documentation/global.html

Summary

Maintainability
Test Coverage
<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="utf-8">
    <title>Global - Documentation</title>

    <script src="scripts/prettify/prettify.js"> </script>
    <!--[if lt IE 9]>
      <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
    <![endif]-->
    <link type="text/css" rel="stylesheet" href="styles/prettify-tomorrow.css">
    <link type="text/css" rel="stylesheet" href="styles/jsdoc-default.css">
    <link type="text/css" rel="stylesheet" href="styles/jsdoc-miew.css">
</head>

<body>

<div id="main">
    <h1 class="page-title">Global</h1>

    




<section>

<header>
    
        <h2></h2>
        
    
</header>

<article>
    <div class="container-overview">
    
        

        


<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>


        
    
    </div>

    

    

    

     

    

    

    

    
        <h3 class="subsection-title">Type Definitions</h3>

        
                
<h4 class="name" id="BallsAndSticksModeOptions">BallsAndSticksModeOptions</h4>




<div class="description">
    <p>Balls and Sticks mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>atom</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Sphere radius as a fraction of Van der Waals atom radius.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bond</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Cylinder radius in angstroms.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>space</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Fraction of the space around one cylinder. Zero means that cylinder fills all
available space.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>multibond</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Toggles rendering of multiple ordered bonds.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>aromrad</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Minor radius of a torus for aromatic loops.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>showarom</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Toggles rendering of aromatic loops.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="CarbonColorerOptions">CarbonColorerOptions</h4>




<div class="description">
    <p>Carbon colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>color</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Single color to paint carbons</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>factor</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Color factor for not carbon atoms.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="CartoonModeOptions">CartoonModeOptions</h4>




<div class="description">
    <p>Cartoon mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>radius</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Standard tube radius.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>depth</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Height of the secondary structure ribbon.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>tension</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Tension for interpolation.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.
polyComplexity must be even for producing symmetric arrows.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>heightSegmentsRatio</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Poly complexity multiplier for height segments.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="ConditionalColorerOptions">ConditionalColorerOptions</h4>




<div class="description">
    <p>Conditional colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>subset</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Selector string.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>color</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Color of selected atoms.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>baseColor</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Color of other atoms.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="ContactSurfaceModeOptions">ContactSurfaceModeOptions</h4>




<div class="description">
    <p>Contact Surface mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>isoValue</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Isovalue of the surface to extract.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>probeRadius</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Probe radius.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>probePositions</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>zClip</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles z-clipping.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>subset</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Only parts of surface close to selected atoms will be visible.
Empty string means whole surface is visible.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>wireframe</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag that specifies whether or not surface rendered in wireframe mode.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Radius scale for the surface being built.
Poly complexity values for render modes. In this case the value corresponds to the grid density.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="ElementColorerOptions">ElementColorerOptions</h4>




<div class="description">
    <p>Element colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>carbon</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Carbon color or -1 to use default.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="HydrophobicityColorerOptions">HydrophobicityColorerOptions</h4>




<div class="description">
    <p>Hydrophobicity colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>gradient</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Name of gradient to use.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="IsoSurfaceSASModeOptions">IsoSurfaceSASModeOptions</h4>




<div class="description">
    <p>Solvent Accessible Surface mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>zClip</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles z-clipping.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>probeRadius</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Radius of the probe.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>subset</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Only parts of surface close to selected atoms will be visible.
Empty string means whole surface is visible.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>wireframe</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag that specifies whether or not surface rendered in wireframe mode.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="IsoSurfaceSESModeOptions">IsoSurfaceSESModeOptions</h4>




<div class="description">
    <p>Solvent Excluded Surface mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>zClip</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles z-clipping.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>probeRadius</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Radius of the probe.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>subset</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Only parts of surface close to selected atoms will be visible.
Empty string means whole surface is visible.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>wireframe</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag that specifies whether or not surface rendered in wireframe mode.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="LicoriceModeOptions">LicoriceModeOptions</h4>




<div class="description">
    <p>Licorice mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>bond</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Bond cylinder radius.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>space</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Fraction of the space around one cylinder. Zero means that cylinder fills all
available space.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>multibond</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles rendering of multiple ordered bonds.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>aromrad</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Minor radius of a torus for aromatic loops.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>showarom</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles rendering of aromatic loops.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Poly complexity values for render modes.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="LinesModeOptions">LinesModeOptions</h4>




<div class="description">
    <p>Lines mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>multibond</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles rendering of multiple ordered bonds.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>showarom</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles rendering of aromatic loops.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>offsarom</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Offset between bonds and aromatic cycle.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>chunkarom</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Number of pieces in a-loop arc, corresponding to atom.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>atom</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Collision radius for atoms picking.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>lineWidth</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Line width in pixels (not used in thin lines).</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="MoleculeColorerOptions">MoleculeColorerOptions</h4>




<div class="description">
    <p>Molecule colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>gradient</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Name of gradient to use.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="OccupancyColorerOptions">OccupancyColorerOptions</h4>




<div class="description">
    <p>Occupancy colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>gradient</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Name of gradient to use.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="PolyComplexity">PolyComplexity</h4>




<div class="description">
    <p>Polygonal complexity settings.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>poor</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>low</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>medium</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>high</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>ultra</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="QuickSurfaceModeOptions">QuickSurfaceModeOptions</h4>




<div class="description">
    <p>Quick Surface mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>isoValue</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Isovalue of the surface to extract.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>scale</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Radius scale for the surface being built.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>zClip</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles z-clipping.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>subset</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Only parts of surface close to selected atoms will be visible.
Empty string means whole surface is visible.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>wireframe</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag that specifies whether or not surface rendered in wireframe mode.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>gaussLim</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Gauss lim for coloring the bigger the value, the smoother our colors are.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>gridSpacing</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Poly complexity values for render modes. In this case the value
corresponds to the grid density.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="SequenceColorerOptions">SequenceColorerOptions</h4>




<div class="description">
    <p>Sequence colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>gradient</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Name of gradient to use.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="TemperatureColorerOptions">TemperatureColorerOptions</h4>




<div class="description">
    <p>Temperature colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>gradient</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Name of gradient to use.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>min</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Minimal temperature.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>max</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Maximal temperature.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="TextModeOptions">TextModeOptions</h4>




<div class="description">
    <p>Text mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>template</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Format string for building output text.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>horizontalAlign</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Text alignment ('left', 'right', 'center').</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>verticalAlign</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Vertical text box alignment ('top', 'bottom', 'middle').</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>dx</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Text offset x in angstroms.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>dy</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Text offset y in angstroms.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>dz</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Text offset z in angstroms.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>fg</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Color rule for foreground.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>bg</code></td>
            

            <td class="type">
            
                
<span class="param-type">string</span>


            
            </td>

            

            

            <td class="description last"><p>Color rule for background.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>showBg</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>Flag, that toggles background rendering.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="TraceModeOptions">TraceModeOptions</h4>




<div class="description">
    <p>Trace mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>radius</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Cylinder radius.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="TubeModeOptions">TubeModeOptions</h4>




<div class="description">
    <p>Tube mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>radius</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Cylinder radius.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>tension</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Tension for interpolation.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>heightSegmentsRatio</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Poly complexity multiplier for height segments.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="UniformColorerOptions">UniformColorerOptions</h4>




<div class="description">
    <p>Uniform colorer options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>color</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Single color to paint with.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="VanDerWaalsModeOptions">VanDerWaalsModeOptions</h4>




<div class="description">
    <p>Van der Waals mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
                
<h4 class="name" id="VolumeDensityModeOptions">VolumeDensityModeOptions</h4>




<div class="description">
    <p>Volume density mode options.</p>
</div>







    <h5 class="subsection-title">Properties:</h5>

    

<table class="props">
    <thead>
    <tr>
        
        <th>Name</th>
        

        <th>Type</th>

        

        

        <th class="last">Description</th>
    </tr>
    </thead>

    <tbody>
    

        <tr>
            
                <td class="name"><code>kSigma</code></td>
            

            <td class="type">
            
                
<span class="param-type">number</span>


            
            </td>

            

            

            <td class="description last"><p>Noise threshold coefficient.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>frame</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>flag, that turns on box frame painting.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>isoMode</code></td>
            

            <td class="type">
            
                
<span class="param-type">boolean</span>


            
            </td>

            

            

            <td class="description last"><p>flag, that turns on IsoSurface mode instead of Volume Rendering.</p></td>
        </tr>

    

        <tr>
            
                <td class="name"><code>polyComplexity</code></td>
            

            <td class="type">
            
                
<span class="param-type"><a href="global.html#PolyComplexity">PolyComplexity</a></span>


            
            </td>

            

            

            <td class="description last"><p>Polygonal complexity settings for different resolutions.</p></td>
        </tr>

    
    </tbody>
</table>




<dl class="details">

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    

    
</dl>






            
    

    
</article>

</section>




</div>

<nav>
    <h2><a href="index.html">Home</a></h2><h3>Namespaces</h3><ul><li><a href="SettingsObject.html">SettingsObject</a></li></ul><h3>Classes</h3><ul><li><a href="EntityList.html">EntityList</a></li><li><a href="EventDispatcher.html">EventDispatcher</a></li><li><a href="GROParser.html">GROParser</a></li><li><a href="GROReader.html">GROReader</a></li><li><a href="Helix.html">Helix</a></li><li><a href="LoaderList.html">LoaderList</a></li><li><a href="Logger.html">Logger</a></li><li><a href="Miew.html">Miew</a></li><li><a href="ParserList.html">ParserList</a></li><li><a href="PDBStream.html">PDBStream</a></li><li><a href="Strand.html">Strand</a></li><li><a href="StructuralElement.html">StructuralElement</a></li></ul><h3>Tutorials</h3><ul><li><a href="tutorial-embed.html">Embedding the Viewer</a></li><li><a href="tutorial-events.html">events</a></li><li><a href="tutorial-selectors.html">Selection Language</a></li><li><a href="tutorial-url.html">URL Query String</a></li></ul><h3><a href="global.html">Global</a></h3>
</nav>

<br class="clear">

<footer>
    Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 3.6.7</a> on Thu Dec 16 2021 21:46:09 GMT+0300 (Москва, стандартное время)
</footer>

<script> prettyPrint(); </script>
<script src="scripts/linenumber.js"> </script>
</body>
</html>