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<hr><h1>sc::IntCoorGen Class Reference</h1><a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> generates a set of simple internal coordinates for a molecule.
<a href="#_details">More...</a>
<p>
<code>#include <<a class="el" href="coor_h-source.html">coor.h</a>></code>
<p>
Inheritance diagram for sc::IntCoorGen<p><center><img src="class_sc__IntCoorGen_inherit_graph.gif" border="0" usemap="#sc::IntCoorGen_inherit_map" alt="Inheritance graph"></center>
<map name="sc::IntCoorGen_inherit_map">
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center>Collaboration diagram for sc::IntCoorGen:<p><center><img src="class_sc__IntCoorGen_coll_graph.gif" border="0" usemap="#sc::IntCoorGen_coll_map" alt="Collaboration graph"></center>
<map name="sc::IntCoorGen_coll_map">
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center><a href="class_sc__IntCoorGen-members.html">List of all members.</a><table border=0 cellpadding=0 cellspacing=0>
<tr><td colspan=2><br><h2>Public Methods</h2></td></tr>
<tr><td nowrap align=right valign=top> </td><td valign=bottom><a class="el" href="class_sc__IntCoorGen.html#a0">IntCoorGen</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &, int nextra=0, int *extra=0)</td></tr>
<tr><td> </td><td><font size=-1><em>Create an <a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> given a <a class="el" href="class_sc__Molecule.html">Molecule</a> and, optionally, extra bonds.</em> <a href="#a0">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top> </td><td valign=bottom><a class="el" href="class_sc__IntCoorGen.html#a1">IntCoorGen</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__KeyVal.html">KeyVal</a> > &)</td></tr>
<tr><td> </td><td><font size=-1><em>The <a class="el" href="class_sc__KeyVal.html">KeyVal</a> constructor.</em> <a href="#a1">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a2" doxytag="sc::IntCoorGen::IntCoorGen"></a>
</td><td valign=bottom><b>IntCoorGen</b> (<a class="el" href="class_sc__StateIn.html">StateIn</a> &)</td></tr>
<tr><td nowrap align=right valign=top><a name="a3" doxytag="sc::IntCoorGen::~IntCoorGen"></a>
</td><td valign=bottom><b>~IntCoorGen</b> ()</td></tr>
<tr><td nowrap align=right valign=top><a name="a4" doxytag="sc::IntCoorGen::save_data_state"></a>
void </td><td valign=bottom><a class="el" href="class_sc__IntCoorGen.html#a4">save_data_state</a> (<a class="el" href="class_sc__StateOut.html">StateOut</a> &)</td></tr>
<tr><td> </td><td><font size=-1><em>Standard member.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a5" doxytag="sc::IntCoorGen::generate"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__IntCoorGen.html#a5">generate</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> > &)</td></tr>
<tr><td> </td><td><font size=-1><em>This generates a set of internal coordinates.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a6" doxytag="sc::IntCoorGen::print"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__IntCoorGen.html#a6">print</a> (std::ostream &out=ExEnv::out0()) const</td></tr>
<tr><td> </td><td><font size=-1><em>Print out information about this.</em></font><br><br></td></tr>
<tr><td colspan=2><br><h2>Protected Methods</h2></td></tr>
<tr><td nowrap align=right valign=top><a name="b0" doxytag="sc::IntCoorGen::init_constants"></a>
void </td><td valign=bottom><b>init_constants</b> ()</td></tr>
<tr><td nowrap align=right valign=top><a name="b1" doxytag="sc::IntCoorGen::cos_ijk"></a>
double </td><td valign=bottom><b>cos_ijk</b> (<a class="el" href="class_sc__Molecule.html">Molecule</a> &m, int i, int j, int k)</td></tr>
<tr><td nowrap align=right valign=top><a name="b2" doxytag="sc::IntCoorGen::hterminal"></a>
int </td><td valign=bottom><b>hterminal</b> (<a class="el" href="class_sc__Molecule.html">Molecule</a> &m, BitArrayLTri &bonds, int i)</td></tr>
<tr><td nowrap align=right valign=top><a name="b3" doxytag="sc::IntCoorGen::nearest_contact"></a>
int </td><td valign=bottom><b>nearest_contact</b> (int i, <a class="el" href="class_sc__Molecule.html">Molecule</a> &m)</td></tr>
<tr><td nowrap align=right valign=top><a name="b4" doxytag="sc::IntCoorGen::add_bonds"></a>
void </td><td valign=bottom><b>add_bonds</b> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> > &list, BitArrayLTri &bonds, <a class="el" href="class_sc__Molecule.html">Molecule</a> &m)</td></tr>
<tr><td nowrap align=right valign=top><a name="b5" doxytag="sc::IntCoorGen::add_bends"></a>
void </td><td valign=bottom><b>add_bends</b> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> > &list, BitArrayLTri &bonds, <a class="el" href="class_sc__Molecule.html">Molecule</a> &m)</td></tr>
<tr><td nowrap align=right valign=top><a name="b6" doxytag="sc::IntCoorGen::add_tors"></a>
void </td><td valign=bottom><b>add_tors</b> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> > &list, BitArrayLTri &bonds, <a class="el" href="class_sc__Molecule.html">Molecule</a> &m)</td></tr>
<tr><td nowrap align=right valign=top><a name="b7" doxytag="sc::IntCoorGen::add_out"></a>
void </td><td valign=bottom><b>add_out</b> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> > &list, BitArrayLTri &bonds, <a class="el" href="class_sc__Molecule.html">Molecule</a> &m)</td></tr>
<tr><td colspan=2><br><h2>Protected Attributes</h2></td></tr>
<tr><td nowrap align=right valign=top><a name="n0" doxytag="sc::IntCoorGen::molecule_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__Molecule.html">Molecule</a>> </td><td valign=bottom><b>molecule_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n1" doxytag="sc::IntCoorGen::linear_bends_"></a>
int </td><td valign=bottom><b>linear_bends_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n2" doxytag="sc::IntCoorGen::linear_lbends_"></a>
int </td><td valign=bottom><b>linear_lbends_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n3" doxytag="sc::IntCoorGen::linear_tors_"></a>
int </td><td valign=bottom><b>linear_tors_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n4" doxytag="sc::IntCoorGen::linear_stors_"></a>
int </td><td valign=bottom><b>linear_stors_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n5" doxytag="sc::IntCoorGen::nextra_bonds_"></a>
int </td><td valign=bottom><b>nextra_bonds_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n6" doxytag="sc::IntCoorGen::extra_bonds_"></a>
int* </td><td valign=bottom><b>extra_bonds_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n7" doxytag="sc::IntCoorGen::linear_bend_thres_"></a>
double </td><td valign=bottom><b>linear_bend_thres_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n8" doxytag="sc::IntCoorGen::linear_tors_thres_"></a>
double </td><td valign=bottom><b>linear_tors_thres_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n9" doxytag="sc::IntCoorGen::radius_scale_factor_"></a>
double </td><td valign=bottom><b>radius_scale_factor_</b></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
<a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> generates a set of simple internal coordinates for a molecule.
<p>
<hr><h2>Constructor & Destructor Documentation</h2>
<a name="a0" doxytag="sc::IntCoorGen::IntCoorGen"></a><p>
<table width="100%" cellpadding="2" cellspacing="0" border="0">
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sc::IntCoorGen::IntCoorGen (
</b></td>
<td valign="bottom"><b>
const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &,
</b></td>
</tr>
<tr>
<td></td>
<td><b>
int <em>nextra</em> = 0,
</b></td>
</tr>
<tr>
<td></td>
<td><b>
int * <em>extra</em> = 0 )
</b></td>
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<td>
<p>
Create an <a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> given a <a class="el" href="class_sc__Molecule.html">Molecule</a> and, optionally, extra bonds.
<p>
<a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> keeps a reference to extra and deletes it when the destructor is called. </td>
</tr>
</table>
<a name="a1" doxytag="sc::IntCoorGen::IntCoorGen"></a><p>
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<td nowrap valign="top"><b>
sc::IntCoorGen::IntCoorGen (
</b></td>
<td valign="bottom"><b>
const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__KeyVal.html">KeyVal</a> > & )
</b></td>
</tr>
</table>
</td>
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</td>
<td>
<p>
The <a class="el" href="class_sc__KeyVal.html">KeyVal</a> constructor.
<p>
<dl compact>
<p>
<dt><code>molecule</code><dd> A <a class="el" href="class_sc__Molecule.html">Molecule</a> object. There is no default.
<p>
<dt><code>radius_scale_factor</code><dd> If the distance between two atoms is less than the radius scale factor times the sum of the atoms' atomic radii, then a bond is placed between the two atoms for the purpose of finding internal coordinates. The default is 1.1.
<p>
<dt><code>linear_bend_threshold</code><dd> A bend angle in degress greater than 180 minus this keyword's floating point value is considered a linear bend. The default is 1.0.
<p>
<dt><code>linear_tors_threshold</code><dd> The angles formed by atoms a-b-c and b-c-d are checked for near linearity. If an angle in degrees is greater than 180 minus this keyword's floating point value, then the torsion is classified as a linear torsion. The default is 1.0.
<p>
<dt><code>linear_bend</code><dd> Generate <a class="el" href="class_sc__BendSimpleCo.html">BendSimpleCo</a> objects to describe linear bends. The default is false.
<p>
<dt><code>linear_lbend</code><dd> Generate pairs of <a class="el" href="class_sc__LinIPSimpleCo.html">LinIPSimpleCo</a> and <a class="el" href="class_sc__LinIPSimpleCo.html">LinIPSimpleCo</a> objects to describe linear bends. The default is true.
<p>
<dt><code>linear_tors</code><dd> Generate <a class="el" href="class_sc__TorsSimpleCo.html">TorsSimpleCo</a> objects to described linear torsions. The default is false.
<p>
<dt><code>linear_stors</code><dd> Generate <a class="el" href="class_sc__ScaledTorsSimpleCo.html">ScaledTorsSimpleCo</a> objects to described linear torsions. The default is true.
<p>
<dt><code>extra_bonds</code><dd> This is a vector of atom numbers, where elements <img align="top" src="form-9.gif">
and <img align="top" src="form-10.gif">
specify the atoms which are bound in extra bond <img align="top" src="form-7.gif">
. The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.
<p>
</dl>
</td>
</tr>
</table>
<hr>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="coor_h-source.html">coor.h</a></ul>
<hr>
<address>
<small>
Generated at Mon Oct 14 14:17:02 2002 for <a
href="http://aros.ca.sandia.gov/~cljanss/mpqc">MPQC</a>
2.1.2 using the documentation package <a
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