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<title>fpocket: asa.h File Reference</title>
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<li><a href="index.html"><span>Main Page</span></a></li>
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<li><a href="annotated.html"><span>Data Structures</span></a></li>
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<div class="contents">
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<h1>asa.h File Reference</h1><code>#include <math.h></code><br>
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<code>#include <stdio.h></code><br>
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<code>#include <stdlib.h></code><br>
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<code>#include <string.h></code><br>
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<code>#include <time.h></code><br>
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<code>#include <ctype.h></code><br>
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<code>#include "<a class="el" href="rpdb_8h-source.html">rpdb.h</a>"</code><br>
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<code>#include "<a class="el" href="voronoi_8h-source.html">voronoi.h</a>"</code><br>
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<code>#include "<a class="el" href="pocket_8h-source.html">pocket.h</a>"</code><br>
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<code>#include "<a class="el" href="psorting_8h-source.html">psorting.h</a>"</code><br>
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<code>#include "<a class="el" href="cluster_8h-source.html">cluster.h</a>"</code><br>
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<code>#include "<a class="el" href="refine_8h-source.html">refine.h</a>"</code><br>
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<code>#include "<a class="el" href="fparams_8h-source.html">fparams.h</a>"</code><br>
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<code>#include "<a class="el" href="memhandler_8h-source.html">memhandler.h</a>"</code><br>
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<p>
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<a href="asa_8h-source.html">Go to the source code of this file.</a><table border="0" cellpadding="0" cellspacing="0">
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<tr><td></td></tr>
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<tr><td colspan="2"><br><h2>Defines</h2></td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#e29930e8c39193c231d3c460904dd2e7">M_NSPIRAL</a> 100</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#056ee2e33f38bebc552b31d932eab912">M_PADDING</a> 1.0</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a> 1.4</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a> 2.2</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#598a3330b3c21701223ee0ca14316eca">PI</a> 3.1415926535897931</td></tr>
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<tr><td colspan="2"><br><h2>Functions</h2></td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#58ec805b7157432fb9de76b01334c0f2">atom_not_in_list</a> (<a class="el" href="structs__atm.html">s_atm</a> *a, <a class="el" href="structs__atm.html">s_atm</a> **atoms, int natoms)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#46b1e19813ef3f501d7ce77892e3bfcd">set_ASA</a> (<a class="el" href="structs__desc.html">s_desc</a> *desc, <a class="el" href="structs__pdb.html">s_pdb</a> *pdb, <a class="el" href="structs__vvertice.html">s_vvertice</a> **tvert, int nvert)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#0ff618e129d637481f9644fd029908b0">get_unique_atoms</a> (<a class="el" href="structs__vvertice.html">s_vvertice</a> **tvert, int nvert, int *n_ua, <a class="el" href="structs__atm.html">s_atm</a> **p, int na)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">float * </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#9df45773e08f04fb69a917e6ba206169">get_points_on_sphere</a> (int nop)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int * </td><td class="memItemRight" valign="bottom"><a class="el" href="asa_8h.html#566de76ed33c4ec6a1ef4d7fefa8a861">get_surrounding_atoms_idx</a> (<a class="el" href="structs__vvertice.html">s_vvertice</a> **tvert, int nvert, <a class="el" href="structs__pdb.html">s_pdb</a> *pdb, int *n_sa)</td></tr>
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</table>
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<hr><h2>Define Documentation</h2>
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<a class="anchor" name="e29930e8c39193c231d3c460904dd2e7"></a><!-- doxytag: member="asa.h::M_NSPIRAL" ref="e29930e8c39193c231d3c460904dd2e7" args="" -->
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<div class="memitem">
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<td class="memname">#define M_NSPIRAL 100 </td>
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</table>
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</div>
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<div class="memdoc">
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<p>
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COPYRIGHT DISCLAIMER<p>
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Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby disclaim all copyright interest in the program “fpocket” (which performs protein cavity detection) written by Vincent Le Guilloux and Peter Schmidtke.<p>
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Vincent Le Guilloux 28 November 2008 Peter Schmidtke 28 November 2008 Pierre Tuffery 28 November 2008<p>
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GNU GPL<p>
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This file is part of the fpocket package.<p>
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fpocket is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.<p>
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fpocket is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.<p>
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You should have received a copy of the GNU General Public License along with fpocket. If not, see <<a href="http://www.gnu.org/licenses/">http://www.gnu.org/licenses/</a>>.
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<p>Definition at line <a class="el" href="asa_8h-source.html#l00061">61</a> of file <a class="el" href="asa_8h-source.html">asa.h</a>.</p>
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<p>Referenced by <a class="el" href="asa_8c-source.html#l00267">set_ASA()</a>.</p>
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</div>
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</div><p>
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<a class="anchor" name="056ee2e33f38bebc552b31d932eab912"></a><!-- doxytag: member="asa.h::M_PADDING" ref="056ee2e33f38bebc552b31d932eab912" args="" -->
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<td class="memname">#define M_PADDING 1.0 </td>
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<p>
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<p>Definition at line <a class="el" href="asa_8h-source.html#l00062">62</a> of file <a class="el" href="asa_8h-source.html">asa.h</a>.</p>
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<p>Referenced by <a class="el" href="asa_8c-source.html#l00107">get_surrounding_atoms_idx()</a>.</p>
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</div>
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</div><p>
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<a class="anchor" name="1c4d87257acc6b058961c30286569414"></a><!-- doxytag: member="asa.h::M_PROBE_SIZE" ref="1c4d87257acc6b058961c30286569414" args="" -->
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<td class="memname">#define M_PROBE_SIZE 1.4 </td>
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<div class="memdoc">
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<p>
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<p>Definition at line <a class="el" href="asa_8h-source.html#l00063">63</a> of file <a class="el" href="asa_8h-source.html">asa.h</a>.</p>
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<p>Referenced by <a class="el" href="asa_8c-source.html#l00267">set_ASA()</a>.</p>
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</div>
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</div><p>
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<a class="anchor" name="13a4860468b1e1aa44b156df0f646a5f"></a><!-- doxytag: member="asa.h::M_PROBE_SIZE2" ref="13a4860468b1e1aa44b156df0f646a5f" args="" -->
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<td class="memname">#define M_PROBE_SIZE2 2.2 </td>
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<div class="memdoc">
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<p>
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<p>Definition at line <a class="el" href="asa_8h-source.html#l00064">64</a> of file <a class="el" href="asa_8h-source.html">asa.h</a>.</p>
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<p>Referenced by <a class="el" href="asa_8c-source.html#l00267">set_ASA()</a>.</p>
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</div>
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</div><p>
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<a class="anchor" name="598a3330b3c21701223ee0ca14316eca"></a><!-- doxytag: member="asa.h::PI" ref="598a3330b3c21701223ee0ca14316eca" args="" -->
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<td class="memname">#define PI 3.1415926535897931 </td>
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<p>
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<p>Definition at line <a class="el" href="asa_8h-source.html#l00065">65</a> of file <a class="el" href="asa_8h-source.html">asa.h</a>.</p>
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<p>Referenced by <a class="el" href="asa_8c-source.html#l00443">get_points_on_sphere()</a>, and <a class="el" href="asa_8c-source.html#l00267">set_ASA()</a>.</p>
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</div><p>
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<hr><h2>Function Documentation</h2>
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<a class="anchor" name="58ec805b7157432fb9de76b01334c0f2"></a><!-- doxytag: member="asa.h::atom_not_in_list" ref="58ec805b7157432fb9de76b01334c0f2" args="(s_atm *a, s_atm **atoms, int natoms)" -->
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<td class="memname">int atom_not_in_list </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structs__atm.html">s_atm</a> * </td>
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<td class="paramname"> <em>a</em>, </td>
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<td></td>
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<td class="paramtype"><a class="el" href="structs__atm.html">s_atm</a> ** </td>
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<td class="paramname"> <em>atoms</em>, </td>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">int </td>
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<td class="paramname"> <em>natoms</em></td><td> </td>
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<td></td>
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<td>)</td>
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<td></td><td></td><td></td>
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<a class="anchor" name="9df45773e08f04fb69a917e6ba206169"></a><!-- doxytag: member="asa.h::get_points_on_sphere" ref="9df45773e08f04fb69a917e6ba206169" args="(int nop)" -->
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<td class="memname">float* get_points_on_sphere </td>
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<td>(</td>
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<td class="paramtype">int </td>
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<td class="paramname"> <em>nop</em> </td>
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<td> ) </td>
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<p>
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## FUNCTION: get_points_on_sphere<p>
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## SPECIFICATION: This function takes an integer as argument and returns a unit sphere with distributed points on its surface according to the Golden Section Spiral Distribution<p>
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## PARAMETRES: @ int nop : number of points to create on the unit sphere (resolution of the surface)<p>
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## RETURN: float* : list of points on the unit sphere
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<p>Definition at line <a class="el" href="asa_8c-source.html#l00443">443</a> of file <a class="el" href="asa_8c-source.html">asa.c</a>.</p>
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<p>References <a class="el" href="asa_8h-source.html#l00065">PI</a>.</p>
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<p>Referenced by <a class="el" href="asa_8c-source.html#l00267">set_ASA()</a>.</p>
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<div class="fragment"><pre class="fragment"><a name="l00443"></a>00443 {
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<a name="l00444"></a>00444 <span class="keywordtype">float</span> *pts =NULL;
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<a name="l00445"></a>00445 pts=(<span class="keywordtype">float</span> *) malloc(<span class="keyword">sizeof</span> (<span class="keywordtype">float</span>) * nop * 3);
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<a name="l00446"></a>00446 <span class="keywordtype">float</span> inc = <a class="code" href="asa_8h.html#598a3330b3c21701223ee0ca14316eca">PI</a> * (3.0 - sqrt(5.0));
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<a name="l00447"></a>00447 <span class="keywordtype">float</span> off = 2.0 / (float) nop;
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<a name="l00448"></a>00448 <span class="keywordtype">float</span> y, r, phi;
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<a name="l00449"></a>00449 <span class="keywordtype">int</span> k;
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<a name="l00450"></a>00450 <span class="keywordflow">for</span> (k = 0; k < nop; k++) {
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<a name="l00451"></a>00451 y = ((float) k) * off - 1.0 + (off / 2.0);
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<a name="l00452"></a>00452 r = sqrt(1.0 - y * y);
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<a name="l00453"></a>00453 phi = k * inc;
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<a name="l00454"></a>00454 pts[3 * k] = cos(phi) * r;
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<a name="l00455"></a>00455 pts[3 * k + 1] = y;
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<a name="l00456"></a>00456 pts[3 * k + 2] = sin(phi) * r;
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<a name="l00457"></a>00457 }
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<a name="l00458"></a>00458 <span class="keywordflow">return</span> pts;
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<a name="l00459"></a>00459 }
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</pre></div>
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<a class="anchor" name="566de76ed33c4ec6a1ef4d7fefa8a861"></a><!-- doxytag: member="asa.h::get_surrounding_atoms_idx" ref="566de76ed33c4ec6a1ef4d7fefa8a861" args="(s_vvertice **tvert, int nvert, s_pdb *pdb, int *n_sa)" -->
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<td class="memname">int* get_surrounding_atoms_idx </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structs__vvertice.html">s_vvertice</a> ** </td>
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<td class="paramname"> <em>tvert</em>, </td>
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<td class="paramtype">int </td>
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<td class="paramtype"><a class="el" href="structs__pdb.html">s_pdb</a> * </td>
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<td class="paramname"> <em>pdb</em>, </td>
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<td class="paramtype">int * </td>
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<td class="paramname"> <em>n_sa</em></td><td> </td>
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## FUNCTION: get_surrounding_atoms_idx<p>
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## SPECIFICATION: Get atom ids around a given set of voronoi vertices<p>
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## PARAMETRES: @ s_vvertices **tvert : List of pointers to voronoi vertices, @ int nvert : Number of Voronoi vertices @ <a class="el" href="structs__pdb.html">s_pdb</a> *pdb : Structure of the protein @ int *n_sa : Pointer to int holding the number of surrounding atoms<p>
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## RETURN: int * : atom ids of surrounding atoms
|
|
<p>Definition at line <a class="el" href="asa_8c-source.html#l00107">107</a> of file <a class="el" href="asa_8c-source.html">asa.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="calc_8c-source.html#l00100">ddist()</a>, <a class="el" href="utils_8c-source.html#l00475">in_tab()</a>, <a class="el" href="rpdb_8h-source.html#l00074">s_pdb::latoms_p</a>, <a class="el" href="asa_8h-source.html#l00062">M_PADDING</a>, <a class="el" href="rpdb_8h-source.html#l00078">s_pdb::natoms</a>, <a class="el" href="voronoi_8h-source.html#l00075">s_vvertice::ray</a>, <a class="el" href="atom_8h-source.html#l00057">s_atm::symbol</a>, <a class="el" href="voronoi_8h-source.html#l00076">s_vvertice::x</a>, <a class="el" href="atom_8h-source.html#l00056">s_atm::x</a>, <a class="el" href="voronoi_8h-source.html#l00076">s_vvertice::y</a>, <a class="el" href="atom_8h-source.html#l00056">s_atm::y</a>, <a class="el" href="voronoi_8h-source.html#l00076">s_vvertice::z</a>, and <a class="el" href="atom_8h-source.html#l00056">s_atm::z</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="asa_8c-source.html#l00267">set_ASA()</a>, and <a class="el" href="writepocket_8c-source.html#l00115">write_pocket_pdb_DB()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00107"></a>00107 {
|
|
<a name="l00108"></a>00108 <a class="code" href="structs__atm.html">s_atm</a> *a=NULL;
|
|
<a name="l00109"></a>00109 <span class="keywordtype">int</span> *sa=NULL;
|
|
<a name="l00110"></a>00110 <span class="keywordtype">int</span> i,z,flag=0;
|
|
<a name="l00111"></a>00111 *n_sa=0;
|
|
<a name="l00112"></a>00112 <span class="keywordflow">for</span>(i=0;i<pdb-><a class="code" href="structs__pdb.html#85aaf7bdb931bb303af1ca736a998b98">natoms</a>;i++){
|
|
<a name="l00113"></a>00113 a=pdb-><a class="code" href="structs__pdb.html#4517e3a82dbf0f34e73d1865e484dbfd">latoms_p</a>[i];
|
|
<a name="l00114"></a>00114 <span class="comment">//consider only heavy atoms for vdw incr.</span>
|
|
<a name="l00115"></a>00115 <span class="keywordflow">if</span>(strncmp(a-><a class="code" href="structs__atm.html#c80daffa94edeadd30433f6653e08054">symbol</a>,<span class="stringliteral">"H"</span>,1)){
|
|
<a name="l00116"></a>00116 flag=0;
|
|
<a name="l00117"></a>00117 <span class="keywordflow">for</span>(z=0;z<nvert && !flag;z++){
|
|
<a name="l00118"></a>00118 <span class="comment">//flag=atom_not_in_list(a,sa,*n_sa);</span>
|
|
<a name="l00119"></a>00119 flag=<a class="code" href="utils_8c.html#c02faf0c5e3cf0b256a1ad1d37d9b8a2">in_tab</a>(sa,*n_sa,i);
|
|
<a name="l00120"></a>00120 <span class="keywordflow">if</span>(!flag && <a class="code" href="calc_8c.html#5fbe8e59e515cf3b7af1c25a1914445c">ddist</a>(a-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>,a-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>,a-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>,tvert[z]-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a>,tvert[z]-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a>,tvert[z]-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a>)<(tvert[z]-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a>+<a class="code" href="asa_8h.html#056ee2e33f38bebc552b31d932eab912">M_PADDING</a>)*(tvert[z]-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a>+<a class="code" href="asa_8h.html#056ee2e33f38bebc552b31d932eab912">M_PADDING</a>)){
|
|
<a name="l00121"></a>00121 *n_sa=*n_sa+1;
|
|
<a name="l00122"></a>00122 <span class="keywordflow">if</span>(sa==NULL){
|
|
<a name="l00123"></a>00123 sa=(<span class="keywordtype">int</span> *)malloc(<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));
|
|
<a name="l00124"></a>00124 sa[*n_sa-1]=i;
|
|
<a name="l00125"></a>00125 }
|
|
<a name="l00126"></a>00126 <span class="keywordflow">else</span> {
|
|
<a name="l00127"></a>00127 sa=(<span class="keywordtype">int</span> *)realloc(sa,<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>)*(*n_sa));
|
|
<a name="l00128"></a>00128 sa[*n_sa-1]=i;
|
|
<a name="l00129"></a>00129 }
|
|
<a name="l00130"></a>00130 }
|
|
<a name="l00131"></a>00131 }
|
|
<a name="l00132"></a>00132 }
|
|
<a name="l00133"></a>00133 }
|
|
<a name="l00134"></a>00134 <span class="keywordflow">return</span> sa;
|
|
<a name="l00135"></a>00135 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="0ff618e129d637481f9644fd029908b0"></a><!-- doxytag: member="asa.h::get_unique_atoms" ref="0ff618e129d637481f9644fd029908b0" args="(s_vvertice **tvert, int nvert, int *n_ua, s_atm **p, int na)" -->
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|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int* get_unique_atoms </td>
|
|
<td>(</td>
|
|
<td class="paramtype"><a class="el" href="structs__vvertice.html">s_vvertice</a> ** </td>
|
|
<td class="paramname"> <em>tvert</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype">int </td>
|
|
<td class="paramname"> <em>nvert</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype">int * </td>
|
|
<td class="paramname"> <em>n_ua</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__atm.html">s_atm</a> ** </td>
|
|
<td class="paramname"> <em>atoms</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype">int </td>
|
|
<td class="paramname"> <em>na</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: get_unique_atoms<p>
|
|
## SPECIFICATION: Get a list of unique atom ids near the pocket<p>
|
|
## PARAMETRES: @ s_vvertices **tvert : List of pointers to voronoi vertices, @ int nvert : Number of Voronoi vertices @ int *n_sa : Pointer to int holding the number of surrounding atoms @ <a class="el" href="structs__atm.html">s_atm</a> **atoms : List of pointers to atoms @ int na : Number of atoms in atoms<p>
|
|
## RETURN: int * : atom ids of unique atoms
|
|
<p>Definition at line <a class="el" href="asa_8c-source.html#l00157">157</a> of file <a class="el" href="asa_8c-source.html">asa.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="atom_8h-source.html#l00063">s_atm::id</a>, <a class="el" href="utils_8c-source.html#l00475">in_tab()</a>, and <a class="el" href="voronoi_8h-source.html#l00084">s_vvertice::neigh</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00157"></a>00157 {
|
|
<a name="l00158"></a>00158 <a class="code" href="structs__atm.html">s_atm</a> *a=NULL;
|
|
<a name="l00159"></a>00159 <span class="keywordtype">int</span> *ua=NULL;
|
|
<a name="l00160"></a>00160 <span class="keywordtype">int</span> z,j;
|
|
<a name="l00161"></a>00161 <span class="keywordtype">int</span> ca_idx;
|
|
<a name="l00162"></a>00162 *n_ua=0;
|
|
<a name="l00163"></a>00163 <span class="keywordtype">int</span> flag=0;
|
|
<a name="l00164"></a>00164
|
|
<a name="l00165"></a>00165 <a class="code" href="structs__vvertice.html">s_vvertice</a> *vcur = NULL ;
|
|
<a name="l00166"></a>00166 <a class="code" href="structs__atm.html">s_atm</a> **neighs = NULL ;
|
|
<a name="l00167"></a>00167 <span class="comment">/*</span>
|
|
<a name="l00168"></a>00168 <span class="comment"> fprintf(stdout, "\nIn get unique atom\n") ;</span>
|
|
<a name="l00169"></a>00169 <span class="comment">*/</span>
|
|
<a name="l00170"></a>00170 <span class="keywordflow">for</span>(z=0;z<nvert;z++){
|
|
<a name="l00171"></a>00171 vcur = tvert[z] ;
|
|
<a name="l00172"></a>00172 neighs = tvert[z]-><a class="code" href="structs__vvertice.html#d8f82150ff5b05ee09b1136a9c09cfd0">neigh</a> ;
|
|
<a name="l00173"></a>00173 <span class="keywordflow">for</span>(j=0;j<4;j++){
|
|
<a name="l00174"></a>00174 a=neighs[j];
|
|
<a name="l00175"></a>00175 flag=<a class="code" href="utils_8c.html#c02faf0c5e3cf0b256a1ad1d37d9b8a2">in_tab</a>(ua,*n_ua,a-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>);
|
|
<a name="l00176"></a>00176 <span class="keywordflow">if</span>(!flag) {
|
|
<a name="l00177"></a>00177 *n_ua=*n_ua+1;
|
|
<a name="l00178"></a>00178 <span class="keywordflow">if</span>(ua==NULL) ua=(<span class="keywordtype">int</span> *)malloc(<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>));
|
|
<a name="l00179"></a>00179 <span class="keywordflow">else</span> ua=(<span class="keywordtype">int</span> *)realloc(ua,<span class="keyword">sizeof</span>(<span class="keywordtype">int</span>)*(*n_ua));
|
|
<a name="l00180"></a>00180
|
|
<a name="l00181"></a>00181 <span class="keywordflow">if</span>(a-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>-1 < na && a==atoms[a-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>-1]) {
|
|
<a name="l00182"></a>00182 ua[*n_ua-1]=a-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>-1;
|
|
<a name="l00183"></a>00183 <span class="comment">/* if(a->id >= 1631) {</span>
|
|
<a name="l00184"></a>00184 <span class="comment"> fprintf(stdout, "\nSetting bad id! %d", a->id ) ;</span>
|
|
<a name="l00185"></a>00185 <span class="comment"> }*/</span>
|
|
<a name="l00186"></a>00186 }
|
|
<a name="l00187"></a>00187 <span class="keywordflow">else</span> {
|
|
<a name="l00188"></a>00188 <span class="keywordflow">for</span>(ca_idx=0;ca_idx<na;ca_idx++){
|
|
<a name="l00189"></a>00189 <span class="keywordflow">if</span>(a==atoms[ca_idx]) {
|
|
<a name="l00190"></a>00190 ua[*n_ua-1]=ca_idx;
|
|
<a name="l00191"></a>00191
|
|
<a name="l00192"></a>00192 <span class="comment">/* if(ca_idx >= 1631) {</span>
|
|
<a name="l00193"></a>00193 <span class="comment"></span>
|
|
<a name="l00194"></a>00194 <span class="comment"> fprintf(stdout, "\nSetting bad id! %d", ca_idx ) ;</span>
|
|
<a name="l00195"></a>00195 <span class="comment"> }*/</span>
|
|
<a name="l00196"></a>00196 <span class="keywordflow">break</span>;
|
|
<a name="l00197"></a>00197 }
|
|
<a name="l00198"></a>00198 }
|
|
<a name="l00199"></a>00199 }
|
|
<a name="l00200"></a>00200 }
|
|
<a name="l00201"></a>00201 }
|
|
<a name="l00202"></a>00202 }
|
|
<a name="l00203"></a>00203
|
|
<a name="l00204"></a>00204 <span class="keywordflow">return</span> ua;
|
|
<a name="l00205"></a>00205 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="46b1e19813ef3f501d7ce77892e3bfcd"></a><!-- doxytag: member="asa.h::set_ASA" ref="46b1e19813ef3f501d7ce77892e3bfcd" args="(s_desc *desc, s_pdb *pdb, s_vvertice **tvert, int nvert)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">void set_ASA </td>
|
|
<td>(</td>
|
|
<td class="paramtype"><a class="el" href="structs__desc.html">s_desc</a> * </td>
|
|
<td class="paramname"> <em>desc</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__pdb.html">s_pdb</a> * </td>
|
|
<td class="paramname"> <em>pdb</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__vvertice.html">s_vvertice</a> ** </td>
|
|
<td class="paramname"> <em>tvert</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype">int </td>
|
|
<td class="paramname"> <em>nvert</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: set_ASA<p>
|
|
## SPECIFICATION: The actual ASA calculation, resulst are written to the descriptor structure<p>
|
|
## PARAMETRES: @ <a class="el" href="structs__desc.html">s_desc</a> *desc : Structure of descriptors @ <a class="el" href="structs__pdb.html">s_pdb</a> *pdb : Structure containing the protein @ s_vvertices **tvert : List of pointers to Voronoi vertices @ int nvert : Number of vertices<p>
|
|
## RETURN: void
|
|
<p>Definition at line <a class="el" href="asa_8c-source.html#l00267">267</a> of file <a class="el" href="asa_8c-source.html">asa.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="calc_8c-source.html#l00100">ddist()</a>, <a class="el" href="atom_8h-source.html#l00070">s_atm::electroneg</a>, <a class="el" href="asa_8c-source.html#l00443">get_points_on_sphere()</a>, <a class="el" href="asa_8c-source.html#l00107">get_surrounding_atoms_idx()</a>, <a class="el" href="asa_8c-source.html#l00208">get_unique_atoms_DEPRECATED()</a>, <a class="el" href="rpdb_8h-source.html#l00074">s_pdb::latoms_p</a>, <a class="el" href="asa_8h-source.html#l00061">M_NSPIRAL</a>, <a class="el" href="asa_8h-source.html#l00063">M_PROBE_SIZE</a>, <a class="el" href="asa_8h-source.html#l00064">M_PROBE_SIZE2</a>, <a class="el" href="memhandler_8c-source.html#l00121">my_malloc()</a>, <a class="el" href="descriptors_8h-source.html#l00108">s_desc::n_abpa</a>, <a class="el" href="asa_8h-source.html#l00065">PI</a>, <a class="el" href="atom_8h-source.html#l00070">s_atm::radius</a>, <a class="el" href="voronoi_8h-source.html#l00075">s_vvertice::ray</a>, <a class="el" href="descriptors_8h-source.html#l00058">s_desc::surf_apol_vdw14</a>, <a class="el" href="descriptors_8h-source.html#l00058">s_desc::surf_apol_vdw22</a>, <a class="el" href="descriptors_8h-source.html#l00058">s_desc::surf_pol_vdw14</a>, <a class="el" href="descriptors_8h-source.html#l00058">s_desc::surf_pol_vdw22</a>, <a class="el" href="descriptors_8h-source.html#l00058">s_desc::surf_vdw14</a>, <a class="el" href="descriptors_8h-source.html#l00058">s_desc::surf_vdw22</a>, <a class="el" href="atom_8h-source.html#l00056">s_atm::x</a>, <a class="el" href="atom_8h-source.html#l00056">s_atm::y</a>, and <a class="el" href="atom_8h-source.html#l00056">s_atm::z</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="descriptors_8c-source.html#l00182">set_descriptors()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00268"></a>00268 {
|
|
<a name="l00269"></a>00269 desc-><a class="code" href="structs__desc.html#b427b3ce5e431f0ca3e3df5c659f2de0">surf_pol_vdw14</a>=0.0;
|
|
<a name="l00270"></a>00270 desc-><a class="code" href="structs__desc.html#7ce0d0f8a0e977c3f5ecbd1a64ec02c7">surf_apol_vdw14</a>=0.0;
|
|
<a name="l00271"></a>00271 desc-><a class="code" href="structs__desc.html#46c2b1ee640b31802839e88bb91f3aac">surf_vdw14</a>=0.0;
|
|
<a name="l00272"></a>00272 desc-><a class="code" href="structs__desc.html#8d64efb827570330fb20cac0a48507f3">surf_vdw22</a>=0.0;
|
|
<a name="l00273"></a>00273 desc-><a class="code" href="structs__desc.html#090bbaf1b3d709e7575ab400ce1848a1">surf_pol_vdw22</a>=0.0;
|
|
<a name="l00274"></a>00274 desc-><a class="code" href="structs__desc.html#30adaa999c80fb0f9c3e357730ab5c3c">surf_apol_vdw22</a>=0.0;
|
|
<a name="l00275"></a>00275 desc-><a class="code" href="structs__desc.html#15d78f3262dcfa80bfba6c1872c51f6e">n_abpa</a>=0;
|
|
<a name="l00276"></a>00276 <span class="keywordtype">int</span> *sa=NULL; <span class="comment">/*surrounding atoms container*/</span>
|
|
<a name="l00277"></a>00277 <span class="comment">/*int *ua=NULL; /*unique atoms contacting vvertices*/</span>
|
|
<a name="l00278"></a>00278 <a class="code" href="structs__atm.html">s_atm</a> ** ua = NULL ;
|
|
<a name="l00279"></a>00279
|
|
<a name="l00280"></a>00280 <span class="keywordtype">int</span> n_sa = 0;
|
|
<a name="l00281"></a>00281 <span class="keywordtype">int</span> n_ua = 0;
|
|
<a name="l00282"></a>00282 <span class="keywordtype">int</span> i;
|
|
<a name="l00283"></a>00283 sa=<a class="code" href="asa_8c.html#566de76ed33c4ec6a1ef4d7fefa8a861">get_surrounding_atoms_idx</a>(tvert,nvert,pdb, &n_sa);
|
|
<a name="l00284"></a>00284 <span class="comment">/*ua=get_unique_atoms_DEPRECATED(tvert,nvert, &n_ua,pdb->latoms_p,pdb->natoms);*/</span>
|
|
<a name="l00285"></a>00285
|
|
<a name="l00286"></a>00286 ua=<a class="code" href="asa_8c.html#8ad36b2d8016490cb8864b3c7016c2a2">get_unique_atoms_DEPRECATED</a>(tvert,nvert, &n_ua);
|
|
<a name="l00287"></a>00287 <span class="keywordtype">float</span> *abpatmp=NULL;
|
|
<a name="l00288"></a>00288 abpatmp=(<span class="keywordtype">float</span> *)<a class="code" href="memhandler_8c.html#52d7260a38c396cb2dd1dd7abcfd61cb">my_malloc</a>(<span class="keyword">sizeof</span>(<span class="keywordtype">float</span>)*n_ua);
|
|
<a name="l00289"></a>00289 <span class="comment">/*</span>
|
|
<a name="l00290"></a>00290 <span class="comment"> for(i = 0 ; i < pdb->natoms ; i++) {</span>
|
|
<a name="l00291"></a>00291 <span class="comment"> if(pdb->latoms_p[i]->id > 1631) {</span>
|
|
<a name="l00292"></a>00292 <span class="comment"> fprintf(stdout, "\nWTF at %d %d", i,pdb->latoms_p[i]->id) ;</span>
|
|
<a name="l00293"></a>00293 <span class="comment"> }</span>
|
|
<a name="l00294"></a>00294 <span class="comment"> }</span>
|
|
<a name="l00295"></a>00295 <span class="comment"> for( i = 0 ; i < n_ua ; i++) {</span>
|
|
<a name="l00296"></a>00296 <span class="comment"> if(ua[i] > 1631)</span>
|
|
<a name="l00297"></a>00297 <span class="comment"> fprintf(stdout, "Atom %d: %d\n", i, ua[i]) ;</span>
|
|
<a name="l00298"></a>00298 <span class="comment"></span>
|
|
<a name="l00299"></a>00299 <span class="comment"> }</span>
|
|
<a name="l00300"></a>00300 <span class="comment">*/</span>
|
|
<a name="l00301"></a>00301
|
|
<a name="l00302"></a>00302 <a class="code" href="structs__atm.html">s_atm</a> *a,*cura;
|
|
<a name="l00303"></a>00303 <span class="keywordtype">float</span> *curpts=NULL,tz,tx,ty,dsq,area;
|
|
<a name="l00304"></a>00304 <span class="keywordtype">int</span> j=0,iv,k,burried,nnburried,vidx,vrefburried;
|
|
<a name="l00305"></a>00305 curpts=<a class="code" href="asa_8c.html#9df45773e08f04fb69a917e6ba206169">get_points_on_sphere</a>(<a class="code" href="asa_8h.html#e29930e8c39193c231d3c460904dd2e7">M_NSPIRAL</a>);
|
|
<a name="l00306"></a>00306 <span class="keywordflow">for</span>(i=0;i<n_ua;i++){
|
|
<a name="l00307"></a>00307 abpatmp[i]=0.0;
|
|
<a name="l00308"></a>00308 <span class="comment">/*</span>
|
|
<a name="l00309"></a>00309 <span class="comment"> fprintf(stdout, "\nUA %d (%d): %d (%d)", i, pdb->natoms, ua [i], n_ua);</span>
|
|
<a name="l00310"></a>00310 <span class="comment">*/</span>
|
|
<a name="l00311"></a>00311 <span class="comment">/*</span>
|
|
<a name="l00312"></a>00312 <span class="comment"> if(ua [i] >= pdb->natoms) {</span>
|
|
<a name="l00313"></a>00313 <span class="comment"> fprintf(stdout, "\nWOOPS at %d! %d \n", i, ua[i]) ;//exit(0) ;</span>
|
|
<a name="l00314"></a>00314 <span class="comment"> }</span>
|
|
<a name="l00315"></a>00315 <span class="comment">*/</span>
|
|
<a name="l00316"></a>00316 <span class="comment">/*</span>
|
|
<a name="l00317"></a>00317 <span class="comment"> cura=pdb->latoms_p[ua[i]];</span>
|
|
<a name="l00318"></a>00318 <span class="comment">*/</span>
|
|
<a name="l00319"></a>00319 cura = ua[i] ;
|
|
<a name="l00320"></a>00320 nnburried=0;
|
|
<a name="l00321"></a>00321
|
|
<a name="l00322"></a>00322 <span class="keywordflow">for</span>(k=0;k<<a class="code" href="asa_8h.html#e29930e8c39193c231d3c460904dd2e7">M_NSPIRAL</a>;k++){
|
|
<a name="l00323"></a>00323 burried=0;
|
|
<a name="l00324"></a>00324 j=0;
|
|
<a name="l00325"></a>00325 tx=cura-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>+curpts[3*k]*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a>);
|
|
<a name="l00326"></a>00326 ty=cura-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>+curpts[3*k+1]*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a>);
|
|
<a name="l00327"></a>00327 tz=cura-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>+curpts[3*k+2]*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a>);
|
|
<a name="l00328"></a>00328 vrefburried=1;
|
|
<a name="l00329"></a>00329 <span class="keywordflow">for</span>(iv=0;iv<nvert;iv++){
|
|
<a name="l00330"></a>00330 <span class="keywordflow">for</span>(vidx=0;vidx<4;vidx++){
|
|
<a name="l00331"></a>00331 <span class="keywordflow">if</span>(cura==tvert[iv]->neigh[vidx]){
|
|
<a name="l00332"></a>00332 <span class="keywordflow">if</span>(<a class="code" href="calc_8c.html#5fbe8e59e515cf3b7af1c25a1914445c">ddist</a>(tx,ty,tz,tvert[iv]->x,tvert[iv]->y,tvert[iv]->z)<=tvert[iv]-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a>*tvert[iv]-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a>) vrefburried=0;
|
|
<a name="l00333"></a>00333 }
|
|
<a name="l00334"></a>00334 }
|
|
<a name="l00335"></a>00335 }
|
|
<a name="l00336"></a>00336 <span class="keywordflow">while</span>(!burried && j< n_sa && !vrefburried){
|
|
<a name="l00337"></a>00337 a=pdb-><a class="code" href="structs__pdb.html#4517e3a82dbf0f34e73d1865e484dbfd">latoms_p</a>[sa[j]];
|
|
<a name="l00338"></a>00338 <span class="keywordflow">if</span>(a!=cura){
|
|
<a name="l00339"></a>00339 dsq=<a class="code" href="calc_8c.html#5fbe8e59e515cf3b7af1c25a1914445c">ddist</a>(tx,ty,tz,a-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>,a-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>,a-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>);
|
|
<a name="l00340"></a>00340 <span class="keywordflow">if</span>(dsq<(a-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a>)*(a-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a>)) burried=1;
|
|
<a name="l00341"></a>00341 }
|
|
<a name="l00342"></a>00342 j++;
|
|
<a name="l00343"></a>00343 }
|
|
<a name="l00344"></a>00344 <span class="keywordflow">if</span>(!burried && !vrefburried) {
|
|
<a name="l00345"></a>00345 nnburried++;
|
|
<a name="l00346"></a>00346 }
|
|
<a name="l00347"></a>00347 }
|
|
<a name="l00348"></a>00348 area=(4*<a class="code" href="asa_8h.html#598a3330b3c21701223ee0ca14316eca">PI</a>*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a>)*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#1c4d87257acc6b058961c30286569414">M_PROBE_SIZE</a>)/(float)M_NSPIRAL)*nnburried;
|
|
<a name="l00349"></a>00349 abpatmp[i]=area;
|
|
<a name="l00350"></a>00350 <span class="keywordflow">if</span>(cura-><a class="code" href="structs__atm.html#f41b525ee3032d47baf2db10387f022c">electroneg</a><2.8) desc-><a class="code" href="structs__desc.html#7ce0d0f8a0e977c3f5ecbd1a64ec02c7">surf_apol_vdw14</a>=desc-><a class="code" href="structs__desc.html#7ce0d0f8a0e977c3f5ecbd1a64ec02c7">surf_apol_vdw14</a>+area;
|
|
<a name="l00351"></a>00351 <span class="keywordflow">else</span> desc-><a class="code" href="structs__desc.html#b427b3ce5e431f0ca3e3df5c659f2de0">surf_pol_vdw14</a>=desc-><a class="code" href="structs__desc.html#b427b3ce5e431f0ca3e3df5c659f2de0">surf_pol_vdw14</a>+area;
|
|
<a name="l00352"></a>00352 desc-><a class="code" href="structs__desc.html#46c2b1ee640b31802839e88bb91f3aac">surf_vdw14</a>=desc-><a class="code" href="structs__desc.html#46c2b1ee640b31802839e88bb91f3aac">surf_vdw14</a>+area;
|
|
<a name="l00353"></a>00353
|
|
<a name="l00354"></a>00354 }
|
|
<a name="l00355"></a>00355
|
|
<a name="l00356"></a>00356
|
|
<a name="l00357"></a>00357 <span class="comment">/*now test with vdw +2.2*/</span>
|
|
<a name="l00358"></a>00358 <span class="keywordflow">for</span>(i=0;i<n_ua;i++){
|
|
<a name="l00359"></a>00359 <span class="comment">/*</span>
|
|
<a name="l00360"></a>00360 <span class="comment"> fprintf(stdout, "\nUA %d (%d): %d (%d)", i, pdb->natoms, ua [i], n_ua);</span>
|
|
<a name="l00361"></a>00361 <span class="comment">*/</span>
|
|
<a name="l00362"></a>00362 <span class="comment">/*</span>
|
|
<a name="l00363"></a>00363 <span class="comment"> if(ua [i] >= pdb->natoms) {</span>
|
|
<a name="l00364"></a>00364 <span class="comment"> fprintf(stdout, "\nWOOPS at %d! %d \n", i, ua[i]) ;//exit(0) ;</span>
|
|
<a name="l00365"></a>00365 <span class="comment"> }</span>
|
|
<a name="l00366"></a>00366 <span class="comment">*/</span>
|
|
<a name="l00367"></a>00367 <span class="comment">/*</span>
|
|
<a name="l00368"></a>00368 <span class="comment"> cura=pdb->latoms_p[ua[i]];</span>
|
|
<a name="l00369"></a>00369 <span class="comment">*/</span>
|
|
<a name="l00370"></a>00370 cura = ua[i] ;
|
|
<a name="l00371"></a>00371 nnburried=0;
|
|
<a name="l00372"></a>00372
|
|
<a name="l00373"></a>00373 <span class="keywordflow">for</span>(k=0;k<M_NSPIRAL;k++){
|
|
<a name="l00374"></a>00374 burried=0;
|
|
<a name="l00375"></a>00375 j=0;
|
|
<a name="l00376"></a>00376 tx=cura-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>+curpts[3*k]*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a>);
|
|
<a name="l00377"></a>00377 ty=cura-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>+curpts[3*k+1]*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a>);
|
|
<a name="l00378"></a>00378 tz=cura-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>+curpts[3*k+2]*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a>);
|
|
<a name="l00379"></a>00379 vrefburried=1;
|
|
<a name="l00380"></a>00380 <span class="keywordflow">for</span>(iv=0;iv<nvert;iv++){
|
|
<a name="l00381"></a>00381 <span class="keywordflow">for</span>(vidx=0;vidx<4;vidx++){
|
|
<a name="l00382"></a>00382 <span class="keywordflow">if</span>(cura==tvert[iv]->neigh[vidx]){
|
|
<a name="l00383"></a>00383 <span class="keywordflow">if</span>(<a class="code" href="calc_8c.html#5fbe8e59e515cf3b7af1c25a1914445c">ddist</a>(tx,ty,tz,tvert[iv]->x,tvert[iv]->y,tvert[iv]->z)<=tvert[iv]-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a>*tvert[iv]-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a>) vrefburried=0;
|
|
<a name="l00384"></a>00384 }
|
|
<a name="l00385"></a>00385 }
|
|
<a name="l00386"></a>00386 }
|
|
<a name="l00387"></a>00387 <span class="keywordflow">while</span>(!burried && j< n_sa && !vrefburried){
|
|
<a name="l00388"></a>00388 a=pdb-><a class="code" href="structs__pdb.html#4517e3a82dbf0f34e73d1865e484dbfd">latoms_p</a>[sa[j]];
|
|
<a name="l00389"></a>00389 <span class="keywordflow">if</span>(a!=cura){
|
|
<a name="l00390"></a>00390 dsq=<a class="code" href="calc_8c.html#5fbe8e59e515cf3b7af1c25a1914445c">ddist</a>(tx,ty,tz,a-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>,a-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>,a-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>);
|
|
<a name="l00391"></a>00391 <span class="keywordflow">if</span>(dsq<(a-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a>)*(a-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a>)) burried=1;
|
|
<a name="l00392"></a>00392 }
|
|
<a name="l00393"></a>00393 j++;
|
|
<a name="l00394"></a>00394 }
|
|
<a name="l00395"></a>00395 <span class="keywordflow">if</span>(!burried && !vrefburried) {
|
|
<a name="l00396"></a>00396 nnburried++;
|
|
<a name="l00397"></a>00397 }
|
|
<a name="l00398"></a>00398 }
|
|
<a name="l00399"></a>00399 area=(4*<a class="code" href="asa_8h.html#598a3330b3c21701223ee0ca14316eca">PI</a>*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a>)*(cura-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>+<a class="code" href="asa_8h.html#13a4860468b1e1aa44b156df0f646a5f">M_PROBE_SIZE2</a>)/(float)M_NSPIRAL)*nnburried;
|
|
<a name="l00400"></a>00400 <span class="keywordflow">if</span>(cura-><a class="code" href="structs__atm.html#f41b525ee3032d47baf2db10387f022c">electroneg</a><2.8) {
|
|
<a name="l00401"></a>00401 <span class="keywordflow">if</span>(area<=abpatmp[i] && abpatmp[i] <=10.0 && area > 0.0){
|
|
<a name="l00402"></a>00402 desc-><a class="code" href="structs__desc.html#15d78f3262dcfa80bfba6c1872c51f6e">n_abpa</a>+=1;
|
|
<a name="l00403"></a>00403 }
|
|
<a name="l00404"></a>00404 desc-><a class="code" href="structs__desc.html#30adaa999c80fb0f9c3e357730ab5c3c">surf_apol_vdw22</a>=desc-><a class="code" href="structs__desc.html#30adaa999c80fb0f9c3e357730ab5c3c">surf_apol_vdw22</a>+area;
|
|
<a name="l00405"></a>00405 }
|
|
<a name="l00406"></a>00406 <span class="keywordflow">else</span> desc-><a class="code" href="structs__desc.html#090bbaf1b3d709e7575ab400ce1848a1">surf_pol_vdw22</a>=desc-><a class="code" href="structs__desc.html#090bbaf1b3d709e7575ab400ce1848a1">surf_pol_vdw22</a>+area;
|
|
<a name="l00407"></a>00407 desc-><a class="code" href="structs__desc.html#8d64efb827570330fb20cac0a48507f3">surf_vdw22</a>=desc-><a class="code" href="structs__desc.html#8d64efb827570330fb20cac0a48507f3">surf_vdw22</a>+area;
|
|
<a name="l00408"></a>00408
|
|
<a name="l00409"></a>00409 }
|
|
<a name="l00410"></a>00410 free(curpts);
|
|
<a name="l00411"></a>00411
|
|
<a name="l00412"></a>00412
|
|
<a name="l00413"></a>00413
|
|
<a name="l00414"></a>00414 curpts=NULL;
|
|
<a name="l00415"></a>00415 <span class="comment">/* for(i=0;i<n_ua-1;i++){</span>
|
|
<a name="l00416"></a>00416 <span class="comment"> free(ua[i]);</span>
|
|
<a name="l00417"></a>00417 <span class="comment"> }*/</span>
|
|
<a name="l00418"></a>00418
|
|
<a name="l00419"></a>00419 free(ua);
|
|
<a name="l00420"></a>00420 free(sa);
|
|
<a name="l00421"></a>00421
|
|
<a name="l00422"></a>00422 sa=NULL;
|
|
<a name="l00423"></a>00423 ua=NULL;
|
|
<a name="l00424"></a>00424 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
</div>
|
|
<hr size="1"><address style="text-align: right;"><small>Generated on Mon Jun 7 16:44:23 2010 for fpocket by
|
|
<a href="http://www.doxygen.org/index.html">
|
|
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.6 </small></address>
|
|
</body>
|
|
</html>
|