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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>
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: MoleculeFileIO.pm,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:47:18 $</span>
18 5 <span class="c"># $Revision: 1.32 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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>
46 33 <span class="k">use</span> <span class="w">FileIO::SDFileIO</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">FileIO::MDLMolFileIO</span><span class="sc">;</span>
48 35
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>
50 37
51 38 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsSupportedMoleculeFileFormat)</span><span class="sc">;</span>
54 41
55 42 <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>
56 43
57 44 <span class="c"># Setup class variables...</span>
58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
60 47
61 48 <span class="c"># Class constructor...</span>
62 <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
63 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
64 51
65 52 <span class="c"># Initialize object...</span>
66 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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">$Class</span><span class="sc">;</span>
68 55 <span class="i">$This</span><span class="i">-&gt;_InitializeMoleculeFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
69 56
70 57 <span class="i">$This</span><span class="i">-&gt;_InitializeMoleculeFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
71 58
72 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
73 60 <span class="s">}</span>
74 61
75 62 <span class="c"># Initialize object data...</span>
76 63 <span class="c">#</span>
77 <a name="_InitializeMoleculeFileIO-"></a> 64 <span class="k">sub </span><span class="m">_InitializeMoleculeFileIO</span> <span class="s">{</span>
78 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
79 66
80 67 <span class="c"># Reference to specific FileIO object...</span>
81 68 <span class="i">$This</span>-&gt;{<span class="w">FileIORef</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
82 69
83 70 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
84 71 <span class="s">}</span>
85 72
86 73 <span class="c"># Initialize class ...</span>
87 <a name="_InitializeClass-"></a> 74 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
88 75 <span class="c">#Class name...</span>
89 76 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
90 77
91 78 <span class="s">}</span>
92 79
93 80 <span class="c"># Initialize object properties......</span>
94 81 <span class="c">#</span>
95 <a name="_InitializeMoleculeFileIOProperties-"></a> 82 <span class="k">sub </span><span class="m">_InitializeMoleculeFileIOProperties</span> <span class="s">{</span>
96 83 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
97 84
98 85 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="s">)</span> <span class="s">{</span>
99 86 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated without specifying file name...&quot;</span><span class="sc">;</span>
100 87 <span class="s">}</span>
101 88
102 89 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Mode</span>}<span class="s">)</span> <span class="s">{</span>
103 90 <span class="i">$NamesAndValues</span>{<span class="w">Mode</span>} = <span class="q">&#39;Read&#39;</span><span class="sc">;</span>
104 91 <span class="s">}</span>
105 92
106 93 <span class="c"># Make sure its a supported format and intialize FileIO object reference...</span>
107 94 <span class="i">$This</span><span class="i">-&gt;_SetFileIORef</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
108 95
109 96 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
110 97 <span class="s">}</span>
111 98
112 99 <span class="c"># Setup FileIO object reference...</span>
113 <a name="_SetFileIORef-"></a> 100 <span class="k">sub </span><span class="m">_SetFileIORef</span> <span class="s">{</span>
114 101 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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>
116 103
117 104 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span>
118 105
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">-&gt;IsSupportedMoleculeFileFormat</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="sc">;</span>
120 107 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Status</span><span class="s">)</span> <span class="s">{</span>
121 108 <span class="w">croak</span> <span class="q">&quot;Error: ${ClassName}-&gt;New: Object can&#39;t be instantiated: File format, $Name, is not supported: Currently supported file formats are: SDF, MDLMol...&quot;</span><span class="sc">;</span>
122 109 <span class="s">}</span>
123 110
124 111 <span class="i">$This</span>-&gt;{<span class="w">FileIORef</span>} = <span class="i">$</span>{<span class="w">IOPackageName</span>}<span class="i">-&gt;new</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
125 112
126 113 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
127 114 <span class="s">}</span>
128 115
129 116 <span class="c"># Is it a supported file format?</span>
130 117 <span class="c">#</span>
131 118 <span class="c"># In scalar context only status is returned; otherwise, file format and file IO package name is also</span>
132 119 <span class="c"># returned.</span>
133 120 <span class="c">#</span>
134 121 <span class="c"># Note:</span>
135 122 <span class="c"># . To support additional file formats, this is the only method which needs to be changed.</span>
136 123 <span class="c">#</span>
137 124 <span class="c"># . Currently supported file formats are:</span>
138 125 <span class="c">#</span>
139 126 <span class="c"># SDF .sdf, .sd</span>
140 127 <span class="c"># MDLMol .mol</span>
141 128 <span class="c">#</span>
142 <a name="IsSupportedMoleculeFileFormat-"></a> 129 <span class="k">sub </span><span class="m">IsSupportedMoleculeFileFormat</span> <span class="s">{</span>
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>
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>
145 132
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> &amp;&amp; <span class="s">(</span><span class="i">_IsMoleculeFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
147 134 <span class="s">(</span><span class="i">$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">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
148 135 <span class="s">}</span>
149 136 <span class="k">else</span> <span class="s">{</span>
150 137 <span class="s">(</span><span class="i">$Name</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="sc">;</span>
151 138 <span class="s">}</span>
152 139 <span class="k">my</span><span class="s">(</span><span class="i">$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>
153 140
154 141 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">&#39;NotSupported&#39;</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">&#39;Unknown&#39;</span><span class="sc">;</span>
155 142
156 143 <span class="j">FORMAT:</span> <span class="s">{</span>
157 144 <span class="k">if</span> <span class="s">(</span><span class="i">FileIO::SDFileIO::IsSDFile</span><span class="s">(</span><span class="i">$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">&#39;SDF&#39;</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">&#39;FileIO::SDFileIO&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
158 145 <span class="k">if</span> <span class="s">(</span><span class="i">FileIO::MDLMolFileIO::IsMDLMolFile</span><span class="s">(</span><span class="i">$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">&#39;MDLMol&#39;</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">&#39;FileIO::MDLMolFileIO&#39;</span><span class="sc">;</span> <span class="k">last</span> <span class="j">FORMAT</span><span class="sc">;</span> <span class="s">}</span>
159 146 <span class="i">$Status</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Format</span> = <span class="q">&#39;NotSupported&#39;</span><span class="sc">;</span> <span class="i">$IOPackageName</span> = <span class="q">&#39;Unknown&#39;</span><span class="sc">;</span>
160 147 <span class="s">}</span>
161 148
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>
163 150 <span class="s">}</span>
164 151
165 152 <span class="c"># Prohibit file ref change...</span>
166 153 <span class="c">#</span>
167 <a name="SetFileIORef-"></a> 154 <span class="k">sub </span><span class="m">SetFileIORef</span> <span class="s">{</span>
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>
169 156
170 157 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetFileIORef: Explicit setting of file ref is not supported...&quot;</span><span class="sc">;</span>
171 158
172 159 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
173 160 <span class="s">}</span>
174 161
175 162 <span class="c"># Prohibit file name change...</span>
176 163 <span class="c">#</span>
177 <a name="SetName-"></a> 164 <span class="k">sub </span><span class="m">SetName</span> <span class="s">{</span>
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>
179 166
180 167 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetName: Explicit setting of file name is not supported: It must be set during object instantiation...&quot;</span><span class="sc">;</span>
181 168
182 169 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
183 170 <span class="s">}</span>
184 171
185 172 <span class="c"># Prohibit file mode change...</span>
186 173 <span class="c">#</span>
187 <a name="SetMode-"></a> 174 <span class="k">sub </span><span class="m">SetMode</span> <span class="s">{</span>
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>
189 176
190 177 <span class="w">carp</span> <span class="q">&quot;Warning: ${ClassName}-&gt;SetMode: Explicit setting of file mode is not supported: It must be set during object instantiation...&quot;</span><span class="sc">;</span>
191 178
192 179 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
193 180 <span class="s">}</span>
194 181
195 182 <span class="c"># Open file in a specific mode; default mode is Read only.</span>
196 183 <span class="c"># Supported mode values are: Read, Write, Append, &lt;, &gt;, &gt;&gt;, r, w, a</span>
197 184 <span class="c">#</span>
198 <a name="Open-"></a> 185 <span class="k">sub </span><span class="m">Open</span> <span class="s">{</span>
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>
200 187
201 188 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">FileIORef</span>}<span class="i">-&gt;Open</span><span class="s">(</span><span class="i">$Mode</span><span class="s">)</span><span class="sc">;</span>
202 189 <span class="s">}</span>
203 190
204 191 <span class="c"># close file...</span>
205 <a name="Close-"></a> 192 <span class="k">sub </span><span class="m">Close</span> <span class="s">{</span>
206 193 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
207 194
208 195 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">FileIORef</span>}<span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
209 196 <span class="s">}</span>
210 197
211 198 <span class="c"># Read molecule string from file and return a molecule object...</span>
212 <a name="ReadMolecule-"></a> 199 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span>
213 200 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
214 201
215 202 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">FileIORef</span>}<span class="i">-&gt;ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
216 203 <span class="s">}</span>
217 204
218 205 <span class="c"># Retrieve molecule string from file...</span>
219 <a name="ReadMoleculeString-"></a> 206 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span>
220 207 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
221 208
222 209 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">FileIORef</span>}<span class="i">-&gt;ReadMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
223 210 <span class="s">}</span>
224 211
225 212 <span class="c"># Write molecule using molecule object...</span>
226 <a name="WriteMolecule-"></a> 213 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span>
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>
228 215
229 216 <span class="k">return</span> <span class="i">$This</span>-&gt;{<span class="w">FileIORef</span>}<span class="i">-&gt;WriteMolecule</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
230 217 <span class="s">}</span>
231 218
232 219 <span class="c"># Is it a MoleculeFileIO object?</span>
233 <a name="_IsMoleculeFileIO-"></a> 220 <span class="k">sub </span><span class="m">_IsMoleculeFileIO</span> <span class="s">{</span>
234 221 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
235 222
236 223 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> &amp;&amp; <span class="i">$Object</span><span class="i">-&gt;isa</span><span class="s">(</span><span class="i">$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>
237 224 <span class="s">}</span>
238 225
239 <a name="EOF-"></a></pre>
240 <p>&nbsp;</p>
241 <br />
242 <center>
243 <img src="../../../images/h2o2.png">
244 </center>
245 </body>
246 </html>