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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: SDToMolFiles.pl,v $
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4 # $Date: 2015/02/28 20:46:20 $
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5 # $Revision: 1.35 $
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6 #
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7 # Author: Manish Sud <msud@san.rr.com>
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8 #
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9 # Copyright (C) 2015 Manish Sud. All rights reserved.
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10 #
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11 # This file is part of MayaChemTools.
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12 #
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13 # MayaChemTools is free software; you can redistribute it and/or modify it under
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14 # the terms of the GNU Lesser General Public License as published by the Free
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15 # Software Foundation; either version 3 of the License, or (at your option) any
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16 # later version.
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17 #
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18 # MayaChemTools is distributed in the hope that it will be useful, but without
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19 # any warranty; without even the implied warranty of merchantability of fitness
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20 # for a particular purpose. See the GNU Lesser General Public License for more
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21 # details.
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22 #
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23 # You should have received a copy of the GNU Lesser General Public License
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24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
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25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
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26 # Boston, MA, 02111-1307, USA.
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27 #
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28
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29 use strict;
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30 use FindBin; use lib "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use SDFileUtil;
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36 use FileUtil;
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37
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38 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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39
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40 # Autoflush STDOUT
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41 $| = 1;
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42
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43 # Starting message...
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44 $ScriptName = basename $0;
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45 print "\n$ScriptName:Starting...\n\n";
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46 $StartTime = new Benchmark;
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47
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48 # Get the options and setup script...
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49 SetupScriptUsage();
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50 if ($Options{help} || @ARGV < 1) {
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51 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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52 }
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53
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54 my(@SDFilesList);
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55 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
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56
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57 # Process options...
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58 print "Processing options...\n";
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59 my(%OptionsInfo);
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60 ProcessOptions();
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61
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62 # Setup information about input files...
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63 print "Checking input SD file(s)...\n";
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64 my(%SDFilesInfo);
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65 RetrieveSDFilesInfo();
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66
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67 # Process input files..
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68 my($FileIndex);
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69 if (@SDFilesList > 1) {
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70 print "\nProcessing SD files...\n";
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71 }
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72 for $FileIndex (0 .. $#SDFilesList) {
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73 if ($SDFilesInfo{FileOkay}[$FileIndex]) {
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74 print "\nProcessing file $SDFilesList[$FileIndex]...\n";
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75 GenerateMolFiles($FileIndex);
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76 }
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77 }
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78 print "\n$ScriptName:Done...\n\n";
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79
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80 $EndTime = new Benchmark;
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81 $TotalTime = timediff ($EndTime, $StartTime);
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82 print "Total time: ", timestr($TotalTime), "\n";
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83
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84 ###############################################################################
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85
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86 # Generate MOL files for a SD file...
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87 #
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88 sub GenerateMolFiles {
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89 my($FileIndex) = @_;
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90 my($SDFile, $MOLFile, $MOLFileRoot, $OutFileRoot, $OverwriteFiles, $UseDataField, $DataFieldName, $UseMolName, $CmpdCount, $MolEndDelimiter, $CmpdString, @CmpdLines, %DataFieldValues);
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91
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92 $SDFile = $SDFilesList[$FileIndex];
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93
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94 if (!open SDFILE, "$SDFile") {
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95 warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
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96 return;
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97 }
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98
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99 $CmpdCount = 0;
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100 $MolEndDelimiter = "M END";
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101
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102 $OutFileRoot = $SDFilesInfo{OutFileRoot}[$FileIndex];
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103 $OverwriteFiles = $OptionsInfo{OverwriteFiles};
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104
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105 $UseDataField = ($OptionsInfo{Mode} =~ /^DataField$/i) ? 1 : 0;
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106 $DataFieldName = $OptionsInfo{DataField};
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107
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108 $UseMolName = ($OptionsInfo{Mode} =~ /^MolName$/i) ? 1 : 0;
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109
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110 CMPDSTRING: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
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111 $CmpdCount++;
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112
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113 # Setup MOL file name...
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114 $MOLFileRoot = '';
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115 if ($UseDataField) {
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116 @CmpdLines = split "\n", $CmpdString;
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117 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
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118 if (exists $DataFieldValues{$DataFieldName}) {
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119 $MOLFileRoot = $DataFieldValues{$DataFieldName};
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120 }
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121 }
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122 elsif ($UseMolName) {
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123 @CmpdLines = split "\n", $CmpdString;
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124 $MOLFileRoot = $CmpdLines[0];
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125 }
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126
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127 # Check for any invalid file name characters in data field or molname values...
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128 if ($MOLFileRoot && $MOLFileRoot =~ /[^a-zA-Z0-9_]/) {
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129 $MOLFileRoot =~ s/[^a-zA-Z0-9_]//g;
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130 }
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131 # Fall back plan for MOL file name...
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132 if (!$MOLFileRoot) {
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133 $MOLFileRoot = "${OutFileRoot}Cmpd${CmpdCount}";
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134 }
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135
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136 $MOLFile = "${MOLFileRoot}.mol";
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137
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138 if (!$OverwriteFiles) {
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139 if (-e $MOLFile) {
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140 warn "Warning: Ignoring compound number, $CmpdCount, in $SDFile: New MOL file, $MOLFile, already exists\n";
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141 next CMPDSTRING;
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142 }
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143 }
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144
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145 if (!($CmpdString =~ /$MolEndDelimiter/)) {
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146 warn "Warning: Ignoring compound number, $CmpdCount, in $SDFile: Invalid compound data\n";
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147 next CMPDSTRING;
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148 }
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149
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150 # Write out MOL file...
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151
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152 print "Generating $MOLFile file...\n";
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153 open MOLFILE, ">$MOLFile" or die "Error: Can't open $MOLFile: $! \n";
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154 ($CmpdString) = split "$MolEndDelimiter", $CmpdString;
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155 print MOLFILE "$CmpdString";
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156 print MOLFILE "$MolEndDelimiter\n";
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157 close MOLFILE;
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158
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159 }
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160
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161 close SDFILE;
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162 }
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163
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164 # Retrieve information about SD files...
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165 #
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166 sub RetrieveSDFilesInfo {
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167 my($SDFile, $Index, $FileDir, $FileName, $FileExt, $OutFileRoot);
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168
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169 %SDFilesInfo = ();
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170 @{$SDFilesInfo{FileOkay}} = ();
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171 @{$SDFilesInfo{OutFileRoot}} = ();
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172
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173 FILELIST: for $Index (0 .. $#SDFilesList) {
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174 $SDFile = $SDFilesList[$Index];
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175
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176 $SDFilesInfo{FileOkay}[$Index] = 0;
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177 $SDFilesInfo{OutFileRoot}[$Index] = '';
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178
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179 $SDFile = $SDFilesList[$Index];
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180 if (!(-e $SDFile)) {
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181 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
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182 next FILELIST;
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183 }
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184 if (!CheckFileType($SDFile, "sd sdf")) {
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185 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
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186 next FILELIST;
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187 }
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188
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189 # Setup output file root...
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190 $FileDir = ""; $FileName = ""; $FileExt = "";
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191 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
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192
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193 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
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194 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
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195 if ($RootFileName && $RootFileExt) {
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196 $FileName = $RootFileName;
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197 }
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198 else {
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199 $FileName = $OptionsInfo{OutFileRoot};
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200 }
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201 $OutFileRoot = $FileName;
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202 }
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203 else {
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204 $OutFileRoot = "$FileName";
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205 }
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206
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207 $SDFilesInfo{FileOkay}[$Index] = 1;
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208 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
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209 }
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210 }
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211
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212 # Process option values...
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213 sub ProcessOptions {
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214 %OptionsInfo = ();
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215
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216 $OptionsInfo{Mode} = $Options{mode};
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217
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218 $OptionsInfo{DataField} = '';
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219 if ($Options{mode} =~ /^DataField$/i) {
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220 if (!$Options{datafield}) {
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221 die "Error: You must specify a value for \"-d, --DataField\" option in \"DataField\" \"-m, --mode\". \n";
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222 }
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223 $OptionsInfo{DataField} = $Options{datafield};
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224 }
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225
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226 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
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227
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228 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
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229 }
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230
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231 # Setup script usage and retrieve command line arguments specified using various options...
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232 sub SetupScriptUsage {
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233
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234 # Retrieve all the options...
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235 %Options = ();
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236
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237 $Options{mode} = 'RootPrefix';
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238
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239 if (!GetOptions(\%Options, "datafield|d=s", "help|h", "mode|m=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
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240 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
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241 }
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242 if ($Options{workingdir}) {
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243 if (! -d $Options{workingdir}) {
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244 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
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245 }
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246 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
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247 }
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248
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249 if ($Options{mode} !~ /^(DataField|MolName|RootPrefix)$/i) {
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250 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: DataField, MolName, RootPrefix\n";
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251 }
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252 }
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253
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254 __END__
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255
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256 =head1 NAME
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257
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258 SDToMolFiles.pl - Generate MDLMOL file(s) from SD file(s)
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259
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260 =head1 SYNOPSIS
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261
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262 SDToMolFiles.pl SDFile(s)...
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263
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264 SDToMolFiles.pl [B<-d, --DataField> DataFieldName]
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265 [B<-m, --mode> DataField | MolName | RootPrefix] [B<-h, --help>]
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266 [B<-o, --overwrite>] [B<-r, --root> rootname]
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267 [B<-w, --workingdir> dirname] SDFile(s)...
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268
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269 =head1 DESCRIPTION
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270
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271 Generate MDLMOL file(s) from I<SDFile(s)>. All header data labels and values in
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272 SDFile(s) are simply ignored; other appopriate data from SDFile(s) is transferred to MDLMOL
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273 files. Multiple I<SDFile(s)> names are separated by spaces. The valid file extensions are
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274 I<.sdf> and I<.sd>. All other file names are ignored. All the SD files in a current
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275 directory can be specified either by I<*.sdf> or the current directory name.
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276
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277 =head1 OPTIONS
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278
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279 =over 4
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280
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281 =item B<-d, --DataField> I<DataFieldName>
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282
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283 Specify I<SDFile(s)> datafield label name whose value is used for generation of MDLMOL
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284 file names. Default value: I<None>.
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285
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286 =item B<-h, --help>
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287
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288 Print this help message.
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289
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290 =item B<-m, --mode> I<DataField | MolName | RootPrefix>
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291
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292 Specify how to generate MDLMOL file names: use a I<SDFile(s)> datafield value; use
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293 molname line from I<SDFile(s)>; generate a sequential ID using root prefix specified
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294 by B<-r, --root> option.
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295
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296 Possible values: I<DataField | MolName | RootPrefix | RootPrefix>.
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297 Default: I<RootPrefix>.
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298
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299 For empty I<MolName> and I<DataField> values during these specified modes, file
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300 name is automatically generated using I<RootPrefix>.
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301
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302 For I<RootPrefix> value of B<-m, --mode> option, MDLMOL file names are generated
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303 using by appending compound record number to value of B<-r, --root> option. For
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304 example: I<RootName>Cmd<RecordNumber>.mol.
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305
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306 Allowed characters in file names are: a-zA-Z0-9_. All other characters in datafield
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307 values, molname line, and root prefix are ignore during generation of file names.
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308
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309 =item B<-o, --overwrite>
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310
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311 Overwrite existing files.
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312
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313 =item B<-r, --root> I<rootname>
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314
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315 Specify root name to used during I<RootPrefix> B<-m, --mode> option value.
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316 New MDLMOL file names are generated using the root: <Root>Cmpd<RecordNumber>.mol
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317 Default for new file names: <InitialSDFileName>Cmpd<RecordNumber>.mol. This option
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318 is ignored for multiple input files.
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319
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320 =item B<-w, --workingdir> I<dirname>
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321
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322 Location of working directory. Default: current directory.
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323
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324 =back
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325
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326 =head1 EXAMPLES
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327
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328 To generate MDLMOL files from Sample1*.sdf and Sample2*.sd files, type:
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329
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330 % SDToMolFiles.pl -o Sample1*.sdf Sample2*.sd
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331
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332 To generate Sample*.mol files from Sample1.sdf, type:
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333
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334 % SDToMolFiles.pl -r Sample -o Sample1.sdf
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335
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336 To generate MOL files from Sample1.sdf using molname line data for generating
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337 MOL file names, type:
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338
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339 % SDToMolFiles.pl -m MolName -r Sample -o Sample1.sdf
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340
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341 To generate MOL files from Sample1.sdf using a specific data field values for
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342 generating MOL file names, type:
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343
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344 % SDToMolFiles.pl -m DataField --DataField MolID -r Sample
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345 -o Sample1.sdf
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346
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347 =head1 AUTHOR
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348
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349
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350 =head1 AUTHOR
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351
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352 Manish Sud <msud@san.rr.com>
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353
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354 =head1 SEE ALSO
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355
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356 InfoSDFiles.pl, MolFilesToSD.pl
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357
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358 =head1 COPYRIGHT
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359
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360 Copyright (C) 2015 Manish Sud. All rights reserved.
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361
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362 This file is part of MayaChemTools.
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363
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364 MayaChemTools is free software; you can redistribute it and/or modify it under
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365 the terms of the GNU Lesser General Public License as published by the Free
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366 Software Foundation; either version 3 of the License, or (at your option)
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367 any later version.
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368
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369 =cut
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