|
0
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Code:FileIO::SDFileIO.pm</title>
|
|
|
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
|
|
|
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
|
|
|
6 </head>
|
|
|
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
|
|
|
8 <br/>
|
|
|
9 <center>
|
|
|
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
|
|
|
11 </center>
|
|
|
12 <br/>
|
|
|
13 <pre>
|
|
|
14 <a name="package-FileIO::SDFileIO-"></a> 1 <span class="k">package </span><span class="i">FileIO::SDFileIO</span><span class="sc">;</span>
|
|
|
15 2 <span class="c">#</span>
|
|
|
16 3 <span class="c"># $RCSfile: SDFileIO.pm,v $</span>
|
|
|
17 4 <span class="c"># $Date: 2015/02/28 20:48:43 $</span>
|
|
|
18 5 <span class="c"># $Revision: 1.35 $</span>
|
|
|
19 6 <span class="c">#</span>
|
|
|
20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></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 <http://www.gnu.org/licenses/> 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">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
47 34 <span class="k">use</span> <span class="w">FileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
48 35 <span class="k">use</span> <span class="w">SDFileUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
49 36 <span class="k">use</span> <span class="w">FileIO::FileIO</span><span class="sc">;</span>
|
|
|
50 37 <span class="k">use</span> <span class="w">FileIO::MDLMolFileIO</span><span class="sc">;</span>
|
|
|
51 38 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span>
|
|
|
52 39
|
|
|
53 40 <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>
|
|
|
54 41
|
|
|
55 42 <span class="i">@ISA</span> = <span class="q">qw(FileIO::FileIO Exporter)</span><span class="sc">;</span>
|
|
|
56 43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
|
|
|
57 44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(IsSDFile)</span><span class="sc">;</span>
|
|
|
58 45
|
|
|
59 46 <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>
|
|
|
60 47
|
|
|
61 48 <span class="c"># Setup class variables...</span>
|
|
|
62 49 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
63 50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
64 51
|
|
|
65 52 <span class="c"># Class constructor...</span>
|
|
|
66 <a name="new-"></a> 53 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
|
|
|
67 54 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
68 55
|
|
|
69 56 <span class="c"># Initialize object...</span>
|
|
|
70 57 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
71 58 <span class="k">bless</span> <span class="i">$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>
|
|
|
72 59 <span class="i">$This</span><span class="i">->_InitializeSDFileIO</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
73 60
|
|
|
74 61 <span class="i">$This</span><span class="i">->_InitializeSDFileIOProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
75 62
|
|
|
76 63 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
77 64 <span class="s">}</span>
|
|
|
78 65
|
|
|
79 66 <span class="c"># Initialize any local object data...</span>
|
|
|
80 67 <span class="c">#</span>
|
|
|
81 <a name="_InitializeSDFileIO-"></a> 68 <span class="k">sub </span><span class="m">_InitializeSDFileIO</span> <span class="s">{</span>
|
|
|
82 69 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
83 70
|
|
|
84 71 <span class="c"># Sorting of MDL data fields during output: Keep the initial order or write 'em out alphabetically...</span>
|
|
|
85 72 <span class="i">$This</span>->{<span class="w">SortDataFieldsDuringOutput</span>} = <span class="q">'No'</span><span class="sc">;</span>
|
|
|
86 73
|
|
|
87 74 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
88 75 <span class="s">}</span>
|
|
|
89 76
|
|
|
90 77 <span class="c"># Initialize class ...</span>
|
|
|
91 <a name="_InitializeClass-"></a> 78 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
|
|
|
92 79 <span class="c">#Class name...</span>
|
|
|
93 80 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
|
|
|
94 81
|
|
|
95 82 <span class="s">}</span>
|
|
|
96 83
|
|
|
97 84 <span class="c"># Initialize object values...</span>
|
|
|
98 <a name="_InitializeSDFileIOProperties-"></a> 85 <span class="k">sub </span><span class="m">_InitializeSDFileIOProperties</span> <span class="s">{</span>
|
|
|
99 86 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
100 87
|
|
|
101 88 <span class="c"># All other property names and values along with all Set/Get<PropertyName> methods</span>
|
|
|
102 89 <span class="c"># are implemented on-demand using ObjectProperty class.</span>
|
|
|
103 90
|
|
|
104 91 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span>
|
|
|
105 92 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span>
|
|
|
106 93 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span>
|
|
|
107 94 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span>
|
|
|
108 95 <span class="s">}</span>
|
|
|
109 96
|
|
|
110 97 <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>
|
|
|
111 98 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying file name..."</span><span class="sc">;</span>
|
|
|
112 99 <span class="s">}</span>
|
|
|
113 100
|
|
|
114 101 <span class="c"># Make sure it's a SD file...</span>
|
|
|
115 102 <span class="i">$Name</span> = <span class="i">$NamesAndValues</span>{<span class="w">Name</span>}<span class="sc">;</span>
|
|
|
116 103 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->IsSDFile</span><span class="s">(</span><span class="i">$Name</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
117 104 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be SDF format..."</span><span class="sc">;</span>
|
|
|
118 105 <span class="s">}</span>
|
|
|
119 106
|
|
|
120 107 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
121 108 <span class="s">}</span>
|
|
|
122 109
|
|
|
123 110 <span class="c"># Is it a SD file?</span>
|
|
|
124 <a name="IsSDFile-"></a> 111 <span class="k">sub </span><span class="m">IsSDFile ($;$)</span> <span class="s">{</span>
|
|
|
125 112 <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>
|
|
|
126 113 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$Status</span><span class="s">)</span><span class="sc">;</span>
|
|
|
127 114
|
|
|
128 115 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">@_</span> == <span class="n">2</span><span class="s">)</span> && <span class="s">(</span><span class="i">_IsSDFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
129 116 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$FileName</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>
|
|
|
130 117 <span class="s">}</span>
|
|
|
131 118 <span class="k">else</span> <span class="s">{</span>
|
|
|
132 119 <span class="i">$FileName</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
|
|
|
133 120 <span class="s">}</span>
|
|
|
134 121
|
|
|
135 122 <span class="c"># Check file extension...</span>
|
|
|
136 123 <span class="i">$Status</span> = <span class="i">FileUtil::CheckFileType</span><span class="s">(</span><span class="i">$FileName</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="sc">;</span>
|
|
|
137 124
|
|
|
138 125 <span class="k">return</span> <span class="i">$Status</span><span class="sc">;</span>
|
|
|
139 126 <span class="s">}</span>
|
|
|
140 127
|
|
|
141 128 <span class="c"># Read molecule from file and return molecule object...</span>
|
|
|
142 <a name="ReadMolecule-"></a> 129 <span class="k">sub </span><span class="m">ReadMolecule</span> <span class="s">{</span>
|
|
|
143 130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
144 131 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
|
|
|
145 132
|
|
|
146 133 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
147 134 <span class="k">return</span> <span class="i">$This</span><span class="i">->ParseMoleculeString</span><span class="s">(</span><span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
|
|
|
148 135 <span class="s">}</span>
|
|
|
149 136
|
|
|
150 137 <span class="c"># Write compound data along with any data field label and values using Molecule object...</span>
|
|
|
151 <a name="WriteMolecule-"></a> 138 <span class="k">sub </span><span class="m">WriteMolecule</span> <span class="s">{</span>
|
|
|
152 139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
153 140
|
|
|
154 141 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> && <span class="i">$Molecule</span><span class="i">->IsMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
155 142 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->WriteMolecule: No data written: Molecule object is not specified..."</span><span class="sc">;</span>
|
|
|
156 143 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
157 144 <span class="s">}</span>
|
|
|
158 145 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
|
|
|
159 146 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
160 147
|
|
|
161 148 <span class="k">print</span> <span class="i">$FileHandle</span> <span class="i">$This</span><span class="i">->GenerateMoleculeString</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> . <span class="q">"\n"</span><span class="sc">;</span>
|
|
|
162 149
|
|
|
163 150 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
164 151 <span class="s">}</span>
|
|
|
165 152
|
|
|
166 153 <span class="c"># Retrieve molecule string...</span>
|
|
|
167 <a name="ReadMoleculeString-"></a> 154 <span class="k">sub </span><span class="m">ReadMoleculeString</span> <span class="s">{</span>
|
|
|
168 155 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
169 156 <span class="k">my</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
|
|
|
170 157
|
|
|
171 158 <span class="i">$FileHandle</span> = <span class="i">$This</span><span class="i">->GetFileHandle</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
172 159 <span class="k">return</span> <span class="i">SDFileUtil::ReadCmpdString</span><span class="s">(</span><span class="i">$FileHandle</span><span class="s">)</span><span class="sc">;</span>
|
|
|
173 160 <span class="s">}</span>
|
|
|
174 161
|
|
|
175 162 <span class="c"># Parse molecule string and return molecule object. ParseMoleculeString supports two invocation methods: class</span>
|
|
|
176 163 <span class="c"># method or a package function.</span>
|
|
|
177 164 <span class="c">#</span>
|
|
|
178 <a name="ParseMoleculeString-"></a> 165 <span class="k">sub </span><span class="m">ParseMoleculeString</span> <span class="s">{</span>
|
|
|
179 166 <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>
|
|
|
180 167 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
181 168
|
|
|
182 169 <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">_IsSDFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
183 170 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
184 171 <span class="s">}</span>
|
|
|
185 172 <span class="k">else</span> <span class="s">{</span>
|
|
|
186 173 <span class="i">$MoleculeString</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
|
|
|
187 174 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
188 175 <span class="s">}</span>
|
|
|
189 176 <span class="k">if</span> <span class="s">(</span>!<span class="i">$MoleculeString</span><span class="s">)</span> <span class="s">{</span>
|
|
|
190 177 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
191 178 <span class="s">}</span>
|
|
|
192 179 <span class="c"># Parse molecule data...</span>
|
|
|
193 180 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
194 181 <span class="i">$Molecule</span> = <span class="i">FileIO::MDLMolFileIO::ParseMoleculeString</span><span class="s">(</span><span class="i">$MoleculeString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
195 182
|
|
|
196 183 <span class="c"># Process data label/value pairs...</span>
|
|
|
197 184 <span class="k">my</span><span class="s">(</span><span class="i">@MoleculeLines</span><span class="cm">,</span> <span class="i">@DataLabels</span><span class="cm">,</span> <span class="i">%DataLabelsAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
198 185
|
|
|
199 186 <span class="i">%DataLabelsAndValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
200 187 <span class="i">@MoleculeLines</span> = <span class="k">split</span> <span class="q">/\n/</span><span class="cm">,</span> <span class="i">$MoleculeString</span><span class="sc">;</span>
|
|
|
201 188 <span class="i">@DataLabels</span> = <span class="i">SDFileUtil::GetCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
202 189 <span class="i">%DataLabelsAndValues</span> = <span class="i">SDFileUtil::GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@MoleculeLines</span><span class="s">)</span><span class="sc">;</span>
|
|
|
203 190
|
|
|
204 191 <span class="c"># Store reference to data labels to keep track of their initial order in SD file...</span>
|
|
|
205 192 <span class="i">$Molecule</span><span class="i">->SetDataFieldLabels</span><span class="s">(</span>\<span class="i">@DataLabels</span><span class="s">)</span><span class="sc">;</span>
|
|
|
206 193
|
|
|
207 194 <span class="c"># Store reference to SD data label/value pairs hash as a generic property of molecule...</span>
|
|
|
208 195 <span class="i">$Molecule</span><span class="i">->SetDataFieldLabelAndValues</span><span class="s">(</span>\<span class="i">%DataLabelsAndValues</span><span class="s">)</span><span class="sc">;</span>
|
|
|
209 196
|
|
|
210 197 <span class="k">return</span> <span class="i">$Molecule</span><span class="sc">;</span>
|
|
|
211 198 <span class="s">}</span>
|
|
|
212 199
|
|
|
213 200 <span class="c"># Generate molecule string using molecule object...</span>
|
|
|
214 <a name="GenerateMoleculeString-"></a> 201 <span class="k">sub </span><span class="m">GenerateMoleculeString</span> <span class="s">{</span>
|
|
|
215 202 <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>
|
|
|
216 203 <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="sc">;</span>
|
|
|
217 204
|
|
|
218 205 <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">_IsSDFileIO</span><span class="s">(</span><span class="i">$FirstParameter</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
219 206 <span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="s">(</span><span class="i">$FirstParameter</span><span class="cm">,</span> <span class="i">$SecondParameter</span><span class="s">)</span><span class="sc">;</span>
|
|
|
220 207 <span class="s">}</span>
|
|
|
221 208 <span class="k">else</span> <span class="s">{</span>
|
|
|
222 209 <span class="i">$Molecule</span> = <span class="i">$FirstParameter</span><span class="sc">;</span>
|
|
|
223 210 <span class="i">$This</span> = <span class="k">undef</span><span class="sc">;</span>
|
|
|
224 211 <span class="s">}</span>
|
|
|
225 212 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
226 213 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
|
|
|
227 214 <span class="s">}</span>
|
|
|
228 215 <span class="c"># Generate CTAB data...</span>
|
|
|
229 216 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
230 217 <span class="i">$CmpdString</span> = <span class="i">FileIO::MDLMolFileIO::GenerateMoleculeString</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
|
|
|
231 218
|
|
|
232 219 <span class="c"># Generate any data field labels and values...</span>
|
|
|
233 220 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelsAndValuesString</span><span class="s">)</span><span class="sc">;</span>
|
|
|
234 221
|
|
|
235 222 <span class="i">$DataFieldLabelsAndValuesString</span> = <span class="q">''</span><span class="sc">;</span>
|
|
|
236 223 <span class="k">if</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->HasProperty</span><span class="s">(</span><span class="q">'DataFieldLabels'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
237 224 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelsRef</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="cm">,</span> <span class="i">$SortDataFields</span><span class="s">)</span><span class="sc">;</span>
|
|
|
238 225
|
|
|
239 226 <span class="i">$SortDataFields</span> = <span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">SortDataFieldsDuringOutput</span>}<span class="s">)</span> && <span class="i">$This</span>->{<span class="w">SortDataFieldsDuringOutput</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
|
|
|
240 227
|
|
|
241 228 <span class="i">$DataFieldLabelsRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
242 229 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
243 230 <span class="i">$DataFieldLabelsAndValuesString</span> = <span class="k">join</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">SDFileUtil::GenerateCmpdDataHeaderLabelsAndValuesLines</span><span class="s">(</span><span class="i">$DataFieldLabelsRef</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="cm">,</span> <span class="i">$SortDataFields</span><span class="s">)</span><span class="sc">;</span>
|
|
|
244 231 <span class="s">}</span>
|
|
|
245 232
|
|
|
246 233 <span class="k">return</span> <span class="q">"${CmpdString }\n${DataFieldLabelsAndValuesString}\n\$\$\$\$"</span><span class="sc">;</span>
|
|
|
247 234 <span class="s">}</span>
|
|
|
248 235
|
|
|
249 236
|
|
|
250 237 <span class="c"># Is it a SDFileIO object?</span>
|
|
|
251 <a name="_IsSDFileIO-"></a> 238 <span class="k">sub </span><span class="m">_IsSDFileIO</span> <span class="s">{</span>
|
|
|
252 239 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
253 240
|
|
|
254 241 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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>
|
|
|
255 242 <span class="s">}</span>
|
|
|
256 243
|
|
|
257 <a name="EOF-"></a></pre>
|
|
|
258 <p> </p>
|
|
|
259 <br />
|
|
|
260 <center>
|
|
|
261 <img src="../../../images/h2o2.png">
|
|
|
262 </center>
|
|
|
263 </body>
|
|
|
264 </html>
|
