1 package MoleculeFileIO;
   2 #
   3 # File: MoleculeFileIO.pm
   4 # Author: Manish Sud <msud@san.rr.com>
   5 #
   6 # Copyright (C) 2024 Manish Sud. All rights reserved.
   7 #
   8 # This file is part of MayaChemTools.
   9 #
  10 # MayaChemTools is free software; you can redistribute it and/or modify it under
  11 # the terms of the GNU Lesser General Public License as published by the Free
  12 # Software Foundation; either version 3 of the License, or (at your option) any
  13 # later version.
  14 #
  15 # MayaChemTools is distributed in the hope that it will be useful, but without
  16 # any warranty; without even the implied warranty of merchantability of fitness
  17 # for a particular purpose.  See the GNU Lesser General Public License for more
  18 # details.
  19 #
  20 # You should have received a copy of the GNU Lesser General Public License
  21 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
  22 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
  23 # Boston, MA, 02111-1307, USA.
  24 #
  25 
  26 use strict;
  27 use Carp;
  28 use Exporter;
  29 use Scalar::Util ();
  30 use FileIO::SDFileIO;
  31 use FileIO::MDLMolFileIO;
  32 
  33 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
  34 
  35 @ISA = qw(Exporter);
  36 @EXPORT = qw();
  37 @EXPORT_OK = qw(IsSupportedMoleculeFileFormat);
  38 
  39 %EXPORT_TAGS = (all  => [@EXPORT, @EXPORT_OK]);
  40 
  41 # Setup class variables...
  42 my($ClassName);
  43 _InitializeClass();
  44 
  45 # Class constructor...
  46 sub new {
  47   my($Class, %NamesAndValues) = @_;
  48 
  49   # Initialize object...
  50   my $This = {};
  51   bless $This, ref($Class) || $Class;
  52   $This->_InitializeMoleculeFileIO();
  53 
  54   $This->_InitializeMoleculeFileIOProperties(%NamesAndValues);
  55 
  56   return $This;
  57 }
  58 
  59 # Initialize object data...
  60 #
  61 sub _InitializeMoleculeFileIO {
  62   my($This) = @_;
  63 
  64   # Reference to specific FileIO object...
  65   $This->{FileIORef} = '';
  66 
  67   return $This;
  68 }
  69 
  70 # Initialize class ...
  71 sub _InitializeClass {
  72   #Class name...
  73   $ClassName = __PACKAGE__;
  74 
  75 }
  76 
  77 # Initialize object properties......
  78 #
  79 sub _InitializeMoleculeFileIOProperties {
  80   my($This, %NamesAndValues) = @_;
  81 
  82   if (!exists $NamesAndValues{Name}) {
  83     croak "Error: ${ClassName}->New: Object can't be instantiated without specifying file name...";
  84   }
  85 
  86   if (!exists $NamesAndValues{Mode}) {
  87     $NamesAndValues{Mode} = 'Read';
  88   }
  89 
  90   # Make sure its a supported format and intialize FileIO object reference...
  91   $This->_SetFileIORef(%NamesAndValues);
  92 
  93   return $This;
  94 }
  95 
  96 # Setup FileIO object reference...
  97 sub _SetFileIORef {
  98   my($This, %NamesAndValues) = @_;
  99   my($Name, $Status, $Format, $IOPackageName);
 100 
 101   $Name = $NamesAndValues{Name};
 102 
 103   ($Status, $Format, $IOPackageName) = $This->IsSupportedMoleculeFileFormat($Name);
 104   if (!$Status) {
 105     croak "Error: ${ClassName}->New: Object can't be instantiated: File format, $Name, is not supported: Currently supported file formats are: SDF, MDLMol...";
 106   }
 107 
 108   $This->{FileIORef} = ${IOPackageName}->new(%NamesAndValues);
 109 
 110   return $This;
 111 }
 112 
 113 # Is it a supported file format?
 114 #
 115 # In scalar context only status is returned; otherwise, file format and file IO package name is also
 116 # returned.
 117 #
 118 # Note:
 119 #   . To support additional file formats, this is the only method which needs to be changed.
 120 #
 121 #   . Currently supported file formats are:
 122 #
 123 #      SDF         .sdf, .sd
 124 #      MDLMol   .mol
 125 #
 126 sub IsSupportedMoleculeFileFormat {
 127   my($FirstParameter, $SecondParameter) = @_;
 128   my($This, $Name);
 129 
 130   if ((@_ == 2) && (_IsMoleculeFileIO($FirstParameter))) {
 131     ($This, $Name) = ($FirstParameter, $SecondParameter);
 132   }
 133   else {
 134     ($Name) = ($FirstParameter);
 135   }
 136   my($Status, $Format, $IOPackageName);
 137 
 138   $Status = 0; $Format = 'NotSupported'; $IOPackageName = 'Unknown';
 139 
 140   FORMAT: {
 141     if (FileIO::SDFileIO::IsSDFile($Name)) { $Status = 1; $Format = 'SDF'; $IOPackageName = 'FileIO::SDFileIO'; last FORMAT; }
 142     if (FileIO::MDLMolFileIO::IsMDLMolFile($Name)) { $Status = 1; $Format = 'MDLMol'; $IOPackageName = 'FileIO::MDLMolFileIO'; last FORMAT; }
 143     $Status = 0; $Format = 'NotSupported'; $IOPackageName = 'Unknown';
 144   }
 145 
 146   return wantarray ? ($Status, $Format, $IOPackageName) : $Status;
 147 }
 148 
 149 # Prohibit file ref change...
 150 #
 151 sub SetFileIORef {
 152   my($This, $Value) = @_;
 153 
 154   carp "Warning: ${ClassName}->SetFileIORef: Explicit setting of file ref is not supported...";
 155 
 156   return $This;
 157 }
 158 
 159 # Prohibit file name change...
 160 #
 161 sub SetName {
 162   my($This, $Name) = @_;
 163 
 164   carp "Warning: ${ClassName}->SetName: Explicit setting of file name is not supported: It must be set during object instantiation...";
 165 
 166   return $This;
 167 }
 168 
 169 # Prohibit file mode change...
 170 #
 171 sub SetMode {
 172   my($This, $Mode) = @_;
 173 
 174   carp "Warning: ${ClassName}->SetMode: Explicit setting of file mode is not supported: It must be set during object instantiation...";
 175 
 176   return $This;
 177 }
 178 
 179 # Open file in a specific mode; default mode is Read only.
 180 # Supported mode values are: Read, Write, Append, <, >, >>, r, w, a
 181 #
 182 sub Open {
 183   my($This, $Mode) = @_;
 184 
 185   return $This->{FileIORef}->Open($Mode);
 186 }
 187 
 188 # close file...
 189 sub Close {
 190   my($This) = @_;
 191 
 192   return $This->{FileIORef}->Close();
 193 }
 194 
 195 # Read molecule string from file and return a molecule object...
 196 sub ReadMolecule {
 197   my($This) = @_;
 198 
 199   return $This->{FileIORef}->ReadMolecule();
 200 }
 201 
 202 # Retrieve molecule string from file...
 203 sub ReadMoleculeString {
 204   my($This) = @_;
 205 
 206   return $This->{FileIORef}->ReadMoleculeString();
 207 }
 208 
 209 # Write molecule using molecule object...
 210 sub WriteMolecule {
 211   my($This, $Molecule) = @_;
 212 
 213   return $This->{FileIORef}->WriteMolecule($Molecule);
 214 }
 215 
 216 # Is it a MoleculeFileIO object?
 217 sub _IsMoleculeFileIO {
 218   my($Object) = @_;
 219 
 220   return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
 221 }
 222