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

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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.