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<h1>Valist class</h1>Container class for list of atom objects.
<a href="#_details">More...</a>
<p>
<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="structsValist.html">sValist</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Container class for list of atom objects. <a href="structsValist.html#_details">More...</a><br></td></tr>
<tr><td colspan="2"><br><h2>Files</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">file </td><td class="memItemRight" valign="bottom"><a class="el" href="valist_8h.html">valist.h</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Contains declarations for class Valist. <br></td></tr>
<p>
<tr><td colspan="2"><br><h2>Typedefs</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="gad14444b05c0349e90134d0184af1188"></a><!-- doxytag: member="Valist::Valist" ref="gad14444b05c0349e90134d0184af1188" args="" -->
typedef struct <a class="el" href="structsValist.html">sValist</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Valist.html#gad14444b05c0349e90134d0184af1188">Valist</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Declaration of the Valist class as the Valist structure. <br></td></tr>
<tr><td colspan="2"><br><h2>Functions</h2></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__Valist.html#ga6b04488b680202d8de65ce87ed9b586">Valist_getAtomList</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get actual array of atom objects from the list. <a href="#ga6b04488b680202d8de65ce87ed9b586"></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__Valist.html#g621fbdbd50e1498274df95f078cdde44">Valist_getCenterX</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get x-coordinate of molecule center. <a href="#g621fbdbd50e1498274df95f078cdde44"></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__Valist.html#ge9a682cd35ecdf1826c2eb43b0740049">Valist_getCenterY</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get y-coordinate of molecule center. <a href="#ge9a682cd35ecdf1826c2eb43b0740049"></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__Valist.html#gbe56a5254fd6cc0f724cbee2105d16d3">Valist_getCenterZ</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get z-coordinate of molecule center. <a href="#gbe56a5254fd6cc0f724cbee2105d16d3"></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__Valist.html#g2aea567c031963b275f4e6e31f9c3e74">Valist_getNumberAtoms</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get number of atoms in the list. <a href="#g2aea567c031963b275f4e6e31f9c3e74"></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__Valist.html#g6e228909b1e2c178ee292ae97c5bce62">Valist_getAtom</a> (<a class="el" href="structsValist.html">Valist</a> *thee, int i)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get pointer to particular atom in list. <a href="#g6e228909b1e2c178ee292ae97c5bce62"></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__Valist.html#gca9784596feb23190c376fe10c85265f">Valist_memChk</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get total memory allocated for this object and its members. <a href="#gca9784596feb23190c376fe10c85265f"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structsValist.html">Valist</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Valist.html#g161c8bda69f6a37578011cc39b5630be">Valist_ctor</a> ()</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Construct the atom list object. <a href="#g161c8bda69f6a37578011cc39b5630be"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Valist.html#g3a45cdb67596f6289b4b4a27f3515af4">Valist_ctor2</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub to construct the atom list object. <a href="#g3a45cdb67596f6289b4b4a27f3515af4"></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__Valist.html#gaf04de8da79be6d12a2cfe7e001b24fd">Valist_dtor</a> (<a class="el" href="structsValist.html">Valist</a> **thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Destroys atom list object. <a href="#gaf04de8da79be6d12a2cfe7e001b24fd"></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__Valist.html#g8b18b21fa58e5250ed419c246d22a4d0">Valist_dtor2</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub to destroy atom list object. <a href="#g8b18b21fa58e5250ed419c246d22a4d0"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Valist.html#g501998331453e488840902156653ef18">Valist_readPQR</a> (<a class="el" href="structsValist.html">Valist</a> *thee, <a class="el" href="structVparam.html">Vparam</a> *param, Vio *sock)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill atom list with information from a PQR file. <a href="#g501998331453e488840902156653ef18"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Valist.html#g155ec618d8938ccf2cff609d9811b7db">Valist_readPDB</a> (<a class="el" href="structsValist.html">Valist</a> *thee, <a class="el" href="structVparam.html">Vparam</a> *param, Vio *sock)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill atom list with information from a PDB file. <a href="#g155ec618d8938ccf2cff609d9811b7db"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Valist.html#g79d3ae98e4903139c3f0172286c48d8a">Valist_readXML</a> (<a class="el" href="structsValist.html">Valist</a> *thee, <a class="el" href="structVparam.html">Vparam</a> *param, Vio *sock)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Fill atom list with information from an XML file. <a href="#g79d3ae98e4903139c3f0172286c48d8a"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">Vrc_Codes </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Valist.html#g902e23e51a90ae7d7dec67c904e83049">Valist_getStatistics</a> (<a class="el" href="structsValist.html">Valist</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Load up Valist with various statistics. <a href="#g902e23e51a90ae7d7dec67c904e83049"></a><br></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
Container class for list of atom objects. <hr><h2>Function Documentation</h2>
<a class="anchor" name="g161c8bda69f6a37578011cc39b5630be"></a><!-- doxytag: member="valist.h::Valist_ctor" ref="g161c8bda69f6a37578011cc39b5630be" args="()" -->
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<td class="memname"><a class="el" href="structsValist.html">Valist</a>* Valist_ctor </td>
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<p>
Construct the atom list object.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Pointer to newly allocated (empty) atom list </dd></dl>
<p>References <a class="el" href="valist_8c-source.html#l00154">Valist_ctor2()</a>, and <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l00112">loadMolecules()</a>.</p>
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Here is the call graph for this function:</div>
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<p><center><img src="group__Valist_g161c8bda69f6a37578011cc39b5630be_cgraph.png" border="0" usemap="#group__Valist_g161c8bda69f6a37578011cc39b5630be_cgraph_map" alt=""></center>
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<a class="anchor" name="g3a45cdb67596f6289b4b4a27f3515af4"></a><!-- doxytag: member="valist.h::Valist_ctor2" ref="g3a45cdb67596f6289b4b4a27f3515af4" args="(Valist *thee)" -->
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<td class="memname">Vrc_Codes Valist_ctor2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
FORTRAN stub to construct the atom list object.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker, Yong Huang </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Success enumeration </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Storage for new atom list </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8h-source.html#l00084">sValist::atoms</a>, <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>, <a class="el" href="valist_8h-source.html#l00085">sValist::vmem</a>, and <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>.</p>
<p>Referenced by <a class="el" href="valist_8c-source.html#l00137">Valist_ctor()</a>.</p>
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<a class="anchor" name="gaf04de8da79be6d12a2cfe7e001b24fd"></a><!-- doxytag: member="valist.h::Valist_dtor" ref="gaf04de8da79be6d12a2cfe7e001b24fd" args="(Valist **thee)" -->
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<td class="memname">void Valist_dtor </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> ** </td>
<td class="paramname"> <em>thee</em> </td>
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<p>
Destroys atom list object.
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<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Pointer to storage for atom list </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8c-source.html#l00175">Valist_dtor2()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l00248">killMolecules()</a>, and <a class="el" href="routines_8c-source.html#l00112">loadMolecules()</a>.</p>
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<p><center><img src="group__Valist_gaf04de8da79be6d12a2cfe7e001b24fd_cgraph.png" border="0" usemap="#group__Valist_gaf04de8da79be6d12a2cfe7e001b24fd_cgraph_map" alt=""></center>
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<a class="anchor" name="g8b18b21fa58e5250ed419c246d22a4d0"></a><!-- doxytag: member="valist.h::Valist_dtor2" ref="g8b18b21fa58e5250ed419c246d22a4d0" args="(Valist *thee)" -->
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<td class="memname">void Valist_dtor2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
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<p>
FORTRAN stub to destroy atom list object.
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<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Pointer to atom list object </td></tr>
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</dl>
<p>References <a class="el" href="valist_8h-source.html#l00084">sValist::atoms</a>, <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>, and <a class="el" href="valist_8h-source.html#l00085">sValist::vmem</a>.</p>
<p>Referenced by <a class="el" href="valist_8c-source.html#l00166">Valist_dtor()</a>.</p>
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<a class="anchor" name="g6e228909b1e2c178ee292ae97c5bce62"></a><!-- doxytag: member="valist.h::Valist_getAtom" ref="g6e228909b1e2c178ee292ae97c5bce62" args="(Valist *thee, int i)" -->
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<td class="memname"><a class="el" href="structsVatom.html">Vatom</a>* Valist_getAtom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td class="paramname"> <em>i</em></td><td> </td>
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<p>
Get pointer to particular atom in list.
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<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Pointer to atom object i </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
<tr><td valign="top"><em>i</em> </td><td>
Index of atom in list </td></tr>
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<p>References <a class="el" href="valist_8h-source.html#l00084">sValist::atoms</a>, and <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l01056">energyMG()</a>, <a class="el" href="vpmg_8c-source.html#l02127">extEnergy()</a>, <a class="el" href="vpmg_8c-source.html#l04623">fillcoChargeSpline1()</a>, <a class="el" href="vpmg_8c-source.html#l04759">fillcoChargeSpline2()</a>, <a class="el" href="vpmg_8c-source.html#l03976">fillcoCoefMolDielNoSmooth()</a>, <a class="el" href="vpmg_8c-source.html#l03868">fillcoCoefMolIon()</a>, <a class="el" href="vpmg_8c-source.html#l04255">fillcoCoefSpline()</a>, <a class="el" href="vpmg_8c-source.html#l09624">fillcoCoefSpline3()</a>, <a class="el" href="vpmg_8c-source.html#l09134">fillcoCoefSpline4()</a>, <a class="el" href="vpmg_8c-source.html#l06435">fillcoPermanentMultipole()</a>, <a class="el" href="routines_8c-source.html#l03910">forceAPOL()</a>, <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>, <a class="el" href="routines_8c-source.html#l00762">initMG()</a>, <a class="el" href="vpmg_8c-source.html#l05509">qfForceSpline1()</a>, <a class="el" href="vpmg_8c-source.html#l05645">qfForceSpline2()</a>, <a class="el" href="vpmg_8c-source.html#l05757">qfForceSpline4()</a>, <a class="el" href="routines_8c-source.html#l01344">storeAtomEnergy()</a>, <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>, <a class="el" href="vacc_8c-source.html#l00143">Vacc_storeParms()</a>, <a class="el" href="vcsm_8c-source.html#l00079">Vcsm_getAtom()</a>, <a class="el" href="vcsm_8c-source.html#l00172">Vcsm_init()</a>, <a class="el" href="vcsm_8c-source.html#l00324">Vcsm_update()</a>, <a class="el" href="vfetk_8c-source.html#l00520">Vfetk_getAtomColor()</a>, <a class="el" href="vfetk_8c-source.html#l00806">Vfetk_setAtomColors()</a>, <a class="el" href="vgreen_8c-source.html#l00223">Vgreen_coulomb_direct()</a>, <a class="el" href="vgreen_8c-source.html#l00309">Vgreen_coulombD_direct()</a>, <a class="el" href="vpbe_8c-source.html#l00212">Vpbe_ctor2()</a>, <a class="el" href="vpbe_8c-source.html#l00413">Vpbe_getCoulombEnergy1()</a>, <a class="el" href="vpmg_8c-source.html#l05211">Vpmg_dbForce()</a>, <a class="el" href="vpmg_8c-source.html#l05047">Vpmg_ibForce()</a>, <a class="el" href="vpmg_8c-source.html#l01064">Vpmg_polarizEnergy()</a>, <a class="el" href="vpmg_8c-source.html#l01507">Vpmg_qfEnergyPoint()</a>, <a class="el" href="vpmg_8c-source.html#l00553">Vpmg_setPart()</a>, and <a class="el" href="vpmg_8c-source.html#l00798">Vpmg_unsetPart()</a>.</p>
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<a class="anchor" name="ga6b04488b680202d8de65ce87ed9b586"></a><!-- doxytag: member="valist.h::Valist_getAtomList" ref="ga6b04488b680202d8de65ce87ed9b586" args="(Valist *thee)" -->
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<td class="memname"><a class="el" href="structsVatom.html">Vatom</a>* Valist_getAtomList </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
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<p>
Get actual array of atom objects from the list.
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<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Array of atom objects </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8h-source.html#l00084">sValist::atoms</a>.</p>
</div>
</div><p>
<a class="anchor" name="g621fbdbd50e1498274df95f078cdde44"></a><!-- doxytag: member="valist.h::Valist_getCenterX" ref="g621fbdbd50e1498274df95f078cdde44" args="(Valist *thee)" -->
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<td class="memname">double Valist_getCenterX </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
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<div class="memdoc">
<p>
Get x-coordinate of molecule center.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>X-coordinate of molecule center </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8h-source.html#l00079">sValist::center</a>.</p>
</div>
</div><p>
<a class="anchor" name="ge9a682cd35ecdf1826c2eb43b0740049"></a><!-- doxytag: member="valist.h::Valist_getCenterY" ref="ge9a682cd35ecdf1826c2eb43b0740049" args="(Valist *thee)" -->
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<td class="memname">double Valist_getCenterY </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Get y-coordinate of molecule center.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Y-coordinate of molecule center </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8h-source.html#l00079">sValist::center</a>.</p>
</div>
</div><p>
<a class="anchor" name="gbe56a5254fd6cc0f724cbee2105d16d3"></a><!-- doxytag: member="valist.h::Valist_getCenterZ" ref="gbe56a5254fd6cc0f724cbee2105d16d3" args="(Valist *thee)" -->
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<td class="memname">double Valist_getCenterZ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Get z-coordinate of molecule center.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Z-coordinate of molecule center </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8h-source.html#l00079">sValist::center</a>.</p>
</div>
</div><p>
<a class="anchor" name="g2aea567c031963b275f4e6e31f9c3e74"></a><!-- doxytag: member="valist.h::Valist_getNumberAtoms" ref="g2aea567c031963b275f4e6e31f9c3e74" args="(Valist *thee)" -->
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<td class="memname">int Valist_getNumberAtoms </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
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<div class="memdoc">
<p>
Get number of atoms in the list.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Number of atoms in list </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l01056">energyMG()</a>, <a class="el" href="vpmg_8c-source.html#l02127">extEnergy()</a>, <a class="el" href="vpmg_8c-source.html#l04623">fillcoChargeSpline1()</a>, <a class="el" href="vpmg_8c-source.html#l04759">fillcoChargeSpline2()</a>, <a class="el" href="vpmg_8c-source.html#l03976">fillcoCoefMolDielNoSmooth()</a>, <a class="el" href="vpmg_8c-source.html#l03868">fillcoCoefMolIon()</a>, <a class="el" href="vpmg_8c-source.html#l04255">fillcoCoefSpline()</a>, <a class="el" href="vpmg_8c-source.html#l09624">fillcoCoefSpline3()</a>, <a class="el" href="vpmg_8c-source.html#l09134">fillcoCoefSpline4()</a>, <a class="el" href="vpmg_8c-source.html#l06435">fillcoPermanentMultipole()</a>, <a class="el" href="routines_8c-source.html#l03910">forceAPOL()</a>, <a class="el" href="routines_8c-source.html#l01120">forceMG()</a>, <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>, <a class="el" href="routines_8c-source.html#l00762">initMG()</a>, <a class="el" href="routines_8c-source.html#l00112">loadMolecules()</a>, <a class="el" href="routines_8c-source.html#l01344">storeAtomEnergy()</a>, <a class="el" href="vacc_8c-source.html#l00182">Vacc_allocate()</a>, <a class="el" href="vacc_8c-source.html#l00240">Vacc_dtor2()</a>, <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>, <a class="el" href="vacc_8c-source.html#l00143">Vacc_storeParms()</a>, <a class="el" href="vacc_8c-source.html#l01620">Vacc_wcaEnergy()</a>, <a class="el" href="vcsm_8c-source.html#l00172">Vcsm_init()</a>, <a class="el" href="vfetk_8c-source.html#l00520">Vfetk_getAtomColor()</a>, <a class="el" href="vfetk_8c-source.html#l00698">Vfetk_qfEnergy()</a>, <a class="el" href="vfetk_8c-source.html#l00806">Vfetk_setAtomColors()</a>, <a class="el" href="vgreen_8c-source.html#l00257">Vgreen_coulomb()</a>, <a class="el" href="vgreen_8c-source.html#l00223">Vgreen_coulomb_direct()</a>, <a class="el" href="vgreen_8c-source.html#l00361">Vgreen_coulombD()</a>, <a class="el" href="vgreen_8c-source.html#l00309">Vgreen_coulombD_direct()</a>, <a class="el" href="vpbe_8c-source.html#l00212">Vpbe_ctor2()</a>, <a class="el" href="vpbe_8c-source.html#l00413">Vpbe_getCoulombEnergy1()</a>, <a class="el" href="vpmg_8c-source.html#l01064">Vpmg_polarizEnergy()</a>, <a class="el" href="vpmg_8c-source.html#l01507">Vpmg_qfEnergyPoint()</a>, <a class="el" href="vpmg_8c-source.html#l00553">Vpmg_setPart()</a>, and <a class="el" href="vpmg_8c-source.html#l00798">Vpmg_unsetPart()</a>.</p>
</div>
</div><p>
<a class="anchor" name="g902e23e51a90ae7d7dec67c904e83049"></a><!-- doxytag: member="valist.h::Valist_getStatistics" ref="g902e23e51a90ae7d7dec67c904e83049" args="(Valist *thee)" -->
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<td class="memname">Vrc_Codes Valist_getStatistics </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Load up Valist with various statistics.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker, Yong Huang </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Success enumeration </dd></dl>
<p>References <a class="el" href="valist_8h-source.html#l00084">sValist::atoms</a>, <a class="el" href="valist_8h-source.html#l00079">sValist::center</a>, <a class="el" href="vatom_8h-source.html#l00077">sVatom::charge</a>, <a class="el" href="valist_8h-source.html#l00083">sValist::charge</a>, <a class="el" href="valist_8h-source.html#l00081">sValist::maxcrd</a>, <a class="el" href="valist_8h-source.html#l00082">sValist::maxrad</a>, <a class="el" href="valist_8h-source.html#l00080">sValist::mincrd</a>, <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>, <a class="el" href="vatom_8h-source.html#l00075">sVatom::position</a>, <a class="el" href="vatom_8h-source.html#l00076">sVatom::radius</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, and <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>.</p>
<p>Referenced by <a class="el" href="valist_8c-source.html#l00514">Valist_readPDB()</a>, <a class="el" href="valist_8c-source.html#l00605">Valist_readPQR()</a>, and <a class="el" href="valist_8c-source.html#l00709">Valist_readXML()</a>.</p>
</div>
</div><p>
<a class="anchor" name="gca9784596feb23190c376fe10c85265f"></a><!-- doxytag: member="valist.h::Valist_memChk" ref="gca9784596feb23190c376fe10c85265f" args="(Valist *thee)" -->
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<td class="memname">unsigned long int Valist_memChk </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Get total memory allocated for this object and its members.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Total memory in bytes </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
</table>
</dl>
<p>References <a class="el" href="valist_8h-source.html#l00085">sValist::vmem</a>.</p>
</div>
</div><p>
<a class="anchor" name="g155ec618d8938ccf2cff609d9811b7db"></a><!-- doxytag: member="valist.h::Valist_readPDB" ref="g155ec618d8938ccf2cff609d9811b7db" args="(Valist *thee, Vparam *param, Vio *sock)" -->
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<td class="memname">Vrc_Codes Valist_readPDB </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structVparam.html">Vparam</a> * </td>
<td class="paramname"> <em>param</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Vio * </td>
<td class="paramname"> <em>sock</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Fill atom list with information from a PDB file.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker, Todd Dolinsky, Yong Huang </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Success enumeration </dd></dl>
<dl class="note" compact><dt><b>Note:</b></dt><dd>We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999. </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
<tr><td valign="top"><em>param</em> </td><td>
A pre-initialized parameter object </td></tr>
<tr><td valign="top"><em>sock</em> </td><td>
Socket read for reading PDB file </td></tr>
</table>
</dl>
<p>References <a class="el" href="vparam_8h-source.html#l00088">sVparam_AtomData::charge</a>, <a class="el" href="vparam_8h-source.html#l00090">sVparam_AtomData::epsilon</a>, <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>, <a class="el" href="vparam_8h-source.html#l00089">sVparam_AtomData::radius</a>, <a class="el" href="valist_8c-source.html#l00853">Valist_getStatistics()</a>, <a class="el" href="vatom_8c-source.html#l00090">Vatom_setAtomID()</a>, <a class="el" href="vatom_8c-source.html#l00194">Vatom_setAtomName()</a>, <a class="el" href="vatom_8c-source.html#l00111">Vatom_setCharge()</a>, <a class="el" href="group__Vatom.html#gc17a9120ddc6cfe671e8e27dc9a2600d">Vatom_setEpsilon()</a>, <a class="el" href="vatom_8c-source.html#l00155">Vatom_setPosition()</a>, <a class="el" href="vatom_8c-source.html#l00097">Vatom_setRadius()</a>, <a class="el" href="vatom_8c-source.html#l00179">Vatom_setResName()</a>, <a class="el" href="valist_8h-source.html#l00085">sValist::vmem</a>, <a class="el" href="vparam_8c-source.html#l00270">Vparam_getAtomData()</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, and <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l00112">loadMolecules()</a>.</p>
<p>
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Here is the call graph for this function:</div>
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<p><center><img src="group__Valist_g155ec618d8938ccf2cff609d9811b7db_cgraph.png" border="0" usemap="#group__Valist_g155ec618d8938ccf2cff609d9811b7db_cgraph_map" alt=""></center>
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<a class="anchor" name="g501998331453e488840902156653ef18"></a><!-- doxytag: member="valist.h::Valist_readPQR" ref="g501998331453e488840902156653ef18" args="(Valist *thee, Vparam *param, Vio *sock)" -->
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<td class="memname">Vrc_Codes Valist_readPQR </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structVparam.html">Vparam</a> * </td>
<td class="paramname"> <em>param</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">Vio * </td>
<td class="paramname"> <em>sock</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Fill atom list with information from a PQR file.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker, Yong Huang </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Success enumeration </dd></dl>
<dl class="note" compact><dt><b>Note:</b></dt><dd><ul>
<li>A PQR file has PDB structure with charge and radius in the last two columns instead of weight and occupancy </li>
<li>We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999. </li>
</ul>
</dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
<tr><td valign="top"><em>param</em> </td><td>
A pre-initialized parameter object </td></tr>
<tr><td valign="top"><em>sock</em> </td><td>
Socket reading for reading PQR file </td></tr>
</table>
</dl>
<p>References <a class="el" href="vparam_8h-source.html#l00088">sVparam_AtomData::charge</a>, <a class="el" href="vparam_8h-source.html#l00090">sVparam_AtomData::epsilon</a>, <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>, <a class="el" href="vparam_8h-source.html#l00089">sVparam_AtomData::radius</a>, <a class="el" href="valist_8c-source.html#l00853">Valist_getStatistics()</a>, <a class="el" href="vatom_8c-source.html#l00090">Vatom_setAtomID()</a>, <a class="el" href="vatom_8c-source.html#l00194">Vatom_setAtomName()</a>, <a class="el" href="vatom_8c-source.html#l00111">Vatom_setCharge()</a>, <a class="el" href="group__Vatom.html#gc17a9120ddc6cfe671e8e27dc9a2600d">Vatom_setEpsilon()</a>, <a class="el" href="vatom_8c-source.html#l00155">Vatom_setPosition()</a>, <a class="el" href="vatom_8c-source.html#l00097">Vatom_setRadius()</a>, <a class="el" href="vatom_8c-source.html#l00179">Vatom_setResName()</a>, <a class="el" href="valist_8h-source.html#l00085">sValist::vmem</a>, <a class="el" href="vparam_8c-source.html#l00270">Vparam_getAtomData()</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, and <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l00112">loadMolecules()</a>.</p>
<p>
<div class="dynheader">
Here is the call graph for this function:</div>
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<a class="anchor" name="g79d3ae98e4903139c3f0172286c48d8a"></a><!-- doxytag: member="valist.h::Valist_readXML" ref="g79d3ae98e4903139c3f0172286c48d8a" args="(Valist *thee, Vparam *param, Vio *sock)" -->
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<td class="memname">Vrc_Codes Valist_readXML </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td class="paramtype"><a class="el" href="structVparam.html">Vparam</a> * </td>
<td class="paramname"> <em>param</em>, </td>
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<td class="paramtype">Vio * </td>
<td class="paramname"> <em>sock</em></td><td> </td>
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Fill atom list with information from an XML file.
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<dl class="author" compact><dt><b>Author:</b></dt><dd>Todd Dolinsky, Yong Huang </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Success enumeration </dd></dl>
<dl class="note" compact><dt><b>Note:</b></dt><dd><ul>
<li>The XML file must adhere to some guidelines, notably the presence of an <atom> tag with all other useful information (x, y, z, charge, and radius) as nested elements. </li>
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</dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>thee</em> </td><td>
Atom list object </td></tr>
<tr><td valign="top"><em>param</em> </td><td>
A pre-initialized parameter object </td></tr>
<tr><td valign="top"><em>sock</em> </td><td>
Socket reading for reading PQR file </td></tr>
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<p>References <a class="el" href="valist_8h-source.html#l00078">sValist::number</a>, <a class="el" href="valist_8c-source.html#l00853">Valist_getStatistics()</a>, <a class="el" href="vatom_8c-source.html#l00090">Vatom_setAtomID()</a>, <a class="el" href="vatom_8c-source.html#l00111">Vatom_setCharge()</a>, <a class="el" href="vatom_8c-source.html#l00155">Vatom_setPosition()</a>, <a class="el" href="vatom_8c-source.html#l00097">Vatom_setRadius()</a>, <a class="el" href="valist_8h-source.html#l00085">sValist::vmem</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, and <a class="el" href="vstring_8c-source.html#l00012">Vstring_strcasecmp()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l00112">loadMolecules()</a>.</p>
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