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Merge pull request #3601 from bgruening/ngl_viewer

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NGL Viewer for molecule representation
This commit is contained in:
Dannon Baker
2017-02-15 15:06:01 -05:00
committed by GitHub
parent a7572145e9 7472568fe5
commit 43f2a64823
10 changed files with 240 additions and 4 deletions
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config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
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config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
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config/plugins/visualizations/charts/static/repository/build/registry.js
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config/plugins/visualizations/charts/static/repository/build/registry.js.map
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config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
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define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_basic:require( "visualizations/cytoscape/basic/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ),} } );
define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_basic:require( "visualizations/cytoscape/basic/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ), ngl_viewer:require( "visualizations/ngl/viewer/config" ),} } );
config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
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config/plugins/visualizations/charts/static/repository/registry.json
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"others" : [ "example", "heatmap", "heatmap_cluster" ],
"cytoscape" : [ "basic" ],
"pv" : [ "viewer" ],
"benfred" : [ "venn" ]
"benfred" : [ "venn" ],
"ngl" : [ "viewer" ]
}
config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
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define( [], function() {
return {
title : 'NGL Viewer',
library : 'NGL',
datatypes : [ 'pdb' ],
keywords : 'NGL protein viewer pdb',
description : 'NGL Viewer is a WebGL based molecular visualization hosted at http://arose.github.io/ngl/.',
settings : {
quality : {
label : 'Quality',
help : 'Select the rendering quality.',
type : 'select',
display : 'radio',
value : 'medium',
data : [ { label : 'High', value : 'high' }, { label : 'Medium', value : 'medium' }, { label : 'Low', value : 'low' } ]
},
viewer : {
type : 'conditional',
test_param : {
name : 'mode',
label : 'Display mode',
type : 'select',
display : 'radio',
value : 'cartoon',
help : '',
data : [ { label : 'Axes', value : 'axes' },
{ label : 'Base', value : 'base' },
{ label : 'Backbone', value : 'backbone' },
{ label : 'Ball+Stick', value : 'ball+stick' },
{ label : 'Cartoon', value : 'cartoon' },
{ label : 'Contact', value : 'contact' },
{ label : 'Helixorient', value : 'helixorient' },
{ label : 'Hyperball', value : 'hyperball' },
{ label : 'Label', value : 'label' },
{ label : 'Licorice', value : 'licorice' },
{ label : 'Line', value : 'line' },
{ label : 'Point', value : 'point' },
{ label : 'Ribbon', value : 'ribbon' },
{ label : 'Rocket', value : 'rocket' },
{ label : 'Rope', value : 'rope' },
{ label : 'Spacefill', value : 'spacefill' },
{ label : 'Surface', value : 'surface' },
{ label : 'Trace', value : 'trace' },
{ label : 'Tube', value : 'tube' },
{ label : 'Unitcell', value : 'unitcell' } ]
}
},
radius: {
name : 'radius',
label : 'Radius',
help : 'Select a number providing a fixed radius used for rendering the representation.',
type : 'float',
min : 0.001,
max : 10.0,
value : 0.05
},
scale: {
name : 'scale',
label : 'Scale',
help : 'Select a number that scales the value defined by the *radius* parameter.',
type : 'float',
min : 0.001,
max : 10.0,
value : 0.7
},
colorscheme : {
label : 'Color Scheme',
help : 'Select color scheme of the molecule scene.',
type : 'select',
display : 'radio',
value : 'atomindex',
data : [ { label : 'Element', value : 'element' },
{ label : 'Picking', value : 'picking' },
{ label : 'Random', value : 'random' },
{ label : 'Uniform', value : 'uniform' },
{ label : 'Atomindex', value : 'atomindex' },
{ label : 'Residue Index', value : 'residueindex' },
{ label : 'Chain Index', value : 'chainindex' },
{ label : 'Chain Name', value : 'chainname' },
{ label : 'Chain Id', value : 'chainid' },
{ label : 'Polymer', value : 'polymer' },
{ label : 'Model Index', value : 'modelindex' },
{ label : 'Entity Type', value : 'entitytype' },
{ label : 'Molecule Type', value : 'moleculetype' },
{ label : 'Secondary Structure', value : 'sstruc' },
{ label : 'Bfactor', value : 'bfactor' },
{ label : 'Resname', value : 'resname' },
{ label : 'Hydrophobicity', value : 'hydrophobicity' },
{ label : 'Value', value : 'value' },
{ label : 'Volume', value : 'volume' },
{ label : 'Occupancy', value : 'occupancy' } ]
},
backcolor : {
label : 'Background Color',
help : 'Select background color of the viewer.',
type : 'select',
display : 'radio',
value : 'white',
data : [ { label : 'Light', value : 'white' }, { label : 'Dark', value : 'black' } ]
},
spin : {
label : 'Spin',
help : 'Spin the molecule view.',
type : 'select',
display : 'radio',
value : false,
data : [ { label : 'On', value : true }, { label : 'Off', value : false } ]
},
assembly : {
label : 'Assembly',
help : 'Select a name of an assembly object.',
type : 'select',
display : 'radio',
value : 'default',
data : [ { label : 'Default', value : 'default' }, { label : 'AU', value : '' },
{ label : 'BU1', value : 'BU1' }, { label : 'UNITCELL', value : 'UNITCELL' },
{ label : 'SUPERCELL', value: 'SUPERCELL' } ]
},
opacity : {
name : 'opacity',
label : 'Opacity',
help : 'Select opacity for the molecule scene.',
type : 'float',
min : 0.0,
max : 1.0,
value : 1.0
}
}
}
});
config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
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config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
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define( [ 'utilities/utils', "plugins/ngl/viewer" ], function( Utils, ngl ) {
return Backbone.Model.extend({
initialize: function( options ) {
var dataset = options.dataset,
settings = options.chart.settings,
stage = new ngl.Stage( options.targets[ 0 ], { backgroundColor: settings.get( 'backcolor' ) } ),
viewer_options = {},
representation_parameters = {},
stage_parameters = {};
_.each( settings.attributes, function( value, key ) {
if ( key.startsWith( 'viewer|' ) ) {
viewer_options[ key.replace( 'viewer|', '' ) ] = value;
}
} );
representation_parameters = {
radius: settings.get( 'radius' ),
scale: settings.get( 'scale' ),
assembly: settings.get( 'assembly' ),
color: settings.get( 'colorscheme' ),
opacity: settings.get( 'opacity' )
};
stage_parameters = { ext: dataset.extension, defaultRepresentation: true };
try {
stage.loadFile( dataset.download_url, stage_parameters ).then( function( component ) {
component.addRepresentation( viewer_options.mode, representation_parameters );
options.chart.state( 'ok', 'Chart drawn.' );
options.process.resolve();
} );
} catch( e ) {
options.chart.state( 'failed', 'Could not load PDB file.' );
options.process.resolve();
}
stage.setQuality( settings.get( 'quality' ) );
if( settings.get( 'spin' ) === true || settings.get( 'spin' ) === 'true' ) {
stage.setSpin( [ 0, 1, 0 ], 0.01 );
}
// Re-renders the molecule view when window is resized
$( window ).resize( function() { stage.viewer.handleResize() } );
}
});
});