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.\" ========================================================================
.\"
.IX Title "MOLECULEFILEIO 1"
.TH MOLECULEFILEIO 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
MoleculeFileIO
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use MoleculeFileIO;
.PP
use MoleculeFileIO qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBMoleculeFileIO\fR class provides the following methods:
.PP
new, Close, IsSupportedMoleculeFileFormat, Open, ReadMolecule,
ReadMoleculeString, WriteMolecule
.PP
The following methods can also be used as functions:
.PP
IsSupportedMoleculeFileFormat
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 1
\&    $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);
.Ve
.Sp
Using specified \fIMoleculeFileIO\fR property names and values hash, \fBnew\fR method
creates a new object and returns a reference to newly created \fBMoleculeFileIO\fR object.
By default, following properties are initialized:
.Sp
.Vb 3
\&    Name = ""
\&    Mode = ""
\&    FileIORef = ""
.Ve
.Sp
Based on extension of specified file \fIName\fR, an input class is automatically associated to
provide molecule read and write methods.
.Sp
Examples:
.Sp
.Vb 9
\&    $Name = "Water.mol";
\&    $Mode = "Read";
\&    $MoleculeFileIO = new MoleculeFileIO(\*(AqName\*(Aq => $Name,
\&                                         \*(AqMode\*(Aq => $Mode);
\&    $MoleculeFileIO\->Open();
\&    $Molecule = $MoleculeFileIO\->ReadMolecule();
\&    $Molecule\->DetectRings();
\&    print "$Molecule\en";
\&    $MoleculeFileIO\->Close();
\&
\&    $MoleculeFileIO = new MoleculeFileIO(\*(AqName\*(Aq => \*(AqSample1.sdf\*(Aq,
\&                                         \*(AqMode\*(Aq => \*(AqRead\*(Aq);
\&    $MoleculeFileIO\->Open();
\&    while ($Molecule = $MoleculeFileIO1\->ReadMolecule()) {
\&        $Molecule\->DetectRings();
\&        print "$Molecule\en";
\&
\&        $DataLabelsAndValuesRef =
\&          $Molecule\->GetDataFieldLabelAndValues();
\&        for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
\&            $DataValue = $DataLabelsAndValuesRef\->{$DataLabel};
\&            print "<DataLabel: $DataLabel; DataValue: $DataValue>; ";
\&        }
\&        print "\en";
\&    }
\&    $MoleculeFileIO\->Close();
.Ve
.IP "\fBClose\fR" 4
.IX Item "Close"
.Vb 1
\&    $MoleculeFileIO\->Close();
.Ve
.Sp
Closes an open file
.IP "\fBIsSupportedMoleculeFileFormat\fR" 4
.IX Item "IsSupportedMoleculeFileFormat"
.Vb 4
\&    $Status = $MoleculeFileIO\->IsSupportedMoleculeFileFormat($Name);
\&    $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
\&    ($Status, $FormatType, $IOClassName) =
\&       $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
.Ve
.Sp
Returns 1 or 0 based on whether input file \fIName\fR format is supported. In list context,
value of supported format type and name of associated \s-1IO\s0 class is also returned.
.Sp
File extension is used to determine file format. Currently, following file extensions are
supported:
.Sp
.Vb 1
\&    FileExts \- FormatType \- AssociatedIOClassName
\&
\&    .mol \- MDLMOL \- MDLMolFileIO
\&    .sdf, .sd \- SDF \- SDFileIO
.Ve
.IP "\fBOpen\fR" 4
.IX Item "Open"
.Vb 1
\&    $MoleculeFileIO\->Open([$Mode]);
.Ve
.Sp
Opens a file in a specified \fIMode\fR. Default mode value: \fIRead\fR. Supported mode
values:
.Sp
.Vb 1
\&    Read, Write, Append, <, >, >>, r, w, or a
.Ve
.IP "\fBReadMolecule\fR" 4
.IX Item "ReadMolecule"
.Vb 1
\&    $Molecule = $MoleculeFileIO\->ReadMolecule();
.Ve
.Sp
Reads molecule data from the file and returns a \fIMolecule\fR object.
.IP "\fBReadMoleculeString\fR" 4
.IX Item "ReadMoleculeString"
.Vb 1
\&    $MoleculeString = $MoleculeFileIO\->ReadMoleculeString();
.Ve
.Sp
Reads molecule data from a file and returns a \fIMolecule\fR string.
.IP "\fBWriteMolecule\fR" 4
.IX Item "WriteMolecule"
.Vb 1
\&    $MoleculeFileIO\->WriteMolecule();
.Ve
.Sp
Write molecule data to a file for a \fIMolecule\fR.
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
FileIO.pm, MDLMolFileIO.pm, SDFileIO.pm
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (C) 2015 Manish Sud. All rights reserved.
.PP
This file is part of MayaChemTools.
.PP
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.