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<h1>Vacc class</h1>Solvent- and ion-accessibility oracle.
<a href="#_details">More...</a>
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<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="structsVaccSurf.html">sVaccSurf</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Surface object list of per-atom surface points. <a href="structsVaccSurf.html#_details">More...</a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">struct </td><td class="memItemRight" valign="bottom"><a class="el" href="structsVacc.html">sVacc</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Oracle for solvent- and ion-accessibility around a biomolecule. <a href="structsVacc.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="vacc_8h.html">vacc.h</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Contains declarations for class Vacc. <br></td></tr>
<p>
<tr><td class="memItemLeft" nowrap align="right" valign="top">file </td><td class="memItemRight" valign="bottom"><a class="el" href="vacc_8c.html">vacc.c</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Class Vacc methods. <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="g161302d3e4967f0aff1e29689e809830"></a><!-- doxytag: member="Vacc::VaccSurf" ref="g161302d3e4967f0aff1e29689e809830" args="" -->
typedef struct <a class="el" href="structsVaccSurf.html">sVaccSurf</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#g161302d3e4967f0aff1e29689e809830">VaccSurf</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Declaration of the VaccSurf class as the VaccSurf structure. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="g1a2ce5f1b6f25fd5efadc5ab0aacbc9c"></a><!-- doxytag: member="Vacc::Vacc" ref="g1a2ce5f1b6f25fd5efadc5ab0aacbc9c" args="" -->
typedef struct <a class="el" href="structsVacc.html">sVacc</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#g1a2ce5f1b6f25fd5efadc5ab0aacbc9c">Vacc</a></td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Declaration of the Vacc class as the Vacc structure. <br></td></tr>
<tr><td colspan="2"><br><h2>Functions</h2></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__Vacc.html#g4df8b067a7d87b4b06a3d9adc9b0f0be">Vacc_memChk</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get number of bytes in this object and its members. <a href="#g4df8b067a7d87b4b06a3d9adc9b0f0be"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structsVaccSurf.html">VaccSurf</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#gf645f700c467833a3611fadb606d16e5">VaccSurf_ctor</a> (Vmem *mem, double probe_radius, int nsphere)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Allocate and construct the surface object; do not assign surface points to positions. <a href="#gf645f700c467833a3611fadb606d16e5"></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__Vacc.html#g7b5d73ff3b8ae17c8efad24ce683de78">VaccSurf_ctor2</a> (<a class="el" href="structsVaccSurf.html">VaccSurf</a> *thee, Vmem *mem, double probe_radius, int nsphere)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Construct the surface object using previously allocated memory; do not assign surface points to positions. <a href="#g7b5d73ff3b8ae17c8efad24ce683de78"></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__Vacc.html#gf015a95a7934819baf6ac85a2c19e499">VaccSurf_dtor</a> (<a class="el" href="structsVaccSurf.html">VaccSurf</a> **thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy the surface object and free its memory. <a href="#gf015a95a7934819baf6ac85a2c19e499"></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__Vacc.html#g90b879964a5faa185a82dc2f7c736a15">VaccSurf_dtor2</a> (<a class="el" href="structsVaccSurf.html">VaccSurf</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy the surface object. <a href="#g90b879964a5faa185a82dc2f7c736a15"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structsVaccSurf.html">VaccSurf</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#gb4df080067f12568eb4336687b676cea">VaccSurf_refSphere</a> (Vmem *mem, int npts)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set up an array of points for a reference sphere of unit radius. <a href="#gb4df080067f12568eb4336687b676cea"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structsVaccSurf.html">VaccSurf</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#g6e118e97d0ef09899dd376b6eda231a7">Vacc_atomSurf</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, <a class="el" href="structsVatom.html">Vatom</a> *atom, <a class="el" href="structsVaccSurf.html">VaccSurf</a> *ref, double probe_radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Set up an array of points corresponding to the SAS due to a particular atom. <a href="#g6e118e97d0ef09899dd376b6eda231a7"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structsVacc.html">Vacc</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#gc712e4ab9b88c9e260f6cfb33f0c6646">Vacc_ctor</a> (<a class="el" href="structsValist.html">Valist</a> *alist, <a class="el" href="structsVclist.html">Vclist</a> *clist, double surf_density)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Construct the accessibility object. <a href="#gc712e4ab9b88c9e260f6cfb33f0c6646"></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__Vacc.html#gf6a84e11159cedc6692cb2b254b6530f">Vacc_ctor2</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, <a class="el" href="structsValist.html">Valist</a> *alist, <a class="el" href="structsVclist.html">Vclist</a> *clist, double surf_density)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub to construct the accessibility object. <a href="#gf6a84e11159cedc6692cb2b254b6530f"></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__Vacc.html#gf3712a0a2c431f3754d53776e6c2087c">Vacc_dtor</a> (<a class="el" href="structsVacc.html">Vacc</a> **thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Destroy object. <a href="#gf3712a0a2c431f3754d53776e6c2087c"></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__Vacc.html#g0b80af5fb860c96d52738f65f42a38d6">Vacc_dtor2</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">FORTRAN stub to destroy object. <a href="#g0b80af5fb860c96d52738f65f42a38d6"></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__Vacc.html#g2b52e74285215d0138d3a1bad46b556f">Vacc_vdwAcc</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM])</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report van der Waals accessibility. <a href="#g2b52e74285215d0138d3a1bad46b556f"></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__Vacc.html#g6e3d06de84edfdedec72f6c39fe6b58f">Vacc_ivdwAcc</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report inflated van der Waals accessibility. <a href="#g6e3d06de84edfdedec72f6c39fe6b58f"></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__Vacc.html#g14c8339e2806380b18aad1e88fe66b71">Vacc_molAcc</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report molecular accessibility. <a href="#g14c8339e2806380b18aad1e88fe66b71"></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__Vacc.html#g771fa3d6536e75841ee6fcbead1660f0">Vacc_fastMolAcc</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report molecular accessibility quickly. <a href="#g771fa3d6536e75841ee6fcbead1660f0"></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__Vacc.html#g6f4eb93667854820fbfc4478e60a618e">Vacc_splineAcc</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double win, double infrad)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report spline-based accessibility. <a href="#g6f4eb93667854820fbfc4478e60a618e"></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__Vacc.html#g0e55024fa647abcce69cae081ba795e7">Vacc_splineAccGrad</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double win, double infrad, double *grad)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report gradient of spline-based accessibility. <a href="#g0e55024fa647abcce69cae081ba795e7"></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__Vacc.html#g6c202624954a3bd3fde446182415c769">Vacc_splineAccAtom</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double win, double infrad, <a class="el" href="structsVatom.html">Vatom</a> *atom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report spline-based accessibility for a given atom. <a href="#g6c202624954a3bd3fde446182415c769"></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__Vacc.html#gd54f2225fecac9de987ea3916e241ce4">Vacc_splineAccGradAtomUnnorm</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double win, double infrad, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *force)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report gradient of spline-based accessibility with respect to a particular atom (see Vpmg_splineAccAtom). <a href="#gd54f2225fecac9de987ea3916e241ce4"></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__Vacc.html#g86e395e15ef9298b4f9cc50b9e6da656">Vacc_splineAccGradAtomNorm</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double win, double infrad, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *force)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report gradient of spline-based accessibility with respect to a particular atom normalized by the accessibility value due to that atom at that point (see Vpmg_splineAccAtom). <a href="#g86e395e15ef9298b4f9cc50b9e6da656"></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__Vacc.html#gc90a25448405539eb8f2178874d496f8">Vacc_splineAccGradAtomNorm4</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double win, double infrad, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *force)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report gradient of spline-based accessibility with respect to a particular atom normalized by a 4th order accessibility value due to that atom at that point (see Vpmg_splineAccAtom). <a href="#gc90a25448405539eb8f2178874d496f8"></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__Vacc.html#g9f24abc998c44e87ff1805256e520f15">Vacc_splineAccGradAtomNorm3</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double center[VAPBS_DIM], double win, double infrad, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *force)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Report gradient of spline-based accessibility with respect to a particular atom normalized by a 3rd order accessibility value due to that atom at that point (see Vpmg_splineAccAtom). <a href="#g9f24abc998c44e87ff1805256e520f15"></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__Vacc.html#g7a741d87762baf5906802b6b9a670080">Vacc_SASA</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area. <a href="#g7a741d87762baf5906802b6b9a670080"></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__Vacc.html#g5514738fb5b25bc0a2c76fa165820a73">Vacc_totalSASA</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the total solvent accessible surface area (SASA). <a href="#g5514738fb5b25bc0a2c76fa165820a73"></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__Vacc.html#gea1fe0e1ddebb4f1ae9dac8a78902220">Vacc_atomSASA</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double radius, <a class="el" href="structsVatom.html">Vatom</a> *atom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the atomic solvent accessible surface area (SASA). <a href="#gea1fe0e1ddebb4f1ae9dac8a78902220"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structsVaccSurf.html">VaccSurf</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#g031408ad5ca9a5bdb7fd9ae1b6e08150">Vacc_atomSASPoints</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double radius, <a class="el" href="structsVatom.html">Vatom</a> *atom)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the set of points for this atom's solvent-accessible surface. <a href="#g031408ad5ca9a5bdb7fd9ae1b6e08150"></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__Vacc.html#gedd9cfb498a5c9a62541d6da92b8c347">Vacc_atomdSAV</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double radius, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *dSA)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the derivatve of solvent accessible volume. <a href="#gedd9cfb498a5c9a62541d6da92b8c347"></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__Vacc.html#gcdc19153ae8a5bf67a84b48c0325e57f">Vacc_atomdSASA</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double dpos, double radius, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *dSA)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Get the derivatve of solvent accessible area. <a href="#gcdc19153ae8a5bf67a84b48c0325e57f"></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__Vacc.html#g98dd210e3d60c845ddda30c66dbf52cd">Vacc_totalAtomdSASA</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double dpos, double radius, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *dSA)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Testing purposes only. <a href="#g98dd210e3d60c845ddda30c66dbf52cd"></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__Vacc.html#ge312e96f78bd62c44ad1b269667ce3cc">Vacc_totalAtomdSAV</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, double dpos, double radius, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *dSA, <a class="el" href="structsVclist.html">Vclist</a> *clist)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Total solvent accessible volume. <a href="#ge312e96f78bd62c44ad1b269667ce3cc"></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__Vacc.html#gb044e1d67b1e8df949f7314a82d8a8ca">Vacc_totalSAV</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, <a class="el" href="structsVclist.html">Vclist</a> *clist, <a class="el" href="structsAPOLparm.html">APOLparm</a> *apolparm, double radius)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the total solvent accessible volume (SAV). <a href="#gb044e1d67b1e8df949f7314a82d8a8ca"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#gde3a80a1f4f87a4b41e17df2a8b93d89">Vacc_wcaEnergy</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, <a class="el" href="structsAPOLparm.html">APOLparm</a> *apolparm, <a class="el" href="structsValist.html">Valist</a> *alist, <a class="el" href="structsVclist.html">Vclist</a> *clist)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the WCA integral energy. <a href="#gde3a80a1f4f87a4b41e17df2a8b93d89"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">VPUBLIC int </td><td class="memItemRight" valign="bottom"><a class="el" href="group__Vacc.html#gf36362999a330e766a98355f4fed5f21">Vacc_wcaForceAtom</a> (<a class="el" href="structsVacc.html">Vacc</a> *thee, <a class="el" href="structsAPOLparm.html">APOLparm</a> *apolparm, <a class="el" href="structsVclist.html">Vclist</a> *clist, <a class="el" href="structsVatom.html">Vatom</a> *atom, double *force)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Return the WCA integral force. <a href="#gf36362999a330e766a98355f4fed5f21"></a><br></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
Solvent- and ion-accessibility oracle. <hr><h2>Function Documentation</h2>
<a class="anchor" name="gcdc19153ae8a5bf67a84b48c0325e57f"></a><!-- doxytag: member="vacc.h::Vacc_atomdSASA" ref="gcdc19153ae8a5bf67a84b48c0325e57f" args="(Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)" -->
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<td class="memname">void Vacc_atomdSASA </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>dpos</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>dSA</em></td><td> </td>
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<td>)</td>
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<div class="memdoc">
<p>
Get the derivatve of solvent accessible area.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Jason Wagoner, David Gohara, Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>dpos</em> </td><td>
Acessibility object </td></tr>
<tr><td valign="top"><em>radius</em> </td><td>
Atom position offset </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Probe radius (Å) </td></tr>
<tr><td valign="top"><em>dSA</em> </td><td>
Atom of interest Array holding answers of calc </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03910">forceAPOL()</a>.</p>
</div>
</div><p>
<a class="anchor" name="gedd9cfb498a5c9a62541d6da92b8c347"></a><!-- doxytag: member="vacc.h::Vacc_atomdSAV" ref="gedd9cfb498a5c9a62541d6da92b8c347" args="(Vacc *thee, double radius, Vatom *atom, double *dSA)" -->
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<td class="memname">void Vacc_atomdSAV </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>dSA</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<div class="memdoc">
<p>
Get the derivatve of solvent accessible volume.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Jason Wagoner, Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>radius</em> </td><td>
Acessibility object </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Probe radius (Å) </td></tr>
<tr><td valign="top"><em>dSA</em> </td><td>
Atom of interest Array holding answers of calc </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03910">forceAPOL()</a>.</p>
</div>
</div><p>
<a class="anchor" name="gea1fe0e1ddebb4f1ae9dac8a78902220"></a><!-- doxytag: member="vacc.h::Vacc_atomSASA" ref="gea1fe0e1ddebb4f1ae9dac8a78902220" args="(Vacc *thee, double radius, Vatom *atom)" -->
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<td class="memname">double Vacc_atomSASA </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em></td><td> </td>
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<td></td>
<td>)</td>
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<div class="memdoc">
<p>
Return the atomic solvent accessible surface area (SASA).
<p>
<dl class="note" compact><dt><b>Note:</b></dt><dd>Alias for Vacc_SASA </dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Atomic solvent accessible area (A^2) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>radius</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Probe molecule radius (Å) Atom of interest </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00086">sVaccSurf::area</a>, <a class="el" href="vacc_8h-source.html#l00088">sVaccSurf::probe_radius</a>, <a class="el" href="vacc_8h-source.html#l00111">sVacc::refSphere</a>, <a class="el" href="vacc_8h-source.html#l00112">sVacc::surf</a>, <a class="el" href="vacc_8c-source.html#l00789">Vacc_atomSurf()</a>, <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>, <a class="el" href="vacc_8c-source.html#l00775">VaccSurf_dtor2()</a>, and <a class="el" href="vatom_8c-source.html#l00083">Vatom_getAtomID()</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l03976">fillcoCoefMolDielNoSmooth()</a>, and <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>.</p>
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<a class="anchor" name="g031408ad5ca9a5bdb7fd9ae1b6e08150"></a><!-- doxytag: member="vacc.h::Vacc_atomSASPoints" ref="g031408ad5ca9a5bdb7fd9ae1b6e08150" args="(Vacc *thee, double radius, Vatom *atom)" -->
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<td class="memname"><a class="el" href="structsVaccSurf.html">VaccSurf</a>* Vacc_atomSASPoints </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
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<div class="memdoc">
<p>
Get the set of points for this atom's solvent-accessible surface.
<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 VaccSurf object for this atom </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>radius</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Probe molecule radius (Å) Atom of interest </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00088">sVaccSurf::probe_radius</a>, <a class="el" href="vacc_8h-source.html#l00111">sVacc::refSphere</a>, <a class="el" href="vacc_8h-source.html#l00112">sVacc::surf</a>, <a class="el" href="vacc_8c-source.html#l00789">Vacc_atomSurf()</a>, <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>, <a class="el" href="vacc_8c-source.html#l00775">VaccSurf_dtor2()</a>, and <a class="el" href="vatom_8c-source.html#l00083">Vatom_getAtomID()</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l03976">fillcoCoefMolDielNoSmooth()</a>.</p>
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<a class="anchor" name="g6e118e97d0ef09899dd376b6eda231a7"></a><!-- doxytag: member="vacc.h::Vacc_atomSurf" ref="g6e118e97d0ef09899dd376b6eda231a7" args="(Vacc *thee, Vatom *atom, VaccSurf *ref, double probe_radius)" -->
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<td class="memname"><a class="el" href="structsVaccSurf.html">VaccSurf</a>* Vacc_atomSurf </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVaccSurf.html">VaccSurf</a> * </td>
<td class="paramname"> <em>ref</em>, </td>
</tr>
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<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>probe_radius</em></td><td> </td>
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<td></td>
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<div class="memdoc">
<p>
Set up an array of points corresponding to the SAS due to a particular atom.
<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>Atom sphere surface object </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>atom</em> </td><td>
Accessibility object for molecule </td></tr>
<tr><td valign="top"><em>ref</em> </td><td>
Atom for which the surface should be constructed </td></tr>
<tr><td valign="top"><em>probe_radius</em> </td><td>
Reference sphere which sets the resolution for the surface. <dl class="see" compact><dt><b>See also:</b></dt><dd><a class="el" href="group__Vacc.html#gb4df080067f12568eb4336687b676cea" title="Set up an array of points for a reference sphere of unit radius.">VaccSurf_refSphere</a> Probe radius (in A) </dd></dl>
</td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00086">sVaccSurf::area</a>, <a class="el" href="vacc_8h-source.html#l00084">sVaccSurf::bpts</a>, <a class="el" href="vacc_8c-source.html#l00083">ivdwAccExclus()</a>, <a class="el" href="vacc_8h-source.html#l00105">sVacc::mem</a>, <a class="el" href="vacc_8h-source.html#l00087">sVaccSurf::npts</a>, <a class="el" href="vacc_8c-source.html#l00728">VaccSurf_ctor()</a>, <a class="el" href="vatom_8c-source.html#l00083">Vatom_getAtomID()</a>, <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>, <a class="el" href="vacc_8h-source.html#l00081">sVaccSurf::xpts</a>, <a class="el" href="vacc_8h-source.html#l00082">sVaccSurf::ypts</a>, and <a class="el" href="vacc_8h-source.html#l00083">sVaccSurf::zpts</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03910">forceAPOL()</a>, <a class="el" href="vacc_8c-source.html#l00705">Vacc_atomSASA()</a>, <a class="el" href="vacc_8c-source.html#l00900">Vacc_atomSASPoints()</a>, and <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>.</p>
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<a class="anchor" name="gc712e4ab9b88c9e260f6cfb33f0c6646"></a><!-- doxytag: member="vacc.h::Vacc_ctor" ref="gc712e4ab9b88c9e260f6cfb33f0c6646" args="(Valist *alist, Vclist *clist, double surf_density)" -->
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<td class="memname"><a class="el" href="structsVacc.html">Vacc</a>* Vacc_ctor </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>, </td>
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<td class="paramtype"><a class="el" href="structsVclist.html">Vclist</a> * </td>
<td class="paramname"> <em>clist</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>surf_density</em></td><td> </td>
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<p>
Construct the accessibility 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>Newly allocated Vacc object </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>clist</em> </td><td>
Molecule for accessibility queries </td></tr>
<tr><td valign="top"><em>surf_density</em> </td><td>
Pre-constructed cell list for looking up atoms near specific positions Minimum per-atom solvent accessible surface point density (in pts/A^2) </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8c-source.html#l00201">Vacc_ctor2()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>, and <a class="el" href="vpbe_8c-source.html#l00212">Vpbe_ctor2()</a>.</p>
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<a class="anchor" name="gf6a84e11159cedc6692cb2b254b6530f"></a><!-- doxytag: member="vacc.h::Vacc_ctor2" ref="gf6a84e11159cedc6692cb2b254b6530f" args="(Vacc *thee, Valist *alist, Vclist *clist, double surf_density)" -->
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<td class="memname">int Vacc_ctor2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVclist.html">Vclist</a> * </td>
<td class="paramname"> <em>clist</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>surf_density</em></td><td> </td>
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<td>)</td>
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<p>
FORTRAN stub to construct the accessibility 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>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>alist</em> </td><td>
Memory for Vacc objet </td></tr>
<tr><td valign="top"><em>clist</em> </td><td>
Molecule for accessibility queries </td></tr>
<tr><td valign="top"><em>surf_density</em> </td><td>
Pre-constructed cell list for looking up atoms near specific positions Minimum per-atom solvent accessible surface point density (in pts/A^2) </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00105">sVacc::mem</a>, <a class="el" href="vacc_8h-source.html#l00112">sVacc::surf</a>, <a class="el" href="vacc_8c-source.html#l00182">Vacc_allocate()</a>, and <a class="el" href="vacc_8c-source.html#l00143">Vacc_storeParms()</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00130">Vacc_ctor()</a>.</p>
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<a class="anchor" name="gf3712a0a2c431f3754d53776e6c2087c"></a><!-- doxytag: member="vacc.h::Vacc_dtor" ref="gf3712a0a2c431f3754d53776e6c2087c" args="(Vacc **thee)" -->
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<td class="memname">void Vacc_dtor </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> ** </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Destroy object.
<p>
<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 memory location of object </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8c-source.html#l00240">Vacc_dtor2()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>, and <a class="el" href="vpbe_8c-source.html#l00407">Vpbe_dtor2()</a>.</p>
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<a class="anchor" name="g0b80af5fb860c96d52738f65f42a38d6"></a><!-- doxytag: member="vacc.h::Vacc_dtor2" ref="g0b80af5fb860c96d52738f65f42a38d6" args="(Vacc *thee)" -->
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<td class="memname">void Vacc_dtor2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
FORTRAN stub to destroy object.
<p>
<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 object </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00106">sVacc::alist</a>, <a class="el" href="vacc_8h-source.html#l00108">sVacc::atomFlags</a>, <a class="el" href="vacc_8h-source.html#l00105">sVacc::mem</a>, <a class="el" href="vacc_8h-source.html#l00111">sVacc::refSphere</a>, <a class="el" href="vacc_8h-source.html#l00112">sVacc::surf</a>, <a class="el" href="vacc_8c-source.html#l00762">VaccSurf_dtor()</a>, and <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00230">Vacc_dtor()</a>.</p>
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<a class="anchor" name="g771fa3d6536e75841ee6fcbead1660f0"></a><!-- doxytag: member="vacc.h::Vacc_fastMolAcc" ref="g771fa3d6536e75841ee6fcbead1660f0" args="(Vacc *thee, double center[VAPBS_DIM], double radius)" -->
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<td class="memname">double Vacc_fastMolAcc </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em></td><td> </td>
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<p>
Report molecular accessibility quickly.
<p>
Given a point which is INSIDE the collection of inflated van der Waals spheres, but OUTSIDE the collection of non-inflated van der Waals spheres, determine accessibility of a probe (of radius radius) at a given point, given a collection of atomic spheres. Uses molecular (Connolly) surface definition.<p>
<dl class="note" compact><dt><b>Note:</b></dt><dd>THIS ASSUMES YOU HAVE TESTED THAT THIS POINT IS DEFINITELY INSIDE THE INFLATED AND NON-INFLATED VAN DER WAALS SURFACES!</dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible) </dd></dl>
<dl compact><dt><b><a class="el" href="bug.html#_bug000005">Bug:</a></b></dt><dd>This routine has a slight bug which can generate very small internal regions of high dielectric (thanks to John Mongan and Jess Swanson for finding this) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>radius</em> </td><td>
Probe center coordinates Probe radius (in Å) </td></tr>
</table>
</dl>
<p>References <a class="el" href="vclist_8h-source.html#l00097">sVclistCell::atoms</a>, <a class="el" href="vacc_8h-source.html#l00107">sVacc::clist</a>, <a class="el" href="vclist_8h-source.html#l00098">sVclistCell::natoms</a>, <a class="el" href="vacc_8h-source.html#l00087">sVaccSurf::npts</a>, <a class="el" href="vacc_8h-source.html#l00112">sVacc::surf</a>, <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>, <a class="el" href="vatom_8c-source.html#l00083">Vatom_getAtomID()</a>, <a class="el" href="vclist_8c-source.html#l00426">Vclist_getCell()</a>, <a class="el" href="vacc_8h-source.html#l00081">sVaccSurf::xpts</a>, <a class="el" href="vacc_8h-source.html#l00082">sVaccSurf::ypts</a>, and <a class="el" href="vacc_8h-source.html#l00083">sVaccSurf::zpts</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00550">Vacc_molAcc()</a>.</p>
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<a class="anchor" name="g6e3d06de84edfdedec72f6c39fe6b58f"></a><!-- doxytag: member="vacc.h::Vacc_ivdwAcc" ref="g6e3d06de84edfdedec72f6c39fe6b58f" args="(Vacc *thee, double center[VAPBS_DIM], double radius)" -->
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<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<p>
Report inflated van der Waals accessibility.
<p>
Determines if a point is within the union of the spheres centered at the atomic centers with radii equal to the sum of the atomic van der Waals radius and the probe radius.<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>Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>radius</em> </td><td>
Probe center coordinates Probe radius (Å) </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00550">Vacc_molAcc()</a>, <a class="el" href="vacc_8c-source.html#l01402">Vacc_totalSAV()</a>, <a class="el" href="vacc_8c-source.html#l01655">Vacc_wcaForceAtom()</a>, <a class="el" href="vfetk_8c-source.html#l02215">Vfetk_fillArray()</a>, and <a class="el" href="vpmg_8c-source.html#l00818">Vpmg_fillArray()</a>.</p>
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<a class="anchor" name="g4df8b067a7d87b4b06a3d9adc9b0f0be"></a><!-- doxytag: member="vacc.h::Vacc_memChk" ref="g4df8b067a7d87b4b06a3d9adc9b0f0be" args="(Vacc *thee)" -->
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<td class="memname">unsigned long int Vacc_memChk </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</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 bytes in 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>Number of bytes allocated for object </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>
Object for memory check </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00105">sVacc::mem</a>.</p>
<p>Referenced by <a class="el" href="vpbe_8c-source.html#l00455">Vpbe_memChk()</a>.</p>
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<a class="anchor" name="g14c8339e2806380b18aad1e88fe66b71"></a><!-- doxytag: member="vacc.h::Vacc_molAcc" ref="g14c8339e2806380b18aad1e88fe66b71" args="(Vacc *thee, double center[VAPBS_DIM], double radius)" -->
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<td class="memname">double Vacc_molAcc </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
<td></td><td></td><td></td>
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<p>
Report molecular accessibility.
<p>
Determine accessibility of a probe (of radius radius) at a given point, given a collection of atomic spheres. Uses molecular (Connolly) surface definition.<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>Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible) </dd></dl>
<dl compact><dt><b><a class="el" href="bug.html#_bug000004">Bug:</a></b></dt><dd>This routine has a slight bug which can generate very small internal regions of high dielectric (thanks to John Mongan and Jess Swanson for finding this) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>radius</em> </td><td>
Probe center coordinates Probe radius (in Å) </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8c-source.html#l00579">Vacc_fastMolAcc()</a>, <a class="el" href="group__Vacc.html#g6e3d06de84edfdedec72f6c39fe6b58f">Vacc_ivdwAcc()</a>, and <a class="el" href="group__Vacc.html#g2b52e74285215d0138d3a1bad46b556f">Vacc_vdwAcc()</a>.</p>
<p>Referenced by <a class="el" href="vfetk_8c-source.html#l02215">Vfetk_fillArray()</a>, and <a class="el" href="vpmg_8c-source.html#l00818">Vpmg_fillArray()</a>.</p>
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<a class="anchor" name="g7a741d87762baf5906802b6b9a670080"></a><!-- doxytag: member="vacc.h::Vacc_SASA" ref="g7a741d87762baf5906802b6b9a670080" args="(Vacc *thee, double radius)" -->
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<td class="memname">double Vacc_SASA </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em></td><td> </td>
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<td></td>
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<p>
Build the solvent accessible surface (SAS) and calculate the solvent accessible surface area.
<p>
<dl class="note" compact><dt><b>Note:</b></dt><dd>Similar to UHBD FORTRAN routine by Brock Luty (returns UHBD's asas2) </dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker (original FORTRAN routine by Brock Luty) </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Total solvent accessible area (A^2) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>radius</em> </td><td>
Accessibility object Probe molecule radius (Å) </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00106">sVacc::alist</a>, <a class="el" href="vacc_8h-source.html#l00086">sVaccSurf::area</a>, <a class="el" href="vacc_8h-source.html#l00105">sVacc::mem</a>, <a class="el" href="vacc_8h-source.html#l00088">sVaccSurf::probe_radius</a>, <a class="el" href="vacc_8h-source.html#l00111">sVacc::refSphere</a>, <a class="el" href="vacc_8h-source.html#l00112">sVacc::surf</a>, <a class="el" href="vacc_8c-source.html#l00789">Vacc_atomSurf()</a>, <a class="el" href="vacc_8c-source.html#l00775">VaccSurf_dtor2()</a>, <a class="el" href="valist_8c-source.html#l00114">Valist_getAtom()</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, and <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00705">Vacc_atomSASA()</a>, <a class="el" href="vacc_8c-source.html#l00900">Vacc_atomSASPoints()</a>, <a class="el" href="vacc_8c-source.html#l00579">Vacc_fastMolAcc()</a>, and <a class="el" href="vacc_8c-source.html#l00699">Vacc_totalSASA()</a>.</p>
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<a class="anchor" name="g6f4eb93667854820fbfc4478e60a618e"></a><!-- doxytag: member="vacc.h::Vacc_splineAcc" ref="g6f4eb93667854820fbfc4478e60a618e" args="(Vacc *thee, double center[VAPBS_DIM], double win, double infrad)" -->
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<td class="memname">double Vacc_splineAcc </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em></td><td> </td>
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<p>
Report spline-based accessibility.
<p>
Determine accessibility at a given point, given a collection of atomic spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) definition suitable for force evalation; basically a cubic spline.<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>Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Probe center coordinates </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window (Å) Inflation radius (Å) for ion access. </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00108">sVacc::atomFlags</a>, <a class="el" href="vclist_8h-source.html#l00097">sVclistCell::atoms</a>, <a class="el" href="vacc_8h-source.html#l00107">sVacc::clist</a>, <a class="el" href="vatom_8h-source.html#l00082">sVatom::id</a>, <a class="el" href="vclist_8h-source.html#l00098">sVclistCell::natoms</a>, <a class="el" href="vacc_8c-source.html#l00435">splineAcc()</a>, <a class="el" href="vclist_8c-source.html#l00426">Vclist_getCell()</a>, and <a class="el" href="vclist_8c-source.html#l00071">Vclist_maxRadius()</a>.</p>
<p>Referenced by <a class="el" href="vfetk_8c-source.html#l02215">Vfetk_fillArray()</a>, and <a class="el" href="vpmg_8c-source.html#l00818">Vpmg_fillArray()</a>.</p>
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<a class="anchor" name="g6c202624954a3bd3fde446182415c769"></a><!-- doxytag: member="vacc.h::Vacc_splineAccAtom" ref="g6c202624954a3bd3fde446182415c769" args="(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom)" -->
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<td class="memname">double Vacc_splineAccAtom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
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<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em>, </td>
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<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em></td><td> </td>
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<p>
Report spline-based accessibility for a given atom.
<p>
Determine accessibility at a given point for a given atomic spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) definition suitable for force evalation; basically a cubic spline.<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>Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Probe center coordinates </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window (Å) </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Inflation radius (Å) for ion access. Atom </td></tr>
</table>
</dl>
<p>References <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00435">splineAcc()</a>.</p>
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<a class="anchor" name="g0e55024fa647abcce69cae081ba795e7"></a><!-- doxytag: member="vacc.h::Vacc_splineAccGrad" ref="g0e55024fa647abcce69cae081ba795e7" args="(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, double *grad)" -->
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<td class="memname">void Vacc_splineAccGrad </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>grad</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
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<p>
Report gradient of spline-based accessibility.
<p>
<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>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Probe center coordinates </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window (Å) </td></tr>
<tr><td valign="top"><em>grad</em> </td><td>
Inflation radius (Å) for ion access. 3-vector set to gradient of accessibility </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00108">sVacc::atomFlags</a>, <a class="el" href="vclist_8h-source.html#l00097">sVclistCell::atoms</a>, <a class="el" href="vacc_8h-source.html#l00107">sVacc::clist</a>, <a class="el" href="vatom_8h-source.html#l00082">sVatom::id</a>, <a class="el" href="vclist_8h-source.html#l00098">sVclistCell::natoms</a>, <a class="el" href="vacc_8c-source.html#l00435">splineAcc()</a>, <a class="el" href="vacc_8c-source.html#l00295">Vacc_splineAccGradAtomNorm()</a>, <a class="el" href="vclist_8c-source.html#l00426">Vclist_getCell()</a>, and <a class="el" href="vclist_8c-source.html#l00071">Vclist_maxRadius()</a>.</p>
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<a class="anchor" name="g86e395e15ef9298b4f9cc50b9e6da656"></a><!-- doxytag: member="vacc.h::Vacc_splineAccGradAtomNorm" ref="g86e395e15ef9298b4f9cc50b9e6da656" args="(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)" -->
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<td class="memname">void Vacc_splineAccGradAtomNorm </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Report gradient of spline-based accessibility with respect to a particular atom normalized by the accessibility value due to that atom at that point (see Vpmg_splineAccAtom).
<p>
Determine accessibility at a given point, given a collection of atomic spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) definition suitable for force evalation; basically a cubic spline.<p>
<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>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Probe center coordinates </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window (Å) </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Inflation radius (Å) for ion access. </td></tr>
<tr><td valign="top"><em>force</em> </td><td>
Atom VAPBS_DIM-vector set to gradient of accessibility </td></tr>
</table>
</dl>
<p>References <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00503">Vacc_splineAccGrad()</a>, and <a class="el" href="vpmg_8c-source.html#l01694">Vpmg_splineSelect()</a>.</p>
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<a class="anchor" name="g9f24abc998c44e87ff1805256e520f15"></a><!-- doxytag: member="vacc.h::Vacc_splineAccGradAtomNorm3" ref="g9f24abc998c44e87ff1805256e520f15" args="(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)" -->
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<td class="memname">void Vacc_splineAccGradAtomNorm3 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Report gradient of spline-based accessibility with respect to a particular atom normalized by a 3rd order accessibility value due to that atom at that point (see Vpmg_splineAccAtom).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Probe center coordinates </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window (Å) </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Inflation radius (Å) for ion access. </td></tr>
<tr><td valign="top"><em>force</em> </td><td>
Atom VAPBS_DIM-vector set to gradient of accessibility </td></tr>
</table>
</dl>
<p>References <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l01694">Vpmg_splineSelect()</a>.</p>
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<a class="anchor" name="gc90a25448405539eb8f2178874d496f8"></a><!-- doxytag: member="vacc.h::Vacc_splineAccGradAtomNorm4" ref="gc90a25448405539eb8f2178874d496f8" args="(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)" -->
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<td class="memname">void Vacc_splineAccGradAtomNorm4 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Report gradient of spline-based accessibility with respect to a particular atom normalized by a 4th order accessibility value due to that atom at that point (see Vpmg_splineAccAtom).
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Michael Schnieders </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Probe center coordinates </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window (Å) </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Inflation radius (Å) for ion access. </td></tr>
<tr><td valign="top"><em>force</em> </td><td>
Atom VAPBS_DIM-vector set to gradient of accessibility </td></tr>
</table>
</dl>
<p>References <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>.</p>
<p>Referenced by <a class="el" href="vpmg_8c-source.html#l01694">Vpmg_splineSelect()</a>.</p>
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<a class="anchor" name="gd54f2225fecac9de987ea3916e241ce4"></a><!-- doxytag: member="vacc.h::Vacc_splineAccGradAtomUnnorm" ref="gd54f2225fecac9de987ea3916e241ce4" args="(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, Vatom *atom, double *force)" -->
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<td class="memname">void Vacc_splineAccGradAtomUnnorm </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>win</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>infrad</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>force</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Report gradient of spline-based accessibility with respect to a particular atom (see Vpmg_splineAccAtom).
<p>
Determine accessibility at a given point, given a collection of atomic spheres. Uses Benoit Roux (Im et al, Comp Phys Comm, 111, 59--75, 1998) definition suitable for force evalation; basically a cubic spline.<p>
<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>center</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>win</em> </td><td>
Probe center coordinates </td></tr>
<tr><td valign="top"><em>infrad</em> </td><td>
Spline window (Å) </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Inflation radius (Å) for ion access. </td></tr>
<tr><td valign="top"><em>force</em> </td><td>
Atom VAPBS_DIM-vector set to gradient of accessibility </td></tr>
</table>
</dl>
<p>References <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>.</p>
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<a class="anchor" name="g98dd210e3d60c845ddda30c66dbf52cd"></a><!-- doxytag: member="vacc.h::Vacc_totalAtomdSASA" ref="g98dd210e3d60c845ddda30c66dbf52cd" args="(Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA)" -->
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<td class="memname">void Vacc_totalAtomdSASA </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>dpos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>dSA</em></td><td> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Testing purposes only.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara, Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>dpos</em> </td><td>
Acessibility object </td></tr>
<tr><td valign="top"><em>radius</em> </td><td>
Atom position offset </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Probe radius (Å) </td></tr>
<tr><td valign="top"><em>dSA</em> </td><td>
Atom of interest Array holding answers of calc </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00111">sVacc::refSphere</a>, <a class="el" href="vatom_8c-source.html#l00083">Vatom_getAtomID()</a>, <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>.</p>
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<a class="anchor" name="ge312e96f78bd62c44ad1b269667ce3cc"></a><!-- doxytag: member="vacc.h::Vacc_totalAtomdSAV" ref="ge312e96f78bd62c44ad1b269667ce3cc" args="(Vacc *thee, double dpos, double radius, Vatom *atom, double *dSA, Vclist *clist)" -->
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<td class="memname">void Vacc_totalAtomdSAV </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>dpos</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">double * </td>
<td class="paramname"> <em>dSA</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVclist.html">Vclist</a> * </td>
<td class="paramname"> <em>clist</em></td><td> </td>
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<p>
Total solvent accessible volume.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara, Nathan Baker </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>dpos</em> </td><td>
Acessibility object </td></tr>
<tr><td valign="top"><em>radius</em> </td><td>
Atom position offset </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Probe radius (Å) </td></tr>
<tr><td valign="top"><em>dSA</em> </td><td>
Atom of interest </td></tr>
<tr><td valign="top"><em>clist</em> </td><td>
Array holding answers of calc clist for this calculation </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00111">sVacc::refSphere</a>, <a class="el" href="vacc_8c-source.html#l01402">Vacc_totalSAV()</a>, <a class="el" href="vatom_8c-source.html#l00083">Vatom_getAtomID()</a>, <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, and <a class="el" href="vatom_8c-source.html#l00104">Vatom_getRadius()</a>.</p>
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<a class="anchor" name="g5514738fb5b25bc0a2c76fa165820a73"></a><!-- doxytag: member="vacc.h::Vacc_totalSASA" ref="g5514738fb5b25bc0a2c76fa165820a73" args="(Vacc *thee, double radius)" -->
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<td class="memname">double Vacc_totalSASA </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td class="paramname"> <em>radius</em></td><td> </td>
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<p>
Return the total solvent accessible surface area (SASA).
<p>
<dl class="note" compact><dt><b>Note:</b></dt><dd>Alias for Vacc_SASA </dd></dl>
<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 solvent accessible area (A^2) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>radius</em> </td><td>
Accessibility object Probe molecule radius (Å) </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>.</p>
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<a class="anchor" name="gb044e1d67b1e8df949f7314a82d8a8ca"></a><!-- doxytag: member="vacc.h::Vacc_totalSAV" ref="gb044e1d67b1e8df949f7314a82d8a8ca" args="(Vacc *thee, Vclist *clist, APOLparm *apolparm, double radius)" -->
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<td class="memname">double Vacc_totalSAV </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVclist.html">Vclist</a> * </td>
<td class="paramname"> <em>clist</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsAPOLparm.html">APOLparm</a> * </td>
<td class="paramname"> <em>apolparm</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>radius</em></td><td> </td>
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<td></td>
<td>)</td>
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<p>
Return the total solvent accessible volume (SAV).
<p>
<dl class="note" compact><dt><b>Note:</b></dt><dd>Alias for Vacc_SAV </dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Total solvent accessible volume (A^3) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>clist</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>apolparm</em> </td><td>
Clist for acc object </td></tr>
<tr><td valign="top"><em>radius</em> </td><td>
Apolar parameters -- could be VNULL if none required for this calculation. If VNULL, then default settings are used Probe molecule radius (Å) </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00128">sAPOLparm::grid</a>, <a class="el" href="vclist_8h-source.html#l00121">sVclist::lower_corner</a>, <a class="el" href="apolparm_8h-source.html#l00129">sAPOLparm::setgrid</a>, <a class="el" href="vclist_8h-source.html#l00122">sVclist::upper_corner</a>, and <a class="el" href="group__Vacc.html#g6e3d06de84edfdedec72f6c39fe6b58f">Vacc_ivdwAcc()</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>, and <a class="el" href="vacc_8c-source.html#l01347">Vacc_totalAtomdSAV()</a>.</p>
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<a class="anchor" name="g2b52e74285215d0138d3a1bad46b556f"></a><!-- doxytag: member="vacc.h::Vacc_vdwAcc" ref="g2b52e74285215d0138d3a1bad46b556f" args="(Vacc *thee, double center[VAPBS_DIM])" -->
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<td class="memname">double Vacc_vdwAcc </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramtype">double </td>
<td class="paramname"> <em>center</em>[VAPBS_DIM]</td><td> </td>
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<p>
Report van der Waals accessibility.
<p>
Determines if a point is within the union of the atomic spheres (with radii equal to their van der Waals radii).<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>Characteristic function value between 1.0 (accessible) and 0.0 (inaccessible) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>center</em> </td><td>
Accessibility object Probe center coordinates </td></tr>
</table>
</dl>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00550">Vacc_molAcc()</a>, <a class="el" href="vfetk_8c-source.html#l02215">Vfetk_fillArray()</a>, and <a class="el" href="vpmg_8c-source.html#l00818">Vpmg_fillArray()</a>.</p>
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<a class="anchor" name="gde3a80a1f4f87a4b41e17df2a8b93d89"></a><!-- doxytag: member="vacc.h::Vacc_wcaEnergy" ref="gde3a80a1f4f87a4b41e17df2a8b93d89" args="(Vacc *thee, APOLparm *apolparm, Valist *alist, Vclist *clist)" -->
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<td class="memname">VPUBLIC int Vacc_wcaEnergy </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsAPOLparm.html">APOLparm</a> * </td>
<td class="paramname"> <em>apolparm</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsValist.html">Valist</a> * </td>
<td class="paramname"> <em>alist</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVclist.html">Vclist</a> * </td>
<td class="paramname"> <em>clist</em></td><td> </td>
</tr>
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<td></td>
<td>)</td>
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<p>
Return the WCA integral energy.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>WCA energy (kJ/mol) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>apolparm</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>alist</em> </td><td>
Apolar calculation parameters </td></tr>
<tr><td valign="top"><em>clist</em> </td><td>
Alist for acc object Clist for acc object </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00134">sAPOLparm::bconc</a>, <a class="el" href="apolparm_8h-source.html#l00175">sAPOLparm::setwat</a>, <a class="el" href="valist_8c-source.html#l00104">Valist_getNumberAtoms()</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>, and <a class="el" href="apolparm_8h-source.html#l00172">sAPOLparm::wcaEnergy</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03696">initAPOL()</a>.</p>
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<a class="anchor" name="gf36362999a330e766a98355f4fed5f21"></a><!-- doxytag: member="vacc.h::Vacc_wcaForceAtom" ref="gf36362999a330e766a98355f4fed5f21" args="(Vacc *thee, APOLparm *apolparm, Vclist *clist, Vatom *atom, double *force)" -->
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<td class="memname">VPUBLIC int Vacc_wcaForceAtom </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVacc.html">Vacc</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
</tr>
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<td></td>
<td class="paramtype"><a class="el" href="structsAPOLparm.html">APOLparm</a> * </td>
<td class="paramname"> <em>apolparm</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structsVclist.html">Vclist</a> * </td>
<td class="paramname"> <em>clist</em>, </td>
</tr>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="structsVatom.html">Vatom</a> * </td>
<td class="paramname"> <em>atom</em>, </td>
</tr>
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<td></td>
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<td class="paramname"> <em>force</em></td><td> </td>
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<p>
Return the WCA integral force.
<p>
<dl class="author" compact><dt><b>Author:</b></dt><dd>David Gohara </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>WCA energy (kJ/mol/A) </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>apolparm</em> </td><td>
Accessibility object </td></tr>
<tr><td valign="top"><em>clist</em> </td><td>
Apolar calculation parameters </td></tr>
<tr><td valign="top"><em>atom</em> </td><td>
Clist for acc object </td></tr>
<tr><td valign="top"><em>force</em> </td><td>
Current atom Force for atom </td></tr>
</table>
</dl>
<p>References <a class="el" href="apolparm_8h-source.html#l00134">sAPOLparm::bconc</a>, <a class="el" href="vatom_8h-source.html#l00080">sVatom::epsilon</a>, <a class="el" href="apolparm_8h-source.html#l00128">sAPOLparm::grid</a>, <a class="el" href="vclist_8h-source.html#l00121">sVclist::lower_corner</a>, <a class="el" href="vatom_8h-source.html#l00076">sVatom::radius</a>, <a class="el" href="apolparm_8h-source.html#l00129">sAPOLparm::setgrid</a>, <a class="el" href="apolparm_8h-source.html#l00175">sAPOLparm::setwat</a>, <a class="el" href="apolparm_8h-source.html#l00149">sAPOLparm::srad</a>, <a class="el" href="vclist_8h-source.html#l00122">sVclist::upper_corner</a>, <a class="el" href="group__Vacc.html#g6e3d06de84edfdedec72f6c39fe6b58f">Vacc_ivdwAcc()</a>, <a class="el" href="vatom_8c-source.html#l00062">Vatom_getPosition()</a>, <a class="el" href="vhal_8h-source.html#l00074">VRC_FAILURE</a>, <a class="el" href="vhal_8h-source.html#l00075">VRC_SUCCESS</a>, <a class="el" href="apolparm_8h-source.html#l00169">sAPOLparm::watepsilon</a>, and <a class="el" href="apolparm_8h-source.html#l00168">sAPOLparm::watsigma</a>.</p>
<p>Referenced by <a class="el" href="routines_8c-source.html#l03910">forceAPOL()</a>.</p>
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<a class="anchor" name="gf645f700c467833a3611fadb606d16e5"></a><!-- doxytag: member="vacc.h::VaccSurf_ctor" ref="gf645f700c467833a3611fadb606d16e5" args="(Vmem *mem, double probe_radius, int nsphere)" -->
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<td class="memname"><a class="el" href="structsVaccSurf.html">VaccSurf</a>* VaccSurf_ctor </td>
<td>(</td>
<td class="paramtype">Vmem * </td>
<td class="paramname"> <em>mem</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>probe_radius</em>, </td>
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<td class="paramname"> <em>nsphere</em></td><td> </td>
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<p>
Allocate and construct the surface object; do not assign surface points to positions.
<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>Newly allocated and constructed surface object </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>probe_radius</em> </td><td>
Memory manager (can be VNULL) </td></tr>
<tr><td valign="top"><em>nsphere</em> </td><td>
Probe radius (in A) for this surface Number of points in sphere </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8c-source.html#l00737">VaccSurf_ctor2()</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00789">Vacc_atomSurf()</a>, and <a class="el" href="vacc_8c-source.html#l00844">VaccSurf_refSphere()</a>.</p>
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<a class="anchor" name="g7b5d73ff3b8ae17c8efad24ce683de78"></a><!-- doxytag: member="vacc.h::VaccSurf_ctor2" ref="g7b5d73ff3b8ae17c8efad24ce683de78" args="(VaccSurf *thee, Vmem *mem, double probe_radius, int nsphere)" -->
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<td class="memname">int VaccSurf_ctor2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVaccSurf.html">VaccSurf</a> * </td>
<td class="paramname"> <em>thee</em>, </td>
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<td class="paramtype">Vmem * </td>
<td class="paramname"> <em>mem</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">double </td>
<td class="paramname"> <em>probe_radius</em>, </td>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>nsphere</em></td><td> </td>
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<p>
Construct the surface object using previously allocated memory; do not assign surface points to positions.
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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>1 if successful, 0 otherwise </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>mem</em> </td><td>
Allocated memory </td></tr>
<tr><td valign="top"><em>probe_radius</em> </td><td>
Memory manager (can be VNULL) </td></tr>
<tr><td valign="top"><em>nsphere</em> </td><td>
Probe radius (in A) for this surface Number of points in sphere </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00086">sVaccSurf::area</a>, <a class="el" href="vacc_8h-source.html#l00084">sVaccSurf::bpts</a>, <a class="el" href="vacc_8h-source.html#l00080">sVaccSurf::mem</a>, <a class="el" href="vacc_8h-source.html#l00087">sVaccSurf::npts</a>, <a class="el" href="vacc_8h-source.html#l00088">sVaccSurf::probe_radius</a>, <a class="el" href="vacc_8h-source.html#l00081">sVaccSurf::xpts</a>, <a class="el" href="vacc_8h-source.html#l00082">sVaccSurf::ypts</a>, and <a class="el" href="vacc_8h-source.html#l00083">sVaccSurf::zpts</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00728">VaccSurf_ctor()</a>.</p>
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<a class="anchor" name="gf015a95a7934819baf6ac85a2c19e499"></a><!-- doxytag: member="vacc.h::VaccSurf_dtor" ref="gf015a95a7934819baf6ac85a2c19e499" args="(VaccSurf **thee)" -->
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<td class="memname">void VaccSurf_dtor </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVaccSurf.html">VaccSurf</a> ** </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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<p>
Destroy the surface object and free its memory.
<p>
<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>
Object to be destroyed </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8c-source.html#l00775">VaccSurf_dtor2()</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00240">Vacc_dtor2()</a>.</p>
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<a class="anchor" name="g90b879964a5faa185a82dc2f7c736a15"></a><!-- doxytag: member="vacc.h::VaccSurf_dtor2" ref="g90b879964a5faa185a82dc2f7c736a15" args="(VaccSurf *thee)" -->
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<td class="memname">void VaccSurf_dtor2 </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structsVaccSurf.html">VaccSurf</a> * </td>
<td class="paramname"> <em>thee</em> </td>
<td> ) </td>
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Destroy the surface object.
<p>
<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>
Object to be destroyed </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00084">sVaccSurf::bpts</a>, <a class="el" href="vacc_8h-source.html#l00080">sVaccSurf::mem</a>, <a class="el" href="vacc_8h-source.html#l00087">sVaccSurf::npts</a>, <a class="el" href="vacc_8h-source.html#l00081">sVaccSurf::xpts</a>, <a class="el" href="vacc_8h-source.html#l00082">sVaccSurf::ypts</a>, and <a class="el" href="vacc_8h-source.html#l00083">sVaccSurf::zpts</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00705">Vacc_atomSASA()</a>, <a class="el" href="vacc_8c-source.html#l00900">Vacc_atomSASPoints()</a>, <a class="el" href="vacc_8c-source.html#l00655">Vacc_SASA()</a>, and <a class="el" href="vacc_8c-source.html#l00762">VaccSurf_dtor()</a>.</p>
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<a class="anchor" name="gb4df080067f12568eb4336687b676cea"></a><!-- doxytag: member="vacc.h::VaccSurf_refSphere" ref="gb4df080067f12568eb4336687b676cea" args="(Vmem *mem, int npts)" -->
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<td class="memname"><a class="el" href="structsVaccSurf.html">VaccSurf</a>* VaccSurf_refSphere </td>
<td>(</td>
<td class="paramtype">Vmem * </td>
<td class="paramname"> <em>mem</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"> <em>npts</em></td><td> </td>
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<td></td>
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<p>
Set up an array of points for a reference sphere of unit radius.
<p>
Generates approximately npts # of points (actual number stored in thee->npts) somewhat uniformly distributed across a sphere of unit radius centered at the origin.<p>
<dl class="note" compact><dt><b>Note:</b></dt><dd>This routine was shamelessly ripped off from sphere.f from UHBD as developed by Michael K. Gilson.</dd></dl>
<dl class="author" compact><dt><b>Author:</b></dt><dd>Nathan Baker (original FORTRAN code by Mike Gilson) </dd></dl>
<dl class="return" compact><dt><b>Returns:</b></dt><dd>Reference sphere surface object </dd></dl>
<dl compact><dt><b>Parameters: </b></dt><dd>
<table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em>npts</em> </td><td>
Memory object Requested number of points on sphere </td></tr>
</table>
</dl>
<p>References <a class="el" href="vacc_8h-source.html#l00084">sVaccSurf::bpts</a>, <a class="el" href="vacc_8h-source.html#l00087">sVaccSurf::npts</a>, <a class="el" href="vacc_8c-source.html#l00728">VaccSurf_ctor()</a>, <a class="el" href="vunit_8h-source.html#l00102">Vunit_pi</a>, <a class="el" href="vacc_8h-source.html#l00081">sVaccSurf::xpts</a>, <a class="el" href="vacc_8h-source.html#l00082">sVaccSurf::ypts</a>, and <a class="el" href="vacc_8h-source.html#l00083">sVaccSurf::zpts</a>.</p>
<p>Referenced by <a class="el" href="vacc_8c-source.html#l00143">Vacc_storeParms()</a>.</p>
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