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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_bmark_8cpp">
<title>/Users/bernard/b20/bsoft/src/bmark.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/bmark.cpp</primary></indexterm>
<para>

<para>Program to generate symmetry axes for mark group symmetries. </para>
 
</para>
<programlisting>#include &quot;rwmg.h&quot;
#include &quot;mg_processing.h&quot;
#include &quot;mg_tomography.h&quot;
#include &quot;mg_marker.h&quot;
#include &quot;marker.h&quot;
#include &quot;file_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="_bmark_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627">main</link> (int argc, char **argv)</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bmark_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
            <listitem><para>const char * <link linkend="_bmark_8cpp_1a4de0ad4c7190962494815c0fa7f948df">use</link> []</para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Program to generate symmetry axes for mark group symmetries. </para>

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

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

<para>Created: 20020619 </para>

<para>Modified: 20150212 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bmark_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627"/>    <section>
    <title>main()</title>
<indexterm><primary>main</primary><secondary>bmark.cpp</secondary></indexterm>
<indexterm><primary>bmark.cpp</primary><secondary>main</secondary></indexterm>
<para><computeroutput>int main (int argc, char ** argv)</computeroutput></para><para>
Definition at line 50 of file bmark.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_bmark_8cpp_1a4de0ad4c7190962494815c0fa7f948df"/>    <section>
    <title>use</title>
<indexterm><primary>use</primary><secondary>bmark.cpp</secondary></indexterm>
<indexterm><primary>bmark.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;bmark&#32;[options]&#32;in.star&#32;[in2.star...]&quot;</emphasis>,
<emphasis role="stringliteral">&quot;--------------------------------------------&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Operates&#32;on&#32;sets&#32;of&#32;micrograph&#32;markers.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Actions:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-reconstructions&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Operate&#32;on&#32;reconstruction&#32;parameters&#32;rather&#32;than&#32;micrographs.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-list&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;List&#32;all&#32;micrograph&#32;and&#32;reconstruction&#32;markers.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-rotate&#32;0.3,0.1,-0.5,81&#32;&#32;Rotate&#32;around&#32;an&#32;axis&#32;by&#32;an&#32;angle.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-scale&#32;0.5,3,1&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Scale.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-translate&#32;12.2,0.5,-50&#32;&#32;Shift&#32;after&#32;rotation&#32;and&#32;scaling.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-plane&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Calculate&#32;a&#32;plane&#32;through&#32;the&#32;markers.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-fom&#32;0.55&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Select&#32;markers&#32;with&#32;a&#32;figure-of-merit&#32;above&#32;this&#32;cutoff.&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;-origin&#32;0,22.5,30&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Set&#32;the&#32;origin&#32;for&#32;rotation.&quot;</emphasis>,

<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Output:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-output&#32;out.star&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Output&#32;micrograph&#32;parameter&#32;file.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
NULL
}
</programlisting><para>
Definition at line 24 of file bmark.cpp.</para>
    </section><anchor xml:id="_bmark_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>bmark.cpp</secondary></indexterm>
<indexterm><primary>bmark.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
