       1 #!/usr/bin/perl -w
       2 #
       3 # File: SortSDFiles.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 "$FindBin::Bin/../lib";
      28 use Getopt::Long;
      29 use File::Basename;
      30 use Text::ParseWords;
      31 use Benchmark;
      32 use FileUtil;
      33 use SDFileUtil;
      34 use TextUtil;
      35
      36 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
      37
      38 # Autoflush STDOUT
      39 $| = 1;
      40
      41 # Starting message...
      42 $ScriptName = basename($0);
      43 print "\n$ScriptName: Starting...\n\n";
      44 $StartTime = new Benchmark;
      45
      46 # Get the options and setup script...
      47 SetupScriptUsage();
      48 if ($Options{help} || @ARGV < 1) {
      49   die GetUsageFromPod("$FindBin::Bin/$ScriptName");
      50 }
      51
      52 my(@SDFilesList);
      53 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
      54
      55 print "Processing options...\n";
      56 my(%OptionsInfo);
      57 ProcessOptions();
      58
      59 print "Checking input SD file(s)...\n";
      60 my(%SDFilesInfo);
      61 RetrieveSDFilesInfo();
      62
      63 # Generate output files...
      64 my($FileIndex);
      65 if (@SDFilesList > 1) {
      66   print "\nProcessing SD files...\n";
      67 }
      68 for $FileIndex (0 .. $#SDFilesList) {
      69   if ($SDFilesInfo{FileOkay}[$FileIndex]) {
      70     print "\nProcessing file $SDFilesList[$FileIndex]...\n";
      71     SortSDFile($FileIndex);
      72   }
      73 }
      74 print "\n$ScriptName:Done...\n\n";
      75
      76 $EndTime = new Benchmark;
      77 $TotalTime = timediff ($EndTime, $StartTime);
      78 print "Total time: ", timestr($TotalTime), "\n";
      79
      80 ###############################################################################
      81
      82 # Sort it out...
      83 sub SortSDFile {
      84   my($Index) = @_;
      85   my($SDFile, $NewSDFile, $KeyDataFieldName);
      86
      87   $SDFile = $SDFilesList[$Index];
      88   $NewSDFile = $SDFilesInfo{OutFile}[$Index];
      89   $KeyDataFieldName = $SDFilesInfo{KeyDataFieldName}[$Index];
      90
      91   print "Generating new SD file $NewSDFile...\n";
      92   open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
      93   open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
      94
      95   # Go over all compound records and store 'em using key value as hash...
      96   my(%KeyToCompundRecordsMap, @InvalidCompoundRecords, $CmpdCount, $CmpdString, @CmpdLines, %DataFieldValues, $KeyDataFieldValue);
      97   %KeyToCompundRecordsMap = ();
      98   @InvalidCompoundRecords = ();
      99   $CmpdCount = 0;
     100
     101   COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
     102       $CmpdCount++;
     103       @CmpdLines = split "\n", $CmpdString;
     104       %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
     105       #Make sure data field value is okay...
     106       if (!(IsNotEmpty($DataFieldValues{$KeyDataFieldName}) && ($DataFieldValues{$KeyDataFieldName} !~ /\n/))) {
     107         push @InvalidCompoundRecords, $CmpdString;
     108         if ($OptionsInfo{DetailLevel} >= 3 ) {
     109           print "Ignoring compound record $CmpdCount: Contains empty value for key data field $KeyDataFieldName :\n $CmpdString\n\n";
     110         }
     111         elsif ($OptionsInfo{DetailLevel} >= 2) {
     112           print "Ignoring compound record $CmpdCount: Contains empty value for key data field $KeyDataFieldName...\n";
     113         }
     114         next COMPOUND;
     115       }
     116       $KeyDataFieldValue = $DataFieldValues{$KeyDataFieldName};
     117       if ($OptionsInfo{KeyData} =~ /^numeric$/i) {
     118         if (!IsFloat($KeyDataFieldValue)) {
     119           push @InvalidCompoundRecords, $CmpdString;
     120           if ($OptionsInfo{DetailLevel} >= 3 ) {
     121             print "Ignoring compound record $CmpdCount: Contains non-numerical value for key data field $KeyDataFieldName :\n $CmpdString\n\n";
     122           }
     123           elsif ($OptionsInfo{DetailLevel} >= 2) {
     124             print "Ignoring compound record $CmpdCount: Contains non-numerical value for key data field $KeyDataFieldName...\n";
     125           }
     126           next COMPOUND;
     127         }
     128       }
     129       if (exists($KeyToCompundRecordsMap{$KeyDataFieldValue})) {
     130         # Append to existing coompund data...
     131         $KeyToCompundRecordsMap{$KeyDataFieldValue} .= "\n" . $CmpdString;
     132       }
     133       else {
     134         $KeyToCompundRecordsMap{$KeyDataFieldValue} = $CmpdString;
     135       }
     136   }
     137
     138   if ($OptionsInfo{Sort} =~ /^ascending$/i) {
     139     if ($OptionsInfo{KeyData} =~ /^alphanumeric$/i) {
     140       for $KeyDataFieldValue (sort { lc($a) cmp lc($b) } keys %KeyToCompundRecordsMap ) {
     141         print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
     142       }
     143     }
     144     else {
     145       for $KeyDataFieldValue (sort { $a <=> $b } keys %KeyToCompundRecordsMap ) {
     146         print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
     147       }
     148     }
     149   }
     150   else {
     151     if ($OptionsInfo{KeyData} =~ /^alphanumeric$/i) {
     152       for $KeyDataFieldValue (sort { lc($b) cmp lc($a) } keys %KeyToCompundRecordsMap ) {
     153         print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
     154       }
     155     }
     156     else {
     157       for $KeyDataFieldValue (sort { $b <=> $a } keys %KeyToCompundRecordsMap ) {
     158         print NEWSDFILE "$KeyToCompundRecordsMap{$KeyDataFieldValue}\n";
     159       }
     160     }
     161   }
     162   # Append the records containing data not appropriate for sorting...
     163   if (@InvalidCompoundRecords) {
     164     print "Placing ", scalar(@InvalidCompoundRecords)," compound record(s) with invalid data field key data the end...\n";
     165     for $CmpdString (@InvalidCompoundRecords) {
     166       print NEWSDFILE "$CmpdString\n";
     167     }
     168   }
     169   close NEWSDFILE;
     170   close SDFILE;
     171 }
     172
     173 # Retrieve information about input SD files...
     174 sub RetrieveSDFilesInfo {
     175   my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot,  $OutFile, $DataFieldName);
     176
     177   %SDFilesInfo = ();
     178
     179   @{$SDFilesInfo{FileOkay}} = ();
     180   @{$SDFilesInfo{OutFile}} = ();
     181   @{$SDFilesInfo{KeyDataFieldName}} = ();
     182
     183   FILELIST: for $Index (0 .. $#SDFilesList) {
     184     $SDFile = $SDFilesList[$Index];
     185     $SDFilesInfo{FileOkay}[$Index] = 0;
     186     $SDFilesInfo{OutFile}[$Index] = "";
     187     $SDFilesInfo{KeyDataFieldName}[$Index] = "";
     188
     189     if (!(-e $SDFile)) {
     190       warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
     191       next FILELIST;
     192     }
     193     if (!CheckFileType($SDFile, "sd sdf")) {
     194       warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
     195       next FILELIST;
     196     }
     197     $FileDir = ""; $FileName = ""; $FileExt = "";
     198     ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
     199     if ($Options{root} && (@SDFilesList == 1)) {
     200       my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
     201       if ($RootFileName && $RootFileExt) {
     202         $FileName = $RootFileName;
     203       }
     204       else {
     205         $FileName = $Options{root};
     206       }
     207       $OutFileRoot = $FileName;
     208     }
     209     else {
     210       $OutFileRoot = $FileName . "SortedByDataField";
     211     }
     212
     213     $OutFile = $OutFileRoot . ".$FileExt";
     214     if (lc($OutFile) eq lc($SDFile)) {
     215       warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
     216       next FILELIST;
     217     }
     218     if (!$Options{overwrite}) {
     219       if (-e $OutFile) {
     220         warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
     221         next FILELIST;
     222       }
     223     }
     224     # Setup data field name...
     225     if ($OptionsInfo{SpecifiedDataFieldName}) {
     226       $DataFieldName = $OptionsInfo{SpecifiedDataFieldName};
     227     }
     228     else {
     229       my($CmpdString, @CmpdLines, @DataFieldNames);
     230       @DataFieldNames = ();
     231       if (!open(SDFILE, "$SDFile")) {
     232         warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
     233         next FILELIST;
     234       }
     235       $CmpdString = ReadCmpdString(\*SDFILE);
     236       close SDFILE;
     237
     238       @CmpdLines = split "\n", $CmpdString;
     239       @DataFieldNames = GetCmpdDataHeaderLabels(\@CmpdLines);
     240       $DataFieldName = $DataFieldNames[0];
     241     }
     242
     243     $SDFilesInfo{FileOkay}[$Index] = 1;
     244     $SDFilesInfo{OutFile}[$Index] = "$OutFile";
     245     $SDFilesInfo{KeyDataFieldName}[$Index] = $DataFieldName;
     246   }
     247 }
     248
     249 # Process option values...
     250 sub ProcessOptions {
     251   $OptionsInfo{DetailLevel} = $Options{detail};
     252
     253   $OptionsInfo{Key} = defined $Options{key} ? $Options{key} : undef;
     254   $OptionsInfo{SpecifiedDataFieldName} = "";
     255   if (defined $Options{key}) {
     256     $OptionsInfo{SpecifiedDataFieldName} = $Options{key};
     257   }
     258
     259   $OptionsInfo{KeyData} = $Options{keydata};
     260   $OptionsInfo{Sort} = $Options{sort};
     261
     262   $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
     263   $OptionsInfo{Root} = defined $Options{root} ? $Options{root} : undef;
     264 }
     265
     266 # Setup script usage  and retrieve command line arguments specified using various options...
     267 sub SetupScriptUsage {
     268
     269   # Retrieve all the options...
     270   %Options = ();
     271   $Options{detail} = 1;
     272   $Options{sort} = "ascending";
     273   $Options{keydata} = "numeric";
     274   if (!GetOptions(\%Options, "detail|d=i", "help|h",  "key|k=s", "keydata=s", "overwrite|o", "root|r=s", "sort|s=s", "workingdir|w=s")) {
     275     die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
     276   }
     277   if ($Options{workingdir}) {
     278     if (! -d $Options{workingdir}) {
     279       die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
     280     }
     281     chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
     282   }
     283   if ($Options{keydata} !~ /^(numeric|alphanumeric)$/i) {
     284     die "Error: The value specified, $Options{keydata}, for option \"--keydata\" is not valid. Allowed values: numeric or alphanumeric\n";
     285   }
     286   if ($Options{sort} !~ /^(ascending|descending)$/i) {
     287     die "Error: The value specified, $Options{sort}, for option \"-s --sort\" is not valid. Allowed values: ascending or descending\n";
     288   }
     289   if (!IsPositiveInteger($Options{detail})) {
     290     die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
     291   }
     292 }
     293