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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_dir_d222c3909b771dd1cf1b375528c5865e">
<title>/Users/bernard/b20/bsoft/src/mol Directory Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/mol Directory Reference</primary></indexterm>
<simplesect>
    <title>Files    </title>
        <itemizedlist>
            <listitem><para>file <link linkend="_mol__alpha_8cpp">mol_alpha.cpp</link></para>

<para>Functions to make and analyze alpha helices. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__bonds_8cpp">mol_bonds.cpp</link></para>

<para>Functions for molecular dynamics. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__compare_8cpp">mol_compare.cpp</link></para>

<para>Library routines used to compare sets of atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__edit_8cpp">mol_edit.cpp</link></para>

<para>Library routines used for atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__map__energy_8cpp">mol_map_energy.cpp</link></para>

<para>Functions to calculate estimates of the fitting of molecules to maps. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__md_8cpp">mol_md.cpp</link></para>

<para>Functions for molecular dynamics. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__monte_8cpp">mol_monte.cpp</link></para>

<para>Functions for a monte carlo metroplis algorithm to energy minimize molecular positions. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__param_8cpp">mol_param.cpp</link></para>

<para>Functions to extract parameters from coordinate files. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__select_8cpp">mol_select.cpp</link></para>

<para>Library routines to select atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__symmetry_8cpp">mol_symmetry.cpp</link></para>

<para>Library routines used for symmetry operations on atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__transform_8cpp">mol_transform.cpp</link></para>

<para>Library routines used for atomic coordinate transformations. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__util_8cpp">mol_util.cpp</link></para>

<para>Library routines used for atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_mol__water_8cpp">mol_water.cpp</link></para>

<para>Generating and managing water. </para>
</listitem>
            <listitem><para>file <link linkend="_molecule__to__map_8cpp">molecule_to_map.cpp</link></para>

<para>Functions to calculate a 3D map from atomic coordinates. </para>
</listitem>
            <listitem><para>file <link linkend="_seq__align_8cpp">seq_align.cpp</link></para>

<para>Library routines to generate and analyze dot plots. </para>
</listitem>
            <listitem><para>file <link linkend="_seq__analysis_8cpp">seq_analysis.cpp</link></para>

<para>Analysis of protein sequences. </para>
</listitem>
            <listitem><para>file <link linkend="_seq__util_8cpp">seq_util.cpp</link></para>

<para>Sequence utility functions. </para>
</listitem>
        </itemizedlist>
</simplesect>
</section>
