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<h1>atom.c</h1><a href="atom_8c.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001
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<a name="l00002"></a>00002 <span class="preprocessor">#include "../headers/atom.h"</span>
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<a name="l00003"></a>00003
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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"></span>
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<a name="l00006"></a>00006 <span class="comment">## GENERAL INFORMATION</span>
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<a name="l00007"></a>00007 <span class="comment">##</span>
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<a name="l00008"></a>00008 <span class="comment">## FILE atom.c</span>
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<a name="l00009"></a>00009 <span class="comment">## AUTHORS P. Schmidtke and V. Le Guilloux</span>
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<a name="l00010"></a>00010 <span class="comment">## LAST MODIFIED 01-04-08</span>
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<a name="l00011"></a>00011 <span class="comment">##</span>
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<a name="l00012"></a>00012 <span class="comment">## SPECIFICATIONS</span>
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<a name="l00013"></a>00013 <span class="comment">##</span>
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<a name="l00014"></a>00014 <span class="comment">## This file should be used to deal with atoms. The corresponding</span>
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<a name="l00015"></a>00015 <span class="comment">## header contains a structure that define an atoms and its </span>
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<a name="l00016"></a>00016 <span class="comment">## properties, like it's vdW radius, its coordinates ...</span>
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<a name="l00017"></a>00017 <span class="comment">## Several information related to the PDB format are also available.</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">## In this file one will find most of functions that deal with atoms</span>
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<a name="l00020"></a>00020 <span class="comment">## structures.</span>
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<a name="l00021"></a>00021 <span class="comment">##</span>
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<a name="l00022"></a>00022 <span class="comment">## MODIFICATIONS HISTORY</span>
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<a name="l00023"></a>00023 <span class="comment">##</span>
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<a name="l00024"></a>00024 <span class="comment">## 28-11-08 (v) Comments UTD</span>
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<a name="l00025"></a>00025 <span class="comment">## 01-04-08 (v) Added comments and creation of history</span>
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<a name="l00026"></a>00026 <span class="comment">## 01-01-08 (vp) Created (random date...)</span>
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<a name="l00027"></a>00027 <span class="comment">## </span>
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<a name="l00028"></a>00028 <span class="comment">## TODO or SUGGESTIONS</span>
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<a name="l00029"></a>00029 <span class="comment">##</span>
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<a name="l00030"></a>00030 <span class="comment">## (v) Merge with pertable.c</span>
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<a name="l00031"></a>00031 <span class="comment">## (v) Add a function to write all known atomic properties for a given atom type</span>
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<a name="l00032"></a>00032 <span class="comment">## (v) Maybe implement a structure for a list of atoms instead of a tab.</span>
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<a name="l00033"></a>00033 <span class="comment">## (v) Check and update if necessary comments of each function!!</span>
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<a name="l00034"></a>00034 <span class="comment"></span>
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<a name="l00035"></a>00035 <span class="comment">*/</span>
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<a name="l00036"></a>00036
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<a name="l00037"></a>00037
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<a name="l00038"></a>00038 <span class="comment">/*</span>
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<a name="l00039"></a>00039 <span class="comment"> COPYRIGHT DISCLAIMER</span>
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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"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
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<a name="l00042"></a>00042 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
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<a name="l00043"></a>00043 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
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<a name="l00044"></a>00044 <span class="comment"> Schmidtke.</span>
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<a name="l00045"></a>00045 <span class="comment"></span>
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<a name="l00046"></a>00046 <span class="comment"> Vincent Le Guilloux 28 November 2008</span>
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<a name="l00047"></a>00047 <span class="comment"> Peter Schmidtke 28 November 2008</span>
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<a name="l00048"></a>00048 <span class="comment"> Pierre Tuffery 28 November 2008</span>
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<a name="l00049"></a>00049 <span class="comment"></span>
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<a name="l00050"></a>00050 <span class="comment"> GNU GPL</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"> This file is part of the fpocket package.</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"> fpocket is free software: you can redistribute it and/or modify</span>
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<a name="l00055"></a>00055 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
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<a name="l00056"></a>00056 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
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<a name="l00057"></a>00057 <span class="comment"> (at your option) any later version.</span>
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<a name="l00058"></a>00058 <span class="comment"></span>
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<a name="l00059"></a>00059 <span class="comment"> fpocket is distributed in the hope that it will be useful,</span>
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<a name="l00060"></a>00060 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<a name="l00061"></a>00061 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<a name="l00062"></a>00062 <span class="comment"> GNU General Public License for more details.</span>
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<a name="l00063"></a>00063 <span class="comment"></span>
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<a name="l00064"></a>00064 <span class="comment"> You should have received a copy of the GNU General Public License</span>
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<a name="l00065"></a>00065 <span class="comment"> along with fpocket. If not, see <http://www.gnu.org/licenses/>.</span>
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<a name="l00066"></a>00066 <span class="comment"></span>
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<a name="l00067"></a>00067 <span class="comment">**/</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 <span class="comment"> ## FUNCTION: </span>
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<a name="l00071"></a>00071 <span class="comment"> get_mol_mass</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"> ## SPECIFICATION:</span>
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<a name="l00074"></a>00074 <span class="comment"> Calculate mass of a molecule represented by a list of atoms. (structure)</span>
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<a name="l00075"></a>00075 <span class="comment"> Perform a simple sum of atoms mass.</span>
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<a name="l00076"></a>00076 <span class="comment"> </span>
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<a name="l00077"></a>00077 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00078"></a>00078 <span class="comment"> @ s_atm *atoms : List of atoms structures</span>
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<a name="l00079"></a>00079 <span class="comment"> @ int natoms : Number of atoms</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"> float: mass of the molecule</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="atom_8h.html#fa83a33583c67b9a3a4439b14000b983">00085</a> <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#fa83a33583c67b9a3a4439b14000b983">get_mol_mass</a>(<a class="code" href="structs__atm.html">s_atm</a> *latoms, <span class="keywordtype">int</span> natoms)
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<a name="l00086"></a>00086 {
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<a name="l00087"></a>00087 <span class="keywordtype">float</span> mass = 00.0 ;
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<a name="l00088"></a>00088 <span class="keywordflow">if</span>(latoms) {
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<a name="l00089"></a>00089 <span class="keywordtype">int</span> i ;
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<a name="l00090"></a>00090 <span class="keywordflow">for</span>(i = 0 ; i < natoms ; i++) {
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<a name="l00091"></a>00091 mass += latoms[i].<a class="code" href="structs__atm.html#ebbe1b323a702c23ef5bb21888adb6a8">mass</a> ;
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<a name="l00092"></a>00092 }
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<a name="l00093"></a>00093 }
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<a name="l00094"></a>00094 <span class="keywordflow">return</span> mass ;
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<a name="l00095"></a>00095 }
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<a name="l00096"></a>00096 <span class="comment"></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"> ## FUNCTION: </span>
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<a name="l00099"></a>00099 <span class="comment"> get_mol_mass_ptr</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"> ## SPECIFICATION:</span>
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<a name="l00102"></a>00102 <span class="comment"> Same as previous, but using different input type (array of pointers)</span>
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<a name="l00103"></a>00103 <span class="comment"> </span>
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<a name="l00104"></a>00104 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00105"></a>00105 <span class="comment"> @ s_atm **atoms : List of pointers to atom structures</span>
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<a name="l00106"></a>00106 <span class="comment"> @ int natoms : Number of atoms</span>
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<a name="l00107"></a>00107 <span class="comment"> </span>
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<a name="l00108"></a>00108 <span class="comment"> ## RETURN:</span>
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<a name="l00109"></a>00109 <span class="comment"> float: mass of the molecule</span>
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<a name="l00110"></a>00110 <span class="comment"> </span>
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<a name="l00111"></a>00111 <span class="comment">*/</span>
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<a name="l00112"></a><a class="code" href="atom_8h.html#6c124482d4ea1d4956cb095413e4b3af">00112</a> <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#6c124482d4ea1d4956cb095413e4b3af">get_mol_mass_ptr</a>(<a class="code" href="structs__atm.html">s_atm</a> **latoms, <span class="keywordtype">int</span> natoms)
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<a name="l00113"></a>00113 {
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<a name="l00114"></a>00114 <span class="keywordtype">float</span> mass = 00.0 ;
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<a name="l00115"></a>00115 <span class="keywordflow">if</span>(latoms) {
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<a name="l00116"></a>00116 <span class="keywordtype">int</span> i ;
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<a name="l00117"></a>00117 <span class="keywordflow">for</span>(i = 0 ; i < natoms ; i++) {
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<a name="l00118"></a>00118 mass += latoms[i]-><a class="code" href="structs__atm.html#ebbe1b323a702c23ef5bb21888adb6a8">mass</a> ;
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<a name="l00119"></a>00119 }
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<a name="l00120"></a>00120 }
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<a name="l00121"></a>00121 <span class="keywordflow">return</span> mass ;
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<a name="l00122"></a>00122 }
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<a name="l00123"></a>00123 <span class="comment"></span>
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<a name="l00124"></a>00124 <span class="comment">/**</span>
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<a name="l00125"></a>00125 <span class="comment"> ## FUNCTION: </span>
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<a name="l00126"></a>00126 <span class="comment"> set_mol_barycenter_ptr</span>
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<a name="l00127"></a>00127 <span class="comment"> </span>
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<a name="l00128"></a>00128 <span class="comment"> ## SPECIFICATION:</span>
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<a name="l00129"></a>00129 <span class="comment"> Calculate the barycenter of a molecule represented by a list of atoms </span>
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<a name="l00130"></a>00130 <span class="comment"> pointers.</span>
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<a name="l00131"></a>00131 <span class="comment"> </span>
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<a name="l00132"></a>00132 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00133"></a>00133 <span class="comment"> @ s_atm **atoms : List of pointers to atoms structures</span>
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<a name="l00134"></a>00134 <span class="comment"> @ int natoms : Number of atoms</span>
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<a name="l00135"></a>00135 <span class="comment"> @ float bary[3] : OUTPUT: Where to store the calculated barycenter</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"> ## RETURN:</span>
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<a name="l00138"></a>00138 <span class="comment"> void (the OUTPUT is set using the input parameter bary)</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">*/</span>
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<a name="l00141"></a><a class="code" href="atom_8h.html#6648ca5bb9d7384c43dda5156e333f24">00141</a> <span class="keywordtype">void</span> <a class="code" href="atom_8c.html#6648ca5bb9d7384c43dda5156e333f24">set_mol_barycenter_ptr</a>(<a class="code" href="structs__atm.html">s_atm</a> **latoms, <span class="keywordtype">int</span> natoms, <span class="keywordtype">float</span> bary[3])
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<a name="l00142"></a>00142 {
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<a name="l00143"></a>00143 <span class="keywordtype">float</span> xsum = 0.0,
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<a name="l00144"></a>00144 ysum = 0.0,
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<a name="l00145"></a>00145 zsum = 0.0 ;
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<a name="l00146"></a>00146
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<a name="l00147"></a>00147 <span class="keywordflow">if</span>(latoms) {
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<a name="l00148"></a>00148 <span class="keywordtype">int</span> i ;
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<a name="l00149"></a>00149 <span class="keywordflow">for</span>(i = 0 ; i < natoms ; i++) {
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<a name="l00150"></a>00150 xsum += latoms[i]-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a> ;
|
|
<a name="l00151"></a>00151 ysum += latoms[i]-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a> ;
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<a name="l00152"></a>00152 zsum += latoms[i]-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a> ;
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|
<a name="l00153"></a>00153 }
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<a name="l00154"></a>00154 }
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<a name="l00155"></a>00155
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<a name="l00156"></a>00156 bary[0] = xsum / natoms ;
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<a name="l00157"></a>00157 bary[1] = xsum / natoms ;
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<a name="l00158"></a>00158 bary[2] = xsum / natoms ;
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<a name="l00159"></a>00159 }
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|
<a name="l00160"></a>00160 <span class="comment"></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"> ## FUNCTION: </span>
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<a name="l00163"></a>00163 <span class="comment"> get_mol_volume_ptr</span>
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|
<a name="l00164"></a>00164 <span class="comment"> </span>
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|
<a name="l00165"></a>00165 <span class="comment"> ## SPECIFICATION: </span>
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<a name="l00166"></a>00166 <span class="comment"> Get an monte carlo approximation of the volume occupied by the atoms given </span>
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|
<a name="l00167"></a>00167 <span class="comment"> in argument (list of pointers).</span>
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<a name="l00168"></a>00168 <span class="comment"> </span>
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<a name="l00169"></a>00169 <span class="comment"> ## PARAMETRES:</span>
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<a name="l00170"></a>00170 <span class="comment"> @ s_atm **atoms : List of pointer to atoms</span>
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<a name="l00171"></a>00171 <span class="comment"> @ int natoms : Number of atoms</span>
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<a name="l00172"></a>00172 <span class="comment"> @ int niter : Number of monte carlo iteration to perform</span>
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<a name="l00173"></a>00173 <span class="comment"> </span>
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<a name="l00174"></a>00174 <span class="comment"> ## RETURN:</span>
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<a name="l00175"></a>00175 <span class="comment"> float: calculated volume (approximation).</span>
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<a name="l00176"></a>00176 <span class="comment"> </span>
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<a name="l00177"></a>00177 <span class="comment">*/</span>
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<a name="l00178"></a><a class="code" href="atom_8h.html#d0f577a82cfdb135f707700c2b84e6a5">00178</a> <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#d0f577a82cfdb135f707700c2b84e6a5">get_mol_volume_ptr</a>(<a class="code" href="structs__atm.html">s_atm</a> **atoms, <span class="keywordtype">int</span> natoms, <span class="keywordtype">int</span> niter)
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<a name="l00179"></a>00179 {
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<a name="l00180"></a>00180 <span class="keywordtype">int</span> i = 0, j = 0,
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<a name="l00181"></a>00181 nb_in = 0;
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<a name="l00182"></a>00182
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<a name="l00183"></a>00183 <span class="keywordtype">float</span> xmin = 0.0, xmax = 0.0,
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<a name="l00184"></a>00184 ymin = 0.0, ymax = 0.0,
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<a name="l00185"></a>00185 zmin = 0.0, zmax = 0.0,
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<a name="l00186"></a>00186 xtmp = 0.0, ytmp = 0.0, ztmp = 0.0,
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<a name="l00187"></a>00187 xr = 0.0, yr = 0.0, zr = 0.0,
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<a name="l00188"></a>00188 vbox = 0.0 ;
|
|
<a name="l00189"></a>00189
|
|
<a name="l00190"></a>00190 <a class="code" href="structs__atm.html">s_atm</a> *acur = NULL ;
|
|
<a name="l00191"></a>00191
|
|
<a name="l00192"></a>00192 <span class="comment">/* First, search extrems coordinates to get a contour box of the molecule */</span>
|
|
<a name="l00193"></a>00193 <span class="keywordflow">for</span>(i = 0 ; i < natoms ; i++) {
|
|
<a name="l00194"></a>00194 acur = atoms[i] ;
|
|
<a name="l00195"></a>00195
|
|
<a name="l00196"></a>00196 <span class="keywordflow">if</span>(i == 0) {
|
|
<a name="l00197"></a>00197 xmin = acur-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a> - acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a> ; xmax = acur-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a> + acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a> ;
|
|
<a name="l00198"></a>00198 ymin = acur-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a> - acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a> ; ymax = acur-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a> + acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a> ;
|
|
<a name="l00199"></a>00199 zmin = acur-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a> - acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a> ; zmax = acur-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a> + acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a> ;
|
|
<a name="l00200"></a>00200 }
|
|
<a name="l00201"></a>00201 <span class="keywordflow">else</span> {
|
|
<a name="l00202"></a>00202 <span class="comment">/* Update the minimum and maximum extreme point */</span>
|
|
<a name="l00203"></a>00203 <span class="keywordflow">if</span>(xmin > (xtmp = acur-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a> - acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>)) xmin = xtmp ;
|
|
<a name="l00204"></a>00204 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(xmax < (xtmp = acur-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a> + acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>)) xmax = xtmp ;
|
|
<a name="l00205"></a>00205
|
|
<a name="l00206"></a>00206 <span class="keywordflow">if</span>(ymin > (ytmp = acur-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a> - acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>)) ymin = ytmp ;
|
|
<a name="l00207"></a>00207 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(ymax < (ytmp = acur-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a> + acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>)) ymax = ytmp ;
|
|
<a name="l00208"></a>00208
|
|
<a name="l00209"></a>00209 <span class="keywordflow">if</span>(zmin > (ztmp = acur-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a> - acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>)) zmin = ztmp ;
|
|
<a name="l00210"></a>00210 <span class="keywordflow">else</span> <span class="keywordflow">if</span>(zmax < (ztmp = acur-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a> + acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>)) zmax = ztmp ;
|
|
<a name="l00211"></a>00211 }
|
|
<a name="l00212"></a>00212 }
|
|
<a name="l00213"></a>00213
|
|
<a name="l00214"></a>00214 <span class="comment">/* Next calculate the contour box volume */</span>
|
|
<a name="l00215"></a>00215 vbox = (xmax - xmin)*(ymax - ymin)*(zmax - zmin) ;
|
|
<a name="l00216"></a>00216
|
|
<a name="l00217"></a>00217 <span class="comment">/* Then apply monte carlo approximation of the volume. */</span>
|
|
<a name="l00218"></a>00218 <span class="keywordflow">for</span>(i = 0 ; i < niter ; i++) {
|
|
<a name="l00219"></a>00219 xr = <a class="code" href="utils_8c.html#5492196e16ed2d16bae1df8483ef79ed">rand_uniform</a>(xmin, xmax) ;
|
|
<a name="l00220"></a>00220 yr = <a class="code" href="utils_8c.html#5492196e16ed2d16bae1df8483ef79ed">rand_uniform</a>(ymin, ymax) ;
|
|
<a name="l00221"></a>00221 zr = <a class="code" href="utils_8c.html#5492196e16ed2d16bae1df8483ef79ed">rand_uniform</a>(zmin, zmax) ;
|
|
<a name="l00222"></a>00222
|
|
<a name="l00223"></a>00223 <span class="keywordflow">for</span>(j = 0 ; j < natoms ; j++) {
|
|
<a name="l00224"></a>00224 acur = atoms[j] ;
|
|
<a name="l00225"></a>00225 xtmp = acur-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a> - xr ;
|
|
<a name="l00226"></a>00226 ytmp = acur-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a> - yr ;
|
|
<a name="l00227"></a>00227 ztmp = acur-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a> - zr ;
|
|
<a name="l00228"></a>00228
|
|
<a name="l00229"></a>00229 <span class="comment">/* Compare r^2 and dist(center, random_point)^2 */</span>
|
|
<a name="l00230"></a>00230 <span class="keywordflow">if</span>((acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>*acur-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>) > (xtmp*xtmp + ytmp*ytmp + ztmp*ztmp)) {
|
|
<a name="l00231"></a>00231 <span class="comment">/* The point is inside one of the vertice!! */</span>
|
|
<a name="l00232"></a>00232 nb_in ++ ; break ;
|
|
<a name="l00233"></a>00233 }
|
|
<a name="l00234"></a>00234 }
|
|
<a name="l00235"></a>00235 }
|
|
<a name="l00236"></a>00236
|
|
<a name="l00237"></a>00237 <span class="comment">/* Ok lets just return the volume Vpok = Nb_in/Niter*Vbox */</span>
|
|
<a name="l00238"></a>00238 <span class="keywordflow">return</span> ((<span class="keywordtype">float</span>)nb_in)/((float)niter)*vbox;
|
|
<a name="l00239"></a>00239 }
|
|
<a name="l00240"></a>00240 <span class="comment"></span>
|
|
<a name="l00241"></a>00241 <span class="comment">/**</span>
|
|
<a name="l00242"></a>00242 <span class="comment"> ## FUNCTION: </span>
|
|
<a name="l00243"></a>00243 <span class="comment"> is_in_lst_atm</span>
|
|
<a name="l00244"></a>00244 <span class="comment"> </span>
|
|
<a name="l00245"></a>00245 <span class="comment"> ## SPECIFICATION: </span>
|
|
<a name="l00246"></a>00246 <span class="comment"> Says wether an atom of id atm_id is in a list of atoms or not </span>
|
|
<a name="l00247"></a>00247 <span class="comment"> </span>
|
|
<a name="l00248"></a>00248 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00249"></a>00249 <span class="comment"> @ s_atm **lst_atm : List of atoms</span>
|
|
<a name="l00250"></a>00250 <span class="comment"> @ int nb_atms : Number of atoms in the list</span>
|
|
<a name="l00251"></a>00251 <span class="comment"> @ int atm_id : ID of the atom to look for.</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"> 1 if the atom is in the tab, 0 if not</span>
|
|
<a name="l00255"></a>00255 <span class="comment"> </span>
|
|
<a name="l00256"></a>00256 <span class="comment">*/</span>
|
|
<a name="l00257"></a><a class="code" href="atom_8h.html#a72221368b25d51716e4d59f02a8d753">00257</a> <span class="keywordtype">int</span> <a class="code" href="atom_8c.html#a72221368b25d51716e4d59f02a8d753">is_in_lst_atm</a>(<a class="code" href="structs__atm.html">s_atm</a> **lst_atm, <span class="keywordtype">int</span> nb_atm, <span class="keywordtype">int</span> atm_id)
|
|
<a name="l00258"></a>00258 {
|
|
<a name="l00259"></a>00259 <span class="keywordtype">int</span> i ;
|
|
<a name="l00260"></a>00260 <span class="keywordflow">for</span>(i = 0 ; i < nb_atm ; i++) {
|
|
<a name="l00261"></a>00261 <span class="keywordflow">if</span>(atm_id == lst_atm[i]-><span class="keywordtype">id</span>) <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00262"></a>00262 }
|
|
<a name="l00263"></a>00263
|
|
<a name="l00264"></a>00264 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00265"></a>00265 }
|
|
<a name="l00266"></a>00266
|
|
<a name="l00267"></a>00267 <span class="comment"></span>
|
|
<a name="l00268"></a>00268 <span class="comment">/**</span>
|
|
<a name="l00269"></a>00269 <span class="comment"> ## FUNCTION: </span>
|
|
<a name="l00270"></a>00270 <span class="comment"> atm_corsp</span>
|
|
<a name="l00271"></a>00271 <span class="comment"> </span>
|
|
<a name="l00272"></a>00272 <span class="comment"> ## SPECIFICATION: </span>
|
|
<a name="l00273"></a>00273 <span class="comment"> Calculate correspondance between two list of atoms, using the first list as</span>
|
|
<a name="l00274"></a>00274 <span class="comment"> reference.</span>
|
|
<a name="l00275"></a>00275 <span class="comment"> </span>
|
|
<a name="l00276"></a>00276 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00277"></a>00277 <span class="comment"> @ s_atm **al1 : First list</span>
|
|
<a name="l00278"></a>00278 <span class="comment"> @ int nal1 : Number of atoms of the first list</span>
|
|
<a name="l00279"></a>00279 <span class="comment"> @ s_atm **al2 : Second list</span>
|
|
<a name="l00280"></a>00280 <span class="comment"> @ int nal2 : Number of atoms of the second list</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"> float: % of atoms of the first list present in the second list</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="atom_8h.html#29b02d9d40f326871aa70623cdd97556">00286</a> <span class="keywordtype">float</span> <a class="code" href="atom_8c.html#a960d66d3bd7cce701a12f56999056b4">atm_corsp</a>(<a class="code" href="structs__atm.html">s_atm</a> **al1, <span class="keywordtype">int</span> nal1, <a class="code" href="structs__atm.html">s_atm</a> **al2, <span class="keywordtype">int</span> nal2)
|
|
<a name="l00287"></a>00287 {
|
|
<a name="l00288"></a>00288 <span class="keywordtype">int</span> i, j,
|
|
<a name="l00289"></a>00289 nb_atm_found = 0 ;
|
|
<a name="l00290"></a>00290 <a class="code" href="structs__atm.html">s_atm</a> *cural = NULL,
|
|
<a name="l00291"></a>00291 *curap ;
|
|
<a name="l00292"></a>00292
|
|
<a name="l00293"></a>00293 <span class="keywordflow">if</span>(nal1 <=0 || nal2 <= 0){
|
|
<a name="l00294"></a>00294 <span class="keywordflow">return</span> 0.0 ;
|
|
<a name="l00295"></a>00295 }
|
|
<a name="l00296"></a>00296
|
|
<a name="l00297"></a>00297 <span class="keywordflow">for</span>(i = 0 ; i < nal1 ; i++) {
|
|
<a name="l00298"></a>00298 <span class="keywordflow">for</span>(j = 0 ; j < nal2 ; j++) {
|
|
<a name="l00299"></a>00299 cural = al1[i] ;
|
|
<a name="l00300"></a>00300 curap = al2[j] ;
|
|
<a name="l00301"></a>00301
|
|
<a name="l00302"></a>00302 <span class="keywordflow">if</span>(curap->res_id == cural-><a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a> &&
|
|
<a name="l00303"></a>00303 ( (curap->id == cural-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>) || strcmp(cural-><a class="code" href="structs__atm.html#2f0330a30f640668efdd726a6dd05a93">name</a>, curap->name) == 0 ) ) {
|
|
<a name="l00304"></a>00304 nb_atm_found++ ;
|
|
<a name="l00305"></a>00305 break ;
|
|
<a name="l00306"></a>00306 }
|
|
<a name="l00307"></a>00307 }
|
|
<a name="l00308"></a>00308 }
|
|
<a name="l00309"></a>00309
|
|
<a name="l00310"></a>00310
|
|
<a name="l00311"></a>00311 <span class="keywordflow">return</span> ((<span class="keywordtype">float</span>)nb_atm_found)/((float)nal1)*100.0 ;
|
|
<a name="l00312"></a>00312 }
|
|
<a name="l00313"></a>00313 <span class="comment"></span>
|
|
<a name="l00314"></a>00314 <span class="comment">/**</span>
|
|
<a name="l00315"></a>00315 <span class="comment"> ## FUNCTION: </span>
|
|
<a name="l00316"></a>00316 <span class="comment"> void print_atoms(FILE *f, s_atm *atoms, int natoms) </span>
|
|
<a name="l00317"></a>00317 <span class="comment"> </span>
|
|
<a name="l00318"></a>00318 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00319"></a>00319 <span class="comment"> Print list of atoms...</span>
|
|
<a name="l00320"></a>00320 <span class="comment"> </span>
|
|
<a name="l00321"></a>00321 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00322"></a>00322 <span class="comment"> @ FILE *f : File to write in.</span>
|
|
<a name="l00323"></a>00323 <span class="comment"> @ s_atm *atoms : List of atoms</span>
|
|
<a name="l00324"></a>00324 <span class="comment"> @ int natoms : Number of atoms</span>
|
|
<a name="l00325"></a>00325 <span class="comment"> </span>
|
|
<a name="l00326"></a>00326 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00327"></a>00327 <span class="comment"> </span>
|
|
<a name="l00328"></a>00328 <span class="comment">*/</span>
|
|
<a name="l00329"></a><a class="code" href="atom_8h.html#9c0033f44cb65046ce5209b269da11d7">00329</a> <span class="keywordtype">void</span> <a class="code" href="atom_8c.html#9c0033f44cb65046ce5209b269da11d7">print_atoms</a>(FILE *f, <a class="code" href="structs__atm.html">s_atm</a> *atoms, <span class="keywordtype">int</span> natoms)
|
|
<a name="l00330"></a>00330 {
|
|
<a name="l00331"></a>00331 <a class="code" href="structs__atm.html">s_atm</a> *atom = NULL ;
|
|
<a name="l00332"></a>00332 <span class="keywordtype">int</span> i ;
|
|
<a name="l00333"></a>00333 <span class="keywordflow">for</span>(i = 0 ; i < natoms ; i++) {
|
|
<a name="l00334"></a>00334 atom = atoms + i ;
|
|
<a name="l00335"></a>00335 fprintf(f, <span class="stringliteral">"======== Atom %s (%d) ========\n"</span>, atom-><a class="code" href="structs__atm.html#2f0330a30f640668efdd726a6dd05a93">name</a>, atom-><a class="code" href="structs__atm.html#88237f06aa7a10cd6b382c19b800f230">id</a>) ;
|
|
<a name="l00336"></a>00336 fprintf(f, <span class="stringliteral">"Type: '%s', Residu: '%s' (%d), Chain: '%s'\n"</span>,
|
|
<a name="l00337"></a>00337 atom-><a class="code" href="structs__atm.html#98466fdfcb021884beb229b1dca361ae">type</a>, atom-><a class="code" href="structs__atm.html#e0ff20f2c491a8b16c866d9b1386b6a5">res_name</a>, atom-><a class="code" href="structs__atm.html#7c42c076ce151f4af210bef730b2b88f">res_id</a>, atom-><a class="code" href="structs__atm.html#c5b9464bd67f2cca101f7bf6beabb223">chain</a>);
|
|
<a name="l00338"></a>00338 fprintf(f, <span class="stringliteral">"x: %f, y: %f, z: %f, occ: %f, bfact: %f\n"</span>,
|
|
<a name="l00339"></a>00339 atom-><a class="code" href="structs__atm.html#2bf748fbcd9b6d0a472b292a6b244ed5">x</a>, atom-><a class="code" href="structs__atm.html#72534af707e830760a209fec348bc1af">y</a>, atom-><a class="code" href="structs__atm.html#f7cae749a2d07ffb393317f12745170a">z</a>, atom-><a class="code" href="structs__atm.html#1696926c680a1014360598d54a1dadb0">occupancy</a>, atom-><a class="code" href="structs__atm.html#6a1a5fd32629457dfa14626b25b5ae46">bfactor</a>);
|
|
<a name="l00340"></a>00340 fprintf(f, <span class="stringliteral">"symbol: '%s', charge: %d, mass: %f, vdw: %f\n"</span>,
|
|
<a name="l00341"></a>00341 atom-><a class="code" href="structs__atm.html#c80daffa94edeadd30433f6653e08054">symbol</a>, atom-><a class="code" href="structs__atm.html#a03a199ed11108d7710547df629c7d73">charge</a>, atom-><a class="code" href="structs__atm.html#ebbe1b323a702c23ef5bb21888adb6a8">mass</a>, atom-><a class="code" href="structs__atm.html#28c2d3bc2d95eb928ea6b5d37184d7f4">radius</a>);
|
|
<a name="l00342"></a>00342 }
|
|
<a name="l00343"></a>00343 }
|
|
</pre></div></div>
|
|
<hr size="1"><address style="text-align: right;"><small>Generated on Sun Jul 5 22:10:40 2009 for fpocket by
|
|
<a href="http://www.doxygen.org/index.html">
|
|
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.9 </small></address>
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</body>
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</html>
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