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author | deepakjadmin |
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date | Wed, 20 Jan 2016 09:23:18 -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 <msud@san.rr.com> 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.