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+<a name="package-NucleicAcids-"></a>   1 <span class="k">package </span><span class="i">NucleicAcids</span><span class="sc">;</span>
+   2 <span class="c">#</span>
+   3 <span class="c"># $RCSfile: NucleicAcids.pm,v $</span>
+   4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span>
+   5 <span class="c"># $Revision: 1.25 $</span>
+   6 <span class="c">#</span>
+   7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</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 &lt;http://www.gnu.org/licenses/&gt; 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(GetNucleicAcids GetNucleicAcidsByType GetNucleicAcidPropertiesData GetNucleicAcidPropertiesNames IsNucleicAcid IsNucleicAcidProperty IsNucleicAcidType)</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">=&gt;</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 nucleic acids data...</span>
+  45 <span class="c">#</span>
+  46 <span class="k">my</span><span class="s">(</span><span class="i">%NucleicAcidDataMap</span><span class="cm">,</span> <span class="i">%NucleicAcidCodeMap</span><span class="cm">,</span> <span class="i">%NucleicAcidOtherCodeMap</span><span class="cm">,</span> <span class="i">%NucleicAcidNameMap</span><span class="cm">,</span> <span class="i">@NucleicAcidCodes</span><span class="cm">,</span> <span class="i">@NucleicAcidPropertyNames</span><span class="cm">,</span> <span class="i">%NucleicAcidPropertyNamesMap</span><span class="cm">,</span> <span class="i">%NucleicAcidTypesMap</span><span class="s">)</span><span class="sc">;</span>
+  47 <span class="i">_LoadNucleicAcidsData</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 nucleic acids as one of these values:</span>
+  51 <span class="c"># code or nucleic acid name...</span>
+  52 <span class="c">#</span>
+<a name="GetNucleicAcids-"></a>  53 <span class="k">sub </span><span class="m">GetNucleicAcids</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">$Code</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
+  55 
+  56   <span class="i">$NameType</span> = <span class="q">&#39;Code&#39;</span><span class="sc">;</span>
+  57   <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> &gt;= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  58     <span class="s">(</span><span class="i">$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">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  63   <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span>
+  64     <span class="j">NAME :</span> <span class="s">{</span>
+  65       <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</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="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span>
+  67     <span class="s">}</span>
+  68     <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
+  69   <span class="s">}</span>
+  70 
+  71   <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
+  72 <span class="s">}</span>
+  73 
+  74 <span class="c">#</span>
+  75 <span class="c"># Get a list of all known nucleic acids by one of these specified types:</span>
+  76 <span class="c"># Nucleobase, Nucleoside, Deoxynucleoside, Nucleotide, Deoxynucleotide. Default: Nucleoside</span>
+  77 <span class="c">#</span>
+<a name="GetNucleicAcidsByType-"></a>  78 <span class="k">sub </span><span class="m">GetNucleicAcidsByType</span> <span class="s">{</span>
+  79   <span class="k">my</span><span class="s">(</span><span class="i">$NameType</span><span class="cm">,</span> <span class="i">$Type</span><span class="cm">,</span> <span class="i">$Code</span><span class="cm">,</span> <span class="i">$Name</span><span class="cm">,</span> <span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
+  80 
+  81   <span class="i">$Type</span> = <span class="q">&#39;Nucleoside&#39;</span><span class="sc">;</span>
+  82   <span class="i">$NameType</span> = <span class="q">&#39;Code&#39;</span><span class="sc">;</span>
+  83   <span class="k">if</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
+  84     <span class="s">(</span><span class="i">$Type</span><span class="cm">,</span> <span class="i">$NameType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  85   <span class="s">}</span>
+  86   <span class="k">elsif</span> <span class="s">(</span><span class="i">@_</span> == <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
+  87     <span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+  88   <span class="s">}</span>
+  89 
+  90   <span class="c"># Collect names...</span>
+  91   <span class="i">@NucleicAcidNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+  92   <span class="j">CODE:</span> <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="i">@NucleicAcidCodes</span><span class="s">)</span> <span class="s">{</span>
+  93     <span class="k">if</span> <span class="s">(</span><span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>} !~ <span class="q">/^$Type$/i</span> <span class="s">)</span> <span class="s">{</span>
+  94       <span class="k">next</span> <span class="j">CODE</span><span class="sc">;</span>
+  95     <span class="s">}</span>
+  96     <span class="j">NAME :</span> <span class="s">{</span>
+  97       <span class="k">if</span> <span class="s">(</span><span class="i">$NameType</span> =~ <span class="q">/^Name$/i</span><span class="s">)</span> <span class="s">{</span><span class="i">$Name</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span> <span class="k">last</span> <span class="j">NAME</span><span class="sc">;</span> <span class="s">}</span>
+  98       <span class="i">$Name</span> = <span class="i">$Code</span><span class="sc">;</span>
+  99     <span class="s">}</span>
+ 100     <span class="k">push</span> <span class="i">@NucleicAcidNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
+ 101   <span class="s">}</span>
+ 102 
+ 103   <span class="k">return</span> <span class="s">(</span><span class="k">wantarray</span> ? <span class="i">@NucleicAcidNames</span> <span class="co">:</span> \<span class="i">@NucleicAcidNames</span><span class="s">)</span><span class="sc">;</span>
+ 104 <span class="s">}</span>
+ 105 
+ 106 <span class="c">#</span>
+ 107 <span class="c"># Get all available properties data for an nucleic acid using any of these symbols:</span>
+ 108 <span class="c"># code, other code or name.</span>
+ 109 <span class="c">#</span>
+ 110 <span class="c"># A reference to a hash array is returned with keys and values representing property</span>
+ 111 <span class="c"># name and its values respectively.</span>
+ 112 <span class="c">#</span>
+<a name="GetNucleicAcidPropertiesData-"></a> 113 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesData</span> <span class="s">{</span>
+ 114   <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 115   <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span><span class="sc">;</span>
+ 116 
+ 117   <span class="k">if</span> <span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 118     <span class="k">return</span> \<span class="i">%</span>{<span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}}<span class="sc">;</span>
+ 119   <span class="s">}</span>
+ 120   <span class="k">else</span> <span class="s">{</span>
+ 121     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 122   <span class="s">}</span>
+ 123 <span class="s">}</span>
+ 124 
+ 125 <span class="c">#</span>
+ 126 <span class="c"># Get names of all available nucleic acid properties. A reference to  an array containing</span>
+ 127 <span class="c"># names of all available properties is returned.</span>
+ 128 <span class="c">#</span>
+<a name="GetNucleicAcidPropertiesNames-"></a> 129 <span class="k">sub </span><span class="m">GetNucleicAcidPropertiesNames</span> <span class="s">{</span>
+ 130   <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span>
+ 131   <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="cm">,</span> <span class="i">@PropertyNames</span><span class="s">)</span><span class="sc">;</span>
+ 132 
+ 133   <span class="i">$Mode</span> = <span class="q">&#39;ByGroup&#39;</span><span class="sc">;</span>
+ 134   <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>
+ 135     <span class="s">(</span><span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 136   <span class="s">}</span>
+ 137 
+ 138   <span class="i">@PropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 139   <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^Alphabetical$/i</span><span class="s">)</span> <span class="s">{</span>
+ 140     <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span><span class="sc">;</span>
+ 141     <span class="c"># Code, OtherCodes and Name are always listed first...</span>
+ 142     <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="q">qw(Code OtherCodes Name)</span><span class="sc">;</span>
+ 143     <span class="k">for</span> <span class="i">$PropertyName</span> <span class="s">(</span><span class="k">sort</span> <span class="k">keys</span> <span class="i">%NucleicAcidPropertyNamesMap</span><span class="s">)</span> <span class="s">{</span>
+ 144       <span class="k">if</span> <span class="s">(</span><span class="i">$PropertyName</span> !~ <span class="q">/^(Code|OtherCodes|Name)$/</span><span class="s">)</span> <span class="s">{</span>
+ 145         <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">$PropertyName</span><span class="sc">;</span>
+ 146       <span class="s">}</span>
+ 147     <span class="s">}</span>
+ 148   <span class="s">}</span>
+ 149   <span class="k">else</span> <span class="s">{</span>
+ 150     <span class="k">push</span> <span class="i">@PropertyNames</span><span class="cm">,</span> <span class="i">@NucleicAcidPropertyNames</span><span class="sc">;</span>
+ 151   <span class="s">}</span>
+ 152   <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>
+ 153 <span class="s">}</span>
+ 154 
+ 155 <span class="c">#</span>
+ 156 <span class="c"># Is it a known nucleic acid? Input is either a code or a name</span>
+ 157 <span class="c">#</span>
+<a name="IsNucleicAcid-"></a> 158 <span class="k">sub </span><span class="m">IsNucleicAcid</span> <span class="s">{</span>
+ 159   <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 160   <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
+ 161 
+ 162   <span class="i">$Status</span> = <span class="s">(</span><span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</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>
+ 163 
+ 164   <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
+ 165 <span class="s">}</span>
+ 166 
+ 167 <span class="c">#</span>
+ 168 <span class="c"># Is it an available nucleic acid property?</span>
+ 169 <span class="c">#</span>
+<a name="IsNucleicAcidProperty-"></a> 170 <span class="k">sub </span><span class="m">IsNucleicAcidProperty</span> <span class="s">{</span>
+ 171   <span class="k">my</span><span class="s">(</span><span class="i">$PropertyName</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 172   <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
+ 173 
+ 174   <span class="i">$Status</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$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>
+ 175 
+ 176   <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
+ 177 <span class="s">}</span>
+ 178 
+ 179 <span class="c">#</span>
+ 180 <span class="c"># Is it an available nucleic acid type?</span>
+ 181 <span class="c">#</span>
+<a name="IsNucleicAcidType-"></a> 182 <span class="k">sub </span><span class="m">IsNucleicAcidType</span> <span class="s">{</span>
+ 183   <span class="k">my</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 184   <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
+ 185 
+ 186   <span class="i">$Status</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$NucleicAcidTypesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$Type</span><span class="s">)</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>
+ 187 
+ 188   <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
+ 189 <span class="s">}</span>
+ 190 
+ 191 <span class="c">#</span>
+ 192 <span class="c"># Implents GetNucleicAcid&lt;PropertyName&gt; for a valid proprty name.</span>
+ 193 <span class="c">#</span>
+<a name="AUTOLOAD-"></a> 194 <span class="k">sub </span><span class="m">AUTOLOAD</span> <span class="s">{</span>
+ 195   <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 196   <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">$PropertyValue</span><span class="cm">,</span> <span class="i">$Code</span><span class="s">)</span><span class="sc">;</span>
+ 197 
+ 198   <span class="i">$PropertyValue</span> = <span class="k">undef</span><span class="sc">;</span>
+ 199 
+ 200   <span class="k">use</span> <span class="w">vars</span> <span class="q">qw($AUTOLOAD)</span><span class="sc">;</span>
+ 201   <span class="i">$FunctionName</span> = <span class="i">$AUTOLOAD</span><span class="sc">;</span>
+ 202   <span class="i">$FunctionName</span> =~ <span class="q">s/.*:://</span><span class="sc">;</span>
+ 203 
+ 204   <span class="c"># Only Get&lt;PropertyName&gt; functions are supported...</span>
+ 205   <span class="k">if</span> <span class="s">(</span><span class="i">$FunctionName</span> !~ <span class="q">/^Get/</span><span class="s">)</span> <span class="s">{</span>
+ 206     <span class="w">croak</span> <span class="q">&quot;Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Only Get&lt;PropertyName&gt; functions are implemented...&quot;</span><span class="sc">;</span>
+ 207   <span class="s">}</span>
+ 208 
+ 209   <span class="i">$PropertyName</span> = <span class="i">$FunctionName</span><span class="sc">;</span>
+ 210   <span class="i">$PropertyName</span> =~  <span class="q">s/^GetNucleicAcid//</span><span class="sc">;</span>
+ 211   <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$PropertyName</span>}<span class="s">)</span> <span class="s">{</span>
+ 212     <span class="w">croak</span> <span class="q">&quot;Error: Function, NucleicAcid::$FunctionName, is not supported by AUTOLOAD in NucleicAcid module: Unknown nucleic acid property name, $PropertyName, specified...&quot;</span><span class="sc">;</span>
+ 213   <span class="s">}</span>
+ 214 
+ 215   <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">$Code</span> = <span class="i">_ValidateNucleicAcidID</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 216     <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
+ 217   <span class="s">}</span>
+ 218   <span class="i">$PropertyValue</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$PropertyName</span>}<span class="sc">;</span>
+ 219   <span class="k">return</span> <span class="i">$PropertyValue</span><span class="sc">;</span>
+ 220 <span class="s">}</span>
+ 221 
+ 222 <span class="c">#</span>
+ 223 <span class="c"># Load NucleicAcidsData.csv files from &lt;MayaChemTools&gt;/lib directory...</span>
+ 224 <span class="c">#</span>
+<a name="_LoadNucleicAcidsData-"></a> 225 <span class="k">sub </span><span class="m">_LoadNucleicAcidsData</span> <span class="s">{</span>
+ 226   <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span>
+ 227 
+ 228   <span class="i">$MayaChemToolsLibDir</span> = <span class="i">GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 229 
+ 230   <span class="i">$NucleicAcidsDataFile</span> =  <span class="q">&quot;$MayaChemToolsLibDir&quot;</span> . <span class="q">&quot;/data/NucleicAcidsData.csv&quot;</span><span class="sc">;</span>
+ 231 
+ 232   <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">&quot;$NucleicAcidsDataFile&quot;</span><span class="s">)</span> <span class="s">{</span>
+ 233     <span class="w">croak</span> <span class="q">&quot;Error: MayaChemTools package file, $NucleicAcidsDataFile, is missing: Possible installation problems...&quot;</span><span class="sc">;</span>
+ 234   <span class="s">}</span>
+ 235 
+ 236   <span class="i">_LoadData</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span><span class="sc">;</span>
+ 237 <span class="s">}</span>
+ 238 
+ 239 <span class="c">#</span>
+ 240 <span class="c"># Load NucleicAcidsData.csv file from &lt;MayaChemTools&gt;/lib directory...</span>
+ 241 <span class="c">#</span>
+<a name="_LoadData-"></a> 242 <span class="k">sub </span><span class="m">_LoadData</span> <span class="s">{</span>
+ 243   <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidsDataFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 244 
+ 245   <span class="i">%NucleicAcidDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 246   <span class="i">@NucleicAcidCodes</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 247   <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 248   <span class="i">%NucleicAcidPropertyNamesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 249   <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 250   <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 251   <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 252   <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 253 
+ 254   <span class="c"># Load property data for all nucleic acids...</span>
+ 255   <span class="c">#</span>
+ 256   <span class="c"># File Format:</span>
+ 257   <span class="c"># &quot;Code&quot;,&quot;OtherCodes&quot;,&quot;BasePair&quot;,&quot;Name&quot;,&quot;Type&quot;,&quot;ChemicalFormula&quot;,&quot;ChemicalFormulaAtpH7.5&quot;,&quot;MolecularWeight&quot;,&quot;ExactMass&quot;,&quot;ElementalComposition&quot;</span>
+ 258   <span class="c">#</span>
+ 259   <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="cm">,</span> <span class="i">$OtherCodes</span><span class="cm">,</span> <span class="i">$NucleicAcidName</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">$Units</span><span class="cm">,</span> <span class="i">@LineWords</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
+ 260 
+ 261   <span class="i">$InDelim</span> = <span class="q">&quot;\,&quot;</span><span class="sc">;</span>
+ 262   <span class="k">open</span> <span class="w">NUCLEICACIDSDATAFILE</span><span class="cm">,</span> <span class="q">&quot;$NucleicAcidsDataFile&quot;</span> <span class="k">or</span> <span class="w">croak</span> <span class="q">&quot;Couldn&#39;t open $NucleicAcidsDataFile: $! ...&quot;</span><span class="sc">;</span>
+ 263 
+ 264   <span class="c"># Skip lines up to column labels...</span>
+ 265   <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*NUCLEICACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 266     <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> !~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
+ 267       <span class="k">last</span> <span class="j">LINE</span><span class="sc">;</span>
+ 268     <span class="s">}</span>
+ 269   <span class="s">}</span>
+ 270   <span class="i">@ColLabels</span>= <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
+ 271   <span class="i">$NumOfCols</span> = <span class="i">@ColLabels</span><span class="sc">;</span>
+ 272 
+ 273   <span class="c"># Extract property names from column labels...</span>
+ 274   <span class="i">@NucleicAcidPropertyNames</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 275   <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>
+ 276     <span class="i">$Name</span> = <span class="i">$ColLabels</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 277     <span class="k">push</span> <span class="i">@NucleicAcidPropertyNames</span><span class="cm">,</span> <span class="i">$Name</span><span class="sc">;</span>
+ 278 
+ 279     <span class="c"># Store property names...</span>
+ 280     <span class="i">$NucleicAcidPropertyNamesMap</span>{<span class="i">$Name</span>} = <span class="i">$Name</span><span class="sc">;</span>
+ 281   <span class="s">}</span>
+ 282 
+ 283   <span class="c"># Process nucleic acid data...</span>
+ 284   <span class="j">LINE:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Line</span> = <span class="i">GetTextLine</span><span class="s">(</span>\<span class="i">*NUCLEICACIDSDATAFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
+ 285     <span class="k">if</span> <span class="s">(</span><span class="i">$Line</span> =~ <span class="q">/^#/</span><span class="s">)</span> <span class="s">{</span>
+ 286       <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
+ 287     <span class="s">}</span>
+ 288     <span class="i">@LineWords</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 289     <span class="i">@LineWords</span> = <span class="i">quotewords</span><span class="s">(</span><span class="i">$InDelim</span><span class="cm">,</span> <span class="n">0</span><span class="cm">,</span> <span class="i">$Line</span><span class="s">)</span><span class="sc">;</span>
+ 290     <span class="k">if</span> <span class="s">(</span><span class="i">@LineWords</span> != <span class="i">$NumOfCols</span><span class="s">)</span> <span class="s">{</span>
+ 291       <span class="w">croak</span> <span class="q">&quot;Error: The number of data fields, @LineWords, in $NucleicAcidsDataFile must be $NumOfCols.\nLine: $Line...&quot;</span><span class="sc">;</span>
+ 292     <span class="s">}</span>
+ 293     <span class="i">$Code</span> = <span class="i">$LineWords</span>[<span class="n">0</span>]<span class="sc">;</span> <span class="i">$OtherCodes</span> = <span class="i">$LineWords</span>[<span class="n">1</span>]<span class="sc">;</span> <span class="i">$NucleicAcidName</span> = <span class="i">$LineWords</span>[<span class="n">3</span>]<span class="sc">;</span>
+ 294     <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}<span class="s">)</span> <span class="s">{</span>
+ 295       <span class="w">carp</span> <span class="q">&quot;Warning: Ignoring data for nucleic acid $Code: It has already been loaded.\nLine: $Line....&quot;</span><span class="sc">;</span>
+ 296       <span class="k">next</span> <span class="j">LINE</span><span class="sc">;</span>
+ 297     <span class="s">}</span>
+ 298 
+ 299     <span class="c"># Store all the values...</span>
+ 300     <span class="k">push</span> <span class="i">@NucleicAcidCodes</span><span class="cm">,</span> <span class="i">$Code</span><span class="sc">;</span>
+ 301     <span class="i">%</span>{<span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 302     <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>
+ 303       <span class="i">$Name</span> = <span class="i">$NucleicAcidPropertyNames</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 304       <span class="i">$Value</span> = <span class="i">$LineWords</span>[<span class="i">$Index</span>]<span class="sc">;</span>
+ 305       <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="i">$Name</span>} = <span class="i">$Value</span><span class="sc">;</span>
+ 306     <span class="s">}</span>
+ 307   <span class="s">}</span>
+ 308   <span class="k">close</span> <span class="w">NUCLEICACIDSDATAFILE</span><span class="sc">;</span>
+ 309 
+ 310   <span class="c"># Setup one letter and nucleic acid name maps...</span>
+ 311   <span class="i">_SetupNucleicAcidIDMap</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 312 <span class="s">}</span>
+ 313 
+ 314 <span class="c">#</span>
+ 315 <span class="c"># Setup lowercase other codes and name maps pointing</span>
+ 316 <span class="c"># to code as show in data file.</span>
+ 317 <span class="c">#</span>
+<a name="_SetupNucleicAcidIDMap-"></a> 318 <span class="k">sub </span><span class="m">_SetupNucleicAcidIDMap</span> <span class="s">{</span>
+ 319   <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="cm">,</span> <span class="i">@OtherCodes</span><span class="cm">,</span> <span class="i">$OtherCode</span><span class="cm">,</span> <span class="i">$NucleicAcidName</span><span class="cm">,</span> <span class="i">$NucleicAcidType</span><span class="s">)</span><span class="sc">;</span>
+ 320 
+ 321   <span class="i">%NucleicAcidCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 322   <span class="i">%NucleicAcidOtherCodeMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 323   <span class="i">%NucleicAcidNameMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 324   <span class="i">%NucleicAcidTypesMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
+ 325 
+ 326   <span class="k">for</span> <span class="i">$Code</span> <span class="s">(</span><span class="k">keys</span> <span class="i">%NucleicAcidDataMap</span><span class="s">)</span> <span class="s">{</span>
+ 327     <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span>
+ 328 
+ 329     <span class="i">$NucleicAcidName</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Name</span>}<span class="sc">;</span>
+ 330     <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidName</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span>
+ 331 
+ 332     <span class="i">$NucleicAcidType</span> = <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">Type</span>}<span class="sc">;</span>
+ 333     <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$NucleicAcidTypesMap</span>{<span class="i">$NucleicAcidType</span>}<span class="s">)</span> <span class="s">{</span>
+ 334       <span class="i">$NucleicAcidTypesMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidType</span><span class="s">)</span>} = <span class="i">$NucleicAcidType</span><span class="sc">;</span>
+ 335     <span class="s">}</span>
+ 336 
+ 337     <span class="i">@OtherCodes</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$NucleicAcidDataMap</span>{<span class="i">$Code</span>}{<span class="w">OtherCodes</span>}<span class="sc">;</span>
+ 338     <span class="j">OTHERCODE:</span> <span class="k">for</span> <span class="i">$OtherCode</span> <span class="s">(</span><span class="i">@OtherCodes</span><span class="s">)</span> <span class="s">{</span>
+ 339       <span class="k">if</span> <span class="s">(</span>!<span class="i">$OtherCode</span><span class="s">)</span> <span class="s">{</span>
+ 340         <span class="k">next</span> <span class="j">OTHERCODE</span><span class="sc">;</span>
+ 341       <span class="s">}</span>
+ 342       <span class="i">$OtherCode</span> = <span class="i">RemoveLeadingAndTrailingWhiteSpaces</span><span class="s">(</span><span class="i">$OtherCode</span><span class="s">)</span><span class="sc">;</span>
+ 343       <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$OtherCode</span><span class="s">)</span>} = <span class="i">$Code</span><span class="sc">;</span>
+ 344     <span class="s">}</span>
+ 345   <span class="s">}</span>
+ 346 <span class="s">}</span>
+ 347 
+ 348 <span class="c"># Validate Nucleic acid ID...</span>
+<a name="_ValidateNucleicAcidID-"></a> 349 <span class="k">sub </span><span class="m">_ValidateNucleicAcidID</span> <span class="s">{</span>
+ 350   <span class="k">my</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
+ 351   <span class="k">my</span><span class="s">(</span><span class="i">$Code</span><span class="s">)</span> = <span class="k">undef</span><span class="sc">;</span>
+ 352 
+ 353   <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+ 354     <span class="i">$Code</span> = <span class="i">$NucleicAcidCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span>
+ 355   <span class="s">}</span>
+ 356   <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+ 357     <span class="i">$Code</span> = <span class="i">$NucleicAcidOtherCodeMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span>
+ 358   <span class="s">}</span>
+ 359   <span class="k">elsif</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="s">)</span> <span class="s">{</span>
+ 360     <span class="i">$Code</span> = <span class="i">$NucleicAcidNameMap</span>{<span class="k">lc</span><span class="s">(</span><span class="i">$NucleicAcidID</span><span class="s">)</span>}<span class="sc">;</span>
+ 361   <span class="s">}</span>
+ 362   <span class="k">return</span> <span class="i">$Code</span><span class="sc">;</span>
+ 363 <span class="s">}</span>
+ 364 
+ 365 
+<a name="EOF-"></a></pre>
+<p>&nbsp;</p>
+<br />
+<center>
+<img src="../../../images/h2o2.png">
+</center>
+</body>
+</html>