comparison mayachemtools/docs/modules/man3/MoleculeFileIO.3 @ 0:73ae111cf86f draft

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124 .\" ========================================================================
125 .\"
126 .IX Title "MOLECULEFILEIO 1"
127 .TH MOLECULEFILEIO 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
129 .\" way too many mistakes in technical documents.
130 .if n .ad l
131 .nh
132 .SH "NAME"
133 MoleculeFileIO
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use MoleculeFileIO;
137 .PP
138 use MoleculeFileIO qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBMoleculeFileIO\fR class provides the following methods:
142 .PP
143 new, Close, IsSupportedMoleculeFileFormat, Open, ReadMolecule,
144 ReadMoleculeString, WriteMolecule
145 .PP
146 The following methods can also be used as functions:
147 .PP
148 IsSupportedMoleculeFileFormat
149 .SS "\s-1METHODS\s0"
150 .IX Subsection "METHODS"
151 .IP "\fBnew\fR" 4
152 .IX Item "new"
153 .Vb 1
154 \& $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);
155 .Ve
156 .Sp
157 Using specified \fIMoleculeFileIO\fR property names and values hash, \fBnew\fR method
158 creates a new object and returns a reference to newly created \fBMoleculeFileIO\fR object.
159 By default, following properties are initialized:
160 .Sp
161 .Vb 3
162 \& Name = ""
163 \& Mode = ""
164 \& FileIORef = ""
165 .Ve
166 .Sp
167 Based on extension of specified file \fIName\fR, an input class is automatically associated to
168 provide molecule read and write methods.
169 .Sp
170 Examples:
171 .Sp
172 .Vb 9
173 \& $Name = "Water.mol";
174 \& $Mode = "Read";
175 \& $MoleculeFileIO = new MoleculeFileIO(\*(AqName\*(Aq => $Name,
176 \& \*(AqMode\*(Aq => $Mode);
177 \& $MoleculeFileIO\->Open();
178 \& $Molecule = $MoleculeFileIO\->ReadMolecule();
179 \& $Molecule\->DetectRings();
180 \& print "$Molecule\en";
181 \& $MoleculeFileIO\->Close();
182 \&
183 \& $MoleculeFileIO = new MoleculeFileIO(\*(AqName\*(Aq => \*(AqSample1.sdf\*(Aq,
184 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq);
185 \& $MoleculeFileIO\->Open();
186 \& while ($Molecule = $MoleculeFileIO1\->ReadMolecule()) {
187 \& $Molecule\->DetectRings();
188 \& print "$Molecule\en";
189 \&
190 \& $DataLabelsAndValuesRef =
191 \& $Molecule\->GetDataFieldLabelAndValues();
192 \& for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
193 \& $DataValue = $DataLabelsAndValuesRef\->{$DataLabel};
194 \& print "<DataLabel: $DataLabel; DataValue: $DataValue>; ";
195 \& }
196 \& print "\en";
197 \& }
198 \& $MoleculeFileIO\->Close();
199 .Ve
200 .IP "\fBClose\fR" 4
201 .IX Item "Close"
202 .Vb 1
203 \& $MoleculeFileIO\->Close();
204 .Ve
205 .Sp
206 Closes an open file
207 .IP "\fBIsSupportedMoleculeFileFormat\fR" 4
208 .IX Item "IsSupportedMoleculeFileFormat"
209 .Vb 4
210 \& $Status = $MoleculeFileIO\->IsSupportedMoleculeFileFormat($Name);
211 \& $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
212 \& ($Status, $FormatType, $IOClassName) =
213 \& $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
214 .Ve
215 .Sp
216 Returns 1 or 0 based on whether input file \fIName\fR format is supported. In list context,
217 value of supported format type and name of associated \s-1IO\s0 class is also returned.
218 .Sp
219 File extension is used to determine file format. Currently, following file extensions are
220 supported:
221 .Sp
222 .Vb 1
223 \& FileExts \- FormatType \- AssociatedIOClassName
224 \&
225 \& .mol \- MDLMOL \- MDLMolFileIO
226 \& .sdf, .sd \- SDF \- SDFileIO
227 .Ve
228 .IP "\fBOpen\fR" 4
229 .IX Item "Open"
230 .Vb 1
231 \& $MoleculeFileIO\->Open([$Mode]);
232 .Ve
233 .Sp
234 Opens a file in a specified \fIMode\fR. Default mode value: \fIRead\fR. Supported mode
235 values:
236 .Sp
237 .Vb 1
238 \& Read, Write, Append, <, >, >>, r, w, or a
239 .Ve
240 .IP "\fBReadMolecule\fR" 4
241 .IX Item "ReadMolecule"
242 .Vb 1
243 \& $Molecule = $MoleculeFileIO\->ReadMolecule();
244 .Ve
245 .Sp
246 Reads molecule data from the file and returns a \fIMolecule\fR object.
247 .IP "\fBReadMoleculeString\fR" 4
248 .IX Item "ReadMoleculeString"
249 .Vb 1
250 \& $MoleculeString = $MoleculeFileIO\->ReadMoleculeString();
251 .Ve
252 .Sp
253 Reads molecule data from a file and returns a \fIMolecule\fR string.
254 .IP "\fBWriteMolecule\fR" 4
255 .IX Item "WriteMolecule"
256 .Vb 1
257 \& $MoleculeFileIO\->WriteMolecule();
258 .Ve
259 .Sp
260 Write molecule data to a file for a \fIMolecule\fR.
261 .SH "AUTHOR"
262 .IX Header "AUTHOR"
263 Manish Sud <msud@san.rr.com>
264 .SH "SEE ALSO"
265 .IX Header "SEE ALSO"
266 FileIO.pm, MDLMolFileIO.pm, SDFileIO.pm
267 .SH "COPYRIGHT"
268 .IX Header "COPYRIGHT"
269 Copyright (C) 2015 Manish Sud. All rights reserved.
270 .PP
271 This file is part of MayaChemTools.
272 .PP
273 MayaChemTools is free software; you can redistribute it and/or modify it under
274 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
275 Software Foundation; either version 3 of the License, or (at your option)
276 any later version.