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<li><a href="index.html"><span>Main Page</span></a></li>
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<li><a href="annotated.html"><span>Data Structures</span></a></li>
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<h1>atom.h</h1><a href="atom_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 <span class="comment">/*</span>
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<a name="l00003"></a>00003 <span class="comment"> COPYRIGHT DISCLAIMER</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"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
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<a name="l00006"></a>00006 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
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<a name="l00007"></a>00007 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
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<a name="l00008"></a>00008 <span class="comment"> Schmidtke.</span>
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<a name="l00009"></a>00009 <span class="comment"></span>
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<a name="l00010"></a>00010 <span class="comment"> Vincent Le Guilloux 28 November 2008</span>
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<a name="l00011"></a>00011 <span class="comment"> Peter Schmidtke 28 November 2008</span>
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<a name="l00012"></a>00012 <span class="comment"> Pierre Tuffery 28 November 2008</span>
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<a name="l00013"></a>00013 <span class="comment"></span>
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<a name="l00014"></a>00014 <span class="comment"> GNU GPL</span>
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<a name="l00015"></a>00015 <span class="comment"></span>
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<a name="l00016"></a>00016 <span class="comment"> This file is part of the fpocket package.</span>
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<a name="l00017"></a>00017 <span class="comment"></span>
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<a name="l00018"></a>00018 <span class="comment"> fpocket is free software: you can redistribute it and/or modify</span>
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<a name="l00019"></a>00019 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
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<a name="l00020"></a>00020 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
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<a name="l00021"></a>00021 <span class="comment"> (at your option) any later version.</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"> fpocket is distributed in the hope that it will be useful,</span>
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<a name="l00024"></a>00024 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<a name="l00025"></a>00025 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<a name="l00026"></a>00026 <span class="comment"> GNU General Public License for more details.</span>
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<a name="l00027"></a>00027 <span class="comment"></span>
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<a name="l00028"></a>00028 <span class="comment"> You should have received a copy of the GNU General Public License</span>
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<a name="l00029"></a>00029 <span class="comment"> along with fpocket. If not, see <http://www.gnu.org/licenses/>.</span>
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<a name="l00030"></a>00030 <span class="comment"></span>
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<a name="l00031"></a>00031 <span class="comment">**/</span>
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<a name="l00032"></a>00032
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<a name="l00033"></a>00033 <span class="preprocessor">#ifndef DH_ATOM</span>
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<a name="l00034"></a>00034 <span class="preprocessor"></span><span class="preprocessor">#define DH_ATOM</span>
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<a name="l00035"></a>00035 <span class="preprocessor"></span>
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<a name="l00036"></a>00036 <span class="preprocessor">#include <stdio.h></span>
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<a name="l00037"></a>00037 <span class="preprocessor">#include <stdlib.h></span>
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<a name="l00038"></a>00038 <span class="preprocessor">#include <string.h></span>
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<a name="l00039"></a>00039 <span class="preprocessor">#include <ctype.h></span>
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<a name="l00040"></a>00040
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<a name="l00041"></a>00041 <span class="preprocessor">#include "<a class="code" href="utils_8h.html">utils.h</a>"</span>
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<a name="l00042"></a>00042
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<a name="l00043"></a>00043 <span class="comment">// --------------------------------MACROS------------------------------------ */</span>
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<a name="l00044"></a>00044
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<a name="l00045"></a>00045
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<a name="l00046"></a>00046
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<a name="l00047"></a>00047 <span class="comment">// -------------------------- PUBLIC STRUCTURES ----------------------------- */</span>
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<a name="l00048"></a>00048 <span class="comment"></span>
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<a name="l00049"></a>00049 <span class="comment">/**</span>
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<a name="l00050"></a>00050 <span class="comment"> A structure for the modelisation of an atom</span>
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<a name="l00051"></a>00051 <span class="comment">*/</span>
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<a name="l00052"></a><a class="code" href="structs__atm.html">00052</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structs__atm.html">s_atm</a>
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<a name="l00053"></a>00053 {
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<a name="l00054"></a><a class="code" href="structs__atm.html#05407d7638ff7f6fc210026306def9b5">00054</a> <span class="keywordtype">int</span> <a class="code" href="structs__atm.html#05407d7638ff7f6fc210026306def9b5">sort_x</a>; <span class="comment">/**< Index in the sorted tab by X coord */</span>
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<a name="l00055"></a>00055
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<a name="l00056"></a><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">00056</a> <span class="keywordtype">float</span> <a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>, <a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>, <a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a> ; <span class="comment">/**< Coords */</span>
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<a name="l00057"></a><a class="code" href="structs__atm.html#98466fdfcb021884beb229b1dca361ae">00057</a> <span class="keywordtype">char</span> <a class="code" href="structs__atm.html#2f0330a30f640668efdd726a6dd05a93">name</a>[5], <span class="comment">/**< Atom name */</span>
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<a name="l00058"></a>00058 <a class="code" href="structs__atm.html#98466fdfcb021884beb229b1dca361ae">type</a>[7], <span class="comment">/**< Atom type */</span>
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<a name="l00059"></a>00059 <a class="code" href="structs__atm.html#c5b9464bd67f2cca101f7bf6beabb223">chain</a>[2], <span class="comment">/**< Chain name */</span>
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<a name="l00060"></a>00060 <a class="code" href="structs__atm.html#c80daffa94edeadd30433f6653e08054">symbol</a>[3], <span class="comment">/**< Chemical symbol of the atom */</span>
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<a name="l00061"></a>00061 <a class="code" href="structs__atm.html#e0ff20f2c491a8b16c866d9b1386b6a5">res_name</a>[8]; <span class="comment">/**< Atom residue name */</span>
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<a name="l00062"></a>00062
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<a name="l00063"></a><a class="code" href="structs__atm.html#46d588698400fc19733301d687cf98bd">00063</a> <span class="keywordtype">int</span> <a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>, <span class="comment">/**< Atom id */</span>
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<a name="l00064"></a>00064 <a class="code" href="structs__atm.html#46d588698400fc19733301d687cf98bd">seen</a>, <span class="comment">/**< Say if we have seen this atom during a neighbor search */</span>
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<a name="l00065"></a>00065 <a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a>, <span class="comment">/**< Atom residue ID */</span>
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<a name="l00066"></a>00066 <a class="code" href="structs__atm.html#de270d849563cffcab038bcb5f5c6e97">atype</a>,
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<a name="l00067"></a>00067 <a class="code" href="structs__atm.html#a03a199ed11108d7710547df629c7d73">charge</a> ; <span class="comment">/**< Atom charge */</span>
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<a name="l00068"></a>00068
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<a name="l00069"></a>00069 <span class="comment">/* Optional fields */</span>
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<a name="l00070"></a><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">00070</a> <span class="keywordtype">float</span> <a class="code" href="structs__atm.html#ebbe1b323a702c23ef5bb21888adb6a8">mass</a>, <span class="comment">/**< Mass */</span>
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<a name="l00071"></a>00071 <a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>, <span class="comment">/**< Vdw radius */</span>
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<a name="l00072"></a>00072 <a class="code" href="structs__atm.html#f41b525ee3032d47baf2db10387f022c">electroneg</a>, <span class="comment">/**< Electronegativity */</span>
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<a name="l00073"></a>00073 <a class="code" href="structs__atm.html#1696926c680a1014360598d54a1dadb0">occupancy</a>, <span class="comment">/**< Occupancy */</span>
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<a name="l00074"></a>00074 <a class="code" href="structs__atm.html#6a1a5fd32629457dfa14626b25b5ae46">bfactor</a> ; <span class="comment">/**< B-factor for christal structures */</span>
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<a name="l00075"></a>00075
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<a name="l00076"></a><a class="code" href="structs__atm.html#bfd1f905200f69dd9cd9750fd305cf46">00076</a> <span class="keywordtype">char</span> <a class="code" href="structs__atm.html#bfd1f905200f69dd9cd9750fd305cf46">pdb_insert</a>, <span class="comment">/**< PDB insertion code */</span>
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<a name="l00077"></a>00077 <a class="code" href="structs__atm.html#58eeb8a80942caa3bd2374f3175cb77d">pdb_aloc</a>; <span class="comment">/**< PDB alternate location code */</span>
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<a name="l00078"></a>00078
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<a name="l00079"></a><a class="code" href="structs__atm.html#e490809411c7c78662727873d499c730">00079</a> <span class="keywordtype">int</span> <a class="code" href="structs__atm.html#e490809411c7c78662727873d499c730">atomic_num</a> ; <span class="comment">/**< Atomic number */</span>
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<a name="l00080"></a>00080
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<a name="l00081"></a>00081 } <a class="code" href="structs__atm.html">s_atm</a> ;
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<a name="l00082"></a>00082
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<a name="l00083"></a>00083 <span class="comment">/* --------------------------------PROTOTYPES--------------------------------- */</span>
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<a name="l00084"></a>00084
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<a name="l00085"></a>00085 <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#fa83a33583c67b9a3a4439b14000b983">get_mol_mass</a>(<a class="code" href="structs__atm.html">s_atm</a> *latoms, <span class="keywordtype">int</span> natoms) ;
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<a name="l00086"></a>00086 <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#6c124482d4ea1d4956cb095413e4b3af">get_mol_mass_ptr</a>(<a class="code" href="structs__atm.html">s_atm</a> **latoms, <span class="keywordtype">int</span> natoms);
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<a name="l00087"></a>00087 <span class="keywordtype">void</span> <a class="code" href="atom_8c.html#6648ca5bb9d7384c43dda5156e333f24">set_mol_barycenter_ptr</a>(<a class="code" href="structs__atm.html">s_atm</a> **latoms, <span class="keywordtype">int</span> natoms, <span class="keywordtype">float</span> bary[3]) ;
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<a name="l00088"></a>00088 <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#d0f577a82cfdb135f707700c2b84e6a5">get_mol_volume_ptr</a>(<a class="code" href="structs__atm.html">s_atm</a> **atoms, <span class="keywordtype">int</span> natoms, <span class="keywordtype">int</span> niter) ;
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<a name="l00089"></a>00089
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<a name="l00090"></a>00090 <span class="keywordtype">int</span> <a class="code" href="atom_8c.html#a72221368b25d51716e4d59f02a8d753">is_in_lst_atm</a>(<a class="code" href="structs__atm.html">s_atm</a> **lst_atm, <span class="keywordtype">int</span> nb_atm, <span class="keywordtype">int</span> atm_id) ;
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<a name="l00091"></a>00091 <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#a960d66d3bd7cce701a12f56999056b4">atm_corsp</a>(<a class="code" href="structs__atm.html">s_atm</a> **al1, <span class="keywordtype">int</span> nl1, <a class="code" href="structs__atm.html">s_atm</a> **pocket_neigh, <span class="keywordtype">int</span> nal2) ;
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<a name="l00092"></a>00092
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<a name="l00093"></a>00093 <span class="keywordtype">void</span> <a class="code" href="atom_8c.html#9c0033f44cb65046ce5209b269da11d7">print_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="l00094"></a>00094
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<a name="l00095"></a>00095 <span class="preprocessor">#endif</span>
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</pre></div></div>
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