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comparison mayachemtools/docs/modules/html/code/AminoAcids.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:AminoAcids.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-AminoAcids-"></a> 1 <span class="k">package </span><span class="i">AminoAcids</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: AminoAcids.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span> | |
| 18 5 <span class="c"># $Revision: 1.25 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> | |
| 47 34 | |
| 48 35 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> | |
| 49 36 | |
| 50 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> | |
| 51 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 52 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetAminoAcids GetAminoAcidPropertiesData GetAminoAcidPropertiesNames IsAminoAcid IsAminoAcidProperty)</span><span class="sc">;</span> | |
| 53 40 | |
| 54 41 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> | |
| 55 42 | |
| 56 43 <span class="c">#</span> | |
| 57 44 <span class="c"># Load amino acids data...</span> | |
| 58 45 <span class="c">#</span> | |
| 59 46 <span class="k">my</span><span class="s">(</span><span class="i">%AminoAcidDataMap</span><span class="cm">,</span> <span class="i">%AminoAcidThreeLetterCodeMap</span><span class="cm">,</span> <span class="i">%AminoAcidOneLetterCodeMap</span><span class="cm">,</span> <span class="i">%AminoAcidNameMap</span><span class="cm">,</span> <span class="i">@AminoAcidPropertyNames</span><span class="cm">,</span> <span class="i">%AminoAcidPropertyNamesMap</span><span class="cm">,</span> <span class="s">)</span><span class="sc">;</span> | |
| 60 47 <span class="i">_LoadAminoAcidsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 61 48 | |
| 62 49 <span class="c">#</span> | |
| 63 50 <span class="c"># Get a list of all known amino acids as one of these values:</span> | |
| 64 51 <span class="c"># one letter code, three letter code, or amino acid name...</span> | |
| 65 52 <span class="c">#</span> | |
| 66 <a name="GetAminoAcids-"></a> 53 <span class="k">sub </span><span class="m">GetAminoAcids</span> <span class="s">{</span> | |
| 67 54 <span class="k">my</span><span class="s">(</span><span class="i">$NameType</span><span class="cm">,</span> <span class="i">$ThreeLetterCode</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">@AminoAcidNames</span><span class="cm">,</span> <span class="i">%AminoAcidNamesMap</span><span class="s">)</span><span class="sc">;</span> | |
| 68 55 | |
| 69 56 <span class="i">$NameType</span> = <span class="q">'ThreeLetterCode'</span><span class="sc">;</span> | |
| 70 57 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 71 58 <span class="s">(</span><span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 72 59 <span class="s">}</span> | |
| 73 60 | |
| 74 61 <span class="c"># Collect names...</span> | |
| 75 62 <span class="i">%AminoAcidNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 76 63 <span class="k">for</span> <span class="i">$ThreeLetterCode</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AminoAcidDataMap</span><span class="s">)</span> <span class="s">{</span> | |
| 77 64 <span class="j">NAME :</span> <span class="s">{</span> | |
| 78 65 <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^OneLetterCode$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="w">OneLetterCode</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span> | |
| 79 66 <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^AminoAcid$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="w">AminoAcid</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span> | |
| 80 67 <span class="i">$Name</span> = <span class="i">$ThreeLetterCode</span><span class="sc">;</span> | |
| 81 68 <span class="s">}</span> | |
| 82 69 <span class="i">$AminoAcidNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span> | |
| 83 70 <span class="s">}</span> | |
| 84 71 | |
| 85 72 <span class="c"># Sort 'em out</span> | |
| 86 73 <span class="i">@AminoAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 87 74 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%AminoAcidNamesMap</span><span class="s">)</span> <span class="s">{</span> | |
| 88 75 <span class="k">push</span> <span class="i">@AminoAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> | |
| 89 76 <span class="s">}</span> | |
| 90 77 | |
| 91 78 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@AminoAcidNames</span> <span class="co">:</span> \<span class="i">@AminoAcidNames</span><span class="s">)</span><span class="sc">;</span> | |
| 92 79 <span class="s">}</span> | |
| 93 80 | |
| 94 81 | |
| 95 82 <span class="c">#</span> | |
| 96 83 <span class="c"># Get all available properties data for an amino acid using any of these symbols:</span> | |
| 97 84 <span class="c"># three letter code; one letter code; name.</span> | |
| 98 85 <span class="c">#</span> | |
| 99 86 <span class="c"># A reference to a hash array is returned with keys and values representing property</span> | |
| 100 87 <span class="c"># name and its values respectively.</span> | |
| 101 88 <span class="c">#</span> | |
| 102 <a name="GetAminoAcidPropertiesData-"></a> 89 <span class="k">sub </span><span class="m">GetAminoAcidPropertiesData</span> <span class="s">{</span> | |
| 103 90 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 104 91 <span class="k">my</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span> | |
| 105 92 | |
| 106 93 <span class="k">if</span> <span class="s">(</span><span class="i">$ThreeLetterCode</span> = <span class="i">_ValidateAminoAcidID</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 107 94 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}}<span class="sc">;</span> | |
| 108 95 <span class="s">}</span> | |
| 109 96 <span class="k">else</span> <span class="s">{</span> | |
| 110 97 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 111 98 <span class="s">}</span> | |
| 112 99 <span class="s">}</span> | |
| 113 100 | |
| 114 101 <span class="c">#</span> | |
| 115 102 <span class="c"># Get names of all available amino acid properties. A reference to an array containing</span> | |
| 116 103 <span class="c"># names of all available properties is returned.</span> | |
| 117 104 <span class="c">#</span> | |
| 118 <a name="GetAminoAcidPropertiesNames-"></a> 105 <span class="k">sub </span><span class="m">GetAminoAcidPropertiesNames</span> <span class="s">{</span> | |
| 119 106 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span> | |
| 120 107 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> | |
| 121 108 | |
| 122 109 <span class="i">$Mode</span> = <span class="q">'ByGroup'</span><span class="sc">;</span> | |
| 123 110 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 124 111 <span class="s">(</span><span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 125 112 <span class="s">}</span> | |
| 126 113 | |
| 127 114 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 128 115 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 129 116 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span> | |
| 130 117 <span class="c"># ThreeLetterCode, OneLetterCode, and AminoAcid are always listed first...</span> | |
| 131 118 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="q">qw(ThreeLetterCode OneLetterCode AminoAcid)</span><span class="sc">;</span> | |
| 132 119 <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%AminoAcidPropertyNamesMap</span><span class="s">)</span> <span class="s">{</span> | |
| 133 120 <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyName</span> !~ <span class="q">/^(ThreeLetterCode|OneLetterCode|AminoAcid)$/</span><span class="s">)</span> <span class="s">{</span> | |
| 134 121 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span> | |
| 135 122 <span class="s">}</span> | |
| 136 123 <span class="s">}</span> | |
| 137 124 <span class="s">}</span> | |
| 138 125 <span class="k">else</span> <span class="s">{</span> | |
| 139 126 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@AminoAcidPropertyNames</span><span class="sc">;</span> | |
| 140 127 <span class="s">}</span> | |
| 141 128 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@PropertyNames</span> <span class="co">:</span> \<span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> | |
| 142 129 <span class="s">}</span> | |
| 143 130 | |
| 144 131 <span class="c">#</span> | |
| 145 132 <span class="c"># Is it a known amino acid? Input is either an one/three letter code or a name.</span> | |
| 146 133 <span class="c">#</span> | |
| 147 <a name="IsAminoAcid-"></a> 134 <span class="k">sub </span><span class="m">IsAminoAcid</span> <span class="s">{</span> | |
| 148 135 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 149 136 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 150 137 | |
| 151 138 <span class="i">$Status</span> = <span class="s">(</span><span class="i">_ValidateAminoAcidID</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 152 139 | |
| 153 140 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 154 141 <span class="s">}</span> | |
| 155 142 | |
| 156 143 | |
| 157 144 <span class="c">#</span> | |
| 158 145 <span class="c"># Is it an available amino acid property?</span> | |
| 159 146 <span class="c">#</span> | |
| 160 <a name="IsAminoAcidProperty-"></a> 147 <span class="k">sub </span><span class="m">IsAminoAcidProperty</span> <span class="s">{</span> | |
| 161 148 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 162 149 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> | |
| 163 150 | |
| 164 151 <span class="i">$Status</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$AminoAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 165 152 | |
| 166 153 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> | |
| 167 154 <span class="s">}</span> | |
| 168 155 | |
| 169 156 <span class="c">#</span> | |
| 170 157 <span class="c"># Implents GetAminoAcid<PropertyName> for a valid proprty name.</span> | |
| 171 158 <span class="c">#</span> | |
| 172 <a name="AUTOLOAD-"></a> 159 <span class="k">sub </span><span class="m">AUTOLOAD</span> <span class="s">{</span> | |
| 173 160 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 174 161 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionName</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">$PropertyValue</span><span class="cm">,</span> <span class="i">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span> | |
| 175 162 | |
| 176 163 <span class="i">$PropertyValue</span> = <span class="k">undef</span><span class="sc">;</span> | |
| 177 164 | |
| 178 165 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw($AUTOLOAD)</span><span class="sc">;</span> | |
| 179 166 <span class="i">$FunctionName</span> = <span class="i">$AUTOLOAD</span><span class="sc">;</span> | |
| 180 167 <span class="i">$FunctionName</span> =~ <span class="q">s/.*:://</span><span class="sc">;</span> | |
| 181 168 | |
| 182 169 <span class="c"># Only Get<PropertyName> functions are supported...</span> | |
| 183 170 <span class="k">if</span> <span class="s">(</span><span class="i">$FunctionName</span> !~ <span class="q">/^Get/</span><span class="s">)</span> <span class="s">{</span> | |
| 184 171 <span class="w">croak</span> <span class="q">"Error: Function, AminoAcid::$FunctionName, is not supported by AUTOLOAD in AminoAcid module: Only Get<PropertyName> functions are implemented..."</span><span class="sc">;</span> | |
| 185 172 <span class="s">}</span> | |
| 186 173 | |
| 187 174 <span class="i">$PropertyName</span> = <span class="i">$FunctionName</span><span class="sc">;</span> | |
| 188 175 <span class="i">$PropertyName</span> =~ <span class="q">s/^GetAminoAcid//</span><span class="sc">;</span> | |
| 189 176 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AminoAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span> | |
| 190 177 <span class="w">croak</span> <span class="q">"Error: Function, AminoAcid::$FunctionName, is not supported by AUTOLOAD in AminoAcid module: Unknown amino acid property name, $PropertyName, specified..."</span><span class="sc">;</span> | |
| 191 178 <span class="s">}</span> | |
| 192 179 | |
| 193 180 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$ThreeLetterCode</span> = <span class="i">_ValidateAminoAcidID</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 194 181 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 195 182 <span class="s">}</span> | |
| 196 183 <span class="i">$PropertyValue</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="i">$PropertyName</span>}<span class="sc">;</span> | |
| 197 184 <span class="k">return</span> <span class="i">$PropertyValue</span><span class="sc">;</span> | |
| 198 185 <span class="s">}</span> | |
| 199 186 | |
| 200 187 | |
| 201 188 <span class="c">#</span> | |
| 202 189 <span class="c"># Load AminoAcidsData.csv files from <MayaChemTools>/lib directory...</span> | |
| 203 190 <span class="c">#</span> | |
| 204 <a name="_LoadAminoAcidsData-"></a> 191 <span class="k">sub </span><span class="m">_LoadAminoAcidsData</span> <span class="s">{</span> | |
| 205 192 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidsDataFile</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> | |
| 206 193 | |
| 207 194 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 208 195 | |
| 209 196 <span class="i">$AminoAcidsDataFile</span> = <span class="q">"$MayaChemToolsLibDir"</span> . <span class="q">"/data/AminoAcidsData.csv"</span><span class="sc">;</span> | |
| 210 197 | |
| 211 198 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$AminoAcidsDataFile"</span><span class="s">)</span> <span class="s">{</span> | |
| 212 199 <span class="w">croak</span> <span class="q">"Error: MayaChemTools package file, $AminoAcidsDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> | |
| 213 200 <span class="s">}</span> | |
| 214 201 | |
| 215 202 <span class="i">_LoadData</span><span class="s">(</span><span class="i">$AminoAcidsDataFile</span><span class="s">)</span><span class="sc">;</span> | |
| 216 203 <span class="s">}</span> | |
| 217 204 | |
| 218 205 <span class="c">#</span> | |
| 219 206 <span class="c"># Load AminoAcidsData.csv file from <MayaChemTools>/lib directory...</span> | |
| 220 207 <span class="c">#</span> | |
| 221 <a name="_LoadData-"></a> 208 <span class="k">sub </span><span class="m">_LoadData</span> <span class="s">{</span> | |
| 222 209 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidsDataFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 223 210 | |
| 224 211 <span class="i">%AminoAcidDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 225 212 <span class="i">@AminoAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 226 213 <span class="i">%AminoAcidPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 227 214 <span class="i">%AminoAcidThreeLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 228 215 <span class="i">%AminoAcidOneLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 229 216 <span class="i">%AminoAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 230 217 | |
| 231 218 <span class="c"># Load property data for all amino acids...</span> | |
| 232 219 <span class="c">#</span> | |
| 233 220 <span class="c"># File Format:</span> | |
| 234 221 <span class="c">#"ThreeLetterCode","OneLetterCode","AminoAcid","AcidicBasic","PolarNonpolar","Charged","Aromatic","HydrophobicHydophilic","IsoelectricPoint","pKCOOH","pKNH3+","MolecularWeight","MolecularWeightMinusH2O(18.01524)","ExactMass","ExactMassMinusH2O(18.01056)","vanderWaalsVolume","%AccessibleResidues","%BuriedResidues","AlphaHelixChouAndFasman","AlphaHelixDeleageAndRoux","AlphaHelixLevitt","AminoAcidsComposition","AminoAcidsCompositionInSwissProt","AntiparallelBetaStrand","AverageAreaBuried","AverageFlexibility","BetaSheetChouAndFasman","BetaSheetDeleageAndRoux","BetaSheetLevitt","BetaTurnChouAndFasman","BetaTurnDeleageAndRoux","BetaTurnLevitt","Bulkiness","CoilDeleageAndRoux","HPLCHFBARetention","HPLCRetentionAtpH2.1","HPLCRetentionAtpH7.4","HPLCTFARetention","HydrophobicityAbrahamAndLeo","HydrophobicityBlack","HydrophobicityBullAndBreese","HydrophobicityChothia","HydrophobicityEisenbergAndOthers","HydrophobicityFauchereAndOthers","HydrophobicityGuy","HydrophobicityHPLCAtpH3.4Cowan","HydrophobicityHPLCAtpH7.5Cowan","HydrophobicityHPLCParkerAndOthers","HydrophobicityHPLCWilsonAndOthers","HydrophobicityHoppAndWoods","HydrophobicityJanin","HydrophobicityKyteAndDoolittle","HydrophobicityManavalanAndOthers","HydrophobicityMiyazawaAndOthers","HydrophobicityOMHSweetAndOthers","HydrophobicityRaoAndArgos","HydrophobicityRfMobility","HydrophobicityRoseAndOthers","HydrophobicityRoseman","HydrophobicityWellingAndOthers","HydrophobicityWolfendenAndOthers","MolecularWeight","NumberOfCodons","ParallelBetaStrand","PolarityGrantham","PolarityZimmerman","RatioHeteroEndToSide","RecognitionFactors","Refractivity","RelativeMutability","TotalBetaStrand","LinearStructure","LinearStructureAtpH7.4"</span> | |
| 235 222 <span class="c">#</span> | |
| 236 223 <span class="c">#</span> | |
| 237 224 <span class="k">my</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="cm">,</span> <span class="i">$OneLetterCode</span><span class="cm">,</span> <span class="i">$AminoAcidName</span><span class="cm">,</span> <span class="i">$Line</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$InDelim</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$Units</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span> | |
| 238 225 | |
| 239 226 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> | |
| 240 227 <span class="k">open</span> <span class="w">AMINOACIDSDATAFILE</span><span class="cm">,</span> <span class="q">"$AminoAcidsDataFile"</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">"Couldn't open $AminoAcidsDataFile: $! ..."</span><span class="sc">;</span> | |
| 241 228 | |
| 242 229 <span class="c"># Skip lines up to column labels...</span> | |
| 243 230 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*AMINOACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 244 231 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> | |
| 245 232 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 246 233 <span class="s">}</span> | |
| 247 234 <span class="s">}</span> | |
| 248 235 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 249 236 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span> | |
| 250 237 | |
| 251 238 <span class="c"># Extract property names from column labels...</span> | |
| 252 239 <span class="i">@AminoAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 253 240 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#ColLabels</span><span class="s">)</span> <span class="s">{</span> | |
| 254 241 <span class="i">$Name</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 255 242 <span class="k">push</span> <span class="i">@AminoAcidPropertyNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> | |
| 256 243 | |
| 257 244 <span class="c"># Store property names...</span> | |
| 258 245 <span class="i">$AminoAcidPropertyNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span> | |
| 259 246 <span class="s">}</span> | |
| 260 247 | |
| 261 248 <span class="c"># Process amino acid data...</span> | |
| 262 249 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*AMINOACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 263 250 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> | |
| 264 251 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 265 252 <span class="s">}</span> | |
| 266 253 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 267 254 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> | |
| 268 255 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span> | |
| 269 256 <span class="w">croak</span> <span class="q">"Error: The number of data fields, @LineWords, in $AminoAcidsDataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> | |
| 270 257 <span class="s">}</span> | |
| 271 258 <span class="i">$ThreeLetterCode</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$OneLetterCode</span> = <span class="i">$LineWords</span>[<span class="n">1</span>]<span class="sc">;</span> <span class="i">$AminoAcidName</span> = <span class="i">$LineWords</span>[<span class="n">3</span>]<span class="sc">;</span> | |
| 272 259 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}<span class="s">)</span> <span class="s">{</span> | |
| 273 260 <span class="w">carp</span> <span class="q">"Warning: Ignoring data for amino acid $ThreeLetterCode: It has already been loaded.\nLine: $Line...."</span><span class="sc">;</span> | |
| 274 261 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> | |
| 275 262 <span class="s">}</span> | |
| 276 263 | |
| 277 264 <span class="c"># Store all the values...</span> | |
| 278 265 <span class="i">%</span>{<span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 279 266 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#LineWords</span><span class="s">)</span> <span class="s">{</span> | |
| 280 267 <span class="i">$Name</span> = <span class="i">$AminoAcidPropertyNames</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 281 268 <span class="i">$Value</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span> | |
| 282 269 <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span> | |
| 283 270 <span class="s">}</span> | |
| 284 271 <span class="s">}</span> | |
| 285 272 <span class="k">close</span> <span class="w">AMINOACIDSDATAFILE</span><span class="sc">;</span> | |
| 286 273 | |
| 287 274 <span class="c"># Setup one letter and amino acid name maps...</span> | |
| 288 275 <span class="i">_SetupAminoAcidIDMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 289 276 <span class="s">}</span> | |
| 290 277 | |
| 291 278 | |
| 292 279 <span class="c">#</span> | |
| 293 280 <span class="c"># Setup lowercase three/one letter code and name maps pointing</span> | |
| 294 281 <span class="c"># to three letter code as show in data file.</span> | |
| 295 282 <span class="c">#</span> | |
| 296 <a name="_SetupAminoAcidIDMap-"></a> 283 <span class="k">sub </span><span class="m">_SetupAminoAcidIDMap</span> <span class="s">{</span> | |
| 297 284 <span class="k">my</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="cm">,</span> <span class="i">$OneLetterCode</span><span class="cm">,</span> <span class="i">$AminoAcidName</span><span class="s">)</span><span class="sc">;</span> | |
| 298 285 | |
| 299 286 <span class="i">%AminoAcidThreeLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 300 287 <span class="i">%AminoAcidOneLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 301 288 <span class="i">%AminoAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 302 289 | |
| 303 290 <span class="k">for</span> <span class="i">$ThreeLetterCode</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AminoAcidDataMap</span><span class="s">)</span> <span class="s">{</span> | |
| 304 291 <span class="i">$OneLetterCode</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="w">OneLetterCode</span>}<span class="sc">;</span> | |
| 305 292 <span class="i">$AminoAcidName</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="w">AminoAcid</span>}<span class="sc">;</span> | |
| 306 293 | |
| 307 294 <span class="i">$AminoAcidThreeLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="s">)</span>} = <span class="i">$ThreeLetterCode</span><span class="sc">;</span> | |
| 308 295 <span class="i">$AminoAcidOneLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$OneLetterCode</span><span class="s">)</span>} = <span class="i">$ThreeLetterCode</span><span class="sc">;</span> | |
| 309 296 <span class="i">$AminoAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidName</span><span class="s">)</span>} = <span class="i">$ThreeLetterCode</span><span class="sc">;</span> | |
| 310 297 <span class="s">}</span> | |
| 311 298 <span class="s">}</span> | |
| 312 299 | |
| 313 300 <span class="c"># Validate amino acid ID...</span> | |
| 314 <a name="_ValidateAminoAcidID-"></a> 301 <span class="k">sub </span><span class="m">_ValidateAminoAcidID</span> <span class="s">{</span> | |
| 315 302 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 316 303 <span class="k">my</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span> | |
| 317 304 | |
| 318 305 | |
| 319 306 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> | |
| 320 307 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$AminoAcidThreeLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> | |
| 321 308 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 322 309 <span class="s">}</span> | |
| 323 310 <span class="i">$ThreeLetterCode</span> = <span class="i">$AminoAcidThreeLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="sc">;</span> | |
| 324 311 <span class="s">}</span> | |
| 325 312 <span class="k">elsif</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> | |
| 326 313 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$AminoAcidOneLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> | |
| 327 314 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 328 315 <span class="s">}</span> | |
| 329 316 <span class="i">$ThreeLetterCode</span> = <span class="i">$AminoAcidOneLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="sc">;</span> | |
| 330 317 <span class="s">}</span> | |
| 331 318 <span class="k">else</span> <span class="s">{</span> | |
| 332 319 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$AminoAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> | |
| 333 320 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 334 321 <span class="s">}</span> | |
| 335 322 <span class="i">$ThreeLetterCode</span> = <span class="i">$AminoAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="sc">;</span> | |
| 336 323 <span class="s">}</span> | |
| 337 324 <span class="k">return</span> <span class="i">$ThreeLetterCode</span><span class="sc">;</span> | |
| 338 325 <span class="s">}</span> | |
| 339 326 | |
| 340 327 | |
| 341 <a name="EOF-"></a></pre> | |
| 342 <p> </p> | |
| 343 <br /> | |
| 344 <center> | |
| 345 <img src="../../../images/h2o2.png"> | |
| 346 </center> | |
| 347 </body> | |
| 348 </html> |