diff mayachemtools/lib/MoleculeFileIO.pm @ 0:73ae111cf86f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/lib/MoleculeFileIO.pm	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,371 @@
+package MoleculeFileIO;
+#
+# $RCSfile: MoleculeFileIO.pm,v $
+# $Date: 2015/02/28 20:47:18 $
+# $Revision: 1.32 $
+#
+# Author: Manish Sud <[e-mail]>
+#
+# Copyright (C) 2015 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.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of fitness
+# for a particular purpose.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use Carp;
+use Exporter;
+use Scalar::Util ();
+use FileIO::SDFileIO;
+use FileIO::MDLMolFileIO;
+
+use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
+
+@ISA = qw(Exporter);
+@EXPORT = qw();
+@EXPORT_OK = qw(IsSupportedMoleculeFileFormat);
+
+%EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);
+
+# Setup class variables...
+my($ClassName);
+_InitializeClass();
+
+# Class constructor...
+sub new {
+  my($Class, %NamesAndValues) = @_;
+
+  # Initialize object...
+  my $This = {};
+  bless $This, ref($Class) || $Class;
+  $This->_InitializeMoleculeFileIO();
+
+  $This->_InitializeMoleculeFileIOProperties(%NamesAndValues);
+
+  return $This;
+}
+
+# Initialize object data...
+#
+sub _InitializeMoleculeFileIO {
+  my($This) = @_;
+
+  # Reference to specific FileIO object...
+  $This->{FileIORef} = '';
+
+  return $This;
+}
+
+# Initialize class ...
+sub _InitializeClass {
+  #Class name...
+  $ClassName = __PACKAGE__;
+
+}
+
+# Initialize object properties......
+#
+sub _InitializeMoleculeFileIOProperties {
+  my($This, %NamesAndValues) = @_;
+
+  if (!exists $NamesAndValues{Name}) {
+    croak "Error: ${ClassName}->New: Object can't be instantiated without specifying file name...";
+  }
+
+  if (!exists $NamesAndValues{Mode}) {
+    $NamesAndValues{Mode} = 'Read';
+  }
+
+  # Make sure its a supported format and intialize FileIO object reference...
+  $This->_SetFileIORef(%NamesAndValues);
+
+  return $This;
+}
+
+# Setup FileIO object reference...
+sub _SetFileIORef {
+  my($This, %NamesAndValues) = @_;
+  my($Name, $Status, $Format, $IOPackageName);
+
+  $Name = $NamesAndValues{Name};
+
+  ($Status, $Format, $IOPackageName) = $This->IsSupportedMoleculeFileFormat($Name);
+  if (!$Status) {
+    croak "Error: ${ClassName}->New: Object can't be instantiated: File format, $Name, is not supported: Currently supported file formats are: SDF, MDLMol...";
+  }
+
+  $This->{FileIORef} = ${IOPackageName}->new(%NamesAndValues);
+
+  return $This;
+}
+
+# Is it a supported file format?
+#
+# In scalar context only status is returned; otherwise, file format and file IO package name is also
+# returned.
+#
+# Note:
+#   . To support additional file formats, this is the only method which needs to be changed.
+#
+#   . Currently supported file formats are:
+#
+#      SDF         .sdf, .sd
+#      MDLMol   .mol
+#
+sub IsSupportedMoleculeFileFormat {
+  my($FirstParameter, $SecondParameter) = @_;
+  my($This, $Name);
+
+  if ((@_ == 2) && (_IsMoleculeFileIO($FirstParameter))) {
+    ($This, $Name) = ($FirstParameter, $SecondParameter);
+  }
+  else {
+    ($Name) = ($FirstParameter);
+  }
+  my($Status, $Format, $IOPackageName);
+
+  $Status = 0; $Format = 'NotSupported'; $IOPackageName = 'Unknown';
+
+  FORMAT: {
+    if (FileIO::SDFileIO::IsSDFile($Name)) { $Status = 1; $Format = 'SDF'; $IOPackageName = 'FileIO::SDFileIO'; last FORMAT; }
+    if (FileIO::MDLMolFileIO::IsMDLMolFile($Name)) { $Status = 1; $Format = 'MDLMol'; $IOPackageName = 'FileIO::MDLMolFileIO'; last FORMAT; }
+    $Status = 0; $Format = 'NotSupported'; $IOPackageName = 'Unknown';
+  }
+
+  return wantarray ? ($Status, $Format, $IOPackageName) : $Status;
+}
+
+# Prohibit file ref change...
+#
+sub SetFileIORef {
+  my($This, $Value) = @_;
+
+  carp "Warning: ${ClassName}->SetFileIORef: Explicit setting of file ref is not supported...";
+
+  return $This;
+}
+
+# Prohibit file name change...
+#
+sub SetName {
+  my($This, $Name) = @_;
+
+  carp "Warning: ${ClassName}->SetName: Explicit setting of file name is not supported: It must be set during object instantiation...";
+
+  return $This;
+}
+
+# Prohibit file mode change...
+#
+sub SetMode {
+  my($This, $Mode) = @_;
+
+  carp "Warning: ${ClassName}->SetMode: Explicit setting of file mode is not supported: It must be set during object instantiation...";
+
+  return $This;
+}
+
+# Open file in a specific mode; default mode is Read only.
+# Supported mode values are: Read, Write, Append, <, >, >>, r, w, a
+#
+sub Open {
+  my($This, $Mode) = @_;
+
+  return $This->{FileIORef}->Open($Mode);
+}
+
+# close file...
+sub Close {
+  my($This) = @_;
+
+  return $This->{FileIORef}->Close();
+}
+
+# Read molecule string from file and return a molecule object...
+sub ReadMolecule {
+  my($This) = @_;
+
+  return $This->{FileIORef}->ReadMolecule();
+}
+
+# Retrieve molecule string from file...
+sub ReadMoleculeString {
+  my($This) = @_;
+
+  return $This->{FileIORef}->ReadMoleculeString();
+}
+
+# Write molecule using molecule object...
+sub WriteMolecule {
+  my($This, $Molecule) = @_;
+
+  return $This->{FileIORef}->WriteMolecule($Molecule);
+}
+
+# Is it a MoleculeFileIO object?
+sub _IsMoleculeFileIO {
+  my($Object) = @_;
+
+  return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+MoleculeFileIO
+
+=head1 SYNOPSIS
+
+use MoleculeFileIO;
+
+use MoleculeFileIO qw(:all);
+
+=head1 DESCRIPTION
+
+B<MoleculeFileIO> class provides the following methods:
+
+new, Close, IsSupportedMoleculeFileFormat, Open, ReadMolecule,
+ReadMoleculeString, WriteMolecule
+
+The following methods can also be used as functions:
+
+IsSupportedMoleculeFileFormat
+
+=head2 METHODS
+
+=over 4
+
+=item B<new>
+
+    $NewMoleculeFileIO = new MoleculeFileIO([%PropertyNameAndValues]);
+
+Using specified I<MoleculeFileIO> property names and values hash, B<new> method
+creates a new object and returns a reference to newly created B<MoleculeFileIO> object.
+By default, following properties are initialized:
+
+    Name = ""
+    Mode = ""
+    FileIORef = ""
+
+Based on extension of specified file I<Name>, an input class is automatically associated to
+provide molecule read and write methods.
+
+Examples:
+
+    $Name = "Water.mol";
+    $Mode = "Read";
+    $MoleculeFileIO = new MoleculeFileIO('Name' => $Name,
+                                         'Mode' => $Mode);
+    $MoleculeFileIO->Open();
+    $Molecule = $MoleculeFileIO->ReadMolecule();
+    $Molecule->DetectRings();
+    print "$Molecule\n";
+    $MoleculeFileIO->Close();
+
+    $MoleculeFileIO = new MoleculeFileIO('Name' => 'Sample1.sdf',
+                                         'Mode' => 'Read');
+    $MoleculeFileIO->Open();
+    while ($Molecule = $MoleculeFileIO1->ReadMolecule()) {
+        $Molecule->DetectRings();
+        print "$Molecule\n";
+
+        $DataLabelsAndValuesRef =
+          $Molecule->GetDataFieldLabelAndValues();
+        for $DataLabel (sort keys %{$DataLabelsAndValuesRef} ) {
+            $DataValue = $DataLabelsAndValuesRef->{$DataLabel};
+            print "<DataLabel: $DataLabel; DataValue: $DataValue>; ";
+        }
+        print "\n";
+    }
+    $MoleculeFileIO->Close();
+
+=item B<Close>
+
+    $MoleculeFileIO->Close();
+
+Closes an open file
+
+=item B<IsSupportedMoleculeFileFormat>
+
+    $Status = $MoleculeFileIO->IsSupportedMoleculeFileFormat($Name);
+    $Status = MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
+    ($Status, $FormatType, $IOClassName) =
+       $MoleculeFileIO::IsSupportedMoleculeFileFormat($Name);
+
+Returns 1 or 0 based on whether input file I<Name> format is supported. In list context,
+value of supported format type and name of associated IO class is also returned.
+
+File extension is used to determine file format. Currently, following file extensions are
+supported:
+
+    FileExts - FormatType - AssociatedIOClassName
+
+    .mol - MDLMOL - MDLMolFileIO
+    .sdf, .sd - SDF - SDFileIO
+
+=item B<Open>
+
+    $MoleculeFileIO->Open([$Mode]);
+
+Opens a file in a specified I<Mode>. Default mode value: I<Read>. Supported mode
+values:
+
+    Read, Write, Append, <, >, >>, r, w, or a
+
+=item B<ReadMolecule>
+
+    $Molecule = $MoleculeFileIO->ReadMolecule();
+
+Reads molecule data from the file and returns a I<Molecule> object.
+
+=item B<ReadMoleculeString>
+
+    $MoleculeString = $MoleculeFileIO->ReadMoleculeString();
+
+Reads molecule data from a file and returns a I<Molecule> string.
+
+=item B<WriteMolecule>
+
+    $MoleculeFileIO->WriteMolecule();
+
+Write molecule data to a file for a I<Molecule>.
+
+=back
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+FileIO.pm, MDLMolFileIO.pm, SDFileIO.pm
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 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.
+
+=cut