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<h1>vatom.h File Reference</h1>Contains declarations for class Vatom.
<a href="#_details">More...</a>
<p>
<code>#include "maloc/maloc.h"</code><br>
<code>#include "<a class="el" href="vhal_8h-source.html">apbs/vhal.h</a>"</code><br>
<p>
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Include dependency graph for vatom.h:</div>
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This graph shows which files directly or indirectly include this file:</div>
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<area shape="rect" href="vopot_8h.html" title="Potential oracle for Cartesian mesh data." alt="" coords="790,381,857,408"><area shape="rect" href="apbs_8h.html" title="Top-level header for APBS." alt="" coords="481,456,542,482"><area shape="rect" href="vacc_8h.html" title="Contains declarations for class Vacc." alt="" coords="552,232,613,258"><area shape="rect" href="vpbe_8h.html" title="Contains declarations for class Vpbe." alt="" coords="685,306,749,333"><area shape="rect" href="vfetk_8h.html" title="Contains declarations for class Vfetk." alt="" coords="150,381,214,408"><area shape="rect" href="valist_8h.html" title="Contains declarations for class Valist." alt="" coords="478,82,545,109"><area shape="rect" href="vclist_8h.html" title="Contains declarations for class Vclist." alt="" coords="688,157,752,184"><area shape="rect" href="vgreen_8h.html" title="Contains declarations for class Vgreen." alt="" coords="184,157,258,184"><area shape="rect" href="vatom_8c.html" title="Class Vatom methods." alt="" coords="978,82,1048,109"><area shape="rect" href="vopot_8c.html" title="Class Vopot methods." alt="" coords="790,456,857,482"><area shape="rect" href="mgparm_8c.html" title="Class MGparm methods." alt="" coords="476,530,556,557"><area shape="rect" href="main_8c.html" title="APBS "front end" program using formatted input files." alt="" coords="408,605,469,632"><area shape="rect" href="routines_8h.html" title="Header file for front end auxiliary routines." alt="" coords="268,530,350,557"><area shape="rect" href="routines_8c.html" title="Supporting routines for APBS front end." alt="" coords="214,605,294,632"><area shape="rect" href="vpmg_8h.html" title="Contains declarations for class Vpmg." alt="" coords="600,381,666,408"><area shape="rect" href="vacc_8c.html" title="Class Vacc methods." alt="" coords="600,306,661,333"><area shape="rect" href="vpmg-private_8h.html" title="Class Vpmg private method declaration." alt="" coords="572,456,684,482"><area shape="rect" href="vpmg_8c.html" title="Class Vpmg methods." alt="" coords="661,530,728,557"><area shape="rect" href="vpbe_8c.html" title="Class Vpbe methods." alt="" coords="690,381,752,408"><area shape="rect" href="vfetk_8c.html" title="Class Vfetk methods." alt="" coords="102,456,164,482"><area shape="rect" href="nosh_8h.html" title="Contains declarations for class NOsh." alt="" coords="289,381,350,408"><area shape="rect" href="valist_8c.html" title="Class Valist methods." alt="" coords="549,157,613,184"><area shape="rect" href="vcsm_8h.html" title="Contains declarations for the Vcsm class." alt="" coords="306,157,373,184"><area shape="rect" href="nosh_8c.html" title="Class NOsh methods." alt="" coords="289,456,350,482"><area shape="rect" href="vclist_8c.html" title="Class Vclist methods." alt="" coords="688,232,752,258"><area shape="rect" href="vgreen_8c.html" title="Class Vgreen methods." alt="" coords="109,232,184,258"><area shape="rect" href="vcsm_8c.html" title="Class Vcsm methods." alt="" coords="309,232,373,258"></map>
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<a href="vatom_8h-source.html">Go to the source code of this file.</a><table border="0" cellpadding="0" cellspacing="0">
<tr><td></td></tr>
<tr><td colspan="2"><br><h2>Data Structures</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">struct </td><td class="memItemRight" valign="bottom"><a class="el" href="structsVatom.html">sVatom</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Contains public data members for Vatom class/module. <a href="structsVatom.html#_details">More...</a><br></td></tr>
<tr><td colspan="2"><br><h2>Typedefs</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="gc92bd9ea60d3453a4ffc63e1b8deabc1"></a><!-- doxytag: member="vatom.h::Vatom" ref="gc92bd9ea60d3453a4ffc63e1b8deabc1" args="" -->
typedef struct <a class="el" href="structsVatom.html">sVatom</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gc92bd9ea60d3453a4ffc63e1b8deabc1">Vatom</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Declaration of the Vatom class as the Vatom structure. <br></td></tr>
<tr><td colspan="2"><br><h2>Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">double * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gbe19ed4ab35365a2e8f7505bcbb6bca2">Vatom_getPosition</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get atomic position. <a href="group__Vatom.html#gbe19ed4ab35365a2e8f7505bcbb6bca2"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gb7f8af75a9fe695fafcec2d8dcfe1f74">Vatom_setRadius</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, double radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set atomic radius. <a href="group__Vatom.html#gb7f8af75a9fe695fafcec2d8dcfe1f74"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gd3538039818c4279eb8a6b0e806dea7b">Vatom_getRadius</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get atomic position. <a href="group__Vatom.html#gd3538039818c4279eb8a6b0e806dea7b"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g208e36b834b3839119d472c13b0a34e6">Vatom_setPartID</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, int partID)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set partition ID. <a href="group__Vatom.html#g208e36b834b3839119d472c13b0a34e6"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g90459dff61fcde8c0da53f073deabdad">Vatom_getPartID</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get partition ID. <a href="group__Vatom.html#g90459dff61fcde8c0da53f073deabdad"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g619690d8845221f0319fddf78bf883d9">Vatom_setAtomID</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, int id)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set atom ID. <a href="group__Vatom.html#g619690d8845221f0319fddf78bf883d9"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g37404117f53ad617e4371df8a7c849bb">Vatom_getAtomID</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get atom ID. <a href="group__Vatom.html#g37404117f53ad617e4371df8a7c849bb"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g804cb2136cc1ff6105b37b176d58b804">Vatom_setCharge</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, double charge)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set atomic charge. <a href="group__Vatom.html#g804cb2136cc1ff6105b37b176d58b804"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g6123ac049c637301d5aa730c18c94756">Vatom_getCharge</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get atomic charge. <a href="group__Vatom.html#g6123ac049c637301d5aa730c18c94756"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gc17a9120ddc6cfe671e8e27dc9a2600d">Vatom_setEpsilon</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, double epsilon)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set atomic epsilon. <a href="group__Vatom.html#gc17a9120ddc6cfe671e8e27dc9a2600d"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">double </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g42729978e8ff788d0295f873fe600c2f">Vatom_getEpsilon</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get atomic epsilon. <a href="group__Vatom.html#g42729978e8ff788d0295f873fe600c2f"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">unsigned long int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g8bfa45d75ccf029ffb500bda6e890476">Vatom_memChk</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the memory used by this structure (and its contents) in bytes. <a href="group__Vatom.html#g8bfa45d75ccf029ffb500bda6e890476"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g4bfc689ba5d955b8b96034b920923409">Vatom_setResName</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, char resName[VMAX_RECLEN])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set residue name. <a href="group__Vatom.html#g4bfc689ba5d955b8b96034b920923409"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gb1012d7d66dd93f1b9c5678d93de840f">Vatom_setAtomName</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, char atomName[VMAX_RECLEN])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set atom name. <a href="group__Vatom.html#gb1012d7d66dd93f1b9c5678d93de840f"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g1d1948cb306b3db8fb882d711a66ea2c">Vatom_getResName</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, char resName[VMAX_RECLEN])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Retrieve residue name. <a href="group__Vatom.html#g1d1948cb306b3db8fb882d711a66ea2c"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g4482fd0b1ed012249c4111315691f24d">Vatom_getAtomName</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, char atomName[VMAX_RECLEN])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Retrieve atom name. <a href="group__Vatom.html#g4482fd0b1ed012249c4111315691f24d"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structsVatom.html">Vatom</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gda235c901fbc52dd99450621d03b02a3">Vatom_ctor</a> ()</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Constructor for the Vatom class. <a href="group__Vatom.html#gda235c901fbc52dd99450621d03b02a3"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g843695817897592b03ed140fa4583c9a">Vatom_ctor2</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub constructor for the Vatom class. <a href="group__Vatom.html#g843695817897592b03ed140fa4583c9a"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g6d47f9b36f0c3b94e69eaa470107e6ed">Vatom_dtor</a> (<a class="el" href="structsVatom.html">Vatom</a> **thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Object destructor. <a href="group__Vatom.html#g6d47f9b36f0c3b94e69eaa470107e6ed"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gcac2e720f850e668c12337b1eb6e8755">Vatom_dtor2</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub object destructor. <a href="group__Vatom.html#gcac2e720f850e668c12337b1eb6e8755"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#gd233011217b9aeeea2907cead69a09f4">Vatom_setPosition</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, double position[3])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set the atomic position. <a href="group__Vatom.html#gd233011217b9aeeea2907cead69a09f4"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g5e1d3015b43d46c4a013b7d69a7f465e">Vatom_copyTo</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, <a class="el" href="structsVatom.html">Vatom</a> *dest)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Copy information to another atom. <a href="group__Vatom.html#g5e1d3015b43d46c4a013b7d69a7f465e"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vatom.html#g3d0f4824838542e20bd9e086f34fb405">Vatom_copyFrom</a> (<a class="el" href="structsVatom.html">Vatom</a> *thee, <a class="el" href="structsVatom.html">Vatom</a> *src)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Copy information to another atom. <a href="group__Vatom.html#g3d0f4824838542e20bd9e086f34fb405"></a><br></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
Contains declarations for class Vatom.
<p>
<dl class="version" compact><dt><b>Version:</b></dt><dd></dd></dl>
<dl class="rcs" compact><dt><b>Id</b></dt><dd><a class="el" href="vatom_8h.html" title="Contains declarations for class Vatom.">vatom.h</a> 1350 2009-02-12 00:38:48Z yhuang01 </dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan A. Baker</dd></dl>
<dl class="attention" compact><dt><b>Attention:</b></dt><dd><div class="fragment"><pre class="fragment">
*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (baker@biochem.wustl.edu)
* Dept. of Biochemistry and Molecular Biophysics
* Center for Computational Biology
* Washington University in St. Louis
*
* Additional contributing authors listed in the code documentation.
*
* Copyright (c) 2002-2009, Washington University in St. Louis.
* Portions Copyright (c) 2002-2009. Nathan A. Baker
* Portions Copyright (c) 1999-2002. The Regents of the University of California.
* Portions Copyright (c) 1995. Michael Holst
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* - Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* - Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* - Neither the name of Washington University in St. Louis nor the names of its
* contributors may be used to endorse or promote products derived from this
* software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
* </pre></div> </dd></dl>
</div>
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