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diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/AminoAcids.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,348 @@ +<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>