1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: SplitSDFiles.pl,v $ 4 # $Date: 2015/02/28 20:46:21 $ 5 # $Revision: 1.36 $ 6 # 7 # Author: Manish Sud <msud@san.rr.com> 8 # 9 # Copyright (C) 2015 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 29 use strict; 30 use FindBin; use lib "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Benchmark; 34 use SDFileUtil; 35 use FileUtil; 36 37 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 38 39 # Autoflush STDOUT 40 $| = 1; 41 42 # Starting message... 43 $ScriptName = basename $0; 44 print "\n$ScriptName:Starting...\n\n"; 45 $StartTime = new Benchmark; 46 47 # Get the options and setup script... 48 SetupScriptUsage(); 49 if ($Options{help} || @ARGV < 1) { 50 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 51 } 52 53 my(@SDFilesList); 54 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); 55 56 # Process options... 57 print "Processing options...\n"; 58 my(%OptionsInfo); 59 ProcessOptions(); 60 61 # Setup information about input files... 62 my(%SDFilesInfo); 63 print "Checking input SD file(s)...\n"; 64 RetrieveSDFilesInfo(); 65 66 # Process input files.. 67 my($FileIndex); 68 if (@SDFilesList > 1) { 69 print "\nProcessing SD files...\n"; 70 } 71 for $FileIndex (0 .. $#SDFilesList) { 72 if ($SDFilesInfo{FileOkay}[$FileIndex]) { 73 print "\nProcessing file $SDFilesList[$FileIndex]...\n"; 74 SplitSDFile($FileIndex); 75 } 76 } 77 print "\n$ScriptName:Done...\n\n"; 78 79 $EndTime = new Benchmark; 80 $TotalTime = timediff ($EndTime, $StartTime); 81 print "Total time: ", timestr($TotalTime), "\n"; 82 83 ############################################################################### 84 85 # Split a SD file... 86 # 87 sub SplitSDFile { 88 my($FileIndex) = @_; 89 90 if ($OptionsInfo{Mode} =~ /^Files$/i) { 91 SplitSDFileByNumOfFiles($FileIndex); 92 } 93 elsif ($OptionsInfo{Mode} =~ /^Cmpds$/i) { 94 SplitSDFileByNumOfCmpds($FileIndex); 95 } 96 } 97 98 # Split SD into specified number of files... 99 # 100 sub SplitSDFileByNumOfFiles { 101 my($FileIndex) = @_; 102 my($SDFile, $CmpdCount, $MaxCmpdsPerFile, $MaxNumOfFiles); 103 104 $SDFile = $SDFilesList[$FileIndex]; 105 106 if (!open SDFILE, "$SDFile") { 107 warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n"; 108 return; 109 } 110 111 $MaxNumOfFiles = $OptionsInfo{NumOfFiles}; 112 113 # Count number of compounds to figure out maximum number of compound per file... 114 $CmpdCount = 0; 115 while (<SDFILE>) { 116 if (/^\$\$\$\$/) { 117 $CmpdCount++; 118 } 119 } 120 close SDFILE; 121 122 if ($CmpdCount < $MaxNumOfFiles) { 123 warn "Warning: Ignoring file $SDFile: Total number of compounds, $CmpdCount, is smaller than number of new files, $MaxNumOfFiles\n"; 124 return; 125 } 126 127 $MaxCmpdsPerFile = int $CmpdCount / $MaxNumOfFiles; 128 129 SplitSDFileByNumOfFilesAndCmpds($FileIndex, $MaxNumOfFiles, $MaxCmpdsPerFile); 130 } 131 132 # Split SD into files containing specified number of compounds... 133 # 134 sub SplitSDFileByNumOfCmpds { 135 my($FileIndex) = @_; 136 137 if ($OptionsInfo{NumOfCmpds} == 1) { 138 SplitSDFileByOneCmpdPerFile($FileIndex); 139 } 140 else { 141 SplitSDFileByNumOfCmpdsPerFile($FileIndex); 142 } 143 } 144 145 # Split SD into files containing one compound per file... 146 # 147 sub SplitSDFileByOneCmpdPerFile { 148 my($FileIndex) = @_; 149 my($SDFile, $NewSDFile, $NewSDFileRoot, $FileExt, $OutFileRoot, $OverwriteFiles, $UseDataField, $DataFieldName, $UseMolName, $CmpdCount, $CmpdString, @CmpdLines, %DataFieldValues); 150 151 $SDFile = $SDFilesList[$FileIndex]; 152 153 if (!open SDFILE, "$SDFile") { 154 warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n"; 155 return; 156 } 157 158 print "\n"; 159 160 $CmpdCount = 0; 161 162 $FileExt = $SDFilesInfo{FileExt}[$FileIndex]; 163 164 $OutFileRoot = $SDFilesInfo{OutFileRoot}[$FileIndex]; 165 $OverwriteFiles = $OptionsInfo{OverwriteFiles}; 166 167 $UseDataField = ($OptionsInfo{CmpdsMode} =~ /^DataField$/i) ? 1 : 0; 168 $DataFieldName = $OptionsInfo{DataField}; 169 170 $UseMolName = ($OptionsInfo{CmpdsMode} =~ /^MolName$/i) ? 1 : 0; 171 172 CMPDSTRING: while ($CmpdString = ReadCmpdString(\*SDFILE)) { 173 $CmpdCount++; 174 175 # Setup SD file name... 176 $NewSDFileRoot = ''; 177 if ($UseDataField) { 178 @CmpdLines = split "\n", $CmpdString; 179 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines); 180 if (exists $DataFieldValues{$DataFieldName}) { 181 $NewSDFileRoot = $DataFieldValues{$DataFieldName}; 182 } 183 } 184 elsif ($UseMolName) { 185 @CmpdLines = split "\n", $CmpdString; 186 $NewSDFileRoot = $CmpdLines[0]; 187 } 188 189 # Check for any invalid file name characters in data field or molname values... 190 if ($NewSDFileRoot && $NewSDFileRoot =~ /[^a-zA-Z0-9_]/) { 191 $NewSDFileRoot =~ s/[^a-zA-Z0-9_]//g; 192 } 193 194 # Fall back plan for SD file name... 195 if (!$NewSDFileRoot) { 196 $NewSDFileRoot = "${OutFileRoot}Cmpd${CmpdCount}"; 197 } 198 199 $NewSDFile = "${NewSDFileRoot}.${FileExt}"; 200 201 if (!$OverwriteFiles) { 202 if (-e $NewSDFile) { 203 warn "Warning: Ignoring compound number, $CmpdCount, in $SDFile: New SD file, $NewSDFile, already exists\n"; 204 next CMPDSTRING; 205 } 206 } 207 208 # Write out new SD file... 209 210 print "Generating $NewSDFile file\n"; 211 open NEWSDFILE, ">$NewSDFile" or die "Error: Can't open $NewSDFile: $! \n"; 212 print NEWSDFILE "$CmpdString\n"; 213 close NEWSDFILE; 214 215 } 216 close SDFILE; 217 } 218 219 # Split SD into files containing specified number of compounds per file... 220 # 221 sub SplitSDFileByNumOfCmpdsPerFile { 222 my($FileIndex) = @_; 223 my($SDFile, $CmpdCount, $MaxCmpdsPerFile, $MaxNumOfFiles); 224 225 $SDFile = $SDFilesList[$FileIndex]; 226 227 if (!open SDFILE, "$SDFile") { 228 warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n"; 229 return; 230 } 231 232 $MaxCmpdsPerFile = $OptionsInfo{NumOfCmpds}; 233 234 # Count number of compounds to figure out maximum number of files... 235 $CmpdCount = 0; 236 while (<SDFILE>) { 237 if (/^\$\$\$\$/) { 238 $CmpdCount++; 239 } 240 } 241 close SDFILE; 242 243 $MaxNumOfFiles = int $CmpdCount / $MaxCmpdsPerFile; 244 245 if (($MaxNumOfFiles * $MaxCmpdsPerFile) < $CmpdCount) { 246 $MaxNumOfFiles++; 247 } 248 249 if ($CmpdCount <= $MaxCmpdsPerFile) { 250 warn "Warning: Ignoring file $SDFile: Total number of compounds, $CmpdCount, is <= specified number of compunds per file, $MaxCmpdsPerFile\n"; 251 return; 252 } 253 254 SplitSDFileByNumOfFilesAndCmpds($FileIndex, $MaxNumOfFiles, $MaxCmpdsPerFile); 255 } 256 257 # Split SD files into specified number of files with specified number of compounds 258 # in each file... 259 # 260 sub SplitSDFileByNumOfFilesAndCmpds { 261 my($FileIndex, $NumOfFiles, $NumOfCmpdsPerFile) = @_; 262 my($SDFile, $CmpdCount, $NewFileIndex, $NewFileName, $MaxCmpdsCount, @NewSDFilesList); 263 264 $SDFile = $SDFilesList[$FileIndex]; 265 266 if (!open SDFILE, "$SDFile") { 267 warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n"; 268 return; 269 } 270 271 # Setup new file names list... 272 @NewSDFilesList = (); 273 for $NewFileIndex (1 .. $NumOfFiles) { 274 $NewFileName = $SDFilesInfo{OutFileRoot}[$FileIndex] . "Part${NewFileIndex}." . $SDFilesInfo{FileExt}[$FileIndex]; 275 if (!$OptionsInfo{OverwriteFiles}) { 276 if (-e $NewFileName) { 277 warn "Warning: Ignoring file $SDFile: New SD file, $NewFileName, already exists\n"; 278 return; 279 } 280 } 281 push @NewSDFilesList, $NewFileName; 282 } 283 284 $MaxCmpdsCount = $NumOfCmpdsPerFile; 285 286 $CmpdCount = 0; 287 $NewFileIndex = 1; 288 289 open NEWSDFILE, ">$NewSDFilesList[$NewFileIndex - 1]" or die "Error: Can't open $NewSDFilesList[$NewFileIndex -1]: $! \n"; 290 print "\nGenerating $NewSDFilesList[$NewFileIndex - 1] file\n"; 291 292 open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n"; 293 294 while (<SDFILE>) { 295 s/(\r\n)|(\r)/\n/g; 296 print NEWSDFILE; 297 298 if ( /^\$\$\$\$/ ) { 299 $CmpdCount++; 300 if ($NewFileIndex <= $NumOfFiles) { 301 if ($CmpdCount >= $MaxCmpdsCount) { 302 if ($NewFileIndex < $NumOfFiles) { 303 close NEWSDFILE; 304 } 305 $NewFileIndex++; 306 $MaxCmpdsCount = $NumOfCmpdsPerFile * $NewFileIndex; 307 308 if ($NewFileIndex <= $NumOfFiles) { 309 open NEWSDFILE, ">$NewSDFilesList[$NewFileIndex - 1]" or die "Error: Can't open $NewSDFilesList[$NewFileIndex - 1]: $! \n"; 310 print "Generating $NewSDFilesList[$NewFileIndex - 1] file...\n"; 311 } 312 } 313 } 314 } 315 } 316 close NEWSDFILE; 317 } 318 319 # Retrieve information about SD files... 320 # 321 sub RetrieveSDFilesInfo { 322 my($SDFile, $Index, $FileDir, $FileName, $FileExt, $OutFileRoot); 323 324 %SDFilesInfo = (); 325 @{$SDFilesInfo{FileOkay}} = (); 326 @{$SDFilesInfo{FileExt}} = (); 327 @{$SDFilesInfo{OutFileRoot}} = (); 328 329 FILELIST: for $Index (0 .. $#SDFilesList) { 330 $SDFile = $SDFilesList[$Index]; 331 332 $SDFilesInfo{FileOkay}[$Index] = 0; 333 $SDFilesInfo{FileExt}[$Index] = ''; 334 $SDFilesInfo{OutFileRoot}[$Index] = ''; 335 336 $SDFile = $SDFilesList[$Index]; 337 if (!(-e $SDFile)) { 338 warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; 339 next FILELIST; 340 } 341 if (!CheckFileType($SDFile, "sd sdf")) { 342 warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; 343 next FILELIST; 344 } 345 346 # Setup output file root... 347 $FileDir = ""; $FileName = ""; $FileExt = ""; 348 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile); 349 350 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) { 351 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot}); 352 if ($RootFileName && $RootFileExt) { 353 $FileName = $RootFileName; 354 } 355 else { 356 $FileName = $OptionsInfo{OutFileRoot}; 357 } 358 $OutFileRoot = $FileName; 359 } 360 else { 361 $OutFileRoot = "$FileName"; 362 } 363 364 $SDFilesInfo{FileOkay}[$Index] = 1; 365 $SDFilesInfo{FileExt}[$Index] = $FileExt; 366 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot; 367 } 368 } 369 370 # Process option values... 371 sub ProcessOptions { 372 %OptionsInfo = (); 373 374 $OptionsInfo{Mode} = $Options{mode}; 375 376 $OptionsInfo{CmpdsMode} = $Options{cmpdsmode}; 377 378 $OptionsInfo{NumOfFiles} = $Options{numfiles}; 379 $OptionsInfo{NumOfCmpds} = $Options{numcmpds}; 380 381 $OptionsInfo{DataField} = ''; 382 if ($Options{mode} =~ /^Cmpds$/i && $Options{cmpdsmode} =~ /^DataField$/i) { 383 if (!$Options{datafield}) { 384 die "Error: You must specify a value for \"-d, --DataField\" option in \"DataField\" value of \"-c, --CmpdsMode\" during \"Cmpds\" \"-m, --mode\" value. \n"; 385 } 386 $OptionsInfo{DataField} = $Options{datafield}; 387 } 388 389 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0; 390 391 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0; 392 } 393 394 395 # Setup script usage and retrieve command line arguments specified using various options... 396 sub SetupScriptUsage { 397 398 # Retrieve all the options... 399 %Options = (); 400 401 $Options{cmpdsmode} = 'RootPrefix'; 402 $Options{mode} = 'Files'; 403 404 $Options{numfiles} = 2; 405 $Options{numcmpds} = 1; 406 407 408 if (!GetOptions(\%Options, "cmpdsmode|c=s", "datafield|d=s", "help|h", "mode|m=s", "numfiles|n=i", "numcmpds=i", "overwrite|o", "root|r=s", "workingdir|w=s")) { 409 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 410 } 411 if ($Options{workingdir}) { 412 if (! -d $Options{workingdir}) { 413 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 414 } 415 chdir $Options{workingdir} or die "Error: Error: Couldn't chdir $Options{workingdir}: $! \n"; 416 } 417 if ($Options{cmpdsmode} !~ /^(DataField|MolName|RootPrefix)$/i) { 418 die "Error: The value specified, $Options{cmpdsmode}, for option \"-c, --CmpdsMode\" is not valid. Allowed values: DataField, MolName, RootPrefix\n"; 419 } 420 if ($Options{mode} !~ /^(Cmpds|Files)$/i) { 421 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: Cmpds, Files\n"; 422 } 423 if ($Options{numfiles} < 2) { 424 die "Error: The value specified, $Options{numfiles}, for option \"-n --numfiles\" is not valid. Allowed values: >= 2 \n"; 425 } 426 if ($Options{numcmpds} < 1) { 427 die "Error: The value specified, $Options{numcmpds}, for option \"-n --numcmpds\" is not valid. Allowed values: >= 1 \n"; 428 } 429 } 430