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

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+++ b/docs/modules/txt/SDFileIO.txt	Wed Jan 20 09:23:18 2016 -0500
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+NAME
+    SDFileIO
+
+SYNOPSIS
+    use FileIO::SDFileIO;
+
+    use FileIO::SDFileIO qw(:all);
+
+DESCRIPTION
+    SDFIleIO class provides the following methods:
+
+    new, GenerateMoleculeString, IsSDFile, ParseMoleculeString,
+    ReadMolecule, ReadMoleculeString, WriteMolecule
+
+    The following methods can also be used as functions:
+
+    GenerateMoleculeString, IsSDFile, ParseMoleculeString
+
+    Data specific to SDFileIO class not directly used by Molecule, Atom and
+    Bond objects - data label/value pairs, atom SteroParity and so on - is
+    associated to and retrieved from approptiate objects using following
+    methods:
+
+        SetMDL<PropertyName>
+        GetMDL<PropertyName>.
+
+    SD data label and values are attached to Molecule object as a refernece
+    to a hash using SetDataFieldLabelAndValues and can be retrieved using
+    GetDataFieldLabelAndValues method.
+
+    SDFileIO class is derived from *FileIO* class and uses its methods to
+    support generic file related functionality.
+
+  METHODS
+    new
+            $NewSDFileIO = new FileIO::SDFileIO(%NamesAndValues);
+
+        Using specified *SDFileIO* property names and values hash, new
+        method creates a new object and returns a reference to newly created
+        SDFileIO object.
+
+    GenerateMoleculeString
+            $MoleculeString = $SDFileIO->GenerateMoleculeString($Molecule);
+            $MoleculeString = FileIO::SDFileIO::GenerateMoleculeString($Molecule);
+
+        Returns a MoleculeString in SD format corresponding to *Molecule*.
+
+    IsSDFile
+            $Status = $SDFileIO->IsSDFile($FileName);
+            $Status = FileIO::SDFileIO::IsSDFile($FileName);
+
+        Returns 1 or 0 based on whether *FileName* is a SD file.
+
+    ParseMoleculeString
+            $Molecule = $SDFileIO->ParseMoleculeString($MoleculeString);
+            $Molecule = FileIO::SDFileIO::ParseMoleculeString($MoleculeString);
+
+        Parses *MoleculeString* and returns a Molecule object. SD data field
+        label and value pairs are associated to Molecule object as a
+        reference to a hash using:
+
+            $Molecule->SetDataFieldLabelAndValues(\%DataLabelsAndValues)
+
+        The reference to hash can be retrieved by:
+
+            $DataLabelsAndValues = $Molecule->GetDataFieldLabelAndValues();
+            for $DataLabel (sort keys %{$DataLabelsAndValues}) {
+                $DataValue = $DataLabelsAndValues->{$DataLabel};
+            }
+
+    ReadMolecule
+            $Molecule = $SDFileIO->ReadMolecule($FileHandle);
+
+        Reads data for the next compound in a file using already opened
+        *FileHandle*, creates, and returns a Molecule object.
+
+    ReadMoleculeString
+            $MoleculeString = $SDFileIO->ReadMoleculeString($FileHandle);
+
+        Reads data for the next compound in a file using already opened
+        *FileHandle* and returns a MoleculeString corresponding to compound
+        structure and other associated data.
+
+    WriteMolecule
+            $SDFileIO->WriteMolecule($Molecule);
+
+        Writes *Molecule* data to a file in MDLMol format and returns
+        SDFileIO.
+
+AUTHOR
+    Manish Sud <[e-mail]>
+
+SEE ALSO
+    MoleculeFileIO.pm, MDLMolFileIO.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.
+