1 #!/usr/bin/perl -w 2 # 3 # File: SortSDFiles.pl 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 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