diff mayachemtools/docs/modules/man3/SDFileIO.3 @ 0:73ae111cf86f draft

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+.\" ========================================================================
+.\"
+.IX Title "SDFILEIO 1"
+.TH SDFILEIO 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.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.