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365 lines
13 KiB
HTML
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365 lines
13 KiB
HTML
Executable file
<?xml version="1.0" encoding="ascii"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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"DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<title>Scientific.Visualization.PyMOL</title>
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<a href="Scientific-module.html">Package Scientific</a> ::
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<a href="Scientific.Visualization-module.html">Package Visualization</a> ::
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Module PyMOL
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</span>
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</td>
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<td>
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<table cellpadding="0" cellspacing="0">
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<!-- hide/show private -->
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<tr><td align="right"><span class="options"
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>[<a href="frames.html" target="_top">frames</a
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target="_top">no frames</a>]</span></td></tr>
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</table>
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<!-- ==================== MODULE DESCRIPTION ==================== -->
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<h1 class="epydoc">Module PyMOL</h1><p class="nomargin-top"></p>
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<p>Definitions of simple 3D graphics objects and scenes containing them,
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in a form that can be fed to the molecular visualization program
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PyMOL</p>
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<p>Scripts that use this module, directly or indirectly, must be run from
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inside PyMOL, otherwise they will terminate with an error message.</p>
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<p>This module is almost compatible with the modules VRML and VRML2,
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which provide visualization by VRML browsers. There are no Polygon
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objects, and the only material attribute supported is diffuse_color.</p>
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<p>Example:</p>
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<pre class="literalblock">
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>>> from Scientific.Visualization.PyMOL import *
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>>> scene = Scene([])
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>>> scale = ColorScale(10.)
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>>> for x in range(11):
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>>> color = scale(x)
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>>> scene.addObject(Cube(Vector(x, 0., 0.), 0.2,
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>>> material=Material(diffuse_color = color)))
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>>> scene.view()
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</pre>
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<!-- ==================== CLASSES ==================== -->
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<a name="section-Classes"></a>
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<table class="summary" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr bgcolor="#70b0f0" class="table-header">
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<td align="left" colspan="2" class="table-header">
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<span class="table-header">Classes</span></td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Arrow-class.html" class="summary-name">Arrow</a><br />
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Arrow
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Cone-class.html" class="summary-name">Cone</a><br />
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Cone
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Cube-class.html" class="summary-name">Cube</a><br />
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Cube
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Cylinder-class.html" class="summary-name">Cylinder</a><br />
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Cylinder
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Group-class.html" class="summary-name">Group</a><br />
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Base class for composite objects
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Line-class.html" class="summary-name">Line</a><br />
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Line
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Material-class.html" class="summary-name">Material</a><br />
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Material specification for graphics objects
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Molecules-class.html" class="summary-name">Molecules</a><br />
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Molecules from a PDB file
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.PyMOLObject-class.html" class="summary-name">PyMOLObject</a><br />
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Graphics object for PyMOL
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Scene-class.html" class="summary-name">Scene</a><br />
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PyMOL scene
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.ShapeObject-class.html" class="summary-name">ShapeObject</a><br />
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Graphics objects representing geometrical shapes
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<a href="Scientific.Visualization.PyMOL.Sphere-class.html" class="summary-name">Sphere</a><br />
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Sphere
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</td>
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</tr>
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</table>
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<!-- ==================== FUNCTIONS ==================== -->
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<a name="section-Functions"></a>
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<table class="summary" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr bgcolor="#70b0f0" class="table-header">
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<td align="left" colspan="2" class="table-header">
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<span class="table-header">Functions</span></td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"><a href="Scientific.Visualization.PyMOL.Material-class.html"
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class="link">Material</a></span>
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="Scientific.Visualization.PyMOL-module.html#DiffuseMaterial" class="summary-sig-name">DiffuseMaterial</a>(<span class="summary-sig-arg">color</span>)</span><br />
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Returns:
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a material with the 'diffuse color' attribute set to color</td>
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<td align="right" valign="top">
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</td>
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</tr>
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</table>
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"><a href="Scientific.Visualization.PyMOL.Material-class.html"
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class="link">Material</a></span>
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a href="Scientific.Visualization.PyMOL-module.html#EmissiveMaterial" class="summary-sig-name">EmissiveMaterial</a>(<span class="summary-sig-arg">color</span>)</span><br />
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Returns:
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a material with the 'diffuse color' attribute set to color</td>
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<td align="right" valign="top">
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</td>
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</tr>
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</table>
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</td>
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</tr>
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<tr>
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<td width="15%" align="right" valign="top" class="summary">
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<span class="summary-type"> </span>
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</td><td class="summary">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr>
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<td><span class="summary-sig"><a name="isGroup"></a><span class="summary-sig-name">isGroup</span>(<span class="summary-sig-arg">x</span>)</span></td>
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<td align="right" valign="top">
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</td>
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</tr>
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</table>
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</td>
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</tr>
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</table>
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<!-- ==================== FUNCTION DETAILS ==================== -->
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<a name="section-FunctionDetails"></a>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr bgcolor="#70b0f0" class="table-header">
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<td align="left" colspan="2" class="table-header">
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<span class="table-header">Function Details</span></td>
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</tr>
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</table>
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<a name="DiffuseMaterial"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr><td>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">DiffuseMaterial</span>(<span class="sig-arg">color</span>)</span>
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</h3>
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</td><td align="right" valign="top"
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>
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</td>
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</tr></table>
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>color</code></strong> (<a href="Scientific.Visualization.Color.Color-class.html"
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class="link">Color</a> or <code>str</code>) - a color object or a predefined color name</li>
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</ul></dd>
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<dt>Returns: <a href="Scientific.Visualization.PyMOL.Material-class.html"
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class="link">Material</a></dt>
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<dd>a material with the 'diffuse color' attribute set to color</dd>
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</dl>
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</td></tr></table>
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</div>
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<a name="EmissiveMaterial"></a>
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<div>
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<table class="details" border="1" cellpadding="3"
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cellspacing="0" width="100%" bgcolor="white">
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<tr><td>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<tr valign="top"><td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">EmissiveMaterial</span>(<span class="sig-arg">color</span>)</span>
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</h3>
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</td><td align="right" valign="top"
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>
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</td>
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</tr></table>
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<dl class="fields">
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<dt>Parameters:</dt>
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<dd><ul class="nomargin-top">
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<li><strong class="pname"><code>color</code></strong> (<a href="Scientific.Visualization.Color.Color-class.html"
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class="link">Color</a> or <code>str</code>) - a color object or a predefined color name</li>
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</ul></dd>
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<dt>Returns: <a href="Scientific.Visualization.PyMOL.Material-class.html"
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class="link">Material</a></dt>
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<dd>a material with the 'diffuse color' attribute set to color</dd>
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</dl>
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</td></tr></table>
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</div>
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<br />
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