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<title>fpocket: dpocket.h File Reference</title>
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<h1>dpocket.h File Reference</h1><code>#include &lt;math.h&gt;</code><br>
<code>#include &lt;stdio.h&gt;</code><br>
<code>#include &lt;stdlib.h&gt;</code><br>
<code>#include &lt;string.h&gt;</code><br>
<code>#include &lt;ctype.h&gt;</code><br>
<code>#include &quot;<a class="el" href="fpocket_8h-source.html">fpocket.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="fpout_8h-source.html">fpout.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="tpocket_8h-source.html">tpocket.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="dparams_8h-source.html">dparams.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="descriptors_8h-source.html">descriptors.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="neighbor_8h-source.html">neighbor.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="pocket_8h-source.html">pocket.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="cluster_8h-source.html">cluster.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="refine_8h-source.html">refine.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="aa_8h-source.html">aa.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="utils_8h-source.html">utils.h</a>&quot;</code><br>
<code>#include &quot;<a class="el" href="memhandler_8h-source.html">memhandler.h</a>&quot;</code><br>
<p>
<a href="dpocket_8h-source.html">Go to the source code of this file.</a><table border="0" cellpadding="0" cellspacing="0">
<tr><td></td></tr>
<tr><td colspan="2"><br><h2>Defines</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#a72b0de64b5a328f4d0ec58b301a09cb">M_DP_EXPLICIT</a>&nbsp;&nbsp;&nbsp;1</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#abec32b77566930d75d509609ed55f5a">M_DP_POCKET</a>&nbsp;&nbsp;&nbsp;2</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#52024d2ce52b224170f20fa9fa78f8e5">M_DP_POCETLIG</a>&nbsp;&nbsp;&nbsp;3</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#23343f9b8e0f8438a1e800f657eebc55">M_DP_OUTP_HEADER</a>&nbsp;&nbsp;&nbsp;&quot;pdb lig overlap PP-crit PP-dst crit4 crit5 crit6 crit6_continue lig_vol pock_vol nb_AS nb_AS_norm mean_as_ray mean_as_solv_acc apol_as_prop apol_as_prop_norm mean_loc_hyd_dens mean_loc_hyd_dens_norm hydrophobicity_score volume_score polarity_score polarity_score_norm charge_score flex prop_polar_atm as_density as_density_norm as_max_dst as_max_dst_norm drug_score&quot;</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#37abd6af8ee30c796fbb1515bb8b8254">M_DP_OUTP_FORMAT</a>&nbsp;&nbsp;&nbsp;&quot;%s %s %6.2f %2d %6.2f %4.2f %4.2f %2d %5.2f %8.2f %10.2f %5d %4.2f %6.2f %6.2f %5.2f %4.2f %7.2f %4.2f %9.2f %7.2f %5d %5.2f %5d %6.2f %7.2f %5.2f %5.2f %5.2f %5.2f %5.2f&quot;</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">#define&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#f3b98e7b7baf7f23c259c71912aa40d9">M_DP_OUTP_VAR</a>(fc, l, ovlp, status, dst, c4, c5, c6, c6_c, lv, d)</td></tr>
<tr><td colspan="2"><br><h2>Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#7b962a8ea0d00ac566609fb14336c17b">dpocket</a> (<a class="el" href="structs__dparams.html">s_dparams</a> *par)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#5413a47106630839ae6ecd90ba9bf9fd">desc_pocket</a> (char fcomplexe[], const char ligname[], <a class="el" href="structs__dparams.html">s_dparams</a> *par, FILE *f[3])</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structs__atm.html">s_atm</a> **&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#fca470f9d8d1c8e84528205c7aeed723">get_explicit_desc</a> (<a class="el" href="structs__pdb.html">s_pdb</a> *pdb_cplx_l, <a class="el" href="structs__lst__vvertice.html">s_lst_vvertice</a> *verts, <a class="el" href="structs__atm.html">s_atm</a> **lig, int nal, <a class="el" href="structs__dparams.html">s_dparams</a> *par, int *nai, <a class="el" href="structs__desc.html">s_desc</a> *desc)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="dpocket_8h.html#c32aae31fed030bdb0f31f447fd2e79f">write_pocket_desc</a> (const char fc[], const char l[], <a class="el" href="structs__desc.html">s_desc</a> *d, float lv, float ovlp, float dst, float c4, float c5, FILE *f)</td></tr>
</table>
<hr><h2>Define Documentation</h2>
<a class="anchor" name="a72b0de64b5a328f4d0ec58b301a09cb"></a><!-- doxytag: member="dpocket.h::M_DP_EXPLICIT" ref="a72b0de64b5a328f4d0ec58b301a09cb" args="" -->
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<td class="memname">#define M_DP_EXPLICIT&nbsp;&nbsp;&nbsp;1 </td>
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<p>Definition at line <a class="el" href="dpocket_8h-source.html#l00060">60</a> of file <a class="el" href="dpocket_8h-source.html">dpocket.h</a>.</p>
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<a class="anchor" name="37abd6af8ee30c796fbb1515bb8b8254"></a><!-- doxytag: member="dpocket.h::M_DP_OUTP_FORMAT" ref="37abd6af8ee30c796fbb1515bb8b8254" args="" -->
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<td class="memname">#define M_DP_OUTP_FORMAT&nbsp;&nbsp;&nbsp;&quot;%s %s %6.2f %2d %6.2f %4.2f %4.2f %2d %5.2f %8.2f %10.2f %5d %4.2f %6.2f %6.2f %5.2f %4.2f %7.2f %4.2f %9.2f %7.2f %5d %5.2f %5d %6.2f %7.2f %5.2f %5.2f %5.2f %5.2f %5.2f&quot; </td>
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format for the dpocket output
<p>Definition at line <a class="el" href="dpocket_8h-source.html#l00066">66</a> of file <a class="el" href="dpocket_8h-source.html">dpocket.h</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00403">write_pocket_desc()</a>.</p>
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</div><p>
<a class="anchor" name="23343f9b8e0f8438a1e800f657eebc55"></a><!-- doxytag: member="dpocket.h::M_DP_OUTP_HEADER" ref="23343f9b8e0f8438a1e800f657eebc55" args="" -->
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<td class="memname">#define M_DP_OUTP_HEADER&nbsp;&nbsp;&nbsp;&quot;pdb lig overlap PP-crit PP-dst crit4 crit5 crit6 crit6_continue lig_vol pock_vol nb_AS nb_AS_norm mean_as_ray mean_as_solv_acc apol_as_prop apol_as_prop_norm mean_loc_hyd_dens mean_loc_hyd_dens_norm hydrophobicity_score volume_score polarity_score polarity_score_norm charge_score flex prop_polar_atm as_density as_density_norm as_max_dst as_max_dst_norm drug_score&quot; </td>
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<p>
header for the dpocket output
<p>Definition at line <a class="el" href="dpocket_8h-source.html#l00064">64</a> of file <a class="el" href="dpocket_8h-source.html">dpocket.h</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00116">dpocket()</a>.</p>
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<a class="anchor" name="f3b98e7b7baf7f23c259c71912aa40d9"></a><!-- doxytag: member="dpocket.h::M_DP_OUTP_VAR" ref="f3b98e7b7baf7f23c259c71912aa40d9" args="(fc, l, ovlp, status, dst, c4, c5, c6, c6_c, lv, d)" -->
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<td class="memname">#define M_DP_OUTP_VAR </td>
<td>(</td>
<td class="paramtype">fc, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">l, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">ovlp, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">status, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">dst, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">c4, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">c5, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">c6, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">c6_c, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">lv, <tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">d&nbsp;</td>
<td class="paramname"> </td>
<td>&nbsp;)&nbsp;</td>
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<b>Value:</b><div class="fragment"><pre class="fragment">fc, l, ovlp, status, dst, c4, c5, c6, c6_c, lv, \
d-&gt;volume, \
d-&gt;nb_asph, d-&gt;nas_norm,\
d-&gt;mean_asph_ray, \
d-&gt;masph_sacc, \
d-&gt;apolar_asphere_prop, \
d-&gt;prop_asapol_norm, \
d-&gt;mean_loc_hyd_dens, \
d-&gt;mean_loc_hyd_dens_norm, \
d-&gt;hydrophobicity_score, \
d-&gt;volume_score, \
d-&gt;polarity_score, \
d-&gt;polarity_score_norm, \
d-&gt;charge_score, \
d-&gt;flex, \
d-&gt;prop_polar_atm, \
d-&gt;as_density, \
d-&gt;as_density_norm, \
d-&gt;as_max_dst, \
d-&gt;as_max_dst_norm, \
d-&gt;drug_score
</pre></div>list of descriptors to output in the dpocket output
<p>Definition at line <a class="el" href="dpocket_8h-source.html#l00067">67</a> of file <a class="el" href="dpocket_8h-source.html">dpocket.h</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00403">write_pocket_desc()</a>.</p>
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</div><p>
<a class="anchor" name="52024d2ce52b224170f20fa9fa78f8e5"></a><!-- doxytag: member="dpocket.h::M_DP_POCETLIG" ref="52024d2ce52b224170f20fa9fa78f8e5" args="" -->
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<td class="memname">#define M_DP_POCETLIG&nbsp;&nbsp;&nbsp;3 </td>
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<p>Definition at line <a class="el" href="dpocket_8h-source.html#l00062">62</a> of file <a class="el" href="dpocket_8h-source.html">dpocket.h</a>.</p>
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<a class="anchor" name="abec32b77566930d75d509609ed55f5a"></a><!-- doxytag: member="dpocket.h::M_DP_POCKET" ref="abec32b77566930d75d509609ed55f5a" args="" -->
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<td class="memname">#define M_DP_POCKET&nbsp;&nbsp;&nbsp;2 </td>
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<p>Definition at line <a class="el" href="dpocket_8h-source.html#l00061">61</a> of file <a class="el" href="dpocket_8h-source.html">dpocket.h</a>.</p>
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<hr><h2>Function Documentation</h2>
<a class="anchor" name="5413a47106630839ae6ecd90ba9bf9fd"></a><!-- doxytag: member="dpocket.h::desc_pocket" ref="5413a47106630839ae6ecd90ba9bf9fd" args="(char fcomplexe[], const char ligname[], s_dparams *par, FILE *f[3])" -->
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<td class="memname">void desc_pocket </td>
<td>(</td>
<td class="paramtype">char&nbsp;</td>
<td class="paramname"> <em>fcomplexe</em>[], </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char&nbsp;</td>
<td class="paramname"> <em>ligname</em>[], </td>
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<td class="paramkey"></td>
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<td class="paramtype"><a class="el" href="structs__dparams.html">s_dparams</a> *&nbsp;</td>
<td class="paramname"> <em>par</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">FILE *&nbsp;</td>
<td class="paramname"> <em>f</em>[3]</td><td>&nbsp;</td>
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<td>)</td>
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## FUNCTION: desc_pocket<p>
## SPECIFICATION: @ const char fcomplexe[] : File containing the PDB @ const char ligname[] : Ligand resname identifier @ <a class="el" href="structs__dparams.html">s_dparams</a> *par : Parameters @ FILE *f[3] : The 3 FILE * to write output in<p>
## PARAMETRES:<p>
## RETURN:
<p>Definition at line <a class="el" href="dpocket_8c-source.html#l00184">184</a> of file <a class="el" href="dpocket_8c-source.html">dpocket.c</a>.</p>
<p>References <a class="el" href="descriptors_8c-source.html#l00086">allocate_s_desc()</a>, <a class="el" href="atom_8c-source.html#l00287">atm_corsp()</a>, <a class="el" href="pocket_8h-source.html#l00064">s_pocket::bary</a>, <a class="el" href="pocket_8c-source.html#l01214">c_lst_pocket_free()</a>, <a class="el" href="neighbor_8c-source.html#l00610">count_atm_prop_vert_neigh()</a>, <a class="el" href="neighbor_8c-source.html#l00503">count_pocket_lig_vert_ovlp()</a>, <a class="el" href="calc_8c-source.html#l00075">dist()</a>, <a class="el" href="pocket_8h-source.html#l00089">c_lst_pockets::first</a>, <a class="el" href="dparams_8h-source.html#l00120">s_dparams::fpar</a>, <a class="el" href="rpdb_8c-source.html#l00794">free_pdb_atoms()</a>, <a class="el" href="dpocket_8c-source.html#l00336">get_explicit_desc()</a>, <a class="el" href="atom_8c-source.html#l00179">get_mol_volume_ptr()</a>, <a class="el" href="pocket_8c-source.html#l01369">get_pocket_pvertices()</a>, <a class="el" href="voronoi__lst_8c-source.html#l00225">get_vert_contacted_atms()</a>, <a class="el" href="rpdb_8h-source.html#l00076">s_pdb::latm_lig</a>, <a class="el" href="tpocket_8h-source.html#l00053">M_CRIT4_D</a>, <a class="el" href="tpocket_8h-source.html#l00054">M_CRIT5_D</a>, <a class="el" href="rpdb_8h-source.html#l00050">M_DONT_KEEP_LIG</a>, <a class="el" href="rpdb_8h-source.html#l00049">M_KEEP_LIG</a>, <a class="el" href="memhandler_8c-source.html#l00255">my_free()</a>, <a class="el" href="rpdb_8h-source.html#l00078">s_pdb::natm_lig</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::nb_mcv_iter</a>, <a class="el" href="pocket_8h-source.html#l00080">node_pocket::next</a>, <a class="el" href="pocket_8h-source.html#l00061">s_pocket::pdesc</a>, <a class="el" href="pocket_8h-source.html#l00082">node_pocket::pocket</a>, <a class="el" href="atom_8h-source.html#l00063">s_atm::res_id</a>, <a class="el" href="rpdb_8c-source.html#l00478">rpdb_open()</a>, <a class="el" href="rpdb_8c-source.html#l00599">rpdb_read()</a>, <a class="el" href="fpocket_8c-source.html#l00082">search_pocket()</a>, <a class="el" href="pocket_8h-source.html#l00070">s_pocket::size</a>, <a class="el" href="pocket_8h-source.html#l00063">s_pocket::v_lst</a>, <a class="el" href="pocket_8h-source.html#l00094">c_lst_pockets::vertices</a>, and <a class="el" href="dpocket_8c-source.html#l00403">write_pocket_desc()</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00116">dpocket()</a>.</p>
<div class="fragment"><pre class="fragment"><a name="l00186"></a>00186 {
<a name="l00187"></a>00187 <a class="code" href="structc__lst__pockets.html">c_lst_pockets</a> *pockets = NULL ;
<a name="l00188"></a>00188 <a class="code" href="structs__lst__vvertice.html">s_lst_vvertice</a> *verts = NULL ;
<a name="l00189"></a>00189
<a name="l00190"></a>00190 <a class="code" href="structs__atm.html">s_atm</a> **interface = NULL ;
<a name="l00191"></a>00191 <a class="code" href="structs__desc.html">s_desc</a> *edesc ;
<a name="l00192"></a>00192 <a class="code" href="structs__atm.html">s_atm</a> **lig = NULL,
<a name="l00193"></a>00193 **patoms ;
<a name="l00194"></a>00194
<a name="l00195"></a>00195 <span class="keywordtype">float</span> vol, ovlp, dst = 0.0, tmp, c4, c5 ;
<a name="l00196"></a>00196 <span class="keywordtype">int</span> nal = 0,
<a name="l00197"></a>00197 nai = 0, <span class="comment">/* Number of atoms in the interface */</span>
<a name="l00198"></a>00198 nbpa ;
<a name="l00199"></a>00199 <span class="keywordtype">int</span> j ;
<a name="l00200"></a>00200
<a name="l00201"></a>00201 <span class="comment">/*</span>
<a name="l00202"></a>00202 <span class="comment"> fprintf(stdout, "dpocket: Loading pdb... ") ; fflush(stdout) ;</span>
<a name="l00203"></a>00203 <span class="comment">*/</span>
<a name="l00204"></a>00204 <a class="code" href="structs__pdb.html">s_pdb</a> *pdb_cplx_l = <a class="code" href="rpdb_8c.html#29ed3bff6fdc59fd8bf806a35c3127d7">rpdb_open</a>(fcomplexe, ligname, <a class="code" href="rpdb_8h.html#66a6a8deb20e74fd1fd4e597b46ead20">M_KEEP_LIG</a>);
<a name="l00205"></a>00205 <a class="code" href="structs__pdb.html">s_pdb</a> *pdb_cplx_nl = <a class="code" href="rpdb_8c.html#29ed3bff6fdc59fd8bf806a35c3127d7">rpdb_open</a>(fcomplexe, ligname, <a class="code" href="rpdb_8h.html#067223f2b95bbd02c1861d7d45f393b7">M_DONT_KEEP_LIG</a>) ;
<a name="l00206"></a>00206
<a name="l00207"></a>00207 <span class="keywordflow">if</span>(! pdb_cplx_l || !pdb_cplx_nl || pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#659b83804ffc576f1307beac00c1486b">natm_lig</a> &lt;= 0) {
<a name="l00208"></a>00208 <span class="keywordflow">if</span>(pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#659b83804ffc576f1307beac00c1486b">natm_lig</a> &lt;= 0) {
<a name="l00209"></a>00209 fprintf(stdout, <span class="stringliteral">"ERROR - No ligand %s found in %s.\n"</span>, ligname, fcomplexe) ;
<a name="l00210"></a>00210
<a name="l00211"></a>00211 }
<a name="l00212"></a>00212 <span class="keywordflow">else</span> fprintf(stdout, <span class="stringliteral">"ERROR - PDB file %s could not be opened\n"</span>, fcomplexe) ;
<a name="l00213"></a>00213
<a name="l00214"></a>00214 return ;
<a name="l00215"></a>00215 }
<a name="l00216"></a>00216
<a name="l00217"></a>00217 <a class="code" href="rpdb_8c.html#1ec399102f369c72b06a9944616715b0">rpdb_read</a>(pdb_cplx_l, ligname, <a class="code" href="rpdb_8h.html#66a6a8deb20e74fd1fd4e597b46ead20">M_KEEP_LIG</a>) ;
<a name="l00218"></a>00218 <a class="code" href="rpdb_8c.html#1ec399102f369c72b06a9944616715b0">rpdb_read</a>(pdb_cplx_nl, ligname, <a class="code" href="rpdb_8h.html#067223f2b95bbd02c1861d7d45f393b7">M_DONT_KEEP_LIG</a>) ;
<a name="l00219"></a>00219 <span class="comment">/*</span>
<a name="l00220"></a>00220 <span class="comment"> fprintf(stdout, " OK\n") ;</span>
<a name="l00221"></a>00221 <span class="comment">*/</span>
<a name="l00222"></a>00222
<a name="l00223"></a>00223 lig = pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#fe85c6dd76ee9c740d2869ee30621ea5">latm_lig</a> ;
<a name="l00224"></a>00224 nal = pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#659b83804ffc576f1307beac00c1486b">natm_lig</a> ;
<a name="l00225"></a>00225
<a name="l00226"></a>00226 <span class="comment">/*check if there are multiple ligand mols*/</span>
<a name="l00227"></a>00227 <span class="keywordtype">int</span> n_lig_molecules=1;
<a name="l00228"></a>00228 <span class="keywordtype">char</span> chain_tmp[2];
<a name="l00229"></a>00229 <span class="keywordtype">int</span> resnumber_tmp;
<a name="l00230"></a>00230 strcpy(chain_tmp,lig[0]-&gt;chain);
<a name="l00231"></a>00231 resnumber_tmp = lig[0]-&gt;<a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a>;
<a name="l00232"></a>00232
<a name="l00233"></a>00233 <span class="keywordflow">for</span> (j = 1 ; j &lt; nal ; j++) {
<a name="l00234"></a>00234 <span class="keywordflow">if</span>(strcmp(chain_tmp,lig[j]-&gt;chain) !=0 || resnumber_tmp!=lig[j]-&gt;res_id){
<a name="l00235"></a>00235 n_lig_molecules++;
<a name="l00236"></a>00236 strcpy(chain_tmp,lig[j]-&gt;chain);
<a name="l00237"></a>00237 resnumber_tmp =lig[j]-&gt;<a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a>;
<a name="l00238"></a>00238 }
<a name="l00239"></a>00239 }
<a name="l00240"></a>00240
<a name="l00241"></a>00241 <span class="comment">/* Getting explicit interface using the known ligand */</span>
<a name="l00242"></a>00242 <span class="comment">/*</span>
<a name="l00243"></a>00243 <span class="comment"> fprintf(stdout, "dpocket: Explicit pocket definition... \n") ; </span>
<a name="l00244"></a>00244 <span class="comment"> fflush(stdout) ;</span>
<a name="l00245"></a>00245 <span class="comment">*/</span>
<a name="l00246"></a>00246 pockets = <a class="code" href="fpocket_8c.html#23faf120fcf6ef1442496cba08d4fbd1">search_pocket</a>(pdb_cplx_nl, par-&gt;<a class="code" href="structs__dparams.html#84c3e94630fcd2402fd190aad5a0ffbf">fpar</a>,pdb_cplx_l) ;
<a name="l00247"></a>00247 <span class="keywordflow">if</span>(pockets == NULL) {
<a name="l00248"></a>00248 fprintf(stdout, <span class="stringliteral">"ERROR - No pocket found for %s\n"</span>, fcomplexe) ;
<a name="l00249"></a>00249 return ;
<a name="l00250"></a>00250 }
<a name="l00251"></a>00251 <span class="comment">//else write_out_fpocket(pockets, pdb_cplx_nl, fcomplexe);</span>
<a name="l00252"></a>00252 <span class="comment">/*</span>
<a name="l00253"></a>00253 <span class="comment"> verts = load_vvertices(pdb_cplx_nl, 3, par-&gt;fpar-&gt;asph_min_size,</span>
<a name="l00254"></a>00254 <span class="comment"> par-&gt;fpar-&gt;asph_max_size) ;</span>
<a name="l00255"></a>00255 <span class="comment">*/</span>
<a name="l00256"></a>00256
<a name="l00257"></a>00257 verts = pockets-&gt;<a class="code" href="structc__lst__pockets.html#8d86cfec23ef9aa0079cf8258b39863e">vertices</a> ;
<a name="l00258"></a>00258 edesc = <a class="code" href="descriptors_8c.html#0313250c68f4a7a8e292b674c30ae9fa">allocate_s_desc</a>() ;
<a name="l00259"></a>00259 interface = <a class="code" href="dpocket_8c.html#fca470f9d8d1c8e84528205c7aeed723">get_explicit_desc</a>(pdb_cplx_l, verts, lig, nal, par,
<a name="l00260"></a>00260 &amp;nai, edesc) ;
<a name="l00261"></a>00261
<a name="l00262"></a>00262 <span class="comment">/* Writing output */</span>
<a name="l00263"></a>00263 vol = <a class="code" href="atom_8c.html#d0f577a82cfdb135f707700c2b84e6a5">get_mol_volume_ptr</a>(lig, nal, par-&gt;<a class="code" href="structs__dparams.html#84c3e94630fcd2402fd190aad5a0ffbf">fpar</a>-&gt;<a class="code" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">nb_mcv_iter</a>) ;
<a name="l00264"></a>00264 <a class="code" href="dpocket_8c.html#c32aae31fed030bdb0f31f447fd2e79f">write_pocket_desc</a>(fcomplexe, ligname, edesc, vol, 100.0, 0.0, 1.0, 1.0, f[0]) ;
<a name="l00265"></a>00265
<a name="l00266"></a>00266 <a class="code" href="structnode__pocket.html">node_pocket</a> *cur = pockets-&gt;<a class="code" href="structc__lst__pockets.html#cf82eb35ce757228759a9af7675f5ad9">first</a> ;
<a name="l00267"></a>00267 <a class="code" href="structs__vvertice.html">s_vvertice</a> **pvert = NULL ;
<a name="l00268"></a>00268 <span class="keywordflow">while</span>(cur) {
<a name="l00269"></a>00269 <span class="comment">/* Get the natomic overlap */</span>
<a name="l00270"></a>00270 patoms = <a class="code" href="voronoi__lst_8c.html#1aea5e4bcd4dae927a55f7c4dafa194d">get_vert_contacted_atms</a>(cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>, &amp;nbpa) ;
<a name="l00271"></a>00271 ovlp = <a class="code" href="atom_8c.html#a960d66d3bd7cce701a12f56999056b4">atm_corsp</a>(interface, nai, patoms, nbpa) ;
<a name="l00272"></a>00272
<a name="l00273"></a>00273 <span class="comment">/* Get the smallest distance of the ligand to the pocket</span>
<a name="l00274"></a>00274 <span class="comment"> (PocketPicker criteria) */</span>
<a name="l00275"></a>00275 <span class="keywordflow">for</span> (j = 0 ; j &lt; nal ; j++) {
<a name="l00276"></a>00276 tmp = <a class="code" href="calc_8c.html#615f3353fc9ccc88069adb4000b21e73">dist</a>(lig[j]-&gt;x, lig[j]-&gt;y, lig[j]-&gt;z,
<a name="l00277"></a>00277 cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#45fdf0337674ecb9e96cc7d52a08926f">bary</a>[0], cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#45fdf0337674ecb9e96cc7d52a08926f">bary</a>[1],
<a name="l00278"></a>00278 cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#45fdf0337674ecb9e96cc7d52a08926f">bary</a>[2]) ;
<a name="l00279"></a>00279 <span class="keywordflow">if</span>(j == 0) dst = tmp ;
<a name="l00280"></a>00280 <span class="keywordflow">else</span> {
<a name="l00281"></a>00281 <span class="keywordflow">if</span>(tmp &lt; dst) dst = tmp ;
<a name="l00282"></a>00282 }
<a name="l00283"></a>00283 }
<a name="l00284"></a>00284
<a name="l00285"></a>00285 <span class="comment">/* Get the consensus criteria too */</span>
<a name="l00286"></a>00286 pvert = <a class="code" href="pocket_8c.html#86288d8af02eeeb7c4a1b18df3a82af3">get_pocket_pvertices</a>(cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>) ;
<a name="l00287"></a>00287
<a name="l00288"></a>00288 c4 = <a class="code" href="neighbor_8c.html#72eb34a8654b78fc8fe8e64b8d49b31a">count_atm_prop_vert_neigh</a>( lig, pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#659b83804ffc576f1307beac00c1486b">natm_lig</a>,
<a name="l00289"></a>00289 pvert, cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#50722d86f4f1bf5b66b092b2bcbc661f">size</a>, <a class="code" href="tpocket_8h.html#bfe7ce08e878d91f96ca004bace09338">M_CRIT4_D</a>,n_lig_molecules) ;
<a name="l00290"></a>00290 c5 = <a class="code" href="neighbor_8c.html#3740ecf8c19f6a9a230fc19553ec23ba">count_pocket_lig_vert_ovlp</a>(lig, pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#659b83804ffc576f1307beac00c1486b">natm_lig</a>,
<a name="l00291"></a>00291 pvert, cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#50722d86f4f1bf5b66b092b2bcbc661f">size</a>, <a class="code" href="tpocket_8h.html#ae4ceec65f3391993a39f87da79e798b">M_CRIT5_D</a>) ;
<a name="l00292"></a>00292
<a name="l00293"></a>00293 <span class="comment">/* */</span>
<a name="l00294"></a>00294 <span class="keywordflow">if</span>(ovlp &gt; 40.0 || dst &lt; 4.0) {
<a name="l00295"></a>00295 <a class="code" href="dpocket_8c.html#c32aae31fed030bdb0f31f447fd2e79f">write_pocket_desc</a>(fcomplexe, ligname, cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>, vol,
<a name="l00296"></a>00296 ovlp, dst, c4, c5, f[1]) ;
<a name="l00297"></a>00297 }
<a name="l00298"></a>00298 <span class="keywordflow">else</span> {
<a name="l00299"></a>00299 <a class="code" href="dpocket_8c.html#c32aae31fed030bdb0f31f447fd2e79f">write_pocket_desc</a>(fcomplexe, ligname, cur-&gt;<a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-&gt;<a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>, vol,
<a name="l00300"></a>00300 ovlp, dst, c4, c5, f[2]) ;
<a name="l00301"></a>00301 }
<a name="l00302"></a>00302 <a class="code" href="memhandler_8c.html#a49400242a007d208c641f79856ea4c6">my_free</a>(patoms) ;
<a name="l00303"></a>00303 cur = cur-&gt;<a class="code" href="structnode__pocket.html#a33c910dd9e6996001374199f250267e">next</a> ;
<a name="l00304"></a>00304 }
<a name="l00305"></a>00305
<a name="l00306"></a>00306 <span class="comment">/* Free memory */</span>
<a name="l00307"></a>00307 <a class="code" href="pocket_8c.html#a9afcc69c1f7bdce1f22b0c48397b242">c_lst_pocket_free</a>(pockets) ;
<a name="l00308"></a>00308 <a class="code" href="memhandler_8c.html#a49400242a007d208c641f79856ea4c6">my_free</a>(interface) ;
<a name="l00309"></a>00309 <a class="code" href="rpdb_8c.html#fda283d39ae56654675e9e858f5ffdea">free_pdb_atoms</a>(pdb_cplx_l) ;
<a name="l00310"></a>00310 <a class="code" href="rpdb_8c.html#fda283d39ae56654675e9e858f5ffdea">free_pdb_atoms</a>(pdb_cplx_nl) ;
<a name="l00311"></a>00311
<a name="l00312"></a>00312 }
</pre></div>
<p>
</div>
</div><p>
<a class="anchor" name="7b962a8ea0d00ac566609fb14336c17b"></a><!-- doxytag: member="dpocket.h::dpocket" ref="7b962a8ea0d00ac566609fb14336c17b" args="(s_dparams *par)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void dpocket </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structs__dparams.html">s_dparams</a> *&nbsp;</td>
<td class="paramname"> <em>par</em> </td>
<td>&nbsp;)&nbsp;</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
## FUNCTION: dpocket<p>
## SPECIFICATION: Dpocket main function. Simple loop is performed over all files.<p>
## PARAMETRES: @ <a class="el" href="structs__dparams.html">s_dparams</a> *par: Parameters of the programm<p>
## RETURN: void
<p>Definition at line <a class="el" href="dpocket_8c-source.html#l00116">116</a> of file <a class="el" href="dpocket_8c-source.html">dpocket.c</a>.</p>
<p>References <a class="el" href="dpocket_8c-source.html#l00184">desc_pocket()</a>, <a class="el" href="dparams_8h-source.html#l00111">s_dparams::f_exp</a>, <a class="el" href="dparams_8h-source.html#l00111">s_dparams::f_fpcknp</a>, <a class="el" href="dparams_8h-source.html#l00111">s_dparams::f_fpckp</a>, <a class="el" href="dparams_8h-source.html#l00108">s_dparams::fcomplex</a>, <a class="el" href="aa_8c-source.html#l00117">get_aa_name3()</a>, <a class="el" href="dparams_8h-source.html#l00108">s_dparams::ligs</a>, <a class="el" href="dpocket_8h-source.html#l00064">M_DP_OUTP_HEADER</a>, and <a class="el" href="dparams_8h-source.html#l00117">s_dparams::nfiles</a>.</p>
<p>Referenced by <a class="el" href="dpmain_8c-source.html#l00067">main()</a>.</p>
<div class="fragment"><pre class="fragment"><a name="l00117"></a>00117 {
<a name="l00118"></a>00118 <span class="keywordtype">int</span> i, j ;
<a name="l00119"></a>00119 FILE *fout[3] ;
<a name="l00120"></a>00120
<a name="l00121"></a>00121 <span class="keywordflow">if</span>(par) {
<a name="l00122"></a>00122 <span class="comment">/* Opening output file file */</span>
<a name="l00123"></a>00123
<a name="l00124"></a>00124 fout[0] = fopen(par-&gt;<a class="code" href="structs__dparams.html#eed722b226fde5c51dfa3e2f83d9a6d3">f_exp</a>,<span class="stringliteral">"w"</span>) ;
<a name="l00125"></a>00125 fout[1] = fopen(par-&gt;<a class="code" href="structs__dparams.html#3f14e5f303fbf919cd6f9abab8505c68">f_fpckp</a>,<span class="stringliteral">"w"</span>) ;
<a name="l00126"></a>00126 fout[2] = fopen(par-&gt;<a class="code" href="structs__dparams.html#b1b7fc562b81d0670f3044252a2d4c34">f_fpcknp</a>,<span class="stringliteral">"w"</span>) ;
<a name="l00127"></a>00127
<a name="l00128"></a>00128 <span class="keywordflow">if</span>(fout[0] &amp;&amp; fout[1] &amp;&amp; fout[2]) {
<a name="l00129"></a>00129
<a name="l00130"></a>00130 <span class="comment">/* Writing column names */</span>
<a name="l00131"></a>00131
<a name="l00132"></a>00132 <span class="keywordflow">for</span>( i = 0 ; i &lt; 3 ; i++ ) {
<a name="l00133"></a>00133 fprintf(fout[i], <a class="code" href="dpocket_8h.html#23343f9b8e0f8438a1e800f657eebc55">M_DP_OUTP_HEADER</a>) ;
<a name="l00134"></a>00134 <span class="keywordflow">for</span>( j = 0 ; j &lt; 20 ; j++ ) fprintf(fout[i], <span class="stringliteral">" %s"</span>, <a class="code" href="aa_8c.html#f071a7d6353978202a07fd66f2ff68d8">get_aa_name3</a>(j));
<a name="l00135"></a>00135 fprintf(fout[i], <span class="stringliteral">"\n"</span>);
<a name="l00136"></a>00136 }
<a name="l00137"></a>00137
<a name="l00138"></a>00138 <span class="comment">/* Begins dpocket */</span>
<a name="l00139"></a>00139 <span class="keywordflow">for</span>(i = 0 ; i &lt; par-&gt;<a class="code" href="structs__dparams.html#04c48f5eb6778c9a5022588e507043d3">nfiles</a> ; i++) {
<a name="l00140"></a>00140 fprintf(stdout, <span class="stringliteral">"&lt;dpocket&gt;s %d/%d - %s:"</span>,
<a name="l00141"></a>00141 i+1, par-&gt;<a class="code" href="structs__dparams.html#04c48f5eb6778c9a5022588e507043d3">nfiles</a>, par-&gt;<a class="code" href="structs__dparams.html#a98295f566006ae97eef0628a9c94a86">fcomplex</a>[i]) ;
<a name="l00142"></a>00142
<a name="l00143"></a>00143 <a class="code" href="dpocket_8c.html#5413a47106630839ae6ecd90ba9bf9fd">desc_pocket</a>(par-&gt;<a class="code" href="structs__dparams.html#a98295f566006ae97eef0628a9c94a86">fcomplex</a>[i], par-&gt;<a class="code" href="structs__dparams.html#d3fbaf401c68c3abf7ef662259e547d6">ligs</a>[i], par, fout) ;
<a name="l00144"></a>00144 <span class="keywordflow">if</span>(i == par-&gt;<a class="code" href="structs__dparams.html#04c48f5eb6778c9a5022588e507043d3">nfiles</a> - 1) fprintf(stdout,<span class="stringliteral">"\n"</span>) ;
<a name="l00145"></a>00145 <span class="keywordflow">else</span> fprintf(stdout,<span class="stringliteral">"\r"</span>) ;
<a name="l00146"></a>00146
<a name="l00147"></a>00147 fflush(stdout) ;
<a name="l00148"></a>00148 }
<a name="l00149"></a>00149
<a name="l00150"></a>00150 <span class="keywordflow">for</span>( i = 0 ; i &lt; 3 ; i++ ) fclose(fout[i]) ;
<a name="l00151"></a>00151 }
<a name="l00152"></a>00152 <span class="keywordflow">else</span> {
<a name="l00153"></a>00153 <span class="keywordflow">if</span>(! fout[0]) {
<a name="l00154"></a>00154 fprintf(stdout, <span class="stringliteral">"! Output file &lt;%s&gt; couldn't be opened.\n"</span>,
<a name="l00155"></a>00155 par-&gt;<a class="code" href="structs__dparams.html#eed722b226fde5c51dfa3e2f83d9a6d3">f_exp</a>) ;
<a name="l00156"></a>00156 }
<a name="l00157"></a>00157 <span class="keywordflow">else</span> <span class="keywordflow">if</span> (! fout[1]) {
<a name="l00158"></a>00158 fprintf(stdout, <span class="stringliteral">"! Output file &lt;%s&gt; couldn't be opened.\n"</span>,
<a name="l00159"></a>00159 par-&gt;<a class="code" href="structs__dparams.html#3f14e5f303fbf919cd6f9abab8505c68">f_fpckp</a>) ;
<a name="l00160"></a>00160 }
<a name="l00161"></a>00161 <span class="keywordflow">else</span> {
<a name="l00162"></a>00162 fprintf(stdout, <span class="stringliteral">"! Output file &lt;%s&gt; couldn't be opened.\n"</span>,
<a name="l00163"></a>00163 par-&gt;<a class="code" href="structs__dparams.html#b1b7fc562b81d0670f3044252a2d4c34">f_fpcknp</a>) ;
<a name="l00164"></a>00164 }
<a name="l00165"></a>00165 }
<a name="l00166"></a>00166 }
<a name="l00167"></a>00167 }
</pre></div>
<p>
</div>
</div><p>
<a class="anchor" name="fca470f9d8d1c8e84528205c7aeed723"></a><!-- doxytag: member="dpocket.h::get_explicit_desc" ref="fca470f9d8d1c8e84528205c7aeed723" args="(s_pdb *pdb_cplx_l, s_lst_vvertice *verts, s_atm **lig, int nal, s_dparams *par, int *nai, s_desc *desc)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structs__atm.html">s_atm</a>** get_explicit_desc </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structs__pdb.html">s_pdb</a> *&nbsp;</td>
<td class="paramname"> <em>pdb_cplx_l</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structs__lst__vvertice.html">s_lst_vvertice</a> *&nbsp;</td>
<td class="paramname"> <em>verts</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structs__atm.html">s_atm</a> **&nbsp;</td>
<td class="paramname"> <em>lig</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int&nbsp;</td>
<td class="paramname"> <em>nal</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structs__dparams.html">s_dparams</a> *&nbsp;</td>
<td class="paramname"> <em>par</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int *&nbsp;</td>
<td class="paramname"> <em>nai</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structs__desc.html">s_desc</a> *&nbsp;</td>
<td class="paramname"> <em>desc</em></td><td>&nbsp;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
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</div>
<div class="memdoc">
<p>
## FUNCTION: get_explicit_desc<p>
## SPECIFICATION: Determine the explicit pocket (see comments at the top of the file), and calculate descriptors (and fill the input structure)<p>
## PARAMETRES: @ <a class="el" href="structs__pdb.html">s_pdb</a> *pdb_cplx_l : The pdb structure @ <a class="el" href="structs__lst__vvertice.html">s_lst_vvertice</a> *verts : The vertices found @ <a class="el" href="structs__atm.html">s_atm</a> **lig : Atoms of the ligand @ int nal : Number of atom in the ligand @ <a class="el" href="structs__dparams.html">s_dparams</a> *par : Parameters @ int *nai : OUTPUT Number of atom in the interface @ <a class="el" href="structs__desc.html">s_desc</a> *desc : OUTPUT Descriptors<p>
## RETURN: <a class="el" href="structs__atm.html">s_atm</a> **: List of pointer to atoms defining the explicit pocket. plus nai and desc are filled.
<p>Definition at line <a class="el" href="dpocket_8c-source.html#l00336">336</a> of file <a class="el" href="dpocket_8c-source.html">dpocket.c</a>.</p>
<p>References <a class="el" href="fparams_8h-source.html#l00139">s_fparams::flag_do_asa_and_volume_calculations</a>, <a class="el" href="dparams_8h-source.html#l00120">s_dparams::fpar</a>, <a class="el" href="neighbor_8c-source.html#l00090">get_mol_atm_neigh()</a>, <a class="el" href="neighbor_8c-source.html#l00332">get_mol_ctd_atm_neigh()</a>, <a class="el" href="neighbor_8c-source.html#l00213">get_mol_vert_neigh()</a>, <a class="el" href="dparams_8h-source.html#l00115">s_dparams::interface_dist_crit</a>, <a class="el" href="dparams_8h-source.html#l00117">s_dparams::interface_method</a>, <a class="el" href="rpdb_8h-source.html#l00074">s_pdb::latoms_p</a>, <a class="el" href="dparams_8h-source.html#l00066">M_INTERFACE_METHOD2</a>, <a class="el" href="neighbor_8h-source.html#l00053">M_INTERFACE_SEARCH</a>, <a class="el" href="memhandler_8c-source.html#l00255">my_free()</a>, <a class="el" href="rpdb_8h-source.html#l00078">s_pdb::natoms</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::nb_mcv_iter</a>, <a class="el" href="voronoi_8h-source.html#l00100">s_lst_vvertice::nvert</a>, <a class="el" href="voronoi_8h-source.html#l00096">s_lst_vvertice::pvertices</a>, and <a class="el" href="descriptors_8c-source.html#l00182">set_descriptors()</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00184">desc_pocket()</a>.</p>
<div class="fragment"><pre class="fragment"><a name="l00338"></a>00338 {
<a name="l00339"></a>00339 <span class="keywordtype">int</span> nvn = 0 ; <span class="comment">/* Number of vertices in the interface */</span>
<a name="l00340"></a>00340
<a name="l00341"></a>00341 <a class="code" href="structs__atm.html">s_atm</a> **interface = NULL ;
<a name="l00342"></a>00342
<a name="l00343"></a>00343 <span class="comment">/*</span>
<a name="l00344"></a>00344 <span class="comment"> fprintf(stdout, "dpocket: Determning explicit interface... ") ; </span>
<a name="l00345"></a>00345 <span class="comment"> fflush(stdout) ;</span>
<a name="l00346"></a>00346 <span class="comment">*/</span>
<a name="l00347"></a>00347
<a name="l00348"></a>00348 <span class="keywordflow">if</span>(par-&gt;<a class="code" href="structs__dparams.html#f48783ed6b360f7a3e83eb4c7ae11300">interface_method</a> == <a class="code" href="dparams_8h.html#8364a85272afb754f95f5f76832a82ac">M_INTERFACE_METHOD2</a>) {
<a name="l00349"></a>00349 <span class="comment">/* Use the distance-based method to define the interface */</span>
<a name="l00350"></a>00350 interface = <a class="code" href="neighbor_8c.html#48bd2094854cf343b3f75e93997bea04">get_mol_atm_neigh</a>( lig, nal, pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#4517e3a82dbf0f34e73d1865e484dbfd">latoms_p</a>,
<a name="l00351"></a>00351 pdb_cplx_l-&gt;<a class="code" href="structs__pdb.html#85aaf7bdb931bb303af1ca736a998b98">natoms</a>,
<a name="l00352"></a>00352 par-&gt;<a class="code" href="structs__dparams.html#09b829e05d79410ee1471242ab622cac">interface_dist_crit</a>, nai) ;
<a name="l00353"></a>00353 }
<a name="l00354"></a>00354 <span class="keywordflow">else</span> {
<a name="l00355"></a>00355 <span class="comment">/* Use the voronoi vertices-based method to define the interface */</span>
<a name="l00356"></a>00356
<a name="l00357"></a>00357 interface = <a class="code" href="neighbor_8c.html#60519bcf15270301f71419d124eb930c">get_mol_ctd_atm_neigh</a>(lig, nal, verts-&gt;<a class="code" href="structs__lst__vvertice.html#638d9ede844bca411ed99cb8e22b0e56">pvertices</a>, verts-&gt;<a class="code" href="structs__lst__vvertice.html#c6b07ac45ca65ccd944b68afd4c18bfb">nvert</a>,
<a name="l00358"></a>00358 par-&gt;<a class="code" href="structs__dparams.html#09b829e05d79410ee1471242ab622cac">interface_dist_crit</a>,
<a name="l00359"></a>00359 <a class="code" href="neighbor_8h.html#1c318ac74ea9b85f4cc72cc40b4709c8">M_INTERFACE_SEARCH</a>, nai) ;
<a name="l00360"></a>00360 }
<a name="l00361"></a>00361
<a name="l00362"></a>00362 <span class="comment">/* Get a tab of pointer for interface's vertices to send a correct argument </span>
<a name="l00363"></a>00363 <span class="comment"> * type to set_descriptors */</span>
<a name="l00364"></a>00364 <a class="code" href="structs__vvertice.html">s_vvertice</a> **tpverts = <a class="code" href="neighbor_8c.html#7bed24829e9d106de97de75a5538199a">get_mol_vert_neigh</a>(lig, nal, verts-&gt;<a class="code" href="structs__lst__vvertice.html#638d9ede844bca411ed99cb8e22b0e56">pvertices</a>, verts-&gt;<a class="code" href="structs__lst__vvertice.html#c6b07ac45ca65ccd944b68afd4c18bfb">nvert</a>,
<a name="l00365"></a>00365 par-&gt;<a class="code" href="structs__dparams.html#09b829e05d79410ee1471242ab622cac">interface_dist_crit</a>, &amp;nvn) ;
<a name="l00366"></a>00366
<a name="l00367"></a>00367 <span class="comment">/* Ok we have the interface and the correct vertices list, now calculate </span>
<a name="l00368"></a>00368 <span class="comment"> * descriptors and write it.</span>
<a name="l00369"></a>00369 <span class="comment"> **/</span>
<a name="l00370"></a>00370 <span class="comment">/*</span>
<a name="l00371"></a>00371 <span class="comment"> fprintf(stdout, "dpocket: Calculating descriptors... ") ; fflush(stdout) ;</span>
<a name="l00372"></a>00372 <span class="comment">*/</span>
<a name="l00373"></a>00373 <a class="code" href="descriptors_8c.html#9cfae44d2e72d4c92d38a4b73538d8c4">set_descriptors</a>(interface, *nai, tpverts, nvn, desc, par-&gt;<a class="code" href="structs__dparams.html#84c3e94630fcd2402fd190aad5a0ffbf">fpar</a>-&gt;<a class="code" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">nb_mcv_iter</a>,pdb_cplx_l,par-&gt;<a class="code" href="structs__dparams.html#84c3e94630fcd2402fd190aad5a0ffbf">fpar</a>-&gt;<a class="code" href="structs__fparams.html#771a10e1c94346d353eb6cb87b4abb18">flag_do_asa_and_volume_calculations</a>);
<a name="l00374"></a>00374 <span class="comment">/*</span>
<a name="l00375"></a>00375 <span class="comment"> fprintf(stdout, " OK\n") ;</span>
<a name="l00376"></a>00376 <span class="comment">*/</span>
<a name="l00377"></a>00377
<a name="l00378"></a>00378 <span class="comment">/* Free memory */</span>
<a name="l00379"></a>00379 <a class="code" href="memhandler_8c.html#a49400242a007d208c641f79856ea4c6">my_free</a>(tpverts) ;
<a name="l00380"></a>00380
<a name="l00381"></a>00381 <span class="keywordflow">return</span> interface ;
<a name="l00382"></a>00382 }
</pre></div>
<p>
</div>
</div><p>
<a class="anchor" name="c32aae31fed030bdb0f31f447fd2e79f"></a><!-- doxytag: member="dpocket.h::write_pocket_desc" ref="c32aae31fed030bdb0f31f447fd2e79f" args="(const char fc[], const char l[], s_desc *d, float lv, float ovlp, float dst, float c4, float c5, FILE *f)" -->
<div class="memitem">
<div class="memproto">
<table class="memname">
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<td class="memname">void write_pocket_desc </td>
<td>(</td>
<td class="paramtype">const char&nbsp;</td>
<td class="paramname"> <em>fc</em>[], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char&nbsp;</td>
<td class="paramname"> <em>l</em>[], </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structs__desc.html">s_desc</a> *&nbsp;</td>
<td class="paramname"> <em>d</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float&nbsp;</td>
<td class="paramname"> <em>lv</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float&nbsp;</td>
<td class="paramname"> <em>ovlp</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float&nbsp;</td>
<td class="paramname"> <em>dst</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float&nbsp;</td>
<td class="paramname"> <em>c4</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">float&nbsp;</td>
<td class="paramname"> <em>c5</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">FILE *&nbsp;</td>
<td class="paramname"> <em>f</em></td><td>&nbsp;</td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
## FUNCTION: write_pocket_desc<p>
## SPECIFICATION: Write pocket descriptors into a file.<p>
## PARAMETRES: @ const char fc[] : Name of the pdb file @ const char l[] : Resname of the ligand @ <a class="el" href="structs__desc.html">s_desc</a> *d : Stucture of descriptors @ float lv : Ligand volume @ float ovlp : Overlap @ FILE *f : Buffer to write in<p>
## RETURN: void
<p>Definition at line <a class="el" href="dpocket_8c-source.html#l00403">403</a> of file <a class="el" href="dpocket_8c-source.html">dpocket.c</a>.</p>
<p>References <a class="el" href="descriptors_8h-source.html#l00094">s_desc::aa_compo</a>, <a class="el" href="tpocket_8h-source.html#l00059">M_CRIT4_VAL</a>, <a class="el" href="tpocket_8h-source.html#l00060">M_CRIT5_VAL</a>, <a class="el" href="dpocket_8h-source.html#l00066">M_DP_OUTP_FORMAT</a>, and <a class="el" href="dpocket_8h-source.html#l00067">M_DP_OUTP_VAR</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00184">desc_pocket()</a>.</p>
<div class="fragment"><pre class="fragment"><a name="l00405"></a>00405 {
<a name="l00406"></a>00406 <span class="keywordtype">int</span> status = 0 ;
<a name="l00407"></a>00407 <span class="keywordflow">if</span>(dst &lt; 4.0) status = 1 ;
<a name="l00408"></a>00408
<a name="l00409"></a>00409 <span class="keywordtype">int</span> c6 = (c4 &gt;= <a class="code" href="tpocket_8h.html#e6144aeda44c4bb02f1f9497785d2510">M_CRIT4_VAL</a> &amp;&amp; c5 &gt;= <a class="code" href="tpocket_8h.html#8e29f7a52f508cd17213fe9e6d7f9b03">M_CRIT5_VAL</a>) ?1:0 ;
<a name="l00410"></a>00410 <span class="keywordtype">float</span> c6_c = ((c4 - <a class="code" href="tpocket_8h.html#e6144aeda44c4bb02f1f9497785d2510">M_CRIT4_VAL</a>)/ (1-<a class="code" href="tpocket_8h.html#e6144aeda44c4bb02f1f9497785d2510">M_CRIT4_VAL</a>)) + ((c5 - <a class="code" href="tpocket_8h.html#8e29f7a52f508cd17213fe9e6d7f9b03">M_CRIT5_VAL</a>)/ (1-<a class="code" href="tpocket_8h.html#8e29f7a52f508cd17213fe9e6d7f9b03">M_CRIT5_VAL</a>)) ;
<a name="l00411"></a>00411
<a name="l00412"></a>00412 fprintf(f, <a class="code" href="dpocket_8h.html#37abd6af8ee30c796fbb1515bb8b8254">M_DP_OUTP_FORMAT</a>, <a class="code" href="dpocket_8h.html#f3b98e7b7baf7f23c259c71912aa40d9">M_DP_OUTP_VAR</a>(fc, l, ovlp, status, dst, c4, c5, c6, c6_c, lv, d)) ;
<a name="l00413"></a>00413
<a name="l00414"></a>00414 <span class="keywordtype">int</span> i ;
<a name="l00415"></a>00415 <span class="keywordflow">for</span>(i = 0 ; i &lt; 20 ; i++) fprintf(f, <span class="stringliteral">" %3d"</span>, d-&gt;<a class="code" href="structs__desc.html#12f239c0748ce08dba80fac61722117f">aa_compo</a>[i]) ;
<a name="l00416"></a>00416
<a name="l00417"></a>00417 fprintf(f, <span class="stringliteral">"\n"</span>) ;
<a name="l00418"></a>00418 }
</pre></div>
<p>
</div>
</div><p>
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