1 #!/usr/bin/perl -w 2 # 3 # $RCSfile: ModifySDFilesDataFields.pl,v $ 4 # $Date: 2015/02/28 20:46:20 $ 5 # $Revision: 1.27 $ 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 "$FindBin::Bin/../lib"; 31 use Getopt::Long; 32 use File::Basename; 33 use Text::ParseWords; 34 use Benchmark; 35 use FileUtil; 36 use SDFileUtil; 37 use TextUtil; 38 39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime); 40 41 # Autoflush STDOUT 42 $| = 1; 43 44 # Starting message... 45 $ScriptName = basename($0); 46 print "\n$ScriptName: Starting...\n\n"; 47 $StartTime = new Benchmark; 48 49 # Get the options and setup script... 50 SetupScriptUsage(); 51 if ($Options{help} || @ARGV < 1) { 52 die GetUsageFromPod("$FindBin::Bin/$ScriptName"); 53 } 54 55 my(@SDFilesList); 56 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd"); 57 58 # Process options... 59 print "Processing options...\n"; 60 my(%OptionsInfo); 61 ProcessOptions(); 62 63 print "Checking input SD file(s)...\n"; 64 my(%SDFilesInfo); 65 RetrieveSDFilesInfo(); 66 67 # Generate output files... 68 my($FileIndex); 69 if (@SDFilesList > 1) { 70 print "\nProcessing SD files...\n"; 71 } 72 for $FileIndex (0 .. $#SDFilesList) { 73 if ($SDFilesInfo{FileOkay}[$FileIndex]) { 74 print "\nProcessing file $SDFilesList[$FileIndex]...\n"; 75 ModifySDFile($FileIndex); 76 } 77 } 78 print "\n$ScriptName:Done...\n\n"; 79 80 $EndTime = new Benchmark; 81 $TotalTime = timediff ($EndTime, $StartTime); 82 print "Total time: ", timestr($TotalTime), "\n"; 83 84 ############################################################################### 85 86 # Modify SD file data fields.... 87 sub ModifySDFile { 88 my($Index) = @_; 89 my($SDFile, $NewSDFile); 90 91 $SDFile = $SDFilesList[$Index]; 92 $NewSDFile = $SDFilesInfo{OutFile}[$Index]; 93 94 print "Generating new SD file $NewSDFile...\n"; 95 open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n"; 96 open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n"; 97 98 my($CmpdCount, $CmpdString, $CmpdData, $MolName, $OldSDField, $NewSDField, $CommonSDField, $Label, $Value, $FieldValues, $MolNameDataField, $URLCmpdIdFieldName, @CmpdLines, %DataFieldAndValues, @DataFieldLabels); 99 $CmpdCount = 0; 100 101 COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) { 102 $CmpdCount++; 103 @CmpdLines = split "\n", $CmpdString; 104 if ($OptionsInfo{UseDataFieldForMolName} || $OptionsInfo{ModifyDataFields}) { 105 %DataFieldAndValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines); 106 } 107 if ($OptionsInfo{ModifyMolName}) { 108 if ($OptionsInfo{AlwaysReplaceMolName} || !IsNotEmpty($CmpdLines[0])) { 109 $MolNameDataField = $OptionsInfo{MolNameDataField}; 110 if ($OptionsInfo{UseDataFieldForMolName} && exists($DataFieldAndValues{$MolNameDataField})) { 111 $MolName = $DataFieldAndValues{$MolNameDataField}; 112 if (length($MolName) > 80) { 113 $MolName = substr($MolName, 0, 80); 114 } 115 } 116 else { 117 $MolName = "$OptionsInfo{MolNamePrefix}${CmpdCount}"; 118 } 119 $CmpdLines[0] = $MolName; 120 $CmpdString = join "\n", @CmpdLines; 121 } 122 } 123 if (!$OptionsInfo{ModifyDataFields}) { 124 # Just write the data and get the next compound... 125 print NEWSDFILE "$CmpdString\n"; 126 next COMPOUND; 127 } 128 # Write out the structure data now and handle the old data fields later... 129 ($CmpdData) = split /\n>/, $CmpdString; 130 print NEWSDFILE "$CmpdData\n"; 131 132 # Modify specified data fields... 133 for $NewSDField (sort keys %{$OptionsInfo{SpecifiedNewToOldSDFieldMap}}) { 134 $FieldValues = ""; 135 for $OldSDField (@{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}}) { 136 if (exists($DataFieldAndValues{$OldSDField}) && length($DataFieldAndValues{$OldSDField})) { 137 $Value = $DataFieldAndValues{$OldSDField}; 138 $FieldValues .= ($FieldValues) ? "\n$Value" : $Value; 139 } 140 } 141 print NEWSDFILE "> <$NewSDField>\n$FieldValues\n\n"; 142 } 143 # Add specified common fields... 144 for $CommonSDField (sort keys %{$OptionsInfo{SpecifiedCommonFieldMap}}) { 145 $Value = $OptionsInfo{SpecifiedCommonFieldMap}{$CommonSDField}; 146 print NEWSDFILE "> <$CommonSDField>\n$Value\n\n"; 147 } 148 if ($OptionsInfo{CreateDataFieldURL}) { 149 $Value = ""; 150 $URLCmpdIdFieldName = $OptionsInfo{URLCmpdIdFieldName}; 151 if (exists($DataFieldAndValues{$URLCmpdIdFieldName}) && length($DataFieldAndValues{$URLCmpdIdFieldName})) { 152 $Value = $DataFieldAndValues{$URLCmpdIdFieldName}; 153 $Value = "$OptionsInfo{URLCGIScriptName}?$OptionsInfo{URLParamName}=${Value}"; 154 } 155 print NEWSDFILE "> <$OptionsInfo{URLDataFieldLabel}>\n$Value\n\n"; 156 } 157 158 # Handle old data fields and write 'em in the same order as they appear in the input 159 # files... 160 if ($OptionsInfo{KeepAllOldDataFields} || $OptionsInfo{KeepUnMappedOldDataFields}) { 161 my($KeepLabel); 162 @DataFieldLabels = GetCmpdDataHeaderLabels(\@CmpdLines); 163 LABEL: for $Label (@DataFieldLabels) { 164 $KeepLabel = $OptionsInfo{KeepAllOldDataFields} ? 1 : ( exists($OptionsInfo{SpecifiedOldToNewSDFieldMap}{$Label}) ? 0 : 1 ); 165 if (!$KeepLabel) { 166 next LABEL; 167 } 168 $Value = $DataFieldAndValues{$Label}; 169 print NEWSDFILE "> <$Label>\n$Value\n\n"; 170 } 171 } 172 173 print NEWSDFILE "\$\$\$\$\n"; 174 } 175 close NEWSDFILE; 176 close SDFILE; 177 } 178 179 # Process option values... 180 sub ProcessOptions { 181 %OptionsInfo = (); 182 183 $OptionsInfo{Mode} = $Options{mode}; 184 185 $OptionsInfo{ModifyMolName} = 1; $OptionsInfo{ModifyDataFields} = 0; 186 if ($Options{mode} =~ /^both$/i) { 187 $OptionsInfo{ModifyMolName} = 1; $OptionsInfo{ModifyDataFields} = 1; 188 } 189 elsif ($Options{mode} =~ /^datafields$/i) { 190 $OptionsInfo{ModifyMolName} = 0; $OptionsInfo{ModifyDataFields} = 1; 191 } 192 193 $OptionsInfo{KeepOldDataFields} = $Options{keepolddatafields}; 194 $OptionsInfo{KeepAllOldDataFields} = ($Options{keepolddatafields} =~ /^all$/i) ? 1 : 0; 195 $OptionsInfo{KeepUnMappedOldDataFields} = ($Options{keepolddatafields} =~ /^unmappedonly$/i) ? 1 : 0; 196 197 $OptionsInfo{MolNameMode} = $Options{molnamemode}; 198 $OptionsInfo{UseDataFieldForMolName} = ($Options{molnamemode} =~ /^datafield$/i) ? 1 : 0; 199 200 $OptionsInfo{MolName} = $Options{molname}; 201 $OptionsInfo{MolNameDataField} = ""; $OptionsInfo{MolNamePrefix} = "Cmpd"; 202 if ($Options{molname}) { 203 if ($OptionsInfo{UseDataFieldForMolName}) { 204 $OptionsInfo{MolNameDataField} = $Options{molname}; 205 } 206 else { 207 $OptionsInfo{MolNamePrefix} = $Options{molname}; 208 } 209 } 210 211 $OptionsInfo{MolNameReplace} = $Options{molnamereplace}; 212 $OptionsInfo{AlwaysReplaceMolName} = ($Options{molnamereplace} =~ /^always$/i) ? 1 : 0; 213 214 if ($Options{datafieldsmap} && $Options{datafieldsmapfile}) { 215 die "Error: Both \"--datafieldsmap\" and \"--datafieldsmapfile\" options specified: only one is allowed at a time\n"; 216 } 217 218 $OptionsInfo{DataFieldsMap} = $Options{datafieldsmap} ? $Options{datafieldsmap} : ''; 219 $OptionsInfo{DataFieldsMapFile} = $Options{datafieldsmapfile} ? $Options{datafieldsmapfile} : ''; 220 221 my($SpecifiedDataFieldMap); 222 223 %{$OptionsInfo{SpecifiedNewToOldSDFieldMap}} = (); 224 %{$OptionsInfo{SpecifiedOldToNewSDFieldMap}} = (); 225 226 $SpecifiedDataFieldMap = ""; 227 if ($Options{datafieldsmap}) { 228 $SpecifiedDataFieldMap = $Options{datafieldsmap}; 229 } 230 elsif ($Options{datafieldsmapfile}) { 231 my($Line, @LineWords); 232 open DATAFIELDSFILE, "$Options{datafieldsmapfile}" or die "Couldn't open $Options{datafieldsmapfile}: $! \n"; 233 while ($Line = GetTextLine(\*DATAFIELDSFILE)) { 234 @LineWords = quotewords(";", 0, $Line); 235 $SpecifiedDataFieldMap .= JoinWords(\@LineWords, ";", 0); 236 } 237 close DATAFIELDSFILE; 238 } 239 240 if ($SpecifiedDataFieldMap) { 241 my($DataFieldMap, $DataField, $NewSDField, @OldSDFields, @DataFieldMapSplit, @DataFieldsSplit, $FirstField); 242 @DataFieldMapSplit = split ";", $SpecifiedDataFieldMap; 243 for $DataFieldMap (@DataFieldMapSplit) { 244 @DataFieldsSplit = split ",", $DataFieldMap; 245 if (@DataFieldsSplit == 1) { 246 die "Error: Invalid number of comma delimited values, ", scalar(@DataFieldsSplit), ", specified, @DataFieldsSplit, using \"--datafieldsmap or --datafieldsmapfile\" option: it must contain more than one value.\n"; 247 } 248 $FirstField = 1; 249 @OldSDFields = (); 250 for $DataField (@DataFieldsSplit) { 251 if (!(defined($DataField) && length($DataField))) { 252 die "Error: One of the comma delimited values, \"", join(",", @DataFieldsSplit), "\", specified using \"--datafieldsmap or --datafieldsmapfile\" option is empty.\n"; 253 } 254 if ($FirstField) { 255 $FirstField = 0; 256 $NewSDField = $DataField; 257 } 258 else { 259 push @OldSDFields, $DataField; 260 } 261 } 262 # Make sure a datafield is only specified once... 263 if (exists $OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}) { 264 die "Error: New data field, $NewSDField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n"; 265 } 266 @{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}} = (); 267 push @{$OptionsInfo{SpecifiedNewToOldSDFieldMap}{$NewSDField}}, @OldSDFields; 268 for $DataField (@OldSDFields) { 269 if (exists $OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataField} ) { 270 die "Error: SD field, $DataField, specified more than once using \"--datafieldsmap or --datafieldsmapfile\" option.\n"; 271 } 272 else { 273 $OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataField} = $NewSDField; 274 } 275 } 276 277 } 278 } 279 280 $OptionsInfo{DataFieldsCommon} = $Options{datafieldscommon} ? $Options{datafieldscommon} : ''; 281 %{$OptionsInfo{SpecifiedCommonFieldMap}} = (); 282 283 if ($Options{datafieldscommon}) { 284 my($DataFieldName, $DataFieldValue, $Index, @CommonDataFieldsSplit); 285 @CommonDataFieldsSplit = split ",", $Options{datafieldscommon}; 286 if (@CommonDataFieldsSplit % 2) { 287 die "Error: Invalid number of comma delimited values, ", scalar(@CommonDataFieldsSplit), ", specified \"", join(",", @CommonDataFieldsSplit), "\" using \"--datafieldscommon\" option: it must contain even number of values.\n"; 288 } 289 for ($Index = 0; $Index < @CommonDataFieldsSplit; $Index += 2) { 290 $DataFieldName = $CommonDataFieldsSplit[$Index]; 291 $DataFieldValue = $CommonDataFieldsSplit[$Index + 1]; 292 if (exists $OptionsInfo{SpecifiedCommonFieldMap}{$DataFieldName}) { 293 die "Error: Common data field, $DataFieldName, specified more than once using \"--datafieldscommon\" option.\n"; 294 } 295 if (exists($OptionsInfo{SpecifiedNewToOldSDFieldMap}{$DataFieldName}) || exists($OptionsInfo{SpecifiedOldToNewSDFieldMap}{$DataFieldName})) { 296 die "Error: Common data field, $DataFieldName, specified using \"--datafieldscommon\" option cannot be specified in \"--datafieldsmap or --datafieldsmapfile\" option.\n"; 297 } 298 $OptionsInfo{SpecifiedCommonFieldMap}{$DataFieldName} = $DataFieldValue; 299 } 300 } 301 302 $OptionsInfo{DataFieldURL} = $Options{datafieldurl} ? $Options{datafieldurl} : ''; 303 $OptionsInfo{CreateDataFieldURL} = (exists($Options{datafieldurl}) && length($Options{datafieldurl}) ) ? 1 : 0; 304 305 $OptionsInfo{URLDataFieldLabel} = ""; $OptionsInfo{URLCGIScriptName} = ""; 306 $OptionsInfo{URLParamName} = ""; $OptionsInfo{URLCmpdIdFieldName} = ""; 307 308 if ($OptionsInfo{CreateDataFieldURL}) { 309 my(@DataFieldURLSplit, $Value); 310 @DataFieldURLSplit = split ",", $Options{datafieldurl}; 311 if (@DataFieldURLSplit != 4) { 312 die "Error: Invalid number of values, ", scalar(@DataFieldURLSplit), ", specified using \"--datafieldURL\" option: it must contain 4 values.\n"; 313 } 314 for $Value (@DataFieldURLSplit) { 315 if (!IsNotEmpty($Value)) { 316 die "Error: One of the values, $Options{datafieldurl}, specified using \"--datafieldURL\" option is empty.\n"; 317 } 318 } 319 $OptionsInfo{URLDataFieldLabel} = $DataFieldURLSplit[0]; 320 $OptionsInfo{URLCGIScriptName} = $DataFieldURLSplit[1]; 321 $OptionsInfo{URLParamName} = $DataFieldURLSplit[2]; 322 $OptionsInfo{URLCmpdIdFieldName} = $DataFieldURLSplit[3]; 323 } 324 325 } 326 327 # Retrieve information about input SD files... 328 sub RetrieveSDFilesInfo { 329 my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot, $OutFile, $DataFieldName); 330 331 %SDFilesInfo = (); 332 @{$SDFilesInfo{FileOkay}} = (); 333 @{$SDFilesInfo{OutFile}} = (); 334 335 FILELIST: for $Index (0 .. $#SDFilesList) { 336 $SDFile = $SDFilesList[$Index]; 337 338 $SDFilesInfo{FileOkay}[$Index] = 0; 339 $SDFilesInfo{OutFile}[$Index] = ''; 340 341 if (!(-e $SDFile)) { 342 warn "Warning: Ignoring file $SDFile: It doesn't exist\n"; 343 next FILELIST; 344 } 345 if (!CheckFileType($SDFile, "sd sdf")) { 346 warn "Warning: Ignoring file $SDFile: It's not a SD file\n"; 347 next FILELIST; 348 } 349 $FileDir = ""; $FileName = ""; $FileExt = ""; 350 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile); 351 if ($Options{root} && (@SDFilesList == 1)) { 352 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root}); 353 if ($RootFileName && $RootFileExt) { 354 $FileName = $RootFileName; 355 } 356 else { 357 $FileName = $Options{root}; 358 } 359 $OutFileRoot = $FileName; 360 } 361 else { 362 $OutFileRoot = $FileName . "ModifiedDataFields"; 363 } 364 365 $OutFile = $OutFileRoot . ".$FileExt"; 366 if (lc($OutFile) eq lc($SDFile)) { 367 warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n"; 368 next FILELIST; 369 } 370 if (!$Options{overwrite}) { 371 if (-e $OutFile) { 372 warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n"; 373 next FILELIST; 374 } 375 } 376 377 $SDFilesInfo{FileOkay}[$Index] = 1; 378 $SDFilesInfo{OutFile}[$Index] = $OutFile; 379 } 380 } 381 382 # Setup script usage and retrieve command line arguments specified using various options... 383 sub SetupScriptUsage { 384 385 # Retrieve all the options... 386 %Options = (); 387 $Options{detail} = 1; 388 $Options{keepolddatafields} = "none"; 389 $Options{mode} = "molname"; 390 $Options{molnamemode} = "labelprefix"; 391 $Options{molnamereplace} = "empty"; 392 393 if (!GetOptions(\%Options, "detail|d=i", "datafieldscommon=s", "datafieldsmap=s", "datafieldsmapfile=s", "datafieldurl=s", "help|h", "keepolddatafields|k=s", "mode|m=s", "molname=s", "molnamemode=s", "molnamereplace=s", "overwrite|o", "root|r=s", "workingdir|w=s")) { 394 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"; 395 } 396 if ($Options{workingdir}) { 397 if (! -d $Options{workingdir}) { 398 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"; 399 } 400 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n"; 401 } 402 if ($Options{keepolddatafields} !~ /^(all|unmappedonly|none)$/i) { 403 die "Error: The value specified, $Options{keepolddatafields}, for option \"-k --keepolddatafields\" is not valid. Allowed values: all, unmappedonly, or none\n"; 404 } 405 if ($Options{mode} !~ /^(molname|datafields|both)$/i) { 406 die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: molname, datafields, or both\n"; 407 } 408 if ($Options{molnamemode} !~ /^(datafield|labelprefix)$/i) { 409 die "Error: The value specified, $Options{molnamemode}, for option \"--molnamemode\" is not valid. Allowed values: datafield or labelprefix\n"; 410 } 411 if ($Options{molnamereplace} !~ /^(always|empty)$/i) { 412 die "Error: The value specified, $Options{molnamereplace}, for option \"--molnamereplace\" is not valid. Allowed values: always or empty\n"; 413 } 414 if (!IsPositiveInteger($Options{detail})) { 415 die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n"; 416 } 417 } 418