TmMolStar/src/tmdet-extension

Caution

This doc written for TmMol* viewer. Things changed due to heavy refactoring to adjust for saguaro usage.

TMDET Extension

TmMol* is a Mol* extension to visualize transmembrane regions and topology according to data of http://pdbtm.enzim.hu/ served by PDBe.

Usage

loadWithUNITMPMembraneRepresentation call on an initialized PluginUIContext object downloads structure and annotation data from the given URLs.

For example:

<script type="text/javascript" src="./tm_molstar.js"></script>
<script type="text/javascript">
    // init viewer
    var viewer = new tm_molstar.Viewer('app', {
        layoutShowControls: false,
        layoutIsExpanded: false,
        viewportShowExpand: true,
        collapseLeftPanel: true
    });

    var pdbId = '1a0s';

    tm_molstar.loadWithUNITMPMembraneRepresentation(viewer.plugin, {

        // URL to get mmCIF/PDBx data
        structureUrl: `https://cs.litemol.org/${pdbId}/full`,

        // URL to load PDBTM information according to FunPDBe Data Exchange Format
        regionDescriptorUrl: `http://localhost:8000/tmdet-data/${pdbId}.json`,
    });
...

Please see the index.html and index.ts files of the demo application in the src/apps/tm-viwer folder and example data files in data/tmdet-example-annotations folder for more details.

Authors

• Gabor Tusnady (tusnady.gabor at ttk.hu), Protein Bioinformatics Research Group, RCNS.
• Csongor Gerdan (gerdan.csongor at ttk.hu), Protein Bioinformatics Research Group, RCNS.

License

Creative Commons Attribution-NonCommercial 4.0 International Public License

Please see the LICENSE file for more details or visit https://creativecommons.org/licenses/by-nc/4.0/.