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1 package AminoAcids;
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2 #
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3 # $RCSfile: AminoAcids.pm,v $
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4 # $Date: 2015/02/28 20:47:02 $
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5 # $Revision: 1.25 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use Carp;
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31 use Text::ParseWords;
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32 use TextUtil;
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33 use FileUtil;
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34
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35 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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36
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37 @ISA = qw(Exporter);
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38 @EXPORT = qw();
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39 @EXPORT_OK = qw(GetAminoAcids GetAminoAcidPropertiesData GetAminoAcidPropertiesNames IsAminoAcid IsAminoAcidProperty);
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40
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41 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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42
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43 #
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44 # Load amino acids data...
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45 #
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46 my(%AminoAcidDataMap, %AminoAcidThreeLetterCodeMap, %AminoAcidOneLetterCodeMap, %AminoAcidNameMap, @AminoAcidPropertyNames, %AminoAcidPropertyNamesMap, );
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47 _LoadAminoAcidsData();
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48
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49 #
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50 # Get a list of all known amino acids as one of these values:
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51 # one letter code, three letter code, or amino acid name...
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52 #
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53 sub GetAminoAcids {
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54 my($NameType, $ThreeLetterCode, $Name, @AminoAcidNames, %AminoAcidNamesMap);
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55
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56 $NameType = 'ThreeLetterCode';
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57 if (@_ >= 1) {
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58 ($NameType) = @_;
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59 }
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60
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61 # Collect names...
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62 %AminoAcidNamesMap = ();
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63 for $ThreeLetterCode (keys %AminoAcidDataMap) {
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64 NAME : {
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65 if ($NameType =~ /^OneLetterCode$/i) {$Name = $AminoAcidDataMap{$ThreeLetterCode}{OneLetterCode}; last NAME; }
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66 if ($NameType =~ /^AminoAcid$/i) {$Name = $AminoAcidDataMap{$ThreeLetterCode}{AminoAcid}; last NAME; }
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67 $Name = $ThreeLetterCode;
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68 }
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69 $AminoAcidNamesMap{$Name} = $Name;
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70 }
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71
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72 # Sort 'em out
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73 @AminoAcidNames = ();
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74 for $Name (sort keys %AminoAcidNamesMap) {
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75 push @AminoAcidNames, $Name;
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76 }
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77
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78 return (wantarray ? @AminoAcidNames : \@AminoAcidNames);
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79 }
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80
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81
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82 #
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83 # Get all available properties data for an amino acid using any of these symbols:
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84 # three letter code; one letter code; name.
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85 #
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86 # A reference to a hash array is returned with keys and values representing property
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87 # name and its values respectively.
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88 #
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89 sub GetAminoAcidPropertiesData {
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90 my($AminoAcidID) = @_;
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91 my($ThreeLetterCode);
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92
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93 if ($ThreeLetterCode = _ValidateAminoAcidID($AminoAcidID)) {
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94 return \%{$AminoAcidDataMap{$ThreeLetterCode}};
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95 }
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96 else {
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97 return undef;
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98 }
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99 }
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100
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101 #
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102 # Get names of all available amino acid properties. A reference to an array containing
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103 # names of all available properties is returned.
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104 #
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105 sub GetAminoAcidPropertiesNames {
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106 my($Mode);
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107 my($PropertyName, @PropertyNames);
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108
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109 $Mode = 'ByGroup';
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110 if (@_ == 1) {
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111 ($Mode) = @_;
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112 }
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113
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114 @PropertyNames = ();
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115 if ($Mode =~ /^Alphabetical$/i) {
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116 my($PropertyName);
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117 # ThreeLetterCode, OneLetterCode, and AminoAcid are always listed first...
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118 push @PropertyNames, qw(ThreeLetterCode OneLetterCode AminoAcid);
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119 for $PropertyName (sort keys %AminoAcidPropertyNamesMap) {
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120 if ($PropertyName !~ /^(ThreeLetterCode|OneLetterCode|AminoAcid)$/) {
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121 push @PropertyNames, $PropertyName;
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122 }
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123 }
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124 }
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125 else {
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126 push @PropertyNames, @AminoAcidPropertyNames;
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127 }
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128 return (wantarray ? @PropertyNames : \@PropertyNames);
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129 }
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130
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131 #
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132 # Is it a known amino acid? Input is either an one/three letter code or a name.
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133 #
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134 sub IsAminoAcid {
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135 my($AminoAcidID) = @_;
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136 my($Status);
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137
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138 $Status = (_ValidateAminoAcidID($AminoAcidID)) ? 1 : 0;
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139
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140 return $Status;
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141 }
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142
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143
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144 #
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145 # Is it an available amino acid property?
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146 #
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147 sub IsAminoAcidProperty {
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148 my($PropertyName) = @_;
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149 my($Status);
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150
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151 $Status = (exists($AminoAcidPropertyNamesMap{$PropertyName})) ? 1 : 0;
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152
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153 return $Status;
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154 }
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155
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156 #
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157 # Implents GetAminoAcid<PropertyName> for a valid proprty name.
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158 #
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159 sub AUTOLOAD {
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160 my($AminoAcidID) = @_;
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161 my($FunctionName, $PropertyName, $PropertyValue, $ThreeLetterCode);
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162
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163 $PropertyValue = undef;
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164
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165 use vars qw($AUTOLOAD);
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166 $FunctionName = $AUTOLOAD;
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167 $FunctionName =~ s/.*:://;
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168
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169 # Only Get<PropertyName> functions are supported...
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170 if ($FunctionName !~ /^Get/) {
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171 croak "Error: Function, AminoAcid::$FunctionName, is not supported by AUTOLOAD in AminoAcid module: Only Get<PropertyName> functions are implemented...";
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172 }
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173
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174 $PropertyName = $FunctionName;
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175 $PropertyName =~ s/^GetAminoAcid//;
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176 if (!exists $AminoAcidPropertyNamesMap{$PropertyName}) {
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177 croak "Error: Function, AminoAcid::$FunctionName, is not supported by AUTOLOAD in AminoAcid module: Unknown amino acid property name, $PropertyName, specified...";
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178 }
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179
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180 if (!($ThreeLetterCode = _ValidateAminoAcidID($AminoAcidID))) {
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181 return undef;
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182 }
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183 $PropertyValue = $AminoAcidDataMap{$ThreeLetterCode}{$PropertyName};
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184 return $PropertyValue;
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185 }
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186
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187
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188 #
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189 # Load AminoAcidsData.csv files from <MayaChemTools>/lib directory...
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190 #
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191 sub _LoadAminoAcidsData {
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192 my($AminoAcidsDataFile, $MayaChemToolsLibDir);
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193
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194 $MayaChemToolsLibDir = GetMayaChemToolsLibDirName();
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195
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196 $AminoAcidsDataFile = "$MayaChemToolsLibDir" . "/data/AminoAcidsData.csv";
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197
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198 if (! -e "$AminoAcidsDataFile") {
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199 croak "Error: MayaChemTools package file, $AminoAcidsDataFile, is missing: Possible installation problems...";
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200 }
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201
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202 _LoadData($AminoAcidsDataFile);
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203 }
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204
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205 #
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206 # Load AminoAcidsData.csv file from <MayaChemTools>/lib directory...
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207 #
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208 sub _LoadData {
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209 my($AminoAcidsDataFile) = @_;
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210
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211 %AminoAcidDataMap = ();
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212 @AminoAcidPropertyNames = ();
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213 %AminoAcidPropertyNamesMap = ();
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214 %AminoAcidThreeLetterCodeMap = ();
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215 %AminoAcidOneLetterCodeMap = ();
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216 %AminoAcidNameMap = ();
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217
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218 # Load property data for all amino acids...
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219 #
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220 # File Format:
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221 #"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"
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222 #
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223 #
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224 my($ThreeLetterCode, $OneLetterCode, $AminoAcidName, $Line, $NumOfCols, $InDelim, $Index, $Name, $Value, $Units, @LineWords, @ColLabels);
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225
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226 $InDelim = "\,";
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227 open AMINOACIDSDATAFILE, "$AminoAcidsDataFile" or croak "Couldn't open $AminoAcidsDataFile: $! ...";
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228
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229 # Skip lines up to column labels...
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230 LINE: while ($Line = GetTextLine(\*AMINOACIDSDATAFILE)) {
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231 if ($Line !~ /^#/) {
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232 last LINE;
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233 }
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234 }
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235 @ColLabels= quotewords($InDelim, 0, $Line);
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236 $NumOfCols = @ColLabels;
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237
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238 # Extract property names from column labels...
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239 @AminoAcidPropertyNames = ();
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240 for $Index (0 .. $#ColLabels) {
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241 $Name = $ColLabels[$Index];
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242 push @AminoAcidPropertyNames, $Name;
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243
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244 # Store property names...
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245 $AminoAcidPropertyNamesMap{$Name} = $Name;
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246 }
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247
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248 # Process amino acid data...
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249 LINE: while ($Line = GetTextLine(\*AMINOACIDSDATAFILE)) {
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250 if ($Line =~ /^#/) {
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251 next LINE;
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252 }
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253 @LineWords = ();
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254 @LineWords = quotewords($InDelim, 0, $Line);
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255 if (@LineWords != $NumOfCols) {
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256 croak "Error: The number of data fields, @LineWords, in $AminoAcidsDataFile must be $NumOfCols.\nLine: $Line...";
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257 }
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258 $ThreeLetterCode = $LineWords[0]; $OneLetterCode = $LineWords[1]; $AminoAcidName = $LineWords[3];
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259 if (exists $AminoAcidDataMap{$ThreeLetterCode}) {
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260 carp "Warning: Ignoring data for amino acid $ThreeLetterCode: It has already been loaded.\nLine: $Line....";
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261 next LINE;
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262 }
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263
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264 # Store all the values...
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265 %{$AminoAcidDataMap{$ThreeLetterCode}} = ();
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266 for $Index (0 .. $#LineWords) {
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267 $Name = $AminoAcidPropertyNames[$Index];
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268 $Value = $LineWords[$Index];
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269 $AminoAcidDataMap{$ThreeLetterCode}{$Name} = $Value;
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270 }
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271 }
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272 close AMINOACIDSDATAFILE;
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273
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274 # Setup one letter and amino acid name maps...
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275 _SetupAminoAcidIDMap();
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276 }
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277
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278
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279 #
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280 # Setup lowercase three/one letter code and name maps pointing
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281 # to three letter code as show in data file.
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282 #
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283 sub _SetupAminoAcidIDMap {
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284 my($ThreeLetterCode, $OneLetterCode, $AminoAcidName);
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285
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286 %AminoAcidThreeLetterCodeMap = ();
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287 %AminoAcidOneLetterCodeMap = ();
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288 %AminoAcidNameMap = ();
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289
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290 for $ThreeLetterCode (keys %AminoAcidDataMap) {
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291 $OneLetterCode = $AminoAcidDataMap{$ThreeLetterCode}{OneLetterCode};
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292 $AminoAcidName = $AminoAcidDataMap{$ThreeLetterCode}{AminoAcid};
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293
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294 $AminoAcidThreeLetterCodeMap{lc($ThreeLetterCode)} = $ThreeLetterCode;
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295 $AminoAcidOneLetterCodeMap{lc($OneLetterCode)} = $ThreeLetterCode;
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296 $AminoAcidNameMap{lc($AminoAcidName)} = $ThreeLetterCode;
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297 }
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298 }
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299
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300 # Validate amino acid ID...
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301 sub _ValidateAminoAcidID {
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302 my($AminoAcidID) = @_;
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303 my($ThreeLetterCode);
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304
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305
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306 if (length($AminoAcidID) == 3) {
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307 if (! exists $AminoAcidThreeLetterCodeMap{lc($AminoAcidID)}) {
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308 return undef;
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309 }
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310 $ThreeLetterCode = $AminoAcidThreeLetterCodeMap{lc($AminoAcidID)};
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311 }
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312 elsif (length($AminoAcidID) == 1) {
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313 if (! exists $AminoAcidOneLetterCodeMap{lc($AminoAcidID)}) {
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314 return undef;
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315 }
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316 $ThreeLetterCode = $AminoAcidOneLetterCodeMap{lc($AminoAcidID)};
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317 }
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318 else {
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319 if (! exists $AminoAcidNameMap{lc($AminoAcidID)}) {
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320 return undef;
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321 }
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322 $ThreeLetterCode = $AminoAcidNameMap{lc($AminoAcidID)};
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323 }
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324 return $ThreeLetterCode;
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325 }
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326
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327
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328 1;
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329
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330 __END__
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331
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332 =head1 NAME
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333
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334 AminoAcids
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335
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336 =head1 SYNOPSIS
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337
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338 use AminoAcids;
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339
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340 use AminoAcids qw(:all);
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341
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342 =head1 DESCRIPTION
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343
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344 B<AminoAcids> module provides the following functions:
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345
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346 GetAminoAcidPropertiesData, GetAminoAcidPropertiesNames, GetAminoAcid<PropertyName>,
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347 GetAminoAcids, IsAminoAcid, IsAminoAcidProperty
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348
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349 =head1 FUNCTIONS
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350
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351 =over 4
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352
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353 =item B<GetAminoAcidPropertiesData>
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354
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355 $DataHashRef = GetAminoAcidPropertiesData($AminoAcidID);
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356
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357 Returns a reference to hash containing property names and values for a specified
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358 amino acid.
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359
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360 =item B<GetAminoAcidPropertiesNames>
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361
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362 @Names = GetAminoAcidPropertiesNames([$Mode]);
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363 $NamesRef = GetAminoAcidPropertiesNames([$Mode]);
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364
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365 Returns an array or a reference to an array containing names of amino acids
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366 properties. Order of amino acids properties is controlled by optional parameter
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367 I<Mode>. Possible values for I<Mode>: I<Alphabetical or ByGroup>; Default: I<ByGroup>
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368
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369 =item B<GetAminoAcidPropertyName>
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370
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371 $Value = GetAminoAcid<PropertyName>($AminoAcidID);
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372
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373 Returns amino acid property value for a specified amino acid. These functions are
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374 not defined in this modules; these are implemented on the fly using Perl's AUTOLOAD
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375 funcion. Here is the list of known amino acids I<property names>: DNACodons, RNACodons,
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376 AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint,
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377 pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O,
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378 MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume,
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379 %AccessibleResidues, %BuriedResidues, AlphaHelixChouAndFasman,
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380 AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition,
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381 AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility,
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382 BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt,
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383 BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness,
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384 CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4,
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385 HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack,
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386 HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers,
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387 HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan,
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388 HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers,
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389 HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin,
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390 HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers,
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391 HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers,
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392 HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers,
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393 HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers,
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394 ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide,
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395 RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure,
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396 LinearStructureAtpH7.4
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397
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398 =item B<GetAminoAcids>
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399
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400 $NamesRef = GetAminoAcids([$NameType]);
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401 (@Names) = GetAminoAcids([$NameType]);
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402
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403 Returns an array or a reference to an array containing names of amino acids
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404 as one letter code, three letter code, or amino acid name controlled by optional
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405 parameter $NameType. By default, amino acids names are returned as three
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406 letter code. Possible values for I<NameType>: I<ThreeLetterCode, OneLetterCode, or
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407 AminoAcid>.
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408
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409 =item B<IsAminoAcid>
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410
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411 $Status = IsAminoAcid($AminoAcidID);
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412
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413 Returns a flag indicating whether or not its a known amino acid ID.
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414
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415 =item B<IsAminoAcidProperty>
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416
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417 $Status = IsAminoAcid($PropertyName);
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418
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419 Returns a flag indicating whether or not its a known amino acid property name.
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420
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421 =back
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422
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423 =head1 AUTHOR
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424
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425 Manish Sud <msud@san.rr.com>
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426
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427 =head1 SEE ALSO
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428
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429 NucleicAcids.pm, PeriodicTable.pm
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430
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431 =head1 COPYRIGHT
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432
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433 Copyright (C) 2015 Manish Sud. All rights reserved.
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434
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435 This file is part of MayaChemTools.
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436
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437 MayaChemTools is free software; you can redistribute it and/or modify it under
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438 the terms of the GNU Lesser General Public License as published by the Free
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439 Software Foundation; either version 3 of the License, or (at your option)
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440 any later version.
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441
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442 =cut
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