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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><a class="code" href="pertable_8c.html#cdcf0f499b84258ffeff11ca58cfdafc">00078</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="l00079"></a>00079 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="l00080"></a>00080 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="l00081"></a>00081 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="l00082"></a>00082 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="l00083"></a>00083 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="l00084"></a>00084 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="l00085"></a>00085 -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="l00086"></a>00086 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="l00087"></a>00087 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="l00088"></a>00088 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="l00089"></a>00089 -1.0, -1.0
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<a name="l00090"></a>00090 } ; <span class="comment">/**< electronegativity list*/</span>
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<a name="l00091"></a>00091
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<a name="l00092"></a><a class="code" href="pertable_8c.html#2e1ab5c465d5c0542933f9c8f322ae5a">00092</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="l00093"></a>00093 <span class="comment">/* X */</span> 0.00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,
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|
<a name="l00094"></a>00094 <span class="comment">/* C */</span> 12.0107, 14.0067, 15.9994, 18.9984032, 20.1797,
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|
<a name="l00095"></a>00095 <span class="comment">/* Na */</span> 22.989770, 24.3050, 26.981538, 28.0855, 30.973761,
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|
<a name="l00096"></a>00096 <span class="comment">/* S */</span> 32.065, 35.453, 39.948, 39.0983, 40.078, 44.955910,
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<a name="l00097"></a>00097 <span class="comment">/* Ti */</span> 47.867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,
|
|
<a name="l00098"></a>00098 <span class="comment">/* Ni */</span> 58.6934, 63.546, 65.409, 69.723, 72.64, 74.92160,
|
|
<a name="l00099"></a>00099 <span class="comment">/* Se */</span> 78.96, 79.904, 83.798, 85.4678, 87.62, 88.90585,
|
|
<a name="l00100"></a>00100 <span class="comment">/* Zr */</span> 91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550,
|
|
<a name="l00101"></a>00101 <span class="comment">/* Pd */</span> 106.42, 107.8682, 112.411, 114.818, 118.710, 121.760,
|
|
<a name="l00102"></a>00102 <span class="comment">/* Te */</span> 127.60, 126.90447, 131.293, 132.90545, 137.327,
|
|
<a name="l00103"></a>00103 <span class="comment">/* La */</span> 138.9055, 140.116, 140.90765, 144.24, 145.0, 150.36,
|
|
<a name="l00104"></a>00104 <span class="comment">/* Eu */</span> 151.964, 157.25, 158.92534, 162.500, 164.93032,
|
|
<a name="l00105"></a>00105 <span class="comment">/* Er */</span> 167.259, 168.93421, 173.04, 174.967, 178.49, 180.9479,
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|
<a name="l00106"></a>00106 <span class="comment">/* W */</span> 183.84, 186.207, 190.23, 192.217, 195.078, 196.96655,
|
|
<a name="l00107"></a>00107 <span class="comment">/* Hg */</span> 200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0,
|
|
<a name="l00108"></a>00108 <span class="comment">/* Fr */</span> 223.0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,
|
|
<a name="l00109"></a>00109 <span class="comment">/* Np */</span> 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,
|
|
<a name="l00110"></a>00110 <span class="comment">/* Md */</span> 258.0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,
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<a name="l00111"></a>00111 <span class="comment">/* Mt */</span> 268.0, 271.0, 272.0
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<a name="l00112"></a>00112 }; <span class="comment">/**< atomic masses*/</span>
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<a name="l00113"></a>00113
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<a name="l00114"></a>00114 <span class="comment">/*</span>
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<a name="l00115"></a>00115 <span class="comment"> A. Bondi, J. Phys. Chem., 68, 441 - 452, 1964, </span>
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<a name="l00116"></a>00116 <span class="comment"> .Phys.Chem., 100, 7384 - 7391, 1996.</span>
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<a name="l00117"></a>00117 <span class="comment"> */</span>
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<a name="l00118"></a><a class="code" href="pertable_8c.html#d218d21e3e71e1b659ce8ccd48b9f540">00118</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>[] = {
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<a name="l00119"></a>00119 <span class="comment">/* X */</span> 1.5, 1.2, 1.4, 1.82, 2.0, 2.0,
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<a name="l00120"></a>00120 <span class="comment">/* C */</span> 1.7, 1.55, 1.52, 1.47, 1.54,
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<a name="l00121"></a>00121 <span class="comment">/* Na */</span> 2.27, 1.73, 2.0, 2.1, 1.8,
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<a name="l00122"></a>00122 <span class="comment">/* S */</span> 1.8, 1.75, 1.88, 2.75, 2.0, 2.0,
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<a name="l00123"></a>00123 <span class="comment">/* Ti */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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<a name="l00124"></a>00124 <span class="comment">/* Ni */</span> 1.63, 1.4, 1.39, 1.07, 2.0, 1.85,
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<a name="l00125"></a>00125 <span class="comment">/* Se */</span> 1.9, 1.85, 2.02, 2.0, 2.0, 2.0,
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<a name="l00126"></a>00126 <span class="comment">/* Zr */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
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<a name="l00127"></a>00127 <span class="comment">/* Pd */</span> 1.63, 1.72, 1.58, 1.93, 2.17, 2.0,
|
|
<a name="l00128"></a>00128 <span class="comment">/* Te */</span> 2.06, 1.98, 2.16, 2.0, 2.0,
|
|
<a name="l00129"></a>00129 <span class="comment">/* La */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00130"></a>00130 <span class="comment">/* Eu */</span> 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00131"></a>00131 <span class="comment">/* Er */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00132"></a>00132 <span class="comment">/* W */</span> 2.0, 2.0, 2.0, 2.0, 1.72, 1.66,
|
|
<a name="l00133"></a>00133 <span class="comment">/* Hg */</span> 1.55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00134"></a>00134 <span class="comment">/* Fr */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 1.86,
|
|
<a name="l00135"></a>00135 <span class="comment">/* Np */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00136"></a>00136 <span class="comment">/* Md */</span> 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
|
|
<a name="l00137"></a>00137 <span class="comment">/* Mt */</span> 2.0, 2.0, 2.0
|
|
<a name="l00138"></a>00138 }; <span class="comment">/**< VDW radii for different elements*/</span>
|
|
<a name="l00139"></a>00139 <span class="comment"></span>
|
|
<a name="l00140"></a>00140 <span class="comment">/**</span>
|
|
<a name="l00141"></a>00141 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00142"></a>00142 <span class="comment"> pte_get_mass</span>
|
|
<a name="l00143"></a>00143 <span class="comment"> </span>
|
|
<a name="l00144"></a>00144 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00145"></a>00145 <span class="comment"> Returns the mass for a given element</span>
|
|
<a name="l00146"></a>00146 <span class="comment"> </span>
|
|
<a name="l00147"></a>00147 <span class="comment"> ## PARAMETERS: </span>
|
|
<a name="l00148"></a>00148 <span class="comment"> @ const char *symbol: The symbol of the element in the periodic table</span>
|
|
<a name="l00149"></a>00149 <span class="comment"> </span>
|
|
<a name="l00150"></a>00150 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00151"></a>00151 <span class="comment"> float: mass corresponding to symbol</span>
|
|
<a name="l00152"></a>00152 <span class="comment"> </span>
|
|
<a name="l00153"></a>00153 <span class="comment">*/</span>
|
|
<a name="l00154"></a><a class="code" href="pertable_8h.html#3eeaf52663f6057aee4f869d5c78a8c8">00154</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="l00155"></a>00155 {
|
|
<a name="l00156"></a>00156 <span class="keywordtype">char</span> atom[3] ;
|
|
<a name="l00157"></a>00157 <span class="keywordflow">if</span> (symbol != NULL) {
|
|
<a name="l00158"></a>00158 atom[0] = (char) toupper((<span class="keywordtype">int</span>) symbol[0]);
|
|
<a name="l00159"></a>00159 atom[1] = (char) tolower((<span class="keywordtype">int</span>) symbol[1]);
|
|
<a name="l00160"></a>00160 atom[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00161"></a>00161
|
|
<a name="l00162"></a>00162 <span class="keywordtype">int</span> i ;
|
|
<a name="l00163"></a>00163 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00164"></a>00164 <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="l00165"></a>00165
|
|
<a name="l00166"></a>00166 <span class="keywordflow">return</span> <a class="code" href="pertable_8c.html#2e1ab5c465d5c0542933f9c8f322ae5a">ST_pte_mass</a>[i] ;
|
|
<a name="l00167"></a>00167 }
|
|
<a name="l00168"></a>00168 }
|
|
<a name="l00169"></a>00169 }
|
|
<a name="l00170"></a>00170
|
|
<a name="l00171"></a>00171
|
|
<a name="l00172"></a>00172 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00173"></a>00173 }
|
|
<a name="l00174"></a>00174 <span class="comment"></span>
|
|
<a name="l00175"></a>00175 <span class="comment">/**</span>
|
|
<a name="l00176"></a>00176 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00177"></a>00177 <span class="comment"> pte_get_vdw_ray</span>
|
|
<a name="l00178"></a>00178 <span class="comment"> </span>
|
|
<a name="l00179"></a>00179 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00180"></a>00180 <span class="comment"> Returns the van der walls radius for a given element</span>
|
|
<a name="l00181"></a>00181 <span class="comment"> </span>
|
|
<a name="l00182"></a>00182 <span class="comment"> ## PARAMETERS: </span>
|
|
<a name="l00183"></a>00183 <span class="comment"> @ const char *symbol: The symbol of the element in the periodic table</span>
|
|
<a name="l00184"></a>00184 <span class="comment"> </span>
|
|
<a name="l00185"></a>00185 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00186"></a>00186 <span class="comment"> float: vdw radius corresponding to symbol</span>
|
|
<a name="l00187"></a>00187 <span class="comment"> </span>
|
|
<a name="l00188"></a>00188 <span class="comment">*/</span>
|
|
<a name="l00189"></a><a class="code" href="pertable_8h.html#e4452b6c03cdbc3ea402b7f4ef183eee">00189</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="l00190"></a>00190 {
|
|
<a name="l00191"></a>00191 <span class="keywordtype">char</span> atom[3] ;
|
|
<a name="l00192"></a>00192
|
|
<a name="l00193"></a>00193 <span class="keywordflow">if</span> (symbol != NULL) {
|
|
<a name="l00194"></a>00194 atom[0] = (char) toupper((<span class="keywordtype">int</span>) symbol[0]);
|
|
<a name="l00195"></a>00195 atom[1] = (char) tolower((<span class="keywordtype">int</span>) symbol[1]);
|
|
<a name="l00196"></a>00196 atom[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00197"></a>00197
|
|
<a name="l00198"></a>00198 <span class="keywordtype">int</span> i ;
|
|
<a name="l00199"></a>00199 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00200"></a>00200 <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="l00201"></a>00201 <span class="keywordflow">return</span> <a class="code" href="pertable_8c.html#d218d21e3e71e1b659ce8ccd48b9f540">ST_pte_rvdw</a>[i] ;
|
|
<a name="l00202"></a>00202 }
|
|
<a name="l00203"></a>00203 }
|
|
<a name="l00204"></a>00204 }
|
|
<a name="l00205"></a>00205
|
|
<a name="l00206"></a>00206 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00207"></a>00207 }
|
|
<a name="l00208"></a>00208 <span class="comment"></span>
|
|
<a name="l00209"></a>00209 <span class="comment">/**</span>
|
|
<a name="l00210"></a>00210 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00211"></a>00211 <span class="comment"> pte_get_enegativity</span>
|
|
<a name="l00212"></a>00212 <span class="comment"> </span>
|
|
<a name="l00213"></a>00213 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00214"></a>00214 <span class="comment"> Returns the electronegativity (Pauling) value for a given element</span>
|
|
<a name="l00215"></a>00215 <span class="comment"> </span>
|
|
<a name="l00216"></a>00216 <span class="comment"> ## PARAMETERS: </span>
|
|
<a name="l00217"></a>00217 <span class="comment"> @ const char *symbol: The symbol of the element in the periodic table</span>
|
|
<a name="l00218"></a>00218 <span class="comment"> </span>
|
|
<a name="l00219"></a>00219 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00220"></a>00220 <span class="comment"> float: electrobegativity of Pauling corresponding to symbol</span>
|
|
<a name="l00221"></a>00221 <span class="comment"> </span>
|
|
<a name="l00222"></a>00222 <span class="comment">*/</span>
|
|
<a name="l00223"></a><a class="code" href="pertable_8h.html#5dda7fa72655b6d311e2a41ef049d5d6">00223</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="l00224"></a>00224 {
|
|
<a name="l00225"></a>00225 <span class="keywordtype">char</span> atom[3] = <span class="stringliteral">""</span> ;
|
|
<a name="l00226"></a>00226
|
|
<a name="l00227"></a>00227 <span class="keywordflow">if</span> (symbol != NULL) {
|
|
<a name="l00228"></a>00228 atom[0] = (char) toupper((<span class="keywordtype">int</span>) symbol[0]);
|
|
<a name="l00229"></a>00229 atom[1] = (char) tolower((<span class="keywordtype">int</span>) symbol[1]);
|
|
<a name="l00230"></a>00230 atom[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00231"></a>00231
|
|
<a name="l00232"></a>00232 <span class="keywordtype">int</span> i ;
|
|
<a name="l00233"></a>00233 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00234"></a>00234 <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="l00235"></a>00235 <span class="keywordflow">return</span> <a class="code" href="pertable_8c.html#cdcf0f499b84258ffeff11ca58cfdafc">ST_pte_electronegativity</a>[i] ;
|
|
<a name="l00236"></a>00236 }
|
|
<a name="l00237"></a>00237 }
|
|
<a name="l00238"></a>00238 }
|
|
<a name="l00239"></a>00239
|
|
<a name="l00240"></a>00240 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00241"></a>00241 }
|
|
<a name="l00242"></a>00242 <span class="comment"></span>
|
|
<a name="l00243"></a>00243 <span class="comment">/**</span>
|
|
<a name="l00244"></a>00244 <span class="comment"> ## FUNCTION:</span>
|
|
<a name="l00245"></a>00245 <span class="comment"> is_valid_element</span>
|
|
<a name="l00246"></a>00246 <span class="comment"> </span>
|
|
<a name="l00247"></a>00247 <span class="comment"> ## SPECIFICATION:</span>
|
|
<a name="l00248"></a>00248 <span class="comment"> Check if a given string corresponds to an atom element.</span>
|
|
<a name="l00249"></a>00249 <span class="comment"> </span>
|
|
<a name="l00250"></a>00250 <span class="comment"> ## PARAMETERS:</span>
|
|
<a name="l00251"></a>00251 <span class="comment"> @ const char *str : The string to test</span>
|
|
<a name="l00252"></a>00252 <span class="comment"> @ int tcase : If = 1, dont take into account the case.</span>
|
|
<a name="l00253"></a>00253 <span class="comment"> </span>
|
|
<a name="l00254"></a>00254 <span class="comment"> ## RETURN:</span>
|
|
<a name="l00255"></a>00255 <span class="comment"> int: -1 if the strig is not an atom element, the index in the periodic table if so.</span>
|
|
<a name="l00256"></a>00256 <span class="comment"> </span>
|
|
<a name="l00257"></a>00257 <span class="comment">*/</span>
|
|
<a name="l00258"></a><a class="code" href="pertable_8h.html#6b05e53b42f5fe5907683fddc430cd39">00258</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="l00259"></a>00259 {
|
|
<a name="l00260"></a>00260 <span class="keywordflow">if</span>(str == NULL) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00261"></a>00261 <span class="keywordflow">if</span>(strlen(str) <= 0) <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00262"></a>00262
|
|
<a name="l00263"></a>00263 <span class="comment">/* Use temporary variable to work on the string */</span>
|
|
<a name="l00264"></a>00264 <span class="keywordtype">int</span> i ;
|
|
<a name="l00265"></a>00265 <span class="keywordtype">char</span> str_tmp[strlen(str)+1] ;
|
|
<a name="l00266"></a>00266 strcpy(str_tmp, str) ;
|
|
<a name="l00267"></a>00267
|
|
<a name="l00268"></a>00268 <span class="comment">/* Remove spaces and case if asked*/</span>
|
|
<a name="l00269"></a>00269 <a class="code" href="utils_8c.html#ed930c5e93a75d90a96195282790d467">str_trim</a>(str_tmp) ;
|
|
<a name="l00270"></a>00270 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00271"></a>00271 str_tmp[0] = tolower(str_tmp[0]) ;
|
|
<a name="l00272"></a>00272 str_tmp[1] = tolower(str_tmp[1]) ;
|
|
<a name="l00273"></a>00273 }
|
|
<a name="l00274"></a>00274
|
|
<a name="l00275"></a>00275 <span class="comment">/* Loop over */</span>
|
|
<a name="l00276"></a>00276 <span class="keywordflow">for</span> (i = 0; i < <a class="code" href="pertable_8c.html#f392ae272dc7d28e673d28319a8164f0">ST_nelem</a> ; i++) {
|
|
<a name="l00277"></a>00277 <span class="keywordtype">char</span> tmp[3] ;
|
|
<a name="l00278"></a>00278 tmp[0] = <a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][0] ;
|
|
<a name="l00279"></a>00279 tmp[1] = <a class="code" href="pertable_8c.html#7e2d2a03ee87a83bd3f82a9786b80418">ST_pte_symbol</a>[i][1] ;
|
|
<a name="l00280"></a>00280
|
|
<a name="l00281"></a>00281 <span class="comment">/* Remove case if asked */</span>
|
|
<a name="l00282"></a>00282 <span class="keywordflow">if</span>(ignore_case == 1) {
|
|
<a name="l00283"></a>00283 tmp[0] = tolower(tmp[0]) ;
|
|
<a name="l00284"></a>00284 tmp[1] = tolower(tmp[1]) ;
|
|
<a name="l00285"></a>00285 }
|
|
<a name="l00286"></a>00286 tmp[2] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00287"></a>00287
|
|
<a name="l00288"></a>00288 <span class="comment">/* Do the comparison*/</span>
|
|
<a name="l00289"></a>00289 <span class="keywordflow">if</span>(strcmp(str_tmp, tmp) == 0) <span class="keywordflow">return</span> i ;
|
|
<a name="l00290"></a>00290 }
|
|
<a name="l00291"></a>00291
|
|
<a name="l00292"></a>00292 <span class="keywordflow">return</span> -1 ;
|
|
<a name="l00293"></a>00293 }
|
|
</pre></div></div>
|
|
<hr size="1"><address style="text-align: right;"><small>Generated on Sun Jul 5 22:10:40 2009 for fpocket by
|
|
<a href="http://www.doxygen.org/index.html">
|
|
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.9 </small></address>
|
|
</body>
|
|
</html>
|