diff docs/modules/txt/MoleculeFileIO.txt @ 0:4816e4a8ae95 draft default tip

Uploaded

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+++ b/docs/modules/txt/MoleculeFileIO.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    MoleculeFileIO
+
+SYNOPSIS
+    use MoleculeFileIO;
+
+    use MoleculeFileIO qw(:all);
+
+DESCRIPTION
+    MoleculeFileIO class provides the following methods:
+
+    new, Close, IsSupportedMoleculeFileFormat, Open, ReadMolecule,
+    ReadMoleculeString, WriteMolecule
+
+    The following methods can also be used as functions:
+
+    IsSupportedMoleculeFileFormat
+
+  METHODS
+    new
+            $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);
+
+        Using specified *MoleculeFileIO* property names and values hash, new
+        method creates a new object and returns a reference to newly created
+        MoleculeFileIO object. By default, following properties are
+        initialized:
+
+            Name = ""
+            Mode = ""
+            FileIORef = ""
+
+        Based on extension of specified file *Name*, an input class is
+        automatically associated to provide molecule read and write methods.
+
+        Examples:
+
+            $Name = "Water.mol";
+            $Mode = "Read";
+            $MoleculeFileIO = new MoleculeFileIO('Name' => $Name,
+                                                 'Mode' => $Mode);
+            $MoleculeFileIO->Open();
+            $Molecule = $MoleculeFileIO->ReadMolecule();
+            $Molecule->DetectRings();
+            print "$Molecule\n";
+            $MoleculeFileIO->Close();
+
+            $MoleculeFileIO = new MoleculeFileIO('Name' => 'Sample1.sdf',
+                                                 'Mode' => 'Read');
+            $MoleculeFileIO->Open();
+            while ($Molecule = $MoleculeFileIO1->ReadMolecule()) {
+                $Molecule->DetectRings();
+                print "$Molecule\n";
+
+                $DataLabelsAndValuesRef =
+                  $Molecule->GetDataFieldLabelAndValues();
+                for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
+                    $DataValue = $DataLabelsAndValuesRef->{$DataLabel};
+                    print "<DataLabel: $DataLabel; DataValue: $DataValue>; ";
+                }
+                print "\n";
+            }
+            $MoleculeFileIO->Close();
+
+    Close
+            $MoleculeFileIO->Close();
+
+        Closes an open file
+
+    IsSupportedMoleculeFileFormat
+            $Status = $MoleculeFileIO->IsSupportedMoleculeFileFormat($Name);
+            $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
+            ($Status, $FormatType, $IOClassName) =
+               $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
+
+        Returns 1 or 0 based on whether input file *Name* format is
+        supported. In list context, value of supported format type and name
+        of associated IO class is also returned.
+
+        File extension is used to determine file format. Currently,
+        following file extensions are supported:
+
+            FileExts - FormatType - AssociatedIOClassName
+
+            .mol - MDLMOL - MDLMolFileIO
+            .sdf, .sd - SDF - SDFileIO
+
+    Open
+            $MoleculeFileIO->Open([$Mode]);
+
+        Opens a file in a specified *Mode*. Default mode value: *Read*.
+        Supported mode values:
+
+            Read, Write, Append, <, >, >>, r, w, or a
+
+    ReadMolecule
+            $Molecule = $MoleculeFileIO->ReadMolecule();
+
+        Reads molecule data from the file and returns a *Molecule* object.
+
+    ReadMoleculeString
+            $MoleculeString = $MoleculeFileIO->ReadMoleculeString();
+
+        Reads molecule data from a file and returns a *Molecule* string.
+
+    WriteMolecule
+            $MoleculeFileIO->WriteMolecule();
+
+        Write molecule data to a file for a *Molecule*.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    FileIO.pm, MDLMolFileIO.pm, SDFileIO.pm
+
+COPYRIGHT
+    Copyright (C) 2015 Manish Sud. All rights reserved.
+
+    This file is part of MayaChemTools.
+
+    MayaChemTools is free software; you can redistribute it and/or modify it
+    under the terms of the GNU Lesser General Public License as published by
+    the Free Software Foundation; either version 3 of the License, or (at
+    your option) any later version.
+