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<h1>writepocket.c</h1><a href="writepocket_8c.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001
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<a name="l00002"></a>00002 <span class="preprocessor">#include "../headers/writepocket.h"</span>
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<a name="l00003"></a>00003 <span class="comment">/*</span>
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<a name="l00004"></a>00004 <span class="comment"></span>
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<a name="l00005"></a>00005 <span class="comment">## GENERAL INFORMATION</span>
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<a name="l00006"></a>00006 <span class="comment">##</span>
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<a name="l00007"></a>00007 <span class="comment">## FILE writepocket.c</span>
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<a name="l00008"></a>00008 <span class="comment">## AUTHORS P. Schmidtke and V. Le Guilloux</span>
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<a name="l00009"></a>00009 <span class="comment">## LAST MODIFIED 02-12-08</span>
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<a name="l00010"></a>00010 <span class="comment">##</span>
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<a name="l00011"></a>00011 <span class="comment">## SPECIFICATIONS</span>
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<a name="l00012"></a>00012 <span class="comment">##</span>
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<a name="l00013"></a>00013 <span class="comment">## Output routine for pockets.</span>
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<a name="l00014"></a>00014 <span class="comment">##</span>
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<a name="l00015"></a>00015 <span class="comment">## MODIFICATIONS HISTORY</span>
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<a name="l00016"></a>00016 <span class="comment">##</span>
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<a name="l00017"></a>00017 <span class="comment">## 02-12-08 (v) Comments UTD</span>
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<a name="l00018"></a>00018 <span class="comment">## 01-04-08 (v) Added template for comments and creation of history</span>
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<a name="l00019"></a>00019 <span class="comment">## 01-01-08 (vp) Created (random date...)</span>
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<a name="l00020"></a>00020 <span class="comment">## </span>
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<a name="l00021"></a>00021 <span class="comment">## TODO or SUGGESTIONS</span>
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<a name="l00022"></a>00022 <span class="comment">##</span>
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<a name="l00023"></a>00023 <span class="comment"></span>
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<a name="l00024"></a>00024 <span class="comment">*/</span>
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<a name="l00025"></a>00025
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<a name="l00026"></a>00026 <span class="comment">/*</span>
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<a name="l00027"></a>00027 <span class="comment"> COPYRIGHT DISCLAIMER</span>
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<a name="l00028"></a>00028 <span class="comment"></span>
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<a name="l00029"></a>00029 <span class="comment"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
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<a name="l00030"></a>00030 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
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<a name="l00031"></a>00031 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
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<a name="l00032"></a>00032 <span class="comment"> Schmidtke.</span>
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<a name="l00033"></a>00033 <span class="comment"></span>
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<a name="l00034"></a>00034 <span class="comment"> Vincent Le Guilloux 28 November 2008</span>
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<a name="l00035"></a>00035 <span class="comment"> Peter Schmidtke 28 November 2008</span>
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<a name="l00036"></a>00036 <span class="comment"> Pierre Tuffery 28 November 2008</span>
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<a name="l00037"></a>00037 <span class="comment"></span>
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<a name="l00038"></a>00038 <span class="comment"> GNU GPL</span>
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<a name="l00039"></a>00039 <span class="comment"></span>
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<a name="l00040"></a>00040 <span class="comment"> This file is part of the fpocket package.</span>
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<a name="l00041"></a>00041 <span class="comment"></span>
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<a name="l00042"></a>00042 <span class="comment"> fpocket is free software: you can redistribute it and/or modify</span>
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<a name="l00043"></a>00043 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
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<a name="l00044"></a>00044 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
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<a name="l00045"></a>00045 <span class="comment"> (at your option) any later version.</span>
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<a name="l00046"></a>00046 <span class="comment"></span>
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<a name="l00047"></a>00047 <span class="comment"> fpocket is distributed in the hope that it will be useful,</span>
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<a name="l00048"></a>00048 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<a name="l00049"></a>00049 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<a name="l00050"></a>00050 <span class="comment"> GNU General Public License for more details.</span>
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<a name="l00051"></a>00051 <span class="comment"></span>
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<a name="l00052"></a>00052 <span class="comment"> You should have received a copy of the GNU General Public License</span>
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<a name="l00053"></a>00053 <span class="comment"> along with fpocket. If not, see <http://www.gnu.org/licenses/>.</span>
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<a name="l00054"></a>00054 <span class="comment"></span>
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<a name="l00055"></a>00055 <span class="comment">**/</span>
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<a name="l00056"></a>00056
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<a name="l00057"></a>00057 <span class="comment"></span>
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<a name="l00058"></a>00058 <span class="comment">/**</span>
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<a name="l00059"></a>00059 <span class="comment"> ## FUNCTION: </span>
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<a name="l00060"></a>00060 <span class="comment"> write_single_pdb</span>
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<a name="l00061"></a>00061 <span class="comment"> </span>
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<a name="l00062"></a>00062 <span class="comment"> ## SPECIFICATION: </span>
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<a name="l00063"></a>00063 <span class="comment"> Write atoms and vertices given in argument in the following standard v2.2 </span>
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<a name="l00064"></a>00064 <span class="comment"> pdb format.</span>
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<a name="l00065"></a>00065 <span class="comment"></span>
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<a name="l00066"></a>00066 <span class="comment"> </span>
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<a name="l00067"></a>00067 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00068"></a>00068 <span class="comment"> @ const char out[] : Output file name</span>
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<a name="l00069"></a>00069 <span class="comment"> @ s_pdb *pdb : PDB infos</span>
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<a name="l00070"></a>00070 <span class="comment"> @ c_lst_pockets *pockets : All pockets</span>
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<a name="l00071"></a>00071 <span class="comment"> </span>
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<a name="l00072"></a>00072 <span class="comment"> ## RETURN:</span>
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<a name="l00073"></a>00073 <span class="comment"> </span>
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<a name="l00074"></a>00074 <span class="comment">*/</span>
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<a name="l00075"></a><a class="code" href="writepocket_8h.html#5392484596cd363d8322062b67dd3a7f">00075</a> <span class="keywordtype">void</span> <a class="code" href="writepocket_8c.html#5392484596cd363d8322062b67dd3a7f">write_pockets_single_pdb</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> out[], <a class="code" href="structs__pdb.html">s_pdb</a> *pdb, <a class="code" href="structc__lst__pockets.html">c_lst_pockets</a> *pockets)
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<a name="l00076"></a>00076 {
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<a name="l00077"></a>00077 <a class="code" href="structnode__pocket.html">node_pocket</a> *nextPocket ;
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<a name="l00078"></a>00078 <a class="code" href="structnode__vertice.html">node_vertice</a> *nextVertice ;
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<a name="l00079"></a>00079 FILE *f = fopen(out, <span class="stringliteral">"w"</span>) ;
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<a name="l00080"></a>00080 <span class="keywordflow">if</span>(f) {
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<a name="l00081"></a>00081 <span class="keywordflow">if</span>(pdb) {
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<a name="l00082"></a>00082 <span class="keywordflow">if</span>(pdb-><a class="code" href="structs__pdb.html#3b0fff968487b66aa1c88e55d45120e4">latoms</a>) <a class="code" href="writepocket_8c.html#2ee381dad55af0f621f92ab393954dbb">write_pdb_atoms</a>(f, pdb-><a class="code" href="structs__pdb.html#3b0fff968487b66aa1c88e55d45120e4">latoms</a>, pdb-><a class="code" href="structs__pdb.html#85aaf7bdb931bb303af1ca736a998b98">natoms</a> ) ;
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<a name="l00083"></a>00083 }
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<a name="l00084"></a>00084
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<a name="l00085"></a>00085 <span class="keywordflow">if</span>(pockets){
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<a name="l00086"></a>00086 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a> = pockets-><a class="code" href="structc__lst__pockets.html#cf82eb35ce757228759a9af7675f5ad9">first</a> ;
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<a name="l00087"></a>00087
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<a name="l00088"></a>00088 <span class="keywordflow">while</span>(pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>){
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<a name="l00089"></a>00089 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a> = pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#72562067d308bcfcf32605e112e30c1a">first</a> ;
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<a name="l00090"></a>00090
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<a name="l00091"></a>00091 <span class="keywordflow">while</span>(pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a>){
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<a name="l00092"></a>00092 <a class="code" href="voronoi_8c.html#624ae3215f4659770cd761d5bbb70a39">write_pdb_vert</a>(f, pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a>-><a class="code" href="structnode__vertice.html#7e7063f6403dfd8f0a8f83462e27729b">vertice</a>) ;
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<a name="l00093"></a>00093
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<a name="l00094"></a>00094 nextVertice = pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a>-><a class="code" href="structnode__vertice.html#61b34ff349d05cc65a4d8b9e2c77ff3e">next</a>;
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<a name="l00095"></a>00095 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a> = nextVertice;
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<a name="l00096"></a>00096 }
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<a name="l00097"></a>00097
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<a name="l00098"></a>00098 nextPocket=pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#a33c910dd9e6996001374199f250267e">next</a>;
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<a name="l00099"></a>00099 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>=nextPocket;
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<a name="l00100"></a>00100 }
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<a name="l00101"></a>00101 }
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<a name="l00102"></a>00102
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<a name="l00103"></a>00103 fclose(f) ;
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<a name="l00104"></a>00104 }
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<a name="l00105"></a>00105 <span class="keywordflow">else</span> {
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<a name="l00106"></a>00106 fprintf(stderr, <span class="stringliteral">"! The file %s could not be opened!\n"</span>, out);
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<a name="l00107"></a>00107 }
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<a name="l00108"></a>00108 }
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<a name="l00109"></a>00109 <span class="comment"></span>
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<a name="l00110"></a>00110 <span class="comment">/**</span>
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<a name="l00111"></a>00111 <span class="comment"> ## FUNCTION: </span>
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<a name="l00112"></a>00112 <span class="comment"> write_pdb_atoms</span>
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<a name="l00113"></a>00113 <span class="comment"> </span>
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<a name="l00114"></a>00114 <span class="comment"> ## SPECIFICATION:</span>
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<a name="l00115"></a>00115 <span class="comment"> Print list of atoms as pdb format in given buffer</span>
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<a name="l00116"></a>00116 <span class="comment"> </span>
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<a name="l00117"></a>00117 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00118"></a>00118 <span class="comment"> @ FILE *f : Buffer to write in.</span>
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<a name="l00119"></a>00119 <span class="comment"> @ s_atm *atoms : List of atoms</span>
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<a name="l00120"></a>00120 <span class="comment"> @ int natoms : Number of atoms</span>
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<a name="l00121"></a>00121 <span class="comment"> </span>
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<a name="l00122"></a>00122 <span class="comment"> ## RETURN:</span>
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<a name="l00123"></a>00123 <span class="comment"> </span>
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<a name="l00124"></a>00124 <span class="comment">*/</span>
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<a name="l00125"></a><a class="code" href="writepocket_8h.html#2ee381dad55af0f621f92ab393954dbb">00125</a> <span class="keywordtype">void</span> <a class="code" href="writepocket_8c.html#2ee381dad55af0f621f92ab393954dbb">write_pdb_atoms</a>(FILE *f, <a class="code" href="structs__atm.html">s_atm</a> *atoms, <span class="keywordtype">int</span> natoms)
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<a name="l00126"></a>00126 {
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<a name="l00127"></a>00127 <a class="code" href="structs__atm.html">s_atm</a> *atom = NULL ;
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<a name="l00128"></a>00128 <span class="keywordtype">int</span> i = 0 ;
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<a name="l00129"></a>00129 <span class="keywordflow">for</span>(i = 0 ; i < natoms ; i++) {
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<a name="l00130"></a>00130 atom = atoms + i ;
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<a name="l00131"></a>00131 <a class="code" href="writepdb_8c.html#c1826cac257476a6fe47825b31cafb4d">write_pdb_atom_line</a>(f, atom-><a class="code" href="structs__atm.html#98466fdfcb021884beb229b1dca361ae">type</a>, atom-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>, atom-><a class="code" href="structs__atm.html#2f0330a30f640668efdd726a6dd05a93">name</a>, atom-><a class="code" href="structs__atm.html#58eeb8a80942caa3bd2374f3175cb77d">pdb_aloc</a>,
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<a name="l00132"></a>00132 atom-><a class="code" href="structs__atm.html#e0ff20f2c491a8b16c866d9b1386b6a5">res_name</a>, atom-><a class="code" href="structs__atm.html#c5b9464bd67f2cca101f7bf6beabb223">chain</a>, atom-><a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a>,
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<a name="l00133"></a>00133 atom-><a class="code" href="structs__atm.html#bfd1f905200f69dd9cd9750fd305cf46">pdb_insert</a>, atom-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>, atom-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>, atom-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>,
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<a name="l00134"></a>00134 atom-><a class="code" href="structs__atm.html#1696926c680a1014360598d54a1dadb0">occupancy</a>, atom-><a class="code" href="structs__atm.html#6a1a5fd32629457dfa14626b25b5ae46">bfactor</a>, atom-><a class="code" href="structs__atm.html#c80daffa94edeadd30433f6653e08054">symbol</a>,
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<a name="l00135"></a>00135 atom-><a class="code" href="structs__atm.html#a03a199ed11108d7710547df629c7d73">charge</a>);
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<a name="l00136"></a>00136 }
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<a name="l00137"></a>00137 }
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<a name="l00138"></a>00138 <span class="comment"></span>
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<a name="l00139"></a>00139 <span class="comment">/**</span>
|
|
<a name="l00140"></a>00140 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00141"></a>00141 <span class="comment"> write_pockets_single_pqr</span>
|
|
<a name="l00142"></a>00142 <span class="comment"> </span>
|
|
<a name="l00143"></a>00143 <span class="comment"> ## SPECIFICATION: </span>
|
|
<a name="l00144"></a>00144 <span class="comment"> Write only pockets (alpha sphere) given in argument in the pqr format.</span>
|
|
<a name="l00145"></a>00145 <span class="comment"></span>
|
|
<a name="l00146"></a>00146 <span class="comment"> !! No atoms writen here, only all pockets in a single pqr file.</span>
|
|
<a name="l00147"></a>00147 <span class="comment"> </span>
|
|
<a name="l00148"></a>00148 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00149"></a>00149 <span class="comment"> @ const char out[] : Output file path</span>
|
|
<a name="l00150"></a>00150 <span class="comment"> @ c_lst_pockets *pockets : List of pockets</span>
|
|
<a name="l00151"></a>00151 <span class="comment"> </span>
|
|
<a name="l00152"></a>00152 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00153"></a>00153 <span class="comment"> </span>
|
|
<a name="l00154"></a>00154 <span class="comment">*/</span>
|
|
<a name="l00155"></a><a class="code" href="writepocket_8h.html#1702b849e7e173b193d42d92aa45ea14">00155</a> <span class="keywordtype">void</span> <a class="code" href="writepocket_8c.html#1702b849e7e173b193d42d92aa45ea14">write_pockets_single_pqr</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> out[], <a class="code" href="structc__lst__pockets.html">c_lst_pockets</a> *pockets)
|
|
<a name="l00156"></a>00156 {
|
|
<a name="l00157"></a>00157 <a class="code" href="structnode__pocket.html">node_pocket</a> *nextPocket ;
|
|
<a name="l00158"></a>00158 <a class="code" href="structnode__vertice.html">node_vertice</a> *nextVertice ;
|
|
<a name="l00159"></a>00159
|
|
<a name="l00160"></a>00160 FILE *f = fopen(out, <span class="stringliteral">"w"</span>) ;
|
|
<a name="l00161"></a>00161 <span class="keywordflow">if</span>(f) {
|
|
<a name="l00162"></a>00162
|
|
<a name="l00163"></a>00163 <span class="keywordflow">if</span>(pockets){
|
|
<a name="l00164"></a>00164 fprintf(f, <span class="stringliteral">"HEADER\n"</span>) ;
|
|
<a name="l00165"></a>00165 fprintf(f, <span class="stringliteral">"HEADER This is a pqr format file writen by the programm fpocket. \n"</span>) ;
|
|
<a name="l00166"></a>00166 fprintf(f, <span class="stringliteral">"HEADER It contains all the pockets vertices found by fpocket. \n"</span>) ;
|
|
<a name="l00167"></a>00167 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a> = pockets-><a class="code" href="structc__lst__pockets.html#cf82eb35ce757228759a9af7675f5ad9">first</a> ;
|
|
<a name="l00168"></a>00168
|
|
<a name="l00169"></a>00169 <span class="keywordflow">while</span>(pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>){
|
|
<a name="l00170"></a>00170 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a> = pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#72562067d308bcfcf32605e112e30c1a">first</a> ;
|
|
<a name="l00171"></a>00171
|
|
<a name="l00172"></a>00172 <span class="keywordflow">while</span>(pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a>){
|
|
<a name="l00173"></a>00173 <a class="code" href="voronoi_8c.html#0fc0360fbb0a071ba6d49dedd57ba397">write_pqr_vert</a>(f, pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a>-><a class="code" href="structnode__vertice.html#7e7063f6403dfd8f0a8f83462e27729b">vertice</a>) ;
|
|
<a name="l00174"></a>00174
|
|
<a name="l00175"></a>00175 nextVertice = pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a>-><a class="code" href="structnode__vertice.html#61b34ff349d05cc65a4d8b9e2c77ff3e">next</a>;
|
|
<a name="l00176"></a>00176 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#2853ff31eafd457b0d17c142541ad1ce">current</a> = nextVertice;
|
|
<a name="l00177"></a>00177 }
|
|
<a name="l00178"></a>00178
|
|
<a name="l00179"></a>00179 nextPocket=pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>-><a class="code" href="structnode__pocket.html#a33c910dd9e6996001374199f250267e">next</a>;
|
|
<a name="l00180"></a>00180 pockets-><a class="code" href="structc__lst__pockets.html#d19d42ddff486b5a89ddb717c28ab803">current</a>=nextPocket;
|
|
<a name="l00181"></a>00181 }
|
|
<a name="l00182"></a>00182 }
|
|
<a name="l00183"></a>00183
|
|
<a name="l00184"></a>00184 fprintf(f, <span class="stringliteral">"TER\nEND\n"</span>) ;
|
|
<a name="l00185"></a>00185 fclose(f) ;
|
|
<a name="l00186"></a>00186 }
|
|
<a name="l00187"></a>00187 <span class="keywordflow">else</span> {
|
|
<a name="l00188"></a>00188 fprintf(stderr, <span class="stringliteral">"! The file %s could not be opened!\n"</span>, out);
|
|
<a name="l00189"></a>00189 }
|
|
<a name="l00190"></a>00190 }
|
|
<a name="l00191"></a>00191 <span class="comment"></span>
|
|
<a name="l00192"></a>00192 <span class="comment">/**</span>
|
|
<a name="l00193"></a>00193 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00194"></a>00194 <span class="comment"> write_each_pocket</span>
|
|
<a name="l00195"></a>00195 <span class="comment"> </span>
|
|
<a name="l00196"></a>00196 <span class="comment"> ## SPECIFICATION: </span>
|
|
<a name="l00197"></a>00197 <span class="comment"> Write each pocket in a single pqr (vertices) and pdb (atoms) file format.</span>
|
|
<a name="l00198"></a>00198 <span class="comment"> </span>
|
|
<a name="l00199"></a>00199 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00200"></a>00200 <span class="comment"> @ const char out[] : Output file path</span>
|
|
<a name="l00201"></a>00201 <span class="comment"> @ c_lst_pockets *pockets : List of pockets</span>
|
|
<a name="l00202"></a>00202 <span class="comment"> </span>
|
|
<a name="l00203"></a>00203 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00204"></a>00204 <span class="comment"> </span>
|
|
<a name="l00205"></a>00205 <span class="comment">*/</span>
|
|
<a name="l00206"></a><a class="code" href="writepocket_8h.html#13ed4f98eaa10e2615280d4a6491f30e">00206</a> <span class="keywordtype">void</span> <a class="code" href="writepocket_8c.html#13ed4f98eaa10e2615280d4a6491f30e">write_each_pocket</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> out_path[], <a class="code" href="structc__lst__pockets.html">c_lst_pockets</a> *pockets)
|
|
<a name="l00207"></a>00207 {
|
|
<a name="l00208"></a>00208 <span class="keywordtype">int</span> out_len = strlen(out_path) ;
|
|
<a name="l00209"></a>00209 <span class="keywordtype">char</span> out[out_len+20] ;
|
|
<a name="l00210"></a>00210 out[0] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00211"></a>00211
|
|
<a name="l00212"></a>00212 <a class="code" href="structnode__pocket.html">node_pocket</a> *pcur ;
|
|
<a name="l00213"></a>00213
|
|
<a name="l00214"></a>00214 <span class="keywordtype">int</span> i = 0 ;
|
|
<a name="l00215"></a>00215 <span class="keywordflow">if</span>(pockets){
|
|
<a name="l00216"></a>00216 pcur = pockets-><a class="code" href="structc__lst__pockets.html#cf82eb35ce757228759a9af7675f5ad9">first</a> ;
|
|
<a name="l00217"></a>00217
|
|
<a name="l00218"></a>00218 <span class="keywordflow">while</span>(pcur){
|
|
<a name="l00219"></a>00219 sprintf(out, <span class="stringliteral">"%s/pocket%d_vert.pqr"</span>, out_path, i) ;
|
|
<a name="l00220"></a>00220 <a class="code" href="writepocket_8c.html#83b9d39c911e264bc513c19c9908cec4">write_pocket_pqr</a>(out, pcur-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>) ;
|
|
<a name="l00221"></a>00221
|
|
<a name="l00222"></a>00222 sprintf(out, <span class="stringliteral">"%s/pocket%d_atm.pdb"</span>, out_path, i) ;
|
|
<a name="l00223"></a>00223 <a class="code" href="writepocket_8c.html#1cd3364bc225d7d762300a6f8f691491">write_pocket_pdb</a>(out, pcur-><a class="code" href="structnode__pocket.html#8dbdbb50f893fa45bba2d8c03aff6553">pocket</a>) ;
|
|
<a name="l00224"></a>00224
|
|
<a name="l00225"></a>00225 pcur = pcur-><a class="code" href="structnode__pocket.html#a33c910dd9e6996001374199f250267e">next</a> ;
|
|
<a name="l00226"></a>00226 i++ ;
|
|
<a name="l00227"></a>00227 }
|
|
<a name="l00228"></a>00228 }
|
|
<a name="l00229"></a>00229 <span class="keywordflow">else</span> {
|
|
<a name="l00230"></a>00230 fprintf(stderr, <span class="stringliteral">"! The file %s could not be opened!\n"</span>, out);
|
|
<a name="l00231"></a>00231 }
|
|
<a name="l00232"></a>00232 }
|
|
<a name="l00233"></a>00233 <span class="comment"></span>
|
|
<a name="l00234"></a>00234 <span class="comment">/**</span>
|
|
<a name="l00235"></a>00235 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00236"></a>00236 <span class="comment"> void write_pocket_pqr</span>
|
|
<a name="l00237"></a>00237 <span class="comment"> </span>
|
|
<a name="l00238"></a>00238 <span class="comment"> ## SPECIFICATION: </span>
|
|
<a name="l00239"></a>00239 <span class="comment"> Write vertices of the pocket given in argument in the pqr format.</span>
|
|
<a name="l00240"></a>00240 <span class="comment"></span>
|
|
<a name="l00241"></a>00241 <span class="comment"> </span>
|
|
<a name="l00242"></a>00242 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00243"></a>00243 <span class="comment"> @ const char out[] : Output file path</span>
|
|
<a name="l00244"></a>00244 <span class="comment"> @ s_pocket *pocket : The pocket to write</span>
|
|
<a name="l00245"></a>00245 <span class="comment"> </span>
|
|
<a name="l00246"></a>00246 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00247"></a>00247 <span class="comment"> </span>
|
|
<a name="l00248"></a>00248 <span class="comment">*/</span>
|
|
<a name="l00249"></a><a class="code" href="writepocket_8h.html#83b9d39c911e264bc513c19c9908cec4">00249</a> <span class="keywordtype">void</span> <a class="code" href="writepocket_8c.html#83b9d39c911e264bc513c19c9908cec4">write_pocket_pqr</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> out[], <a class="code" href="structs__pocket.html">s_pocket</a> *pocket)
|
|
<a name="l00250"></a>00250 {
|
|
<a name="l00251"></a>00251 <a class="code" href="structnode__vertice.html">node_vertice</a> *vcur = NULL ;
|
|
<a name="l00252"></a>00252
|
|
<a name="l00253"></a>00253 FILE *f = fopen(out, <span class="stringliteral">"w"</span>) ;
|
|
<a name="l00254"></a>00254 <span class="keywordflow">if</span>(f && pocket) {
|
|
<a name="l00255"></a>00255 fprintf(f, <span class="stringliteral">"HEADER\n"</span>) ;
|
|
<a name="l00256"></a>00256 fprintf(f, <span class="stringliteral">"HEADER This is a pqr format file writen by the programm fpocket. \n"</span>) ;
|
|
<a name="l00257"></a>00257 fprintf(f, <span class="stringliteral">"HEADER It represent the voronoi vertices of a single pocket found by the \n"</span>) ;
|
|
<a name="l00258"></a>00258 fprintf(f, <span class="stringliteral">"HEADER algorithm. \n"</span>) ;
|
|
<a name="l00259"></a>00259 fprintf(f, <span class="stringliteral">"HEADER \n"</span>) ;
|
|
<a name="l00260"></a>00260 fprintf(f, <span class="stringliteral">"HEADER Information about the pocket %5d:\n"</span>, pocket-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#72562067d308bcfcf32605e112e30c1a">first</a>-><a class="code" href="structnode__vertice.html#7e7063f6403dfd8f0a8f83462e27729b">vertice</a>-><a class="code" href="structs__vvertice.html#54bc1b392d46ab9a9a1ec164c1a2b431">resid</a>) ;
|
|
<a name="l00261"></a>00261 fprintf(f, <span class="stringliteral">"HEADER 0 - Pocket Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#1ae9bc01b675565e5321c525f8e88eb4">score</a>) ;
|
|
<a name="l00262"></a>00262 fprintf(f, <span class="stringliteral">"HEADER 1 - Number of V. Vertices : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#d481d25ff964a6858975b5abfb671412">nb_asph</a>) ;
|
|
<a name="l00263"></a>00263 fprintf(f, <span class="stringliteral">"HEADER 2 - Mean alpha-sphere radius : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#6e455ee4a61943b81a09fb9c4a816967">mean_asph_ray</a>) ;
|
|
<a name="l00264"></a>00264 fprintf(f, <span class="stringliteral">"HEADER 3 - Mean alpha-sphere SA : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#8d8c1b492a8f07602c496ffe907a7135">masph_sacc</a>) ;
|
|
<a name="l00265"></a>00265 fprintf(f, <span class="stringliteral">"HEADER 4 - Mean B-factor : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#537c647e77f9ca129c77b31e3d15b2ca">flex</a>) ;
|
|
<a name="l00266"></a>00266 fprintf(f, <span class="stringliteral">"HEADER 5 - Hydrophobicity Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#ec451be95312187f418e20b87ebc0c1c">hydrophobicity_score</a>) ;
|
|
<a name="l00267"></a>00267 fprintf(f, <span class="stringliteral">"HEADER 6 - Polarity Score : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#d612b029bba06646381771d4b61dc5e6">polarity_score</a>) ;
|
|
<a name="l00268"></a>00268 fprintf(f, <span class="stringliteral">"HEADER 7 - Volume Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#0bf245c3d85f2fc8dec41d560313588a">volume_score</a>) ;
|
|
<a name="l00269"></a>00269 fprintf(f, <span class="stringliteral">"HEADER 8 - Real volume (approximation) : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#ec106f2a35f5676a6af920311aa4260e">volume</a>) ;
|
|
<a name="l00270"></a>00270 fprintf(f, <span class="stringliteral">"HEADER 9 - Charge Score : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#00da80b684d1bb1af13ec779e282c7e0">charge_score</a>) ;
|
|
<a name="l00271"></a>00271 fprintf(f, <span class="stringliteral">"HEADER 10 - Local hydrophobic density Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#b48b3533d79c147285ca50eabc12ef63">mean_loc_hyd_dens</a>) ;
|
|
<a name="l00272"></a>00272 fprintf(f, <span class="stringliteral">"HEADER 11 - Number of apolar alpha sphere : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#bf347ec0386c3b075470ea7c63c87381">nAlphaApol</a>) ;
|
|
<a name="l00273"></a>00273 fprintf(f, <span class="stringliteral">"HEADER 12 - Proportion of apolar alpha sphere : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#1e842880419a0616060301b4eacf858f">apolar_asphere_prop</a>) ;
|
|
<a name="l00274"></a>00274
|
|
<a name="l00275"></a>00275 vcur = pocket-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#72562067d308bcfcf32605e112e30c1a">first</a> ;
|
|
<a name="l00276"></a>00276
|
|
<a name="l00277"></a>00277 <span class="keywordflow">while</span>(vcur){
|
|
<a name="l00278"></a>00278 <a class="code" href="voronoi_8c.html#0fc0360fbb0a071ba6d49dedd57ba397">write_pqr_vert</a>(f, vcur-><a class="code" href="structnode__vertice.html#7e7063f6403dfd8f0a8f83462e27729b">vertice</a>) ;
|
|
<a name="l00279"></a>00279
|
|
<a name="l00280"></a>00280 vcur = vcur-><a class="code" href="structnode__vertice.html#61b34ff349d05cc65a4d8b9e2c77ff3e">next</a> ;
|
|
<a name="l00281"></a>00281 }
|
|
<a name="l00282"></a>00282
|
|
<a name="l00283"></a>00283 fprintf(f, <span class="stringliteral">"TER\nEND\n"</span>) ;
|
|
<a name="l00284"></a>00284 fclose(f) ;
|
|
<a name="l00285"></a>00285 }
|
|
<a name="l00286"></a>00286 <span class="keywordflow">else</span> {
|
|
<a name="l00287"></a>00287 <span class="keywordflow">if</span>(!f) fprintf(stderr, <span class="stringliteral">"! The file %s could not be opened!\n"</span>, out);
|
|
<a name="l00288"></a>00288 <span class="keywordflow">else</span> fprintf(stderr, <span class="stringliteral">"! Invalid pocket to write in write_pocket_pqr !\n"</span>);
|
|
<a name="l00289"></a>00289 }
|
|
<a name="l00290"></a>00290 }
|
|
<a name="l00291"></a>00291 <span class="comment"></span>
|
|
<a name="l00292"></a>00292 <span class="comment">/**</span>
|
|
<a name="l00293"></a>00293 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00294"></a>00294 <span class="comment"> write_pocket_pdb</span>
|
|
<a name="l00295"></a>00295 <span class="comment"> </span>
|
|
<a name="l00296"></a>00296 <span class="comment"> ## SPECIFICATION: </span>
|
|
<a name="l00297"></a>00297 <span class="comment"> Write atoms contacted by vertices of the pocket given in argument in </span>
|
|
<a name="l00298"></a>00298 <span class="comment"> the pdb format.</span>
|
|
<a name="l00299"></a>00299 <span class="comment"></span>
|
|
<a name="l00300"></a>00300 <span class="comment"> </span>
|
|
<a name="l00301"></a>00301 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00302"></a>00302 <span class="comment"> @ const char out[] : Output file path</span>
|
|
<a name="l00303"></a>00303 <span class="comment"> @ s_pocket *pocket : The pocket to write</span>
|
|
<a name="l00304"></a>00304 <span class="comment"> </span>
|
|
<a name="l00305"></a>00305 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00306"></a>00306 <span class="comment"> </span>
|
|
<a name="l00307"></a>00307 <span class="comment">*/</span>
|
|
<a name="l00308"></a><a class="code" href="writepocket_8h.html#1cd3364bc225d7d762300a6f8f691491">00308</a> <span class="keywordtype">void</span> <a class="code" href="writepocket_8c.html#1cd3364bc225d7d762300a6f8f691491">write_pocket_pdb</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> out[], <a class="code" href="structs__pocket.html">s_pocket</a> *pocket)
|
|
<a name="l00309"></a>00309 {
|
|
<a name="l00310"></a>00310 <a class="code" href="structnode__vertice.html">node_vertice</a> *vcur = NULL ;
|
|
<a name="l00311"></a>00311 <span class="keywordtype">int</span> i = 0 ;
|
|
<a name="l00312"></a>00312 <span class="keywordtype">int</span> cur_size = 0,
|
|
<a name="l00313"></a>00313 cur_allocated = 10 ;
|
|
<a name="l00314"></a>00314
|
|
<a name="l00315"></a>00315 <a class="code" href="structs__atm.html">s_atm</a> **atms = (<a class="code" href="structs__atm.html">s_atm</a>**)<a class="code" href="memhandler_8c.html#52d7260a38c396cb2dd1dd7abcfd61cb">my_malloc</a>(<span class="keyword">sizeof</span>(<a class="code" href="structs__atm.html">s_atm</a>*)*10) ;
|
|
<a name="l00316"></a>00316 <a class="code" href="structs__atm.html">s_atm</a> *atom = NULL ;
|
|
<a name="l00317"></a>00317
|
|
<a name="l00318"></a>00318 FILE *f = fopen(out, <span class="stringliteral">"w"</span>) ;
|
|
<a name="l00319"></a>00319 <span class="keywordflow">if</span>(f && pocket) {
|
|
<a name="l00320"></a>00320
|
|
<a name="l00321"></a>00321 fprintf(f, <span class="stringliteral">"HEADER\n"</span>) ;
|
|
<a name="l00322"></a>00322 fprintf(f, <span class="stringliteral">"HEADER This is a pdb format file writen by the programm fpocket. \n"</span>) ;
|
|
<a name="l00323"></a>00323 fprintf(f, <span class="stringliteral">"HEADER It represents the atoms contacted by the voronoi vertices of the pocket. \n"</span>) ;
|
|
<a name="l00324"></a>00324 fprintf(f, <span class="stringliteral">"HEADER \n"</span>) ;
|
|
<a name="l00325"></a>00325 fprintf(f, <span class="stringliteral">"HEADER Information about the pocket %5d:\n"</span>, pocket-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#72562067d308bcfcf32605e112e30c1a">first</a>-><a class="code" href="structnode__vertice.html#7e7063f6403dfd8f0a8f83462e27729b">vertice</a>-><a class="code" href="structs__vvertice.html#54bc1b392d46ab9a9a1ec164c1a2b431">resid</a>) ;
|
|
<a name="l00326"></a>00326 fprintf(f, <span class="stringliteral">"HEADER 0 - Pocket Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#1ae9bc01b675565e5321c525f8e88eb4">score</a>) ;
|
|
<a name="l00327"></a>00327 fprintf(f, <span class="stringliteral">"HEADER 1 - Number of V. Vertices : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#d481d25ff964a6858975b5abfb671412">nb_asph</a>) ;
|
|
<a name="l00328"></a>00328 fprintf(f, <span class="stringliteral">"HEADER 2 - Mean alpha-sphere radius : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#6e455ee4a61943b81a09fb9c4a816967">mean_asph_ray</a>) ;
|
|
<a name="l00329"></a>00329 fprintf(f, <span class="stringliteral">"HEADER 3 - Mean alpha-sphere SA : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#8d8c1b492a8f07602c496ffe907a7135">masph_sacc</a>) ;
|
|
<a name="l00330"></a>00330 fprintf(f, <span class="stringliteral">"HEADER 4 - Mean B-factor : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#537c647e77f9ca129c77b31e3d15b2ca">flex</a>) ;
|
|
<a name="l00331"></a>00331 fprintf(f, <span class="stringliteral">"HEADER 5 - Hydrophobicity Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#ec451be95312187f418e20b87ebc0c1c">hydrophobicity_score</a>) ;
|
|
<a name="l00332"></a>00332 fprintf(f, <span class="stringliteral">"HEADER 6 - Polarity Score : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#d612b029bba06646381771d4b61dc5e6">polarity_score</a>) ;
|
|
<a name="l00333"></a>00333 fprintf(f, <span class="stringliteral">"HEADER 7 - Volume Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#0bf245c3d85f2fc8dec41d560313588a">volume_score</a>) ;
|
|
<a name="l00334"></a>00334 fprintf(f, <span class="stringliteral">"HEADER 8 - Real volume (approximation) : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#ec106f2a35f5676a6af920311aa4260e">volume</a>) ;
|
|
<a name="l00335"></a>00335 fprintf(f, <span class="stringliteral">"HEADER 9 - Charge Score : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#00da80b684d1bb1af13ec779e282c7e0">charge_score</a>) ;
|
|
<a name="l00336"></a>00336 fprintf(f, <span class="stringliteral">"HEADER 10 - Local hydrophobic density Score : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#b48b3533d79c147285ca50eabc12ef63">mean_loc_hyd_dens</a>) ;
|
|
<a name="l00337"></a>00337 fprintf(f, <span class="stringliteral">"HEADER 11 - Number of apolar alpha sphere : %5d\n"</span>, pocket-><a class="code" href="structs__pocket.html#bf347ec0386c3b075470ea7c63c87381">nAlphaApol</a>) ;
|
|
<a name="l00338"></a>00338 fprintf(f, <span class="stringliteral">"HEADER 12 - Proportion of apolar alpha sphere : %.4f\n"</span>, pocket-><a class="code" href="structs__pocket.html#aba02d3ca1a41adf62ad69884c85fed5">pdesc</a>-><a class="code" href="structs__desc.html#1e842880419a0616060301b4eacf858f">apolar_asphere_prop</a>) ;
|
|
<a name="l00339"></a>00339
|
|
<a name="l00340"></a>00340 <span class="comment">/* First get the list of atoms */</span>
|
|
<a name="l00341"></a>00341 vcur = pocket-><a class="code" href="structs__pocket.html#cf07f539404d23c1956373f8c93a4fcc">v_lst</a>-><a class="code" href="structc__lst__vertices.html#72562067d308bcfcf32605e112e30c1a">first</a> ;
|
|
<a name="l00342"></a>00342
|
|
<a name="l00343"></a>00343 <span class="keywordflow">while</span>(vcur){
|
|
<a name="l00344"></a>00344 <span class="keywordflow">for</span>(i = 0 ; i < 4 ; i++) {
|
|
<a name="l00345"></a>00345 <span class="keywordflow">if</span>(!<a class="code" href="atom_8c.html#a72221368b25d51716e4d59f02a8d753">is_in_lst_atm</a>(atms, cur_size, vcur-><a class="code" href="structnode__vertice.html#7e7063f6403dfd8f0a8f83462e27729b">vertice</a>-><a class="code" href="structs__vvertice.html#d8f82150ff5b05ee09b1136a9c09cfd0">neigh</a>[i]-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>)) {
|
|
<a name="l00346"></a>00346 <span class="keywordflow">if</span>(cur_size >= cur_allocated-1) {
|
|
<a name="l00347"></a>00347 cur_allocated *= 2 ;
|
|
<a name="l00348"></a>00348 atms = (<a class="code" href="structs__atm.html">s_atm</a>**)<a class="code" href="memhandler_8c.html#ede15d67c845c05e9b2bfb59b8ab6cf7">my_realloc</a>(atms, <span class="keyword">sizeof</span>(<a class="code" href="structs__atm.html">s_atm</a>)*cur_allocated) ;
|
|
<a name="l00349"></a>00349 }
|
|
<a name="l00350"></a>00350 atms[cur_size] = vcur-><a class="code" href="structnode__vertice.html#7e7063f6403dfd8f0a8f83462e27729b">vertice</a>-><a class="code" href="structs__vvertice.html#d8f82150ff5b05ee09b1136a9c09cfd0">neigh</a>[i] ;
|
|
<a name="l00351"></a>00351 cur_size ++ ;
|
|
<a name="l00352"></a>00352 }
|
|
<a name="l00353"></a>00353
|
|
<a name="l00354"></a>00354 }
|
|
<a name="l00355"></a>00355 vcur = vcur-><a class="code" href="structnode__vertice.html#61b34ff349d05cc65a4d8b9e2c77ff3e">next</a> ;
|
|
<a name="l00356"></a>00356 }
|
|
<a name="l00357"></a>00357
|
|
<a name="l00358"></a>00358 <span class="comment">/* Then write atoms... */</span>
|
|
<a name="l00359"></a>00359
|
|
<a name="l00360"></a>00360 <span class="keywordflow">for</span>(i = 0 ; i < cur_size ; i++) {
|
|
<a name="l00361"></a>00361 atom = atms[i] ;
|
|
<a name="l00362"></a>00362
|
|
<a name="l00363"></a>00363 <a class="code" href="writepdb_8c.html#c1826cac257476a6fe47825b31cafb4d">write_pdb_atom_line</a>(f, atom-><a class="code" href="structs__atm.html#98466fdfcb021884beb229b1dca361ae">type</a>, atom-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>, atom-><a class="code" href="structs__atm.html#2f0330a30f640668efdd726a6dd05a93">name</a>, atom-><a class="code" href="structs__atm.html#58eeb8a80942caa3bd2374f3175cb77d">pdb_aloc</a>,
|
|
<a name="l00364"></a>00364 atom-><a class="code" href="structs__atm.html#e0ff20f2c491a8b16c866d9b1386b6a5">res_name</a>, atom-><a class="code" href="structs__atm.html#c5b9464bd67f2cca101f7bf6beabb223">chain</a>, atom-><a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a>,
|
|
<a name="l00365"></a>00365 atom-><a class="code" href="structs__atm.html#bfd1f905200f69dd9cd9750fd305cf46">pdb_insert</a>, atom-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>, atom-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>, atom-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>,
|
|
<a name="l00366"></a>00366 atom-><a class="code" href="structs__atm.html#1696926c680a1014360598d54a1dadb0">occupancy</a>, atom-><a class="code" href="structs__atm.html#6a1a5fd32629457dfa14626b25b5ae46">bfactor</a>, atom-><a class="code" href="structs__atm.html#c80daffa94edeadd30433f6653e08054">symbol</a>,
|
|
<a name="l00367"></a>00367 atom-><a class="code" href="structs__atm.html#a03a199ed11108d7710547df629c7d73">charge</a>);
|
|
<a name="l00368"></a>00368 }
|
|
<a name="l00369"></a>00369
|
|
<a name="l00370"></a>00370 fprintf(f, <span class="stringliteral">"TER\nEND\n"</span>) ;
|
|
<a name="l00371"></a>00371 fclose(f) ;
|
|
<a name="l00372"></a>00372 }
|
|
<a name="l00373"></a>00373 <span class="keywordflow">else</span> {
|
|
<a name="l00374"></a>00374 <span class="keywordflow">if</span>(!f) fprintf(stderr, <span class="stringliteral">"! The file %s could not be opened!\n"</span>, out);
|
|
<a name="l00375"></a>00375 <span class="keywordflow">else</span> fprintf(stderr, <span class="stringliteral">"! Invalid pocket to write in write_pocket_pqr !\n"</span>);
|
|
<a name="l00376"></a>00376 }
|
|
<a name="l00377"></a>00377
|
|
<a name="l00378"></a>00378 <a class="code" href="memhandler_8c.html#a49400242a007d208c641f79856ea4c6">my_free</a>(atms) ;
|
|
<a name="l00379"></a>00379 }
|
|
</pre></div></div>
|
|
<hr size="1"><address style="text-align: right;"><small>Generated on Sun Jul 5 22:10:40 2009 for fpocket by
|
|
<a href="http://www.doxygen.org/index.html">
|
|
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.9 </small></address>
|
|
</body>
|
|
</html>
|