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<h1>aa.c</h1><a href="aa_8c.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="preprocessor">#include "../headers/aa.h"</span>
<a name="l00002"></a>00002
<a name="l00003"></a>00003 <span class="comment">/*</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">## GENERAL INFORMATION</span>
<a name="l00006"></a>00006 <span class="comment">##</span>
<a name="l00007"></a>00007 <span class="comment">## FILE aa.c</span>
<a name="l00008"></a>00008 <span class="comment">## AUTHORS P. Schmidtke and V. Le Guilloux</span>
<a name="l00009"></a>00009 <span class="comment">## LAST MODIFIED 28-11-08 (v)</span>
<a name="l00010"></a>00010 <span class="comment">##</span>
<a name="l00011"></a>00011 <span class="comment">## SPECIFICATIONS</span>
<a name="l00012"></a>00012 <span class="comment">##</span>
<a name="l00013"></a>00013 <span class="comment">## This file contains severals functions that allow one to</span>
<a name="l00014"></a>00014 <span class="comment">## deal with amino-acids and their properties. Properties</span>
<a name="l00015"></a>00015 <span class="comment">## should be stored in the static variable ST_aa, that</span>
<a name="l00016"></a>00016 <span class="comment">## contains for each amino-acids, several properties</span>
<a name="l00017"></a>00017 <span class="comment">## stored in a specific structure.</span>
<a name="l00018"></a>00018 <span class="comment">##</span>
<a name="l00019"></a>00019 <span class="comment">## MODIFICATIONS HISTORY</span>
<a name="l00020"></a>00020 <span class="comment">##</span>
<a name="l00021"></a>00021 <span class="comment">## 28-11-08 (v) Comments UTD</span>
<a name="l00022"></a>00022 <span class="comment">## 20-11-08 (v) Added molecular weight</span>
<a name="l00023"></a>00023 <span class="comment">## 01-04-08 (v) Added comments and creation of history</span>
<a name="l00024"></a>00024 <span class="comment">## 01-01-08 (vp) Created (random date...)</span>
<a name="l00025"></a>00025 <span class="comment">## </span>
<a name="l00026"></a>00026 <span class="comment">## TODO or SUGGESTIONS</span>
<a name="l00027"></a>00027 <span class="comment">##</span>
<a name="l00028"></a>00028 <span class="comment">## (v) Get more accurate descriptors, namely for the volume and charge *score*</span>
<a name="l00029"></a>00029 <span class="comment">## (v) Check and update if necessary comments of each function!!</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
<a name="l00034"></a>00034 <span class="comment">/*</span>
<a name="l00035"></a>00035 <span class="comment"> COPYRIGHT DISCLAIMER</span>
<a name="l00036"></a>00036 <span class="comment"></span>
<a name="l00037"></a>00037 <span class="comment"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
<a name="l00038"></a>00038 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
<a name="l00039"></a>00039 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
<a name="l00040"></a>00040 <span class="comment"> Schmidtke.</span>
<a name="l00041"></a>00041 <span class="comment"></span>
<a name="l00042"></a>00042 <span class="comment"> Vincent Le Guilloux 28 November 2008</span>
<a name="l00043"></a>00043 <span class="comment"> Peter Schmidtke 28 November 2008</span>
<a name="l00044"></a>00044 <span class="comment"> Pierre Tuffery 28 November 2008</span>
<a name="l00045"></a>00045 <span class="comment"></span>
<a name="l00046"></a>00046 <span class="comment"> GNU GPL</span>
<a name="l00047"></a>00047 <span class="comment"></span>
<a name="l00048"></a>00048 <span class="comment"> This file is part of the fpocket package.</span>
<a name="l00049"></a>00049 <span class="comment"></span>
<a name="l00050"></a>00050 <span class="comment"> fpocket is free software: you can redistribute it and/or modify</span>
<a name="l00051"></a>00051 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
<a name="l00052"></a>00052 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
<a name="l00053"></a>00053 <span class="comment"> (at your option) any later version.</span>
<a name="l00054"></a>00054 <span class="comment"></span>
<a name="l00055"></a>00055 <span class="comment"> fpocket is distributed in the hope that it will be useful,</span>
<a name="l00056"></a>00056 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00057"></a>00057 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00058"></a>00058 <span class="comment"> GNU General Public License for more details.</span>
<a name="l00059"></a>00059 <span class="comment"></span>
<a name="l00060"></a>00060 <span class="comment"> You should have received a copy of the GNU General Public License</span>
<a name="l00061"></a>00061 <span class="comment"> along with fpocket. If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
<a name="l00062"></a>00062 <span class="comment"></span>
<a name="l00063"></a>00063 <span class="comment">**/</span>
<a name="l00064"></a>00064 <span class="comment"></span>
<a name="l00065"></a>00065 <span class="comment">/**</span>
<a name="l00066"></a>00066 <span class="comment"> Several amino-acid properties, taken from:</span>
<a name="l00067"></a>00067 <span class="comment"> http://www.info.univ-angers.fr/~gh/Idas/proprietes.htm</span>
<a name="l00068"></a>00068 <span class="comment"></span>
<a name="l00069"></a>00069 <span class="comment"> Hydrophobicity taken from :</span>
<a name="l00070"></a>00070 <span class="comment"> http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/PolyAmino_Acids/Reference_Chart.html</span>
<a name="l00071"></a>00071 <span class="comment"></span>
<a name="l00072"></a>00072 <span class="comment"> Monera &amp; al. Journal of Protein Science 1, 319-329 (1995)</span>
<a name="l00073"></a>00073 <span class="comment"></span>
<a name="l00074"></a>00074 <span class="comment"> Molecular weight taken from:</span>
<a name="l00075"></a>00075 <span class="comment"> http://www.expasy.ch/tools/pscale/Molecularweight.html</span>
<a name="l00076"></a>00076 <span class="comment"> </span>
<a name="l00077"></a>00077 <span class="comment">*/</span>
<a name="l00078"></a><a class="code" href="aa_8c.html#c01f5927476c0edf657f6d3400cc5abf">00078</a> <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="structs__amino__a.html">s_amino_a</a> <a class="code" href="aa_8c.html#c01f5927476c0edf657f6d3400cc5abf">ST_aa</a>[20] =
<a name="l00079"></a>00079 {
<a name="l00080"></a>00080 <span class="comment">// Name Code Molecular weight VolumeScore Hydrophobicity Charge Polatity func_grp</span>
<a name="l00081"></a>00081 { <span class="stringliteral">"ALA"</span>, <span class="charliteral">'A'</span>, 89.0, 2.0, 41.0, 0, 0, 2 },
<a name="l00082"></a>00082 { <span class="stringliteral">"ARG"</span>, <span class="charliteral">'R'</span>, 174.0, 7.0, -14.0, 1, 1, 5 },
<a name="l00083"></a>00083 { <span class="stringliteral">"ASN"</span>, <span class="charliteral">'N'</span>, 132.0, 3.0, -28.0, 0, 1, 3 },
<a name="l00084"></a>00084 { <span class="stringliteral">"ASP"</span>, <span class="charliteral">'D'</span>, 133.0, 3.0, -55.0, -1, 1, 3 },
<a name="l00085"></a>00085 { <span class="stringliteral">"CYS"</span>, <span class="charliteral">'C'</span>, 121.0, 3.0, 49.0, 0, 0, 6 },
<a name="l00086"></a>00086 { <span class="stringliteral">"GLN"</span>, <span class="charliteral">'Q'</span>, 146.0, 4.0, -10.0, 0, 1, 3 },
<a name="l00087"></a>00087 { <span class="stringliteral">"GLU"</span>, <span class="charliteral">'E'</span>, 147.0, 4.0, -31.0, -1, 1, 3 },
<a name="l00088"></a>00088 { <span class="stringliteral">"GLY"</span>, <span class="charliteral">'G'</span>, 75.0, 1.0, 0.0, 0, 0, 2 },
<a name="l00089"></a>00089 { <span class="stringliteral">"HIS"</span>, <span class="charliteral">'H'</span>, 155.0, 4.0, 8.0, 1, 1, 1 },
<a name="l00090"></a>00090 { <span class="stringliteral">"ILE"</span>, <span class="charliteral">'I'</span>, 131.0, 5.0, 99.0, 0, 0, 2 },
<a name="l00091"></a>00091 { <span class="stringliteral">"LEU"</span>, <span class="charliteral">'L'</span>, 131.0, 5.0, 97.0, 0, 0, 2 },
<a name="l00092"></a>00092 { <span class="stringliteral">"LYS"</span>, <span class="charliteral">'K'</span>, 146.0, 6.0, -23.0, 1, 1, 5 },
<a name="l00093"></a>00093 { <span class="stringliteral">"MET"</span>, <span class="charliteral">'M'</span>, 149.0, 5.0, 74.0, 0, 0, 5 },
<a name="l00094"></a>00094 { <span class="stringliteral">"PHE"</span>, <span class="charliteral">'F'</span>, 165.0, 6.0, 100.0, 0, 0, 1 },
<a name="l00095"></a>00095 { <span class="stringliteral">"PRO"</span>, <span class="charliteral">'P'</span>, 115.0, 3.0, -46.0, 0, 0, 2 },
<a name="l00096"></a>00096 { <span class="stringliteral">"SER"</span>, <span class="charliteral">'S'</span>, 105.0, 2.0, -5.0, 0, 1, 4 },
<a name="l00097"></a>00097 { <span class="stringliteral">"THR"</span>, <span class="charliteral">'T'</span>, 119.0, 3.0, 13.0, 0, 1, 4 },
<a name="l00098"></a>00098 { <span class="stringliteral">"TRP"</span>, <span class="charliteral">'W'</span>, 204.0, 8.0, 97.0, 0, 1, 1 },
<a name="l00099"></a>00099 { <span class="stringliteral">"TYR"</span>, <span class="charliteral">'Y'</span>, 181.0, 7.0, 63.0, 0, 1, 1 },
<a name="l00100"></a>00100 { <span class="stringliteral">"VAL"</span>, <span class="charliteral">'V'</span>, 117.0, 4.0, 76.0, 0, 0, 2 }
<a name="l00101"></a>00101 } ;
<a name="l00102"></a>00102 <span class="comment"></span>
<a name="l00103"></a>00103 <span class="comment">/**</span>
<a name="l00104"></a>00104 <span class="comment"> ## FUNCTION: </span>
<a name="l00105"></a>00105 <span class="comment"> get_aa_name3</span>
<a name="l00106"></a>00106 <span class="comment"> </span>
<a name="l00107"></a>00107 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00108"></a>00108 <span class="comment"> Return the name of AA given in argument (index in the static table)</span>
<a name="l00109"></a>00109 <span class="comment"> </span>
<a name="l00110"></a>00110 <span class="comment"> ## PARAMETRES:</span>
<a name="l00111"></a>00111 <span class="comment"> @ const int index: Index of the AA in the tab</span>
<a name="l00112"></a>00112 <span class="comment"> </span>
<a name="l00113"></a>00113 <span class="comment"> ## RETURN:</span>
<a name="l00114"></a>00114 <span class="comment"> char *: Name if index is valid, NULL if not.</span>
<a name="l00115"></a>00115 <span class="comment"> </span>
<a name="l00116"></a>00116 <span class="comment">*/</span>
<a name="l00117"></a><a class="code" href="aa_8h.html#f071a7d6353978202a07fd66f2ff68d8">00117</a> <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="l00118"></a>00118 {
<a name="l00119"></a>00119 <span class="keywordflow">if</span>(index &lt; M_NB_AA &amp;&amp; index &gt;= 0) {
<a name="l00120"></a>00120 <span class="keywordflow">return</span> (<span class="keywordtype">char</span>*)ST_aa[index].<a class="code" href="structs__amino__a.html#ea8b997108e6468326b00183bd6eb0c7">name3</a> ;
<a name="l00121"></a>00121 }
<a name="l00122"></a>00122 <span class="keywordflow">return</span> NULL ;
<a name="l00123"></a>00123 }
<a name="l00124"></a>00124 <span class="comment"></span>
<a name="l00125"></a>00125 <span class="comment">/**</span>
<a name="l00126"></a>00126 <span class="comment"> ## FUNCTION: </span>
<a name="l00127"></a>00127 <span class="comment"> get_aa_index</span>
<a name="l00128"></a>00128 <span class="comment"> </span>
<a name="l00129"></a>00129 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00130"></a>00130 <span class="comment"> Return the index of AA given in argument (3letter code representation) in the</span>
<a name="l00131"></a>00131 <span class="comment"> static AA tab.</span>
<a name="l00132"></a>00132 <span class="comment"> </span>
<a name="l00133"></a>00133 <span class="comment"> ## PARAMETRES:</span>
<a name="l00134"></a>00134 <span class="comment"> @ const char *name: Amno acid name (3 letter code representation)</span>
<a name="l00135"></a>00135 <span class="comment"> </span>
<a name="l00136"></a>00136 <span class="comment"> ## RETURN:</span>
<a name="l00137"></a>00137 <span class="comment"> int: index of the given amino acid, -1 if not found in the tab</span>
<a name="l00138"></a>00138 <span class="comment"> </span>
<a name="l00139"></a>00139 <span class="comment">*/</span>
<a name="l00140"></a><a class="code" href="aa_8h.html#f10857d7d319ed08d91b2a91e8dfa73f">00140</a> <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="l00141"></a>00141 {
<a name="l00142"></a>00142 <span class="keywordtype">int</span> i,
<a name="l00143"></a>00143 aa_index = -1 ;
<a name="l00144"></a>00144
<a name="l00145"></a>00145 <span class="keywordflow">for</span>(i = 0 ; i &lt; <a class="code" href="aa_8h.html#473a70533737641d73e56c3a2c4292ff">M_NB_AA</a> ; i++) {
<a name="l00146"></a>00146 <span class="keywordflow">if</span>(toupper(name[0]) == ST_aa[i].name3[0] &amp;&amp; toupper(name[1]) == ST_aa[i].name3[1]
<a name="l00147"></a>00147 &amp;&amp; toupper(name[2]) == ST_aa[i].name3[2] ) {
<a name="l00148"></a>00148 aa_index = i ;
<a name="l00149"></a>00149 break ;
<a name="l00150"></a>00150 }
<a name="l00151"></a>00151 }
<a name="l00152"></a>00152
<a name="l00153"></a>00153 <span class="keywordflow">return</span> aa_index ;
<a name="l00154"></a>00154 }
<a name="l00155"></a>00155
<a name="l00156"></a>00156 <span class="comment">/*********** Getting information from an AA name in the static tab ***********/</span>
<a name="l00157"></a>00157
<a name="l00158"></a>00158 <span class="comment"></span>
<a name="l00159"></a>00159 <span class="comment">/**</span>
<a name="l00160"></a>00160 <span class="comment"> ## FUNCTION: </span>
<a name="l00161"></a>00161 <span class="comment"> get_aa_mw</span>
<a name="l00162"></a>00162 <span class="comment"> </span>
<a name="l00163"></a>00163 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00164"></a>00164 <span class="comment"> Return the molecular weight of AA given in argument</span>
<a name="l00165"></a>00165 <span class="comment"> </span>
<a name="l00166"></a>00166 <span class="comment"> ## PARAMETRES:</span>
<a name="l00167"></a>00167 <span class="comment"> @ const int index: Index of the AA in the tab</span>
<a name="l00168"></a>00168 <span class="comment"> </span>
<a name="l00169"></a>00169 <span class="comment"> ## RETURN:</span>
<a name="l00170"></a>00170 <span class="comment"> float: Molecular weight if the index is valid, NULL if not.</span>
<a name="l00171"></a>00171 <span class="comment"> </span>
<a name="l00172"></a>00172 <span class="comment">*/</span>
<a name="l00173"></a><a class="code" href="aa_8h.html#c8205bded5bf0a2077fc2aa928435fb0">00173</a> <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="l00174"></a>00174 {
<a name="l00175"></a>00175 <span class="keywordtype">int</span> aa_index = <a class="code" href="aa_8c.html#f10857d7d319ed08d91b2a91e8dfa73f">get_aa_index</a>(name) ;
<a name="l00176"></a>00176
<a name="l00177"></a>00177 <span class="keywordflow">if</span>(aa_index != -1) {
<a name="l00178"></a>00178 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#0c82f3a8524b934028b8289a41c8ee91">mw</a> ;
<a name="l00179"></a>00179 }<span class="comment">/*</span>
<a name="l00180"></a>00180 <span class="comment"> else {</span>
<a name="l00181"></a>00181 <span class="comment"> fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);</span>
<a name="l00182"></a>00182 <span class="comment"> }*/</span>
<a name="l00183"></a>00183
<a name="l00184"></a>00184 <span class="keywordflow">return</span> -1.0 ;
<a name="l00185"></a>00185 }
<a name="l00186"></a>00186 <span class="comment"></span>
<a name="l00187"></a>00187 <span class="comment">/**</span>
<a name="l00188"></a>00188 <span class="comment"> ## FUNCTION: </span>
<a name="l00189"></a>00189 <span class="comment"> get_aa_volume_score</span>
<a name="l00190"></a>00190 <span class="comment"> </span>
<a name="l00191"></a>00191 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00192"></a>00192 <span class="comment"> Return the volume score of given amino acid (very approximative...)</span>
<a name="l00193"></a>00193 <span class="comment"> </span>
<a name="l00194"></a>00194 <span class="comment"> ## PARAMETRES:</span>
<a name="l00195"></a>00195 <span class="comment"> @ const char *name: Amno acid name (3 letter code representation)</span>
<a name="l00196"></a>00196 <span class="comment"> </span>
<a name="l00197"></a>00197 <span class="comment"> ## RETURN:</span>
<a name="l00198"></a>00198 <span class="comment"> float: volume score, -1 if aa not found in the tab</span>
<a name="l00199"></a>00199 <span class="comment"> </span>
<a name="l00200"></a>00200 <span class="comment">*/</span>
<a name="l00201"></a><a class="code" href="aa_8h.html#e8721edaf9b5027df8fcb9932497568c">00201</a> <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="l00202"></a>00202 {
<a name="l00203"></a>00203 <span class="keywordtype">int</span> aa_index = <a class="code" href="aa_8c.html#f10857d7d319ed08d91b2a91e8dfa73f">get_aa_index</a>(name) ;
<a name="l00204"></a>00204
<a name="l00205"></a>00205 <span class="keywordflow">if</span>(aa_index != -1) {
<a name="l00206"></a>00206 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#4ddae5fde18856a3dab901009673d4f6">volume</a> ;
<a name="l00207"></a>00207 }<span class="comment">/*</span>
<a name="l00208"></a>00208 <span class="comment"> else {</span>
<a name="l00209"></a>00209 <span class="comment"> fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);</span>
<a name="l00210"></a>00210 <span class="comment"> }*/</span>
<a name="l00211"></a>00211
<a name="l00212"></a>00212 <span class="keywordflow">return</span> -1.0 ;
<a name="l00213"></a>00213 }
<a name="l00214"></a>00214 <span class="comment"></span>
<a name="l00215"></a>00215 <span class="comment">/**</span>
<a name="l00216"></a>00216 <span class="comment"> ## FUNCTION: </span>
<a name="l00217"></a>00217 <span class="comment"> get_aa_hydrophobicity_score</span>
<a name="l00218"></a>00218 <span class="comment"> </span>
<a name="l00219"></a>00219 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00220"></a>00220 <span class="comment"> Return the hydrophobicity score of given amino acid</span>
<a name="l00221"></a>00221 <span class="comment"> </span>
<a name="l00222"></a>00222 <span class="comment"> ## PARAMETRES:</span>
<a name="l00223"></a>00223 <span class="comment"> @ const char *name: Amno acid name (3 letter code representation)</span>
<a name="l00224"></a>00224 <span class="comment"> </span>
<a name="l00225"></a>00225 <span class="comment"> ## RETURN:</span>
<a name="l00226"></a>00226 <span class="comment"> float: hydrophobicity score, -1 if aa not found in the tab</span>
<a name="l00227"></a>00227 <span class="comment"> </span>
<a name="l00228"></a>00228 <span class="comment">*/</span>
<a name="l00229"></a><a class="code" href="aa_8h.html#acfe4be9ac7a7111d65a1dba7b7a11b9">00229</a> <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="l00230"></a>00230 {
<a name="l00231"></a>00231 <span class="keywordtype">int</span> aa_index = <a class="code" href="aa_8c.html#f10857d7d319ed08d91b2a91e8dfa73f">get_aa_index</a>(name) ;
<a name="l00232"></a>00232
<a name="l00233"></a>00233 <span class="keywordflow">if</span>(aa_index != -1) {
<a name="l00234"></a>00234 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#8c7db917f840ebd0dad9a378a4be4b92">hydrophobicity</a> ;
<a name="l00235"></a>00235 }<span class="comment">/*</span>
<a name="l00236"></a>00236 <span class="comment"> else {</span>
<a name="l00237"></a>00237 <span class="comment"> fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);</span>
<a name="l00238"></a>00238 <span class="comment"> }*/</span>
<a name="l00239"></a>00239
<a name="l00240"></a>00240 <span class="keywordflow">return</span> -1.0 ;
<a name="l00241"></a>00241 }
<a name="l00242"></a>00242 <span class="comment"></span>
<a name="l00243"></a>00243 <span class="comment">/**</span>
<a name="l00244"></a>00244 <span class="comment"> ## FUNCTION: </span>
<a name="l00245"></a>00245 <span class="comment"> get_aa_charge</span>
<a name="l00246"></a>00246 <span class="comment"> </span>
<a name="l00247"></a>00247 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00248"></a>00248 <span class="comment"> Return the charge score of given amino acid</span>
<a name="l00249"></a>00249 <span class="comment"> </span>
<a name="l00250"></a>00250 <span class="comment"> ## PARAMETRES:</span>
<a name="l00251"></a>00251 <span class="comment"> const char *name: Amno acid name (3 letter code representation)</span>
<a name="l00252"></a>00252 <span class="comment"> </span>
<a name="l00253"></a>00253 <span class="comment"> ## RETURN:</span>
<a name="l00254"></a>00254 <span class="comment"> charge (positiv, negativ, neutral, see header for more details), 0 if aa </span>
<a name="l00255"></a>00255 <span class="comment"> not found in the tab</span>
<a name="l00256"></a>00256 <span class="comment"> </span>
<a name="l00257"></a>00257 <span class="comment">*/</span>
<a name="l00258"></a><a class="code" href="aa_8h.html#adf25cee3c6ea3b956dbe776356b198d">00258</a> <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="l00259"></a>00259 {
<a name="l00260"></a>00260 <span class="keywordtype">int</span> aa_index = <a class="code" href="aa_8c.html#f10857d7d319ed08d91b2a91e8dfa73f">get_aa_index</a>(name) ;
<a name="l00261"></a>00261
<a name="l00262"></a>00262 <span class="keywordflow">if</span>(aa_index != -1) {
<a name="l00263"></a>00263 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#0f912bcd04ae9f99a8f3a45e736d9d16">charge</a> ;
<a name="l00264"></a>00264 }<span class="comment">/*</span>
<a name="l00265"></a>00265 <span class="comment"> else {</span>
<a name="l00266"></a>00266 <span class="comment"> fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);</span>
<a name="l00267"></a>00267 <span class="comment"> }*/</span>
<a name="l00268"></a>00268
<a name="l00269"></a>00269 <span class="keywordflow">return</span> 0 ;
<a name="l00270"></a>00270 }
<a name="l00271"></a>00271 <span class="comment"></span>
<a name="l00272"></a>00272 <span class="comment">/**</span>
<a name="l00273"></a>00273 <span class="comment"> ## FUNCTION: </span>
<a name="l00274"></a>00274 <span class="comment"> get_aa_polarity</span>
<a name="l00275"></a>00275 <span class="comment"> </span>
<a name="l00276"></a>00276 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00277"></a>00277 <span class="comment"> Return the polarity score of given amino acid</span>
<a name="l00278"></a>00278 <span class="comment"> </span>
<a name="l00279"></a>00279 <span class="comment"> ## PARAMETRES:</span>
<a name="l00280"></a>00280 <span class="comment"> @ const char *name: Amno acid name (3 letter code representation)</span>
<a name="l00281"></a>00281 <span class="comment"> </span>
<a name="l00282"></a>00282 <span class="comment"> ## RETURN:</span>
<a name="l00283"></a>00283 <span class="comment"> int polarity (polar, apolar), 0 if aa not found in the tab</span>
<a name="l00284"></a>00284 <span class="comment"> </span>
<a name="l00285"></a>00285 <span class="comment">*/</span>
<a name="l00286"></a><a class="code" href="aa_8h.html#a12288b5ca620ff78a9a4a5b48d4abb0">00286</a> <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="l00287"></a>00287 {
<a name="l00288"></a>00288 <span class="keywordtype">int</span> aa_index = <a class="code" href="aa_8c.html#f10857d7d319ed08d91b2a91e8dfa73f">get_aa_index</a>(name) ;
<a name="l00289"></a>00289
<a name="l00290"></a>00290 <span class="keywordflow">if</span>(aa_index != -1) {
<a name="l00291"></a>00291 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#e6101783dcf52f5de7ed94729c55096b">polarity</a> ;
<a name="l00292"></a>00292 }<span class="comment">/*</span>
<a name="l00293"></a>00293 <span class="comment"> else {</span>
<a name="l00294"></a>00294 <span class="comment"> fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);</span>
<a name="l00295"></a>00295 <span class="comment"> }*/</span>
<a name="l00296"></a>00296
<a name="l00297"></a>00297 <span class="keywordflow">return</span> -1 ;
<a name="l00298"></a>00298 }
<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"> ## FUNCTION: </span>
<a name="l00302"></a>00302 <span class="comment"> get_func_grp_from_idx</span>
<a name="l00303"></a>00303 <span class="comment"> </span>
<a name="l00304"></a>00304 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00305"></a>00305 <span class="comment"> Return the functional group type of the given amino acid</span>
<a name="l00306"></a>00306 <span class="comment"> </span>
<a name="l00307"></a>00307 <span class="comment"> ## PARAMETRES:</span>
<a name="l00308"></a>00308 <span class="comment"> @ const char *name: Amno acid name (3 letter code representation)</span>
<a name="l00309"></a>00309 <span class="comment"> </span>
<a name="l00310"></a>00310 <span class="comment"> ## RETURN:</span>
<a name="l00311"></a>00311 <span class="comment"> int: functional group id</span>
<a name="l00312"></a>00312 <span class="comment"> </span>
<a name="l00313"></a>00313 <span class="comment">*/</span>
<a name="l00314"></a><a class="code" href="aa_8h.html#365325c4571c0c23235f7e58f3cd9f5d">00314</a> <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="l00315"></a>00315 {
<a name="l00316"></a>00316 <span class="keywordtype">int</span> aa_index = <a class="code" href="aa_8c.html#f10857d7d319ed08d91b2a91e8dfa73f">get_aa_index</a>(name) ;
<a name="l00317"></a>00317
<a name="l00318"></a>00318 <span class="keywordflow">if</span>(aa_index != -1) {
<a name="l00319"></a>00319 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#1e4bec2abdf9140e3490fac980a5702c">func_grp</a> ;
<a name="l00320"></a>00320 }<span class="comment">/*</span>
<a name="l00321"></a>00321 <span class="comment"> else {</span>
<a name="l00322"></a>00322 <span class="comment"> fprintf(stderr, "! Amino acid '%s' could not be found in property table...\n", name);</span>
<a name="l00323"></a>00323 <span class="comment"> }*/</span>
<a name="l00324"></a>00324
<a name="l00325"></a>00325 <span class="keywordflow">return</span> -1 ;
<a name="l00326"></a>00326 }
<a name="l00327"></a>00327
<a name="l00328"></a>00328
<a name="l00329"></a>00329 <span class="comment">/************** Getting information from an AA index in the static tab **************/</span>
<a name="l00330"></a>00330
<a name="l00331"></a>00331 <span class="comment"></span>
<a name="l00332"></a>00332 <span class="comment">/**</span>
<a name="l00333"></a>00333 <span class="comment"> ## FUNCTION: </span>
<a name="l00334"></a>00334 <span class="comment"> get_volume_score_from_idx</span>
<a name="l00335"></a>00335 <span class="comment"> </span>
<a name="l00336"></a>00336 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00337"></a>00337 <span class="comment"> Return the volume score of given amino acid</span>
<a name="l00338"></a>00338 <span class="comment"> </span>
<a name="l00339"></a>00339 <span class="comment"> ## PARAMETRES:</span>
<a name="l00340"></a>00340 <span class="comment"> @ int aa_index: Index of the amino acid in the tab</span>
<a name="l00341"></a>00341 <span class="comment"> </span>
<a name="l00342"></a>00342 <span class="comment"> ## RETURN:</span>
<a name="l00343"></a>00343 <span class="comment"> float: volume score, -1 if aa not found in the tab</span>
<a name="l00344"></a>00344 <span class="comment"> </span>
<a name="l00345"></a>00345 <span class="comment">*/</span>
<a name="l00346"></a><a class="code" href="aa_8h.html#ce98533a9358aec6dcc325fe567c26fe">00346</a> <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="l00347"></a>00347 {
<a name="l00348"></a>00348 <span class="keywordflow">if</span>(aa_index &lt; M_NB_AA &amp;&amp; aa_index &gt;= 0){
<a name="l00349"></a>00349 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#4ddae5fde18856a3dab901009673d4f6">volume</a> ;
<a name="l00350"></a>00350 }<span class="comment">/*</span>
<a name="l00351"></a>00351 <span class="comment"> else {</span>
<a name="l00352"></a>00352 <span class="comment"> fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);</span>
<a name="l00353"></a>00353 <span class="comment"> }*/</span>
<a name="l00354"></a>00354
<a name="l00355"></a>00355 <span class="keywordflow">return</span> -1.0 ;
<a name="l00356"></a>00356 }
<a name="l00357"></a>00357 <span class="comment"></span>
<a name="l00358"></a>00358 <span class="comment">/**</span>
<a name="l00359"></a>00359 <span class="comment"> ## FUNCTION: </span>
<a name="l00360"></a>00360 <span class="comment"> get_hydrophobicity_score_from_idx</span>
<a name="l00361"></a>00361 <span class="comment"> </span>
<a name="l00362"></a>00362 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00363"></a>00363 <span class="comment"> Return the hydrophobicity score of given amino acid</span>
<a name="l00364"></a>00364 <span class="comment"> </span>
<a name="l00365"></a>00365 <span class="comment"> ## PARAMETRES:</span>
<a name="l00366"></a>00366 <span class="comment"> @ int aa_index: Index of the amino acid in the tab</span>
<a name="l00367"></a>00367 <span class="comment"> </span>
<a name="l00368"></a>00368 <span class="comment"> ## RETURN:</span>
<a name="l00369"></a>00369 <span class="comment"> float hydrophobicity score, -1 if aa not found in the tab</span>
<a name="l00370"></a>00370 <span class="comment"> </span>
<a name="l00371"></a>00371 <span class="comment">*/</span>
<a name="l00372"></a><a class="code" href="aa_8h.html#3988fc0beb2f06dee9ebb04ef491f9d7">00372</a> <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="l00373"></a>00373 {
<a name="l00374"></a>00374 <span class="keywordflow">if</span>(aa_index &lt; M_NB_AA &amp;&amp; aa_index &gt;= 0) {
<a name="l00375"></a>00375 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#8c7db917f840ebd0dad9a378a4be4b92">hydrophobicity</a> ;
<a name="l00376"></a>00376 }<span class="comment">/*</span>
<a name="l00377"></a>00377 <span class="comment"> else {</span>
<a name="l00378"></a>00378 <span class="comment"> fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);</span>
<a name="l00379"></a>00379 <span class="comment"> }*/</span>
<a name="l00380"></a>00380
<a name="l00381"></a>00381 <span class="keywordflow">return</span> -1.0 ;
<a name="l00382"></a>00382 }
<a name="l00383"></a>00383 <span class="comment"></span>
<a name="l00384"></a>00384 <span class="comment">/**</span>
<a name="l00385"></a>00385 <span class="comment"> ## FUNCTION: </span>
<a name="l00386"></a>00386 <span class="comment"> get_charge_from_idx</span>
<a name="l00387"></a>00387 <span class="comment"> </span>
<a name="l00388"></a>00388 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00389"></a>00389 <span class="comment"> Return the charge score of given amino acid</span>
<a name="l00390"></a>00390 <span class="comment"> </span>
<a name="l00391"></a>00391 <span class="comment"> ## PARAMETRES:</span>
<a name="l00392"></a>00392 <span class="comment"> @ int aa_index: Index of the amino acid in the tab</span>
<a name="l00393"></a>00393 <span class="comment"> </span>
<a name="l00394"></a>00394 <span class="comment"> ## RETURN:</span>
<a name="l00395"></a>00395 <span class="comment"> int charge (positiv, negativ, neutral, see header for more details), 0 if aa </span>
<a name="l00396"></a>00396 <span class="comment"> not found in the tab</span>
<a name="l00397"></a>00397 <span class="comment"> </span>
<a name="l00398"></a>00398 <span class="comment">*/</span>
<a name="l00399"></a><a class="code" href="aa_8h.html#641c90c89a2f096c09ee972cf05d8b71">00399</a> <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="l00400"></a>00400 {
<a name="l00401"></a>00401 <span class="keywordflow">if</span>(aa_index &lt; M_NB_AA &amp;&amp; aa_index &gt;= 0){
<a name="l00402"></a>00402 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#0f912bcd04ae9f99a8f3a45e736d9d16">charge</a> ;
<a name="l00403"></a>00403 }<span class="comment">/*</span>
<a name="l00404"></a>00404 <span class="comment"> else {</span>
<a name="l00405"></a>00405 <span class="comment"> fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);</span>
<a name="l00406"></a>00406 <span class="comment"> }*/</span>
<a name="l00407"></a>00407
<a name="l00408"></a>00408 <span class="keywordflow">return</span> 0 ;
<a name="l00409"></a>00409 }
<a name="l00410"></a>00410 <span class="comment"></span>
<a name="l00411"></a>00411 <span class="comment">/**</span>
<a name="l00412"></a>00412 <span class="comment"> ## FUNCTION: </span>
<a name="l00413"></a>00413 <span class="comment"> get_polarity_from_idx</span>
<a name="l00414"></a>00414 <span class="comment"> </span>
<a name="l00415"></a>00415 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00416"></a>00416 <span class="comment"> Return the polarity score of given amino acid</span>
<a name="l00417"></a>00417 <span class="comment"> </span>
<a name="l00418"></a>00418 <span class="comment"> ## PARAMETRES:</span>
<a name="l00419"></a>00419 <span class="comment"> @ int aa_index: Index of the amino acid in the tab</span>
<a name="l00420"></a>00420 <span class="comment"> </span>
<a name="l00421"></a>00421 <span class="comment"> ## RETURN:</span>
<a name="l00422"></a>00422 <span class="comment"> int: polarity (polar, apolar), -1 if aa not found in the tab</span>
<a name="l00423"></a>00423 <span class="comment"> </span>
<a name="l00424"></a>00424 <span class="comment">*/</span>
<a name="l00425"></a><a class="code" href="aa_8h.html#6b1242df111921659782dc1285ac101a">00425</a> <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="l00426"></a>00426 {
<a name="l00427"></a>00427 <span class="keywordflow">if</span>(aa_index &lt; M_NB_AA &amp;&amp; aa_index &gt;= 0) {
<a name="l00428"></a>00428 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#e6101783dcf52f5de7ed94729c55096b">polarity</a> ;
<a name="l00429"></a>00429 }<span class="comment">/*</span>
<a name="l00430"></a>00430 <span class="comment"> else {</span>
<a name="l00431"></a>00431 <span class="comment"> fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);</span>
<a name="l00432"></a>00432 <span class="comment"> }*/</span>
<a name="l00433"></a>00433
<a name="l00434"></a>00434 <span class="keywordflow">return</span> -1 ;
<a name="l00435"></a>00435 }
<a name="l00436"></a>00436 <span class="comment"></span>
<a name="l00437"></a>00437 <span class="comment">/**</span>
<a name="l00438"></a>00438 <span class="comment"> ## FUNCTION: </span>
<a name="l00439"></a>00439 <span class="comment"> get_func_grp_from_idx</span>
<a name="l00440"></a>00440 <span class="comment"> </span>
<a name="l00441"></a>00441 <span class="comment"> ## SPECIFICATION: </span>
<a name="l00442"></a>00442 <span class="comment"> Return the functional group type of the given amino acid</span>
<a name="l00443"></a>00443 <span class="comment"> </span>
<a name="l00444"></a>00444 <span class="comment"> ## PARAMETRES:</span>
<a name="l00445"></a>00445 <span class="comment"> @ int aa_index: Index of the amino acid in the tab</span>
<a name="l00446"></a>00446 <span class="comment"> </span>
<a name="l00447"></a>00447 <span class="comment"> ## RETURN:</span>
<a name="l00448"></a>00448 <span class="comment"> int: functional group id</span>
<a name="l00449"></a>00449 <span class="comment"> </span>
<a name="l00450"></a>00450 <span class="comment">*/</span>
<a name="l00451"></a><a class="code" href="aa_8h.html#f0ed06f72d932ca26aebc22b8e3dec46">00451</a> <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="l00452"></a>00452 {
<a name="l00453"></a>00453 <span class="keywordflow">if</span>(aa_index &lt; M_NB_AA &amp;&amp; aa_index &gt;= 0) {
<a name="l00454"></a>00454 <span class="keywordflow">return</span> ST_aa[aa_index].<a class="code" href="structs__amino__a.html#1e4bec2abdf9140e3490fac980a5702c">func_grp</a> ;
<a name="l00455"></a>00455 }<span class="comment">/*</span>
<a name="l00456"></a>00456 <span class="comment"> else {</span>
<a name="l00457"></a>00457 <span class="comment"> fprintf(stderr, "! Amino acid %d could not be found in property table...\n", aa_index);</span>
<a name="l00458"></a>00458 <span class="comment"> }*/</span>
<a name="l00459"></a>00459
<a name="l00460"></a>00460 <span class="keywordflow">return</span> -1 ;
<a name="l00461"></a>00461 }
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