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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_bflat_8cpp">
<title>/Users/bernard/b20/bsoft/src/bflat.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/bflat.cpp</primary></indexterm>
<para>

<para>Solvent flattening. </para>
 
</para>
<programlisting>#include &quot;rwimg.h&quot;
#include &quot;symmetry.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="_bflat_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627">main</link> (int argc, char **argv)</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_bflat_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
            <listitem><para>const char * <link linkend="_bflat_8cpp_1a4de0ad4c7190962494815c0fa7f948df">use</link> []</para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Solvent flattening. </para>

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

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

<para>Created: 20041113 </para>

<para>Modified: 20150717 <literallayout><computeroutput>An implementation based on the method proposed in:
van Heel, M. (2001). &quot;Do single (ribosome) molecules phase themselves?&quot; Cold Spring Harb Symp Quant Biol 66: 77-86.
</computeroutput></literallayout> </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_bflat_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627"/>    <section>
    <title>main()</title>
<indexterm><primary>main</primary><secondary>bflat.cpp</secondary></indexterm>
<indexterm><primary>bflat.cpp</primary><secondary>main</secondary></indexterm>
<para><computeroutput>int main (int argc, char ** argv)</computeroutput></para><para>
Definition at line 51 of file bflat.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_bflat_8cpp_1a4de0ad4c7190962494815c0fa7f948df"/>    <section>
    <title>use</title>
<indexterm><primary>use</primary><secondary>bflat.cpp</secondary></indexterm>
<indexterm><primary>bflat.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;bflat&#32;[options]&#32;input.img&#32;output.img&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-------------------------------------------&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Does&#32;phase&#32;extension&#32;by&#32;solvent&#32;flattening.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;The&#32;amplitudes&#32;are&#32;defined&#32;in&#32;three&#32;possible&#32;mutually&#32;exclusive&#32;ways:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;1.&#32;Derived&#32;from&#32;the&#32;input&#32;map&#32;(default).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;2.&#32;Derived&#32;from&#32;a&#32;reference&#32;map.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;3.&#32;Specified&#32;in&#32;an&#32;external&#32;amplitude&#32;map.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Actions:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-symmetrize&#32;C5&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Apply&#32;point&#32;group&#32;symmetry.&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;-datatype&#32;u&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Force&#32;writing&#32;of&#32;a&#32;new&#32;data&#32;type.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-resolution&#32;35,15.5,1.5&#32;&#32;Resolution&#32;limit&#32;start,&#32;end&#32;and&#32;step&#32;(default&#32;30,20,1).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-iterations&#32;80&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Iterations&#32;(default&#32;1).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-exit&#32;0.1&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Exit&#32;condition&#32;based&#32;on&#32;amplitude&#32;RMSD&#32;(default&#32;0.01).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-output&#32;5&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Number&#32;of&#32;iterations&#32;between&#32;writing&#32;output&#32;maps&#32;(default&#32;100).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
<emphasis role="stringliteral">&quot;Input:&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-Reference&#32;file.map&#32;&#32;&#32;&#32;&#32;&#32;File&#32;to&#32;generate&#32;amplitudes&#32;from&#32;(default&#32;amplitudes&#32;from&#32;input&#32;map).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-Amplitudes&#32;file.map&#32;&#32;&#32;&#32;&#32;File&#32;with&#32;amplitudes&#32;(default&#32;amplitudes&#32;from&#32;input&#32;map).&quot;</emphasis>,
<emphasis role="stringliteral">&quot;-Mask&#32;mask.tif&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;&#32;Mask&#32;file.&quot;</emphasis>,
<emphasis role="stringliteral">&quot;&#32;&quot;</emphasis>,
NULL
}
</programlisting><para>
Definition at line 22 of file bflat.cpp.</para>
    </section><anchor xml:id="_bflat_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>bflat.cpp</secondary></indexterm>
<indexterm><primary>bflat.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
