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NAME

MDLMolFileIO

SYNOPSIS

use FileIO::MDLMolFileIO;

use FileIO::MDLMolFileIO qw(:all);

DESCRIPTION

MDLMolFIleIO class provides the following methods:

new, GenerateMoleculeString, IsMDLMolFile, ParseMoleculeString, ReadMolecule, ReadMoleculeString, WriteMolecule

The following methods can also be used as functions:

GenerateMoleculeString, IsMDLMolFile, ParseMoleculeString

Data specific to MDLMolFileIO class not directly used by Molecule, Atom and Bond objects - data label/value pairs, atom SteroParity and so on - is associated to and retrieved from appropriate objects using following methods:

SetMDL<PropertyName>
GetMDL<PropertyName>.

MDLMolFileIO class is derived from FileIO class and uses its methods to support generic file related functionality.

METHODS

new
$NewMDLMolFileIO = new FileIO::MDLMolFileIO(%NamesAndValues);

Using specified MDLMolFileIO property names and values hash, new method creates a new object and returns a reference to newly created MDLMolFileIO object.

GenerateMoleculeString
$MoleculeString = $MDLMolFileIO->GenerateMoleculeString($Molecule);
$MoleculeString = FileIO::MDLMolFileIO::GenerateMoleculeString($Molecule);

Returns a MoleculeString in MDLMol format corresponding to Molecule.

IsMDLMolFile
$Status = $MDLMolFileIO->IsMDLMolFile($FileName);
$Status = FileIO::MDLMolFileIO::IsMDLMolFile($FileName);

Returns 1 or 0 based on whether FileName is a MDLMol file.

ParseMoleculeString
$Molecule = $MDLMolFileIO->ParseMoleculeString($MoleculeString);
$Molecule = FileIO::MDLMolFileIO::ParseMoleculeString($MoleculeString);

Parses MoleculeString and returns a Molecule object.

ReadMolecule
$Molecule = $MDLMolFileIO->ReadMolecule($FileHandle);

Reads data for the compound in a file using already opened FileHandle, creates, and returns a Molecule object.

ReadMoleculeString
$MoleculeString = $MDLMolFileIO->ReadMoleculeString($FileHandle);

Reads data for the compound in a file using already opened FileHandle and returns a MoleculeString corresponding to compound structure and other associated data.

WriteMolecule
$MDLMolFileIO->WriteMolecule($Molecule);

Writes Molecule data to a file in MDLMol format and returns MDLMolFileIO.

AUTHOR

Manish Sud

SEE ALSO

MoleculeFileIO.pm, SDFileIO.pm

COPYRIGHT

Copyright (C) 2019 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.

 

 

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