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<h1>Glossary<a class="headerlink" href="#glossary" title="Permalink to this headline">¶</a></h1>
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<dt id="term-abstract-base-class">Abstract base class</dt>
<dd>A <a class="reference internal" href="#term-base-class"><em class="xref std std-term">Base Class</em></a> that is not
directly usable by itself, but which defines the common properties
of several subclasses. Example: the class
<a class="reference internal" href="modules.html#MMTK.ChemicalObjects.ChemicalObject" title="MMTK.ChemicalObjects.ChemicalObject"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicalObjects.ChemicalObject</span></tt></a> is
an abstract base class which defines the common properties of its
subclasses <a class="reference internal" href="modules.html#MMTK.ChemicalObjects.Atom" title="MMTK.ChemicalObjects.Atom"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicalObjects.Atom</span></tt></a>,
<a class="reference internal" href="modules.html#MMTK.ChemicalObjects.Group" title="MMTK.ChemicalObjects.Group"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicalObjects.Group</span></tt></a>,
<a class="reference internal" href="modules.html#MMTK.ChemicalObjects.Molecule" title="MMTK.ChemicalObjects.Molecule"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicalObjects.Molecule</span></tt></a>,
<tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicaObjects.Complex</span></tt>, and
<a class="reference internal" href="modules.html#MMTK.ChemicalObjects.AtomCluster" title="MMTK.ChemicalObjects.AtomCluster"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicalObjects.AtomCluster</span></tt></a>. A <a class="reference internal" href="#term-mix-in-class"><em class="xref std std-term">Mix-in class</em></a>
is a special kind of abstract base class.</dd>
<dt id="term-base-class">Base class</dt>
<dd>A class from which another class inherits. In most
cases, the inheriting class is a specialization of the base class.
For example, the class <a class="reference internal" href="modules.html#MMTK.ChemicalObjects.Molecule" title="MMTK.ChemicalObjects.Molecule"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicalObjects.Molecule</span></tt></a> is a
base class of <a class="reference internal" href="modules.html#MMTK.Proteins.PeptideChain" title="MMTK.Proteins.PeptideChain"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.Proteins.PeptideChain</span></tt></a>,
because peptide chains are special molecules. Another common
application is the <a class="reference internal" href="#term-abstract-base-class"><em class="xref std std-term">Abstract base class</em></a>.</dd>
<dt id="term-mix-in-class">Mix-in class</dt>
<dd>A class that is used as a <a class="reference internal" href="#term-base-class"><em class="xref std std-term">Base class</em></a>
in other classes with the sole intention of providing methods
that are common to these classes. Mix-in classes cannot be used
to create instances. They are a special kind of
<a class="reference internal" href="#term-abstract-base-class"><em class="xref std std-term">Abstract base class</em></a>.
Example: class <a class="reference internal" href="modules.html#MMTK.Collections.GroupOfAtoms" title="MMTK.Collections.GroupOfAtoms"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.Collections.GroupOfAtoms</span></tt></a>.</dd>
<dt id="term-subclass">Subclass</dt>
<dd>A class that has another class as its <a class="reference internal" href="#term-base-class"><em class="xref std std-term">Base class</em></a>.
The subclass is usually a specialization of the base class, and can
use all of the methods defined in the base class.
Example: class <a class="reference internal" href="modules.html#MMTK.Proteins.Residue" title="MMTK.Proteins.Residue"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.Proteins.Residue</span></tt></a> is
a subclass of <a class="reference internal" href="modules.html#MMTK.ChemicalObjects.Group" title="MMTK.ChemicalObjects.Group"><tt class="xref py py-class docutils literal"><span class="pre">MMTK.ChemicalObjects.Group</span></tt></a>.</dd>
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