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

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+.\" ========================================================================
+.\"
+.IX Title "MOLECULEFILEIO 1"
+.TH MOLECULEFILEIO 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"
+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.