       1 #!/usr/bin/perl -w
       2 #
       3 # File: JoinSDFiles.pl
       4 # Author: Manish Sud <msud@san.rr.com>
       5 #
       6 # Copyright (C) 2018 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 FindBin; use lib "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Benchmark;
      31 use SDFileUtil;
      32 use FileUtil;
      33
      34 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      35
      36 # Autoflush STDOUT
      37 $| = 1;
      38
      39 # Starting message...
      40 $ScriptName = basename $0;
      41 print "\n$ScriptName:Starting...\n\n";
      42 $StartTime = new Benchmark;
      43
      44 # Get the options and setup script...
      45 SetupScriptUsage();
      46 if ($Options{help} || @ARGV < 1) {
      47   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      48 }
      49
      50 my(@SDFilesList);
      51 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      52 if (@SDFilesList == 1) {
      53   die "Error: Specify more than one SD file.\n";
      54 }
      55
      56 # Process options...
      57 print "Processing options...\n";
      58 my(%OptionsInfo);
      59 ProcessOptions();
      60
      61 # Setup information about input files...
      62 print "Checking input SD files...\n";
      63 my(%SDFilesInfo);
      64 RetrieveSDFilesInfo();
      65
      66 # Join files...
      67 print "\nGenerating new SD file $OptionsInfo{NewSDFile}...\n";
      68 JoinSDFiles();
      69
      70 print "\n$ScriptName:Done...\n\n";
      71
      72 $EndTime = new Benchmark;
      73 $TotalTime = timediff ($EndTime, $StartTime);
      74 print "Total time: ", timestr($TotalTime), "\n";
      75
      76 ###############################################################################
      77
      78 # Join all valid SD files...
      79 sub JoinSDFiles {
      80   my($FileIndex, $SDFile, $NewSDFile);
      81
      82   $NewSDFile = $OptionsInfo{NewSDFile};
      83
      84   open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
      85   FILELIST: for $FileIndex (0 .. $#SDFilesList) {
      86     if (!$SDFilesInfo{FileOkay}[$FileIndex]) {
      87       next FILELIST;
      88     }
      89     $SDFile = $SDFilesList[$FileIndex];
      90     print "\nProcessing file $SDFile...\n";
      91
      92     open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
      93     while (<SDFILE>) {
      94       s/(\r\n)|(\r)/\n/g;
      95       print NEWSDFILE;
      96     }
      97     close SDFILE;
      98   }
      99
     100   close NEWSDFILE;
     101 }
     102
     103 # Retrieve information about SD files...
     104 sub RetrieveSDFilesInfo {
     105   my($Index, $SDFile);
     106
     107   %SDFilesInfo = ();
     108   @{$SDFilesInfo{FileOkay}} = ();
     109
     110   FILELIST: for $Index (0 .. $#SDFilesList) {
     111     $SDFilesInfo{FileOkay}[$Index] = 0;
     112
     113     $SDFile = $SDFilesList[$Index];
     114     if (!(-e $SDFile)) {
     115       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     116       next FILELIST;
     117     }
     118     if (!CheckFileType($SDFile, "sdf sd")) {
     119       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     120       next FILELIST;
     121     }
     122     if (! open SDFILE, "$SDFile") {
     123       warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
     124       next FILELIST;
     125     }
     126     close SDFILE;
     127
     128     $SDFilesInfo{FileOkay}[$Index] = 1;
     129   }
     130 }
     131
     132 # Process option values...
     133 sub ProcessOptions {
     134   my($FileDir, $FileName, $FileExt, $NewSDFile);
     135
     136   %OptionsInfo = ();
     137
     138   $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : undef;
     139   $OptionsInfo{Overwrite} = $Options{overwrite} ? $Options{overwrite} : undef;
     140
     141   if ($Options{root}) {
     142     $FileDir = ""; $FileName = ""; $FileExt = "";
     143     ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root});
     144     if ($FileName && $FileExt) {
     145       $NewSDFile = $FileName . "." . $FileExt;
     146     }
     147     else {
     148       $NewSDFile =  $Options{root} . ".sdf";
     149     }
     150   }
     151   else {
     152     $FileDir = ""; $FileName = ""; $FileExt = "";
     153     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFilesList[0]);
     154     $NewSDFile = $FileName . "1To" . @SDFilesList . "Joined.sdf";
     155   }
     156
     157   if (!$Options{overwrite}) {
     158     if (-e $NewSDFile) {
     159       die "Error: The file $NewSDFile already exists.\n";
     160     }
     161   }
     162   if ($Options{root}) {
     163     my($FileIndex);
     164     for $FileIndex (0 .. $#SDFilesList) {
     165       if (lc($NewSDFile) eq lc($SDFilesList[$FileIndex])) {
     166         die "Error: Output filename, $NewSDFile, is similar to a input file name.\nSpecify a different name using \"-r --root\" option or use default name.\n";
     167       }
     168     }
     169   }
     170   $OptionsInfo{NewSDFile} = $NewSDFile;
     171
     172 }
     173
     174 # Setup script usage  and retrieve command line arguments specified using various options...
     175 sub SetupScriptUsage {
     176
     177   # Retrieve all the options...
     178   %Options = ();
     179   if (!GetOptions(\%Options, "help|h", "overwrite|o", "root|r=s", "workingdir|w=s")) {
     180     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     181   }
     182   if ($Options{workingdir}) {
     183     if (! -d $Options{workingdir}) {
     184       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     185     }
     186     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     187   }
     188 }
     189