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<h1>descriptors.c</h1><a href="descriptors_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/descriptors.h"</span>
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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"></span>
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<a name="l00005"></a>00005 <span class="comment">## GENERAL INFORMATION</span>
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<a name="l00006"></a>00006 <span class="comment">##</span>
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<a name="l00007"></a>00007 <span class="comment">## FILE descriptors.c</span>
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<a name="l00008"></a>00008 <span class="comment">## AUTHORS P. Schmidtke and V. Le Guilloux</span>
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<a name="l00009"></a>00009 <span class="comment">## LAST MODIFIED 01-04-08</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">## SPECIFICATIONS</span>
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<a name="l00012"></a>00012 <span class="comment">##</span>
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<a name="l00013"></a>00013 <span class="comment">## This file is used to calculate descriptors using a set of atoms</span>
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<a name="l00014"></a>00014 <span class="comment">## and/or alpha spheres, using structures defined in atoms.c and</span>
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<a name="l00015"></a>00015 <span class="comment">## voronoi/voronoi_lst.c.</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">## </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">## MODIFICATIONS HISTORY</span>
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<a name="l00020"></a>00020 <span class="comment">##</span>
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<a name="l00021"></a>00021 <span class="comment">## 09-02-09 (v) Maximum distance between two alpha sphere added</span>
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<a name="l00022"></a>00022 <span class="comment">## 29-01-09 (v) Normalized density and polarity score added</span>
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<a name="l00023"></a>00023 <span class="comment">## 21-01-09 (v) Density descriptor Added</span>
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<a name="l00024"></a>00024 <span class="comment">## 14-01-09 (v) Some normalized descriptors added</span>
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<a name="l00025"></a>00025 <span class="comment">## 28-11-08 (v) Comments UTD + relooking + mean_asph_ray set to float -_-'</span>
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<a name="l00026"></a>00026 <span class="comment">## 01-04-08 (v) Added comments and creation of history</span>
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<a name="l00027"></a>00027 <span class="comment">## 01-01-08 (vp) Created (random date...)</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">## TODO or SUGGESTIONS</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">## (v) Some descriptors need urgent improvement (amino-acids volume </span>
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<a name="l00032"></a>00032 <span class="comment">## score is the best example: maybe replace by the molecular weight </span>
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<a name="l00033"></a>00033 <span class="comment">## for example, although the way we use this kind of descriptors </span>
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<a name="l00034"></a>00034 <span class="comment">## might not be relevant at all anyway...)</span>
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<a name="l00035"></a>00035 <span class="comment">## (v) Possible improvement:</span>
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<a name="l00036"></a>00036 <span class="comment">## Use the sorted structure to calculate the apolar density.</span>
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<a name="l00037"></a>00037 <span class="comment"></span>
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<a name="l00038"></a>00038 <span class="comment">*/</span>
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<a name="l00039"></a>00039
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<a name="l00040"></a>00040 <span class="comment">/*</span>
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<a name="l00041"></a>00041 <span class="comment"> COPYRIGHT DISCLAIMER</span>
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<a name="l00042"></a>00042 <span class="comment"></span>
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<a name="l00043"></a>00043 <span class="comment"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
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<a name="l00044"></a>00044 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
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<a name="l00045"></a>00045 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
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<a name="l00046"></a>00046 <span class="comment"> Schmidtke.</span>
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<a name="l00047"></a>00047 <span class="comment"></span>
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<a name="l00048"></a>00048 <span class="comment"> Vincent Le Guilloux 28 November 2008</span>
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<a name="l00049"></a>00049 <span class="comment"> Peter Schmidtke 28 November 2008</span>
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<a name="l00050"></a>00050 <span class="comment"> Pierre Tuffery 28 November 2008</span>
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<a name="l00051"></a>00051 <span class="comment"></span>
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<a name="l00052"></a>00052 <span class="comment"> GNU GPL</span>
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<a name="l00053"></a>00053 <span class="comment"></span>
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<a name="l00054"></a>00054 <span class="comment"> This file is part of the fpocket package.</span>
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<a name="l00055"></a>00055 <span class="comment"></span>
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<a name="l00056"></a>00056 <span class="comment"> fpocket is free software: you can redistribute it and/or modify</span>
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<a name="l00057"></a>00057 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
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<a name="l00058"></a>00058 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
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<a name="l00059"></a>00059 <span class="comment"> (at your option) any later version.</span>
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<a name="l00060"></a>00060 <span class="comment"></span>
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<a name="l00061"></a>00061 <span class="comment"> fpocket is distributed in the hope that it will be useful,</span>
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<a name="l00062"></a>00062 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<a name="l00063"></a>00063 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<a name="l00064"></a>00064 <span class="comment"> GNU General Public License for more details.</span>
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<a name="l00065"></a>00065 <span class="comment"></span>
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<a name="l00066"></a>00066 <span class="comment"> You should have received a copy of the GNU General Public License</span>
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<a name="l00067"></a>00067 <span class="comment"> along with fpocket. If not, see <http://www.gnu.org/licenses/>.</span>
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<a name="l00068"></a>00068 <span class="comment"></span>
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<a name="l00069"></a>00069 <span class="comment">*/</span>
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<a name="l00070"></a>00070
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<a name="l00071"></a>00071 <span class="comment"></span>
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<a name="l00072"></a>00072 <span class="comment">/**</span>
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<a name="l00073"></a>00073 <span class="comment"> ## FUNCTION: </span>
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<a name="l00074"></a>00074 <span class="comment"> allocate_s_desc </span>
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<a name="l00075"></a>00075 <span class="comment"> </span>
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<a name="l00076"></a>00076 <span class="comment"> ## SPECIFICATION: </span>
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<a name="l00077"></a>00077 <span class="comment"> Allocate a descroptor structure</span>
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<a name="l00078"></a>00078 <span class="comment"> </span>
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<a name="l00079"></a>00079 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00080"></a>00080 <span class="comment"> </span>
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<a name="l00081"></a>00081 <span class="comment"> ## RETURN:</span>
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<a name="l00082"></a>00082 <span class="comment"> s_desc*</span>
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<a name="l00083"></a>00083 <span class="comment"> </span>
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<a name="l00084"></a>00084 <span class="comment">*/</span>
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<a name="l00085"></a><a class="code" href="descriptors_8h.html#0313250c68f4a7a8e292b674c30ae9fa">00085</a> <a class="code" href="structs__desc.html">s_desc</a>* <a class="code" href="descriptors_8c.html#0313250c68f4a7a8e292b674c30ae9fa">allocate_s_desc</a>(<span class="keywordtype">void</span>)
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<a name="l00086"></a>00086 {
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<a name="l00087"></a>00087 <a class="code" href="structs__desc.html">s_desc</a> *desc = (<a class="code" href="structs__desc.html">s_desc</a>*)<a class="code" href="memhandler_8c.html#52d7260a38c396cb2dd1dd7abcfd61cb">my_malloc</a>(<span class="keyword">sizeof</span>(<a class="code" href="structs__desc.html">s_desc</a>)) ;
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<a name="l00088"></a>00088
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<a name="l00089"></a>00089 <a class="code" href="descriptors_8c.html#9380470e1ad56a99f5a0597355eeb5ea">reset_desc</a>(desc) ;
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<a name="l00090"></a>00090
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<a name="l00091"></a>00091 <span class="keywordflow">return</span> desc ;
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<a name="l00092"></a>00092 }
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<a name="l00093"></a>00093 <span class="comment"></span>
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<a name="l00094"></a>00094 <span class="comment">/**</span>
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<a name="l00095"></a>00095 <span class="comment"> ## FUNCTION: </span>
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<a name="l00096"></a>00096 <span class="comment"> reset_s_desc</span>
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<a name="l00097"></a>00097 <span class="comment"> </span>
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<a name="l00098"></a>00098 <span class="comment"> ## SPECIFICATION: </span>
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<a name="l00099"></a>00099 <span class="comment"> Reset descriptors to 0 values.</span>
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<a name="l00100"></a>00100 <span class="comment"> </span>
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<a name="l00101"></a>00101 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00102"></a>00102 <span class="comment"> </span>
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<a name="l00103"></a>00103 <span class="comment"> ## RETURN:</span>
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<a name="l00104"></a>00104 <span class="comment"> void</span>
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<a name="l00105"></a>00105 <span class="comment"> </span>
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<a name="l00106"></a>00106 <span class="comment">*/</span>
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<a name="l00107"></a><a class="code" href="descriptors_8h.html#9380470e1ad56a99f5a0597355eeb5ea">00107</a> <span class="keywordtype">void</span> <a class="code" href="descriptors_8c.html#9380470e1ad56a99f5a0597355eeb5ea">reset_desc</a>(<a class="code" href="structs__desc.html">s_desc</a> *desc)
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<a name="l00108"></a>00108 {
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<a name="l00109"></a>00109 desc-><a class="code" href="structs__desc.html#ec451be95312187f418e20b87ebc0c1c">hydrophobicity_score</a> = 0.0 ;
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<a name="l00110"></a>00110 desc-><a class="code" href="structs__desc.html#0bf245c3d85f2fc8dec41d560313588a">volume_score</a> = 0.0 ;
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<a name="l00111"></a>00111 desc-><a class="code" href="structs__desc.html#ec106f2a35f5676a6af920311aa4260e">volume</a> = 0.0 ;
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<a name="l00112"></a>00112 desc-><a class="code" href="structs__desc.html#6363a7adfb5bc485f3524b8d4f0b5326">prop_polar_atm</a> = 0.0 ;
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<a name="l00113"></a>00113 desc-><a class="code" href="structs__desc.html#6e455ee4a61943b81a09fb9c4a816967">mean_asph_ray</a> = 0.0 ;
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<a name="l00114"></a>00114 desc-><a class="code" href="structs__desc.html#8d8c1b492a8f07602c496ffe907a7135">masph_sacc</a> = 0.0 ;
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<a name="l00115"></a>00115 desc-><a class="code" href="structs__desc.html#1e842880419a0616060301b4eacf858f">apolar_asphere_prop</a> = 0.0 ;
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<a name="l00116"></a>00116 desc-><a class="code" href="structs__desc.html#b48b3533d79c147285ca50eabc12ef63">mean_loc_hyd_dens</a> = 0.0 ;
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<a name="l00117"></a>00117 desc-><a class="code" href="structs__desc.html#2aeb19cfc5f53e2d22f1a2065ede1010">as_density</a> = 0.0 ;
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<a name="l00118"></a>00118 desc-><a class="code" href="structs__desc.html#6620d6b2cdaaa469b32a66a5e5260a80">as_max_dst</a> = 0.0 ;
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<a name="l00119"></a>00119
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<a name="l00120"></a>00120 desc-><a class="code" href="structs__desc.html#537c647e77f9ca129c77b31e3d15b2ca">flex</a> = 0.0 ;
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<a name="l00121"></a>00121 desc-><a class="code" href="structs__desc.html#8c4599be9319ff05ecf42dd6c70d0d6d">nas_norm</a> = 0.0 ;
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<a name="l00122"></a>00122 desc-><a class="code" href="structs__desc.html#a18101e18ed5d1714470a026621037f3">prop_asapol_norm</a> = 0.0 ;
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<a name="l00123"></a>00123 desc-><a class="code" href="structs__desc.html#3a111a68d68713a0c9b2d5e904951820">mean_loc_hyd_dens_norm</a> = 0.0 ;
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<a name="l00124"></a>00124 desc-><a class="code" href="structs__desc.html#a97dfcc5ad6152e55ef0ebe9985cce5c">as_density_norm</a> = 0.0 ;
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<a name="l00125"></a>00125 desc-><a class="code" href="structs__desc.html#15f213905d46949ade4dc9ec9e413d4f">polarity_score_norm</a> = 0.0 ;
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<a name="l00126"></a>00126 desc-><a class="code" href="structs__desc.html#9a9c0a666cb104843a278525e556087a">as_max_dst_norm</a> = 0.0 ;
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<a name="l00127"></a>00127
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<a name="l00128"></a>00128 desc-><a class="code" href="structs__desc.html#d481d25ff964a6858975b5abfb671412">nb_asph</a> = 0 ;
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<a name="l00129"></a>00129 desc-><a class="code" href="structs__desc.html#d612b029bba06646381771d4b61dc5e6">polarity_score</a> = 0 ;
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<a name="l00130"></a>00130 desc-><a class="code" href="structs__desc.html#00da80b684d1bb1af13ec779e282c7e0">charge_score</a> = 0 ;
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<a name="l00131"></a>00131
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<a name="l00132"></a>00132 <span class="keywordtype">int</span> i ;
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<a name="l00133"></a>00133 <span class="keywordflow">for</span>(i = 0 ; i < 20 ; i++) desc-><a class="code" href="structs__desc.html#12f239c0748ce08dba80fac61722117f">aa_compo</a>[i] = 0 ;
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<a name="l00134"></a>00134 }
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<a name="l00135"></a>00135 <span class="comment"></span>
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<a name="l00136"></a>00136 <span class="comment">/**</span>
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<a name="l00137"></a>00137 <span class="comment"> ## FUNCTION: </span>
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<a name="l00138"></a>00138 <span class="comment"> set_descriptors</span>
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<a name="l00139"></a>00139 <span class="comment"> </span>
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<a name="l00140"></a>00140 <span class="comment"> ## SPECIFICATION: </span>
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<a name="l00141"></a>00141 <span class="comment"> Set descriptors using a set of atoms with corresponding voronoi vertices.</span>
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<a name="l00142"></a>00142 <span class="comment"> Current descriptors (need to be improved...) includes atom/AA based descriptors</span>
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<a name="l00143"></a>00143 <span class="comment"> and voronoi vertice based descriptors.</span>
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<a name="l00144"></a>00144 <span class="comment"> A word on several descriptors:</span>
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<a name="l00145"></a>00145 <span class="comment"> - The "solvent accessibility" of a sphere (which is rather the buriedness</span>
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<a name="l00146"></a>00146 <span class="comment"> degree...) is defined as the distance of the barycenter of the sphere</span>
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<a name="l00147"></a>00147 <span class="comment"> (defined using the 4 contacted atoms) from the center of the sphere.</span>
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<a name="l00148"></a>00148 <span class="comment"> - The mean_loc_hyd_dens is the mean value of apolar density calculated</span>
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<a name="l00149"></a>00149 <span class="comment"> for each vertice and defined in the next function (see comments or doc)</span>
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<a name="l00150"></a>00150 <span class="comment"> </span>
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<a name="l00151"></a>00151 <span class="comment"> </span>
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<a name="l00152"></a>00152 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00153"></a>00153 <span class="comment"> @ s_atm **atoms : The list of atoms</span>
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<a name="l00154"></a>00154 <span class="comment"> @ int natoms : The number of atoms</span>
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<a name="l00155"></a>00155 <span class="comment"> @ s_vvertice **tvert : The list of vertices</span>
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<a name="l00156"></a>00156 <span class="comment"> @ int nvert : The number of vertices</span>
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<a name="l00157"></a>00157 <span class="comment"> @ s_desc *desc : OUTPUT: The descriptor structure to fill</span>
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<a name="l00158"></a>00158 <span class="comment"> </span>
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<a name="l00159"></a>00159 <span class="comment"> ## RETURN:</span>
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<a name="l00160"></a>00160 <span class="comment"> void: s_desc is filled</span>
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<a name="l00161"></a>00161 <span class="comment"> </span>
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<a name="l00162"></a>00162 <span class="comment">*/</span>
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<a name="l00163"></a><a class="code" href="descriptors_8h.html#cef259d58bb6952caf98c16e7c85b82c">00163</a> <span class="keywordtype">void</span> <a class="code" href="descriptors_8c.html#c7884a89b2fea911c75f796df23690de">set_descriptors</a>(<a class="code" href="structs__atm.html">s_atm</a> **atoms, <span class="keywordtype">int</span> natoms, <a class="code" href="structs__vvertice.html">s_vvertice</a> **tvert, <span class="keywordtype">int</span> nvert,
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<a name="l00164"></a>00164 <a class="code" href="structs__desc.html">s_desc</a> *desc,<span class="keywordtype">int</span> niter)
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<a name="l00165"></a>00165 {
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<a name="l00166"></a>00166 <span class="comment">/* Setting atom-based descriptors */</span>
|
|
<a name="l00167"></a>00167 <a class="code" href="descriptors_8c.html#e025b1c81cd0d590bf6efc2db82cea70">set_atom_based_descriptors</a>(atoms, natoms, desc) ;
|
|
<a name="l00168"></a>00168
|
|
<a name="l00169"></a>00169 <span class="comment">/* Setting vertice-based descriptors */</span>
|
|
<a name="l00170"></a>00170 <span class="keywordflow">if</span>(! tvert) return ;
|
|
<a name="l00171"></a>00171
|
|
<a name="l00172"></a>00172 <span class="keywordtype">float</span> d = 0.0, vx, vy, vz, vrad,
|
|
<a name="l00173"></a>00173 masph_sacc = 0.0, <span class="comment">/* Mean alpha sphere solvent accessibility */</span>
|
|
<a name="l00174"></a>00174 mean_ashape_radius = 0.0,
|
|
<a name="l00175"></a>00175 as_density = 0.0, as_max_dst = -1.0,
|
|
<a name="l00176"></a>00176 dtmp = 0.0 ;
|
|
<a name="l00177"></a>00177
|
|
<a name="l00178"></a>00178 <span class="keywordtype">int</span> i, j,
|
|
<a name="l00179"></a>00179 napol_neigh = 0,
|
|
<a name="l00180"></a>00180 nAlphaApol = 0 ;
|
|
<a name="l00181"></a>00181
|
|
<a name="l00182"></a>00182 <span class="keywordtype">float</span> as_max_r = -1.0 ;
|
|
<a name="l00183"></a>00183
|
|
<a name="l00184"></a>00184 <a class="code" href="structs__vvertice.html">s_vvertice</a> *vcur = NULL,
|
|
<a name="l00185"></a>00185 *vc = NULL ;
|
|
<a name="l00186"></a>00186
|
|
<a name="l00187"></a>00187 desc-><a class="code" href="structs__desc.html#b48b3533d79c147285ca50eabc12ef63">mean_loc_hyd_dens</a> = 0.0 ;
|
|
<a name="l00188"></a>00188 <span class="keywordflow">for</span>(i = 0 ; i < nvert ; i++) {
|
|
<a name="l00189"></a>00189 vcur = tvert[i] ;
|
|
<a name="l00190"></a>00190 <span class="keywordflow">if</span>(vcur-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a> > as_max_r) as_max_r = vcur-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a> ;
|
|
<a name="l00191"></a>00191
|
|
<a name="l00192"></a>00192 vx = vcur-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a> ; vy = vcur-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a> ; vz = vcur-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a> ; vrad = vcur-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a> ;
|
|
<a name="l00193"></a>00193
|
|
<a name="l00194"></a>00194 <span class="comment">/* Calculate apolar density if necessary, and pocket density */</span>
|
|
<a name="l00195"></a>00195 j = 0 ;
|
|
<a name="l00196"></a>00196 <span class="keywordflow">if</span>(vcur-><a class="code" href="structs__vvertice.html#7cd4bd55a93f3400449ef354b49bb4c3">type</a> == <a class="code" href="voronoi_8h.html#e90a1520c3ca5a4b829d387d4d06b004">M_APOLAR_AS</a>) {
|
|
<a name="l00197"></a>00197 napol_neigh = 0 ;
|
|
<a name="l00198"></a>00198 <span class="keywordflow">for</span>(j = 0 ; j < nvert ; j++) {
|
|
<a name="l00199"></a>00199 vc = tvert[j] ;
|
|
<a name="l00200"></a>00200
|
|
<a name="l00201"></a>00201 <span class="comment">/* Increment the number of apolar neighbor */</span>
|
|
<a name="l00202"></a>00202 <span class="keywordflow">if</span>(vc != vcur && vc-><a class="code" href="structs__vvertice.html#7cd4bd55a93f3400449ef354b49bb4c3">type</a> == <a class="code" href="voronoi_8h.html#e90a1520c3ca5a4b829d387d4d06b004">M_APOLAR_AS</a> &&
|
|
<a name="l00203"></a>00203 <a class="code" href="calc_8c.html#615f3353fc9ccc88069adb4000b21e73">dist</a>(vx, vy, vz, vc->x, vc->y, vc->z)-(vc->ray + vrad) <= 0.) {
|
|
<a name="l00204"></a>00204 napol_neigh += 1 ;
|
|
<a name="l00205"></a>00205 }
|
|
<a name="l00206"></a>00206
|
|
<a name="l00207"></a>00207 <span class="comment">/* Update density by the way... */</span>
|
|
<a name="l00208"></a>00208 <span class="keywordflow">if</span>(j > i) {
|
|
<a name="l00209"></a>00209 dtmp = <a class="code" href="calc_8c.html#615f3353fc9ccc88069adb4000b21e73">dist</a>(vcur-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a>, vcur-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a>, vcur-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a>,
|
|
<a name="l00210"></a>00210 vc->x, vc->y, vc->z);
|
|
<a name="l00211"></a>00211
|
|
<a name="l00212"></a>00212 <span class="keywordflow">if</span>(dtmp > as_max_dst) as_max_dst = dtmp ;
|
|
<a name="l00213"></a>00213 as_density += dtmp ;
|
|
<a name="l00214"></a>00214 }
|
|
<a name="l00215"></a>00215 }
|
|
<a name="l00216"></a>00216 desc-><a class="code" href="structs__desc.html#b48b3533d79c147285ca50eabc12ef63">mean_loc_hyd_dens</a> += (float) napol_neigh ;
|
|
<a name="l00217"></a>00217 nAlphaApol += 1 ;
|
|
<a name="l00218"></a>00218 }
|
|
<a name="l00219"></a>00219 <span class="keywordflow">else</span> {
|
|
<a name="l00220"></a>00220 <span class="comment">/* Update density */</span>
|
|
<a name="l00221"></a>00221 <span class="keywordflow">for</span>(j = i+1 ; j < nvert ; j++) {
|
|
<a name="l00222"></a>00222 dtmp = <a class="code" href="calc_8c.html#615f3353fc9ccc88069adb4000b21e73">dist</a>(vcur-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a>, vcur-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a>, vcur-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a>,
|
|
<a name="l00223"></a>00223 tvert[j]-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a>, tvert[j]-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a>, tvert[j]-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a>) ;
|
|
<a name="l00224"></a>00224
|
|
<a name="l00225"></a>00225 <span class="keywordflow">if</span>(dtmp > as_max_dst) as_max_dst = dtmp ;
|
|
<a name="l00226"></a>00226 as_density += dtmp ;
|
|
<a name="l00227"></a>00227 }
|
|
<a name="l00228"></a>00228 }
|
|
<a name="l00229"></a>00229
|
|
<a name="l00230"></a>00230 mean_ashape_radius += vcur-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a> ;
|
|
<a name="l00231"></a>00231 <span class="comment">/* Estimating solvent accessibility of the sphere */</span>
|
|
<a name="l00232"></a>00232 d = <a class="code" href="calc_8c.html#615f3353fc9ccc88069adb4000b21e73">dist</a>(vcur-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a>, vcur-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a>, vcur-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a>,
|
|
<a name="l00233"></a>00233 vcur-><a class="code" href="structs__vvertice.html#158f2fc12fef57205ad4f951bf20caea">bary</a>[0], vcur-><a class="code" href="structs__vvertice.html#158f2fc12fef57205ad4f951bf20caea">bary</a>[1], vcur-><a class="code" href="structs__vvertice.html#158f2fc12fef57205ad4f951bf20caea">bary</a>[2]) ;
|
|
<a name="l00234"></a>00234 masph_sacc += d/vcur-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a> ;
|
|
<a name="l00235"></a>00235 }
|
|
<a name="l00236"></a>00236
|
|
<a name="l00237"></a>00237 <span class="keywordflow">if</span>(nAlphaApol>0) desc-><a class="code" href="structs__desc.html#b48b3533d79c147285ca50eabc12ef63">mean_loc_hyd_dens</a> /= (float)nAlphaApol ;
|
|
<a name="l00238"></a>00238 <span class="keywordflow">else</span> desc-><a class="code" href="structs__desc.html#b48b3533d79c147285ca50eabc12ef63">mean_loc_hyd_dens</a>= 0.0;
|
|
<a name="l00239"></a>00239
|
|
<a name="l00240"></a>00240 desc-><a class="code" href="structs__desc.html#6620d6b2cdaaa469b32a66a5e5260a80">as_max_dst</a> = as_max_dst ;
|
|
<a name="l00241"></a>00241 desc-><a class="code" href="structs__desc.html#1e842880419a0616060301b4eacf858f">apolar_asphere_prop</a> = (float)nAlphaApol / (<span class="keywordtype">float</span>)nvert ;
|
|
<a name="l00242"></a>00242 desc-><a class="code" href="structs__desc.html#8d8c1b492a8f07602c496ffe907a7135">masph_sacc</a> = masph_sacc / nvert ;
|
|
<a name="l00243"></a>00243 desc-><a class="code" href="structs__desc.html#6e455ee4a61943b81a09fb9c4a816967">mean_asph_ray</a> = mean_ashape_radius / (float)nvert ;
|
|
<a name="l00244"></a>00244 desc-><a class="code" href="structs__desc.html#d481d25ff964a6858975b5abfb671412">nb_asph</a> = nvert ;
|
|
<a name="l00245"></a>00245 desc-><a class="code" href="structs__desc.html#2aeb19cfc5f53e2d22f1a2065ede1010">as_density</a> = as_density / ((nvert*nvert - nvert) * 0.5) ;
|
|
<a name="l00246"></a>00246
|
|
<a name="l00247"></a>00247 desc-><a class="code" href="structs__desc.html#ec106f2a35f5676a6af920311aa4260e">volume</a> = <a class="code" href="voronoi_8c.html#621631ed13a0e6d72412f1551969a655">get_verts_volume_ptr</a>(tvert, nvert, niter,-1.6) ;
|
|
<a name="l00248"></a>00248 desc-><a class="code" href="structs__desc.html#eb15aebab64687c1c18d261e40b96901">as_max_r</a> = as_max_r ;
|
|
<a name="l00249"></a>00249 }
|
|
<a name="l00250"></a>00250 <span class="comment"></span>
|
|
<a name="l00251"></a>00251 <span class="comment">/**</span>
|
|
<a name="l00252"></a>00252 <span class="comment"> ## FUNCTION: </span>
|
|
<a name="l00253"></a>00253 <span class="comment"> get_vert_apolar_density</span>
|
|
<a name="l00254"></a>00254 <span class="comment"> </span>
|
|
<a name="l00255"></a>00255 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00256"></a>00256 <span class="comment"> Here we calculate the number of apolar vertices (vertices that contact at </span>
|
|
<a name="l00257"></a>00257 <span class="comment"> least 3 atoms having their electronegativity > 2.7) that lie within a range </span>
|
|
<a name="l00258"></a>00258 <span class="comment"> of 0-r () from a given reference vertice, r being its own radius.</span>
|
|
<a name="l00259"></a>00259 <span class="comment"> </span>
|
|
<a name="l00260"></a>00260 <span class="comment"> It provides the apolar density for a given vertice, that will be used for</span>
|
|
<a name="l00261"></a>00261 <span class="comment"> the calculation of the total apolar density of the pocket, defined as the</span>
|
|
<a name="l00262"></a>00262 <span class="comment"> mean value of it.</span>
|
|
<a name="l00263"></a>00263 <span class="comment"> </span>
|
|
<a name="l00264"></a>00264 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00265"></a>00265 <span class="comment"> @ s_vvertice **tvert : The list of vertices</span>
|
|
<a name="l00266"></a>00266 <span class="comment"> @ int nvert : The number of vertices</span>
|
|
<a name="l00267"></a>00267 <span class="comment"> @ s_vvertice *vert : The reference vertice.</span>
|
|
<a name="l00268"></a>00268 <span class="comment"> </span>
|
|
<a name="l00269"></a>00269 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00270"></a>00270 <span class="comment"> int: The apolar density as defined previously.</span>
|
|
<a name="l00271"></a>00271 <span class="comment"> </span>
|
|
<a name="l00272"></a>00272 <span class="comment">*/</span>
|
|
<a name="l00273"></a><a class="code" href="descriptors_8h.html#9759d226e51f3e4829391181ead808b9">00273</a> <span class="keywordtype">int</span> <a class="code" href="descriptors_8c.html#9759d226e51f3e4829391181ead808b9">get_vert_apolar_density</a>(<a class="code" href="structs__vvertice.html">s_vvertice</a> **tvert, <span class="keywordtype">int</span> nvert, <a class="code" href="structs__vvertice.html">s_vvertice</a> *vert)
|
|
<a name="l00274"></a>00274 {
|
|
<a name="l00275"></a>00275 <span class="keywordtype">int</span> apol_neighbours = 0,
|
|
<a name="l00276"></a>00276 i = 0 ;
|
|
<a name="l00277"></a>00277
|
|
<a name="l00278"></a>00278 <a class="code" href="structs__vvertice.html">s_vvertice</a> *vc = NULL ;
|
|
<a name="l00279"></a>00279
|
|
<a name="l00280"></a>00280 <span class="keywordtype">float</span> vx = vert-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a>,
|
|
<a name="l00281"></a>00281 vy = vert-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a>,
|
|
<a name="l00282"></a>00282 vz = vert-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a>,
|
|
<a name="l00283"></a>00283 vray = vert-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a> ;
|
|
<a name="l00284"></a>00284
|
|
<a name="l00285"></a>00285 <span class="keywordflow">for</span>(i = 0 ; i < nvert ; i++) {
|
|
<a name="l00286"></a>00286 vc = tvert[i] ;
|
|
<a name="l00287"></a>00287 <span class="keywordflow">if</span>(vc != vert && vc-><a class="code" href="structs__vvertice.html#7cd4bd55a93f3400449ef354b49bb4c3">type</a> == <a class="code" href="voronoi_8h.html#e90a1520c3ca5a4b829d387d4d06b004">M_APOLAR_AS</a>){
|
|
<a name="l00288"></a>00288 <span class="keywordflow">if</span>(<a class="code" href="calc_8c.html#615f3353fc9ccc88069adb4000b21e73">dist</a>(vx, vy, vz, vc-><a class="code" href="structs__vvertice.html#017f9695c923d87d851231bf13967b22">x</a>, vc-><a class="code" href="structs__vvertice.html#250642d688398e4186819f63d54247bc">y</a>, vc-><a class="code" href="structs__vvertice.html#3e03d11fd3b1d0ffb623481fa1b497b6">z</a>)-(vc-><a class="code" href="structs__vvertice.html#0aadc589bd2213f3c6246e873cc69a83">ray</a> + vray) <= 0.) {
|
|
<a name="l00289"></a>00289 apol_neighbours += 1 ;
|
|
<a name="l00290"></a>00290 }
|
|
<a name="l00291"></a>00291 }
|
|
<a name="l00292"></a>00292 }
|
|
<a name="l00293"></a>00293
|
|
<a name="l00294"></a>00294 <span class="keywordflow">return</span> apol_neighbours ;
|
|
<a name="l00295"></a>00295 }
|
|
<a name="l00296"></a>00296 <span class="comment"></span>
|
|
<a name="l00297"></a>00297 <span class="comment">/**</span>
|
|
<a name="l00298"></a>00298 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00299"></a>00299 <span class="comment"> set_atom_based_descriptors</span>
|
|
<a name="l00300"></a>00300 <span class="comment"> </span>
|
|
<a name="l00301"></a>00301 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00302"></a>00302 <span class="comment"> Update atomic descriptors of the pocket for the given atom. Here, we just</span>
|
|
<a name="l00303"></a>00303 <span class="comment"> update mean bfactor, electronegativity, amino-acids scores...</span>
|
|
<a name="l00304"></a>00304 <span class="comment"> </span>
|
|
<a name="l00305"></a>00305 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00306"></a>00306 <span class="comment"> @ s_atom *atoms : The atoms</span>
|
|
<a name="l00307"></a>00307 <span class="comment"> @ int natoms : Number of atoms</span>
|
|
<a name="l00308"></a>00308 <span class="comment"> @ s_desc *desc : OUTPUT : The descriptor structure to fill</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"> void</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="descriptors_8h.html#e025b1c81cd0d590bf6efc2db82cea70">00314</a> <span class="keywordtype">void</span> <a class="code" href="descriptors_8c.html#e025b1c81cd0d590bf6efc2db82cea70">set_atom_based_descriptors</a>(<a class="code" href="structs__atm.html">s_atm</a> **atoms, <span class="keywordtype">int</span> natoms, <a class="code" href="structs__desc.html">s_desc</a> *desc)
|
|
<a name="l00315"></a>00315 {
|
|
<a name="l00316"></a>00316 <a class="code" href="structs__atm.html">s_atm</a> *curatom = NULL ;
|
|
<a name="l00317"></a>00317
|
|
<a name="l00318"></a>00318 <span class="keywordtype">int</span> i,
|
|
<a name="l00319"></a>00319 res_ids[natoms], <span class="comment">/* Maximum natoms residues contacting the pocket */</span>
|
|
<a name="l00320"></a>00320 nb_res_ids = 0 ; <span class="comment">/* Current number of residus */</span>
|
|
<a name="l00321"></a>00321
|
|
<a name="l00322"></a>00322 <span class="keywordtype">int</span> nb_polar_atm = 0 ;
|
|
<a name="l00323"></a>00323
|
|
<a name="l00324"></a>00324 <span class="keywordflow">for</span>(i = 0 ; i < natoms ; i++) {
|
|
<a name="l00325"></a>00325 curatom = atoms[i] ;
|
|
<a name="l00326"></a>00326
|
|
<a name="l00327"></a>00327 <span class="comment">/* Setting amino acid descriptor of the current atom */</span>
|
|
<a name="l00328"></a>00328 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#c02faf0c5e3cf0b256a1ad1d37d9b8a2">in_tab</a>(res_ids, nb_res_ids, curatom-><a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a>) == 0) {
|
|
<a name="l00329"></a>00329 <a class="code" href="descriptors_8c.html#4fae028d2c83da127914b336e71f8340">set_aa_desc</a>(desc, atoms[i]->res_name) ;
|
|
<a name="l00330"></a>00330 res_ids[nb_res_ids] = curatom-><a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a> ;
|
|
<a name="l00331"></a>00331 nb_res_ids ++ ;
|
|
<a name="l00332"></a>00332 }
|
|
<a name="l00333"></a>00333
|
|
<a name="l00334"></a>00334 <span class="comment">/* Setting atom descriptor */</span>
|
|
<a name="l00335"></a>00335 desc-><a class="code" href="structs__desc.html#537c647e77f9ca129c77b31e3d15b2ca">flex</a> += curatom-><a class="code" href="structs__atm.html#6a1a5fd32629457dfa14626b25b5ae46">bfactor</a> ;
|
|
<a name="l00336"></a>00336 <span class="keywordflow">if</span>(curatom-><a class="code" href="structs__atm.html#f41b525ee3032d47baf2db10387f022c">electroneg</a> > 2.7) nb_polar_atm += 1 ;
|
|
<a name="l00337"></a>00337 }
|
|
<a name="l00338"></a>00338
|
|
<a name="l00339"></a>00339 desc-><a class="code" href="structs__desc.html#ec451be95312187f418e20b87ebc0c1c">hydrophobicity_score</a> = desc-><a class="code" href="structs__desc.html#ec451be95312187f418e20b87ebc0c1c">hydrophobicity_score</a>/ (float) nb_res_ids ;
|
|
<a name="l00340"></a>00340 desc-><a class="code" href="structs__desc.html#0bf245c3d85f2fc8dec41d560313588a">volume_score</a> = desc-><a class="code" href="structs__desc.html#0bf245c3d85f2fc8dec41d560313588a">volume_score</a> / (float) nb_res_ids ;
|
|
<a name="l00341"></a>00341
|
|
<a name="l00342"></a>00342 desc-><a class="code" href="structs__desc.html#537c647e77f9ca129c77b31e3d15b2ca">flex</a> /= natoms ;
|
|
<a name="l00343"></a>00343 desc-><a class="code" href="structs__desc.html#6363a7adfb5bc485f3524b8d4f0b5326">prop_polar_atm</a> = ((float) nb_polar_atm) / ((float) natoms) * 100.0 ;
|
|
<a name="l00344"></a>00344 }
|
|
<a name="l00345"></a>00345 <span class="comment"></span>
|
|
<a name="l00346"></a>00346 <span class="comment">/**</span>
|
|
<a name="l00347"></a>00347 <span class="comment"> ## FUNCTION: </span>
|
|
<a name="l00348"></a>00348 <span class="comment"> set_aa_desc</span>
|
|
<a name="l00349"></a>00349 <span class="comment"> </span>
|
|
<a name="l00350"></a>00350 <span class="comment"> ## SPECIFICATION: </span>
|
|
<a name="l00351"></a>00351 <span class="comment"> Set amino-acid based descriptors.</span>
|
|
<a name="l00352"></a>00352 <span class="comment"> </span>
|
|
<a name="l00353"></a>00353 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00354"></a>00354 <span class="comment"> @ s_desc *desc : OUTPUT: Structure of descriptors to fill</span>
|
|
<a name="l00355"></a>00355 <span class="comment"> @ const char *aa_name : The amino acid name</span>
|
|
<a name="l00356"></a>00356 <span class="comment"> </span>
|
|
<a name="l00357"></a>00357 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00358"></a>00358 <span class="comment"> s_desc*</span>
|
|
<a name="l00359"></a>00359 <span class="comment"> </span>
|
|
<a name="l00360"></a>00360 <span class="comment">*/</span>
|
|
<a name="l00361"></a><a class="code" href="descriptors_8h.html#4fae028d2c83da127914b336e71f8340">00361</a> <span class="keywordtype">void</span> <a class="code" href="descriptors_8c.html#4fae028d2c83da127914b336e71f8340">set_aa_desc</a>(<a class="code" href="structs__desc.html">s_desc</a> *desc, <span class="keyword">const</span> <span class="keywordtype">char</span> *aa_name)
|
|
<a name="l00362"></a>00362 {
|
|
<a name="l00363"></a>00363 <span class="keywordtype">int</span> aa_idx = -1;
|
|
<a name="l00364"></a>00364 <span class="keywordtype">char</span> l1 = aa_name[0],
|
|
<a name="l00365"></a>00365 l2 = aa_name[1],
|
|
<a name="l00366"></a>00366 l3 = aa_name[2] ;
|
|
<a name="l00367"></a>00367
|
|
<a name="l00368"></a>00368 <span class="comment">/* Ok, lets use the less comparisons possible... (may be used in the aa.c</span>
|
|
<a name="l00369"></a>00369 <span class="comment"> * file later!) </span>
|
|
<a name="l00370"></a>00370 <span class="comment"> * Only A, C, G, H, I, L, M, P, S, T and V possibility for the first letter:</span>
|
|
<a name="l00371"></a>00371 <span class="comment"> **/</span>
|
|
<a name="l00372"></a>00372 <span class="keywordflow">switch</span>(l1) {
|
|
<a name="l00373"></a>00373 <span class="keywordflow">case</span> <span class="charliteral">'A'</span> : <span class="comment">/* Either ALA, ASP, ASN or ARG */</span>
|
|
<a name="l00374"></a>00374 <span class="keywordflow">if</span>(l2 == <span class="charliteral">'L'</span>) aa_idx = <a class="code" href="aa_8h.html#1b0c9070ecb3ea0befd683ce92dfa925">M_ALA_IDX</a> ; <span class="comment">/* ALA amino acid! */</span>
|
|
<a name="l00375"></a>00375 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(l2 == <span class="charliteral">'R'</span>) aa_idx = <a class="code" href="aa_8h.html#6cb6aa2cef5eaa616d3c5f4fc4acd710">M_ARG_IDX</a> ; <span class="comment">/* ARG amino acid! */</span>
|
|
<a name="l00376"></a>00376 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(l2 == <span class="charliteral">'S'</span> && l3 == <span class="charliteral">'P'</span>)
|
|
<a name="l00377"></a>00377 aa_idx = <a class="code" href="aa_8h.html#93845fafca07848ed53cb4d454be12ac">M_ASP_IDX</a> ; <span class="comment">/* ASP amino acid! */</span>
|
|
<a name="l00378"></a>00378 <span class="keywordflow">else</span> aa_idx = <a class="code" href="aa_8h.html#84516b2203e073e9dbc63ccaf7a3628b">M_ASN_IDX</a> ; break ; <span class="comment">/* ASN amino acid! */</span>
|
|
<a name="l00379"></a>00379
|
|
<a name="l00380"></a>00380 <span class="keywordflow">case</span> <span class="charliteral">'C'</span> : aa_idx = <a class="code" href="aa_8h.html#7e417b6b18144cb3417f86c100e26210">M_CYS_IDX</a> ; break ; <span class="comment">/* CYS amino acid! */</span>
|
|
<a name="l00381"></a>00381
|
|
<a name="l00382"></a>00382 <span class="keywordflow">case</span> <span class="charliteral">'G'</span> : <span class="comment">/* Either GLU, GLY, or GLN, so just check the 3rd letter */</span>
|
|
<a name="l00383"></a>00383 <span class="keywordflow">if</span>(l3 == <span class="charliteral">'U'</span>) aa_idx = <a class="code" href="aa_8h.html#ee64fbe3bf2b3700be47e73710ba9b2e">M_GLU_IDX</a> ; <span class="comment">/* GLU amino acid! */</span>
|
|
<a name="l00384"></a>00384 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(l3 == <span class="charliteral">'Y'</span>) aa_idx = <a class="code" href="aa_8h.html#8af8b421277f5bac3dd71ecb39912a68">M_GLY_IDX</a> ; <span class="comment">/* GLY amino acid! */</span>
|
|
<a name="l00385"></a>00385 <span class="keywordflow">else</span> aa_idx = <a class="code" href="aa_8h.html#a50e956ceccc8383378ce2c86a0650c7">M_GLN_IDX</a> ; break ; <span class="comment">/* GLN amino acid! */</span>
|
|
<a name="l00386"></a>00386
|
|
<a name="l00387"></a>00387 <span class="keywordflow">case</span> <span class="charliteral">'H'</span> : aa_idx = <a class="code" href="aa_8h.html#ad66b8237a731e8b9284cf2c0f5bf1a8">M_HIS_IDX</a> ; break ; <span class="comment">/* HIS amino acid! */</span>
|
|
<a name="l00388"></a>00388 <span class="keywordflow">case</span> <span class="charliteral">'I'</span> : aa_idx = <a class="code" href="aa_8h.html#f7ed4c3826357ffd5ca1430960b01323">M_ILE_IDX</a> ; break ; <span class="comment">/* ILE amino acid! */</span>
|
|
<a name="l00389"></a>00389
|
|
<a name="l00390"></a>00390 <span class="keywordflow">case</span> <span class="charliteral">'L'</span> : <span class="comment">/* Either ALA, ASP, ASN or ARG */</span>
|
|
<a name="l00391"></a>00391 <span class="keywordflow">if</span>(l2 == <span class="charliteral">'Y'</span>) aa_idx = <a class="code" href="aa_8h.html#9c48ce33c40ed282161be85f00e5c358">M_LYS_IDX</a> ; <span class="comment">/* LYS amino acid! */</span>
|
|
<a name="l00392"></a>00392 <span class="keywordflow">else</span> aa_idx = <a class="code" href="aa_8h.html#6f298038ea813adf7ce7591d8aebc24f">M_LEU_IDX</a> ; break ; <span class="comment">/* LEU amino acid! */</span>
|
|
<a name="l00393"></a>00393
|
|
<a name="l00394"></a>00394 <span class="keywordflow">case</span> <span class="charliteral">'M'</span> : aa_idx = <a class="code" href="aa_8h.html#7552b2c0cb98c2ec24839aa18761321d">M_MET_IDX</a> ; break ; <span class="comment">/* MET amino acid! */</span>
|
|
<a name="l00395"></a>00395 <span class="keywordflow">case</span> <span class="charliteral">'P'</span> : <span class="comment">/* Either ALA, ASP, ASN or ARG */</span>
|
|
<a name="l00396"></a>00396 <span class="keywordflow">if</span>(l2 == <span class="charliteral">'H'</span>) aa_idx = <a class="code" href="aa_8h.html#0ce108eda73a67d937d4a9a95742e7e2">M_PHE_IDX</a> ; <span class="comment">/* PHE amino acid! */</span>
|
|
<a name="l00397"></a>00397 <span class="keywordflow">else</span> aa_idx = <a class="code" href="aa_8h.html#f67fd842e620788b97ebf0ed4c062d6f">M_PRO_IDX</a> ; break ; <span class="comment">/* PRO amino acid! */</span>
|
|
<a name="l00398"></a>00398
|
|
<a name="l00399"></a>00399 <span class="keywordflow">case</span> <span class="charliteral">'S'</span> : aa_idx = <a class="code" href="aa_8h.html#bd333adb6a0180ddb95da74027d34693">M_SER_IDX</a> ; break ; <span class="comment">/* SER amino acid! */</span>
|
|
<a name="l00400"></a>00400
|
|
<a name="l00401"></a>00401 <span class="keywordflow">case</span> <span class="charliteral">'T'</span> : <span class="comment">/* Either ALA, ASP, ASN or ARG */</span>
|
|
<a name="l00402"></a>00402 <span class="keywordflow">if</span>(l2 == <span class="charliteral">'H'</span>) aa_idx = <a class="code" href="aa_8h.html#cd98aae4f40d8e2c19435b5d79abcb53">M_THR_IDX</a> ; <span class="comment">/* THR amino acid! */</span>
|
|
<a name="l00403"></a>00403 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(l2 == <span class="charliteral">'R'</span>) aa_idx = <a class="code" href="aa_8h.html#ae2397ccd1d8baefaf8beecb9ebf4128">M_TRP_IDX</a> ; <span class="comment">/* TRP amino acid! */</span>
|
|
<a name="l00404"></a>00404 <span class="keywordflow">else</span> aa_idx = <a class="code" href="aa_8h.html#d894f46b7d2e41ec7a1bdf2f66d6d530">M_TYR_IDX</a> ; break ; <span class="comment">/* TYR amino acid! */</span>
|
|
<a name="l00405"></a>00405
|
|
<a name="l00406"></a>00406 <span class="keywordflow">case</span> <span class="charliteral">'V'</span> : aa_idx = <a class="code" href="aa_8h.html#93cd02b2888b078a6c3c0461bda79841">M_VAL_IDX</a> ; break ; <span class="comment">/* VAL amino acid! */</span>
|
|
<a name="l00407"></a>00407
|
|
<a name="l00408"></a>00408 <span class="keywordflow">default</span>: <span class="comment">/*fprintf(stderr, "! Amno acid %s does not exists!\n", aa_name) ;*/</span>
|
|
<a name="l00409"></a>00409 break ;
|
|
<a name="l00410"></a>00410 }
|
|
<a name="l00411"></a>00411
|
|
<a name="l00412"></a>00412 <span class="comment">/* Ok now we have our amino acid, lets update statistics! */</span>
|
|
<a name="l00413"></a>00413
|
|
<a name="l00414"></a>00414 <span class="keywordflow">if</span>(aa_idx != -1) {
|
|
<a name="l00415"></a>00415 desc-><a class="code" href="structs__desc.html#12f239c0748ce08dba80fac61722117f">aa_compo</a>[aa_idx] ++ ;
|
|
<a name="l00416"></a>00416
|
|
<a name="l00417"></a>00417 desc-><a class="code" href="structs__desc.html#ec451be95312187f418e20b87ebc0c1c">hydrophobicity_score</a> += <a class="code" href="aa_8c.html#3988fc0beb2f06dee9ebb04ef491f9d7">get_hydrophobicity_score_from_idx</a>(aa_idx) ;
|
|
<a name="l00418"></a>00418 desc-><a class="code" href="structs__desc.html#d612b029bba06646381771d4b61dc5e6">polarity_score</a> += <a class="code" href="aa_8c.html#6b1242df111921659782dc1285ac101a">get_polarity_from_idx</a>(aa_idx) ;
|
|
<a name="l00419"></a>00419 desc-><a class="code" href="structs__desc.html#0bf245c3d85f2fc8dec41d560313588a">volume_score</a> += <a class="code" href="aa_8c.html#ce98533a9358aec6dcc325fe567c26fe">get_volume_score_from_idx</a>(aa_idx) ;
|
|
<a name="l00420"></a>00420 desc-><a class="code" href="structs__desc.html#00da80b684d1bb1af13ec779e282c7e0">charge_score</a> += <a class="code" href="aa_8c.html#641c90c89a2f096c09ee972cf05d8b71">get_charge_from_idx</a>(aa_idx) ;
|
|
<a name="l00421"></a>00421 }
|
|
<a name="l00422"></a>00422 }
|
|
<a name="l00423"></a>00423
|
|
</pre></div></div>
|
|
<hr size="1"><address style="text-align: right;"><small>Generated on Sun Jul 5 22:10:40 2009 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> 1.5.9 </small></address>
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</body>
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