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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_bcatmol_8cpp">
<title>/Users/bernard/b20/bsoft/src/bcatmol.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/bcatmol.cpp</primary></indexterm>
<para>

<para>A program to concatenate coordinates from different files. </para>
 
</para>
<programlisting>#include &quot;rwmolecule.h&quot;
#include &quot;mol_transform.h&quot;
#include &quot;mol_util.h&quot;
#include &quot;utilities.h&quot;
#include &quot;options.h&quot;
#include &quot;timer.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bcatmol_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627">main</link> (int argc, char **argv)</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bcatmol_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
            <listitem><para>const char * <link linkend="_bcatmol_8cpp_1a4de0ad4c7190962494815c0fa7f948df">use</link> []</para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>A program to concatenate coordinates from different files. </para>

<para><formalpara><title>Author: </title>

<para>Bernard Heymann </para>
</formalpara>
<formalpara><title>Date: </title>

<para>Created: 20031018 </para>

<para>Modified: 20170123 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bcatmol_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627"/>    <section>
    <title>main()</title>
<indexterm><primary>main</primary><secondary>bcatmol.cpp</secondary></indexterm>
<indexterm><primary>bcatmol.cpp</primary><secondary>main</secondary></indexterm>
<para><computeroutput>int main (int argc, char ** argv)</computeroutput></para><para>
Definition at line 45 of file bcatmol.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_bcatmol_8cpp_1a4de0ad4c7190962494815c0fa7f948df"/>    <section>
    <title>use</title>
<indexterm><primary>use</primary><secondary>bcatmol.cpp</secondary></indexterm>
<indexterm><primary>bcatmol.cpp</primary><secondary>use</secondary></indexterm>
<para><computeroutput>const char* use[]</computeroutput></para><emphasis role="strong">Initial value:</emphasis><programlisting>=&#32;{
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Usage:&#32;bcatmol&#32;[options]&#32;input.pdb&#32;[input2.pdb&#32;...]&quot;</emphasis>,
<emphasis role="stringliteral">&quot;---------------------------------------------------&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Concatenates&#32;sets&#32;of&#32;coordinates&#32;with&#32;shifts&#32;from&#32;sets&#32;of&#32;files.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Actions:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-select&#32;CA&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Atom&#32;selection&#32;(default&#32;all).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-rename&#32;D&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Rename&#32;molecules&#32;from&#32;the&#32;given&#32;letter.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Parameters:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-verbose&#32;7&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Verbosity&#32;of&#32;output.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-box&#32;10,10,10&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Size&#32;of&#32;enclosing&#32;box&#32;(angstrom,&#32;default&#32;from&#32;coordinates).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-pbc&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Resolve&#32;periodic&#32;boundary&#32;bonds&#32;before&#32;catenation.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Input:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-parameters&#32;parm.star&#32;&#32;&#32;&#32;Atomic&#32;properties&#32;parameter&#32;file&#32;(default&#32;atom_prop.star).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Output:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-output&#32;output.pdb&#32;&#32;&#32;&#32;&#32;&#32;&#32;Output&#32;coordinate&#32;file&#32;(default&#32;temp.pdb).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
NULL
}
</programlisting><para>
Definition at line 21 of file bcatmol.cpp.</para>
    </section><anchor xml:id="_bcatmol_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>bcatmol.cpp</secondary></indexterm>
<indexterm><primary>bcatmol.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
