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3 <title>MayaChemTools:Code:AminoAcids.pm</title>
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13 <pre>
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14 <a name="package-AminoAcids-"></a> 1 <span class="k">package </span><span class="i">AminoAcids</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: AminoAcids.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:02 $</span>
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18 5 <span class="c"># $Revision: 1.25 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
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47 34
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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>
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49 36
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50 37 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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51 38 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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52 39 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetAminoAcids GetAminoAcidPropertiesData GetAminoAcidPropertiesNames IsAminoAcid IsAminoAcidProperty)</span><span class="sc">;</span>
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53 40
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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>
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55 42
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56 43 <span class="c">#</span>
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57 44 <span class="c"># Load amino acids data...</span>
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58 45 <span class="c">#</span>
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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>
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60 47 <span class="i">_LoadAminoAcidsData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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61 48
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62 49 <span class="c">#</span>
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63 50 <span class="c"># Get a list of all known amino acids as one of these values:</span>
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64 51 <span class="c"># one letter code, three letter code, or amino acid name...</span>
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65 52 <span class="c">#</span>
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66 <a name="GetAminoAcids-"></a> 53 <span class="k">sub </span><span class="m">GetAminoAcids</span> <span class="s">{</span>
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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>
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68 55
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69 56 <span class="i">$NameType</span> = <span class="q">'ThreeLetterCode'</span><span class="sc">;</span>
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70 57 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> >= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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71 58 <span class="s">(</span><span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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72 59 <span class="s">}</span>
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73 60
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74 61 <span class="c"># Collect names...</span>
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75 62 <span class="i">%AminoAcidNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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76 63 <span class="k">for</span> <span class="i">$ThreeLetterCode</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%AminoAcidDataMap</span><span class="s">)</span> <span class="s">{</span>
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77 64 <span class="j">NAME :</span> <span class="s">{</span>
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78 65 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
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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">$ThreeLetterCode</span>}{<span class="w">AminoAcid</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span>
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80 67 <span class="i">$Name</span> = <span class="i">$ThreeLetterCode</span><span class="sc">;</span>
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81 68 <span class="s">}</span>
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82 69 <span class="i">$AminoAcidNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span>
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83 70 <span class="s">}</span>
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84 71
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85 72 <span class="c"># Sort 'em out</span>
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86 73 <span class="i">@AminoAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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87 74 <span class="k">for</span> <span class="i">$Name</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%AminoAcidNamesMap</span><span class="s">)</span> <span class="s">{</span>
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88 75 <span class="k">push</span> <span class="i">@AminoAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
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89 76 <span class="s">}</span>
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90 77
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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>
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92 79 <span class="s">}</span>
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93 80
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94 81
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95 82 <span class="c">#</span>
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96 83 <span class="c"># Get all available properties data for an amino acid using any of these symbols:</span>
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97 84 <span class="c"># three letter code; one letter code; name.</span>
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98 85 <span class="c">#</span>
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99 86 <span class="c"># A reference to a hash array is returned with keys and values representing property</span>
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100 87 <span class="c"># name and its values respectively.</span>
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101 88 <span class="c">#</span>
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102 <a name="GetAminoAcidPropertiesData-"></a> 89 <span class="k">sub </span><span class="m">GetAminoAcidPropertiesData</span> <span class="s">{</span>
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103 90 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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104 91 <span class="k">my</span><span class="s">(</span><span class="i">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span>
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105 92
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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>
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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>
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108 95 <span class="s">}</span>
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109 96 <span class="k">else</span> <span class="s">{</span>
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110 97 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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111 98 <span class="s">}</span>
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112 99 <span class="s">}</span>
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113 100
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114 101 <span class="c">#</span>
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115 102 <span class="c"># Get names of all available amino acid properties. A reference to an array containing</span>
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116 103 <span class="c"># names of all available properties is returned.</span>
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117 104 <span class="c">#</span>
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118 <a name="GetAminoAcidPropertiesNames-"></a> 105 <span class="k">sub </span><span class="m">GetAminoAcidPropertiesNames</span> <span class="s">{</span>
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119 106 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span>
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120 107 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
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121 108
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122 109 <span class="i">$Mode</span> = <span class="q">'ByGroup'</span><span class="sc">;</span>
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123 110 <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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124 111 <span class="s">(</span><span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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125 112 <span class="s">}</span>
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126 113
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127 114 <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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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>
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129 116 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span>
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130 117 <span class="c"># ThreeLetterCode, OneLetterCode, and AminoAcid are always listed first...</span>
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131 118 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="q">qw(ThreeLetterCode OneLetterCode AminoAcid)</span><span class="sc">;</span>
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132 119 <span class="k">for</span> <span class="i">$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>
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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>
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134 121 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
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135 122 <span class="s">}</span>
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136 123 <span class="s">}</span>
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137 124 <span class="s">}</span>
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138 125 <span class="k">else</span> <span class="s">{</span>
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139 126 <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@AminoAcidPropertyNames</span><span class="sc">;</span>
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140 127 <span class="s">}</span>
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141 128 <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@PropertyNames</span> <span class="co">:</span> \<span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
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142 129 <span class="s">}</span>
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143 130
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144 131 <span class="c">#</span>
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145 132 <span class="c"># Is it a known amino acid? Input is either an one/three letter code or a name.</span>
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146 133 <span class="c">#</span>
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147 <a name="IsAminoAcid-"></a> 134 <span class="k">sub </span><span class="m">IsAminoAcid</span> <span class="s">{</span>
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148 135 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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149 136 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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150 137
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151 138 <span class="i">$Status</span> = <span class="s">(</span><span class="i">_ValidateAminoAcidID</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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152 139
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153 140 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
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154 141 <span class="s">}</span>
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155 142
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156 143
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157 144 <span class="c">#</span>
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158 145 <span class="c"># Is it an available amino acid property?</span>
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159 146 <span class="c">#</span>
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160 <a name="IsAminoAcidProperty-"></a> 147 <span class="k">sub </span><span class="m">IsAminoAcidProperty</span> <span class="s">{</span>
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161 148 <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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162 149 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
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163 150
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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">$PropertyName</span>}<span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
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165 152
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166 153 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
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167 154 <span class="s">}</span>
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168 155
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169 156 <span class="c">#</span>
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170 157 <span class="c"># Implents GetAminoAcid<PropertyName> for a valid proprty name.</span>
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171 158 <span class="c">#</span>
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172 <a name="AUTOLOAD-"></a> 159 <span class="k">sub </span><span class="m">AUTOLOAD</span> <span class="s">{</span>
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173 160 <span class="k">my</span><span class="s">(</span><span class="i">$AminoAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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174 161 <span class="k">my</span><span class="s">(</span><span class="i">$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">$ThreeLetterCode</span><span class="s">)</span><span class="sc">;</span>
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175 162
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176 163 <span class="i">$PropertyValue</span> = <span class="k">undef</span><span class="sc">;</span>
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177 164
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178 165 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw($AUTOLOAD)</span><span class="sc">;</span>
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179 166 <span class="i">$FunctionName</span> = <span class="i">$AUTOLOAD</span><span class="sc">;</span>
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180 167 <span class="i">$FunctionName</span> =~ <span class="q">s/.*:://</span><span class="sc">;</span>
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181 168
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182 169 <span class="c"># Only Get<PropertyName> functions are supported...</span>
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183 170 <span class="k">if</span> <span class="s">(</span><span class="i">$FunctionName</span> !~ <span class="q">/^Get/</span><span class="s">)</span> <span class="s">{</span>
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184 171 <span class="w">croak</span> <span class="q">"Error: Function, AminoAcid::$FunctionName, is not supported by AUTOLOAD in AminoAcid module: Only Get<PropertyName> functions are implemented..."</span><span class="sc">;</span>
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185 172 <span class="s">}</span>
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186 173
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187 174 <span class="i">$PropertyName</span> = <span class="i">$FunctionName</span><span class="sc">;</span>
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188 175 <span class="i">$PropertyName</span> =~ <span class="q">s/^GetAminoAcid//</span><span class="sc">;</span>
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189 176 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$AminoAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span>
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190 177 <span class="w">croak</span> <span class="q">"Error: Function, AminoAcid::$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 />
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344 <center>
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345 <img src="../../../images/h2o2.png">
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346 </center>
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347 </body>
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348 </html>
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