diff lib/FileIO/SDFileIO.pm @ 0:4816e4a8ae95 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/FileIO/SDFileIO.pm	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,367 @@
+package FileIO::SDFileIO;
+#
+# $RCSfile: SDFileIO.pm,v $
+# $Date: 2015/02/28 20:48:43 $
+# $Revision: 1.35 $
+#
+# 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 TextUtil ();
+use FileUtil ();
+use SDFileUtil ();
+use FileIO::FileIO;
+use FileIO::MDLMolFileIO;
+use Molecule;
+
+use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
+
+@ISA = qw(FileIO::FileIO Exporter);
+@EXPORT = qw();
+@EXPORT_OK = qw(IsSDFile);
+
+%EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);
+
+# Setup class variables...
+my($ClassName);
+_InitializeClass();
+
+# Class constructor...
+sub new {
+  my($Class, %NamesAndValues) = @_;
+
+  # Initialize object...
+  my $This = $Class->SUPER::new();
+  bless $This, ref($Class) || $Class;
+  $This->_InitializeSDFileIO();
+
+  $This->_InitializeSDFileIOProperties(%NamesAndValues);
+
+  return $This;
+}
+
+# Initialize any local object data...
+#
+sub _InitializeSDFileIO {
+  my($This) = @_;
+
+  # Sorting of MDL data fields during output: Keep the initial order or write 'em out alphabetically...
+  $This->{SortDataFieldsDuringOutput} = 'No';
+
+  return $This;
+}
+
+# Initialize class ...
+sub _InitializeClass {
+  #Class name...
+  $ClassName = __PACKAGE__;
+
+}
+
+# Initialize object values...
+sub _InitializeSDFileIOProperties {
+  my($This, %NamesAndValues) = @_;
+
+  # All other property names and values along with all Set/Get<PropertyName> methods
+  # are implemented on-demand using ObjectProperty class.
+
+  my($Name, $Value, $MethodName);
+  while (($Name, $Value) = each  %NamesAndValues) {
+    $MethodName = "Set${Name}";
+    $This->$MethodName($Value);
+  }
+
+  if (!exists $NamesAndValues{Name}) {
+    croak "Error: ${ClassName}->New: Object can't be instantiated without specifying file name...";
+  }
+
+  # Make sure it's a SD file...
+  $Name = $NamesAndValues{Name};
+  if (!$This->IsSDFile($Name)) {
+    croak "Error: ${ClassName}->New: Object can't be instantiated: File, $Name, doesn't appear to be SDF format...";
+  }
+
+  return $This;
+}
+
+# Is it a SD file?
+sub IsSDFile ($;$) {
+  my($FirstParameter, $SecondParameter) = @_;
+  my($This, $FileName, $Status);
+
+  if ((@_ == 2) && (_IsSDFileIO($FirstParameter))) {
+    ($This, $FileName) = ($FirstParameter, $SecondParameter);
+  }
+  else {
+    $FileName = $FirstParameter;
+  }
+
+  # Check file extension...
+  $Status = FileUtil::CheckFileType($FileName, "sd sdf");
+
+  return $Status;
+}
+
+# Read molecule from file and return molecule object...
+sub ReadMolecule {
+  my($This) = @_;
+  my($FileHandle);
+
+  $FileHandle = $This->GetFileHandle();
+  return $This->ParseMoleculeString(SDFileUtil::ReadCmpdString($FileHandle));
+}
+
+# Write compound data along with any data field label and values using Molecule object...
+sub WriteMolecule {
+  my($This, $Molecule) = @_;
+
+  if (!(defined($Molecule) && $Molecule->IsMolecule())) {
+    carp "Warning: ${ClassName}->WriteMolecule: No data written: Molecule object is not specified...";
+    return $This;
+  }
+  my($FileHandle);
+  $FileHandle = $This->GetFileHandle();
+
+  print $FileHandle $This->GenerateMoleculeString($Molecule) . "\n";
+
+  return $This;
+}
+
+# Retrieve molecule string...
+sub ReadMoleculeString {
+  my($This) = @_;
+  my($FileHandle);
+
+  $FileHandle = $This->GetFileHandle();
+  return SDFileUtil::ReadCmpdString($FileHandle);
+}
+
+# Parse molecule string and return molecule object. ParseMoleculeString supports two invocation methods: class
+# method or a package function.
+#
+sub ParseMoleculeString {
+  my($FirstParameter, $SecondParameter) = @_;
+  my($This, $MoleculeString);
+
+  if ((@_ == 2) && (_IsSDFileIO($FirstParameter))) {
+    ($This, $MoleculeString) = ($FirstParameter, $SecondParameter);
+  }
+  else {
+    $MoleculeString = $FirstParameter;
+    $This = undef;
+  }
+  if (!$MoleculeString) {
+    return undef;
+  }
+  # Parse molecule data...
+  my($Molecule);
+  $Molecule = FileIO::MDLMolFileIO::ParseMoleculeString($MoleculeString);
+
+  # Process data label/value pairs...
+  my(@MoleculeLines, @DataLabels, %DataLabelsAndValues);
+
+  %DataLabelsAndValues = ();
+  @MoleculeLines = split /\n/, $MoleculeString;
+  @DataLabels = SDFileUtil::GetCmpdDataHeaderLabels(\@MoleculeLines);
+  %DataLabelsAndValues = SDFileUtil::GetCmpdDataHeaderLabelsAndValues(\@MoleculeLines);
+
+  # Store reference to data labels to keep track of their initial order in SD file...
+  $Molecule->SetDataFieldLabels(\@DataLabels);
+
+  # Store reference to SD data label/value pairs hash as a generic property of molecule...
+  $Molecule->SetDataFieldLabelAndValues(\%DataLabelsAndValues);
+
+  return $Molecule;
+}
+
+# Generate molecule string using molecule object...
+sub GenerateMoleculeString {
+  my($FirstParameter, $SecondParameter) = @_;
+  my($This, $Molecule);
+
+  if ((@_ == 2) && (_IsSDFileIO($FirstParameter))) {
+    ($This, $Molecule) = ($FirstParameter, $SecondParameter);
+  }
+  else {
+    $Molecule = $FirstParameter;
+    $This = undef;
+  }
+  if (!defined($Molecule)) {
+    return undef;
+  }
+  # Generate CTAB data...
+  my($CmpdString);
+  $CmpdString = FileIO::MDLMolFileIO::GenerateMoleculeString($Molecule);
+
+  # Generate any data field labels and values...
+  my($DataFieldLabelsAndValuesString);
+
+  $DataFieldLabelsAndValuesString = '';
+  if ($Molecule->HasProperty('DataFieldLabels')) {
+    my($DataFieldLabelsRef, $DataFieldLabelAndValuesRef, $SortDataFields);
+
+    $SortDataFields = (exists($This->{SortDataFieldsDuringOutput}) && $This->{SortDataFieldsDuringOutput} =~ /^Yes$/i) ? 1 : 0;
+
+    $DataFieldLabelsRef = $Molecule->GetDataFieldLabels();
+    $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
+    $DataFieldLabelsAndValuesString = join "\n", SDFileUtil::GenerateCmpdDataHeaderLabelsAndValuesLines($DataFieldLabelsRef, $DataFieldLabelAndValuesRef, $SortDataFields);
+  }
+
+  return "${CmpdString }\n${DataFieldLabelsAndValuesString}\n\$\$\$\$";
+}
+
+
+# Is it a SDFileIO object?
+sub _IsSDFileIO {
+  my($Object) = @_;
+
+  return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+SDFileIO
+
+=head1 SYNOPSIS
+
+use FileIO::SDFileIO;
+
+use FileIO::SDFileIO qw(:all);
+
+=head1 DESCRIPTION
+
+B<SDFIleIO> class provides the following methods:
+
+new, GenerateMoleculeString, IsSDFile, ParseMoleculeString, ReadMolecule,
+ReadMoleculeString, WriteMolecule
+
+The following methods can also be used as functions:
+
+GenerateMoleculeString, IsSDFile, ParseMoleculeString
+
+Data specific to B<SDFileIO> class not directly used by B<Molecule>, B<Atom> and
+B<Bond> objects - data label/value pairs, atom SteroParity and so on - is associated to
+and retrieved from approptiate objects using following methods:
+
+    SetMDL<PropertyName>
+    GetMDL<PropertyName>.
+
+SD data label and values are attached to B<Molecule> object as a refernece to a hash
+using SetDataFieldLabelAndValues and can be retrieved using GetDataFieldLabelAndValues
+method.
+
+B<SDFileIO> class is derived from I<FileIO> class and uses its methods to support
+generic file related functionality.
+
+=head2 METHODS
+
+=over 4
+
+=item B<new>
+
+    $NewSDFileIO = new FileIO::SDFileIO(%NamesAndValues);
+
+Using specified I<SDFileIO> property names and values hash, B<new> method creates a new object
+and returns a reference to newly created B<SDFileIO> object.
+
+=item B<GenerateMoleculeString>
+
+    $MoleculeString = $SDFileIO->GenerateMoleculeString($Molecule);
+    $MoleculeString = FileIO::SDFileIO::GenerateMoleculeString($Molecule);
+
+Returns a B<MoleculeString> in SD format corresponding to I<Molecule>.
+
+=item B<IsSDFile>
+
+    $Status = $SDFileIO->IsSDFile($FileName);
+    $Status = FileIO::SDFileIO::IsSDFile($FileName);
+
+Returns 1 or 0 based on whether I<FileName> is a SD file.
+
+=item B<ParseMoleculeString>
+
+    $Molecule = $SDFileIO->ParseMoleculeString($MoleculeString);
+    $Molecule = FileIO::SDFileIO::ParseMoleculeString($MoleculeString);
+
+Parses I<MoleculeString> and returns a B<Molecule> object. SD data field label and value pairs
+are associated to B<Molecule> object as a reference to a hash using:
+
+    $Molecule->SetDataFieldLabelAndValues(\%DataLabelsAndValues)
+
+The reference to hash can be retrieved by:
+
+    $DataLabelsAndValues = $Molecule->GetDataFieldLabelAndValues();
+    for $DataLabel (sort keys %{$DataLabelsAndValues}) {
+        $DataValue = $DataLabelsAndValues->{$DataLabel};
+    }
+
+=item B<ReadMolecule>
+
+    $Molecule = $SDFileIO->ReadMolecule($FileHandle);
+
+Reads data for the next compound in a file using already opened I<FileHandle>, creates,
+and returns a B<Molecule> object.
+
+=item B<ReadMoleculeString>
+
+    $MoleculeString = $SDFileIO->ReadMoleculeString($FileHandle);
+
+Reads data for the next compound in a file using already opened I<FileHandle> and
+returns a B<MoleculeString> corresponding to compound structure and other associated
+data.
+
+=item B<WriteMolecule>
+
+    $SDFileIO->WriteMolecule($Molecule);
+
+Writes I<Molecule> data to a file in MDLMol format and returns B<SDFileIO>.
+
+=back
+
+=head1 AUTHOR
+
+Manish Sud <[e-mail]>
+
+=head1 SEE ALSO
+
+MoleculeFileIO.pm, MDLMolFileIO.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