1 package MoleculeFileIO;
   2 #
   3 # $RCSfile: MoleculeFileIO.pm,v $
   4 # $Date: 2008/04/25 00:00:46 $
   5 # $Revision: 1.15 $
   6 #
   7 # Author: Manish Sud <msud@san.rr.com>
   8 #
   9 # Copyright (C) 2004-2008 Manish Sud. All rights reserved.
  10 #
  11 # This file is part of MayaChemTools.
  12 #
  13 # MayaChemTools is free software; you can redistribute it and/or modify it under
  14 # the terms of the GNU Lesser General Public License as published by the Free
  15 # Software Foundation; either version 3 of the License, or (at your option) any
  16 # later version.
  17 #
  18 # MayaChemTools is distributed in the hope that it will be useful, but without
  19 # any warranty; without even the implied warranty of merchantability of fitness
  20 # for a particular purpose.  See the GNU Lesser General Public License for more
  21 # details.
  22 #
  23 # You should have received a copy of the GNU Lesser General Public License
  24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
  25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
  26 # Boston, MA, 02111-1307, USA.
  27 #
  28 use 5.006;
  29 use strict;
  30 use Carp;
  31 use Exporter;
  32 use Scalar::Util ();
  33 use FileIO::SDFileIO;
  34 use FileIO::MDLMolFileIO;
  35 
  36 use vars qw($VERSION @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
  37 
  38 $VERSION = '1.00';
  39 @ISA = qw(Exporter);
  40 @EXPORT = qw();
  41 @EXPORT_OK = qw(IsSupportedMoleculeFileFormat);
  42 
  43 %EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);
  44 
  45 # Setup class variables...
  46 my($ClassName);
  47 _InitializeClass();
  48 
  49 # Class constructor...
  50 sub new {
  51   my($Class, %NamesAndValues) = @_;
  52 
  53   # Initialize object...
  54   my $This = {};
  55   bless $This, ref($Class) || $Class;
  56   $This->_InitializeMoleculeFileIO();
  57 
  58   $This->_InitializeMoleculeFileIOProperties(%NamesAndValues);
  59 
  60   return $This;
  61 }
  62 
  63 # Initialize object data...
  64 #
  65 sub _InitializeMoleculeFileIO {
  66   my($This) = @_;
  67 
  68   # Reference to specific FileIO object...
  69   $This->{FileIORef} = '';
  70 
  71   return $This;
  72 }
  73 
  74 # Initialize class ...
  75 sub _InitializeClass {
  76   #Class name...
  77   $ClassName = __PACKAGE__;
  78 
  79 }
  80 
  81 # Initialize object properties......
  82 #
  83 sub _InitializeMoleculeFileIOProperties {
  84   my($This, %NamesAndValues) = @_;
  85 
  86   if (!exists $NamesAndValues{Name}) {
  87     croak "Error: ${ClassName}->New: Object can't be instantiated without specifying file name...";
  88   }
  89 
  90   if (!exists $NamesAndValues{Mode}) {
  91     $NamesAndValues{Mode} = 'Read';
  92   }
  93 
  94   # Make sure its a supported format and intialize FileIO object reference...
  95   $This->_SetFileIORef(%NamesAndValues);
  96 
  97   return $This;
  98 }
  99 
 100 # Setup FileIO object reference...
 101 sub _SetFileIORef {
 102   my($This, %NamesAndValues) = @_;
 103   my($Name, $Status, $Format, $IOPackageName);
 104 
 105   $Name = $NamesAndValues{Name};
 106 
 107   ($Status, $Format, $IOPackageName) = $This->IsSupportedMoleculeFileFormat($Name);
 108   if (!$Status) {
 109     croak "Error: ${ClassName}->New: Object can't be instantiated: File format, $Name, is not supported: Currently supported file formats are: SDF, MDLMol...";
 110   }
 111 
 112   $This->{FileIORef} = ${IOPackageName}->new(%NamesAndValues);
 113 
 114   return $This;
 115 }
 116 
 117 # Is it a supported file format?
 118 #
 119 # In scalar context only status is returned; otherwise, file format and file IO package name is also
 120 # returned.
 121 #
 122 # Note:
 123 #   . To support additional file formats, this is the only method which needs to be changed.
 124 #
 125 #   . Currently supported file formats are:
 126 #
 127 #      SDF         .sdf, .sd
 128 #      MDLMol   .mol
 129 #
 130 sub IsSupportedMoleculeFileFormat {
 131   my($FirstParameter, $SecondParameter) = @_;
 132   my($This, $Name);
 133 
 134   if ((@_ == 2) && (_IsMoleculeFileIO($FirstParameter))) {
 135     ($This, $Name) = ($FirstParameter, $SecondParameter);
 136   }
 137   else {
 138     ($Name) = ($FirstParameter);
 139   }
 140   my($Status, $Format, $IOPackageName);
 141 
 142   $Status = 0; $Format = 'NotSupported'; $IOPackageName = 'Unknown';
 143 
 144   FORMAT: {
 145     if (SDFileIO::IsSDFile($Name)) { $Status = 1; $Format = 'SDF'; $IOPackageName = 'SDFileIO'; last FORMAT; }
 146     if (MDLMolFileIO::IsMDLMolFile($Name)) { $Status = 1; $Format = 'MDLMol'; $IOPackageName = 'MDLMolFileIO'; last FORMAT; }
 147     $Status = 0; $Format = 'NotSupported'; $IOPackageName = 'Unknown';
 148   }
 149 
 150   return wantarray ? ($Status, $Format, $IOPackageName) : $Status;
 151 }
 152 
 153 # Prohibit file ref change...
 154 #
 155 sub SetFileIORef {
 156   my($This, $Value) = @_;
 157 
 158   carp "Warning: ${ClassName}->SetFileIORef: Explicit setting of file ref is not supported...";
 159 
 160   return $This;
 161 }
 162 
 163 # Prohibit file name change...
 164 #
 165 sub SetName {
 166   my($This, $Name) = @_;
 167 
 168   carp "Warning: ${ClassName}->SetName: Explicit setting of file name is not supported: It must be set during object instantiation...";
 169 
 170   return $This;
 171 }
 172 
 173 # Prohibit file mode change...
 174 #
 175 sub SetMode {
 176   my($This, $Mode) = @_;
 177 
 178   carp "Warning: ${ClassName}->SetMode: Explicit setting of file mode is not supported: It must be set during object instantiation...";
 179 
 180   return $This;
 181 }
 182 
 183 # Open file in a specific mode; default mode is Read only.
 184 # Supported mode values are: Read, Write, Append, <, >, >>, r, w, a
 185 #
 186 sub Open {
 187   my($This, $Mode) = @_;
 188 
 189   return $This->{FileIORef}->Open($Mode);
 190 }
 191 
 192 # close file...
 193 sub Close {
 194   my($This) = @_;
 195 
 196   return $This->{FileIORef}->Close();
 197 }
 198 
 199 # Read molecule string from file and return a molecule object...
 200 sub ReadMolecule {
 201   my($This) = @_;
 202 
 203   return $This->{FileIORef}->ReadMolecule();
 204 }
 205 
 206 # Retrieve molecule string from file...
 207 sub ReadMoleculeString {
 208   my($This) = @_;
 209 
 210   return $This->{FileIORef}->ReadMoleculeString();
 211 }
 212 
 213 # Write molecule using molecule object...
 214 sub WriteMolecule {
 215   my($This, $Molecule) = @_;
 216 
 217   return $This->{FileIORef}->WriteMolecule($Molecule);
 218 }
 219 
 220 # Is it a MoleculeFileIO object?
 221 sub _IsMoleculeFileIO {
 222   my($Object) = @_;
 223 
 224   return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
 225 }
 226