Merge pull request galaxyproject#20101 from guerler/molstar

Add Molstar

Author: guerler

client/gulpfile.js

@@ -37,6 +37,7 @@ const INSTALL_PLUGIN_BUILD_IDS = [
     "heatmap",
     "kepler",
     "ngl",
+    "molstar",
     "msa",
     "niivue",
     "openlayers",

config/plugins/visualizations/molstar/config/molstar.xml

@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Molstar Viewer" embeddable="true">
+    <description>Complex Biomolecular Structures</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test test_attr="ext">pdb</test>
+            <test test_attr="ext">pqr</test>
+            <test test_attr="ext">cif</test>
+            <test test_attr="ext">bcif</test>
+            <test test_attr="ext">mol</test>
+            <test test_attr="ext">mol2</test>
+            <test test_attr="ext">sdf</test>
+            <test test_attr="ext">xyz</test>
+            <test test_attr="ext">gro</test>
+            <test test_attr="ext">top</test>
+            <test test_attr="ext">traj</test>
+        </data_source>
+    </data_sources>
+    <params>
+        <param required="true">dataset_id</param>
+    </params>
+    <requirements>
+        <requirement type="npm" version="0.0.1" package="@galaxyproject/molstar"/>
+    </requirements>
+    <entry_point entry_point_type="script" src="dist/index.js" css="dist/index.css" />
+    <tests>
+        <test>
+            <param name="dataset_id" value="http://cdn.jsdelivr.net/gh/galaxyproject/galaxy-test-data/newbox.pdb" ftype="pdb" />
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+### What is Molstar?
+
+Mol\* (**Molstar**) is a modern, fast, interactive 3D viewer for molecular structures such as proteins, nucleic acids, small molecules, and macromolecular assemblies. It enables detailed exploration of complex biological data directly in your web browser.
+
+Currently, Molstar in this interface supports formats such as **PDB**, **PQR**, **mmCIF**, **BinaryCIF**, **MOL2**, **SDF**, **XYZ**, **GRO**, **TOP**, and **TRAJ**.  
+After selecting a compatible dataset, you'll see a fully interactive 3D visualization where you can rotate, zoom, color, and inspect molecular models.
+
+#### Key Features
+
+- **Real-Time 3D Rendering**: Explore structures smoothly at high performance, even for very large systems.
+- **Advanced Representations**: Display molecules as cartoons, surfaces, ball-and-stick, space-filling, and more.
+- **Chain, Ligand, and Atom Highlighting**: Focus on specific parts of the molecule using flexible selection tools.
+- **Animations and Morphing**: Animate models with multiple conformations (e.g., NMR ensembles).
+- **Volume Data Support**: View cryo-EM and density maps (MRC, DSN6) alongside atomic models.
+- **Extensible Plugin System**: Customize the viewer for specialized workflows.
+
+To learn more about Mol\* Viewer, visit:  
+[https://molstar.org/](https://molstar.org/)
+    ]]></help>
+</visualization>