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<li><a href="annotated.html"><span>Data Structures</span></a></li>
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<h1>fparams.h</h1><a href="fparams_8h.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
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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"> COPYRIGHT DISCLAIMER</span>
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<a name="l00005"></a>00005 <span class="comment"></span>
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<a name="l00006"></a>00006 <span class="comment"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
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<a name="l00007"></a>00007 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
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<a name="l00008"></a>00008 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
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<a name="l00009"></a>00009 <span class="comment"> Schmidtke.</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"> Vincent Le Guilloux 28 November 2008</span>
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<a name="l00012"></a>00012 <span class="comment"> Peter Schmidtke 28 November 2008</span>
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<a name="l00013"></a>00013 <span class="comment"> Pierre Tuffery 28 November 2008</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"> GNU GPL</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"> This file is part of the fpocket package.</span>
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<a name="l00018"></a>00018 <span class="comment"></span>
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<a name="l00019"></a>00019 <span class="comment"> fpocket is free software: you can redistribute it and/or modify</span>
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<a name="l00020"></a>00020 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
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<a name="l00021"></a>00021 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
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<a name="l00022"></a>00022 <span class="comment"> (at your option) any later version.</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"> fpocket is distributed in the hope that it will be useful,</span>
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<a name="l00025"></a>00025 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<a name="l00026"></a>00026 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<a name="l00027"></a>00027 <span class="comment"> GNU General Public License for more details.</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"> You should have received a copy of the GNU General Public License</span>
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<a name="l00030"></a>00030 <span class="comment"> along with fpocket. If not, see <http://www.gnu.org/licenses/>.</span>
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<a name="l00031"></a>00031 <span class="comment"></span>
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<a name="l00032"></a>00032 <span class="comment">**/</span>
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<a name="l00033"></a>00033
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<a name="l00034"></a>00034 <span class="preprocessor">#ifndef DH_FPARAMS</span>
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<a name="l00035"></a>00035 <span class="preprocessor"></span><span class="preprocessor">#define DH_FPARAMS</span>
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<a name="l00036"></a>00036 <span class="preprocessor"></span>
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<a name="l00037"></a>00037 <span class="comment">/* ------------------------------- INCLUDES ----------------------------------*/</span>
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<a name="l00038"></a>00038
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<a name="l00039"></a>00039 <span class="preprocessor">#include <stdio.h></span>
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<a name="l00040"></a>00040 <span class="preprocessor">#include <stdlib.h></span>
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<a name="l00041"></a>00041 <span class="preprocessor">#include <unistd.h></span>
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<a name="l00042"></a>00042 <span class="preprocessor">#include <string.h></span>
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<a name="l00043"></a>00043 <span class="preprocessor">#include <ctype.h></span>
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<a name="l00044"></a>00044 <span class="preprocessor">#include <limits.h></span>
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<a name="l00045"></a>00045 <span class="preprocessor">#include <assert.h></span>
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<a name="l00046"></a>00046
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<a name="l00047"></a>00047 <span class="preprocessor">#include "<a class="code" href="utils_8h.html">utils.h</a>"</span>
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<a name="l00048"></a>00048 <span class="preprocessor">#include "<a class="code" href="memhandler_8h.html">memhandler.h</a>"</span>
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<a name="l00049"></a>00049
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<a name="l00050"></a>00050 <span class="comment">/* ----------------------------- PUBLIC MACROS ------------------------------ */</span>
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<a name="l00051"></a>00051
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<a name="l00052"></a>00052 <span class="comment">/* Options of the pocket finder program */</span>
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<a name="l00053"></a>00053 <span class="comment">/* standard parameters */</span>
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<a name="l00054"></a>00054
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<a name="l00055"></a>00055
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<a name="l00056"></a><a class="code" href="fparams_8h.html#f83d8c1f0a4a16b144b63e88d6b211bf">00056</a> <span class="preprocessor">#define M_MIN_ASHAPE_SIZE_DEFAULT 3.0</span><span class="comment">/**< Use min alpha sphere radius of : 3.0 */</span>
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<a name="l00057"></a>00057
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<a name="l00058"></a><a class="code" href="fparams_8h.html#50c6e2d2eb22a7c7b529c67fc04b56c9">00058</a> <span class="preprocessor">#define M_MAX_ASHAPE_SIZE_DEFAULT 6.0</span><span class="comment">/**< Use max alpha sphere radius of : 6.0 */</span>
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<a name="l00059"></a>00059
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<a name="l00060"></a><a class="code" href="fparams_8h.html#0f6138f1929550d8ff600529496b83b4">00060</a> <span class="preprocessor">#define M_CLUST_MAX_DIST 1.73</span><span class="comment">/**< Use first connection distance (see report) : 2.0 */</span>
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<a name="l00061"></a>00061
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<a name="l00062"></a><a class="code" href="fparams_8h.html#37a7ca05610fcb4aff8759267e83e4af">00062</a> <span class="preprocessor">#define M_REFINE_DIST 4.5</span><span class="comment">/**< use second connection distance (see report) : 4.5 */</span>
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<a name="l00063"></a>00063
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<a name="l00064"></a><a class="code" href="fparams_8h.html#cadff4aad15c6ece2eb248488b4221eb">00064</a> <span class="preprocessor">#define M_REFINE_MIN_PROP_APOL_AS 0.0</span><span class="comment">/**< At least a proportion of M_REFINE_MIN_NAPOL_AS apolar alpha spheres in the pocket 0.0 */</span>
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<a name="l00065"></a>00065
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<a name="l00066"></a><a class="code" href="fparams_8h.html#e5f7357fe7ddb5b03bc18b45159f64c4">00066</a> <span class="preprocessor">#define M_SLCLUST_MAX_DIST 2.5</span><span class="comment">/**< Single linkage clustering connection distance 2.5 */</span>
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<a name="l00067"></a>00067
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<a name="l00068"></a><a class="code" href="fparams_8h.html#721fc2c4a9b89fa4a0c0de0f31967d9a">00068</a> <span class="preprocessor">#define M_SLCLUST_MIN_NUM_NEIGH 2</span><span class="comment">/**< Minimum number of common neighbours for single linkage clustering 5 */</span>
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<a name="l00069"></a>00069
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<a name="l00070"></a><a class="code" href="fparams_8h.html#17764121ba6792298aba0da59482cc60">00070</a> <span class="preprocessor">#define M_MC_ITER 3000</span><span class="comment">/**< Number of iterations for the Monte Carlo volume calculation 3000 */</span>
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<a name="l00071"></a>00071
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<a name="l00072"></a><a class="code" href="fparams_8h.html#4caa4e2b63f97eae1c52a1e7cf51dc5b">00072</a> <span class="preprocessor">#define M_BASIC_VOL_DIVISION -1</span><span class="comment">/**< Precision for "exact" volume integration, set to -1 if not used -1 */</span>
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<a name="l00073"></a>00073
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<a name="l00074"></a><a class="code" href="fparams_8h.html#d6f4bc5db7427ee0e333f483e1632022">00074</a> <span class="preprocessor">#define M_MIN_POCK_NB_ASPH 36</span><span class="comment">/**< Minimum number of alpha spheres for a pocket to be kept */</span>
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<a name="l00075"></a>00075
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<a name="l00076"></a><a class="code" href="fparams_8h.html#243ad6dc96e3f975fb8a224426810bb6">00076</a> <span class="preprocessor">#define M__MIN_APOL_NEIGH_DEFAULT 3</span><span class="comment">/**< Minimum number of atoms having a low electronegativity in order to declare an alpha sphere to be apolar 3 */</span>
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<a name="l00077"></a>00077
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<a name="l00078"></a><a class="code" href="fparams_8h.html#43a40d4fa640254998f4e0cf2a3fd7a6">00078</a> <span class="preprocessor">#define M_DB_RUN 0 </span><span class="comment">/**< default value for running fpocket for populating a database, 0 default*/</span>
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<a name="l00079"></a>00079
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<a name="l00080"></a><a class="code" href="fparams_8h.html#7773b427778268b6569aae255f04c68c">00080</a> <span class="preprocessor">#define M_PAR_PDB_FILE 'f' </span><span class="comment">/**< flag to give a single pdb input file*/</span>
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<a name="l00081"></a><a class="code" href="fparams_8h.html#c9f20b54cb35b4bcc3b7a1b49b6e5ebe">00081</a> <span class="preprocessor">#define M_PAR_PDB_LIST 'F' </span><span class="comment">/**< flag to give a txt file containing paths to multiple pdb files*/</span>
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<a name="l00082"></a><a class="code" href="fparams_8h.html#9fe722d12f7ed6c181c1022aace70e21">00082</a> <span class="preprocessor">#define M_PAR_MAX_ASHAPE_SIZE 'M' </span><span class="comment">/**< flag for the maximum alpha sphere size*/</span>
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<a name="l00083"></a><a class="code" href="fparams_8h.html#c2dcc50d93bac7e0fe16850062556626">00083</a> <span class="preprocessor">#define M_PAR_MIN_ASHAPE_SIZE 'm' </span><span class="comment">/**< flag for the minimum alpha sphere size*/</span>
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<a name="l00084"></a><a class="code" href="fparams_8h.html#6868a969cd3e83643a099bb3a93498fb">00084</a> <span class="preprocessor">#define M_PAR_MIN_APOL_NEIGH 'A' </span><span class="comment">/**< flag for the minimum number of apolar neighbours for an alpha sphere to be considered as apolar*/</span>
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<a name="l00085"></a><a class="code" href="fparams_8h.html#ace76e1ea0d5b9bd44c7833fc257f9d5">00085</a> <span class="preprocessor">#define M_PAR_CLUST_MAX_DIST 'D' </span><span class="comment">/**< flag for the first clustering distance*/</span>
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<a name="l00086"></a><a class="code" href="fparams_8h.html#e5eccb0710c00b2c304cc688b8041f54">00086</a> <span class="preprocessor">#define M_PAR_SL_MAX_DIST 's' </span><span class="comment">/**< flag for the distance crit. of the multiple linkage clustering algorithm*/</span>
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<a name="l00087"></a><a class="code" href="fparams_8h.html#bc2dc478b856e70af235992072620d91">00087</a> <span class="preprocessor">#define M_PAR_SL_MIN_NUM_NEIGH 'n' </span><span class="comment">/**< flag for the single linkage min neighbours*/</span>
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<a name="l00088"></a><a class="code" href="fparams_8h.html#bdef86070652cf4d0fa5493ccf73d4fa">00088</a> <span class="preprocessor">#define M_PAR_MC_ITER 'v' </span><span class="comment">/**< flag for how many iterations for the monte carlo volume calculation algorithm*/</span>
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<a name="l00089"></a><a class="code" href="fparams_8h.html#74ad0900c04fd7855cb4914deabe0ba3">00089</a> <span class="preprocessor">#define M_PAR_BASIC_VOL_DIVISION 'b'</span><span class="comment">/**< flag for the space approximation of the MC*/</span>
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<a name="l00090"></a><a class="code" href="fparams_8h.html#2558ed6c1ac5aefc7366c607caefde34">00090</a> <span class="preprocessor">#define M_PAR_MIN_POCK_NB_ASPH 'i' </span><span class="comment">/**< flag for the min number of alpha spheres in the pocket*/</span>
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<a name="l00091"></a><a class="code" href="fparams_8h.html#9bbf5319350592125ab3504cea9c10e4">00091</a> <span class="preprocessor">#define M_PAR_REFINE_DIST 'r' </span><span class="comment">/**< flag for the refining distance*/</span>
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<a name="l00092"></a><a class="code" href="fparams_8h.html#a53522d41aaa000c99a53f29ea5c60cf">00092</a> <span class="preprocessor">#define M_PAR_REFINE_MIN_NAPOL_AS 'p'</span><span class="comment">/**< flag for minimum proportion of apolar alpha spheres*/</span>
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<a name="l00093"></a><a class="code" href="fparams_8h.html#598416cef61191786dcc416d92da84dd">00093</a> <span class="preprocessor">#define M_PAR_DB_RUN 'd' </span><span class="comment">/**<flag for running fpocket as database run, more silent and special output is produced for automatic grabbing of results using other programs*/</span>
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<a name="l00094"></a>00094
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<a name="l00095"></a><a class="code" href="fparams_8h.html#6148535acc1f81ca26cbaaf678c1cfc5">00095</a> <span class="preprocessor">#define M_FP_USAGE "\n\</span>
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<a name="l00096"></a>00096 <span class="preprocessor">***** USAGE (fpocket) *****\n\</span>
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<a name="l00097"></a>00097 <span class="preprocessor">\n\</span>
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<a name="l00098"></a>00098 <span class="preprocessor">Pocket finding on a pdb - list of pdb - file(s): \n\</span>
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<a name="l00099"></a>00099 <span class="preprocessor">\t./bin/fpocket -f pdb \n\</span>
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<a name="l00100"></a>00100 <span class="preprocessor">\t./bin/fpocket -F pdb_list \n\</span>
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<a name="l00101"></a>00101 <span class="preprocessor">\nOPTIONS (find standard parameters in brackets) \n\n\</span>
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<a name="l00102"></a>00102 <span class="preprocessor">\t-m (float) : Minimum radius of an alpha-sphere. (3.0)\n\</span>
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<a name="l00103"></a>00103 <span class="preprocessor">\t-M (float) : Maximum radius of an alpha-sphere. (6.0)\n\</span>
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<a name="l00104"></a>00104 <span class="preprocessor">\t-A (int) : Minimum number of apolar neighbor for \n\</span>
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<a name="l00105"></a>00105 <span class="preprocessor">\t an a-sphere to be considered as apolar. (3)\n\</span>
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<a name="l00106"></a>00106 <span class="preprocessor">\t-i (int) : Minimum number of a-sphere per pocket. (30)\n\</span>
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<a name="l00107"></a>00107 <span class="preprocessor">\t-D (float) : Maximum distance for first clustering \n\</span>
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<a name="l00108"></a>00108 <span class="preprocessor">\t algorithm. (1.73)\n\</span>
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<a name="l00109"></a>00109 <span class="preprocessor">\t-s (float) : Maximum distance for single linkage \n\</span>
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<a name="l00110"></a>00110 <span class="preprocessor">\t clustering (2.5)\n\</span>
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<a name="l00111"></a>00111 <span class="preprocessor">\t-n (integer): Minimum number of neighbor close from \n\</span>
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<a name="l00112"></a>00112 <span class="preprocessor">\t each other (not merged otherwise). (3)\n\</span>
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<a name="l00113"></a>00113 <span class="preprocessor">\t-r (float) : Maximum distance between two pockets \n\</span>
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<a name="l00114"></a>00114 <span class="preprocessor">\t barycenter (merged otherwise). (4.5)\n\</span>
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<a name="l00115"></a>00115 <span class="preprocessor">\t-p (float) : Minimum proportion of apolar sphere in \n\</span>
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<a name="l00116"></a>00116 <span class="preprocessor">\t a pocket (remove otherwise) (0.0)\n\</span>
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<a name="l00117"></a>00117 <span class="preprocessor">\t-v (integer): Number of Monte-Carlo iteration for the \n\</span>
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<a name="l00118"></a>00118 <span class="preprocessor">\t calculation of each pocket volume. (2500)\n\</span>
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<a name="l00119"></a>00119 <span class="preprocessor">\t-b (integer): Space approximation for the basic method \n\</span>
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<a name="l00120"></a>00120 <span class="preprocessor">\t of the volume calculation. Not used by \n\</span>
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<a name="l00121"></a>00121 <span class="preprocessor">\t default (Monte Carlo approximation is) \n\</span>
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<a name="l00122"></a>00122 <span class="preprocessor">\t-d flag : Put this flag if you want to run fpocket for \n\</span>
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<a name="l00123"></a>00123 <span class="preprocessor">\t database creation \n\</span>
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<a name="l00124"></a>00124 <span class="preprocessor">\nSee the manual (man fpocket), or the full documentation for\n\</span>
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<a name="l00125"></a>00125 <span class="preprocessor">more information.\n\</span>
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<a name="l00126"></a>00126 <span class="preprocessor">***************************\n" </span><span class="comment">/**< the usage print content*/</span>
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<a name="l00127"></a>00127
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<a name="l00128"></a>00128 <span class="comment">/* --------------------------- PUBLIC STRUCTURES ---------------------------- */</span><span class="comment"></span>
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<a name="l00129"></a>00129 <span class="comment">/**</span>
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<a name="l00130"></a>00130 <span class="comment"> Structure containing all necessary parameters that can be changed by the user.</span>
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<a name="l00131"></a>00131 <span class="comment"> This structure is commun to both programs (validation and pocket finding), </span>
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<a name="l00132"></a>00132 <span class="comment"> even if the pocked finding programm doesn't need some parameters.</span>
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<a name="l00133"></a>00133 <span class="comment">*/</span>
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<a name="l00134"></a><a class="code" href="structs__fparams.html">00134</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structs__fparams.html">s_fparams</a>
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<a name="l00135"></a>00135 {
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<a name="l00136"></a><a class="code" href="structs__fparams.html#4e1b3892d1e42947408cdcaed497bf97">00136</a> <span class="keywordtype">char</span> <a class="code" href="structs__fparams.html#4e1b3892d1e42947408cdcaed497bf97">pdb_path</a>[<a class="code" href="utils_8h.html#ea69486910da420cbfe816d80ecc8b0c">M_MAX_PDB_NAME_LEN</a>] ; <span class="comment">/**< The pdb file */</span>
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<a name="l00137"></a><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">00137</a> <span class="keywordtype">char</span> **<a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a> ;
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<a name="l00138"></a><a class="code" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">00138</a> <span class="keywordtype">int</span> <a class="code" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">npdb</a> ; <span class="comment">/**< number of pdb files*/</span>
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<a name="l00139"></a><a class="code" href="structs__fparams.html#771a10e1c94346d353eb6cb87b4abb18">00139</a> <span class="keywordtype">int</span> <a class="code" href="structs__fparams.html#771a10e1c94346d353eb6cb87b4abb18">flag_do_asa_and_volume_calculations</a>; <span class="comment">/**<if 1, asa and volume calculations are performed(slower), if 0, not*/</span>
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<a name="l00140"></a>00140 <span class="keywordtype">int</span> <a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a>, <span class="comment">/**< Min number of apolar neighbours for an a-sphere</span>
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<a name="l00141"></a><a class="code" href="structs__fparams.html#b23279857aaf7861b452cd2bf463f624">00141</a> <span class="comment"> to be an apolar a-sphere */</span>
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<a name="l00142"></a>00142 <a class="code" href="structs__fparams.html#b23279857aaf7861b452cd2bf463f624">sl_clust_min_nneigh</a>, <span class="comment">/**< Min number of neighbours for single linkage</span>
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<a name="l00143"></a>00143 <span class="comment"> clustering */</span>
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<a name="l00144"></a>00144 <a class="code" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">nb_mcv_iter</a>, <span class="comment">/**< Number of iteration for the Monte Carlo volume</span>
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<a name="l00145"></a>00145 <span class="comment"> calculation */</span>
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<a name="l00146"></a>00146 <a class="code" href="structs__fparams.html#289a1193bf0ffa2f737cd9dc914b63e0">basic_volume_div</a>, <span class="comment">/**< Box division factor for basic volume calculation */</span>
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<a name="l00147"></a>00147 <a class="code" href="structs__fparams.html#2ccafe788e970f4e00bdae591d834865">min_pock_nb_asph</a>, <span class="comment">/**< Minimump number of alpha spheres per pocket */</span>
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<a name="l00148"></a>00148 <a class="code" href="structs__fparams.html#b8d794447932a12435a628f3462df7ad">db_run</a>; <span class="comment">/**< flag for running fpocket for db population*/</span>
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<a name="l00149"></a>00149
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<a name="l00150"></a><a class="code" href="structs__fparams.html#71691bbfb98d90e12ca8cb3c79e2688c">00150</a> <span class="keywordtype">float</span> <a class="code" href="structs__fparams.html#cd506e600d2b5077f7925847be38c854">clust_max_dist</a>, <span class="comment">/**< First clustering distance criteria */</span>
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<a name="l00151"></a>00151 <a class="code" href="structs__fparams.html#50d6211ea1f5d9b90c10f866c82e54b8">refine_min_apolar_asphere_prop</a>, <span class="comment">/**< Min proportion of apolar alpha</span>
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<a name="l00152"></a>00152 <span class="comment"> spheres for each pocket */</span>
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<a name="l00153"></a>00153 <a class="code" href="structs__fparams.html#71691bbfb98d90e12ca8cb3c79e2688c">sl_clust_max_dist</a>, <span class="comment">/**< Single linkage clusturing distance criteria */</span>
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<a name="l00154"></a>00154 <a class="code" href="structs__fparams.html#8ba147c559344c3f0406c1e7a86b98d1">refine_clust_dist</a>, <span class="comment">/**< Refine clustering distance criteria */</span>
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<a name="l00155"></a>00155 <a class="code" href="structs__fparams.html#545b7bea97958089689608fff6b8910d">asph_min_size</a>, <span class="comment">/**< Minimum size of alpha spheres to keep */</span>
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<a name="l00156"></a>00156 <a class="code" href="structs__fparams.html#7439af209766e39dad7e39f4c6e19711">asph_max_size</a> ; <span class="comment">/**< Maximum size of alpha spheres to keep */</span>
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<a name="l00157"></a>00157
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<a name="l00158"></a>00158
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<a name="l00159"></a>00159 } <a class="code" href="structs__fparams.html">s_fparams</a> ;
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<a name="l00160"></a>00160
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<a name="l00161"></a>00161 <span class="comment">/* ------------------------------- PROTOTYPES ------------------------------- */</span>
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<a name="l00162"></a>00162
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<a name="l00163"></a>00163 <a class="code" href="structs__fparams.html">s_fparams</a>* <a class="code" href="fparams_8c.html#7f23db4971a109deb1ab5e841ace1607">init_def_fparams</a>(<span class="keywordtype">void</span>) ;
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<a name="l00164"></a>00164 <a class="code" href="structs__fparams.html">s_fparams</a>* <a class="code" href="fparams_8c.html#c1806d3567baea11616fc5fdfca417d7">get_fpocket_args</a>(<span class="keywordtype">int</span> nargs, <span class="keywordtype">char</span> **args) ;
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<a name="l00165"></a>00165
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<a name="l00166"></a>00166 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#8471dca4fb8f09806aed3be18a79c6b2">parse_clust_max_dist</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00167"></a>00167 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#da442addde23a799e50cecae103974bf">parse_sclust_max_dist</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00168"></a>00168 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#39b0715eb1fb67b993d494570f866135">parse_sclust_min_nneigh</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00169"></a>00169 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#40cf684e6c79bc0d5494cf63ee40b8d3">parse_min_apol_neigh</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00170"></a>00170 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#0356665c59c8eda7fb483f47dbbe8d3b">parse_asph_min_size</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00171"></a>00171 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#8ba1cfff825efc1d30099d85f1f85b01">parse_asph_max_size</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00172"></a>00172 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#ffc4eabc99149ff419340f11297312c6">parse_mc_niter</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00173"></a>00173 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#bb8b6f641fc59aea7b6915fd3c197fba">parse_basic_vol_div</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00174"></a>00174 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#cca6c1f10d064997753458d61e052f7d">parse_refine_dist</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00175"></a>00175 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#a08e358edc9c6941f595da45c4741fe0">parse_refine_minaap</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00176"></a>00176 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#c09155f5ca513066b30c9d1485d810a8">parse_min_pock_nb_asph</a>(<span class="keywordtype">char</span> *str, <a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00177"></a>00177
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<a name="l00178"></a>00178 <span class="keywordtype">int</span> <a class="code" href="fparams_8c.html#bdc82d2e467d8dd8765d605d1ae26dc6">is_fpocket_opt</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> opt) ;
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<a name="l00179"></a>00179
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<a name="l00180"></a>00180 <span class="keywordtype">void</span> <a class="code" href="fparams_8c.html#112335ac520ae98bdcf93e0c75c3c5db">free_fparams</a>(<a class="code" href="structs__fparams.html">s_fparams</a> *p) ;
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<a name="l00181"></a>00181 <span class="keywordtype">void</span> <a class="code" href="fparams_8c.html#ab8c5397c1eaa6388ae24aa9ae605481">print_pocket_usage</a>(FILE *f) ;
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<a name="l00182"></a>00182 <span class="keywordtype">void</span> <a class="code" href="fparams_8c.html#00d0d0ea58e0b3fd1f6a785427e6b5f1">print_fparams</a>(<a class="code" href="structs__fparams.html">s_fparams</a> *p, FILE *f) ;
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<a name="l00183"></a>00183
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<a name="l00184"></a>00184 <span class="preprocessor">#endif</span>
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</pre></div></div>
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<hr size="1"><address style="text-align: right;"><small>Generated on Mon Jun 7 16:44:23 2010 for fpocket by
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<a href="http://www.doxygen.org/index.html">
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<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.6 </small></address>
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</body>
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</html>
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