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.\" ========================================================================
.\"
.IX Title "SDFILEIO 1"
.TH SDFILEIO 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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.if n .ad l
.nh
.SH "NAME"
SDFileIO
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use FileIO::SDFileIO;
.PP
use FileIO::SDFileIO qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBSDFIleIO\fR class provides the following methods:
.PP
new, GenerateMoleculeString, IsSDFile, ParseMoleculeString, ReadMolecule,
ReadMoleculeString, WriteMolecule
.PP
The following methods can also be used as functions:
.PP
GenerateMoleculeString, IsSDFile, ParseMoleculeString
.PP
Data specific to \fBSDFileIO\fR class not directly used by \fBMolecule\fR, \fBAtom\fR and
\&\fBBond\fR objects \- data label/value pairs, atom SteroParity and so on \- is associated to
and retrieved from approptiate objects using following methods:
.PP
.Vb 2
\&    SetMDL<PropertyName>
\&    GetMDL<PropertyName>.
.Ve
.PP
\&\s-1SD\s0 data label and values are attached to \fBMolecule\fR object as a refernece to a hash
using SetDataFieldLabelAndValues and can be retrieved using GetDataFieldLabelAndValues
method.
.PP
\&\fBSDFileIO\fR class is derived from \fIFileIO\fR class and uses its methods to support
generic file related functionality.
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 1
\&    $NewSDFileIO = new FileIO::SDFileIO(%NamesAndValues);
.Ve
.Sp
Using specified \fISDFileIO\fR property names and values hash, \fBnew\fR method creates a new object
and returns a reference to newly created \fBSDFileIO\fR object.
.IP "\fBGenerateMoleculeString\fR" 4
.IX Item "GenerateMoleculeString"
.Vb 2
\&    $MoleculeString = $SDFileIO\->GenerateMoleculeString($Molecule);
\&    $MoleculeString = FileIO::SDFileIO::GenerateMoleculeString($Molecule);
.Ve
.Sp
Returns a \fBMoleculeString\fR in \s-1SD\s0 format corresponding to \fIMolecule\fR.
.IP "\fBIsSDFile\fR" 4
.IX Item "IsSDFile"
.Vb 2
\&    $Status = $SDFileIO\->IsSDFile($FileName);
\&    $Status = FileIO::SDFileIO::IsSDFile($FileName);
.Ve
.Sp
Returns 1 or 0 based on whether \fIFileName\fR is a \s-1SD\s0 file.
.IP "\fBParseMoleculeString\fR" 4
.IX Item "ParseMoleculeString"
.Vb 2
\&    $Molecule = $SDFileIO\->ParseMoleculeString($MoleculeString);
\&    $Molecule = FileIO::SDFileIO::ParseMoleculeString($MoleculeString);
.Ve
.Sp
Parses \fIMoleculeString\fR and returns a \fBMolecule\fR object. \s-1SD\s0 data field label and value pairs
are associated to \fBMolecule\fR object as a reference to a hash using:
.Sp
.Vb 1
\&    $Molecule\->SetDataFieldLabelAndValues(\e%DataLabelsAndValues)
.Ve
.Sp
The reference to hash can be retrieved by:
.Sp
.Vb 4
\&    $DataLabelsAndValues = $Molecule\->GetDataFieldLabelAndValues();
\&    for $DataLabel (sort keys %{$DataLabelsAndValues}) {
\&        $DataValue = $DataLabelsAndValues\->{$DataLabel};
\&    }
.Ve
.IP "\fBReadMolecule\fR" 4
.IX Item "ReadMolecule"
.Vb 1
\&    $Molecule = $SDFileIO\->ReadMolecule($FileHandle);
.Ve
.Sp
Reads data for the next compound in a file using already opened \fIFileHandle\fR, creates,
and returns a \fBMolecule\fR object.
.IP "\fBReadMoleculeString\fR" 4
.IX Item "ReadMoleculeString"
.Vb 1
\&    $MoleculeString = $SDFileIO\->ReadMoleculeString($FileHandle);
.Ve
.Sp
Reads data for the next compound in a file using already opened \fIFileHandle\fR and
returns a \fBMoleculeString\fR corresponding to compound structure and other associated
data.
.IP "\fBWriteMolecule\fR" 4
.IX Item "WriteMolecule"
.Vb 1
\&    $SDFileIO\->WriteMolecule($Molecule);
.Ve
.Sp
Writes \fIMolecule\fR data to a file in MDLMol format and returns \fBSDFileIO\fR.
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
MoleculeFileIO.pm, MDLMolFileIO.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.