<a name="Module:Scientific.Visualization.VMD"><h1>Module Scientific.Visualization.VMD</h1></a>

<p>This module provides definitions of simple 3D graphics objects and
scenes containing them, in a form that can be fed to the molecular
visualization program VMD. Scenes can either be written as VMD script
files, or visualized directly by running VMD.</p>

There are a few attributes that are common to all graphics objects:

<p><dl>
<dt>material</dt>
<dd><p>
a Material object defining color and surface properties</p></dd>
<dt>comment</dt>
<dd><p>
a comment string that will be written to the VRML file</p></dd>
<dt>reuse</dt>
<dd><p>
a boolean flag (defaulting to false). If set to one,
           the object may share its VRML definition with other
           objects. This reduces the size of the VRML file, but
           can yield surprising side effects in some cases.</p></dd>
</dl>
</p>

<p>This module is almost compatible with the modules VRML and VRML2, which
provide visualization by VRML browsers. There is no Polygon objects,
and the only material attribute supported is diffuse_color. Note
also that loading a scene with many cubes into VMD is very slow, because
each cube is represented by 12 individual triangles.</p>

<p>Example:</p>

<pre>
from VMD import *
scene = Scene([])
scale = ColorScale(10.)
for x in range(11):
    color = scale(x)
    scene.addObject(Cube(Vector(x, 0., 0.), 0.2,
                         material=Material(diffuse_color = color)))
scene.view()
</pre>
<hr width=70%>
<h2>Functions</h2>

<ul>
<li> <p>

<a name="Function:Scientific.Visualization.VMD.DiffuseMaterial"><b><i>DiffuseMaterial</i></b>(<i>color</i>)</a><br>


</p>

<p>Returns a material with the <tt>diffuse color</tt> attribute set to <i>color</i>.</p></ul>
<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Scene"><h2>Class Scene: VMD scene</h2></a>

<p>A VMD scene is a collection of graphics objects that can be
written to a VMD script file or fed directly to VMD.</p>

<p>Constructor: Scene(<i>objects</i>=None, **|options|)</p>

<p><dl>
<dt><i>objects</i></dt>
<dd><p>
a list of graphics objects or <tt>None</tt> for an empty scene</p></dd>
<dt><i>options</i></dt>
<dd><p>
options as keyword arguments. The only option available
             is "scale", whose value must be a positive number which
             specifies a scale factor applied to all coordinates of
             geometrical objects <i>except</i> for molecule objects, which
             cannot be scaled.
</p></dd>
</dl>
</p>

<b>Methods:</b><br>
<ul>
<li> <b><i>addObject</i></b>(<i>object</i>)
<p>Adds <i>object</i> to the list of graphics objects.</p>

<li> <b><i>writeToFile</i></b>(<i>filename</i>, <i>delete</i>=<tt>0</tt>)
<p>Writes the scene to a VRML file with name <i>filename</i>.</p>

<li> <b><i>view</i></b>()
<p>Start VMD for the scene.</p>

</ul>
<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Molecules"><h2>Class Molecules: Molecules from a PDB file</h2></a>

<p>Constructor: Molecules(<i>pdb_file</i>)
</p>

<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Sphere"><h2>Class Sphere: Sphere</h2></a>

<p>Constructor: Sphere(<i>center</i>, <i>radius</i>, **|attributes|)</p>

<p><dl>
<dt><i>center</i></dt>
<dd><p>
the center of the sphere (a vector)</p></dd>
<dt><i>radius</i></dt>
<dd><p>
the sphere radius (a positive number)</p></dd>
<dt><i>attributes</i></dt>
<dd><p>
any graphics object attribute
</p></dd>
</dl>
</p>

<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Cube"><h2>Class Cube: Cube</h2></a>

<p>Constructor: Cube(<i>center</i>, <i>edge</i>, **|attributes|)</p>

<p><dl>
<dt><i>center</i></dt>
<dd><p>
the center of the cube (a vector)</p></dd>
<dt><i>edge</i></dt>
<dd><p>
the length of an edge  (a positive number)</p></dd>
<dt><i>attributes</i></dt>
<dd><p>
any graphics object attribute</p></dd>
</dl>
</p>

<p>The edges of a cube are always parallel to the coordinate axes.
</p>

<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Cylinder"><h2>Class Cylinder: Cylinder</h2></a>

<p>Constructor: Cylinder(<i>point1</i>, <i>point2</i>, <i>radius</i>,
                      <i>faces</i>=<tt>(1, 1, 1)</tt>, **|attributes|)</p>

<p><dl>
<dt><i>point1</i>, <i>point2</i></dt>
<dd><p>
the end points of the cylinder axis (vectors)</p></dd>
<dt><i>radius</i></dt>
<dd><p>
the radius  (a positive number)</p></dd>
<dt><i>attributes</i></dt>
<dd><p>
any graphics object attribute</p></dd>
<dt><i>faces</i></dt>
<dd><p>
a sequence of three boolean flags, corresponding to
           the cylinder hull and the two circular end pieces,
           specifying for each of these parts whether it is visible
           or not.
</p></dd>
</dl>
</p>

<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Cone"><h2>Class Cone: Cone</h2></a>

<p>Constructor: Cone(<i>point1</i>, <i>point2</i>, <i>radius</i>, <i>face</i>=<tt>1</tt>, **|attributes|)</p>

<p><dl>
<dt><i>point1</i>, <i>point2</i></dt>
<dd><p>
the end points of the cylinder axis (vectors).
                      <i>point1</i> is the tip of the cone.</p></dd>
<dt><i>radius</i></dt>
<dd><p>
the radius  (a positive number)</p></dd>
<dt><i>attributes</i></dt>
<dd><p>
any graphics object attribute</p></dd>
<dt><i>face</i></dt>
<dd><p>
a boolean flag, specifying if the circular bottom is visible
</p></dd>
</dl>
</p>

<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Line"><h2>Class Line: Line</h2></a>

<p>Constructor: Line(<i>point1</i>, <i>point2</i>, **|attributes|)</p>

<p><dl>
<dt><i>point1</i>, <i>point2</i></dt>
<dd><p>
the end points of the line (vectors)</p></dd>
<dt><i>attributes</i></dt>
<dd><p>
any graphics object attribute
</p></dd>
</dl>
</p>

<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Arrow"><h2>Class Arrow: Arrow</h2></a>

<p>An arrow consists of a cylinder and a cone.</p>

<p>Constructor: Arrow(<i>point1</i>, <i>point2</i>, <i>radius</i>, **|attributes|)</p>

<p><dl>
<dt><i>point1</i>, <i>point2</i></dt>
<dd><p>
the end points of the arrow (vectors).
                      <i>point2</i> defines the tip of the arrow.</p></dd>
<dt><i>radius</i></dt>
<dd><p>
the radius of the arrow shaft (a positive number)</p></dd>
<dt><i>attributes</i></dt>
<dd><p>
any graphics object attribute
</p></dd>
</dl>
</p>

<hr width=70%>
<a name="Class:Scientific.Visualization.VMD.Material"><h2>Class Material: Material for graphics objects</h2></a>

<p>A material defines the color and surface properties of an object.</p>

<p>Constructor: Material(**|attributes|)</p>

<p>The accepted attributes are "ambient_color", "diffuse_color",
"specular_color", "emissive_color", "shininess", and "transparency".
Only "diffuse_color" is used, the others are permitted for compatibility
with the VRML modules.
</p>