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<section xmlns="http://docbook.org/ns/docbook" version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink" xml:id="_mol__param_8cpp">
<title>/Users/bernard/b20/bsoft/src/mol/mol_param.cpp File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/src/mol/mol_param.cpp</primary></indexterm>
<para>

<para>Functions to extract parameters from coordinate files. </para>
 
</para>
<programlisting>#include &quot;rwmolecule.h&quot;
#include &quot;rwmd.h&quot;
#include &quot;mol_bonds.h&quot;
#include &quot;Matrix.h&quot;
#include &quot;linked_list.h&quot;
#include &quot;utilities.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_struct_batomtype">Batomtype</link> * <link linkend="_mol__param_8cpp_1a582b16e61e1c849151621088fbaeb499">molgroup_get_atom_types</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, int elements)</para>

<para>Obtains atomic types from molecule groups. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmd">Bmd</link> * <link linkend="_mol__param_8cpp_1aa4165c67208fa1ed0d7a5bfba8750b14">md_calculate_parameters</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, int elements, int show_bond, int show_angle)</para>

<para>Calculates atomic parameters from molecule groups. </para>
</listitem>
        </itemizedlist>
</simplesect>
<simplesect>
    <title>Variables    </title>
        <itemizedlist>
            <listitem><para>int <link linkend="_mol__param_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453">verbose</link></para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Functions to extract parameters from coordinate files. </para>

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

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

<para>Created: 20050304 </para>

<para>Modified: 20090226 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_mol__param_8cpp_1aa4165c67208fa1ed0d7a5bfba8750b14"/>    <section>
    <title>md_calculate_parameters()</title>
<indexterm><primary>md_calculate_parameters</primary><secondary>mol_param.cpp</secondary></indexterm>
<indexterm><primary>mol_param.cpp</primary><secondary>md_calculate_parameters</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmd">Bmd</link>* md_calculate_parameters (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, int elements, int show_bond, int show_angle)</computeroutput></para><para>

<para>Calculates atomic parameters from molecule groups. </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>*molgroup</entry>
                                <entry>
<para>molecule group. </para>
</entry>
                            </row>
                            <row>
                                <entry>elements</entry>
                                <entry>
<para>flag to take atom types from element records. </para>
</entry>
                            </row>
                            <row>
                                <entry>show_bond</entry>
                                <entry>
<para>flag to show bonds. </para>
</entry>
                            </row>
                            <row>
                                <entry>show_angle</entry>
                                <entry>
<para>flag to show angles. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmd* molecular dynamics object, NULL on failure. </para>
</formalpara>
</para>
<para>
Definition at line 73 of file mol_param.cpp.</para>
    </section><anchor xml:id="_mol__param_8cpp_1a582b16e61e1c849151621088fbaeb499"/>    <section>
    <title>molgroup_get_atom_types()</title>
<indexterm><primary>molgroup_get_atom_types</primary><secondary>mol_param.cpp</secondary></indexterm>
<indexterm><primary>mol_param.cpp</primary><secondary>molgroup_get_atom_types</secondary></indexterm>
<para><computeroutput><link linkend="_struct_batomtype">Batomtype</link>* molgroup_get_atom_types (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, int elements)</computeroutput></para><para>

<para>Obtains atomic types from molecule groups. </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>*molgroup</entry>
                                <entry>
<para>molecule group. </para>
</entry>
                            </row>
                            <row>
                                <entry>elements</entry>
                                <entry>
<para>flag to take atom types from element records. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Batomtype* atom property structure, NULL on failure. </para>
</formalpara>
</para>
<para>
Definition at line 26 of file mol_param.cpp.</para>
</section>
</section>
<section>
<title>Variable Documentation</title>
<anchor xml:id="_mol__param_8cpp_1a0b2caeb4b6f130be43e5a2f0267dd453"/>    <section>
    <title>verbose</title>
<indexterm><primary>verbose</primary><secondary>mol_param.cpp</secondary></indexterm>
<indexterm><primary>mol_param.cpp</primary><secondary>verbose</secondary></indexterm>
<para><computeroutput>int verbose</computeroutput></para></section>
</section>
</section>
