Commit 329914a0 authored by Lukas Pravda's avatar Lukas Pravda
Browse files

Merge branch 'dev' -- release 1.0

parents 8dbb3078 f701abb1
Pipeline #176751 passed with stages
in 40 seconds
## RELEASE 1.0 - 28 April 2021
* Support to display atom names
* Use `pdbeccdutils=0.6` data
* Minor bug fixes
## RELEASE 0.2 - 24 February 2020
Component rembranded to `pdb-ligand-env`
Component rebranded to `pdb-ligand-env`
### Features
......
# 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.
This is a web-component to display ligand structure in 2D along with its interactions. Ligand can be perceived as a set of covalently linked pdb residues (refered to as bound molecule) or a single pdb residue. This depiction can be enriched with a substructure highlight, atom names, and binding site interactions.
## Step after cloning (use local server to see demo pages)
......@@ -133,6 +133,8 @@ let uiParams = {
help: false, // allow help option from the component menu
residueLabel: true, // show residue label
tooltip: true // show residue tooltip on mouse hover
menu: true // allow menu to be (not) available
names: true // allow ligand depiction with atom names
};
this.display = new Visualization(this, uiParams, environment);
......@@ -144,8 +146,8 @@ this.display.initCarbohydratePolymerInteractions('5e98', 'bm1','3');
// to display ligand interactions
this.display.initLigandInteractions('1cbs', 200, 'A');
// to display chemical component only
this.display.initLigandDisplay('HEM');
// to display chemical component with atom names only
this.display.initLigandDisplay('HEM', true);
````
## Parameters
......@@ -160,4 +162,5 @@ this.display.initLigandDisplay('HEM');
| 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. |
| names-on | boolean | No | Allow ligand depiction to be displayed with atom names. |
| environment | string | No | What data should be used: one of `production`, `development`, `internal` or a shorthand `prod`, `dev`, `int`. |
......@@ -14,7 +14,7 @@
<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js"
charset="utf-8"></script>
<!--PDBe interactions component-->
<script type="module" src="http://127.0.0.1:8080/pdb-ligand-env-component-0.3.0-min.js"></script>
<script type="module" src="http://127.0.0.1:8080/pdb-ligand-env-component-1.0.0-min.js"></script>
</head>
......@@ -37,7 +37,7 @@
<!--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>
<pdb-ligand-env pdb-res-name="CLR" zoom-on names-on></pdb-ligand-env>
</div>
</div>
......
......@@ -18,7 +18,7 @@
<script src="https://cdn.jsdelivr.net/npm/@webcomponents/webcomponentsjs/custom-elements-es5-adapter.js"
charset="utf-8"></script>
<script type="module" src="pdb-ligand-env-component-0.3.0-min.js"></script>
<script type="module" src="pdb-ligand-env-component-1.0.0-min.js"></script>
<script>
var renderBmInteractions = function (id, bmId) {
var int =
......@@ -126,9 +126,9 @@
<!--
Further use in the app for bound molecule interactions:
<pdb-ligand-env pdb-id="3d12" bound-molecule-id="bm1"></pdb-ligand-env>
for ligand interactions:
<pdb-ligand-env pdb-id="3d12" pdb-chain-id="A" pdb-res-id="200"></pdb-ligand-env>
-->
......
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"license": "Apache License 2.0",
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......@@ -2092,12 +2092,6 @@
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......@@ -2577,7 +2522,7 @@
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