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<h1>pertable.c</h1><a href="pertable_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/pertable.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 pertable.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 28-11-08</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 defines the periodic element table. It's strongly based on the</span>
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<a name="l00015"></a>00015 <span class="comment">## VMD source code.</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">## MODIFICATIONS HISTORY</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">## 17-03-09 (v) Added function testing if a string is a valid element symbol</span>
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<a name="l00020"></a>00020 <span class="comment">## 28-11-08 (v) Comments UTD</span>
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<a name="l00021"></a>00021 <span class="comment">## 01-04-08 (v) Added template for comments and creation of history</span>
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<a name="l00022"></a>00022 <span class="comment">## 01-01-08 (vp) Created (random date...)</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">## TODO or SUGGESTIONS</span>
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<a name="l00025"></a>00025 <span class="comment">##</span>
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<a name="l00026"></a>00026 <span class="comment">## (v) Merge with atom.c</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"></span>
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<a name="l00029"></a>00029 <span class="comment">*/</span>
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<a name="l00030"></a>00030
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<a name="l00031"></a>00031 <span class="comment">/*</span>
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<a name="l00032"></a>00032 <span class="comment"> COPYRIGHT DISCLAIMER</span>
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<a name="l00033"></a>00033 <span class="comment"></span>
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<a name="l00034"></a>00034 <span class="comment"> Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, hereby</span>
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<a name="l00035"></a>00035 <span class="comment"> disclaim all copyright interest in the program “fpocket” (which</span>
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<a name="l00036"></a>00036 <span class="comment"> performs protein cavity detection) written by Vincent Le Guilloux and Peter</span>
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<a name="l00037"></a>00037 <span class="comment"> Schmidtke.</span>
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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"> Vincent Le Guilloux 28 November 2008</span>
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<a name="l00040"></a>00040 <span class="comment"> Peter Schmidtke 28 November 2008</span>
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<a name="l00041"></a>00041 <span class="comment"> Pierre Tuffery 28 November 2008</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"> GNU GPL</span>
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<a name="l00044"></a>00044 <span class="comment"></span>
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<a name="l00045"></a>00045 <span class="comment"> This file is part of the fpocket package.</span>
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<a name="l00046"></a>00046 <span class="comment"></span>
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<a name="l00047"></a>00047 <span class="comment"> fpocket is free software: you can redistribute it and/or modify</span>
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<a name="l00048"></a>00048 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
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<a name="l00049"></a>00049 <span class="comment"> the Free Software Foundation, either version 3 of the License, or</span>
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<a name="l00050"></a>00050 <span class="comment"> (at your option) any later version.</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"> fpocket is distributed in the hope that it will be useful,</span>
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<a name="l00053"></a>00053 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<a name="l00054"></a>00054 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<a name="l00055"></a>00055 <span class="comment"> GNU General Public License for more details.</span>
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<a name="l00056"></a>00056 <span class="comment"></span>
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<a name="l00057"></a>00057 <span class="comment"> You should have received a copy of the GNU General Public License</span>
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<a name="l00058"></a>00058 <span class="comment"> along with fpocket. If not, see <http://www.gnu.org/licenses/>.</span>
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<a name="l00059"></a>00059 <span class="comment"></span>
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<a name="l00060"></a>00060 <span class="comment">**/</span>
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<a name="l00061"></a>00061
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<a name="l00062"></a><a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">00062</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> = 112 ; <span class="comment">/**< number of elements in the @static const char *ST_pte_symbol list*/</span>
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<a name="l00063"></a>00063
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<a name="l00064"></a><a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">00064</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *<a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[] = {
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<a name="l00065"></a>00065 <span class="stringliteral">"X"</span>, <span class="stringliteral">"H"</span>, <span class="stringliteral">"He"</span>, <span class="stringliteral">"Li"</span>, <span class="stringliteral">"Be"</span>, <span class="stringliteral">"B"</span>, <span class="stringliteral">"C"</span>, <span class="stringliteral">"N"</span>, <span class="stringliteral">"O"</span>, <span class="stringliteral">"F"</span>, <span class="stringliteral">"Ne"</span>,
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<a name="l00066"></a>00066 <span class="stringliteral">"Na"</span>, <span class="stringliteral">"Mg"</span>, <span class="stringliteral">"Al"</span>, <span class="stringliteral">"Si"</span>, <span class="stringliteral">"P"</span> , <span class="stringliteral">"S"</span>, <span class="stringliteral">"Cl"</span>, <span class="stringliteral">"Ar"</span>, <span class="stringliteral">"K"</span>, <span class="stringliteral">"Ca"</span>, <span class="stringliteral">"Sc"</span>,
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<a name="l00067"></a>00067 <span class="stringliteral">"Ti"</span>, <span class="stringliteral">"V"</span>, <span class="stringliteral">"Cr"</span>, <span class="stringliteral">"Mn"</span>, <span class="stringliteral">"Fe"</span>, <span class="stringliteral">"Co"</span>, <span class="stringliteral">"Ni"</span>, <span class="stringliteral">"Cu"</span>, <span class="stringliteral">"Zn"</span>, <span class="stringliteral">"Ga"</span>, <span class="stringliteral">"Ge"</span>,
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<a name="l00068"></a>00068 <span class="stringliteral">"As"</span>, <span class="stringliteral">"Se"</span>, <span class="stringliteral">"Br"</span>, <span class="stringliteral">"Kr"</span>, <span class="stringliteral">"Rb"</span>, <span class="stringliteral">"Sr"</span>, <span class="stringliteral">"Y"</span>, <span class="stringliteral">"Zr"</span>, <span class="stringliteral">"Nb"</span>, <span class="stringliteral">"Mo"</span>, <span class="stringliteral">"Tc"</span>,
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<a name="l00069"></a>00069 <span class="stringliteral">"Ru"</span>, <span class="stringliteral">"Rh"</span>, <span class="stringliteral">"Pd"</span>, <span class="stringliteral">"Ag"</span>, <span class="stringliteral">"Cd"</span>, <span class="stringliteral">"In"</span>, <span class="stringliteral">"Sn"</span>, <span class="stringliteral">"Sb"</span>, <span class="stringliteral">"Te"</span>, <span class="stringliteral">"I"</span>, <span class="stringliteral">"Xe"</span>,
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<a name="l00070"></a>00070 <span class="stringliteral">"Cs"</span>, <span class="stringliteral">"Ba"</span>, <span class="stringliteral">"La"</span>, <span class="stringliteral">"Ce"</span>, <span class="stringliteral">"Pr"</span>, <span class="stringliteral">"Nd"</span>, <span class="stringliteral">"Pm"</span>, <span class="stringliteral">"Sm"</span>, <span class="stringliteral">"Eu"</span>, <span class="stringliteral">"Gd"</span>, <span class="stringliteral">"Tb"</span>,
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<a name="l00071"></a>00071 <span class="stringliteral">"Dy"</span>, <span class="stringliteral">"Ho"</span>, <span class="stringliteral">"Er"</span>, <span class="stringliteral">"Tm"</span>, <span class="stringliteral">"Yb"</span>, <span class="stringliteral">"Lu"</span>, <span class="stringliteral">"Hf"</span>, <span class="stringliteral">"Ta"</span>, <span class="stringliteral">"W"</span>, <span class="stringliteral">"Re"</span>, <span class="stringliteral">"Os"</span>,
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<a name="l00072"></a>00072 <span class="stringliteral">"Ir"</span>, <span class="stringliteral">"Pt"</span>, <span class="stringliteral">"Au"</span>, <span class="stringliteral">"Hg"</span>, <span class="stringliteral">"Tl"</span>, <span class="stringliteral">"Pb"</span>, <span class="stringliteral">"Bi"</span>, <span class="stringliteral">"Po"</span>, <span class="stringliteral">"At"</span>, <span class="stringliteral">"Rn"</span>, <span class="stringliteral">"Fr"</span>,
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<a name="l00073"></a>00073 <span class="stringliteral">"Ra"</span>, <span class="stringliteral">"Ac"</span>, <span class="stringliteral">"Th"</span>, <span class="stringliteral">"Pa"</span>, <span class="stringliteral">"U"</span>, <span class="stringliteral">"Np"</span>, <span class="stringliteral">"Pu"</span>, <span class="stringliteral">"Am"</span>, <span class="stringliteral">"Cm"</span>, <span class="stringliteral">"Bk"</span>, <span class="stringliteral">"Cf"</span>,
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<a name="l00074"></a>00074 <span class="stringliteral">"Es"</span>, <span class="stringliteral">"Fm"</span>, <span class="stringliteral">"Md"</span>, <span class="stringliteral">"No"</span>, <span class="stringliteral">"Lr"</span>, <span class="stringliteral">"Rf"</span>, <span class="stringliteral">"Db"</span>, <span class="stringliteral">"Sg"</span>, <span class="stringliteral">"Bh"</span>, <span class="stringliteral">"Hs"</span>, <span class="stringliteral">"Mt"</span>,
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<a name="l00075"></a>00075 <span class="stringliteral">"Ds"</span>, <span class="stringliteral">"Rg"</span>
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<a name="l00076"></a>00076 } ; <span class="comment">/**< element list*/</span>
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<a name="l00077"></a>00077
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<a name="l00078"></a>00078
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<a name="l00079"></a><a class="code" href="pertable_8c.html#04531a8fc2decd1f26e2e6f1b47730e9">00079</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#04531a8fc2decd1f26e2e6f1b47730e9">ST_prot_nelem</a> = 5 ;
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<a name="l00080"></a><a class="code" href="pertable_8c.html#fdecbeb72c5385dcec00ece864eefbb0">00080</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *<a class="code" href="pertable_8c.html#fdecbeb72c5385dcec00ece864eefbb0">ST_pte_prot_symbol</a>[] = {
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<a name="l00081"></a>00081 <span class="stringliteral">"H"</span>, <span class="stringliteral">"C"</span>, <span class="stringliteral">"N"</span>, <span class="stringliteral">"O"</span>, <span class="stringliteral">"S"</span>
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<a name="l00082"></a>00082 } ;
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<a name="l00083"></a>00083
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<a name="l00084"></a><a class="code" href="pertable_8c.html#a39f6df9f0f4fd5b7bda545a8e9005c5">00084</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#a39f6df9f0f4fd5b7bda545a8e9005c5">ST_nucl_acid_nelem</a> = 5 ;
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<a name="l00085"></a><a class="code" href="pertable_8c.html#29ee0fc69813b1ae66b63a82e886cf1c">00085</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *<a class="code" href="pertable_8c.html#29ee0fc69813b1ae66b63a82e886cf1c">ST_pte_nucl_acid_symbol</a>[] = {
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<a name="l00086"></a>00086 <span class="stringliteral">"H"</span>, <span class="stringliteral">"C"</span>, <span class="stringliteral">"N"</span>, <span class="stringliteral">"O"</span>, <span class="stringliteral">"P"</span>
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<a name="l00087"></a>00087 } ;
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<a name="l00088"></a>00088
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<a name="l00089"></a><a class="code" href="pertable_8c.html#732014afeb1ee1a32a9ca967578a1f2e">00089</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#732014afeb1ee1a32a9ca967578a1f2e">ST_n_standard_res_names</a> = 23;
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<a name="l00090"></a><a class="code" href="pertable_8c.html#479c3e9145f096eacda7d060c12ca40a">00090</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *<a class="code" href="pertable_8c.html#479c3e9145f096eacda7d060c12ca40a">ST_standard_res_names</a> [] = {
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<a name="l00091"></a>00091 <span class="stringliteral">"GLY"</span>, <span class="stringliteral">"LEU"</span>, <span class="stringliteral">"ILE"</span>, <span class="stringliteral">"TRP"</span>, <span class="stringliteral">"MET"</span>, <span class="stringliteral">"SER"</span>, <span class="stringliteral">"THR"</span>, <span class="stringliteral">"LYS"</span>, <span class="stringliteral">"ARG"</span>, <span class="stringliteral">"ASN"</span>,
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<a name="l00092"></a>00092 <span class="stringliteral">"GLN"</span>, <span class="stringliteral">"GLU"</span>, <span class="stringliteral">"ASP"</span>, <span class="stringliteral">"CYS"</span>, <span class="stringliteral">"PRO"</span>, <span class="stringliteral">"HIS"</span>, <span class="stringliteral">"TYR"</span>, <span class="stringliteral">"PHE"</span>, <span class="stringliteral">"VAL"</span>, <span class="stringliteral">"ALA"</span>,
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<a name="l00093"></a>00093 <span class="stringliteral">"HIE"</span>, <span class="stringliteral">"HID"</span>, <span class="stringliteral">"HIP"</span>, <span class="stringliteral">"HSD"</span>, <span class="stringliteral">"HSE"</span>, <span class="stringliteral">"HSP"</span>
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<a name="l00094"></a>00094 } ;
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<a name="l00095"></a>00095
|
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<a name="l00096"></a><a class="code" href="pertable_8c.html#6dc30c101ce0857fc53db28b20e05fdb">00096</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#6dc30c101ce0857fc53db28b20e05fdb">ST_n_standard_nucl_acid_names</a> = 9;
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|
<a name="l00097"></a><a class="code" href="pertable_8c.html#b30d971f0ed354b67ae4376ca53a13fb">00097</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span> *<a class="code" href="pertable_8c.html#b30d971f0ed354b67ae4376ca53a13fb">ST_standard_nucl_acid_names</a> [] = {
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<a name="l00098"></a>00098 <span class="stringliteral">"dG"</span>,<span class="stringliteral">"dC"</span>, <span class="stringliteral">"dT"</span>,<span class="stringliteral">"dA"</span>,<span class="stringliteral">"A"</span>,<span class="stringliteral">"C"</span>,<span class="stringliteral">"T"</span>,<span class="stringliteral">"G"</span>,<span class="stringliteral">"U"</span>
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<a name="l00099"></a>00099 } ;
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<a name="l00100"></a>00100
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<a name="l00101"></a>00101
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<a name="l00102"></a><a class="code" href="pertable_8c.html#cdcf0f499b84258ffeff11ca58cfdafc">00102</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">float</span> <a class="code" href="pertable_8c.html#cdcf0f499b84258ffeff11ca58cfdafc">ST_pte_electronegativity</a>[] = {
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<a name="l00103"></a>00103 0.0, 2.1, 0.98, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, -1.0,
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<a name="l00104"></a>00104 0.9, 1.2, 1.5, 1.8, 2.1, 2.5, 3.0, -1.0, 0.8, 1.0, 1.3,
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<a name="l00105"></a>00105 1.5, 1.6, 1.6, 1.5, 1.8, 1.8, 1.9, 1.9, 1.6, 1.8, 2.0,
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<a name="l00106"></a>00106 2.2, 2.4, 2.9, -1.0, 0.8, 1.0, 1.2, 1.3, 1.6, 2.0, 1.9,
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<a name="l00107"></a>00107 2.2, 2.2, 2.3, 1.9, 1.7, 1.7, 1.8, 2.0, 2.1, 2.6, 2.6,
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<a name="l00108"></a>00108 0.8, 0.9, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
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<a name="l00109"></a>00109 -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, 1.3, 1.5, 1.7, 1.9, 2.2,
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<a name="l00110"></a>00110 2.2, 2.2, 2.4, 1.9, 1.8, 1.8, 1.9, 2.0, 2.2, -1.0, 0.7,
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<a name="l00111"></a>00111 0.9, 1.1, 1.3, 1.5, 1.7, 1.3, 1.3, 1.3, 1.3, 1.3, 1.3,
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<a name="l00112"></a>00112 1.3, 1.3, 1.3, 1.3, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0,
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<a name="l00113"></a>00113 -1.0, -1.0
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<a name="l00114"></a>00114 } ; <span class="comment">/**< electronegativity list*/</span>
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<a name="l00115"></a>00115
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<a name="l00116"></a><a class="code" href="pertable_8c.html#2e1ab5c465d5c0542933f9c8f322ae5a">00116</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">float</span> <a class="code" href="pertable_8c.html#2e1ab5c465d5c0542933f9c8f322ae5a">ST_pte_mass</a>[] = {
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<a name="l00117"></a>00117 <span class="comment">/* X */</span> 0.00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,
|
|
<a name="l00118"></a>00118 <span class="comment">/* C */</span> 12.0107, 14.0067, 15.9994, 18.9984032, 20.1797,
|
|
<a name="l00119"></a>00119 <span class="comment">/* Na */</span> 22.989770, 24.3050, 26.981538, 28.0855, 30.973761,
|
|
<a name="l00120"></a>00120 <span class="comment">/* S */</span> 32.065, 35.453, 39.948, 39.0983, 40.078, 44.955910,
|
|
<a name="l00121"></a>00121 <span class="comment">/* Ti */</span> 47.867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,
|
|
<a name="l00122"></a>00122 <span class="comment">/* Ni */</span> 58.6934, 63.546, 65.409, 69.723, 72.64, 74.92160,
|
|
<a name="l00123"></a>00123 <span class="comment">/* Se */</span> 78.96, 79.904, 83.798, 85.4678, 87.62, 88.90585,
|
|
<a name="l00124"></a>00124 <span class="comment">/* Zr */</span> 91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550,
|
|
<a name="l00125"></a>00125 <span class="comment">/* Pd */</span> 106.42, 107.8682, 112.411, 114.818, 118.710, 121.760,
|
|
<a name="l00126"></a>00126 <span class="comment">/* Te */</span> 127.60, 126.90447, 131.293, 132.90545, 137.327,
|
|
<a name="l00127"></a>00127 <span class="comment">/* La */</span> 138.9055, 140.116, 140.90765, 144.24, 145.0, 150.36,
|
|
<a name="l00128"></a>00128 <span class="comment">/* Eu */</span> 151.964, 157.25, 158.92534, 162.500, 164.93032,
|
|
<a name="l00129"></a>00129 <span class="comment">/* Er */</span> 167.259, 168.93421, 173.04, 174.967, 178.49, 180.9479,
|
|
<a name="l00130"></a>00130 <span class="comment">/* W */</span> 183.84, 186.207, 190.23, 192.217, 195.078, 196.96655,
|
|
<a name="l00131"></a>00131 <span class="comment">/* Hg */</span> 200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0,
|
|
<a name="l00132"></a>00132 <span class="comment">/* Fr */</span> 223.0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,
|
|
<a name="l00133"></a>00133 <span class="comment">/* Np */</span> 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,
|
|
<a name="l00134"></a>00134 <span class="comment">/* Md */</span> 258.0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,
|
|
<a name="l00135"></a>00135 <span class="comment">/* Mt */</span> 268.0, 271.0, 272.0
|
|
<a name="l00136"></a>00136 }; <span class="comment">/**< atomic masses*/</span>
|
|
<a name="l00137"></a>00137
|
|
<a name="l00138"></a>00138 <span class="comment">/*</span>
|
|
<a name="l00139"></a>00139 <span class="comment"> A. Bondi, J. Phys. Chem., 68, 441 - 452, 1964, </span>
|
|
<a name="l00140"></a>00140 <span class="comment"> .Phys.Chem., 100, 7384 - 7391, 1996.</span>
|
|
<a name="l00141"></a>00141 <span class="comment"> */</span>
|
|
<a name="l00142"></a><a class="code" href="pertable_8c.html#d218d21e3e71e1b659ce8ccd48b9f540">00142</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">float</span> <a class="code" href="pertable_8c.html#d218d21e3e71e1b659ce8ccd48b9f540">ST_pte_rvdw</a>[] = {
|
|
<a name="l00143"></a>00143 <span class="comment">/* X */</span> 1.5, 1.2, 1.4, 1.82, 2.0, 2.0,
|
|
<a name="l00144"></a>00144 <span class="comment">/* C */</span> 1.7, 1.55, 1.52, 1.47, 1.54,
|
|
<a name="l00145"></a>00145 <span class="comment">/* Na */</span> 2.27, 1.73, 2.0, 2.1, 1.8,
|
|
<a name="l00146"></a>00146 <span class="comment">/* S */</span> 1.8, 1.75, 1.88, 2.75, 2.0, 2.0,
|
|
<a name="l00147"></a>00147 <span class="comment">/* Ti */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00148"></a>00148 <span class="comment">/* Ni */</span> 1.63, 1.4, 1.39, 1.07, 2.0, 1.85,
|
|
<a name="l00149"></a>00149 <span class="comment">/* Se */</span> 1.9, 1.85, 2.02, 2.0, 2.0, 2.0,
|
|
<a name="l00150"></a>00150 <span class="comment">/* Zr */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00151"></a>00151 <span class="comment">/* Pd */</span> 1.63, 1.72, 1.58, 1.93, 2.17, 2.0,
|
|
<a name="l00152"></a>00152 <span class="comment">/* Te */</span> 2.06, 1.98, 2.16, 2.0, 2.0,
|
|
<a name="l00153"></a>00153 <span class="comment">/* La */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00154"></a>00154 <span class="comment">/* Eu */</span> 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00155"></a>00155 <span class="comment">/* Er */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00156"></a>00156 <span class="comment">/* W */</span> 2.0, 2.0, 2.0, 2.0, 1.72, 1.66,
|
|
<a name="l00157"></a>00157 <span class="comment">/* Hg */</span> 1.55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00158"></a>00158 <span class="comment">/* Fr */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 1.86,
|
|
<a name="l00159"></a>00159 <span class="comment">/* Np */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00160"></a>00160 <span class="comment">/* Md */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00161"></a>00161 <span class="comment">/* Mt */</span> 2.0, 2.0, 2.0
|
|
<a name="l00162"></a>00162 }; <span class="comment">/**< VDW radii for different elements*/</span>
|
|
<a name="l00163"></a>00163 <span class="comment"></span>
|
|
<a name="l00164"></a>00164 <span class="comment">/**</span>
|
|
<a name="l00165"></a>00165 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00166"></a>00166 <span class="comment"> pte_get_mass</span>
|
|
<a name="l00167"></a>00167 <span class="comment"> </span>
|
|
<a name="l00168"></a>00168 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00169"></a>00169 <span class="comment"> Returns the mass for a given element</span>
|
|
<a name="l00170"></a>00170 <span class="comment"> </span>
|
|
<a name="l00171"></a>00171 <span class="comment"> ## PARAMETERS: </span>
|
|
<a name="l00172"></a>00172 <span class="comment"> @ const char *symbol: The symbol of the element in the periodic table</span>
|
|
<a name="l00173"></a>00173 <span class="comment"> </span>
|
|
<a name="l00174"></a>00174 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00175"></a>00175 <span class="comment"> float: mass corresponding to symbol</span>
|
|
<a name="l00176"></a>00176 <span class="comment"> </span>
|
|
<a name="l00177"></a>00177 <span class="comment">*/</span>
|
|
<a name="l00178"></a><a class="code" href="pertable_8h.html#3eeaf52663f6057aee4f869d5c78a8c8">00178</a> <span class="keywordtype">float</span> <a class="code" href="pertable_8c.html#3eeaf52663f6057aee4f869d5c78a8c8">pte_get_mass</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *symbol)
|
|
<a name="l00179"></a>00179 {
|
|
<a name="l00180"></a>00180 <span class="keywordtype">char</span> atom[3] ;
|
|
<a name="l00181"></a>00181 <span class="keywordflow">if</span> (symbol != NULL) {
|
|
<a name="l00182"></a>00182 atom[0] = (char) toupper((<span class="keywordtype">int</span>) symbol[0]);
|
|
<a name="l00183"></a>00183 atom[1] = (char) tolower((<span class="keywordtype">int</span>) symbol[1]);
|
|
<a name="l00184"></a>00184 atom[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00185"></a>00185
|
|
<a name="l00186"></a>00186 <span class="keywordtype">int</span> i ;
|
|
<a name="l00187"></a>00187 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00188"></a>00188 <span class="keywordflow">if</span> ( (<a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][0] == atom[0]) && (<a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][1] == atom[1]) ) {
|
|
<a name="l00189"></a>00189
|
|
<a name="l00190"></a>00190 <span class="keywordflow">return</span> <a class="code" href="pertable_8c.html#2e1ab5c465d5c0542933f9c8f322ae5a">ST_pte_mass</a>[i] ;
|
|
<a name="l00191"></a>00191 }
|
|
<a name="l00192"></a>00192 }
|
|
<a name="l00193"></a>00193 }
|
|
<a name="l00194"></a>00194
|
|
<a name="l00195"></a>00195
|
|
<a name="l00196"></a>00196 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00197"></a>00197 }
|
|
<a name="l00198"></a>00198 <span class="comment"></span>
|
|
<a name="l00199"></a>00199 <span class="comment">/**</span>
|
|
<a name="l00200"></a>00200 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00201"></a>00201 <span class="comment"> pte_get_vdw_ray</span>
|
|
<a name="l00202"></a>00202 <span class="comment"> </span>
|
|
<a name="l00203"></a>00203 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00204"></a>00204 <span class="comment"> Returns the van der walls radius for a given element</span>
|
|
<a name="l00205"></a>00205 <span class="comment"> </span>
|
|
<a name="l00206"></a>00206 <span class="comment"> ## PARAMETERS: </span>
|
|
<a name="l00207"></a>00207 <span class="comment"> @ const char *symbol: The symbol of the element in the periodic table</span>
|
|
<a name="l00208"></a>00208 <span class="comment"> </span>
|
|
<a name="l00209"></a>00209 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00210"></a>00210 <span class="comment"> float: vdw radius corresponding to symbol</span>
|
|
<a name="l00211"></a>00211 <span class="comment"> </span>
|
|
<a name="l00212"></a>00212 <span class="comment">*/</span>
|
|
<a name="l00213"></a><a class="code" href="pertable_8h.html#e4452b6c03cdbc3ea402b7f4ef183eee">00213</a> <span class="keywordtype">float</span> <a class="code" href="pertable_8c.html#e4452b6c03cdbc3ea402b7f4ef183eee">pte_get_vdw_ray</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *symbol)
|
|
<a name="l00214"></a>00214 {
|
|
<a name="l00215"></a>00215 <span class="keywordtype">char</span> atom[3] ;
|
|
<a name="l00216"></a>00216
|
|
<a name="l00217"></a>00217 <span class="keywordflow">if</span> (symbol != NULL) {
|
|
<a name="l00218"></a>00218 atom[0] = (char) toupper((<span class="keywordtype">int</span>) symbol[0]);
|
|
<a name="l00219"></a>00219 atom[1] = (char) tolower((<span class="keywordtype">int</span>) symbol[1]);
|
|
<a name="l00220"></a>00220 atom[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00221"></a>00221
|
|
<a name="l00222"></a>00222 <span class="keywordtype">int</span> i ;
|
|
<a name="l00223"></a>00223 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00224"></a>00224 <span class="keywordflow">if</span> ( (<a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][0] == atom[0]) && (<a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][1] == atom[1]) ) {
|
|
<a name="l00225"></a>00225 <span class="keywordflow">return</span> <a class="code" href="pertable_8c.html#d218d21e3e71e1b659ce8ccd48b9f540">ST_pte_rvdw</a>[i] ;
|
|
<a name="l00226"></a>00226 }
|
|
<a name="l00227"></a>00227 }
|
|
<a name="l00228"></a>00228 }
|
|
<a name="l00229"></a>00229
|
|
<a name="l00230"></a>00230 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00231"></a>00231 }
|
|
<a name="l00232"></a>00232 <span class="comment"></span>
|
|
<a name="l00233"></a>00233 <span class="comment">/**</span>
|
|
<a name="l00234"></a>00234 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00235"></a>00235 <span class="comment"> pte_get_enegativity</span>
|
|
<a name="l00236"></a>00236 <span class="comment"> </span>
|
|
<a name="l00237"></a>00237 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00238"></a>00238 <span class="comment"> Returns the electronegativity (Pauling) value for a given element</span>
|
|
<a name="l00239"></a>00239 <span class="comment"> </span>
|
|
<a name="l00240"></a>00240 <span class="comment"> ## PARAMETERS: </span>
|
|
<a name="l00241"></a>00241 <span class="comment"> @ const char *symbol: The symbol of the element in the periodic table</span>
|
|
<a name="l00242"></a>00242 <span class="comment"> </span>
|
|
<a name="l00243"></a>00243 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00244"></a>00244 <span class="comment"> float: electrobegativity of Pauling corresponding to symbol</span>
|
|
<a name="l00245"></a>00245 <span class="comment"> </span>
|
|
<a name="l00246"></a>00246 <span class="comment">*/</span>
|
|
<a name="l00247"></a><a class="code" href="pertable_8h.html#5dda7fa72655b6d311e2a41ef049d5d6">00247</a> <span class="keywordtype">float</span> <a class="code" href="pertable_8c.html#5dda7fa72655b6d311e2a41ef049d5d6">pte_get_enegativity</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *symbol)
|
|
<a name="l00248"></a>00248 {
|
|
<a name="l00249"></a>00249 <span class="keywordtype">char</span> atom[3] = <span class="stringliteral">""</span> ;
|
|
<a name="l00250"></a>00250
|
|
<a name="l00251"></a>00251 <span class="keywordflow">if</span> (symbol != NULL) {
|
|
<a name="l00252"></a>00252 atom[0] = (char) toupper((<span class="keywordtype">int</span>) symbol[0]);
|
|
<a name="l00253"></a>00253 atom[1] = (char) tolower((<span class="keywordtype">int</span>) symbol[1]);
|
|
<a name="l00254"></a>00254 atom[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00255"></a>00255
|
|
<a name="l00256"></a>00256 <span class="keywordtype">int</span> i ;
|
|
<a name="l00257"></a>00257 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00258"></a>00258 <span class="keywordflow">if</span> ( (<a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][0] == atom[0]) && (<a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][1] == atom[1]) ) {
|
|
<a name="l00259"></a>00259 <span class="keywordflow">return</span> <a class="code" href="pertable_8c.html#cdcf0f499b84258ffeff11ca58cfdafc">ST_pte_electronegativity</a>[i] ;
|
|
<a name="l00260"></a>00260 }
|
|
<a name="l00261"></a>00261 }
|
|
<a name="l00262"></a>00262 }
|
|
<a name="l00263"></a>00263
|
|
<a name="l00264"></a>00264 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00265"></a>00265 }
|
|
<a name="l00266"></a>00266 <span class="comment"></span>
|
|
<a name="l00267"></a>00267 <span class="comment">/**</span>
|
|
<a name="l00268"></a>00268 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00269"></a>00269 <span class="comment"> is_valid_element</span>
|
|
<a name="l00270"></a>00270 <span class="comment"> </span>
|
|
<a name="l00271"></a>00271 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00272"></a>00272 <span class="comment"> Check if a given string corresponds to an atom element.</span>
|
|
<a name="l00273"></a>00273 <span class="comment"> </span>
|
|
<a name="l00274"></a>00274 <span class="comment"> ## PARAMETERS:</span>
|
|
<a name="l00275"></a>00275 <span class="comment"> @ const char *str : The string to test</span>
|
|
<a name="l00276"></a>00276 <span class="comment"> @ int tcase : If = 1, dont take into account the case.</span>
|
|
<a name="l00277"></a>00277 <span class="comment"> </span>
|
|
<a name="l00278"></a>00278 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00279"></a>00279 <span class="comment"> int: -1 if the strig is not an atom element, the index in the periodic table if so.</span>
|
|
<a name="l00280"></a>00280 <span class="comment"> </span>
|
|
<a name="l00281"></a>00281 <span class="comment">*/</span>
|
|
<a name="l00282"></a><a class="code" href="pertable_8h.html#6b05e53b42f5fe5907683fddc430cd39">00282</a> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#6b05e53b42f5fe5907683fddc430cd39">is_valid_element</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *str, <span class="keywordtype">int</span> ignore_case)
|
|
<a name="l00283"></a>00283 {
|
|
<a name="l00284"></a>00284 <span class="keywordflow">if</span>(str == NULL) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00285"></a>00285 <span class="keywordflow">if</span>(strlen(str) <= 0) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00286"></a>00286
|
|
<a name="l00287"></a>00287 <span class="comment">/* Use temporary variable to work on the string */</span>
|
|
<a name="l00288"></a>00288 <span class="keywordtype">int</span> i ;
|
|
<a name="l00289"></a>00289 <span class="keywordtype">char</span> str_tmp[strlen(str)+1] ;
|
|
<a name="l00290"></a>00290 strcpy(str_tmp, str) ;
|
|
<a name="l00291"></a>00291
|
|
<a name="l00292"></a>00292 <span class="comment">/* Remove spaces and case if asked*/</span>
|
|
<a name="l00293"></a>00293 <a class="code" href="utils_8c.html#ed930c5e93a75d90a96195282790d467">str_trim</a>(str_tmp) ;
|
|
<a name="l00294"></a>00294 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00295"></a>00295 str_tmp[0] = tolower(str_tmp[0]) ;
|
|
<a name="l00296"></a>00296 str_tmp[1] = tolower(str_tmp[1]) ;
|
|
<a name="l00297"></a>00297 }
|
|
<a name="l00298"></a>00298
|
|
<a name="l00299"></a>00299 <span class="comment">/* Loop over */</span>
|
|
<a name="l00300"></a>00300 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00301"></a>00301 <span class="keywordtype">char</span> tmp[3] ;
|
|
<a name="l00302"></a>00302 tmp[0] = <a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][0] ;
|
|
<a name="l00303"></a>00303 tmp[1] = <a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][1] ;
|
|
<a name="l00304"></a>00304
|
|
<a name="l00305"></a>00305 <span class="comment">/* Remove case if asked */</span>
|
|
<a name="l00306"></a>00306 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00307"></a>00307 tmp[0] = tolower(tmp[0]) ;
|
|
<a name="l00308"></a>00308 tmp[1] = tolower(tmp[1]) ;
|
|
<a name="l00309"></a>00309 }
|
|
<a name="l00310"></a>00310 tmp[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00311"></a>00311
|
|
<a name="l00312"></a>00312 <span class="comment">/* Do the comparison*/</span>
|
|
<a name="l00313"></a>00313 <span class="keywordflow">if</span>(strcmp(str_tmp, tmp) == 0) <span class="keywordflow">return</span> i ;
|
|
<a name="l00314"></a>00314 }
|
|
<a name="l00315"></a>00315
|
|
<a name="l00316"></a>00316 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00317"></a>00317 }
|
|
<a name="l00318"></a>00318 <span class="comment"></span>
|
|
<a name="l00319"></a>00319 <span class="comment">/**-----------------------------------------------------------------------------</span>
|
|
<a name="l00320"></a>00320 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00321"></a>00321 <span class="comment"> int element_in_std_res(char *res_name)</span>
|
|
<a name="l00322"></a>00322 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00323"></a>00323 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00324"></a>00324 <span class="comment"> Compare resname to the list of standard protein resnames. Return 1 if</span>
|
|
<a name="l00325"></a>00325 <span class="comment"> resname is in this list, 0 else.</span>
|
|
<a name="l00326"></a>00326 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00327"></a>00327 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00328"></a>00328 <span class="comment"> @ char *res_name : The current residue name</span>
|
|
<a name="l00329"></a>00329 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00330"></a>00330 <span class="comment"> ## RETURN: int</span>
|
|
<a name="l00331"></a>00331 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00332"></a>00332 <span class="comment">*/</span>
|
|
<a name="l00333"></a><a class="code" href="pertable_8h.html#9ec74074992414a252deb3bdb6f53af5">00333</a> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#9ec74074992414a252deb3bdb6f53af5">element_in_std_res</a>(<span class="keywordtype">char</span> *res_name){
|
|
<a name="l00334"></a>00334 <span class="keywordtype">int</span> i;
|
|
<a name="l00335"></a>00335 <span class="keywordflow">for</span>(i=0;i<<a class="code" href="pertable_8c.html#732014afeb1ee1a32a9ca967578a1f2e">ST_n_standard_res_names</a>;i++){
|
|
<a name="l00336"></a>00336 <span class="keywordflow">if</span>(!strncmp(res_name, <a class="code" href="pertable_8c.html#479c3e9145f096eacda7d060c12ca40a">ST_standard_res_names</a>[i],3)) <span class="keywordflow">return</span> 1;
|
|
<a name="l00337"></a>00337 }
|
|
<a name="l00338"></a>00338 <span class="keywordflow">return</span> 0;
|
|
<a name="l00339"></a>00339 }
|
|
<a name="l00340"></a>00340 <span class="comment"></span>
|
|
<a name="l00341"></a>00341 <span class="comment">/**-----------------------------------------------------------------------------</span>
|
|
<a name="l00342"></a>00342 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00343"></a>00343 <span class="comment"> int element_in_nucl_acid(char *res_name)</span>
|
|
<a name="l00344"></a>00344 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00345"></a>00345 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00346"></a>00346 <span class="comment"> Compare resname to the list of standard nucleic acid residues. Return 1 if</span>
|
|
<a name="l00347"></a>00347 <span class="comment"> resname is in this list, 0 else.</span>
|
|
<a name="l00348"></a>00348 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00349"></a>00349 <span class="comment"> ## PARAMETRES:</span>
|
|
<a name="l00350"></a>00350 <span class="comment"> @ char *res_name : The current residue name</span>
|
|
<a name="l00351"></a>00351 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00352"></a>00352 <span class="comment"> ## RETURN: int</span>
|
|
<a name="l00353"></a>00353 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00354"></a>00354 <span class="comment">*/</span>
|
|
<a name="l00355"></a><a class="code" href="pertable_8h.html#9016391ffac695897fc618911af1077d">00355</a> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#9016391ffac695897fc618911af1077d">element_in_nucl_acid</a>(<span class="keywordtype">char</span> *res_name){
|
|
<a name="l00356"></a>00356 <span class="keywordtype">int</span> i;
|
|
<a name="l00357"></a>00357 <span class="keywordflow">for</span>(i=0;i<<a class="code" href="pertable_8c.html#6dc30c101ce0857fc53db28b20e05fdb">ST_n_standard_nucl_acid_names</a>;i++){
|
|
<a name="l00358"></a>00358 <span class="keywordflow">if</span>(!strncmp(res_name, <a class="code" href="pertable_8c.html#b30d971f0ed354b67ae4376ca53a13fb">ST_standard_nucl_acid_names</a>[i],3)) <span class="keywordflow">return</span> 1;
|
|
<a name="l00359"></a>00359 }
|
|
<a name="l00360"></a>00360 <span class="keywordflow">return</span> 0;
|
|
<a name="l00361"></a>00361 }
|
|
<a name="l00362"></a>00362
|
|
<a name="l00363"></a><a class="code" href="pertable_8h.html#dfc5930a4822e0fa67e7a4541c30c5e2">00363</a> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#dfc5930a4822e0fa67e7a4541c30c5e2">is_water</a>(<span class="keywordtype">char</span> *res_name){
|
|
<a name="l00364"></a>00364 <span class="keywordflow">if</span>(!strncmp(res_name, <span class="stringliteral">"HOH"</span>,3)||!strncmp(res_name, <span class="stringliteral">"WAT"</span>,3)) <span class="keywordflow">return</span> 1;
|
|
<a name="l00365"></a>00365 <span class="keywordflow">return</span> 0;
|
|
<a name="l00366"></a>00366 }
|
|
<a name="l00367"></a>00367
|
|
<a name="l00368"></a>00368 <span class="comment"></span>
|
|
<a name="l00369"></a>00369 <span class="comment">/**-----------------------------------------------------------------------------</span>
|
|
<a name="l00370"></a>00370 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00371"></a>00371 <span class="comment"> is_valid_prot_element</span>
|
|
<a name="l00372"></a>00372 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00373"></a>00373 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00374"></a>00374 <span class="comment"> Check if a given string corresponds to an atom element.</span>
|
|
<a name="l00375"></a>00375 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00376"></a>00376 <span class="comment"> ## PARAMETERS:</span>
|
|
<a name="l00377"></a>00377 <span class="comment"> @ const char *str : The string to test</span>
|
|
<a name="l00378"></a>00378 <span class="comment"> @ int tcase : If = 1, dont take into account the case.</span>
|
|
<a name="l00379"></a>00379 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00380"></a>00380 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00381"></a>00381 <span class="comment"> int: -1 if the strig is not an atom element, the index in the periodic table if so.</span>
|
|
<a name="l00382"></a>00382 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00383"></a>00383 <span class="comment">*/</span>
|
|
<a name="l00384"></a><a class="code" href="pertable_8h.html#d8987379124bf6467d28a571c09327ee">00384</a> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#d8987379124bf6467d28a571c09327ee">is_valid_prot_element</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *str, <span class="keywordtype">int</span> ignore_case)
|
|
<a name="l00385"></a>00385 {
|
|
<a name="l00386"></a>00386 <span class="keywordflow">if</span>(str == NULL) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00387"></a>00387 <span class="keywordflow">if</span>(strlen(str) <= 0) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00388"></a>00388 <span class="comment">/* Use temporary variable to work on the string */</span>
|
|
<a name="l00389"></a>00389 <span class="keywordtype">int</span> i ;
|
|
<a name="l00390"></a>00390 <span class="keywordtype">char</span> str_tmp[strlen(str)+1] ;
|
|
<a name="l00391"></a>00391 strcpy(str_tmp, str) ;
|
|
<a name="l00392"></a>00392
|
|
<a name="l00393"></a>00393
|
|
<a name="l00394"></a>00394 <span class="comment">/* Remove spaces and case if asked*/</span>
|
|
<a name="l00395"></a>00395 <a class="code" href="utils_8c.html#ed930c5e93a75d90a96195282790d467">str_trim</a>(str_tmp) ;
|
|
<a name="l00396"></a>00396 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00397"></a>00397 str_tmp[0] = tolower(str_tmp[0]) ;
|
|
<a name="l00398"></a>00398 str_tmp[1] = tolower(str_tmp[1]) ;
|
|
<a name="l00399"></a>00399 }
|
|
<a name="l00400"></a>00400
|
|
<a name="l00401"></a>00401 <span class="comment">/* Loop over standard protein element table*/</span>
|
|
<a name="l00402"></a>00402 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#04531a8fc2decd1f26e2e6f1b47730e9">ST_prot_nelem</a> ; i++) {
|
|
<a name="l00403"></a>00403 <span class="keywordtype">char</span> tmp[3] ;
|
|
<a name="l00404"></a>00404 tmp[0] = <a class="code" href="pertable_8c.html#fdecbeb72c5385dcec00ece864eefbb0">ST_pte_prot_symbol</a>[i][0] ;
|
|
<a name="l00405"></a>00405 tmp[1] = <a class="code" href="pertable_8c.html#fdecbeb72c5385dcec00ece864eefbb0">ST_pte_prot_symbol</a>[i][1] ;
|
|
<a name="l00406"></a>00406
|
|
<a name="l00407"></a>00407 <span class="comment">/* Remove case if asked */</span>
|
|
<a name="l00408"></a>00408 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00409"></a>00409 tmp[0] = tolower(tmp[0]) ;
|
|
<a name="l00410"></a>00410 tmp[1] = tolower(tmp[1]) ;
|
|
<a name="l00411"></a>00411 }
|
|
<a name="l00412"></a>00412 tmp[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00413"></a>00413
|
|
<a name="l00414"></a>00414 <span class="comment">/* Do the comparison*/</span>
|
|
<a name="l00415"></a>00415 <span class="keywordflow">if</span>(strncmp(str_tmp, tmp,1) == 0) <span class="keywordflow">return</span> i ;
|
|
<a name="l00416"></a>00416 }
|
|
<a name="l00417"></a>00417
|
|
<a name="l00418"></a>00418 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00419"></a>00419 }
|
|
<a name="l00420"></a>00420
|
|
<a name="l00421"></a>00421 <span class="comment"></span>
|
|
<a name="l00422"></a>00422 <span class="comment">/**-----------------------------------------------------------------------------</span>
|
|
<a name="l00423"></a>00423 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00424"></a>00424 <span class="comment"> is_valid_nucl_acid_element</span>
|
|
<a name="l00425"></a>00425 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00426"></a>00426 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00427"></a>00427 <span class="comment"> Check if a given string corresponds to an atom element.</span>
|
|
<a name="l00428"></a>00428 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00429"></a>00429 <span class="comment"> ## PARAMETERS:</span>
|
|
<a name="l00430"></a>00430 <span class="comment"> @ const char *str : The string to test</span>
|
|
<a name="l00431"></a>00431 <span class="comment"> @ int tcase : If = 1, dont take into account the case.</span>
|
|
<a name="l00432"></a>00432 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00433"></a>00433 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00434"></a>00434 <span class="comment"> int: -1 if the strig is not an atom element, the index in the periodic table if so.</span>
|
|
<a name="l00435"></a>00435 <span class="comment"> -----------------------------------------------------------------------------</span>
|
|
<a name="l00436"></a>00436 <span class="comment">*/</span>
|
|
<a name="l00437"></a><a class="code" href="pertable_8h.html#d1ab7881d279190272f4ba8af124dd22">00437</a> <span class="keywordtype">int</span> <a class="code" href="pertable_8c.html#d1ab7881d279190272f4ba8af124dd22">is_valid_nucl_acid_element</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *str, <span class="keywordtype">int</span> ignore_case)
|
|
<a name="l00438"></a>00438 {
|
|
<a name="l00439"></a>00439 <span class="keywordflow">if</span>(str == NULL) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00440"></a>00440 <span class="keywordflow">if</span>(strlen(str) <= 0) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00441"></a>00441 <span class="comment">/* Use temporary variable to work on the string */</span>
|
|
<a name="l00442"></a>00442 <span class="keywordtype">int</span> i ;
|
|
<a name="l00443"></a>00443 <span class="keywordtype">char</span> str_tmp[strlen(str)+1] ;
|
|
<a name="l00444"></a>00444 strcpy(str_tmp, str) ;
|
|
<a name="l00445"></a>00445
|
|
<a name="l00446"></a>00446
|
|
<a name="l00447"></a>00447 <span class="comment">/* Remove spaces and case if asked*/</span>
|
|
<a name="l00448"></a>00448 <a class="code" href="utils_8c.html#ed930c5e93a75d90a96195282790d467">str_trim</a>(str_tmp) ;
|
|
<a name="l00449"></a>00449 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00450"></a>00450 str_tmp[0] = tolower(str_tmp[0]) ;
|
|
<a name="l00451"></a>00451 str_tmp[1] = tolower(str_tmp[1]) ;
|
|
<a name="l00452"></a>00452 }
|
|
<a name="l00453"></a>00453
|
|
<a name="l00454"></a>00454 <span class="comment">/* Loop over standard protein element table*/</span>
|
|
<a name="l00455"></a>00455 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#a39f6df9f0f4fd5b7bda545a8e9005c5">ST_nucl_acid_nelem</a> ; i++) {
|
|
<a name="l00456"></a>00456 <span class="keywordtype">char</span> tmp[3] ;
|
|
<a name="l00457"></a>00457 tmp[0] = <a class="code" href="pertable_8c.html#29ee0fc69813b1ae66b63a82e886cf1c">ST_pte_nucl_acid_symbol</a>[i][0] ;
|
|
<a name="l00458"></a>00458 tmp[1] = <a class="code" href="pertable_8c.html#29ee0fc69813b1ae66b63a82e886cf1c">ST_pte_nucl_acid_symbol</a>[i][1] ;
|
|
<a name="l00459"></a>00459
|
|
<a name="l00460"></a>00460 <span class="comment">/* Remove case if asked */</span>
|
|
<a name="l00461"></a>00461 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00462"></a>00462 tmp[0] = tolower(tmp[0]) ;
|
|
<a name="l00463"></a>00463 tmp[1] = tolower(tmp[1]) ;
|
|
<a name="l00464"></a>00464 }
|
|
<a name="l00465"></a>00465 tmp[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00466"></a>00466
|
|
<a name="l00467"></a>00467 <span class="comment">/* Do the comparison*/</span>
|
|
<a name="l00468"></a>00468 <span class="keywordflow">if</span>(strncmp(str_tmp, tmp,1) == 0) <span class="keywordflow">return</span> i ;
|
|
<a name="l00469"></a>00469 }
|
|
<a name="l00470"></a>00470
|
|
<a name="l00471"></a>00471 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00472"></a>00472 }
|
|
<a name="l00473"></a>00473
|
|
<a name="l00474"></a>00474
|
|
</pre></div></div>
|
|
<hr size="1"><address style="text-align: right;"><small>Generated on Mon Jun 7 16:44:23 2010 for fpocket by
|
|
<a href="http://www.doxygen.org/index.html">
|
|
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.6 </small></address>
|
|
</body>
|
|
</html>
|