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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<h1>dparams.h</h1><a href="dparams_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment"></span>
<a name="l00002"></a>00002 <span class="comment">/**</span>
<a name="l00003"></a>00003 <span class="comment"> COPYRIGHT DISCLAIMER</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
<a name="l00006"></a>00006 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
<a name="l00007"></a>00007 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
<a name="l00008"></a>00008 <span class="comment"> Schmidtke.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment"> Vincent Le Guilloux 28 November 2008</span>
<a name="l00011"></a>00011 <span class="comment"> Peter Schmidtke 28 November 2008</span>
<a name="l00012"></a>00012 <span class="comment"> Pierre Tuffery 28 November 2008</span>
<a name="l00013"></a>00013 <span class="comment"></span>
<a name="l00014"></a>00014 <span class="comment"> GNU GPL</span>
<a name="l00015"></a>00015 <span class="comment"></span>
<a name="l00016"></a>00016 <span class="comment"> This file is part of the fpocket package.</span>
<a name="l00017"></a>00017 <span class="comment"></span>
<a name="l00018"></a>00018 <span class="comment"> fpocket is free software: you can redistribute it and/or modify</span>
<a name="l00019"></a>00019 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
<a name="l00020"></a>00020 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
<a name="l00021"></a>00021 <span class="comment"> (at your option) any later version.</span>
<a name="l00022"></a>00022 <span class="comment"></span>
<a name="l00023"></a>00023 <span class="comment"> fpocket is distributed in the hope that it will be useful,</span>
<a name="l00024"></a>00024 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00025"></a>00025 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00026"></a>00026 <span class="comment"> GNU General Public License for more details.</span>
<a name="l00027"></a>00027 <span class="comment"></span>
<a name="l00028"></a>00028 <span class="comment"> You should have received a copy of the GNU General Public License</span>
<a name="l00029"></a>00029 <span class="comment"> along with fpocket. If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
<a name="l00030"></a>00030 <span class="comment"></span>
<a name="l00031"></a>00031 <span class="comment">**/</span>
<a name="l00032"></a>00032
<a name="l00033"></a>00033 <span class="preprocessor">#ifndef DH_DPARAMS</span>
<a name="l00034"></a>00034 <span class="preprocessor"></span><span class="preprocessor">#define DH_DPARAMS</span>
<a name="l00035"></a>00035 <span class="preprocessor"></span>
<a name="l00036"></a>00036 <span class="comment">/* ----------------------------- INCLUDES ------------------------------------*/</span>
<a name="l00037"></a>00037
<a name="l00038"></a>00038 <span class="preprocessor">#include &lt;stdio.h&gt;</span>
<a name="l00039"></a>00039 <span class="preprocessor">#include &lt;stdlib.h&gt;</span>
<a name="l00040"></a>00040 <span class="preprocessor">#include &lt;unistd.h&gt;</span>
<a name="l00041"></a>00041 <span class="preprocessor">#include &lt;string.h&gt;</span>
<a name="l00042"></a>00042 <span class="preprocessor">#include &lt;ctype.h&gt;</span>
<a name="l00043"></a>00043 <span class="preprocessor">#include &lt;limits.h&gt;</span>
<a name="l00044"></a>00044 <span class="preprocessor">#include &lt;assert.h&gt;</span>
<a name="l00045"></a>00045
<a name="l00046"></a>00046 <span class="preprocessor">#include "<a class="code" href="utils_8h.html">utils.h</a>"</span>
<a name="l00047"></a>00047 <span class="preprocessor">#include "<a class="code" href="memhandler_8h.html">memhandler.h</a>"</span>
<a name="l00048"></a>00048 <span class="preprocessor">#include "<a class="code" href="fparams_8h.html">fparams.h</a>"</span>
<a name="l00049"></a>00049
<a name="l00050"></a>00050 <span class="comment">/* --------------------------- PUBLIC MACROS ---------------------------------*/</span>
<a name="l00051"></a>00051
<a name="l00052"></a>00052
<a name="l00053"></a>00053 <span class="comment">/* Options of the test program */</span>
<a name="l00054"></a><a class="code" href="dparams_8h.html#82c7b59d8b32f307c412e0ecb98a04a1">00054</a> <span class="preprocessor">#define M_DPAR_INTERFACE_METHOD1 'e'</span>
<a name="l00055"></a><a class="code" href="dparams_8h.html#66f452257935ac35b2aff9d9a5b35a5c">00055</a> <span class="preprocessor"></span><span class="preprocessor">#define M_DPAR_INTERFACE_METHOD2 'E'</span>
<a name="l00056"></a><a class="code" href="dparams_8h.html#e1b3066b79046f6dbb5b3ec5537cc6b7">00056</a> <span class="preprocessor"></span><span class="preprocessor">#define M_DPAR_DISTANCE_CRITERIA 'd'</span>
<a name="l00057"></a><a class="code" href="dparams_8h.html#1dd1b9ec6a0f6e786341e70b6e35d994">00057</a> <span class="preprocessor"></span><span class="preprocessor">#define M_DPAR_INPUT_FILE 'f'</span>
<a name="l00058"></a><a class="code" href="dparams_8h.html#c2a49a64021fccfd5ac216bd724c34f4">00058</a> <span class="preprocessor"></span><span class="preprocessor">#define M_DPAR_OUTPUT_FILE 'o'</span>
<a name="l00059"></a>00059 <span class="preprocessor"></span>
<a name="l00060"></a>00060 <span class="comment">/* Two way of defining the interface: */</span>
<a name="l00061"></a>00061 <span class="comment">/* 1 - Get atoms ocontacted by vertices within M_VERT_LIG_NEIG_DIST of the ligand. */</span>
<a name="l00062"></a>00062 <span class="comment">/* 2 - Just get atoms within M_LIG_NEIG_DIST of the ligand, based on each ligand atom. */</span>
<a name="l00063"></a><a class="code" href="dparams_8h.html#cefcbcb3b4a22d32a05b6b2e931334b4">00063</a> <span class="preprocessor">#define M_INTERFACE_METHOD1 1 </span>
<a name="l00064"></a><a class="code" href="dparams_8h.html#7a9d98b0a58c3e4ff49f676ad073686f">00064</a> <span class="preprocessor"></span><span class="preprocessor">#define M_VERT_LIG_NEIG_DIST 4.0</span>
<a name="l00065"></a>00065 <span class="preprocessor"></span>
<a name="l00066"></a><a class="code" href="dparams_8h.html#8364a85272afb754f95f5f76832a82ac">00066</a> <span class="preprocessor">#define M_INTERFACE_METHOD2 2</span>
<a name="l00067"></a><a class="code" href="dparams_8h.html#828cf5a56026b461ab24fdc52364b1a5">00067</a> <span class="preprocessor"></span><span class="preprocessor">#define M_LIG_NEIG_DIST 4.0</span>
<a name="l00068"></a>00068 <span class="preprocessor"></span>
<a name="l00069"></a><a class="code" href="dparams_8h.html#22ad6835c39effbd106823c3c5ca7c0f">00069</a> <span class="preprocessor">#define M_OUTPUT_FILE1_DEFAULT "dpout_explicitp.txt"</span>
<a name="l00070"></a><a class="code" href="dparams_8h.html#f1de078ce38b24912d6da6b73ea8dcc5">00070</a> <span class="preprocessor"></span><span class="preprocessor">#define M_OUTPUT_FILE2_DEFAULT "dpout_fpocketp.txt"</span>
<a name="l00071"></a><a class="code" href="dparams_8h.html#e65d6e015a840528747af72ef2f01caa">00071</a> <span class="preprocessor"></span><span class="preprocessor">#define M_OUTPUT_FILE3_DEFAULT "dpout_fpocketnp.txt"</span>
<a name="l00072"></a>00072 <span class="preprocessor"></span>
<a name="l00073"></a><a class="code" href="dparams_8h.html#8c7b27b7a35d576199e6a8514932bb2b">00073</a> <span class="preprocessor">#define M_MAX_FILE_NAME_LENGTH 300</span>
<a name="l00074"></a><a class="code" href="dparams_8h.html#baa32d51cfc76b1ca87dc19bad704051">00074</a> <span class="preprocessor"></span><span class="preprocessor">#define M_NB_MC_ITER 2500</span>
<a name="l00075"></a><a class="code" href="dparams_8h.html#9d33a35d04aa8828b78e8ee4dd87d3ae">00075</a> <span class="preprocessor"></span><span class="preprocessor">#define M_MIN_ASPH_RAY 2.8</span>
<a name="l00076"></a><a class="code" href="dparams_8h.html#c642406bb0595dbd39d3d111eb27b0ac">00076</a> <span class="preprocessor"></span><span class="preprocessor">#define M_MAX_ASPH_RAY 10.0</span>
<a name="l00077"></a>00077 <span class="preprocessor"></span>
<a name="l00078"></a><a class="code" href="dparams_8h.html#0905e7f06509f8460ef006f086887671">00078</a> <span class="preprocessor">#define M_DP_USAGE "\</span>
<a name="l00079"></a>00079 <span class="preprocessor">\n***** USAGE (dpocket) *****\n\</span>
<a name="l00080"></a>00080 <span class="preprocessor">\n\</span>
<a name="l00081"></a>00081 <span class="preprocessor">The program needs as input a file containing at each \n\</span>
<a name="l00082"></a>00082 <span class="preprocessor">line a pdb file name and a ligand code (3 letters). \n\</span>
<a name="l00083"></a>00083 <span class="preprocessor">The format of each line must be: \n\n\</span>
<a name="l00084"></a>00084 <span class="preprocessor">{PATH/}2fej.pdb LIG \n\n\</span>
<a name="l00085"></a>00085 <span class="preprocessor">The ligand code is the resname of the ligand atoms in \n\</span>
<a name="l00086"></a>00086 <span class="preprocessor">the pdb file and has to separated by a tab from the \n\</span>
<a name="l00087"></a>00087 <span class="preprocessor">pdb structure in the input file. \n\n\</span>
<a name="l00088"></a>00088 <span class="preprocessor">See the manual for more information. \n\n\</span>
<a name="l00089"></a>00089 <span class="preprocessor">Example of command using default parameters: \n\</span>
<a name="l00090"></a>00090 <span class="preprocessor">\t./bin/dpocket -f file_path \n\n\</span>
<a name="l00091"></a>00091 <span class="preprocessor">Options: \n\</span>
<a name="l00092"></a>00092 <span class="preprocessor">\t-o string : Prefix of the output file. (./dpout_*) \n\</span>
<a name="l00093"></a>00093 <span class="preprocessor">\t-e : Use the first protein-ligand explicit \n\</span>
<a name="l00094"></a>00094 <span class="preprocessor">\t interface definition (default). \n\</span>
<a name="l00095"></a>00095 <span class="preprocessor">\t-E : Use the second protein-ligand explicit \n\</span>
<a name="l00096"></a>00096 <span class="preprocessor">\t interface definition. \n\</span>
<a name="l00097"></a>00097 <span class="preprocessor">\t-d float : Distance criteria for the choosen \n\</span>
<a name="l00098"></a>00098 <span class="preprocessor">\t interface definition. (4.0) \n\n\</span>
<a name="l00099"></a>00099 <span class="preprocessor">Options specific to fpocket are usable too. \n\</span>
<a name="l00100"></a>00100 <span class="preprocessor">See the manual/tutorial for mor information. \n\</span>
<a name="l00101"></a>00101 <span class="preprocessor">***************************\n"</span>
<a name="l00102"></a>00102 <span class="preprocessor"></span>
<a name="l00103"></a>00103 <span class="comment">/* --------------------------- PUBLIC STRUCTURES -----------------------------*/</span>
<a name="l00104"></a>00104
<a name="l00105"></a>00105
<a name="l00106"></a><a class="code" href="structs__dparams.html">00106</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structs__dparams.html">s_dparams</a>
<a name="l00107"></a>00107 {
<a name="l00108"></a><a class="code" href="structs__dparams.html#d3fbaf401c68c3abf7ef662259e547d6">00108</a> <span class="keywordtype">char</span> **<a class="code" href="structs__dparams.html#a98295f566006ae97eef0628a9c94a86">fcomplex</a>, <span class="comment">/**&lt; path of the holo form of the structure */</span>
<a name="l00109"></a>00109 **<a class="code" href="structs__dparams.html#d3fbaf401c68c3abf7ef662259e547d6">ligs</a> ; <span class="comment">/**&lt; HET residue name of the ligand */</span>
<a name="l00110"></a>00110
<a name="l00111"></a><a class="code" href="structs__dparams.html#3f14e5f303fbf919cd6f9abab8505c68">00111</a> <span class="keywordtype">char</span> *<a class="code" href="structs__dparams.html#eed722b226fde5c51dfa3e2f83d9a6d3">f_exp</a>, <span class="comment">/**&lt; name of the explicit pocket definition output file*/</span>
<a name="l00112"></a>00112 *<a class="code" href="structs__dparams.html#3f14e5f303fbf919cd6f9abab8505c68">f_fpckp</a>, <span class="comment">/**&lt; name of the pocket definition output file*/</span>
<a name="l00113"></a>00113 *<a class="code" href="structs__dparams.html#b1b7fc562b81d0670f3044252a2d4c34">f_fpcknp</a> ; <span class="comment">/**&lt; name of the non pocket definition output file*/</span>
<a name="l00114"></a>00114
<a name="l00115"></a><a class="code" href="structs__dparams.html#09b829e05d79410ee1471242ab622cac">00115</a> <span class="keywordtype">float</span> <a class="code" href="structs__dparams.html#09b829e05d79410ee1471242ab622cac">interface_dist_crit</a>; <span class="comment">/**&lt; distance for explicit binding pocket definition*/</span>
<a name="l00116"></a>00116
<a name="l00117"></a><a class="code" href="structs__dparams.html#04c48f5eb6778c9a5022588e507043d3">00117</a> <span class="keywordtype">int</span> <a class="code" href="structs__dparams.html#04c48f5eb6778c9a5022588e507043d3">nfiles</a>, <span class="comment">/**&lt; number of files to analyse*/</span>
<a name="l00118"></a>00118 <a class="code" href="structs__dparams.html#f48783ed6b360f7a3e83eb4c7ae11300">interface_method</a> ; <span class="comment">/**&lt; how to identify the explicit binding pocket*/</span>
<a name="l00119"></a>00119
<a name="l00120"></a><a class="code" href="structs__dparams.html#84c3e94630fcd2402fd190aad5a0ffbf">00120</a> <a class="code" href="structs__fparams.html">s_fparams</a> *<a class="code" href="structs__dparams.html#84c3e94630fcd2402fd190aad5a0ffbf">fpar</a> ; <span class="comment">/**&lt; fparams container*/</span>
<a name="l00121"></a>00121
<a name="l00122"></a>00122 } <a class="code" href="structs__dparams.html">s_dparams</a> ;
<a name="l00123"></a>00123
<a name="l00124"></a>00124 <span class="comment">/* ----------------------------- PROTOTYPES --------------------------------- */</span>
<a name="l00125"></a>00125
<a name="l00126"></a>00126 <a class="code" href="structs__dparams.html">s_dparams</a>* <a class="code" href="dparams_8c.html#100b780c898d5b4b3482aba9797f7306">init_def_dparams</a>(<span class="keywordtype">void</span>) ;
<a name="l00127"></a>00127 <a class="code" href="structs__dparams.html">s_dparams</a>* <a class="code" href="dparams_8c.html#ca1e7fb31512b575d498b486be72e318">get_dpocket_args</a>(<span class="keywordtype">int</span> nargs, <span class="keywordtype">char</span> **args) ;
<a name="l00128"></a>00128
<a name="l00129"></a>00129 <span class="keywordtype">int</span> <a class="code" href="dparams_8c.html#415b85de804f291fcd2381c5042b29fa">add_list_complexes</a>(<span class="keywordtype">char</span> *str_list_file, <a class="code" href="structs__dparams.html">s_dparams</a> *par) ;
<a name="l00130"></a>00130 <span class="keywordtype">int</span> <a class="code" href="dparams_8c.html#300ca3e1ebd9d45a74b6be88169fbbd4">add_complexe</a>(<span class="keywordtype">char</span> *complex, <span class="keywordtype">char</span> *ligand, <a class="code" href="structs__dparams.html">s_dparams</a> *par) ;
<a name="l00131"></a>00131 <span class="keywordtype">int</span> <a class="code" href="dparams_8c.html#1e7882763429519c63037bb44787ca4b">parse_dist_crit</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__dparams.html">s_dparams</a> *p) ;
<a name="l00132"></a>00132
<a name="l00133"></a>00133 <span class="keywordtype">void</span> <a class="code" href="dparams_8c.html#06ed3fb78ed2fcd4a491f4b28829e538">print_dparams</a>(<a class="code" href="structs__dparams.html">s_dparams</a> *p, FILE *f) ;
<a name="l00134"></a>00134 <span class="keywordtype">void</span> <a class="code" href="dparams_8c.html#4d9ba39c7b1219bd7758b7d479d1b47e">print_dpocket_usage</a>(FILE *f) ;
<a name="l00135"></a>00135 <span class="keywordtype">void</span> <a class="code" href="dparams_8c.html#828ec187d6c18322a19e51c14759408f">free_dparams</a>(<a class="code" href="structs__dparams.html">s_dparams</a> *p) ;
<a name="l00136"></a>00136
<a name="l00137"></a>00137 <span class="preprocessor">#endif</span>
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