "Lukas Pravda",
"license": "Apache License 2.0"
diff --git a/src/component.js b/src/component.js
deleted file mode 100644
index fa5b743dbd4d3e08b0805e834260f50ea8ac0bb9..0000000000000000000000000000000000000000
--- a/src/component.js
+++ /dev/null
@@ -1,64 +0,0 @@
-// Import the LitElement base class and html helper function
-import { LitElement, html } from 'lit-element';
-
-// Extend the LitElement base class
-class pdbInteractions extends LitElement {
-
- //Get properties / attribute values
- static get properties() {
- return {
- 'pdb-id': { type: String },
- 'bound-molecule-id': { type: String },
- 'pdb-res-id': { type: Number },
- 'pdb-chain-id': { type: String }
- };
- }
-
- constructor() {
- super();
- }
-
- render() {
- return html`
-
- ${!this['pdb-id'] ?
- html`<div style='text-align:center;font-weight:bold;margin-top:20px;'>Error: Specify valid 'pdb-id' attribute to render the component.<div>` :
- html``
- }
- `;
- }
-
- updated(changedProperties) {
- if (this['pdb-id']) {
- this.display = new Visualization(this);
-
- if (this['bound-molecule-id']) {
- this.display.initialiseBoundMolecule(this['pdb-id'], this['bound-molecule-id']);
- }
- else {
- this.display.initialiseLigand(this['pdb-id'], this['pdb-res-id'], this['pdb-chain-id'])
- }
- }
- }
-
- connectedCallback() {
- super.connectedCallback();
-
- this.style.display = 'block';
- this.style.height = '100%';
- this.style.width = '100%';
- this.style.position = 'relative';
-
- }
-
- createRenderRoot() {
- /**
- * Render template in light DOM. Note that shadow DOM features like
- * encapsulated CSS are unavailable.
- */
- return this;
- }
-
-}
-// Register the new element with the browser.
-customElements.define('pdb-interactions', pdbInteractions);
\ No newline at end of file
diff --git a/src/component/component.js b/src/component/component.js
new file mode 100644
index 0000000000000000000000000000000000000000..5787f89e1262bb3e19290753b4feaa158dc241f2
--- /dev/null
+++ b/src/component/component.js
@@ -0,0 +1,93 @@
+// Import the LitElement base class and html helper function
+import { LitElement, html } from 'lit-element';
+import "../styles/pdb-ligand-env.css";
+
+// Extend the LitElement base class
+class pdbLigandEnv extends LitElement {
+
+ //Get properties / attribute values
+ static get properties() {
+ return {
+ pdbId: { type: String, attribute: 'pdb-id' },
+ bmId: { type: String, attribute: 'bound-molecule-id' },
+ resName: { type: String, attribute: 'pdb-res-name' },
+ resId: { type: Number, attribute: 'pdb-res-id' },
+ chainId: { type: String, attribute: 'pdb-chain-id' },
+ substructureHighlight: { type: Array, attribute: 'substructure' },
+ substructureColor: { type: String, attribute: 'color' },
+ zoomOn: { type: Boolean, attribute: 'zoom-on' },
+ };
+ }
+
+ constructor() {
+ super();
+ }
+
+ async connectedCallback() {
+ let uiParams = new Config.UIParameters();
+ uiParams.zoom = this.zoomOn;
+
+ this.display = new Visualization(this, uiParams);
+
+ if (this.pdbId) {
+ if (this.bmId) {
+ this.display.initBoundMoleculeInteractions(this.pdbId, this.bmId);
+ }
+ else {
+ this.display.initLigandInteractions(this.pdbId, this.resId, this.chainId);
+ }
+ }
+ else if (this.resName) {
+ this.display.initLigandDisplay(this.resName).then(() => this.display.centerScene());
+ }
+ }
+
+
+ //#region properties
+ set depiction(data) {
+ if (!data) return;
+
+ this.display.addDepiction(data, false);
+ this.display.centerScene();
+ }
+
+ set ligandHighlight(data) {
+ if (!data || !this.display) {
+ console.log(`Argument needs to be a non empty array of strings.`);
+ return;
+ }
+
+ this.display.addLigandHighlight(data, this.highlightColor);
+ this.substructureHighlight = data;
+ }
+
+ set highlightColor(data) {
+ if (!data || !this.display) return;
+
+ this.highlightColor = data;
+ 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.toogleZoom(data);
+ }
+ //#endregion properties
+
+
+ createRenderRoot() {
+ /**
+ * Render template in light DOM. Note that shadow DOM features like
+ * encapsulated CSS are unavailable.
+ */
+ return this;
+ }
+
+}
+// Register the new element with the browser.
+customElements.define('pdb-ligand-env', pdbLigandEnv);
\ No newline at end of file
diff --git a/src/manager.ts b/src/manager.ts
deleted file mode 100644
index 1e4637cfb9e325811fca9fed68ba22d06ca1c937..0000000000000000000000000000000000000000
--- a/src/manager.ts
+++ /dev/null
@@ -1,644 +0,0 @@
-/// <reference path="./visualsMapping.ts" />
-/// <reference path="./depiction.ts" />
-
-const server: string = "https://wwwdev.ebi.ac.uk/pdbe/graph-api";
-
-const clickEvent = 'PDB.interactions.click';
-const mouseoverEvent = 'PDB.interactions.mouseover';
-const mouseoutEvent = 'PDB.interactions.mouseout'
-
-class Visualization {
- // component related
- private parent: HTMLElement;
-
- // #region svg properties
- private canvas: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
- private simulation: d3.Simulation<d3.SimulationNodeDatum, undefined>;
- private svg: d3.Selection<any, {}, HTMLElement, any>;
- private visualization: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
-
- private nodes: any;
- private links: any
- // #endregion
-
- // #region ui properties
- private residueLabel: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
- private tooltip: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
- // #endregion
-
- // #region data properties
- private pdbId: string;
- private bindingSite: Model.BindingSite;
- private depiction: Depiction;
-
- private visualsMapper: VisualsMapper;
- private interactionsData: any;
- private selectedResidueHash: string;
- // #endregion
-
- constructor(element: HTMLElement) {
- this.parent = element;
- this.visualsMapper = new VisualsMapper();
-
- new UI(this.parent, this).register(new Model.UIParameters());
-
- this.tooltip = d3.select("#int-tooltip");
- this.residueLabel = d3.select('#int-residue-label');
-
- this.canvas = d3.select(this.parent)
- .append('div')
- .attr('id', 'int-canvas');
-
- this.svg = this.canvas
- .append('svg')
- .attr('xmlns', 'http://www.w3.org/2000/svg')
- .attr('width', () => this.parent.offsetWidth)
- .attr('height', () => this.parent.offsetHeight)
-
- document.addEventListener('PDB.molstar.click', e => this.nodeMouseEnterEventHandler(e));
- document.addEventListener('PDB.molstar.mouseover', e => this.nodeMouseEnterEventHandler(e));
- document.addEventListener('PDB.molstar.mouseout', () => this.nodeMouseLeaveEventHandler());
-
- d3.select(window).on('resize', () => this.resize(this));
- }
-
- // #region even handlers
- private nodeMouseEnterEventHandler(e: any) {
- let hash = `${e.eventData.auth_asym_id}${e.eventData.auth_seq_id}${e.eventData.ins_code}`;
-
- if (this.nodes !== undefined) {
- this.nodes.each((node: Model.InteractionNode, index: number, group: any) => {
- if (node.id === hash) {
- this.selectedResidueHash = hash;
- this.nodeHighlight(node, index, group);
- return;
- }
- });
- }
- }
-
- private nodeMouseLeaveEventHandler() {
- if (this.nodes !== undefined) {
- this.nodes.each((node: Model.InteractionNode, index: number, group: any) => {
- if (node.id == this.selectedResidueHash) {
- this.nodeDim(node, index, group);
- return;
- }
- });
- }
- }
-
- private linkMouseClickEventHandler(x: Model.Link) {
- this.fireLinkEvent(x, clickEvent);
- }
-
- private linkMouseOverEventHandler(x: Model.Link) {
- this.tooltip.transition()
- .duration(200)
- .style('opacity', .9);
-
- this.tooltip.html(x.toTooltip());
- this.fireLinkEvent(x, mouseoverEvent);
- }
-
- private linkMouseOutEventHandler() {
- this.tooltip.transition()
- .duration(200)
- .style('opacity', 0);
-
- this.fireLinkLeaveEvent();
- }
-
- private zoom_handler = d3.zoom()
- .scaleExtent([1 / 10, 10])
- .on('zoom', () => d3.select('#vis-root').attr('transform', d3.event.transform));
-
- private drag_handler = d3.drag()
- .on('start', (x: Model.InteractionNode) => {
- if (!d3.event.active) this.simulation.alphaTarget(0.3).restart();
-
- x.fx = x.x;
- x.fy = x.y;
- })
- .on('drag', (x: Model.InteractionNode) => {
- x.fx = d3.event.x;
- x.fy = d3.event.y;
- })
- .on('end', (x: Model.InteractionNode) => {
- if (!d3.event.active) this.simulation.alphaTarget(0);
- x.fx = d3.event.x;
- x.fy = d3.event.y;
- });
-
- // #endregion event handlers
-
- public async initialiseBoundMolecule(pdbid: string, bmId: string) {
- this.pdbId = pdbid;
- this.addMarkers();
-
- d3.json(`${server}/pdb/bound_molecule_interactions/${this.pdbId}/${bmId}`)
- .catch(e => { throw e; })
- .then((data: any) => {
- let key = Object.keys(data)[0];
- this.interactionsData = data;
-
- this.bindingSite = new Model.BindingSite().fromBoundMolecule(key, data[key][0]);
- this.bindingSite.bmId = bmId;
- let ligands = this.bindingSite.residues.filter(x => x.isLigand);
-
- if (ligands.length === 1) this.initialiseLigand(this.pdbId, ligands[0].authorResidueNumber, ligands[0].chainId);
- else this.setupScene();
- });
- }
-
- public async initialiseLigand(pdbId: string, resId: number, chainId: string) {
- this.pdbId = pdbId;
-
- d3.json(`${server}/pdb/bound_ligand_interactions/${pdbId}/${chainId}/${resId}`)
- .catch(e => { throw e; })
- .then((data: any) => {
- let key = Object.keys(data)[0];
- let body = data[key][0];
- this.interactionsData = data;
-
- d3.json(`https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/${body.ligand.chem_comp_id}/annotation`)
- .catch(e => { throw e; })
- .then((d: any) => {
- this.depiction = new Depiction(d);
- this.bindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
- this.setupLigandScene();
- });
- });
- }
-
- // #region menu functions
- public saveSvg(ctx: Visualization) {
- d3.text('pdbe-interactions-svgstyles.css').then(x => {
- let svgToDl = d3.select('#int-canvas');
- svgToDl.select('svg')
- .append('style')
- .text(`/* <![CDATA[ */ \n ${x} \n /* ]]> */`);
-
- let svgData = svgToDl.html();
- let svgBlob = new Blob([svgData], { type: 'image/svg;charset=utf-8' });
- let svgUrl = URL.createObjectURL(svgBlob);
- let downloadLink = document.createElement('a');
-
- downloadLink.href = svgUrl;
- downloadLink.download = `${ctx.pdbId}_${ctx.bindingSite.bmId}.svg`;
-
- document.body.appendChild(downloadLink);
- downloadLink.click();
- document.body.removeChild(downloadLink);
- });
- }
-
-
- public downloadInteractionsData(ctx: Visualization): void {
- let downloadLink = document.createElement('a');
-
- let dataBlob = new Blob([JSON.stringify(ctx.interactionsData, null, 4)], { type: 'application/json' });
-
- downloadLink.href = URL.createObjectURL(dataBlob);
- downloadLink.download = `${ctx.pdbId}_${ctx.bindingSite.bmId}_interactions.json`;
- document.body.appendChild(downloadLink);
- downloadLink.click();
- document.body.removeChild(downloadLink);
- }
-
-
- public reinitialize(ctx: Visualization) {
- ctx.visualization.remove();
-
- if (ctx.depiction === undefined) ctx.setupScene();
- else ctx.setupLigandScene();
-
- ctx.residueLabel.transition()
- .duration(200)
- .style('opacity', 0);
- }
-
- private resize(ctx: Visualization) {
- ctx.svg
- .attr('width', ctx.parent.offsetWidth)
- .attr('height', ctx.parent.offsetHeight);
-
- if (ctx.depiction === undefined) {
- ctx.simulation
- .force('center', d3.forceCenter(this.parent.offsetWidth / 2, this.parent.offsetHeight / 2))
- .restart();
- } else ctx.simulation.restart();
-
- ctx.zoom_handler(ctx.svg);
- }
-
-
- public centerScene(ctx: Visualization) {
- if (ctx.nodes.length === 0)
- return;
-
- // Get the bounding box
- let minX: any = d3.min(ctx.nodes.data().map((x) => x.x));
- let minY: any = d3.min(ctx.nodes.data().map((x) => x.y));
-
- let maxX: any = d3.max(ctx.nodes.data().map((x) => x.x));
- let maxY: any = d3.max(ctx.nodes.data().map((x) => x.y));
-
- // The width and the height of the graph
- let molWidth = maxX - minX;
- let molHeight = maxY - minY;
-
- // how much larger the drawing area is than the width and the height
- let widthRatio = ctx.parent.offsetWidth / molWidth;
- let heightRatio = ctx.parent.offsetHeight / molHeight;
-
- // we need to fit it in both directions, so we scale according to
- // the direction in which we need to shrink the most
- let minRatio = Math.min(widthRatio, heightRatio) * 0.8;
-
- // the new dimensions of the molecule
- let newMolWidth = molWidth * minRatio;
- let newMolHeight = molHeight * minRatio;
-
- // translate so that it's in the center of the window
- let xTrans = -(minX) * minRatio + (ctx.parent.offsetWidth - newMolWidth) / 2;
- let yTrans = -(minY) * minRatio + (ctx.parent.offsetHeight - newMolHeight) / 2;
-
- // do the actual moving
- ctx.visualization.attr('transform', `translate(${xTrans}, ${yTrans}) scale(${minRatio})`);
-
- // tell the zoomer what we did so that next we zoom, it uses the
- // transformation we entered here
- ctx.zoom_handler.transform(ctx.svg, d3.zoomIdentity);
-
-
-
- };
- // #endregion menu functions
-
- // #region mouse events
- //https://stackoverflow.com/questions/40722344/understanding-d3-with-an-example-mouseover-mouseup-with-multiple-arguments
- private fireNodeMouseEnterEvent(x: Model.InteractionNode, i: number, g: any) {
- this.nodeHighlight(x, i, g);
- this.fireNodeEvent(x, mouseoverEvent);
- }
-
- private fireNodeMouseLeaveEvent(x: Model.InteractionNode, i: number, g: any) {
- this.nodeDim(x, i, g);
-
- const e = new CustomEvent(mouseoutEvent, {
- bubbles: true,
- detail: {}
- });
- this.parent.dispatchEvent(e);
- }
-
- private fireLinkEvent(link: Model.Link, eventName: string) {
- let atomsSource = [];
- let atomsTarget = [];
-
- if (link instanceof Model.LigandResidueLink) {
- let tmpSrc = [].concat.apply([], link.interaction.map(x => x.sourceAtoms));
- atomsSource = [].concat.apply([], tmpSrc).filter((v, i, a) => a.indexOf(v) === i);
-
- let tmpTar = [].concat.apply([], link.interaction.map(x => x.targetAtoms));
- atomsTarget = [].concat.apply([], tmpTar).filter((v, i, a) => a.indexOf(v) === i);
- }
-
- const e = new CustomEvent(eventName, {
- bubbles: true,
- detail: {
- interacting_nodes: [
- {
- pdb_res_id: this.pdbId,
- auth_asym_id: link.source.residue.chainId,
- auth_seq_id: link.source.residue.authorResidueNumber,
- auth_ins_code_id: link.source.residue.authorInsertionCode,
- atoms: atomsSource
- },
- {
- pdb_res_id: this.pdbId,
- auth_asym_id: link.target.residue.chainId,
- auth_seq_id: link.target.residue.authorResidueNumber,
- auth_ins_code_id: link.target.residue.authorInsertionCode,
- atoms: atomsTarget
- }
- ]
- }
- });
-
- this.parent.dispatchEvent(e);
- }
-
- private fireNodeEvent(node: Model.InteractionNode, eventName: string) {
- const e = new CustomEvent(eventName, {
- bubbles: true,
- detail: {
- selected_node: {
- pdb_res_id: this.pdbId,
- auth_asym_id: node.residue.chainId,
- auth_seq_id: node.residue.authorResidueNumber,
- auth_ins_code_id: node.residue.authorInsertionCode
- }
- }
- });
-
- this.parent.dispatchEvent(e);
- }
-
- private fireLinkLeaveEvent() {
- const e = new CustomEvent(mouseoutEvent, {
- bubbles: true,
- detail: {}
- });
-
- this.parent.dispatchEvent(e);
- }
-
- // #endregion mouse events
-
- // #region Labels
- private showLabel(x: Model.InteractionNode) {
- this.residueLabel.transition()
- .duration(200)
- .style('opacity', .9);
-
- this.residueLabel.html(x.toTooltip());
- }
- //#endregion labels
-
- private selectLigand(n: Model.InteractionNode, i: number, g: any) {
- this.fireNodeEvent(n, clickEvent);
-
- if (!n.residue.isLigand) return;
-
- this.visualization.remove();
- this.fireNodeMouseLeaveEvent(n, i, g);
- this.showLabel(n);
-
- this.initialiseLigand(this.pdbId, n.residue.authorResidueNumber, n.residue.chainId);
- }
-
- private async setupLigandScene() {
- this.addMarkers();
-
- let xShift = (this.parent.offsetWidth / 2) - (this.depiction.resolution.x / 2);
- let yShift = (this.parent.offsetHeight / 2) - (this.depiction.resolution.y / 2);
-
- this.visualization = this.svg.append('g')
- .attr('id', 'vis-root')
- .append('g')
- .attr('transform', `translate(${xShift}, ${yShift}) scale(1)`);
-
- this.links = this.visualization.append('g')
- .attr('id', 'links')
- .selectAll()
- .data(this.bindingSite.links)
- .enter().append('g');
-
- this.links
- .append('line')
- .classed('svg-shadow-bond', (x: Model.Link) => x.getLinkClass() !== 'hydrophobic')
- .on('click', (x: Model.Link) => this.linkMouseClickEventHandler(x))
- .on('mouseenter', (x: Model.Link) => this.linkMouseOverEventHandler(x))
- .on('mouseleave', () => this.linkMouseOutEventHandler());
-
- this.links
- .append('line')
- .attr('class', (e: Model.LigandResidueLink) => `svg-bond svg-bond-${e.getLinkClass()}`)
- .attr('marker-mid', (e: Model.LigandResidueLink) => e.hasClash() ? 'url(#clash)' : '')
-
- let depictionRoot = this.visualization.append('g').attr('id', 'depiction');
- this.depiction.appendClarityNodes(depictionRoot)
- this.depiction.appendBondVisualsTo(depictionRoot);
- this.depiction.appendTextsTo(depictionRoot);
-
- this.bindingSite.interactionNodes
- .filter((x: Model.InteractionNode) => !x.residue.isLigand)
- .forEach((x: Model.InteractionNode) => {
- let lnks = this.bindingSite.links
- .filter((y: Model.LigandResidueLink) => y.containsInteractionNode(x))
- .map((y: Model.LigandResidueLink) => [].concat.apply([], y.interaction.map(z => z.sourceAtoms)));
-
- let concated = [].concat.apply([], lnks);
- let position: Vector2D = this.depiction.getInitalNodePosition(concated);
-
- x.x = position.x + Math.random() * 110;
- x.y = position.y + Math.random() * 110;
- });
-
-
- //setup nodes
- this.nodes = this.visualization.append('g')
- .attr('id', 'nodes')
- .selectAll()
- .data(this.bindingSite.interactionNodes)
- .enter().append('g');
-
- // draw glycans
- await this.visualsMapper.graphicsPromise;
- await this.visualsMapper.mappingPromise;
-
- this.nodes.filter((x: Model.InteractionNode) => !x.residue.isLigand)
- .attr('class', (x: Model.InteractionNode) => `svg-node svg-${x.residue.getResidueType()}-res`)
- .on('click', (x: Model.InteractionNode) => this.fireNodeEvent(x, clickEvent))
- .on('mouseenter', (x: Model.InteractionNode, i: number, g: any) => this.fireNodeMouseEnterEvent(x, i, g))
- .on('mouseleave', (x: Model.InteractionNode, i: number, g: any) => this.fireNodeMouseLeaveEvent(x, i, g));
-
- this.nodes.filter((x: Model.InteractionNode) => !x.residue.isLigand && this.visualsMapper.glycanMapping.has(x.residue.chemCompId))
- .html((e: Model.InteractionNode) => this.visualsMapper.getGlycanImage(e.residue.chemCompId));
-
- // draw rest
- this.nodes.filter((x: Model.InteractionNode) => !x.residue.isLigand && !this.visualsMapper.glycanMapping.has(x.residue.chemCompId))
- .append('circle')
- .attr('r', (x: Model.InteractionNode) => x.scale * 25);
-
- this.nodes
- .filter((x: Model.InteractionNode) => !x.residue.isLigand)
- .append('text')
- .style('text-anchor', 'middle')
- .style('dominant-baseline', 'central')
- .each(function (e: Model.InteractionNode) {
- let labels = [e.residue.chemCompId, `${e.residue.chainId} ${e.residue.authorResidueNumber}`];
- for (var i = 0; i < labels.length; i++) {
- d3.select(this)
- .append('tspan')
- .attr('dy', (i * 20) - 4)
- .attr('x', 0)
- .text(labels[i]);
- }
- });
-
- // let forceLink = d3.forceLink()
- // .links(visuals.links)
- // .distance(150)
- // .strength(0.5);
-
- //let charge = d3.forceManyBody().strength(-1000).distanceMin(50).distanceMax(150);
- let collision = d3.forceCollide().radius(50)
- //let center = d3.forceCenter(xShift, yShift);
-
- this.simulation = d3.forceSimulation(this.bindingSite.interactionNodes)
- // .force('link', forceLink)
- // .force('charge', charge) //strength
- .force('collision', collision)
- // .force('center', center)
- .on('tick', () => this.simulationStep(this));
-
- this.drag_handler(this.nodes);
- this.zoom_handler(this.svg);
- this.centerScene(this);
- }
-
- private async setupScene() {
- let context = this;
-
- this.visualization = this.svg.append('g').attr('id', 'vis-root');
- this.links = this.visualization.append('g')
- .attr('id', 'links')
- .selectAll()
- .data(context.bindingSite.links)
- .enter().append('g')
-
- this.links
- .append('line')
- .classed('svg-shadow-bond', (x: Model.Link) => x.getLinkClass() !== 'hydrophobic')
- .attr('class', 'svg-shadow-bond')
- .on('click', (x: Model.Link) => this.linkMouseClickEventHandler(x))
- .on('mouseover', (x: Model.Link) => this.linkMouseOverEventHandler(x))
- .on('mouseout', (x: Model.Link) => this.linkMouseOverEventHandler(x));
-
- this.links
- .append('line')
- .attr('class', (x: Model.Link) => `svg-bond svg-bond-${x.getLinkClass()}`)
- .attr('marker-end', (x: Model.Link) => `url(#arrow-${x.getLinkClass()})`);
-
- this.nodes = this.visualization.append('g')
- .attr('id', 'nodes')
- .selectAll()
- .data(this.bindingSite.interactionNodes)
- .enter().append('g')
- .attr('class', (e: Model.InteractionNode) => `svg-node svg-${e.residue.getResidueType()}-res`)
- .on('click', (x: Model.InteractionNode, i: number, g: any) => this.selectLigand(x, i, g))
- .on('mouseover', (x: Model.InteractionNode, i: number, g: any) => this.fireNodeMouseEnterEvent(x, i, g))
- .on('mouseout', (x: Model.InteractionNode, i: number, g: any) => this.fireNodeMouseLeaveEvent(x, i, g));
-
-
- await this.visualsMapper.graphicsPromise;
- await this.visualsMapper.mappingPromise;
-
- this.nodes.filter((n: Model.InteractionNode) =>
- this.visualsMapper.glycanMapping.has(n.residue.chemCompId))
- .html((e: Model.InteractionNode) => this.visualsMapper.getGlycanImage(e.residue.chemCompId));
-
- this.nodes.filter((e: Model.InteractionNode) => !this.visualsMapper.glycanMapping.has(e.residue.chemCompId))
- .append('circle')
- .attr('r', '25');
-
- this.nodes.append('text')
- .style('text-anchor', 'middle')
- .style('dominant-baseline', 'central')
- .each(function (e: Model.InteractionNode) {
- let labels = [e.residue.chemCompId, `${e.residue.chainId} ${e.residue.authorResidueNumber}`];
- for (var i = 0; i < labels.length; i++) {
- d3.select(this)
- .append('tspan')
- .attr('dy', (i * 20) - 4)
- .attr('x', 0)
- .text(labels[i]);
- }
- });
-
- let forceLink = d3.forceLink()
- .links(this.bindingSite.links)
- .distance((x: Model.Link) => (<Model.InteractionNode>x.source).residue.isLigand && (<Model.InteractionNode>x.target).residue.isLigand ? 55 : 150)
- .strength(0.5);
-
- let charge = d3.forceManyBody().strength(-1000).distanceMin(55).distanceMax(250);
- let collision = d3.forceCollide(45);
- let center = d3.forceCenter(this.parent.offsetWidth / 2, this.parent.offsetHeight / 2);
-
- this.simulation = d3.forceSimulation(this.bindingSite.interactionNodes)
- .force('link', forceLink)
- .force('charge', charge) //strength
- .force('collision', collision)
- .force('center', center)
- .on('tick', () => this.simulationStep(this));
-
- this.drag_handler(this.nodes);
- this.zoom_handler(this.svg);
- }
-
- private simulationStep(ctx: Visualization) {
- ctx.nodes.attr('transform', (d) => `translate(${d.x},${d.y}) scale(${d.scale})`);
- ctx.links.selectAll('line').attr('x1', (x: any) => x.source.x)
- .attr('y1', (x: any) => x.source.y)
- .attr('x2', (x: any) => x.target.x)
- .attr('y2', (x: any) => x.target.y);
- }
-
- private nodeHighlight(x: Model.InteractionNode, i: number, g: any) {
- x.scale = 1.5;
-
- if (x.residue.isLigand) d3.select(g[i]).style('cursor', 'pointer');
- d3.select(g[i])
- .attr('transform', () => `translate(${x.x},${x.y}) scale(${x.scale})`);
-
- this.tooltip.transition()
- .duration(200)
- .style('opacity', .9);
-
- this.tooltip.html(x.toTooltip());
- }
-
- private nodeDim(x: Model.InteractionNode, i: number, g: any) {
- x.scale = 1.0;
-
- if (x.residue.isLigand) d3.select(g[i]).style('cursor', 'default');
- d3.select(g[i])
- .attr('transform', `translate(${x.x},${x.y}) scale(${x.scale})`);
-
- this.tooltip.transition()
- .duration(200)
- .style('opacity', 0);
- }
-
- private addMarkers() {
- // let mapping = new Map<string, string>([
- // // ["arrow-electrostatic", "#3F26BF"],
- // // ["arrow-vdw", "#9B7653"],
- // // ["arrow-metal", "#008080"],
- // // ["arrow-aromatic", "#AD4379"],
- // ]);
- this.svg
- .append('defs')
- .append('marker')
- .attr('id', 'clash')
- .attr("markerWidth", 15)
- .attr("markerHeight", 15)
- .attr("refX", 7)
- .attr("refY", 3)
- .attr("orient", "auto")
- .attr('markerUnits', 'strokeWidth')
-
- .append('path')
- .attr('d', 'M22.245,4.015c0.313,0.313,0.313,0.826,0,1.139l-6.276,6.27c-0.313,0.312-0.313,0.826,0,1.14l6.273,6.272 c0.313,0.313,0.313,0.826,0,1.14l-2.285,2.277c-0.314,0.312-0.828,0.312-1.142,0l-6.271-6.271c-0.313-0.313-0.828-0.313-1.141,0 l-6.276,6.267c-0.313,0.313-0.828,0.313-1.141,0l-2.282-2.28c-0.313-0.313-0.313-0.826,0-1.14l6.278-6.269 c0.313-0.312,0.313-0.826,0-1.14L1.709,5.147c-0.314-0.313-0.314-0.827,0-1.14l2.284-2.278C4.308,1.417,4.821,1.417,5.135,1.73 L11.405,8c0.314,0.314,0.828,0.314,1.141,0.001l6.276-6.267c0.312-0.312,0.826-0.312,1.141,0L22.245,4.015z')
- .attr('style', 'stroke:#FF5050;stroke-width:3px;');
-
- // mapping.forEach((x, y) =>
- // d3.select('defs').append('marker')
- // .attr('id', y)
- // .attr("markerWidth", 15)
- // .attr("markerHeight", 15)
- // .attr("refX", 7)
- // .attr("refY", 3)
- // .attr("orient", "auto")
- // .attr('markerUnits', 'strokeWidth')
- // .attr('viewBox', '0 0 20 20')
- // .append('path')
- // .attr('d', 'M0,0 L0,6 L9,3 z')
- // .attr('fill', x)
- // );
- }
-}
-
diff --git a/src/plugin/config.ts b/src/plugin/config.ts
new file mode 100644
index 0000000000000000000000000000000000000000..3aa0c4ab3b88b5a39947db0a6d75c1ccc46da644
--- /dev/null
+++ b/src/plugin/config.ts
@@ -0,0 +1,86 @@
+namespace Config {
+ export const nodeSize: number = 30;
+ export const interactionClickEvent: string = 'PDB.interactions.click';
+ export const interactionMouseoverEvent: string = 'PDB.interactions.mouseover';
+ export const interactionMouseoutEvent: string = 'PDB.interactions.mouseout'
+
+ export const interactionShowLabelEvent: string = 'PDB.interactions.showLabel';
+ export const interactionHideLabelEvent: string = 'PDB.interactions.hideLabel';
+
+ export const molstarClickEvent: string = 'PDB.molstar.click';
+ export const molstarMouseoverEvent: string = 'PDB.molstar.mouseover';
+ export const molstarMouseoutEvent: string = 'PDB.molstar.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')],
+ ['negative', Array<string>('E', 'D')],
+ ['polar', Array<string>('N', 'Q', 'S', 'T')],
+ ['cystein', Array<string>('C', 'U')],
+ ['glycine', Array<string>('G')],
+ ['proline', Array<string>('P')],
+ ['aromatic', Array<string>('H', 'Y')]
+ ]);
+
+ export const aaAbreviations = new Map<string, string>([
+ ['ALA', 'A'],
+ ['ARG', 'R'],
+ ['ASN', 'N'],
+ ['ASP', 'D'],
+ ['CYS', 'C'],
+ ['GLU', 'E'],
+ ['GLN', 'Q'],
+ ['GLY', 'G'],
+ ['HIS', 'H'],
+ ['ILE', 'I'],
+ ['LEU', 'L'],
+ ['LYS', 'K'],
+ ['MET', 'M'],
+ ['PHE', 'F'],
+ ['PRO', 'P'],
+ ['SER', 'S'],
+ ['THR', 'T'],
+ ['TRP', 'W'],
+ ['TYR', 'Y'],
+ ['VAL', 'V']
+ ]);
+
+ export const backboneAtoms: Array<string> = ['N', 'CA', 'C', 'O'];
+
+ export const interactionsClasses = new Map<string, Array<string>>([
+ ["covalent", new Array<string>("covalent")],
+ ["electrostatic", new Array<string>("ionic", "hbond", "weak_hbond", "polar", "weak_polar", "xbond", "carbonyl")],
+ ['amide', new Array<string>("AMIDEAMIDE", "AMIDERING")],
+ ["vdw", new Array<string>("vdw")],
+ ["hydrophobic", new Array<string>("hydrophobic")],
+ ["aromatic", new Array<string>("aromatic", "FF", "OF", "EE", "FT", "OT", "ET", "FE", "OE", "EF")],
+ ["atom-pi", new Array<string>("CARBONPI", "CATIONPI", "DONORPI", "HALOGENPI", "METSULPHURPI")],
+ ["metal", new Array<string>("metal_complex")],
+ ["clashes", new Array<string>("clash", "vdw_clash")]
+ ]);
+
+ export class UIParameters {
+ reinitialize: boolean;
+ zoom: boolean;
+ fullScreen: boolean;
+ downloadImage: boolean;
+ downloadData: boolean;
+ center: boolean;
+ help: boolean;
+ residueLabel: boolean;
+ tooltip: boolean;
+
+ constructor() {
+ this.reinitialize = true;
+ this.zoom = true;
+ this.fullScreen = true;
+ this.downloadImage = true;
+ this.downloadData = true;
+ this.center = true;
+ this.help = true;
+ this.residueLabel = true;
+ this.tooltip = true;
+
+ }
+ }
+}
\ No newline at end of file
diff --git a/src/depiction.ts b/src/plugin/depiction.ts
similarity index 80%
rename from src/depiction.ts
rename to src/plugin/depiction.ts
index 85052471d3f1682e933bd6137e21ae91883f12b4..91b1d14941ef735972a584b1167d7e30b1b0c887 100644
--- a/src/depiction.ts
+++ b/src/plugin/depiction.ts
@@ -17,9 +17,21 @@ class Depiction {
ccdId: string;
atoms: Atom[];
bonds: Bond[];
+
resolution: Vector2D;
- constructor(data: any) {
+ 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>;
+
+ constructor(parent: any, data: any) {
+ this.root = parent
+
+ this.highlight = this.root.append('g').attr('id', 'highlight');
+ 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);
@@ -76,16 +88,55 @@ class Depiction {
return new Vector2D(x, y);
}
+ public draw(withClarityNodes: boolean = false) {
+ this.structure.selectAll("*").remove();
+
+ if (withClarityNodes) this.appendClarityNodes();
+ this.appendBondVisuals();
+ this.appendTexts();
+ }
+
+ public highlightSubgraph(atoms: Array<string>, color: string = undefined) {
+ if (!this.atoms || !atoms) return;
+
+ this.highlight.selectAll('*').remove();
+
+ color = color ? color : "#BFBFBF";
+ let atomsToHighlight = this.atoms.filter(x => atoms.includes(x.name));
+
+ this.highlight.selectAll()
+ .data(atomsToHighlight)
+ .enter()
+ .append('circle')
+ .attr('r', '16.12')
+ .attr('cx', x => x.position.x)
+ .attr('cy', x => x.position.y)
+ .attr('style', `fill:${color};fill-rule:evenodd;stroke:${color};stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1`);
+
+ let bondsToHighlight = this.bonds.filter(x => atoms.includes(x.bgn.name) && atoms.includes(x.end.name))
+
+ this.highlight.selectAll()
+ .data(bondsToHighlight)
+ .enter()
+ .append('path')
+ .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`)
+ }
+
+ public addContour(data: any) {
+ this.contour.selectAll('*').remove();
+
+ this.contour.append('div').text(`'contour data goes here: ${data}`);
+ }
/**
* Appends to a given selection the visual representation of bonds as svg:path elements.
*
- * @param {d3.Selection<d3.BaseType, {}, HTMLElement, any>} selection where to append SVG
* representation of the bond visuals.
* @memberof Depiction
*/
- public appendBondVisualsTo(root: d3.Selection<d3.BaseType, {}, HTMLElement, any>): void {
- root.selectAll()
+ private appendBondVisuals(): void {
+ this.structure.selectAll()
.data(this.bonds)
.enter()
.append('path')
@@ -100,12 +151,10 @@ class Depiction {
* Also there are all sorts of colorful subscripts and superscripts,
* so it is much easier to use it this way.
*
- * @param {d3.Selection<d3.BaseType, {}, HTMLElement, any>} root where to append SVG
- * representation of compounds' labels.
* @memberof Depiction
*/
- public appendTextsTo(root: any): void {
- root.selectAll()
+ private appendTexts(): void {
+ this.structure.selectAll()
.data(this.atoms.filter(x => Object.keys(x.label).length !== 0).map(x => x.label))
.enter()
.append('text')
@@ -126,23 +175,22 @@ class Depiction {
* Add small white circle on the background of atoms with label
* just to make the interaction lines pretty.
*
- * @param {*} root
* @memberof Depiction
*/
- public appendClarityNodes(root: any): void {
- root.selectAll()
+ private appendClarityNodes(): void {
+ this.structure.selectAll()
.data(this.atoms.filter(x => Object.keys(x.label).length != 0))
.enter().append('circle')
- .attr('class', 'svg-shadow-node')
+ .classed('pdb-lig-env-svg-shadow-node', true)
.attr('cx', (x: any) => x.position.x)
.attr('cy', (x: any) => x.position.y)
.attr('r', 15);
-
}
public getCenter(ids: string[]): Vector2D {
let coords = new Array<Vector2D>();
+
ids.forEach(x => {
let pos = this.atoms.find(y => y.name === x).position;
coords.push(pos);
diff --git a/src/plugin/manager.ts b/src/plugin/manager.ts
new file mode 100644
index 0000000000000000000000000000000000000000..061ec174054fe9cdc15148ab49a410c6a2140afc
--- /dev/null
+++ b/src/plugin/manager.ts
@@ -0,0 +1,841 @@
+
+class Visualization {
+ // component related
+ private parent: HTMLElement;
+
+ // #region svg properties
+ private simulation: d3.Simulation<d3.SimulationNodeDatum, undefined>;
+ private svg: d3.Selection<any, {}, HTMLElement, any>;
+ private canvas: d3.Selection<SVGGElement, {}, HTMLElement, any>;
+
+ private depictionRoot: d3.Selection<SVGGElement, {}, HTMLElement, any>;
+ private nodesRoot: d3.Selection<SVGGElement, {}, HTMLElement, any>;
+ private linksRoot: d3.Selection<SVGGElement, {}, HTMLElement, any>;
+
+ private zoomHandler: d3.ZoomBehavior<Element, unknown>
+
+ private nodes: any;
+ private links: any;
+ // #endregion
+
+ // #region data properties
+ private pdbId: string;
+ private bindingSite: Model.BindingSite;
+ private depiction: Depiction;
+
+ private visualsMapper: VisualsMapper;
+ private interactionsData: any;
+ private selectedResidueHash: string;
+
+ private rProvider: ResidueProvider;
+
+ public fullScreen: boolean;
+ // #endregion
+
+ constructor(element: HTMLElement, uiParameters: Config.UIParameters = undefined) {
+ this.parent = element;
+ this.parent.style.cssText += "display: block; height: 100%; width: 100%; position: relative;";
+
+ this.visualsMapper = new VisualsMapper();
+ this.rProvider = ResidueProvider.getInstance();
+ this.fullScreen = false;
+
+ if (uiParameters === undefined) uiParameters = new Config.UIParameters();
+
+ new UI(this.parent, this).register(uiParameters);
+
+ this.svg = d3.select(this.parent)
+ .append('div')
+ .attr('id', 'pdb-lig-env-root')
+ .append('svg')
+ .style('background-color', 'white')
+ .attr('xmlns', 'http://www.w3.org/2000/svg')
+ .attr('width', '100%')
+ .attr('height', '100%');
+
+ this.canvas = this.svg.append('g').attr('id', 'vis-root');
+ this.linksRoot = this.canvas.append('g').attr('id', 'links');
+ this.depictionRoot = this.canvas.append('g').attr('id', 'depiction');
+ this.nodesRoot = this.canvas.append('g').attr('id', 'nodes');
+
+ if (uiParameters.zoom) this.zoomHandler = this.getZoomHandler();
+
+ document.addEventListener(Config.molstarClickEvent, e => this.nodeMouseEnterEventHandler(e));
+ document.addEventListener(Config.molstarMouseoverEvent, e => this.nodeMouseEnterEventHandler(e));
+ document.addEventListener(Config.molstarMouseoutEvent, () => this.nodeMouseLeaveEventHandler());
+
+ d3.select(this.parent).on('resize', () => this.resize());
+ this.addMarkers();
+ }
+
+ // #region even handlers
+ private getZoomHandler() {
+ return d3.zoom()
+ .scaleExtent([1 / 10, 10])
+ .on('zoom', () => this.canvas
+ .attr('transform', d3.event.transform));
+ }
+
+
+ private nodeMouseEnterEventHandler(e: any) {
+ if (this.fullScreen) return;
+
+ 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) => {
+ if (node.id === hash) {
+ this.selectedResidueHash = hash;
+ this.nodeHighlight(node, index, group);
+ return;
+ }
+ });
+
+ }
+
+
+ private nodeMouseLeaveEventHandler() {
+ if (this.fullScreen) return;
+
+ this.nodes?.each((node: Model.InteractionNode, index: number, group: any) => {
+ if (node.id == this.selectedResidueHash) {
+ this.nodeDim(node, index, group);
+ return;
+ }
+ });
+ }
+
+ private linkMouseClickEventHandler(x: Model.Link) {
+ this.fireExternalLinkEvent(x, Config.interactionClickEvent);
+ }
+
+ private linkMouseOverEventHandler(x: Model.Link) {
+ this.fireExternalLinkEvent(x, Config.interactionMouseoverEvent);
+ }
+
+ private linkMouseOutEventHandler() {
+ this.fireExternalLinkLeaveEvent();
+ }
+
+ private dragHandler = d3.drag()
+ .filter((x: Model.InteractionNode) => !x.static)
+ .on('start', (x: Model.InteractionNode) => {
+ if (!d3.event.active) this.simulation.alphaTarget(0.3).restart();
+
+ x.fx = x.x;
+ x.fy = x.y;
+ })
+ .on('drag', (x: Model.InteractionNode) => {
+ x.fx = d3.event.x;
+ x.fy = d3.event.y;
+ })
+ .on('end', (x: Model.InteractionNode) => {
+ if (!d3.event.active) this.simulation.alphaTarget(0);
+ x.fx = d3.event.x;
+ x.fy = d3.event.y;
+ });
+
+ // #endregion event handlers
+
+ // #region public methods
+ /**
+ * Download bound molecule interactions data from PDBe Graph API end point
+ * /pdb/bound_molecule_interactions
+ *
+ * Correct parameters can be obtained using API call:
+ * /pdb/bound_molecules
+ *
+ * @param {string} pdbid
+ * @param {string} bmId bound molecule identifier: e.g. bm1, bm2, ...
+ * @memberof Visualization
+ */
+ public initBoundMoleculeInteractions(pdbid: string, bmId: string) {
+ this.pdbId = pdbid;
+ let url = Resources.boundMoleculeAPI(pdbid, bmId);
+
+ d3.json(url)
+ .catch(e => this.processError(e, 'No interactions to display'))
+ .then((data: any) => this.addBoundMoleculeInteractions(data, bmId))
+ .then(() => new Promise(resolve => setTimeout(resolve, 1500)))
+ .then(() => this.centerScene());
+ }
+
+ /**
+ * Download ligand interactions data from PDBe Graph API end point
+ * /pdb/bound_ligand_interactions.
+ *
+ * Correct parameters can be obtained using API call:
+ * /pdb/bound_molecules
+ *
+ * @param {string} pdbId pdb id
+ * @param {number} resId residue number aka: auth_seq_id
+ * @param {string} chainId chain id aka: auth_asym_id
+ * @memberof Visualization
+ */
+ public initLigandInteractions(pdbId: string, resId: number, chainId: string) {
+ this.pdbId = pdbId;
+ let url = Resources.ligandInteractionsAPI(pdbId, chainId, resId);
+
+ d3.json(url)
+ .catch(e => this.processError(e, 'No interactions to display'))
+ .then((data: any) => this.addLigandInteractions(data))
+ .then(() => new Promise(resolve => setTimeout(resolve, 1500)))
+ .then(() => this.centerScene());
+ }
+
+ /**
+ * Download ligand structure given the anotation generated by the
+ * PDBeChem process.
+ *
+ * @param {string} ligandId
+ * @returns
+ * @memberof Visualization
+ */
+ public async initLigandDisplay(ligandId: string) {
+ const ligandUrl = Resources.ligandAnnotationAPI(ligandId);
+
+ return d3.json(ligandUrl)
+ .catch(e => this.processError(e, `Depiction ${ligandId} not found`))
+ .then((d: any) => this.addDepiction(d, true))
+ .then(() => this.centerScene());
+ }
+
+
+ /**
+ * Add depiction to the canvas from external resource.
+ *
+ * @param {*} depiction Content of annotation.json file generated by
+ * the PDBeChem process.
+ * @param {*} withClarityNodes Control if shadow nodes should be drawn
+ * in the background of nodes with labels
+ * @memberof Visualization
+ */
+ public addDepiction(depiction: any, withClarityNodes: boolean) {
+ this.depiction = new Depiction(this.depictionRoot, depiction);
+ this.depiction.draw(withClarityNodes);
+ }
+
+
+ /**
+ * Add atom highlight to the ligand structure. The previous highlight
+ * is going to be removed.
+ *
+ * @param {string[]} highlight List of atom names to be highlighted.
+ * @param {string} [color=undefined] Color in #HEXHEX format.
+ * @memberof Visualization
+ */
+ public addLigandHighlight(highlight: string[], color: string = undefined) {
+ 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);
+ }
+
+
+ public toogleZoom(active: boolean) {
+ if (active) {
+ this.zoomHandler = this.getZoomHandler();
+ } else {
+ this.zoomHandler = undefined;
+ }
+ }
+
+
+ /**
+ * Add ligand interactions to the canvas
+ *
+ * @param {*} data Data content of the API end point
+ * /pdb/bound_ligand_interactions
+ * @memberof Visualization
+ */
+ public addLigandInteractions(data: any) {
+ let key = Object.keys(data)[0];
+ let body = data[key][0];
+ this.interactionsData = data;
+
+ if (this.depiction === undefined || this.depiction.ccdId !== body.ligand.chem_comp_id) {
+ this.initLigandDisplay(body.ligand.chem_comp_id).then(() => {
+ this.bindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
+ this.setupLigandScene();
+ });
+ } else {
+ this.bindingSite = new Model.BindingSite().fromLigand(key, body, this.depiction);
+ this.setupLigandScene();
+ }
+ }
+
+
+ /**
+ * Add bound molecule interactions to the canvas.
+ *
+ * @param {*} data Data content of the API end point
+ * /pdb/bound_molecule_interactions
+ * @param {string} bmId Bound molecule id
+ * @memberof Visualization
+ */
+ public addBoundMoleculeInteractions(data: any, bmId: string) {
+ let key = Object.keys(data)[0];
+ this.interactionsData = data;
+
+ this.bindingSite = new Model.BindingSite().fromBoundMolecule(key, data[key][0]);
+ this.bindingSite.bmId = bmId;
+ let ligands = this.bindingSite.residues.filter(x => x.isLigand);
+
+ if (ligands.length === 1) this.initLigandInteractions(this.pdbId, ligands[0].authorResidueNumber, ligands[0].chainId);
+ else this.setupScene();
+ }
+
+
+ // #region menu functions
+ public saveSvg() {
+ d3.text(Resources.componentSvgCss)
+ .then(x => {
+ let svgData = `
+ <svg xmlns="http://www.w3.org/2000/svg" width="100%" height="100%" style="background-color: white;">
+ ${this.svg.html()}
+ <style>
+ /* <![CDATA[ */ \n ${x} \n /* ]]> */
+ </style>
+ </svg>`;
+
+ let svgBlob = new Blob([svgData], { type: 'image/svg;charset=utf-8' });
+ let svgUrl = URL.createObjectURL(svgBlob);
+ let downloadLink = document.createElement('a');
+
+ downloadLink.href = svgUrl;
+ downloadLink.download = this.getSVGName();
+
+ document.body.appendChild(downloadLink);
+ downloadLink.click();
+ document.body.removeChild(downloadLink);
+ });
+ }
+
+
+ /**
+ * Download interactions data in the JSON format.
+ *
+ * @memberof Visualization
+ */
+ public downloadInteractionsData(): void {
+ let downloadLink = document.createElement('a');
+ let dataBlob = new Blob([JSON.stringify(this.interactionsData, null, 4)], { type: 'application/json' });
+
+ downloadLink.href = URL.createObjectURL(dataBlob);
+ downloadLink.download = this.interactionsData === undefined ? 'no name.json' : `${this.pdbId}_${this.bindingSite.bmId}_interactions.json`;
+ document.body.appendChild(downloadLink);
+ downloadLink.click();
+ document.body.removeChild(downloadLink);
+ }
+
+
+ /**
+ * Reinitialize the scene (basicaly rerun the simulation to place interaction partners)
+ *
+ * @memberof Visualization
+ */
+ public reinitialize() {
+ if (this.depiction === undefined) this.setupScene();
+ else this.setupLigandScene();
+
+ this.hideLigandLabel();
+ }
+
+
+
+ /**
+ * Center scene to the viewbox
+ *
+ * @memberof Visualization
+ */
+ public centerScene() {
+ // Get the bounding box
+ if (this.nodes !== undefined) {
+ let minX: any = d3.min(this.nodes.data().map((x) => x.x));
+ let minY: any = d3.min(this.nodes.data().map((x) => x.y));
+
+ let maxX: any = d3.max(this.nodes.data().map((x) => x.x));
+ let maxY: any = d3.max(this.nodes.data().map((x) => x.y));
+
+ this.computeBoundingBox(minX, maxX, minY, maxY);
+
+ } else if (this.depiction !== undefined) {
+ let minX: any = d3.min(this.depiction.atoms.map((x: Atom) => x.position.x));
+ let minY: any = d3.min(this.depiction.atoms.map((x: Atom) => x.position.y));
+
+ let maxX: any = d3.max(this.depiction.atoms.map((x: Atom) => x.position.x));
+ let maxY: any = d3.max(this.depiction.atoms.map((x: Atom) => x.position.y));
+
+ this.computeBoundingBox(minX, maxX, minY, maxY);
+ }
+ }
+
+ private computeBoundingBox(minX: number, maxX: number, minY: number, maxY: number) {
+ // The width and the height of the graph
+ let molWidth = maxX - minX;
+ let molHeight = maxY - minY;
+
+ // how much larger the drawing area is than the width and the height
+ let widthRatio = this.parent.offsetWidth / molWidth;
+ let heightRatio = this.parent.offsetHeight / molHeight;
+
+ // we need to fit it in both directions, so we scale according to
+ // the direction in which we need to shrink the most
+ let minRatio = Math.min(widthRatio, heightRatio) * 0.85;
+
+ // the new dimensions of the molecule
+ let newMolWidth = molWidth * minRatio;
+ let newMolHeight = molHeight * minRatio;
+
+ // translate so that it's in the center of the window
+ let xTrans = -(minX) * minRatio + (this.parent.offsetWidth - newMolWidth) / 2;
+ let yTrans = -(minY) * minRatio + (this.parent.offsetHeight - newMolHeight) / 2;
+
+ // do the actual moving
+ this.canvas.attr('transform', `translate(${xTrans}, ${yTrans}) scale(${minRatio})`);
+
+ // tell the zoomer what we did so that next we zoom, it uses the
+ // transformation we entered here
+
+ let translation = d3.zoomIdentity.translate(xTrans, yTrans).scale(minRatio);
+ this.zoomHandler?.transform(this.svg, translation);
+
+ };
+
+ // #endregion menu functions
+
+ // #endregion public methods
+
+ private resize() {
+ this.svg
+ .attr('width', this.parent.offsetWidth)
+ .attr('height', this.parent.offsetHeight);
+
+ if (this.depiction === undefined) {
+ this.simulation
+ .force('center', d3.forceCenter(this.parent.offsetWidth / 2, this.parent.offsetHeight / 2))
+ .restart();
+ } else this.simulation.restart();
+
+ if (this.zoomHandler !== undefined) this.zoomHandler(this.svg);
+ }
+
+ private getSVGName(): string {
+ if (this.bindingSite !== undefined) return `${this.bindingSite.bmId}.svg`;
+ if (this.depiction !== undefined) return `${this.depiction.ccdId}.svg`;
+
+ return 'blank.svg';
+ }
+
+ // #region fire events
+
+ //https://stackoverflow.com/questions/40722344/understanding-d3-with-an-example-mouseover-mouseup-with-multiple-arguments
+ private fireExternalNodeMouseEnterEvent(x: Model.InteractionNode, i: number, g: any) {
+ this.nodeHighlight(x, i, g);
+ this.fireExternalNodeEvent(x, Config.interactionMouseoverEvent);
+ }
+
+ private fireExternalNodeMouseLeaveEvent(x: Model.InteractionNode, i: number, g: any) {
+ this.nodeDim(x, i, g);
+
+ const e = new CustomEvent(Config.interactionMouseoutEvent, {
+ bubbles: true,
+ detail: {}
+ });
+ this.parent.dispatchEvent(e);
+ }
+
+ private fireExternalLinkEvent(link: Model.Link, eventName: string) {
+ let atomsSource = [];
+ let atomsTarget = [];
+
+ if (link instanceof Model.LigandResidueLink) {
+ let tmpSrc = [].concat.apply([], link.interaction.map(x => x.sourceAtoms));
+ atomsSource = [].concat.apply([], tmpSrc).filter((v, i, a) => a.indexOf(v) === i);
+
+ let tmpTar = [].concat.apply([], link.interaction.map(x => x.targetAtoms));
+ atomsTarget = [].concat.apply([], tmpTar).filter((v, i, a) => a.indexOf(v) === i);
+ }
+
+ const e = new CustomEvent(eventName, {
+ bubbles: true,
+ detail: {
+ interacting_nodes: [
+ {
+ pdb_res_id: this.pdbId,
+ auth_asym_id: link.source.residue.chainId,
+ auth_seq_id: link.source.residue.authorResidueNumber,
+ auth_ins_code_id: link.source.residue.authorInsertionCode,
+ atoms: atomsSource
+ },
+ {
+ pdb_res_id: this.pdbId,
+ auth_asym_id: link.target.residue.chainId,
+ auth_seq_id: link.target.residue.authorResidueNumber,
+ auth_ins_code_id: link.target.residue.authorInsertionCode,
+ atoms: atomsTarget
+ }
+ ],
+ tooltip: link.toTooltip()
+ }
+ });
+
+ this.parent.dispatchEvent(e);
+ }
+
+ private fireExternalNodeEvent(node: Model.InteractionNode, eventName: string) {
+ const e = new CustomEvent(eventName, {
+ bubbles: true,
+ detail: {
+ selected_node: {
+ pdb_res_id: this.pdbId,
+ auth_asym_id: node.residue.chainId,
+ auth_seq_id: node.residue.authorResidueNumber,
+ auth_ins_code_id: node.residue.authorInsertionCode
+ },
+ tooltip: node.toTooltip()
+ }
+ });
+
+ this.parent.dispatchEvent(e);
+ }
+
+ private fireExternalLinkLeaveEvent() {
+ const e = new CustomEvent(Config.interactionMouseoutEvent, {
+ bubbles: true,
+ detail: {}
+ });
+
+ this.parent.dispatchEvent(e);
+ }
+
+ // #endregion fire events
+
+
+ //#region setup scene micromethods
+ private wipeOutVisuals() {
+ this.nodesRoot.selectAll('*').remove();
+ this.linksRoot.selectAll('*').remove();
+ }
+
+ private setupLinks() {
+ this.links = this.linksRoot
+ .selectAll()
+ .data(this.bindingSite.links)
+ .enter().append('g');
+
+ this.links
+ .append('line')
+ .classed('pdb-lig-env-svg-shadow-bond', (x: Model.Link) => x.getLinkClass() !== 'hydrophobic')
+ .on('click', (x: Model.Link) => this.linkMouseClickEventHandler(x))
+ .on('mouseenter', (x: Model.Link) => this.linkMouseOverEventHandler(x))
+ .on('mouseleave', () => this.linkMouseOutEventHandler());
+
+ this.links
+ .append('line')
+ .attr('class', (e: Model.Link) => `pdb-lig-env-svg-bond pdb-lig-env-svg-bond-${e.getLinkClass()}`)
+ .attr('marker-mid', (e: Model.Link) => e.hasClash() ? 'url(#clash)' : '')
+ .on('mouseenter', (x: Model.Link) => this.linkMouseOverEventHandler(x))
+ .on('mouseleave', () => this.linkMouseOutEventHandler());
+ }
+
+
+
+ private addNodeLabels(selection: any) {
+ selection
+ .append('text')
+ .style('text-anchor', 'middle')
+ .style('dominant-baseline', 'central')
+ .each(function (e: Model.InteractionNode) {
+ let labels = [e.residue.chemCompId, `${e.residue.chainId} ${e.residue.authorResidueNumber}`];
+ for (var i = 0; i < labels.length; i++) {
+ d3.select(this)
+ .append('tspan')
+ .attr('dy', (i * 20) - 4)
+ .attr('x', 0)
+ .text(labels[i]);
+ }
+ });
+ }
+ //#endregion
+
+ /**
+ * Initialize scene after user selected a part of bound molecule.
+ *
+ * @private
+ * @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) {
+ this.fireExternalNodeEvent(n, Config.interactionClickEvent);
+
+ if (!n.residue.isLigand) return;
+
+ this.fireExternalNodeMouseLeaveEvent(n, i, g);
+ this.showLigandLabel(n);
+
+ this.initLigandInteractions(this.pdbId, n.residue.authorResidueNumber, n.residue.chainId);
+ }
+
+ /**
+ * Display error message on the SVG canvas if any of the resources
+ * are not available.
+ *
+ * @private
+ * @param {*} e error object
+ * @param {string} msg Error message to display
+ * @memberof Visualization
+ */
+ private processError(e: any, msg: string) {
+ this.canvas.append('text')
+ .classed('pdb-lig-env-svg-node', true)
+ .attr('x', this.parent.clientWidth / 3)
+ .attr('y', this.parent.clientHeight / 2)
+ .text(msg)
+
+ throw e;
+
+ }
+
+
+ /**
+ * Setup ligand scene for display of ligand and interactions.
+ * This includes: setup of links, nodes, simulation and subscribing to relevant events.
+ *
+ * Depiction is expected to be downloaded already.
+ *
+ * @private
+ * @memberof Visualization
+ */
+ private async setupLigandScene() {
+ this.wipeOutVisuals();
+ this.setupLinks();
+
+ this.bindingSite.interactionNodes
+ .filter((x: Model.InteractionNode) => !x.residue.isLigand)
+ .forEach((x: Model.InteractionNode) => {
+ let lnks = this.bindingSite.links
+ .filter((y: Model.LigandResidueLink) => y.containsInteractionNode(x))
+ .map((y: Model.LigandResidueLink) => [].concat.apply([], y.interaction.map(z => z.sourceAtoms)));
+
+ let concated = [].concat.apply([], lnks);
+ let position: Vector2D = this.depiction.getInitalNodePosition(concated);
+
+ x.x = position.x + Math.random() * 110;
+ x.y = position.y + Math.random() * 110;
+ });
+
+
+ // setup nodes; wait for resources to be ready
+ this.bindingSite.interactionNodes.forEach(x => this.rProvider.downloadAnnotation(x.residue));
+ await Promise.all(this.rProvider.downloadPromises);
+ await Promise.all([this.visualsMapper.graphicsPromise, this.visualsMapper.mappingPromise]);
+
+ this.nodes = this.nodesRoot.append('g')
+ .selectAll()
+ .data(this.bindingSite.interactionNodes)
+ .enter().append('g');
+
+
+ this.nodes.filter((x: Model.InteractionNode) => !x.residue.isLigand)
+ .on('click', (x: Model.InteractionNode) => this.fireExternalNodeEvent(x, Config.interactionClickEvent))
+ .attr('class', (x: Model.InteractionNode) => `pdb-lig-env-svg-node pdb-lig-env-svg-${x.residue.getResidueType()}-res`)
+ .on('mouseenter', (x: Model.InteractionNode, i: number, g: any) => this.fireExternalNodeMouseEnterEvent(x, i, g))
+ .on('mouseleave', (x: Model.InteractionNode, i: number, g: any) => this.fireExternalNodeMouseLeaveEvent(x, i, g));
+
+ this.nodes.filter((x: Model.InteractionNode) => !x.residue.isLigand && this.visualsMapper.glycanMapping.has(x.residue.chemCompId))
+ .html((e: Model.InteractionNode) => this.visualsMapper.getGlycanImage(e.residue.chemCompId));
+
+ // draw rest
+ this.nodes.filter((x: Model.InteractionNode) => !this.visualsMapper.glycanMapping.has(x.residue.chemCompId))
+ .append('circle')
+ .attr('r', (x: Model.InteractionNode) => x.scale * Config.nodeSize);
+
+ let nodesWithText = this.nodes.filter((x: Model.InteractionNode) => !x.residue.isLigand);
+ this.addNodeLabels(nodesWithText);
+
+ let forceLink = d3.forceLink()
+ .links(this.links.filter((x: Model.LigandResidueLink) => x.getLinkClass() !== 'hydrophobic'))
+ .distance(70)
+ .strength(0.5);
+
+ let charge = d3.forceManyBody().strength(-100).distanceMin(40).distanceMax(80);
+ let collision = d3.forceCollide().radius(45);
+
+ this.simulation = d3.forceSimulation(this.bindingSite.interactionNodes)
+ .force('link', forceLink)
+ .force('charge', charge) //strength
+ .force('collision', collision)
+ .on('tick', () => this.simulationStep());
+
+ this.dragHandler(this.nodes);
+ if (this.zoomHandler !== undefined) this.zoomHandler(this.svg, d3.zoomIdentity);
+ }
+
+
+ /**
+ * Setup display of interactions for bound molecule.
+ * * This includes: setup of links, nodes, simulation and subscribing to relevant events.
+ * No depiction is required for this step.
+ *
+ * @private
+ * @memberof Visualization
+ */
+ private async setupScene() {
+ this.wipeOutVisuals();
+ this.setupLinks();
+
+ // setup nodes; wait for resources to be ready
+ this.bindingSite.interactionNodes.forEach(x => ResidueProvider.getInstance().downloadAnnotation(x.residue));
+ await Promise.all(this.rProvider.downloadPromises);
+ await Promise.all([this.visualsMapper.graphicsPromise, this.visualsMapper.mappingPromise]);
+
+ this.nodes = this.nodesRoot
+ .selectAll()
+ .data(this.bindingSite.interactionNodes)
+ .enter().append('g')
+ .attr('class', (e: Model.InteractionNode) => `pdb-lig-env-svg-node pdb-lig-env-svg-${e.residue.getResidueType()}-res`)
+ .on('click', (x: Model.InteractionNode, i: number, g: any) => this.selectLigand(x, i, g))
+ .on('mouseover', (x: Model.InteractionNode, i: number, g: any) => this.fireExternalNodeMouseEnterEvent(x, i, g))
+ .on('mouseout', (x: Model.InteractionNode, i: number, g: any) => this.fireExternalNodeMouseLeaveEvent(x, i, g));
+
+
+ this.nodes.filter((n: Model.InteractionNode) =>
+ this.visualsMapper.glycanMapping.has(n.residue.chemCompId))
+ .html((e: Model.InteractionNode) => this.visualsMapper.getGlycanImage(e.residue.chemCompId));
+
+ this.nodes.filter((e: Model.InteractionNode) => !this.visualsMapper.glycanMapping.has(e.residue.chemCompId))
+ .append('circle')
+ .attr('r', Config.nodeSize);
+
+ this.addNodeLabels(this.nodes);
+
+ let forceLink = d3.forceLink()
+ .links(this.bindingSite.links)
+ .distance((x: Model.Link) => (<Model.InteractionNode>x.source).residue.isLigand && (<Model.InteractionNode>x.target).residue.isLigand ? 55 : 150)
+ .strength(0.5);
+
+ let charge = d3.forceManyBody().strength(-1000).distanceMin(55).distanceMax(250);
+ let collision = d3.forceCollide(45);
+ let center = d3.forceCenter(this.parent.offsetWidth / 2, this.parent.offsetHeight / 2);
+
+ this.simulation = d3.forceSimulation(this.bindingSite.interactionNodes)
+ .force('link', forceLink)
+ .force('charge', charge) //strength
+ .force('collision', collision)
+ .force('center', center)
+ .on('tick', () => this.simulationStep());
+
+ this.dragHandler(this.nodes);
+
+ if (this.zoomHandler) this.zoomHandler(this.svg);
+ }
+
+
+ /**
+ * This is a tick in a simulation that updates position of nodes and links
+ * Depiction does not change its conformation.
+ *
+ * @private
+ * @memberof Visualization
+ */
+ private simulationStep() {
+ this.nodes.attr('transform', (n: Model.InteractionNode) => `translate(${n.x},${n.y}) scale(${n.scale})`);
+ this.links.selectAll('line').attr('x1', (x: any) => x.source.x)
+ .attr('y1', (x: any) => x.source.y)
+ .attr('x2', (x: any) => x.target.x)
+ .attr('y2', (x: any) => x.target.y);
+ }
+
+
+ private nodeHighlight(x: Model.InteractionNode, i: number, g: any) {
+ x.scale = 1.5;
+
+ if (x.residue.isLigand) d3.select(g[i]).style('cursor', 'pointer');
+ d3.select(g[i])
+ .attr('transform', () => `translate(${x.x},${x.y}) scale(${x.scale})`);
+ }
+
+
+ private nodeDim(x: Model.InteractionNode, i: number, g: any) {
+ x.scale = 1.0;
+
+ if (x.residue.isLigand) d3.select(g[i]).style('cursor', 'default');
+
+ d3.select(g[i])
+ .attr('transform', `translate(${x.x},${x.y}) scale(${x.scale})`);
+ }
+
+
+ private showLigandLabel(x: Model.InteractionNode) {
+ const e = new CustomEvent(Config.interactionShowLabelEvent, {
+ bubbles: true,
+ detail: {
+ label: x.toTooltip()
+ }
+ });
+
+ this.parent.dispatchEvent(e);
+ }
+
+
+ private hideLigandLabel() {
+ const e = new CustomEvent(Config.interactionHideLabelEvent, {
+ bubbles: true,
+ detail: {}
+ });
+
+ this.parent.dispatchEvent(e);
+ }
+
+
+ private addMarkers() {
+ // let mapping = new Map<string, string>([
+ // // ["arrow-electrostatic", "#3F26BF"],
+ // // ["arrow-vdw", "#9B7653"],
+ // // ["arrow-metal", "#008080"],
+ // // ["arrow-aromatic", "#AD4379"],
+ // ]);
+
+ this.svg
+ .append('defs')
+ .append('marker')
+ .attr('id', 'clash')
+ .attr("markerWidth", 15)
+ .attr("markerHeight", 15)
+ .attr("refX", 7)
+ .attr("refY", 3)
+ .attr("orient", "auto")
+ .attr('markerUnits', 'strokeWidth')
+
+ .append('path')
+ .attr('d', 'M22.245,4.015c0.313,0.313,0.313,0.826,0,1.139l-6.276,6.27c-0.313,0.312-0.313,0.826,0,1.14l6.273,6.272 c0.313,0.313,0.313,0.826,0,1.14l-2.285,2.277c-0.314,0.312-0.828,0.312-1.142,0l-6.271-6.271c-0.313-0.313-0.828-0.313-1.141,0 l-6.276,6.267c-0.313,0.313-0.828,0.313-1.141,0l-2.282-2.28c-0.313-0.313-0.313-0.826,0-1.14l6.278-6.269 c0.313-0.312,0.313-0.826,0-1.14L1.709,5.147c-0.314-0.313-0.314-0.827,0-1.14l2.284-2.278C4.308,1.417,4.821,1.417,5.135,1.73 L11.405,8c0.314,0.314,0.828,0.314,1.141,0.001l6.276-6.267c0.312-0.312,0.826-0.312,1.141,0L22.245,4.015z')
+ .attr('style', 'stroke:#FF5050;stroke-width:3px;');
+
+ // mapping.forEach((x, y) =>
+ // d3.select('defs').append('marker')
+ // .attr('id', y)
+ // .attr("markerWidth", 15)
+ // .attr("markerHeight", 15)
+ // .attr("refX", 7)
+ // .attr("refY", 3)
+ // .attr("orient", "auto")
+ // .attr('markerUnits', 'strokeWidth')
+ // .attr('viewBox', '0 0 20 20')
+ // .append('path')
+ // .attr('d', 'M0,0 L0,6 L9,3 z')
+ // .attr('fill', x)
+ // );
+ }
+}
+
diff --git a/src/model.ts b/src/plugin/model.ts
similarity index 67%
rename from src/model.ts
rename to src/plugin/model.ts
index 8384393ed84e85aad554864aca642b5da3bdc288..c0dfe6358e34a5c5677479e89bb9a94e5c05100b 100644
--- a/src/model.ts
+++ b/src/plugin/model.ts
@@ -1,49 +1,6 @@
namespace Model {
"use strict";
- const aminoAcids = new Map<string, Array<string>>([
- ['cystein', new Array<string>('CYS', 'SEC', 'CSO')],
- ['positive', new Array<string>('LYS', 'ARG')],
- ['negative', new Array<string>('ASP', 'GLU')],
- ['polar', new Array<string>('SER', 'SEP', 'THR', 'ASN', 'GLN', 'TPO')],
- ['aliphatic', new Array<string>('ALA', 'VAL', 'ILE', 'LEU', 'MET', 'PRO', 'MSE')],
- ['aromatic', new Array<string>('TRP', 'TYR', 'PHE', 'HIS')]
- ]);
-
- const backboneAtoms = ['N', 'CA', 'C', 'O'];
-
- const interactionsClasses = new Map<string, Array<string>>([
- ["covalent", new Array<string>("covalent")],
- ["electrostatic", new Array<string>("ionic", "hbond", "weak_hbond", "polar", "weak_polar", "xbond", "carbonyl")],
- ['amide', new Array<string>("AMIDEAMIDE", "AMIDERING")],
- ["vdw", new Array<string>("vdw")],
- ["hydrophobic", new Array<string>("hydrophobic")],
- ["aromatic", new Array<string>("aromatic", "FF", "OF", "EE", "FT", "OT", "ET", "FE", "OE", "EF", "CARBONPI", "CATIONPI", "DONORPI", "HALOGENPI", "METSULPHURPI")],
- ["metal", new Array<string>("metal_complex")],
- ["clashes", new Array<string>("clash", "vdw_clash")]
- ]);
-
- export class UIParameters {
- reinitialize: boolean;
- downloadImage: boolean;
- downloadData: boolean;
- center: boolean;
- help: boolean;
- residueLabel: boolean;
- tooltip: boolean;
-
- constructor() {
- this.reinitialize = true;
- this.downloadImage = true;
- this.downloadData = true;
- this.center = true;
- this.help = true;
- this.residueLabel = true;
- this.tooltip = true;
-
- }
- }
-
/**
*
*
@@ -104,7 +61,7 @@ namespace Model {
this.chemCompId = data.chem_comp_id;
this.authorInsertionCode = data.author_insertion_code;
this.id = `${this.chainId}${this.authorResidueNumber}${(this.authorInsertionCode === ' ' ? '' : this.authorInsertionCode)}`;
- this.isLigand = isLigand
+ this.isLigand = isLigand;
}
/**
@@ -120,13 +77,15 @@ namespace Model {
return 'water';
}
- for (let [key, value] of aminoAcids) {
- if (value.includes(this.chemCompId)) {
+ let code = ResidueProvider.getInstance().getAminoAcidAbbreviation(this.chemCompId);
+
+ for (let [key, value] of Config.aaTypes) {
+ if (value.includes(code)) {
return key;
}
}
- return 'others';
+ return 'other';
}
public equals(other: Residue): boolean {
@@ -143,7 +102,8 @@ namespace Model {
export class InteractionNode implements d3.SimulationNodeDatum {
id: string;
residue: Residue;
- scale: number;
+ scale: number; // how is the node scaled up in comparison to its original size
+ static: boolean // whether or not can be dragged and droped
index?: number;
x?: number;
@@ -156,6 +116,7 @@ namespace Model {
constructor(r: Residue, scale: number, id: string, x: number = undefined, y: number = undefined) {
this.residue = r;
this.id = id;
+ this.static = Boolean(scale < 1.0);
this.scale = scale;
if (x !== undefined) {
@@ -188,6 +149,7 @@ namespace Model {
target: InteractionNode;
getLinkClass(): string;
+ hasClash(): boolean;
toTooltip(): string;
}
@@ -215,6 +177,17 @@ namespace Model {
return this.target.equals(n) || this.source.equals(n);
}
+ public hasClash(): boolean {
+ this.interactions.forEach(x => {
+ if (x.includes('clash')) {
+ return true
+ }
+ });
+ return false;
+ }
+
+
+
/**
* Shorthand to check if the link contains particular underlying
* residue.
@@ -247,7 +220,7 @@ namespace Model {
if (this.isBoundMoleculeLink()) return 'ligand';
// JS map preserves order of elements
- for (let [key, value] of interactionsClasses) {
+ for (let [key, value] of Config.interactionsClasses) {
for (let interactionDetails of this.interactions.values()) {
if (interactionDetails.filter(x => -1 !== value.indexOf(x)).length > 0) {
return key;
@@ -299,7 +272,7 @@ namespace Model {
// JS map preserves order of elements
let allInteractions = this.interaction.map(x => x.interactionsClases).reduce((x, y) => x.concat(y));
- for (let [key, value] of interactionsClasses) {
+ for (let [key, value] of Config.interactionsClasses) {
if (allInteractions.filter(x => -1 !== value.indexOf(x)).length > 0) {
return key;
}
@@ -324,15 +297,23 @@ namespace Model {
}
public toTooltip() {
- let msg = [];
+ let msg = new Set();
+ let rProvider = ResidueProvider.getInstance();
+
this.interaction.forEach(x => {
- let isMainChain = !this.target.residue.isLigand && x.targetAtoms.every(y => backboneAtoms.includes(y));
- let interactionFlag = isMainChain ? 'backbone' : 'side chain';
+ let isMainChain = !this.target.residue.isLigand && x.targetAtoms.every(y => Config.backboneAtoms.includes(y));
+ let targetAbbreviation = rProvider.getAminoAcidAbbreviation(this.target.residue.chemCompId);
+ let isResidue = Boolean(targetAbbreviation !== 'X');
+ let interactionFlag = '';
+
+ if (isMainChain && isResidue) interactionFlag = 'backbone';
+ else if (!isMainChain && isResidue) interactionFlag = 'side chain';
+ else interactionFlag = 'ligand';
- msg.push(`<li><span>${interactionFlag}</span> interaction (<b>${x.targetAtoms}</b> | ${x.interactionsClases}): ${x.distance}Ã…</li>`);
+ msg.add(`<li><span>${interactionFlag}</span> interaction (<b>${x.targetAtoms}</b> | ${x.interactionsClases}): ${x.distance}Ã…</li>`);
});
- return `<ul>${msg.join('\n')}</ul>`;
+ return `<ul>${Array.from(msg.values()).join('\n')}</ul>`;
}
}
@@ -350,6 +331,8 @@ namespace Model {
interactionNodes: InteractionNode[];
links: Link[];
+ private tmpResidueSet: ObjectSet<Residue>;
+ private tmpNodesSet: ObjectSet<InteractionNode>;
constructor() {
this.residues = new Array<Residue>();
@@ -362,36 +345,30 @@ namespace Model {
this.pdbId = pdbId;
this.bmId = data.bm_id;
- data.composition.ligands.forEach(x => this.residues.push(new Residue(x, true)));
+ this.tmpResidueSet = new ObjectSet<Residue>();
+ this.tmpNodesSet = new ObjectSet<InteractionNode>();
+
+ data.composition.ligands.forEach(x => this.tmpResidueSet.tryAdd(new Residue(x, true)));
data.interactions.forEach(x => {
- let beginingNode = this.processResidueInteractionPartner(x.begin);
+ let bgnNode = this.processResidueInteractionPartner(x.begin);
let endNode = this.processResidueInteractionPartner(x.end);
- let link = new ResidueResidueLink(beginingNode, endNode, x.interactions)
+
+ let link = new ResidueResidueLink(bgnNode, endNode, x.interactions)
this.links.push(link);
});
+ this.interactionNodes = Array.from(this.tmpNodesSet.values());
+
return this;
}
private processResidueInteractionPartner(r: any): InteractionNode {
- let residue = this.residues.find(x => {
- let hash = `${r.chain_id}${r.author_residue_number}${(r.author_insertion_code === ' ' ? '' : r.author_insertion_code)}`;;
- return hash === x.id;
- });
-
- if (residue === undefined) {
- residue = new Residue(r, false);
- this.residues.push(residue);
- }
-
- let node = this.interactionNodes.find(x => x.id === residue.id);
- if (node === undefined) {
- let node = new InteractionNode(residue, 1.0, residue.id);
- this.interactionNodes.push(node);
- return node;
- }
+ let residue = new Residue(r, false);
+ residue = this.tmpResidueSet.tryAdd(residue);
+ let node = new InteractionNode(residue, 1.0, residue.id);
+ node = this.tmpNodesSet.tryAdd(node);
return node;
}
@@ -403,15 +380,12 @@ namespace Model {
else scale = 1.0
let center = d.getCenter(atom_names);
- let id = `${r.id}_${atom_names.reduce((x, y) => x + "_" + y)}`;
- let nodeProvider = this.interactionNodes.find(x => x.id === id);
+ let id = `${r.id}_${atom_names.sort().reduce((x, y) => x + "_" + y)}`;
- if (nodeProvider === undefined) {
- let tmpNode = new InteractionNode(r, scale, id, center.x, center.y);
- this.interactionNodes.push(tmpNode);
- return tmpNode;
- }
- return nodeProvider;
+ let node = new InteractionNode(r, scale, id, center.x, center.y);
+ node = this.tmpNodesSet.tryAdd(node);
+
+ return node;
}
@@ -419,23 +393,77 @@ namespace Model {
this.pdbId = pdbId;
this.bmId = `${data.ligand.chem_comp_id}_${data.ligand.chain_id}_${data.ligand.author_residue_number}`;
+ this.tmpResidueSet = new ObjectSet<Residue>();
+ this.tmpNodesSet = new ObjectSet<InteractionNode>();
+ let tmpLinks = new Array<LigandResidueLink>();
+
let ligandResidue = new Residue(data.ligand, true);
- this.residues.push(ligandResidue);
+ this.tmpResidueSet.tryAdd(ligandResidue);
+
+ ligand.atoms.forEach(x => this.processLigandInteractionPartner(ligandResidue, ligand, [x.name]));
data.interactions.forEach(x => {
- let beginingNode = this.processLigandInteractionPartner(ligandResidue, ligand, x.ligand_atoms);
+ let bgnNode = this.processLigandInteractionPartner(ligandResidue, ligand, x.ligand_atoms);
let endNode = this.processResidueInteractionPartner(x.end);
- let tmpLink = this.links.find(x => (<LigandResidueLink>x).containsBothNodes(beginingNode, endNode)) as LigandResidueLink;
+
+ if (bgnNode.residue.equals(endNode.residue)) {
+ this.tmpNodesSet.delete(endNode);
+ return; // we do not want to show 'self interactions'
+ }
+
+ let tmpLink = tmpLinks.find(x => (<LigandResidueLink>x).containsBothNodes(bgnNode, endNode)) as LigandResidueLink;
if (tmpLink !== undefined) {
tmpLink.addInteraction(x.ligand_atoms, x.end.atom_names, x.interaction_type, x.interaction_details, x.distance);
} else {
- let link = new LigandResidueLink(beginingNode, endNode, x.ligand_atoms, x.end.atom_names, x.interaction_type, x.interaction_details, x.distance);
- this.links.push(link);
+ let link = new LigandResidueLink(bgnNode, endNode, x.ligand_atoms, x.end.atom_names, x.interaction_type, x.interaction_details, x.distance);
+ tmpLinks.push(link);
}
});
+
+ this.interactionNodes = Array.from(this.tmpNodesSet);
+ this.links = this.filterOutAromaticAtomAtomInteractions(tmpLinks);
+
return this;
}
+
+ /**
+ * Filter out Aromatic atom atom interactions provided there is
+ * an evidence of the same atom being part of the stacking information
+ *
+ * This is for clarity purposes only.
+ *
+ * @private
+ * @param {Array<LigandResidueLink>} src
+ * @returns {Array<LigandResidueLink>}
+ * @memberof BindingSite
+ */
+ private filterOutAromaticAtomAtomInteractions(src: Array<LigandResidueLink>): Array<LigandResidueLink> {
+ let result = new Array<LigandResidueLink>();
+ src.forEach((x: LigandResidueLink) => {
+ let isAtomAtom = x.interaction.map(y => y.interactionType).every(z => z === InteractionType.AtomAtom);
+
+ if (x.getLinkClass() === 'aromatic' && isAtomAtom) {
+ let targetAtoms = x.interaction.map(y => y.targetAtoms).reduce((a, b) => a.concat(b));
+ let otherInteractions = new Set(src.filter(y => y.target.equals(x.target)));
+ otherInteractions.delete(x);
+
+ let otherBoundAtoms = Array.from(otherInteractions)
+ .map(y => y.interaction)
+ .reduce((a, b) => a.concat(b))
+ .map(y => y.targetAtoms)
+ .reduce((a, b) => a.concat(b));
+
+ if (otherBoundAtoms.includes(targetAtoms[0])) {
+ return;
+ }
+ }
+
+ result.push(x);
+ });
+
+ return result;
+ }
}
}
\ No newline at end of file
diff --git a/src/plugin/objectSet.ts b/src/plugin/objectSet.ts
new file mode 100644
index 0000000000000000000000000000000000000000..5ff62f3bc7d3f69984fd9993c4e599371a5afbca
--- /dev/null
+++ b/src/plugin/objectSet.ts
@@ -0,0 +1,30 @@
+/**
+ * Extension class just to get objects and collections work nicely.
+ * Not sure what the javascript way is if you need distinct on
+ *
+ * @export
+ * @class ObjectSet
+ * @extends {Set<T>}
+ * @template T
+ */
+class ObjectSet<T> extends Set<T> {
+
+ public tryAdd(value: T): T {
+ let item = undefined;
+
+ this.forEach((x: any) => {
+ if (x.equals(value)) {
+ item = x;
+ return;
+ }
+ });
+
+ if (item === undefined) {
+ item = value;
+ super.add(value);
+ }
+
+ return item;
+ }
+
+}
\ No newline at end of file
diff --git a/src/plugin/residuefactory.ts b/src/plugin/residuefactory.ts
new file mode 100644
index 0000000000000000000000000000000000000000..cb232afc82807d7e5bb55a085f21fb5ec81647b3
--- /dev/null
+++ b/src/plugin/residuefactory.ts
@@ -0,0 +1,74 @@
+/**
+ * Singleton instance to provide residue abbreviations to the component
+ *
+ * @class ResidueProvider
+ */
+class ResidueProvider {
+ private static instance: ResidueProvider;
+ private mapping: Map<string, string>;
+ public downloadPromises: Array<Promise<any>>;
+
+
+ /**
+ * The Singleton's constructor should always be private to prevent direct
+ * construction calls with the `new` operator.
+ * @memberof ResidueProvider
+ */
+ private constructor() {
+ this.mapping = new Map<string, string>(Config.aaAbreviations);
+ this.downloadPromises = new Array<Promise<any>>();
+ }
+
+
+ /**
+ * The static method that controls the access to the singleton instance.
+ *
+ * This implementation let you subclass the Singleton class while keeping
+ * just one instance of each subclass around.
+ *
+ * @static
+ * @returns {ResidueProvider}
+ * @memberof ResidueProvider
+ */
+ public static getInstance(): ResidueProvider {
+ if (!ResidueProvider.instance) {
+ ResidueProvider.instance = new ResidueProvider();
+ }
+
+ return ResidueProvider.instance;
+ }
+
+
+ /**
+ * Get single letter abbreviation of the ligand.
+ *
+ * @param {string} name Name of the chemical compound
+ * @returns Single letter abbreviation of the ligand
+ * @memberof ResidueProvider
+ */
+ public getAminoAcidAbbreviation(name: string): string {
+ return this.mapping.has(name) ? this.mapping.get(name) : undefined;
+ }
+
+
+ /**
+ * Fetch single letter abbreviations from API if they are not present
+ *
+ * @param {string} n
+ * @returns
+ * @memberof ResidueProvider
+ */
+ public downloadAnnotation(r: Model.Residue): void {
+ if (this.mapping.has(r.chemCompId) || r.isLigand) return;
+
+ let url = Resources.residueTypeAPI(r.chemCompId);
+ let res = d3.json(url).then(x => {
+ let code = x[r.chemCompId][0].one_letter_code;
+ this.mapping.set(r.chemCompId, code);
+
+ return code;
+ });
+
+ this.downloadPromises.push(res);
+ }
+}
\ No newline at end of file
diff --git a/src/plugin/resources.ts b/src/plugin/resources.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7c3148e38047dd70146a1abd05fff139e2280ed0
--- /dev/null
+++ b/src/plugin/resources.ts
@@ -0,0 +1,24 @@
+namespace Resources {
+ export const apiServer: string = 'https://wwwdev.ebi.ac.uk/pdbe/graph-api';
+ export const glycanSymbols: string = 'https://pdbe.gitdocs.ebi.ac.uk/web-components/ligand-env/pdb-snfg-visuals.xml';
+ export const glycanMapping: string = 'https://pdbe.gitdocs.ebi.ac.uk/web-components/ligand-env/het_mapping.json';
+ export const componentSvgCss: string = 'https://pdbe.gitdocs.ebi.ac.uk/web-components/ligand-env/pdb-ligand-env-svg.css';
+
+ export const residueTypeURL: string = "https://www.ebi.ac.uk/pdbe/api/pdb/compound/summary/";
+
+ export function ligandAnnotationAPI(ligandName: string): string {
+ return `https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/${ligandName}/annotation`;
+ }
+
+ export function boundMoleculeAPI(pdbId: string, bmId: string): string {
+ return `${apiServer}/pdb/bound_molecule_interactions/${pdbId}/${bmId}`;
+ }
+
+ export function ligandInteractionsAPI(pdbId: string, chainId: string, resId: number) {
+ return `${apiServer}/pdb/bound_ligand_interactions/${pdbId}/${chainId}/${resId}`;
+ }
+
+ export function residueTypeAPI(chemCompId: string): string {
+ return `${residueTypeURL}${chemCompId}`;
+ }
+}
\ No newline at end of file
diff --git a/src/plugin/ui.ts b/src/plugin/ui.ts
new file mode 100644
index 0000000000000000000000000000000000000000..07518726a44a3f5f6eb336af973af340615ffafe
--- /dev/null
+++ b/src/plugin/ui.ts
@@ -0,0 +1,410 @@
+// #region help
+let helpLigands = `
+ <table class='pdb-lig-env-help-table'>
+ <tr>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #80A0F0; "></div>
+ </td>
+ <td>hydrophobic</td>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #C048C0;"></div>
+ </td>
+ <td>negativelly charged</td>
+ </tr>
+ <tr>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #15A4A4;"></div>
+ </td>
+ <td>aromatic</td>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #15C015;"></div>
+ </td>
+ <td>polar</td>
+ <td>
+ </tr>
+ <tr>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #F08080;"></div>
+ </td>
+ <td>cystein</td>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #00BFFF;"></div>
+ </td>
+ <td>water</td>
+ </tr>
+ <tr>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #F01505;"></div>
+ </td>
+ <td>positivelly charged</td>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #F2F2F2;"></div>
+ </td>
+ <td>other</td>
+ </tr>
+ <tr>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: #F09048;"></div>
+ </td>
+ <td>glycine</td>
+ <td>
+ <div class="pdb-lig-env-help-residue" style="background: white; border: 1.2px solid black;"></div>
+ </td>
+ <td>bound molecule</td>
+ </tr>
+ <tr>
+ <td></td>
+ <td><a href="https://www.ncbi.nlm.nih.gov/glycans/snfg.html" target="blank">glycans (SNFG)</a></td>
+ <td></td>
+ <td></td>
+ </tr>
+ </table>
+ `
+let helpBonds = `
+<table class='pdb-lig-env-help-table' style="border-bottom: 0.5px solid black; padding-bottom: 10px;">
+<tr>
+ <td>
+ <hr style="border: 0 none; border-top: 5px solid #AD4379; background: none; height: 0;" />
+ </td>
+ <td>aromatic</td>
+ <td>
+ <hr style="border: 0 none; border-top: 5px solid #FF5050; background: none; height: 0;" />
+ </td>
+ <td>clashes</td>
+</tr>
+<tr>
+ <td>
+ <hr style="border: 0 none; border-top: 5px solid black; background: none; height: 0;" />
+ </td>
+ <td>covalent</td>
+ <td>
+ <hr style="border: 0 none; border-top: 5px solid #3F26BF; background: none; height: 0;" />
+ </td>
+ <td>electrostatic</td>
+
+</tr>
+<tr>
+ <td>
+ <hr style="border: 0 none; border-top: 5px solid #008080; background: none; height: 0;" />
+ </td>
+ <td>metal</td>
+ <td></td>
+ <td>hydrophobic</td>
+</tr>
+
+<tr>
+ <td>
+ <hr style="border: 0 none; border-top: 5px solid #9B7653; background: none; height: 0;" />
+ </td>
+ <td>vdw</td>
+</tr>
+</table>
+<table class="pdb-lig-env-help-table" style="margin-top: 5px;">
+<tr>
+ <td>
+ <hr style="border: 0 none; border-top: 5px solid black; background: none; height: 0;" />
+ </td>
+ <td>covalent</td>
+ <td>
+ <hr style="border: 0 none; border-top: 5px dashed black; background: none; height: 0;" />
+ </td>
+ <td>non-covalent</td>
+</tr>
+</table>`
+
+// #endregion help
+
+
+
+class UI {
+ private parent: HTMLElement;
+ private display: Visualization;
+
+ private residueLabel: d3.Selection<d3.BaseType, {}, HTMLElement, any>; //label used to display ligand ids
+ private tooltip: d3.Selection<d3.BaseType, {}, HTMLElement, any>; // mouseover tooltips
+
+ private originalWidth: number;
+ private originalHeight: number;
+
+
+ constructor(element: HTMLElement, vis: Visualization) {
+ this.parent = element;
+ this.display = vis;
+
+ this.originalWidth = this.parent.offsetWidth;
+ this.originalHeight = this.parent.offsetHeight;
+
+
+ }
+
+ /**
+ * Registers UI elements on the top of SVG canvas with interactions
+ * and ligands
+ *
+ * @param {Config.UIParameters} params Object with annotation which
+ * UI elements should be created.
+ * @returns
+ * @memberof UI
+ */
+ public register(params: Config.UIParameters) {
+ if (!Object.keys(params).some(x => params[x])) {
+ return;
+ }
+
+ let toolbar = d3.select(this.parent)
+ .append('div')
+ .classed('pdb-lig-env-toolbar-container', true)
+ .on('mouseover', () => this.displayToolbarPanel(true))
+ .on('mouseout', () => this.displayToolbarPanel(false));
+
+ toolbar.append('div')
+ .classed('pdb-lig-env-menu-panel', true)
+ .append('i')
+ .attr('title', 'Menu')
+ .attr('class', 'icon icon-common icon-bars');
+
+ let dynamicPanel = toolbar.append('div')
+ .classed('pdb-lig-env-menu-panel', true)
+ .attr('id', 'pdb-lig-env-menu-dynamic-panel')
+ .style('display', 'none')
+ .style('opacity', 0);
+
+ if (params.help) {
+ dynamicPanel.append('i')
+ .attr('id', 'pdb-lig-env-help-btn')
+ .attr('title', 'Help')
+ .attr('class', 'icon icon-common icon-question-circle')
+ .on('click', () => this.showHelp());
+
+ let cont = d3.select(this.parent).append('div').attr('id', 'pdb-lig-env-help-container')
+ let navbar = cont.append('div').classed('pdb-lig-env-help-navbar', true);
+
+ navbar.append('a')
+ .classed('active', true)
+ .attr('id', 'pdb-lig-env-help-residues-btn')
+ .text('Ligands and residues')
+ .on('click', () => this.changeHelp(true));
+
+ navbar.append('a')
+ .attr('id', 'pdb-lig-env-help-bonds-btn')
+ .text('Interactions')
+ .on('click', () => this.changeHelp(false));
+
+ cont.append('div').attr('id', 'pdb-lig-env-help-ligands').html(helpLigands);
+ cont.append('div').attr('id', 'pdb-lig-env-help-bonds').html(helpBonds);
+ }
+
+ if (params.downloadImage) {
+ dynamicPanel.append('i')
+ .attr('id', 'pdb-lig-env-screenshot-btn')
+ .attr('title', 'Screenshot')
+ .attr('class', 'icon icon-common icon-camera')
+ .on('click', () => this.saveSVG());
+ }
+
+ if (params.downloadData) {
+ dynamicPanel.append('i')
+ .attr('id', 'pdb-lig-env-download-btn')
+ .attr('title', 'Download interactions')
+ .attr('class', 'icon icon-common icon-download')
+ .on('click', () => this.download());
+ }
+
+
+
+
+ if (params.center) {
+ dynamicPanel.append('i')
+ .attr('id', 'pdb-lig-env-center-btn')
+ .attr('title', 'Center screen')
+ .attr('class', 'icon icon-common icon-crosshairs')
+ .on('click', () => this.center());
+ }
+
+ if (params.fullScreen) {
+ dynamicPanel.append('i')
+ .attr('id', 'pdb-lig-env-fullscreen-btn')
+ .attr('title', 'Toggle Expanded')
+ .attr('class', 'icon icon-common icon-fullscreen')
+ .on('click', () => this.fullScreen());
+ }
+
+ if (params.reinitialize) {
+ dynamicPanel.append('i')
+ .attr('id', 'pdb-lig-env-home-btn')
+ .attr('title', 'Reset Camera')
+ .attr('class', 'icon icon-common icon-sync-alt')
+ .on('click', () => this.reinitialize());
+ }
+
+ if (params.tooltip) {
+ this.tooltip = d3.select(this.parent).append('div')
+ .classed('pdb-lig-env-label', true)
+ .attr('id', 'pdb-lig-env-tooltip')
+ .style('opacity', 0)
+ }
+
+ if (params.residueLabel) {
+ this.residueLabel = d3.select(this.parent).append('div')
+ .classed('pdb-lig-env-label', true)
+ .attr('id', 'pdb-lig-env-residue-label')
+ .style('opacity', 0)
+ }
+
+ if (this.tooltip !== undefined) {
+ 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());
+ }
+
+ if (this.residueLabel !== undefined) {
+ this.parent.addEventListener(Config.interactionShowLabelEvent, e => this.showLigandLabel(e));
+ this.parent.addEventListener(Config.interactionHideLabelEvent, () => this.hideLigandLabel());
+ }
+
+ }
+
+ // #region UI methods
+ private saveSVG() {
+ this.display.saveSvg();
+ }
+
+ private reinitialize() {
+ this.display.reinitialize()
+ }
+
+ private download() {
+ this.display.downloadInteractionsData()
+ }
+
+ private center() {
+ this.display.centerScene()
+ }
+
+ private changeHelp(showResidues: boolean) {
+ let ligHelpBtn = d3.select(this.parent).select('#pdb-lig-env-help-residues-btn');
+ let bondHelpBtn = d3.select(this.parent).select('#pdb-lig-env-help-bonds-btn');
+ let bondHelpSection = d3.select(this.parent).select('#pdb-lig-env-help-bonds');
+ let ligHelpSection = d3.select(this.parent).select('#pdb-lig-env-help-ligands');
+
+ if (showResidues) {
+ bondHelpBtn.classed('active', false);
+ ligHelpBtn.classed('active', true);
+ bondHelpSection.style('display', 'none');
+ ligHelpSection.style('display', 'block');
+
+ } else {
+ ligHelpBtn.classed('active', false);
+ bondHelpBtn.classed('active', true);
+ bondHelpSection.style('display', 'block');
+ ligHelpSection.style('display', 'none');
+ }
+ }
+
+ private showHelp() {
+ let el = d3.select(this.parent).select('#pdb-lig-env-help-container');
+ let btn = d3.select(this.parent).select('#pdb-lig-env-help-btn');
+
+ if (el.style('display') === 'block') {
+ el.style('display', 'none');
+ el.style('opacity', 0);
+ btn.style('color', '');
+ } else {
+ el.style('display', 'block');
+ el.style('opacity', 1);
+ btn.style('color', '#637ca0');
+ }
+ }
+
+ private displayToolbarPanel(show: boolean) {
+ let dynPanel = d3.select(this.parent).select('#pdb-lig-env-menu-dynamic-panel');
+ let el = d3.select(this.parent).select('#pdb-lig-env-help-container');
+
+ if (!dynPanel && !el) return;
+
+ if (show || el.style('display') === 'block') {
+ dynPanel.style('display', 'block');
+ dynPanel.style('opacity', 0.9);
+ } else {
+
+ dynPanel.style('display', 'none');
+ dynPanel.style('opacity', 0);
+ }
+ }
+
+ /**
+ * Switch component view and full screen.
+ *
+ * @private
+ * @memberof UI
+ */
+ private fullScreen() {
+ let btn = d3.select(this.parent).select('#pdb-lig-env-fullscreen-btn');
+
+ if (btn.attr('class') === 'icon icon-common icon-fullscreen') {
+ this.display.fullScreen = true;
+
+ this.parent.parentElement.style.width = '100%'
+ this.parent.parentElement.style.height = '100%'
+ this.parent.parentElement.style.position = 'fixed';
+ this.parent.parentElement.style.top = '0';
+ this.parent.parentElement.style.left = '0';
+ this.parent.parentElement.style.zIndex = '10000000000000';
+
+ btn.classed('icon-fullscreen', false);
+ btn.classed('icon-fullscreen-collapse', true);
+
+ this.display.centerScene();
+ } else {
+ this.display.fullScreen = true;
+
+ this.parent.parentElement.style.width = `${this.originalWidth}px`;
+ this.parent.parentElement.style.height = `${this.originalHeight}px`;
+ this.parent.parentElement.style.position = 'relative';
+ this.parent.parentElement.style.zIndex = '';
+
+ btn.classed('icon-fullscreen', true);
+ btn.classed('icon-fullscreen-collapse', false);
+
+ this.display.centerScene();
+
+
+ }
+ }
+ // #endregion UI methods
+
+ // #region event handlers
+ private nodeMouseEnterEventHandler(e: any) {
+
+ this.tooltip.transition()
+ .duration(200)
+ .style('opacity', .9);
+
+ this.tooltip.html(e.detail.tooltip);
+
+ }
+
+ private nodeMouseLeaveEventHandler() {
+ this.tooltip.transition()
+ .duration(200)
+ .style('opacity', 0);
+
+ }
+
+ private showLigandLabel(e: any) {
+ this.residueLabel.transition()
+ .duration(200)
+ .style('opacity', .9);
+
+ this.residueLabel.html(e.detail.label);
+
+ }
+
+ private hideLigandLabel() {
+ this.residueLabel.transition()
+ .duration(200)
+ .style('opacity', 0);
+ }
+ // #endregion event handlers
+
+}
\ No newline at end of file
diff --git a/src/visualsMapping.ts b/src/plugin/visualsMapping.ts
similarity index 88%
rename from src/visualsMapping.ts
rename to src/plugin/visualsMapping.ts
index 79db6dd9e43bd01d4e69531388944fcc294157cd..de34c5cd237673941e11abcaf7f769d2e8ff453e 100644
--- a/src/visualsMapping.ts
+++ b/src/plugin/visualsMapping.ts
@@ -18,8 +18,8 @@ class VisualsMapper {
this.glycanMapping = new Map<string, string>();
this.glycanImages = new Map<string, SVGElement>();
- this.graphicsPromise = this.parseSymbols('https://pdbe.gitdocs.ebi.ac.uk/web-components/interactions/visuals.xml');
- this.mappingPromise = this.parseGlycanMapping('https://pdbe.gitdocs.ebi.ac.uk/web-components/interactions/het_mapping.json');
+ this.graphicsPromise = this.parseSymbols(Resources.glycanSymbols);
+ this.mappingPromise = this.parseGlycanMapping(Resources.glycanMapping);
}
/**
diff --git a/src/styles/pdb-ligand-env-svg.css b/src/styles/pdb-ligand-env-svg.css
new file mode 100644
index 0000000000000000000000000000000000000000..df14ba1bbac29549efbf7b70816fb52e7a39c85c
--- /dev/null
+++ b/src/styles/pdb-ligand-env-svg.css
@@ -0,0 +1,158 @@
+.pdb-lig-env-svg-shadow-node {
+ stroke-width: 0;
+ fill: white;
+}
+
+.pdb-lig-env-svg-shadow-bond {
+ stroke-width: 15px;
+ stroke: transparent;
+}
+
+.pdb-lig-env-svg-bond {
+ fill: none;
+ fill-rule: evenodd;
+ stroke-linecap: butt;
+ stroke-linejoin: miter;
+ stroke-opacity: 1;
+}
+
+.pdb-lig-env-svg-bond-ligand {
+ stroke-width: 4px;
+ stroke: black;
+}
+
+.pdb-lig-env-svg-bond-electrostatic {
+ stroke-width: 2px;
+ stroke-dasharray: 10 10;
+ stroke: #3F26BF;
+}
+
+.pdb-lig-env-svg-bond-stacking {
+ stroke-width: 2px;
+ stroke: green;
+}
+
+.pdb-lig-env-svg-bond-atom-pi {
+ stroke-width: 2px;
+ stroke: #2E8B57;
+}
+
+.pdb-lig-env-svg-bond-amide {
+ stroke-width: 2px;
+ stroke: green;
+}
+
+.pdb-lig-env-svg-bond-vdw {
+ stroke-width: 2px;
+ stroke-dasharray: 10 10;
+ stroke: #9B7653;
+}
+
+.pdb-lig-env-svg-bond-hydrophobic {
+ stroke-width: 0px;
+}
+
+.pdb-lig-env-svg-bond-aromatic {
+ stroke-width: 4px;
+ stroke-dasharray: 1 10;
+ stroke: #AD4379;
+}
+
+.pdb-lig-env-svg-bond-metal {
+ stroke-width: 4px;
+ stroke: #008080;
+}
+
+.pdb-lig-env-svg-bond-clashes {
+ stroke-width: 2px;
+ stroke: #FF5050;
+}
+
+.pdb-lig-env-svg-bond-covalent {
+ stroke-width: 2px;
+ stroke: black;
+}
+
+.pdb-lig-env-svg-bond-other {
+ stroke-width: 1px;
+ stroke: black;
+}
+
+.pdb-lig-env-svg-node circle {
+ stroke-width: 3px;
+}
+
+.pdb-lig-env-svg-node text {
+ cursor: inherit;
+ font-family: sans-serif;
+ stroke: black !important;
+ fill: black !important;
+}
+
+.pdb-lig-env-svg-node text tspan:first-child {
+ cursor: inherit;
+ font-weight: 100;
+ font-size: 1em;
+}
+
+.pdb-lig-env-svg-node text tspan:nth-child(2) {
+ cursor: inherit;
+ font-weight: lighter;
+ font-size: 0.75em;
+}
+
+.pdb-lig-env-svg-ligand-res {
+ stroke: black;
+ fill: white;
+}
+
+.pdb-lig-env-svg-water-res {
+ stroke: #A9A9A9;
+ fill: #00BFFF;
+}
+
+.pdb-lig-env-svg-cystein-res {
+ stroke: #A9A9A9;
+ fill: #F08080;
+}
+
+.pdb-lig-env-svg-positive-res {
+ stroke: #A9A9A9;
+ fill: #F01505;
+}
+
+.pdb-lig-env-svg-negative-res {
+ stroke: #A9A9A9;
+ fill: #C048C0;
+}
+
+.pdb-lig-env-svg-proline-res {
+ stroke: #A9A9A9;
+ fill: #C0C000;
+}
+
+.pdb-lig-env-svg-polar-res {
+ stroke: #A9A9A9;
+ fill: #15C015;
+}
+
+.pdb-lig-env-svg-aromatic-res {
+ stroke: #A9A9A9;
+ fill: #15A4A4;
+}
+
+.pdb-lig-env-svg-hydrophobic-res {
+ stroke: #A9A9A9;
+ fill: #80A0F0;
+}
+
+.pdb-lig-env-svg-glycine-res {
+ stroke: #A9A9A9;
+ fill: #F09048;
+}
+
+.pdb-lig-env-svg-other-res {
+ stroke: #A9A9A9;
+ fill: #F2F2F2;
+
+}
\ No newline at end of file
diff --git a/build/pdbe-interactions-styles.css b/src/styles/pdb-ligand-env.css
similarity index 66%
rename from build/pdbe-interactions-styles.css
rename to src/styles/pdb-ligand-env.css
index f50dfa6126d5b81f21bd53e5ac47e98fc1016790..e6181bf2325e9b62e35aba4c55e5e65ab47096f9 100644
--- a/build/pdbe-interactions-styles.css
+++ b/src/styles/pdb-ligand-env.css
@@ -1,11 +1,11 @@
-#int-canvas {
+#pdb-lig-env-root {
cursor: default;
border-radius: 3px;
width: 100%;
- height: 98.5vh;
+ height: 100%;
}
-.int-label {
+.pdb-lig-env-label {
position: absolute;
height: auto;
padding: 10px;
@@ -16,24 +16,24 @@
word-wrap: normal;
}
-#int-tooltip {
+#pdb-lig-env-tooltip {
margin: 10px 0 0 10px;
bottom: 10px;
}
-#int-tooltip>ul {
+#pdb-lig-env-tooltip>ul {
margin: 0;
padding: 0;
list-style-type: none;
}
-#int-tooltip>ul>li:first-of-type(span) {
+#pdb-lig-env-tooltip>ul>li:first-of-type(span) {
text-align: left;
padding: 0px !important;
font-weight: 900;
}
-.int-menu-panel {
+.pdb-lig-env-menu-panel {
background: #ccd4e0;
opacity: 0.9;
float: right;
@@ -47,28 +47,28 @@
transition: .2s;
}
-.int-menu-panel>i {
+.pdb-lig-env-menu-panel>i {
margin-right: 15px;
cursor: pointer;
font: 12px sans-serif;
}
-.int-menu-panel>i:last-child {
+.pdb-lig-env-menu-panel>i:last-child {
margin-right: 0px;
}
-.int-menu-panel>i:hover {
+.pdb-lig-env-menu-panel>i:hover {
color: #637ca0;
}
-.int-toolbar-container {
+.pdb-lig-env-toolbar-container {
top: 20px;
right: 20px;
position: absolute;
overflow: hidden;
}
-#int-help-container {
+#pdb-lig-env-help-container {
font-family: sans-serif;
background: #f6f5f3;
display: none;
@@ -87,67 +87,77 @@
transition: 1s;
}
-#int-help-container:first-child {
+#pdb-lig-env-help-container:first-child {
font-weight: bold;
}
-#int-residue-label {
+#pdb-lig-env-residue-label {
margin: 0 0 10px 10px;
left: 10px;
top: 10px;
}
-#int-tooltip span:first-child {
+#pdb-lig-env-tooltip span:first-child {
text-align: left;
padding-left: 0px !important;
font-weight: 900;
}
-#int-tooltip span:last-child {
+#pdb-lig-env-tooltip span:last-child {
padding-left: 10px;
}
-.int-help-table tr {
+.pdb-lig-env-help-table {
+ border: none !important;
+ margin: 0 !important;
+ background-color: #f6f5f3 !important;
+}
+
+.pdb-lig-env-help-table td {
+ border: none !important;
+}
+
+.pdb-lig-env-help-table tr {
height: 25px;
}
-.int-help-table tr td:first-child {
+.pdb-lig-env-help-table tr td:first-child {
width: 25px;
min-width: 25px;
max-width: 25px;
}
-.int-help-table tr td:nth-child(2) {
+.pdb-lig-env-help-table tr td:nth-child(2) {
min-width: 100px;
}
-.int-help-table tr td:nth-child(3) {
+.pdb-lig-env-help-table tr td:nth-child(3) {
width: 25px;
min-width: 25px;
max-width: 25px;
}
-#int-help-bonds {
+#pdb-lig-env-help-bonds {
display: none;
}
-.int-btn:hover {
+.pdb-lig-env-btn:hover {
color: #637ca0;
}
-.int-help-residue {
+.pdb-lig-env-help-residue {
width: 20px;
height: 20px;
border-radius: 50%;
border: 1.2px solid #a9a9a9;
}
-.int-help-navbar {
+.pdb-lig-env-help-navbar {
height: 20px;
margin-bottom: 10px;
}
-.int-help-navbar a {
+.pdb-lig-env-help-navbar a {
width: 49%;
padding-bottom: 5px;
border: none;
@@ -158,8 +168,7 @@
cursor: pointer;
}
-.int-help-navbar a.active,
-.int-help-navbar a:hover {
+.pdb-lig-env-help-navbar a.active {
border-bottom: 2px solid #637ca0;
color: #637ca0;
}
\ No newline at end of file
diff --git a/src/ui.ts b/src/ui.ts
deleted file mode 100644
index fb9d01d46c9d5647c80ba7fd5ed800bdc7de1cac..0000000000000000000000000000000000000000
--- a/src/ui.ts
+++ /dev/null
@@ -1,295 +0,0 @@
-/// <reference path="./manager.ts" />
-
-// #region help
-let helpLigands = `
- <table class='int-help-table'>
- <tr>
- <td>
- <div class="int-help-residue" style="background: #808080; "></div>
- </td>
- <td>aliphatic</td>
- <td>
- <div class="int-help-residue" style="background: #FF4500;"></div>
- </td>
- <td>negativelly charged</td>
- </tr>
- <tr>
- <td>
- <div class="int-help-residue" style="background: #FFA2FF;"></div>
- </td>
- <td>aromatic</td>
- <td>
- <div class="int-help-residue" style="background: #C0C0C0;"></div>
- </td>
- <td>other</td>
- </tr>
- <tr>
- <td>
- <div class="int-help-residue" style="background: yellow;"></div>
- </td>
- <td>cystein</td>
- <td>
- <div class="int-help-residue" style="background: #9DC183;"></div>
- </td>
- <td>polar</td>
- <td>
- </tr>
- <tr>
- <td>
- <div class="int-help-residue" style="background: #007FFF;"></div>
- </td>
- <td>positivelly charged</td>
- <td>
- <div class="int-help-residue" style="background: #00BFFF;"></div>
- </td>
- <td>water</td>
- </tr>
- <tr>
- <td>
- <div class="int-help-residue" style="background: white; border: 1.2px solid black;"></div>
- </td>
- <td>bound molecule</td>
- <td></td>
- <td><a href="https://www.ncbi.nlm.nih.gov/glycans/snfg.html" target="blank">glycans (SNFG)</a></td>
- </tr>
- </table>
- `
-let helpBonds = `
-<table class='int-help-table' style="border-bottom: 0.5px solid black; padding-bottom: 10px;">
-<tr>
- <td>
- <hr style="border: 0 none; border-top: 5px solid #AD4379; background: none; height: 0;" />
- </td>
- <td>aromatic</td>
- <td>
- <hr style="border: 0 none; border-top: 5px solid #FF5050; background: none; height: 0;" />
- </td>
- <td>clashes</td>
-</tr>
-<tr>
- <td>
- <hr style="border: 0 none; border-top: 5px solid black; background: none; height: 0;" />
- </td>
- <td>covalent</td>
- <td>
- <hr style="border: 0 none; border-top: 5px solid #3F26BF; background: none; height: 0;" />
- </td>
- <td>electrostatic</td>
-
-</tr>
-<tr>
- <td>
- <hr style="border: 0 none; border-top: 5px solid #008080; background: none; height: 0;" />
- </td>
- <td>metal</td>
- <td></td>
- <td>hydrophobic</td>
-</tr>
-
-<tr>
- <td>
- <hr style="border: 0 none; border-top: 5px solid #9B7653; background: none; height: 0;" />
- </td>
- <td>vdw</td>
-</tr>
-</table>
-<table class="int-help-table" style="margin-top: 5px;">
-<tr>
- <td>
- <hr style="border: 0 none; border-top: 5px solid black; background: none; height: 0;" />
- </td>
- <td>covalent</td>
- <td>
- <hr style="border: 0 none; border-top: 5px dashed black; background: none; height: 0;" />
- </td>
- <td>non-covalent</td>
-</tr>
-</table>`
-
-// #endregion help
-
-
-
-class UI {
- private root: HTMLElement;
- private display: Visualization;
-
- private residueLabel: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
- private tooltip: d3.Selection<d3.BaseType, {}, HTMLElement, any>;
-
-
- constructor(element: HTMLElement, vis: Visualization) {
- this.root = element;
- this.display = vis;
-
- }
-
- public register(params: Model.UIParameters) {
- if (!Object.keys(params).some(x => params[x])) {
- return;
- }
-
- let toolbar = d3.select(this.root)
- .append('div')
- .classed('int-toolbar-container', true)
- .on('mouseover', () => this.displayToolbarPanel(true))
- .on('mouseout', () => this.displayToolbarPanel(false));
-
- toolbar.append('div')
- .classed('int-menu-panel', true)
- .append('i')
- .attr('title', 'Menu')
- .attr('class', 'icon icon-common icon-bars');
-
- let dynamicPanel = toolbar.append('div')
- .classed('int-menu-panel', true)
- .attr('id', 'int-menu-dynamic-panel')
- .style('display', 'none')
- .style('opacity', 0);
-
- if (params.reinitialize) {
- dynamicPanel.append('i')
- .attr('id', 'int-home-btn')
- .attr('title', 'Reset camera')
- .attr('class', 'icon icon-common icon-sync-alt')
- .on('click', () => this.reinitialize());
- }
-
- if (params.downloadImage) {
- dynamicPanel.append('i')
- .attr('id', 'int-screenshot-btn')
- .attr('title', 'Save SVG')
- .attr('class', 'icon icon-common icon-camera')
- .on('click', () => this.saveSVG());
- }
-
- if (params.downloadData) {
- dynamicPanel.append('i')
- .attr('id', 'int-download-btn')
- .attr('title', 'Download interactions')
- .attr('class', 'icon icon-common icon-download')
- .on('click', () => this.download());
- }
-
- if (params.center) {
- dynamicPanel.append('i')
- .attr('id', 'int-center-btn')
- .attr('title', 'Center screeeeeeeeeeeen')
- .attr('class', 'icon icon-common icon-crosshairs')
- .on('click', () => this.center());
- }
-
- if (params.help) {
- dynamicPanel.append('i')
- .attr('id', 'int-help-btn')
- .attr('title', 'Show help')
- .attr('class', 'icon icon-common icon-question-circle')
- .on('click', () => this.showHelp());
-
- let cont = d3.select(this.root).append('div').attr('id', 'int-help-container')
- let navbar = cont.append('div').classed('int-help-navbar', true);
-
- navbar.append('a')
- .classed('active', true)
- .attr('id', 'int-help-residues-btn')
- .text('Ligands and residues')
- .on('click', () => this.changeHelp(true));
-
- navbar.append('a')
- .classed('active', true)
- .attr('id', 'int-help-bonds-btn')
- .text('Interactions')
- .on('click', () => this.changeHelp(false));
-
- cont.append('div').attr('id', 'int-help-ligands').html(helpLigands);
- cont.append('div').attr('id', 'int-help-bonds').html(helpBonds);
- }
-
- if (params.tooltip) {
- this.tooltip = d3.select(this.root).append('div')
- .classed('int-label', true)
- .attr('id', 'int-tooltip')
- .style('opacity', 0)
- }
-
- if (params.residueLabel) {
- this.residueLabel = d3.select(this.root).append('div')
- .classed('int-label', true)
- .attr('id', 'int-residue-label')
- .style('opacity', 0)
- }
-
- console.log(this.residueLabel);
- console.log(this.tooltip);
- }
-
- // #region UI methods
- private saveSVG() {
- this.display.saveSvg(this.display);
- }
-
- private reinitialize() {
- this.display.reinitialize(this.display)
- }
-
- private download() {
- this.display.downloadInteractionsData(this.display)
- }
-
- private center() {
- this.display.centerScene(this.display)
- }
-
- private changeHelp(showResidues: boolean) {
- let ligHelpBtn = d3.select('#int-help-residues-btn');
- let bondHelpBtn = d3.select('#int-help-bonds-btn');
- let bondHelpSection = d3.select('#int-help-bonds');
- let ligHelpSection = d3.select('#int-help-ligands');
-
- if (showResidues) {
- bondHelpBtn.classed('active', false);
- ligHelpBtn.classed('active', true);
- bondHelpSection.style('display', 'none');
- ligHelpSection.style('display', 'block');
-
- } else {
- ligHelpBtn.classed('active', false);
- bondHelpBtn.classed('active', true);
- bondHelpSection.style('display', 'block');
- ligHelpSection.style('display', 'none');
- }
- }
-
- showHelp() {
- let el = d3.select('#int-help-container');
- let btn = d3.select('#int-help-btn');
-
- if (el.style('display') === 'block') {
- el.style('display', 'none');
- el.style('opacity', 0);
- btn.style('color', '');
- } else {
- el.style('display', 'block');
- el.style('opacity', 1);
- btn.style('color', '#637ca0');
- }
- }
-
- displayToolbarPanel(show: boolean) {
- let dynPanel = d3.select('#int-menu-dynamic-panel');
- let el = d3.select('#int-help-container');
-
- if (!dynPanel && !el) return;
-
- if (show || el.style('display') === 'block') {
- dynPanel.style('display', 'block');
- dynPanel.style('opacity', 0.9);
- } else {
-
- dynPanel.style('display', 'none');
- dynPanel.style('opacity', 0);
- }
- }
-
- // #endregion UI methods
-}
\ No newline at end of file
diff --git a/tsconfig.json b/tsconfig.json
index 60d88a78fce6291f10fd7e17e883ce79c524c29d..2fa5b589702ad83a3eceda9794feb05be9e84cc0 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -5,23 +5,17 @@
"noUnusedLocals": true,
"noUnusedParameters": true,
"target": "es2016",
- "lib": [ "es5", "es6", "es7", "es2015.collection", "dom", "es2015.promise"],
+ "lib": ["es5", "es6", "es7", "es2015.collection", "dom", "es2015.promise"],
"sourceMap": false,
"declaration": true,
"module": "none",
- "moduleResolution": "node",
- "out": "build/app.js"
- },
- "files": [
- "src/model.ts",
- "src/ui.ts",
- "src/manager.ts",
- "src/visualsMapping.ts",
- "src/depiction.ts",
- ],
+ "moduleResolution": "node",
+ "out": "build/pdb-ligand-env-plugin.js"
+ },
+ "include": ["src/plugin/**/*", ],
"exclude": [
"node_modules",
"build",
- "dist"
+ "dist"
]
}
\ No newline at end of file
diff --git a/webpack.config.js b/webpack.config.js
index 2d28104fcfbdc73cc527d47b674c11dbbf56e906..3019b60204e44c0646629b34fa65596469538e29 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -4,74 +4,55 @@ const camelCase = require("camelcase");
const CleanWebpackPlugin = require("clean-webpack-plugin");
const PACKAGE_ROOT_PATH = process.cwd();
-const PKG_JSON = require(path.join(PACKAGE_ROOT_PATH, "package.json"));
const config = {
- entry: ["./src/component.js"],
+ entry: ["./src/component/component.js"],
output: {
path: path.resolve(PACKAGE_ROOT_PATH, "build"),
- filename: "component.js"
+ filename: "pdb-ligand-env-component-init.js"
},
target: "web",
devtool: "source-map",
resolve: {
extensions: [".js"]
},
-// externals: {
-// d3: "d3",
-// "protvista-track": "ProtvistaTrack",
-// "protvista-sequence": "ProtvistaSequence",
-// "resize-observer-polyfill": "ResizeObserver"
-// },
-// plugins: [new CleanWebpackPlugin([path.join(PACKAGE_ROOT_PATH, "dist")])],
module: {
rules: [
- // {
- // test: /\.css$/,
- // use: [
- // "style-loader",
- // { loader: "css-loader", options: { importLoaders: 1 } }
- // ]
- // },
- // {
- // test: /.(jpg|jpeg|png|svg)$/,
- // use: ['url-loader'],
- // },
+ {
+ test: /\.css$/,
+ use: [
+ "style-loader",
+ { loader: "css-loader", options: { importLoaders: 1 } }
+ ]
+ },
+ {
+ test: /.(jpg|jpeg|png|svg)$/,
+ use: ['url-loader'],
+ },
{
test: /\.(js)$/,
- exclude: function excludeCondition(path){
-
- const nonEs5SyntaxPackages = [
- 'lit-element',
- 'lit-html'
- ]
-
- // DO transpile these packages
- if (nonEs5SyntaxPackages.some( pkg => path.match(pkg))) {
- return false;
- }
-
- // Ignore all other modules that are in node_modules
- if (path.match(/node_modules\\/)) { return true; }
-
- else return false;
- },
+ exclude: function excludeCondition(path) {
+
+ const nonEs5SyntaxPackages = [
+ 'lit-element',
+ 'lit-html'
+ ]
+
+ // DO transpile these packages
+ if (nonEs5SyntaxPackages.some(pkg => path.match(pkg))) {
+ return false;
+ }
+
+ // Ignore all other modules that are in node_modules
+ if (path.match(/node_modules\\/)) { return true; }
+
+ else return false;
+ },
use: {
loader: "babel-loader",
options: {
babelrc: false,
- presets: [
- // [
- // "@babel/preset-env",
- // {
- // targets: {
- // ie: 11,
- // browsers: "last 2 versions"
- // },
- // modules: false
- // }
- // ]
- ],
+ presets: [],
plugins: [
[
"@babel/plugin-transform-runtime",