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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__alpha_8h">
<title>/Users/bernard/b20/bsoft/include/mol_alpha.h File Reference</title>
<indexterm><primary>/Users/bernard/b20/bsoft/include/mol_alpha.h</primary></indexterm>
<para>

<para>Header for functions to make and analyze alpha helices. </para>
 
</para>
<programlisting>#include &quot;rwmolecule.h&quot;
</programlisting><simplesect>
    <title>Functions    </title>
        <itemizedlist>
            <listitem><para><link linkend="_struct_bmolgroup">Bmolgroup</link> * <link linkend="_mol__alpha_8h_1a9907d81ba9424ab77ffc80f79c9911cc">molgroup_generate_alpha_helix</link> (int <link linkend="__vector3_8h_1a7baf5ed670fcf9bcca9a3a400820e292">length</link>)</para>

<para>Generates an alpha helix of the desired length. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmolecule">Bmolecule</link> * <link linkend="_mol__alpha_8h_1a09993da8a0c1e7413ba48a501210dcc3">mol_generate_alpha_helix</link> (int <link linkend="__vector3_8h_1a7baf5ed670fcf9bcca9a3a400820e292">length</link>)</para>

<para>Generates an alpha helix of the desired length. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__alpha_8h_1a4778e0f1a9ec6198c89072fe3a651a9d">molgroup_set_alpha_helix</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup, int helix_start, int helix_end)</para>

<para>Sets a residue range to an alpha helix in all molecules. </para>
</listitem>
            <listitem><para>int <link linkend="_mol__alpha_8h_1ae1768f69d8e49d79a58b28c2fa9bfc00">molgroup_find_helical_axes</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Calculates the centers and orientations of all alpha helices. </para>
</listitem>
            <listitem><para><link linkend="_class_vector3">Vector3</link>&lt; double &gt; <link linkend="_mol__alpha_8h_1a9ebdc7dbc703102528718669001fdf90">alpha_find_center</link> (<link linkend="_struct_bresidue">Bresidue</link> *resfirst, <link linkend="_struct_bresidue">Bresidue</link> *reslast)</para>

<para>Calculates the center of an alpha helix. </para>
</listitem>
            <listitem><para><link linkend="_class_vector3">Vector3</link>&lt; double &gt; <link linkend="_mol__alpha_8h_1a913b36307fc4e0c871c114b4a2fd0721">alpha_find_orientation</link> (<link linkend="_struct_bresidue">Bresidue</link> *resfirst, <link linkend="_struct_bresidue">Bresidue</link> *reslast)</para>

<para>Calculates the orientation of an alpha helix. </para>
</listitem>
            <listitem><para><link linkend="_class_vector3">Vector3</link>&lt; double &gt; <link linkend="_mol__alpha_8h_1a0942ce93360e5b71f01b9fd81279505b">mol_find_alpha_orientation</link> (<link linkend="_struct_bmolecule">Bmolecule</link> *mol, int set_std)</para>

<para>Calculates the orientation of an alpha helix. </para>
</listitem>
            <listitem><para><link linkend="_class_vector3">Vector3</link>&lt; double &gt; <link linkend="_mol__alpha_8h_1ac496c23bbcbc4d267041265c4e3d7fbf">point_on_helix_axis</link> (<link linkend="_class_vector3">Vector3</link>&lt; double &gt; ca1, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; ca2, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; ca3)</para>

<para>Calculates a point on an alpha helix corresponding to a Ca atom. </para>
</listitem>
            <listitem><para><link linkend="_struct_bmolgroup">Bmolgroup</link> * <link linkend="_mol__alpha_8h_1aca26aaa716d72e585cec9196407443ee">molgroup_consolidate_alpha</link> (<link linkend="_struct_bmolgroup">Bmolgroup</link> *molgroup)</para>

<para>Cluster a set of alpha helices to consolidate helices. </para>
</listitem>
        </itemizedlist>
</simplesect>
<section>
<title>Detailed Description</title>

<para>Header for functions to make and analyze alpha helices. </para>

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

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

<para>Created: 20050315 </para>

<para>Modified: 20060121 </para>
</formalpara>
</para>
</section>
<section>
<title>Function Documentation</title>
<anchor xml:id="_mol__alpha_8h_1a9ebdc7dbc703102528718669001fdf90"/>    <section>
    <title>alpha_find_center()</title>
<indexterm><primary>alpha_find_center</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>alpha_find_center</secondary></indexterm>
<para><computeroutput><link linkend="_class_vector3">Vector3</link>&lt;double&gt; alpha_find_center (<link linkend="_struct_bresidue">Bresidue</link> * resfirst, <link linkend="_struct_bresidue">Bresidue</link> * reslast)</computeroutput></para><para>

<para>Calculates the center of an alpha helix. </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>*resfirst</entry>
                                <entry>
<para>first residue in helix. </para>
</entry>
                            </row>
                            <row>
                                <entry>*reslast</entry>
                                <entry>
<para>last residue in helix. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para><link linkend="_class_vector3">Vector3&lt;double&gt;</link> center. </para>
</formalpara>
</para>
<para>
Definition at line 179 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1a913b36307fc4e0c871c114b4a2fd0721"/>    <section>
    <title>alpha_find_orientation()</title>
<indexterm><primary>alpha_find_orientation</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>alpha_find_orientation</secondary></indexterm>
<para><computeroutput><link linkend="_class_vector3">Vector3</link>&lt;double&gt; alpha_find_orientation (<link linkend="_struct_bresidue">Bresidue</link> * resfirst, <link linkend="_struct_bresidue">Bresidue</link> * reslast)</computeroutput></para><para>

<para>Calculates the orientation of an alpha helix. </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>*resfirst</entry>
                                <entry>
<para>first residue in helix. </para>
</entry>
                            </row>
                            <row>
                                <entry>*reslast</entry>
                                <entry>
<para>last residue in helix. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para><link linkend="_class_vector3">Vector3&lt;double&gt;</link> axis. </para>
</formalpara>
</para>
<para>
Definition at line 208 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1a0942ce93360e5b71f01b9fd81279505b"/>    <section>
    <title>mol_find_alpha_orientation()</title>
<indexterm><primary>mol_find_alpha_orientation</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>mol_find_alpha_orientation</secondary></indexterm>
<para><computeroutput><link linkend="_class_vector3">Vector3</link>&lt;double&gt; mol_find_alpha_orientation (<link linkend="_struct_bmolecule">Bmolecule</link> * mol, int set_std)</computeroutput></para><para>

<para>Calculates the orientation of an alpha helix. </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>*mol</entry>
                                <entry>
<para>molecule. </para>
</entry>
                            </row>
                            <row>
                                <entry>set_std</entry>
                                <entry>
<para>rotate and shift to a standard orientation. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para><link linkend="_class_vector3">Vector3&lt;double&gt;</link> axis. </para>
</formalpara>
</para>
<para>
Definition at line 249 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1a09993da8a0c1e7413ba48a501210dcc3"/>    <section>
    <title>mol_generate_alpha_helix()</title>
<indexterm><primary>mol_generate_alpha_helix</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>mol_generate_alpha_helix</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmolecule">Bmolecule</link>* mol_generate_alpha_helix (int length)</computeroutput></para><para>

<para>Generates an alpha helix of the desired 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>length</entry>
                                <entry>
<para>number of alanines to generate. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 68 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1aca26aaa716d72e585cec9196407443ee"/>    <section>
    <title>molgroup_consolidate_alpha()</title>
<indexterm><primary>molgroup_consolidate_alpha</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>molgroup_consolidate_alpha</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmolgroup">Bmolgroup</link>* molgroup_consolidate_alpha (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Cluster a set of alpha helices to consolidate helices. </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 with alpha helices (deallocated). </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>Bmolgroup* new molecule group. </para>
</formalpara>
</para>
<para>
Definition at line 382 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1ae1768f69d8e49d79a58b28c2fa9bfc00"/>    <section>
    <title>molgroup_find_helical_axes()</title>
<indexterm><primary>molgroup_find_helical_axes</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>molgroup_find_helical_axes</secondary></indexterm>
<para><computeroutput>int molgroup_find_helical_axes (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup)</computeroutput></para><para>

<para>Calculates the centers and orientations of all alpha helices. </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 0. </para>
</formalpara>
</para>
<para>
Definition at line 147 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1a9907d81ba9424ab77ffc80f79c9911cc"/>    <section>
    <title>molgroup_generate_alpha_helix()</title>
<indexterm><primary>molgroup_generate_alpha_helix</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>molgroup_generate_alpha_helix</secondary></indexterm>
<para><computeroutput><link linkend="_struct_bmolgroup">Bmolgroup</link>* molgroup_generate_alpha_helix (int length)</computeroutput></para><para>

<para>Generates an alpha helix of the desired 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>length</entry>
                                <entry>
<para>number of alanines to generate. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 54 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1a4778e0f1a9ec6198c89072fe3a651a9d"/>    <section>
    <title>molgroup_set_alpha_helix()</title>
<indexterm><primary>molgroup_set_alpha_helix</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>molgroup_set_alpha_helix</secondary></indexterm>
<para><computeroutput>int molgroup_set_alpha_helix (<link linkend="_struct_bmolgroup">Bmolgroup</link> * molgroup, int helix_start, int helix_end)</computeroutput></para><para>

<para>Sets a residue range to an alpha helix in all molecules. </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>helix_start</entry>
                                <entry>
<para>first residue in helix. </para>
</entry>
                            </row>
                            <row>
                                <entry>helix_end</entry>
                                <entry>
<para>last residue in helix. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para>int 0. </para>
</formalpara>
</para>
<para>
Definition at line 117 of file mol_alpha.cpp.</para>
    </section><anchor xml:id="_mol__alpha_8h_1ac496c23bbcbc4d267041265c4e3d7fbf"/>    <section>
    <title>point_on_helix_axis()</title>
<indexterm><primary>point_on_helix_axis</primary><secondary>mol_alpha.h</secondary></indexterm>
<indexterm><primary>mol_alpha.h</primary><secondary>point_on_helix_axis</secondary></indexterm>
<para><computeroutput><link linkend="_class_vector3">Vector3</link>&lt;double&gt; point_on_helix_axis (<link linkend="_class_vector3">Vector3</link>&lt; double &gt; ca1, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; ca2, <link linkend="_class_vector3">Vector3</link>&lt; double &gt; ca3)</computeroutput></para><para>

<para>Calculates a point on an alpha helix corresponding to a Ca atom. </para>
</para>

<para><literallayout><computeroutput>The point on the alpha helix corresponding to the second Ca atom 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>ca1</entry>
                                <entry>
<para>first Ca atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>ca2</entry>
                                <entry>
<para>second Ca atom. </para>
</entry>
                            </row>
                            <row>
                                <entry>ca3</entry>
                                <entry>
<para>third Ca atom. </para>
</entry>
                            </row>
                        </tbody>
                        </tgroup>
                    </table>
                    </para>
                </formalpara>
                <formalpara><title>Returns: </title>

<para><link linkend="_class_vector3">Vector3&lt;double&gt;</link> point on alpha helix. </para>
</formalpara>
</para>
<para>
Definition at line 349 of file mol_alpha.cpp.</para>
</section>
</section>
</section>
