Mercurial > repos > deepakjadmin > mayatool3_test3
view mayachemtools/docs/modules/html/code/AminoAcids.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line source
<html> <head> <title>MayaChemTools:Code:AminoAcids.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-AminoAcids-"></a> 1 <span class="k">package </span><span class="i">AminoAcids</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: AminoAcids.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span> 5 <span class="c"># $Revision: 1.25 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 34 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> 36 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span> 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetAminoAcids GetAminoAcidPropertiesData GetAminoAcidPropertiesNames IsAminoAcid IsAminoAcidProperty)</span><span class="sc">;</span> 40 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> 42 43 <span class="c">#</span> 44 <span class="c"># Load amino acids data...</span> 45 <span class="c">#</span> 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> 47 <span class="i">_LoadAminoAcidsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 48 49 <span class="c">#</span> 50 <span class="c"># Get a list of all known amino acids as one of these values:</span> 51 <span class="c"># one letter code, three letter code, or amino acid name...</span> 52 <span class="c">#</span> <a name="GetAminoAcids-"></a> 53 <span class="k">sub </span><span class="m">GetAminoAcids</span> <span class="s">{</span> 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> 55 56 <span class="i">$NameType</span> = <span class="q">'ThreeLetterCode'</span><span class="sc">;</span> 57 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 58 <span class="s">(</span><span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 59 <span class="s">}</span> 60 61 <span class="c"># Collect names...</span> 62 <span class="i">%AminoAcidNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 63 <span class="k">for</span> <span class="i">$ThreeLetterCode</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AminoAcidDataMap</span><span class="s">)</span> <span class="s">{</span> 64 <span class="j">NAME :</span> <span class="s">{</span> 65 <span class="k">if</span> <span class="s">(</span><span class="i">$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> 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">$ThreeLetterCode</span>}{<span class="w">AminoAcid</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span> 67 <span class="i">$Name</span> = <span class="i">$ThreeLetterCode</span><span class="sc">;</span> 68 <span class="s">}</span> 69 <span class="i">$AminoAcidNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span> 70 <span class="s">}</span> 71 72 <span class="c"># Sort 'em out</span> 73 <span class="i">@AminoAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 74 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%AminoAcidNamesMap</span><span class="s">)</span> <span class="s">{</span> 75 <span class="k">push</span> <span class="i">@AminoAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> 76 <span class="s">}</span> 77 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> 79 <span class="s">}</span> 80 81 82 <span class="c">#</span> 83 <span class="c"># Get all available properties data for an amino acid using any of these symbols:</span> 84 <span class="c"># three letter code; one letter code; name.</span> 85 <span class="c">#</span> 86 <span class="c"># A reference to a hash array is returned with keys and values representing property</span> 87 <span class="c"># name and its values respectively.</span> 88 <span class="c">#</span> <a name="GetAminoAcidPropertiesData-"></a> 89 <span class="k">sub </span><span class="m">GetAminoAcidPropertiesData</span> <span class="s">{</span> 90 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 91 <span class="k">my</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span> 92 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> 94 <span class="k">return</span> \<span class="i">%</span>{<span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}}<span class="sc">;</span> 95 <span class="s">}</span> 96 <span class="k">else</span> <span class="s">{</span> 97 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 98 <span class="s">}</span> 99 <span class="s">}</span> 100 101 <span class="c">#</span> 102 <span class="c"># Get names of all available amino acid properties. A reference to an array containing</span> 103 <span class="c"># names of all available properties is returned.</span> 104 <span class="c">#</span> <a name="GetAminoAcidPropertiesNames-"></a> 105 <span class="k">sub </span><span class="m">GetAminoAcidPropertiesNames</span> <span class="s">{</span> 106 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span> 107 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> 108 109 <span class="i">$Mode</span> = <span class="q">'ByGroup'</span><span class="sc">;</span> 110 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 111 <span class="s">(</span><span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 112 <span class="s">}</span> 113 114 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 116 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span> 117 <span class="c"># ThreeLetterCode, OneLetterCode, and AminoAcid are always listed first...</span> 118 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="q">qw(ThreeLetterCode OneLetterCode AminoAcid)</span><span class="sc">;</span> 119 <span class="k">for</span> <span class="i">$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> 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> 121 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span> 122 <span class="s">}</span> 123 <span class="s">}</span> 124 <span class="s">}</span> 125 <span class="k">else</span> <span class="s">{</span> 126 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@AminoAcidPropertyNames</span><span class="sc">;</span> 127 <span class="s">}</span> 128 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@PropertyNames</span> <span class="co">:</span> \<span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span> 129 <span class="s">}</span> 130 131 <span class="c">#</span> 132 <span class="c"># Is it a known amino acid? Input is either an one/three letter code or a name.</span> 133 <span class="c">#</span> <a name="IsAminoAcid-"></a> 134 <span class="k">sub </span><span class="m">IsAminoAcid</span> <span class="s">{</span> 135 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 136 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 137 138 <span class="i">$Status</span> = <span class="s">(</span><span class="i">_ValidateAminoAcidID</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 139 140 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 141 <span class="s">}</span> 142 143 144 <span class="c">#</span> 145 <span class="c"># Is it an available amino acid property?</span> 146 <span class="c">#</span> <a name="IsAminoAcidProperty-"></a> 147 <span class="k">sub </span><span class="m">IsAminoAcidProperty</span> <span class="s">{</span> 148 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 149 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span> 150 151 <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">$PropertyName</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 152 153 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span> 154 <span class="s">}</span> 155 156 <span class="c">#</span> 157 <span class="c"># Implents GetAminoAcid<PropertyName> for a valid proprty name.</span> 158 <span class="c">#</span> <a name="AUTOLOAD-"></a> 159 <span class="k">sub </span><span class="m">AUTOLOAD</span> <span class="s">{</span> 160 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 161 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span> 162 163 <span class="i">$PropertyValue</span> = <span class="k">undef</span><span class="sc">;</span> 164 165 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw($AUTOLOAD)</span><span class="sc">;</span> 166 <span class="i">$FunctionName</span> = <span class="i">$AUTOLOAD</span><span class="sc">;</span> 167 <span class="i">$FunctionName</span> =~ <span class="q">s/.*:://</span><span class="sc">;</span> 168 169 <span class="c"># Only Get<PropertyName> functions are supported...</span> 170 <span class="k">if</span> <span class="s">(</span><span class="i">$FunctionName</span> !~ <span class="q">/^Get/</span><span class="s">)</span> <span class="s">{</span> 171 <span class="w">croak</span> <span class="q">"Error: Function, AminoAcid::$FunctionName, is not supported by AUTOLOAD in AminoAcid module: Only Get<PropertyName> functions are implemented..."</span><span class="sc">;</span> 172 <span class="s">}</span> 173 174 <span class="i">$PropertyName</span> = <span class="i">$FunctionName</span><span class="sc">;</span> 175 <span class="i">$PropertyName</span> =~ <span class="q">s/^GetAminoAcid//</span><span class="sc">;</span> 176 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AminoAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span> 177 <span class="w">croak</span> <span class="q">"Error: Function, AminoAcid::$FunctionName, is not supported by AUTOLOAD in AminoAcid module: Unknown amino acid property name, $PropertyName, specified..."</span><span class="sc">;</span> 178 <span class="s">}</span> 179 180 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$ThreeLetterCode</span> = <span class="i">_ValidateAminoAcidID</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 181 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 182 <span class="s">}</span> 183 <span class="i">$PropertyValue</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="i">$PropertyName</span>}<span class="sc">;</span> 184 <span class="k">return</span> <span class="i">$PropertyValue</span><span class="sc">;</span> 185 <span class="s">}</span> 186 187 188 <span class="c">#</span> 189 <span class="c"># Load AminoAcidsData.csv files from <MayaChemTools>/lib directory...</span> 190 <span class="c">#</span> <a name="_LoadAminoAcidsData-"></a> 191 <span class="k">sub </span><span class="m">_LoadAminoAcidsData</span> <span class="s">{</span> 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> 193 194 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 195 196 <span class="i">$AminoAcidsDataFile</span> = <span class="q">"$MayaChemToolsLibDir"</span> . <span class="q">"/data/AminoAcidsData.csv"</span><span class="sc">;</span> 197 198 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$AminoAcidsDataFile"</span><span class="s">)</span> <span class="s">{</span> 199 <span class="w">croak</span> <span class="q">"Error: MayaChemTools package file, $AminoAcidsDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> 200 <span class="s">}</span> 201 202 <span class="i">_LoadData</span><span class="s">(</span><span class="i">$AminoAcidsDataFile</span><span class="s">)</span><span class="sc">;</span> 203 <span class="s">}</span> 204 205 <span class="c">#</span> 206 <span class="c"># Load AminoAcidsData.csv file from <MayaChemTools>/lib directory...</span> 207 <span class="c">#</span> <a name="_LoadData-"></a> 208 <span class="k">sub </span><span class="m">_LoadData</span> <span class="s">{</span> 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> 210 211 <span class="i">%AminoAcidDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 212 <span class="i">@AminoAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 213 <span class="i">%AminoAcidPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 214 <span class="i">%AminoAcidThreeLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 215 <span class="i">%AminoAcidOneLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 216 <span class="i">%AminoAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 217 218 <span class="c"># Load property data for all amino acids...</span> 219 <span class="c">#</span> 220 <span class="c"># File Format:</span> 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> 222 <span class="c">#</span> 223 <span class="c">#</span> 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">$Units</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span> 225 226 <span class="i">$InDelim</span> = <span class="q">"\,"</span><span class="sc">;</span> 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: $! ..."</span><span class="sc">;</span> 228 229 <span class="c"># Skip lines up to column labels...</span> 230 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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> 231 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 232 <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span> 233 <span class="s">}</span> 234 <span class="s">}</span> 235 <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 236 <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span> 237 238 <span class="c"># Extract property names from column labels...</span> 239 <span class="i">@AminoAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 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> 241 <span class="i">$Name</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span> 242 <span class="k">push</span> <span class="i">@AminoAcidPropertyNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span> 243 244 <span class="c"># Store property names...</span> 245 <span class="i">$AminoAcidPropertyNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span> 246 <span class="s">}</span> 247 248 <span class="c"># Process amino acid data...</span> 249 <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$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> 250 <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span> 251 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 252 <span class="s">}</span> 253 <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 254 <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span> 255 <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span> 256 <span class="w">croak</span> <span class="q">"Error: The number of data fields, @LineWords, in $AminoAcidsDataFile must be $NumOfCols.\nLine: $Line..."</span><span class="sc">;</span> 257 <span class="s">}</span> 258 <span class="i">$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">$LineWords</span>[<span class="n">3</span>]<span class="sc">;</span> 259 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}<span class="s">)</span> <span class="s">{</span> 260 <span class="w">carp</span> <span class="q">"Warning: Ignoring data for amino acid $ThreeLetterCode: It has already been loaded.\nLine: $Line...."</span><span class="sc">;</span> 261 <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span> 262 <span class="s">}</span> 263 264 <span class="c"># Store all the values...</span> 265 <span class="i">%</span>{<span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 266 <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#LineWords</span><span class="s">)</span> <span class="s">{</span> 267 <span class="i">$Name</span> = <span class="i">$AminoAcidPropertyNames</span>[<span class="i">$Index</span>]<span class="sc">;</span> 268 <span class="i">$Value</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span> 269 <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span> 270 <span class="s">}</span> 271 <span class="s">}</span> 272 <span class="k">close</span> <span class="w">AMINOACIDSDATAFILE</span><span class="sc">;</span> 273 274 <span class="c"># Setup one letter and amino acid name maps...</span> 275 <span class="i">_SetupAminoAcidIDMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 276 <span class="s">}</span> 277 278 279 <span class="c">#</span> 280 <span class="c"># Setup lowercase three/one letter code and name maps pointing</span> 281 <span class="c"># to three letter code as show in data file.</span> 282 <span class="c">#</span> <a name="_SetupAminoAcidIDMap-"></a> 283 <span class="k">sub </span><span class="m">_SetupAminoAcidIDMap</span> <span class="s">{</span> 284 <span class="k">my</span><span class="s">(</span><span class="i">$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> 285 286 <span class="i">%AminoAcidThreeLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 287 <span class="i">%AminoAcidOneLetterCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 288 <span class="i">%AminoAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 289 290 <span class="k">for</span> <span class="i">$ThreeLetterCode</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AminoAcidDataMap</span><span class="s">)</span> <span class="s">{</span> 291 <span class="i">$OneLetterCode</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="w">OneLetterCode</span>}<span class="sc">;</span> 292 <span class="i">$AminoAcidName</span> = <span class="i">$AminoAcidDataMap</span>{<span class="i">$ThreeLetterCode</span>}{<span class="w">AminoAcid</span>}<span class="sc">;</span> 293 294 <span class="i">$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> 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">$ThreeLetterCode</span><span class="sc">;</span> 296 <span class="i">$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> 297 <span class="s">}</span> 298 <span class="s">}</span> 299 300 <span class="c"># Validate amino acid ID...</span> <a name="_ValidateAminoAcidID-"></a> 301 <span class="k">sub </span><span class="m">_ValidateAminoAcidID</span> <span class="s">{</span> 302 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 303 <span class="k">my</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span> 304 305 306 <span class="k">if</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> == <span class="n">3</span><span class="s">)</span> <span class="s">{</span> 307 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$AminoAcidThreeLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 308 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 309 <span class="s">}</span> 310 <span class="i">$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> 311 <span class="s">}</span> 312 <span class="k">elsif</span> <span class="s">(</span><span class="k">length</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 313 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$AminoAcidOneLetterCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span> 314 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 315 <span class="s">}</span> 316 <span class="i">$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> 317 <span class="s">}</span> 318 <span class="k">else</span> <span class="s">{</span> 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> 320 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 321 <span class="s">}</span> 322 <span class="i">$ThreeLetterCode</span> = <span class="i">$AminoAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span>}<span class="sc">;</span> 323 <span class="s">}</span> 324 <span class="k">return</span> <span class="i">$ThreeLetterCode</span><span class="sc">;</span> 325 <span class="s">}</span> 326 327 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>