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comparison mayachemtools/docs/modules/man3/MoleculeFileIO.3 @ 0:73ae111cf86f draft
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date | Wed, 20 Jan 2016 11:55:01 -0500 |
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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. |