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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

## 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.

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