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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__bonds_8h">
<title>/Users/bernard/b20/bsoft/include/mol_bonds.h File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/include/mol_bonds.h</primary></indexterm>
<para>

<para>Header for molecular dynamics. </para>
 
</para>
<programlisting>#include &quot;rwmd.h&quot;
#include &quot;rwmolecule.h&quot;
#include &quot;mol_util.h&quot;
#include &quot;utilities.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_struct_bbond">Bbond</link> * <link linkend="_mol__bonds_8h_1a82071e30f389173d52cb38fe9b67f371">md_generate_bond_list</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, <link linkend="_struct_bmd">Bmd</link> *md)</para>

<para>Generates a distance-based bond list. </para>
</listitem>
            <listitem><para><link linkend="_struct_bbond">Bbond</link> * <link linkend="_mol__bonds_8h_1a284fd2d1723a6d24b578755891506784">md_generate_molecular_bond_list</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, <link linkend="_struct_bmd">Bmd</link> *md)</para>

<para>Generates an intramolecular distance-based bond list. </para>
</listitem>
            <listitem><para><link linkend="_struct_bbond">Bbond</link> * <link linkend="_mol__bonds_8h_1afb9f125fd976feaae28962fd41d1bf7a">md_generate_bond_list_with_valence</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, <link linkend="_struct_bmd">Bmd</link> *md, int valence)</para>

<para>Generates a bond list based on a single valence and the shortest current bond lengths. </para>
</listitem>
            <listitem><para>double <link linkend="_mol__bonds_8h_1ada61ddbf0a924df1e0453f37f3047971">md_bond_list_set_parameters</link> (<link linkend="_struct_bbond">Bbond</link> *bondlist, <link linkend="_struct_bbondtype">Bbondtype</link> *bondtype)</para>

<para>Assigns covalent bond lengths to bonds. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__bonds_8h_1a7ce12a42d5adfebc7272a3ad670a68fe">md_show_bonds</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Shows the bonds and bond lengths. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__bonds_8h_1ab146b9627db5f6a6ace82ed64fc03938">md_show_angles</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Shows the angles and angular sizes. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__bonds_8h_1aeae7188cf8383bd44a2ed7c53b348f47">md_show_bond_stats</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Shows the number of bonds and the valency per atom. </para>
</listitem>
            <listitem><para><link linkend="_struct_bangle">Bangle</link> * <link linkend="_mol__bonds_8h_1a30566baa97aae4844587d8d821ca4014">md_generate_angle_list</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, <link linkend="_struct_bmd">Bmd</link> *md)</para>

<para>Generates an angle list. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__bonds_8h_1a45604db3ba3c35d9757c1a7249819aa9">md_angle_list_set_parameters</link> (<link linkend="_struct_bangle">Bangle</link> *anglelist, <link linkend="_struct_bangletype">Bangletype</link> *angletype)</para>

<para>Assigns angles from angle types. </para>
</listitem>
            <listitem><para>double <link linkend="_mol__bonds_8h_1af8659d56988fb97f12888723c6d4460a">md_find_bond_length</link> (<link linkend="_struct_batom">Batom</link> *atom1, <link linkend="_struct_batom">Batom</link> *atom2, <link linkend="_struct_bbondtype">Bbondtype</link> *bondtype)</para>

<para>Finds the reference covalent bond length. </para>
</listitem>
            <listitem><para><link linkend="_struct_bbondtype">Bbondtype</link> * <link linkend="_mol__bonds_8h_1a142f8db66160e96617f9bd1198a36da0">md_find_bond_type</link> (<link linkend="_struct_batom">Batom</link> *atom1, <link linkend="_struct_batom">Batom</link> *atom2, <link linkend="_struct_bbondtype">Bbondtype</link> *bondtype)</para>

<para>Finds the bond type. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__bonds_8h_1a57825d03f4d0b21bd9a3aa04122b250c">md_show_bond_types</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, <link linkend="_struct_bbondtype">Bbondtype</link> *bondtype)</para>

<para>Shows the bond type composition. </para>
</listitem>
            <listitem><para>double <link linkend="_mol__bonds_8h_1a17515e95f0c97cc1a2d15ffa4fccf33a">md_angle</link> (<link linkend="_struct_batom">Batom</link> *atom1, <link linkend="_struct_batom">Batom</link> *atom2, <link linkend="_struct_batom">Batom</link> *atom3)</para>

<para>Calculates the angle between three atoms. </para>
</listitem>
            <listitem><para><link linkend="_struct_bangletype">Bangletype</link> * <link linkend="_mol__bonds_8h_1a5c89c49cc2a3758901a90d97e452d8ea">md_find_angle_type</link> (<link linkend="_struct_batom">Batom</link> *atom1, <link linkend="_struct_batom">Batom</link> *atom2, <link linkend="_struct_batom">Batom</link> *atom3, <link linkend="_struct_bangletype">Bangletype</link> *angletype)</para>

<para>Finds the reference angle type between three atoms. </para>
</listitem>
            <listitem><para>double <link linkend="_mol__bonds_8h_1aef962053af35fecdccd972e5dc90e3c4">md_find_angle</link> (<link linkend="_struct_batom">Batom</link> *atom1, <link linkend="_struct_batom">Batom</link> *atom2, <link linkend="_struct_batom">Batom</link> *atom3, <link linkend="_struct_bangletype">Bangletype</link> *angletype)</para>

<para>Finds the reference angle between three atoms. </para>
</listitem>
            <listitem><para>double <link linkend="_mol__bonds_8h_1a4e67d8d19920ea0e70cd8d1459456007">md_calculate_deviations</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, int wrap)</para>

<para>Calculates deviations from the reference bond lengths and angles. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__bonds_8h_1a67ade9c1669f284c9b30e2472549f482">md_calculate_radial_deviation</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Calculates the radial deviations from the center of the box. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Header for molecular dynamics. </para>

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

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

<para>Created: 20010828 </para>

<para>Modified: 20180228 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_mol__bonds_8h_1a17515e95f0c97cc1a2d15ffa4fccf33a"/>    <section>
    <title>md_angle()</title>
<indexterm><primary>md_angle</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_angle</secondary></indexterm>
<para><computeroutput>double md_angle (<link linkend="_struct_batom">Batom</link> * atom1, <link linkend="_struct_batom">Batom</link> * atom2, <link linkend="_struct_batom">Batom</link> * atom3)</computeroutput></para><para>

<para>Calculates the angle between three atoms. </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>*atom1</entry>
                                <entry>
<para>first atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom2</entry>
                                <entry>
<para>second atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom3</entry>
                                <entry>
<para>third atom. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>double angle. <literallayout><computeroutput>The angle associated with the second atom and between the bonds linking
the first and third atoms is calculated.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 637 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a45604db3ba3c35d9757c1a7249819aa9"/>    <section>
    <title>md_angle_list_set_parameters()</title>
<indexterm><primary>md_angle_list_set_parameters</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_angle_list_set_parameters</secondary></indexterm>
<para><computeroutput>int md_angle_list_set_parameters (<link linkend="_struct_bangle">Bangle</link> * anglelist, <link linkend="_struct_bangletype">Bangletype</link> * angletype)</computeroutput></para><para>

<para>Assigns angles from angle types. </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>*anglelist</entry>
                                <entry>
<para>list of angles. </para>
</entry>
                            </row>
                            <row>
                                <entry>*angletype</entry>
                                <entry>
<para>list of angle types. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>The angles are taken from an angle type list.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 485 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1ada61ddbf0a924df1e0453f37f3047971"/>    <section>
    <title>md_bond_list_set_parameters()</title>
<indexterm><primary>md_bond_list_set_parameters</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_bond_list_set_parameters</secondary></indexterm>
<para><computeroutput>double md_bond_list_set_parameters (<link linkend="_struct_bbond">Bbond</link> * bondlist, <link linkend="_struct_bbondtype">Bbondtype</link> * bondtype)</computeroutput></para><para>

<para>Assigns covalent bond lengths to bonds. </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>*bondlist</entry>
                                <entry>
<para>list of bonds. </para>
</entry>
                            </row>
                            <row>
                                <entry>*bondtype</entry>
                                <entry>
<para>list of bond types. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>double fraction of bond types found. <literallayout><computeroutput>The bond lengths are taken from a bond type list.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 299 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a4e67d8d19920ea0e70cd8d1459456007"/>    <section>
    <title>md_calculate_deviations()</title>
<indexterm><primary>md_calculate_deviations</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_calculate_deviations</secondary></indexterm>
<para><computeroutput>double md_calculate_deviations (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, int wrap)</computeroutput></para><para>

<para>Calculates deviations from the reference bond lengths and angles. </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>wrap</entry>
                                <entry>
<para>flag to wrap around periodic boundaries. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>double angle. </para>
</formalpara>
</para>
<para>
Definition at line 742 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a67ade9c1669f284c9b30e2472549f482"/>    <section>
    <title>md_calculate_radial_deviation()</title>
<indexterm><primary>md_calculate_radial_deviation</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_calculate_radial_deviation</secondary></indexterm>
<para><computeroutput>int md_calculate_radial_deviation (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Calculates the radial deviations from the center of the box. </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>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>double angle. </para>
</formalpara>
</para>
<para>
Definition at line 809 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1aef962053af35fecdccd972e5dc90e3c4"/>    <section>
    <title>md_find_angle()</title>
<indexterm><primary>md_find_angle</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_find_angle</secondary></indexterm>
<para><computeroutput>double md_find_angle (<link linkend="_struct_batom">Batom</link> * atom1, <link linkend="_struct_batom">Batom</link> * atom2, <link linkend="_struct_batom">Batom</link> * atom3, <link linkend="_struct_bangletype">Bangletype</link> * angletype)</computeroutput></para><para>

<para>Finds the reference angle between three atoms. </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>*atom1</entry>
                                <entry>
<para>first atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom2</entry>
                                <entry>
<para>second atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom3</entry>
                                <entry>
<para>third atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*angletype</entry>
                                <entry>
<para>angle type list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>double angle. <literallayout><computeroutput>The angle type is found in the angle type list, and the angle is
set from the angle type structure.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 719 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a5c89c49cc2a3758901a90d97e452d8ea"/>    <section>
    <title>md_find_angle_type()</title>
<indexterm><primary>md_find_angle_type</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_find_angle_type</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bangletype">Bangletype</link>* md_find_angle_type (<link linkend="_struct_batom">Batom</link> * atom1, <link linkend="_struct_batom">Batom</link> * atom2, <link linkend="_struct_batom">Batom</link> * atom3, <link linkend="_struct_bangletype">Bangletype</link> * angletype)</computeroutput></para><para>

<para>Finds the reference angle type between three atoms. </para>
</para>

<para><literallayout><computeroutput>The angle type is found in the angle type list, and the angle type is
returned.
</computeroutput></literallayout></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>*atom1</entry>
                                <entry>
<para>first atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom2</entry>
                                <entry>
<para>second atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom3</entry>
                                <entry>
<para>third atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*angletype</entry>
                                <entry>
<para>angle type list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bangletype* angle type. </para>
</formalpara>
</para>
<para>
Definition at line 663 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1af8659d56988fb97f12888723c6d4460a"/>    <section>
    <title>md_find_bond_length()</title>
<indexterm><primary>md_find_bond_length</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_find_bond_length</secondary></indexterm>
<para><computeroutput>double md_find_bond_length (<link linkend="_struct_batom">Batom</link> * atom1, <link linkend="_struct_batom">Batom</link> * atom2, <link linkend="_struct_bbondtype">Bbondtype</link> * bondtype)</computeroutput></para><para>

<para>Finds the reference covalent bond length. </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>*atom1</entry>
                                <entry>
<para>first atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom2</entry>
                                <entry>
<para>second atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*bondtype</entry>
                                <entry>
<para>bond type list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>double bond length. <literallayout><computeroutput>The bond type is found in the bond type list, and the bond length is
set from the bond type structure.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 510 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a142f8db66160e96617f9bd1198a36da0"/>    <section>
    <title>md_find_bond_type()</title>
<indexterm><primary>md_find_bond_type</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_find_bond_type</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bbondtype">Bbondtype</link>* md_find_bond_type (<link linkend="_struct_batom">Batom</link> * atom1, <link linkend="_struct_batom">Batom</link> * atom2, <link linkend="_struct_bbondtype">Bbondtype</link> * bondtype)</computeroutput></para><para>

<para>Finds the bond type. </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>*atom1</entry>
                                <entry>
<para>first atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*atom2</entry>
                                <entry>
<para>second atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>*bondtype</entry>
                                <entry>
<para>bond type list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bbondtype* bond type structure. <literallayout><computeroutput>The bond type is found in the bond type list.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 542 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a30566baa97aae4844587d8d821ca4014"/>    <section>
    <title>md_generate_angle_list()</title>
<indexterm><primary>md_generate_angle_list</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_generate_angle_list</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bangle">Bangle</link>* md_generate_angle_list (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, <link linkend="_struct_bmd">Bmd</link> * md)</computeroutput></para><para>

<para>Generates an angle list. </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 structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>*md</entry>
                                <entry>
<para>global molecular dynamics structure (can be NULL). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bangle* new angle list. <literallayout><computeroutput>This function uses the bond list for the molecule group to find bonds
to the same atom and set an angle structure with the corresponding angle.
The angle is defined in the molecular dynamics structure.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 415 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a82071e30f389173d52cb38fe9b67f371"/>    <section>
    <title>md_generate_bond_list()</title>
<indexterm><primary>md_generate_bond_list</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_generate_bond_list</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bbond">Bbond</link>* md_generate_bond_list (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, <link linkend="_struct_bmd">Bmd</link> * md)</computeroutput></para><para>

<para>Generates a distance-based bond list. </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 structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>*md</entry>
                                <entry>
<para>global molecular dynamics structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bbond* new bond list. <literallayout><computeroutput>This function assumes very little and defines bonds purely on distance.
This means that the bond distances must already have been defined well.
The bond length is defined in the molecular dynamics structure.
If the molecule group already has a bond list, no new bonds are generated. 
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 30 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1afb9f125fd976feaae28962fd41d1bf7a"/>    <section>
    <title>md_generate_bond_list_with_valence()</title>
<indexterm><primary>md_generate_bond_list_with_valence</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_generate_bond_list_with_valence</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bbond">Bbond</link>* md_generate_bond_list_with_valence (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, <link linkend="_struct_bmd">Bmd</link> * md, int valence)</computeroutput></para><para>

<para>Generates a bond list based on a single valence and the shortest current bond lengths. </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 structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>*md</entry>
                                <entry>
<para>global molecular dynamics structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>valence</entry>
                                <entry>
<para>atom valence. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bbond* new bond list. <literallayout><computeroutput>This function attempts to assign bonds based on atomic valence by
finding the top number of shortests bonds. The current bond length is
encoded in the bond strength variable, k, in the bond structure.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 208 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a284fd2d1723a6d24b578755891506784"/>    <section>
    <title>md_generate_molecular_bond_list()</title>
<indexterm><primary>md_generate_molecular_bond_list</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_generate_molecular_bond_list</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bbond">Bbond</link>* md_generate_molecular_bond_list (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, <link linkend="_struct_bmd">Bmd</link> * md)</computeroutput></para><para>

<para>Generates an intramolecular distance-based bond list. </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 structure. </para>
</entry>
                            </row>
                            <row>
                                <entry>*md</entry>
                                <entry>
<para>global molecular dynamics structure. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bbond* new bond list. <literallayout><computeroutput>This function defines bonds on distance and within molecules.
This means that the bond distances must already have been defined well.
The bond length is defined in the molecular dynamics structure.
If the molecule group already has a bond list, no new bonds are generated. 
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 105 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1ab146b9627db5f6a6ace82ed64fc03938"/>    <section>
    <title>md_show_angles()</title>
<indexterm><primary>md_show_angles</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_show_angles</secondary></indexterm>
<para><computeroutput>int md_show_angles (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Shows the angles and angular sizes. </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>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of angles. <literallayout><computeroutput>Uses the angle list defined for the molecule group.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 350 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1aeae7188cf8383bd44a2ed7c53b348f47"/>    <section>
    <title>md_show_bond_stats()</title>
<indexterm><primary>md_show_bond_stats</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_show_bond_stats</secondary></indexterm>
<para><computeroutput>int md_show_bond_stats (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Shows the number of bonds and the valency per atom. </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>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of bonds. <literallayout><computeroutput>Uses the bond list defined for the molecule group.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 371 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a57825d03f4d0b21bd9a3aa04122b250c"/>    <section>
    <title>md_show_bond_types()</title>
<indexterm><primary>md_show_bond_types</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_show_bond_types</secondary></indexterm>
<para><computeroutput>int md_show_bond_types (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, <link linkend="_struct_bbondtype">Bbondtype</link> * bondtype)</computeroutput></para><para>

<para>Shows the bond type composition. </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>*bondtype</entry>
                                <entry>
<para>bond type list. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. <literallayout><computeroutput>For each bond, the bond type is found in the bond type list.
The number variable for each bond type is used for counting.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 580 of file mol_bonds.cpp.</para>
    </section><anchor xml:id="_mol__bonds_8h_1a7ce12a42d5adfebc7272a3ad670a68fe"/>    <section>
    <title>md_show_bonds()</title>
<indexterm><primary>md_show_bonds</primary><secondary>mol_bonds.h</secondary></indexterm>
<indexterm><primary>mol_bonds.h</primary><secondary>md_show_bonds</secondary></indexterm>
<para><computeroutput>int md_show_bonds (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Shows the bonds and bond lengths. </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>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int number of bonds. <literallayout><computeroutput>Uses the bond list defined for the molecule group.
</computeroutput></literallayout> </para>
</formalpara>
</para>
<para>
Definition at line 329 of file mol_bonds.cpp.</para>
</section>
</section>
</section>
