mirror of
https://github.com/Discngine/fpocket.git
synced 2026-06-04 11:54:21 +08:00
172 lines
17 KiB
HTML
172 lines
17 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
|
<html><head><meta http-equiv="Content-Type" content="text/html;charset=UTF-8">
|
|
<title>fpocket: aa.h Source File</title>
|
|
<link href="tabs.css" rel="stylesheet" type="text/css">
|
|
<link href="doxygen.css" rel="stylesheet" type="text/css">
|
|
</head><body>
|
|
<img src="fpocket_logo_small.png" width="545" height="150">
|
|
<!-- Generated by Doxygen 1.5.9 -->
|
|
<script type="text/javascript">
|
|
<!--
|
|
function changeDisplayState (e){
|
|
var num=this.id.replace(/[^[0-9]/g,'');
|
|
var button=this.firstChild;
|
|
var sectionDiv=document.getElementById('dynsection'+num);
|
|
if (sectionDiv.style.display=='none'||sectionDiv.style.display==''){
|
|
sectionDiv.style.display='block';
|
|
button.src='open.gif';
|
|
}else{
|
|
sectionDiv.style.display='none';
|
|
button.src='closed.gif';
|
|
}
|
|
}
|
|
function initDynSections(){
|
|
var divs=document.getElementsByTagName('div');
|
|
var sectionCounter=1;
|
|
for(var i=0;i<divs.length-1;i++){
|
|
if(divs[i].className=='dynheader'&&divs[i+1].className=='dynsection'){
|
|
var header=divs[i];
|
|
var section=divs[i+1];
|
|
var button=header.firstChild;
|
|
if (button!='IMG'){
|
|
divs[i].insertBefore(document.createTextNode(' '),divs[i].firstChild);
|
|
button=document.createElement('img');
|
|
divs[i].insertBefore(button,divs[i].firstChild);
|
|
}
|
|
header.style.cursor='pointer';
|
|
header.onclick=changeDisplayState;
|
|
header.id='dynheader'+sectionCounter;
|
|
button.src='closed.gif';
|
|
section.id='dynsection'+sectionCounter;
|
|
section.style.display='none';
|
|
section.style.marginLeft='14px';
|
|
sectionCounter++;
|
|
}
|
|
}
|
|
}
|
|
window.onload = initDynSections;
|
|
-->
|
|
</script>
|
|
<div class="navigation" id="top">
|
|
<div class="tabs">
|
|
<ul>
|
|
<li><a href="index.html"><span>Main Page</span></a></li>
|
|
<li><a href="annotated.html"><span>Data Structures</span></a></li>
|
|
<li class="current"><a href="files.html"><span>Files</span></a></li>
|
|
</ul>
|
|
</div>
|
|
<div class="tabs">
|
|
<ul>
|
|
<li><a href="files.html"><span>File List</span></a></li>
|
|
<li><a href="globals.html"><span>Globals</span></a></li>
|
|
</ul>
|
|
</div>
|
|
<h1>aa.h</h1><a href="aa_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001
|
|
<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 <http://www.gnu.org/licenses/>.</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_AA</span>
|
|
<a name="l00034"></a>00034 <span class="preprocessor"></span><span class="preprocessor">#define DH_AA</span>
|
|
<a name="l00035"></a>00035 <span class="preprocessor"></span>
|
|
<a name="l00036"></a>00036 <span class="preprocessor">#include <stdio.h></span>
|
|
<a name="l00037"></a>00037 <span class="preprocessor">#include <stdlib.h></span>
|
|
<a name="l00038"></a>00038 <span class="preprocessor">#include <string.h></span>
|
|
<a name="l00039"></a>00039 <span class="preprocessor">#include <ctype.h></span>
|
|
<a name="l00040"></a>00040
|
|
<a name="l00041"></a>00041 <span class="comment">/* ------------------------------MACROS---------------------------------------*/</span>
|
|
<a name="l00042"></a>00042
|
|
<a name="l00043"></a><a class="code" href="aa_8h.html#473a70533737641d73e56c3a2c4292ff">00043</a> <span class="preprocessor">#define M_NB_AA 20 </span><span class="comment">/**< number of amino acid macros*/</span>
|
|
<a name="l00044"></a><a class="code" href="aa_8h.html#1b0c9070ecb3ea0befd683ce92dfa925">00044</a> <span class="preprocessor">#define M_ALA_IDX 0 </span><span class="comment">/**< 0 for ALA*/</span>
|
|
<a name="l00045"></a><a class="code" href="aa_8h.html#7e417b6b18144cb3417f86c100e26210">00045</a> <span class="preprocessor">#define M_CYS_IDX 1 </span><span class="comment">/**< 1 for CYS*/</span>
|
|
<a name="l00046"></a><a class="code" href="aa_8h.html#93845fafca07848ed53cb4d454be12ac">00046</a> <span class="preprocessor">#define M_ASP_IDX 2 </span><span class="comment">/**< 2 for ASP*/</span>
|
|
<a name="l00047"></a><a class="code" href="aa_8h.html#ee64fbe3bf2b3700be47e73710ba9b2e">00047</a> <span class="preprocessor">#define M_GLU_IDX 3 </span><span class="comment">/**< 3 for GLU*/</span>
|
|
<a name="l00048"></a><a class="code" href="aa_8h.html#0ce108eda73a67d937d4a9a95742e7e2">00048</a> <span class="preprocessor">#define M_PHE_IDX 4 </span><span class="comment">/**< 4 for PHE*/</span>
|
|
<a name="l00049"></a><a class="code" href="aa_8h.html#8af8b421277f5bac3dd71ecb39912a68">00049</a> <span class="preprocessor">#define M_GLY_IDX 5 </span><span class="comment">/**< 5 for GLY*/</span>
|
|
<a name="l00050"></a><a class="code" href="aa_8h.html#ad66b8237a731e8b9284cf2c0f5bf1a8">00050</a> <span class="preprocessor">#define M_HIS_IDX 6 </span><span class="comment">/**< 6 for HIS*/</span>
|
|
<a name="l00051"></a><a class="code" href="aa_8h.html#f7ed4c3826357ffd5ca1430960b01323">00051</a> <span class="preprocessor">#define M_ILE_IDX 7 </span><span class="comment">/**< 7 for ILE*/</span>
|
|
<a name="l00052"></a><a class="code" href="aa_8h.html#9c48ce33c40ed282161be85f00e5c358">00052</a> <span class="preprocessor">#define M_LYS_IDX 8 </span><span class="comment">/**< 8 for LYS*/</span>
|
|
<a name="l00053"></a><a class="code" href="aa_8h.html#6f298038ea813adf7ce7591d8aebc24f">00053</a> <span class="preprocessor">#define M_LEU_IDX 9 </span><span class="comment">/**< 9 for LEU*/</span>
|
|
<a name="l00054"></a><a class="code" href="aa_8h.html#7552b2c0cb98c2ec24839aa18761321d">00054</a> <span class="preprocessor">#define M_MET_IDX 10 </span><span class="comment">/**< 10 for MET*/</span>
|
|
<a name="l00055"></a><a class="code" href="aa_8h.html#84516b2203e073e9dbc63ccaf7a3628b">00055</a> <span class="preprocessor">#define M_ASN_IDX 11 </span><span class="comment">/**< 11 for ASN*/</span>
|
|
<a name="l00056"></a><a class="code" href="aa_8h.html#f67fd842e620788b97ebf0ed4c062d6f">00056</a> <span class="preprocessor">#define M_PRO_IDX 12 </span><span class="comment">/**< 12 for PRO*/</span>
|
|
<a name="l00057"></a><a class="code" href="aa_8h.html#a50e956ceccc8383378ce2c86a0650c7">00057</a> <span class="preprocessor">#define M_GLN_IDX 13 </span><span class="comment">/**< 13 for GLN*/</span>
|
|
<a name="l00058"></a><a class="code" href="aa_8h.html#6cb6aa2cef5eaa616d3c5f4fc4acd710">00058</a> <span class="preprocessor">#define M_ARG_IDX 14 </span><span class="comment">/**< 14 for ARG*/</span>
|
|
<a name="l00059"></a><a class="code" href="aa_8h.html#bd333adb6a0180ddb95da74027d34693">00059</a> <span class="preprocessor">#define M_SER_IDX 15 </span><span class="comment">/**< 15 for SER*/</span>
|
|
<a name="l00060"></a><a class="code" href="aa_8h.html#cd98aae4f40d8e2c19435b5d79abcb53">00060</a> <span class="preprocessor">#define M_THR_IDX 16 </span><span class="comment">/**< 16 for THR*/</span>
|
|
<a name="l00061"></a><a class="code" href="aa_8h.html#93cd02b2888b078a6c3c0461bda79841">00061</a> <span class="preprocessor">#define M_VAL_IDX 17 </span><span class="comment">/**< 17 for VAL*/</span>
|
|
<a name="l00062"></a><a class="code" href="aa_8h.html#ae2397ccd1d8baefaf8beecb9ebf4128">00062</a> <span class="preprocessor">#define M_TRP_IDX 18 </span><span class="comment">/**< 18 for TRP*/</span>
|
|
<a name="l00063"></a><a class="code" href="aa_8h.html#d894f46b7d2e41ec7a1bdf2f66d6d530">00063</a> <span class="preprocessor">#define M_TYR_IDX 19 </span><span class="comment">/**< 19 for TYR*/</span>
|
|
<a name="l00064"></a>00064
|
|
<a name="l00065"></a>00065 <span class="comment">/* --------------------------- PUBLIC STRUCTURES ------------------------------*/</span>
|
|
<a name="l00066"></a>00066 <span class="comment"></span>
|
|
<a name="l00067"></a>00067 <span class="comment">/**</span>
|
|
<a name="l00068"></a>00068 <span class="comment"> A structure for the modelisation of an amino acid</span>
|
|
<a name="l00069"></a>00069 <span class="comment">*/</span>
|
|
<a name="l00070"></a><a class="code" href="structs__amino__a.html">00070</a> <span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structs__amino__a.html">s_amino_a</a>
|
|
<a name="l00071"></a>00071 {
|
|
<a name="l00072"></a><a class="code" href="structs__amino__a.html#ea8b997108e6468326b00183bd6eb0c7">00072</a> <span class="keywordtype">char</span> <a class="code" href="structs__amino__a.html#ea8b997108e6468326b00183bd6eb0c7">name3</a>[4] ; <span class="comment">/**< name of the amino-acid (3 letter code)*/</span>
|
|
<a name="l00073"></a><a class="code" href="structs__amino__a.html#f55283d22dfd4128a6475c517819ee06">00073</a> <span class="keywordtype">char</span> <a class="code" href="structs__amino__a.html#f55283d22dfd4128a6475c517819ee06">code</a> ; <span class="comment">/**< one letter code for the amino acid*/</span>
|
|
<a name="l00074"></a>00074
|
|
<a name="l00075"></a><a class="code" href="structs__amino__a.html#0c82f3a8524b934028b8289a41c8ee91">00075</a> <span class="keywordtype">float</span> <a class="code" href="structs__amino__a.html#0c82f3a8524b934028b8289a41c8ee91">mw</a> ; <span class="comment">/**< molecular weight of the amino acid*/</span>
|
|
<a name="l00076"></a><a class="code" href="structs__amino__a.html#4ddae5fde18856a3dab901009673d4f6">00076</a> <span class="keywordtype">float</span> <a class="code" href="structs__amino__a.html#4ddae5fde18856a3dab901009673d4f6">volume</a>; <span class="comment">/**< volume score for each aa taken from http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm*/</span>
|
|
<a name="l00077"></a><a class="code" href="structs__amino__a.html#8c7db917f840ebd0dad9a378a4be4b92">00077</a> <span class="keywordtype">float</span> <a class="code" href="structs__amino__a.html#8c7db917f840ebd0dad9a378a4be4b92">hydrophobicity</a>; <span class="comment">/**< hydrophobicity score for each aa taken from Monera & al. Journal of Protein Science 1, 319-329 (1995)*/</span>
|
|
<a name="l00078"></a><a class="code" href="structs__amino__a.html#e6101783dcf52f5de7ed94729c55096b">00078</a> <span class="keywordtype">int</span> <a class="code" href="structs__amino__a.html#0f912bcd04ae9f99a8f3a45e736d9d16">charge</a>, <span class="comment">/**< crude net charge of each amino acid in pH 7*/</span>
|
|
<a name="l00079"></a>00079 <a class="code" href="structs__amino__a.html#e6101783dcf52f5de7ed94729c55096b">polarity</a>, <span class="comment">/**< polarity of each aa taken from http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm*/</span>
|
|
<a name="l00080"></a>00080 <a class="code" href="structs__amino__a.html#1e4bec2abdf9140e3490fac980a5702c">func_grp</a> ; <span class="comment">/**< funct. groups of each aa taken from http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm*/</span>
|
|
<a name="l00081"></a>00081
|
|
<a name="l00082"></a>00082 } <a class="code" href="structs__amino__a.html">s_amino_a</a> ;
|
|
<a name="l00083"></a>00083
|
|
<a name="l00084"></a>00084 <span class="comment">/* -----------------------------PROTOTYPES------------------------------------*/</span>
|
|
<a name="l00085"></a>00085
|
|
<a name="l00086"></a>00086 <span class="keywordtype">int</span> <a class="code" href="aa_8c.html#f10857d7d319ed08d91b2a91e8dfa73f">get_aa_index</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *name) ;
|
|
<a name="l00087"></a>00087 <span class="keywordtype">char</span>* <a class="code" href="aa_8c.html#f071a7d6353978202a07fd66f2ff68d8">get_aa_name3</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> index) ;
|
|
<a name="l00088"></a>00088
|
|
<a name="l00089"></a>00089 <span class="keywordtype">float</span> <a class="code" href="aa_8c.html#c8205bded5bf0a2077fc2aa928435fb0">get_aa_mw</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *name) ;
|
|
<a name="l00090"></a>00090 <span class="keywordtype">float</span> <a class="code" href="aa_8c.html#e8721edaf9b5027df8fcb9932497568c">get_aa_volume_score</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *name) ;
|
|
<a name="l00091"></a>00091 <span class="keywordtype">float</span> <a class="code" href="aa_8c.html#acfe4be9ac7a7111d65a1dba7b7a11b9">get_aa_hydrophobicity_score</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *name) ;
|
|
<a name="l00092"></a>00092 <span class="keywordtype">int</span> <a class="code" href="aa_8c.html#adf25cee3c6ea3b956dbe776356b198d">get_aa_charge</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *name) ;
|
|
<a name="l00093"></a>00093 <span class="keywordtype">int</span> <a class="code" href="aa_8c.html#a12288b5ca620ff78a9a4a5b48d4abb0">get_aa_polarity</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *name) ;
|
|
<a name="l00094"></a>00094 <span class="keywordtype">int</span> <a class="code" href="aa_8c.html#365325c4571c0c23235f7e58f3cd9f5d">get_aa_func_grp</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *name) ;
|
|
<a name="l00095"></a>00095
|
|
<a name="l00096"></a>00096 <span class="keywordtype">float</span> <a class="code" href="aa_8c.html#ce98533a9358aec6dcc325fe567c26fe">get_volume_score_from_idx</a>(<span class="keywordtype">int</span> aa_index) ;
|
|
<a name="l00097"></a>00097 <span class="keywordtype">float</span> <a class="code" href="aa_8c.html#3988fc0beb2f06dee9ebb04ef491f9d7">get_hydrophobicity_score_from_idx</a>(<span class="keywordtype">int</span> aa_index) ;
|
|
<a name="l00098"></a>00098 <span class="keywordtype">int</span> <a class="code" href="aa_8c.html#641c90c89a2f096c09ee972cf05d8b71">get_charge_from_idx</a>(<span class="keywordtype">int</span> aa_index) ;
|
|
<a name="l00099"></a>00099 <span class="keywordtype">int</span> <a class="code" href="aa_8c.html#6b1242df111921659782dc1285ac101a">get_polarity_from_idx</a>(<span class="keywordtype">int</span> aa_index) ;
|
|
<a name="l00100"></a>00100 <span class="keywordtype">int</span> <a class="code" href="aa_8c.html#f0ed06f72d932ca26aebc22b8e3dec46">get_func_grp_from_idx</a>(<span class="keywordtype">int</span> aa_index) ;
|
|
<a name="l00101"></a>00101
|
|
<a name="l00102"></a>00102 <span class="preprocessor">#endif</span>
|
|
</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>
|