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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_jviews_8cpp">
<title>/Users/bernard/b20/bsoft/src/jviews.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/jviews.cpp</primary></indexterm>
<para>

<para>Generates views covering an asymmetric unit or all symmetry related views. </para>
 
</para>
<programlisting>#include &quot;rwstar.h&quot;
#include &quot;rwmg.h&quot;
#include &quot;utilities.h&quot;
#include &quot;options.h&quot;
#include &quot;timer.h&quot;
#include &quot;mg_processing.h&quot;
#include &quot;mg_extract.h&quot;
#include &quot;mg_subtomo.h&quot;
#include &quot;spline.h&quot;
#include &quot;random_numbers.h&quot;
#include &lt;fstream&gt;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_jviews_8cpp_1a6b991a49a3ad87a3f229f91fba822c10">pdb_matrices_from_particles</link> (<link linkend="_struct_bparticle">Bparticle</link> *part, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; sampling, <link linkend="_class_bstring">Bstring</link> &amp;filename)</para>

<para>Generates PDB file matrices from particle views and locations. </para>
</listitem>
            <listitem><para>int <link linkend="_jviews_8cpp_1a526776ad1347407f26edbbcb5b2ee5f5">cmm_views</link> (<link linkend="_class_bstring">Bstring</link> &amp;filename, <link linkend="_struct_bparticle">Bparticle</link> *part, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; sampling, long part_sel, double fom_cutoff, double colorfom_min, double colorfom_max, <link linkend="_class_r_g_b">RGB</link>&lt; double &gt; color, double diameter, double <link linkend="__vector3_8h_1a7baf5ed670fcf9bcca9a3a400820e292">length</link>, double thickness)</para>
</listitem>
            <listitem><para>int <link linkend="_jviews_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627">main</link> (int argc, char **argv)</para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_jviews_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
            <listitem><para>const char * <link linkend="_jviews_8cpp_1a4de0ad4c7190962494815c0fa7f948df">use</link> []</para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Generates views covering an asymmetric unit or all symmetry related views. </para>

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

<para>Juha Huiskonen </para>

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

<para>Created: 20071203 </para>

<para>Modified: 20080925 </para>

<para>Modified: 20081126 added shift option </para>

<para>Modified: 20090204 added asymmetric unit views </para>

<para>Modified: 20090205 added random views </para>

<para>Modified: 20090206 added PDB output </para>

<para>Modified: 20090408 added generate views option </para>

<para>Modified: 20100527 added -Grid option </para>

<para>Modified: 20110510 changed the orientation of the views when creating a Chimera marker file </para>

<para>Modified: 20111208 added -Top option </para>

<para>Modified: 20120123 (BH) </para>

<para>Modified: 20120316 added -randomizealpha option </para>

<para>Modified: 20150108 (BH) - incorporated into Bsoft <literallayout><computeroutput>Writes particle views into a Chimera markerfile for visualization
Writes particle orientations into a PDB file as BIOIMT matrices 
(these can be combined with a pseudoatomic model of the template, and all orientations 
can be visualized in Chimera)
</computeroutput></literallayout> </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_jviews_8cpp_1a526776ad1347407f26edbbcb5b2ee5f5"/>    <section>
    <title>cmm_views()</title>
<indexterm><primary>cmm_views</primary><secondary>jviews.cpp</secondary></indexterm>
<indexterm><primary>jviews.cpp</primary><secondary>cmm_views</secondary></indexterm>
<para><computeroutput>int cmm_views (<link linkend="_class_bstring">Bstring</link> &amp; filename, <link linkend="_struct_bparticle">Bparticle</link> * part, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; sampling, long part_sel, double fom_cutoff, double colorfom_min, double colorfom_max, <link linkend="_class_r_g_b">RGB</link>&lt; double &gt; color, double diameter, double length, double thickness)</computeroutput></para><para>
Definition at line 78 of file jviews.cpp.</para>
    </section><anchor xml:id="_jviews_8cpp_1a3c04138a5bfe5d72780bb7e82a18e627"/>    <section>
    <title>main()</title>
<indexterm><primary>main</primary><secondary>jviews.cpp</secondary></indexterm>
<indexterm><primary>jviews.cpp</primary><secondary>main</secondary></indexterm>
<para><computeroutput>int main (int argc, char ** argv)</computeroutput></para><para>
Definition at line 208 of file jviews.cpp.</para>
    </section><anchor xml:id="_jviews_8cpp_1a6b991a49a3ad87a3f229f91fba822c10"/>    <section>
    <title>pdb_matrices_from_particles()</title>
<indexterm><primary>pdb_matrices_from_particles</primary><secondary>jviews.cpp</secondary></indexterm>
<indexterm><primary>jviews.cpp</primary><secondary>pdb_matrices_from_particles</secondary></indexterm>
<para><computeroutput>int pdb_matrices_from_particles (<link linkend="_struct_bparticle">Bparticle</link> * part, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; sampling, <link linkend="_class_bstring">Bstring</link> &amp; filename)</computeroutput></para><para>

<para>Generates PDB file matrices from particle views and locations. </para>
</para>

<para>
                <formalpara>
                    <title>
Parameters                    </title>
                    <para>
                    <table frame="all">
                        <tgroup cols="2" align="left" colsep="1" rowsep="1">
                        <colspec colwidth="1*"/>
                        <colspec colwidth="4*"/>
                        <tbody>
                            <row>
                                <entry>*part</entry>
                                <entry>
<para>list of particles. </para>
</entry>
                            </row>
                            <row>
                                <entry>sampling</entry>
                                <entry>
<para>spatial sampling. </para>
</entry>
                            </row>
                            <row>
                                <entry>&amp;filename</entry>
                                <entry>
<para>PDB file with matrices. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. Writes a PDB file. Uses the BIOMT records. </para>
</formalpara>
</para>
<para>
Definition at line 51 of file jviews.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_jviews_8cpp_1a4de0ad4c7190962494815c0fa7f948df"/>    <section>
    <title>use</title>
<indexterm><primary>use</primary><secondary>jviews.cpp</secondary></indexterm>
<indexterm><primary>jviews.cpp</primary><secondary>use</secondary></indexterm>
<para><computeroutput>const char* use[]</computeroutput></para><para>
Definition at line 162 of file jviews.cpp.</para>
    </section><anchor xml:id="_jviews_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>jviews.cpp</secondary></indexterm>
<indexterm><primary>jviews.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
