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3 <title>MayaChemTools:Code:MoleculeFileIO.pm</title>
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13 <pre>
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14 <a name="package-MoleculeFileIO-"></a> 1 <span class="k">package </span><span class="i">MoleculeFileIO</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: MoleculeFileIO.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span>
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18 5 <span class="c"># $Revision: 1.32 $</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">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">FileIO::SDFileIO</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">FileIO::MDLMolFileIO</span><span class="sc">;</span>
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48 35
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49 36 <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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50 37
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51 38 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsSupportedMoleculeFileFormat)</span><span class="sc">;</span>
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54 41
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55 42 <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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56 43
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57 44 <span class="c"># Setup class variables...</span>
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58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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60 47
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61 48 <span class="c"># Class constructor...</span>
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62 <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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63 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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64 51
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65 52 <span class="c"># Initialize object...</span>
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66 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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67 54 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
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68 55 <span class="i">$This</span><span class="i">->_InitializeMoleculeFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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69 56
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70 57 <span class="i">$This</span><span class="i">->_InitializeMoleculeFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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71 58
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72 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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73 60 <span class="s">}</span>
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74 61
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75 62 <span class="c"># Initialize object data...</span>
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76 63 <span class="c">#</span>
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77 <a name="_InitializeMoleculeFileIO-"></a> 64 <span class="k">sub </span><span class="m">_InitializeMoleculeFileIO</span> <span class="s">{</span>
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78 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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79 66
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80 67 <span class="c"># Reference to specific FileIO object...</span>
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81 68 <span class="i">$This</span>->{<span class="w">FileIORef</span>} = <span class="q">''</span><span class="sc">;</span>
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82 69
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83 70 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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84 71 <span class="s">}</span>
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85 72
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86 73 <span class="c"># Initialize class ...</span>
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87 <a name="_InitializeClass-"></a> 74 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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88 75 <span class="c">#Class name...</span>
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89 76 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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90 77
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91 78 <span class="s">}</span>
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92 79
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93 80 <span class="c"># Initialize object properties......</span>
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94 81 <span class="c">#</span>
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95 <a name="_InitializeMoleculeFileIOProperties-"></a> 82 <span class="k">sub </span><span class="m">_InitializeMoleculeFileIOProperties</span> <span class="s">{</span>
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96 83 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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97 84
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98 85 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="s">)</span> <span class="s">{</span>
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99 86 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span>
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100 87 <span class="s">}</span>
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101 88
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102 89 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span>
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103 90 <span class="i">$NamesAndValues</span>{<span class="w">Mode</span>} = <span class="q">'Read'</span><span class="sc">;</span>
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104 91 <span class="s">}</span>
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105 92
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106 93 <span class="c"># Make sure its a supported format and intialize FileIO object reference...</span>
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107 94 <span class="i">$This</span><span class="i">->_SetFileIORef</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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108 95
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109 96 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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110 97 <span class="s">}</span>
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111 98
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112 99 <span class="c"># Setup FileIO object reference...</span>
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113 <a name="_SetFileIORef-"></a> 100 <span class="k">sub </span><span class="m">_SetFileIORef</span> <span class="s">{</span>
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114 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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115 102 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span><span class="sc">;</span>
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116 103
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117 104 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span>
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118 105
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119 106 <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->IsSupportedMoleculeFileFormat</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span>
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120 107 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
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121 108 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File format, $Name, is not supported: Currently supported file formats are: SDF, MDLMol..."</span><span class="sc">;</span>
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122 109 <span class="s">}</span>
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123 110
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124 111 <span class="i">$This</span>->{<span class="w">FileIORef</span>} = <span class="i">$</span>{<span class="w">IOPackageName</span>}<span class="i">->new</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
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125 112
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126 113 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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127 114 <span class="s">}</span>
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128 115
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129 116 <span class="c"># Is it a supported file format?</span>
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130 117 <span class="c">#</span>
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131 118 <span class="c"># In scalar context only status is returned; otherwise, file format and file IO package name is also</span>
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132 119 <span class="c"># returned.</span>
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133 120 <span class="c">#</span>
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134 121 <span class="c"># Note:</span>
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135 122 <span class="c"># . To support additional file formats, this is the only method which needs to be changed.</span>
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136 123 <span class="c">#</span>
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137 124 <span class="c"># . Currently supported file formats are:</span>
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138 125 <span class="c">#</span>
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139 126 <span class="c"># SDF .sdf, .sd</span>
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140 127 <span class="c"># MDLMol .mol</span>
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141 128 <span class="c">#</span>
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142 <a name="IsSupportedMoleculeFileFormat-"></a> 129 <span class="k">sub </span><span class="m">IsSupportedMoleculeFileFormat</span> <span class="s">{</span>
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143 130 <span class="k">my</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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144 131 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span><span class="sc">;</span>
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145 132
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146 133 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsMoleculeFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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147 134 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
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148 135 <span class="s">}</span>
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149 136 <span class="k">else</span> <span class="s">{</span>
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150 137 <span class="s">(</span><span class="i">$Name</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span>
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151 138 <span class="s">}</span>
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152 139 <span class="k">my</span><span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span><span class="sc">;</span>
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153 140
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154 141 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'NotSupported'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'Unknown'</span><span class="sc">;</span>
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155 142
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156 143 <span class="j">FORMAT:</span> <span class="s">{</span>
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157 144 <span class="k">if</span> <span class="s">(</span><span class="i">FileIO::SDFileIO::IsSDFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'SDF'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'FileIO::SDFileIO'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
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158 145 <span class="k">if</span> <span class="s">(</span><span class="i">FileIO::MDLMolFileIO::IsMDLMolFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> <span class="i">$Status</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'MDLMol'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'FileIO::MDLMolFileIO'</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
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159 146 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">'NotSupported'</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">'Unknown'</span><span class="sc">;</span>
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160 147 <span class="s">}</span>
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161 148
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162 149 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="s">(</span><span class="i">$Status</span><span class="cm">,</span> <span class="i">$Format</span><span class="cm">,</span> <span class="i">$IOPackageName</span><span class="s">)</span> <span class="co">:</span> <span class="i">$Status</span><span class="sc">;</span>
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163 150 <span class="s">}</span>
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164 151
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165 152 <span class="c"># Prohibit file ref change...</span>
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166 153 <span class="c">#</span>
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167 <a name="SetFileIORef-"></a> 154 <span class="k">sub </span><span class="m">SetFileIORef</span> <span class="s">{</span>
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168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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169 156
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170 157 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetFileIORef: Explicit setting of file ref is not supported..."</span><span class="sc">;</span>
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171 158
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172 159 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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173 160 <span class="s">}</span>
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174 161
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175 162 <span class="c"># Prohibit file name change...</span>
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176 163 <span class="c">#</span>
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177 <a name="SetName-"></a> 164 <span class="k">sub </span><span class="m">SetName</span> <span class="s">{</span>
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178 165 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Name</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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179 166
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180 167 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetName: Explicit setting of file name is not supported: It must be set during object instantiation..."</span><span class="sc">;</span>
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181 168
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182 169 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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183 170 <span class="s">}</span>
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184 171
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185 172 <span class="c"># Prohibit file mode change...</span>
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186 173 <span class="c">#</span>
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187 <a name="SetMode-"></a> 174 <span class="k">sub </span><span class="m">SetMode</span> <span class="s">{</span>
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188 175 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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189 176
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190 177 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetMode: Explicit setting of file mode is not supported: It must be set during object instantiation..."</span><span class="sc">;</span>
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191 178
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192 179 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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193 180 <span class="s">}</span>
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194 181
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195 182 <span class="c"># Open file in a specific mode; default mode is Read only.</span>
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196 183 <span class="c"># Supported mode values are: Read, Write, Append, <, >, >>, r, w, a</span>
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197 184 <span class="c">#</span>
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198 <a name="Open-"></a> 185 <span class="k">sub </span><span class="m">Open</span> <span class="s">{</span>
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199 186 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Mode</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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200 187
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201 188 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->Open</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span>
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202 189 <span class="s">}</span>
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203 190
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204 191 <span class="c"># close file...</span>
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205 <a name="Close-"></a> 192 <span class="k">sub </span><span class="m">Close</span> <span class="s">{</span>
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206 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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207 194
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208 195 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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209 196 <span class="s">}</span>
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210 197
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211 198 <span class="c"># Read molecule string from file and return a molecule object...</span>
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212 <a name="ReadMolecule-"></a> 199 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span>
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213 200 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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214 201
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215 202 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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216 203 <span class="s">}</span>
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217 204
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218 205 <span class="c"># Retrieve molecule string from file...</span>
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219 <a name="ReadMoleculeString-"></a> 206 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span>
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220 207 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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221 208
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222 209 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->ReadMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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223 210 <span class="s">}</span>
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224 211
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225 212 <span class="c"># Write molecule using molecule object...</span>
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226 <a name="WriteMolecule-"></a> 213 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span>
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227 214 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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228 215
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229 216 <span class="k">return</span> <span class="i">$This</span>->{<span class="w">FileIORef</span>}<span class="i">->WriteMolecule</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
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230 217 <span class="s">}</span>
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231 218
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232 219 <span class="c"># Is it a MoleculeFileIO object?</span>
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233 <a name="_IsMoleculeFileIO-"></a> 220 <span class="k">sub </span><span class="m">_IsMoleculeFileIO</span> <span class="s">{</span>
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234 221 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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235 222
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236 223 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</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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237 224 <span class="s">}</span>
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238 225
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239 <a name="EOF-"></a></pre>
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240 <p> </p>
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241 <br />
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242 <center>
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243 <img src="../../../images/h2o2.png">
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244 </center>
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245 </body>
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246 </html>
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