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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: MolFilesToSD.pl,v $
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4 # $Date: 2015/02/28 20:46:20 $
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5 # $Revision: 1.38 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use SDFileUtil;
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36 use FileUtil;
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37 use TextUtil;
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38
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39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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40
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41 # Autoflush STDOUT
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42 $| = 1;
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43
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44 # Starting message...
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45 $ScriptName = basename $0;
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46 print "\n$ScriptName:Starting...\n\n";
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47 $StartTime = new Benchmark;
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48
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49 # Get the options and setup script...
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50 SetupScriptUsage();
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51 if ($Options{help} || @ARGV < 1) {
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52 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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53 }
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54
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55 my(@MOLFilesList);
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56 @MOLFilesList = ExpandFileNames(\@ARGV, "mol");
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57
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58 # Process options...
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59 print "Processing options...\n";
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60 my(%OptionsInfo);
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61 ProcessOptions();
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62
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63 print "Generating SD file $OptionsInfo{SDFile}...\n";
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64 GenerateSDFile();
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65
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66 print "\n$ScriptName:Done...\n\n";
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67
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68 $EndTime = new Benchmark;
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69 $TotalTime = timediff ($EndTime, $StartTime);
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70 print "Total time: ", timestr($TotalTime), "\n";
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71
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72 ###############################################################################
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73
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74 # Generate a SD file using all valid MDL MOL files...
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75 sub GenerateSDFile {
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76 my($MOLFile, $Index, $FileCount, $FileOkayCount, $MolNameLine, $CmpdID, $FileDir, $FileName, $FileExt);
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77
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78 open SDFILE, ">$OptionsInfo{SDFile}" or die "Error: Can't open $OptionsInfo{SDFile}: $! \n";
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79 $FileCount = 0;
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80 $FileOkayCount = 0;
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81
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82 FILELIST: for $Index (0 .. $#MOLFilesList) {
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83 $MOLFile = $MOLFilesList[$Index];
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84 $FileCount++;
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85
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86 print "Processing file $MOLFile...\n";
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87
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88 if (!(-e $MOLFile)) {
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89 warn "Warning: Ignoring file $MOLFile: It doesn't exist\n";
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90 next FILELIST;
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91 }
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92
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93 if (!CheckFileType($MOLFile, "mol")) {
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94 warn "Warning: Ignoring file $MOLFile: It's not a MDLMOL file\n";
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95 next FILELIST;
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96 }
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97
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98 if (!open MOLFILE, "$MOLFile") {
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99 warn "Warning: Ignoring file $MOLFile: Couldn't open it: $! \n";
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100 next FILELIST;
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101 }
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102
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103 $FileOkayCount++;
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104
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105 if ($OptionsInfo{ModifyData}) {
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106 $MolNameLine = <MOLFILE>;
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107 if ($OptionsInfo{UseFilePrefix}) {
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108 ($FileDir, $FileName, $FileExt) = ParseFileName($MOLFile);
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109 $CmpdID = $FileName;
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110 }
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111 else {
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112 $CmpdID = $OptionsInfo{CompoundID} . "$FileCount";
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113 }
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114
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115 if ($OptionsInfo{AddMolNameLine}) {
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116 print SDFILE "$CmpdID\n";
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117 }
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118 else {
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119 $MolNameLine =~ s/(\r\n)|(\r)/\n/g;
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120 print SDFILE $MolNameLine;
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121 }
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122
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123 while (<MOLFILE>) {
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124 s/(\r\n)|(\r)/\n/g;
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125 print SDFILE;
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126 }
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127
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128 if ($OptionsInfo{AddDataField}) {
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129 print SDFILE "> <$OptionsInfo{DataFieldLabel}>\n${CmpdID}\n";
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130 }
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131 }
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132 else {
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133 while (<MOLFILE>) {
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134 s/(\r\n)|(\r)/\n/g;
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135 print SDFILE;
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136 }
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137 }
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138 print SDFILE "\n\$\$\$\$\n";
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139 close MOLFILE;
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140 }
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141 close SDFILE;
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142
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143 print "\nNumber of files: $FileCount\n";
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144 print "Number of files processed successfully: $FileOkayCount\n";
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145 print "Number of files ignored: " . ($FileCount - $FileOkayCount) . "\n";
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146 }
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147
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148 # Process option values...
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149 sub ProcessOptions {
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150 %OptionsInfo = ();
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151
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152 $OptionsInfo{Mode} = $Options{mode};
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153
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154 $OptionsInfo{CompoundID} = $Options{compoundid};
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155 $OptionsInfo{DataFieldLabel} = $Options{datafieldlabel};
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156
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157 $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
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158 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
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159
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160 $OptionsInfo{AddMolNameLine} = ($Options{mode} =~ /^(molnameline|both)$/i) ? 1 : 0;
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161 $OptionsInfo{AddDataField} = ($Options{mode} =~ /^(datafield|both)$/i) ? 1 : 0;
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162
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163 $OptionsInfo{AddMolNameLine} = ($Options{mode} =~ /^(molnameline|both)$/i) ? 1 : 0;
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164 $OptionsInfo{AddDataField} = ($Options{mode} =~ /^(datafield|both)$/i) ? 1 : 0;
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165
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166 $OptionsInfo{ModifyData} = ($OptionsInfo{AddMolNameLine} || $OptionsInfo{AddDataField}) ? 1 : 0;
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167
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168 $OptionsInfo{UseFilePrefix} = ($Options{compoundid} =~ /^usefileprefix$/i) ? 1 : 0;
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169
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170 # Setup SD file name...
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171 my($FileDir, $FileName, $FileExt, $SDFile);
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172 if ($Options{root}) {
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173 $FileDir = ""; $FileName = ""; $FileExt = "";
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174 ($FileDir, $FileName, $FileExt) = ParseFileName($Options{root});
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175 if ($FileName && $FileExt) {
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176 $SDFile = $FileName;
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177 }
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178 else {
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179 $SDFile = $Options{root};
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180 }
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181 $SDFile .= ".sdf";
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182 }
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183 else {
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184 $FileDir = ""; $FileName = ""; $FileExt = "";
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185 ($FileDir, $FileName, $FileExt) = ParseFileName($MOLFilesList[0]);
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186 $SDFile = $FileName . "1To" . @MOLFilesList . ".sdf";
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187 }
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188
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189 if (!$Options{overwrite}) {
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190 if (-e $SDFile) {
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191 die "Error: The file $SDFile already exists.\n";
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192 }
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193 }
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194 $OptionsInfo{SDFile} = $SDFile;
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195
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196 }
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197
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198 # Setup script usage and retrieve command line arguments specified using various options...
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199 sub SetupScriptUsage {
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200
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201 # Retrieve all the options...
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202 %Options = ();
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203 $Options{compoundid} = "Cmpd";
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204 $Options{datafieldlabel} = "Cmpd_ID";
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205 $Options{mode} = "none";
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206
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207 if (!GetOptions(\%Options, "compoundid|c=s", "datafieldlabel|d=s", "help|h", "mode|m=s", "overwrite|o", "root|r=s", "workingdir|w=s")) {
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208 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
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209 }
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210 if ($Options{workingdir}) {
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211 if (! -d $Options{workingdir}) {
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212 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
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213 }
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214 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
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215 }
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216 if ($Options{mode} !~ /^(molnameline|datafield|both|none)$/i ) {
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217 die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: molnameline, datafield, both, or none\n";
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218 }
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219 }
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220
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221 __END__
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222
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223 =head1 NAME
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224
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225 MolFilesToSD.pl - Generate a SD file from MDLMOL File(s)
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226
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227 =head1 SYNOPSIS
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228
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229 MolFilesToSD.pl MDLMOLFile(s)...
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230
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231 MolFilesToSD.pl [B<-c, --compoundid> usefileprefix | idlabel] [B<-d, --datafieldlabel> fieldlabel]
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232 [B<-h, --help>] [B<-m, --mode> molnameline | datafield | both | none] [B<-o, --overwrite>]
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233 [B<-r, --root> rootname] [B<-w, --workingdir> dirname] MDLMOLFile(s)...
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234
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235 =head1 DESCRIPTION
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236
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237 Generate a SD file from I<MDLMOL File(s)>. Multiple file names are separated by spaces.
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238 The valid file extension is I<.mol>. All other file names are ignored. All the files in a current
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239 directory can be specified by I<*.mol>, or the current directory name.
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240
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241 =head1 OPTIONS
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242
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243 =over 4
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244
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245 =item B<-c, --compoundid> I<usefileprefix | idlabel>
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246
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247 Specify how to generate compound IDs: use MOL filename prefix or generate
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248 a new compound ID by combining I<idlabel> with compound number. Possible
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249 values: I<usefileprefix | idlabel>. By default, I<Cmd> is used as a I<idlabel> to generate
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250 these types of compound IDs: Cmpd1, Cmpd2 and so on.
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251
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252 Example: To generate compound IDs like Mol_ID1, Mol_ID2 and so on, specify
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253 "MolID" value for this option.
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254
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255 =item B<-d, --datafieldlabel> I<fieldlabel>
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256
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257 Specify data field label for adding compound ID field into SD file during I<datafield | both>
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258 values of B<-m, --mode> option. Default: <Cmpd_ID>.
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259
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260 =item B<-h, --help>
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261
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262 Print this help message.
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263
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264 =item B<-m, --mode> I<molnameline | datafield | both | none>
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265
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266 Specify how to add compopund ID into SD file: relplace the molname line,
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267 add a new data field, replace the molname line and add data field, or do
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268 nothing. Possible values: I<molnameline | datafield | both | none>.
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269 Default: I<nothing>.
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270
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271 Use B<-c, --compoundid> to specify compound ID generation process.
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272
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273 =item B<-o, --overwrite>
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274
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275 Overwrite existing files.
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276
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277 =item B<-r, --root> I<rootname>
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278
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279 New SD file name is generated using the root: <Root>.sdf. Default new file
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280 name: <InitialMOLFileName>1To<Count>.sdf.
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281
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282 =item B<-w, --workingdir> I<dirname>
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283
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284 Location of working directory. Default: current directory.
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285
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286 =back
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287
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288 =head1 EXAMPLES
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289
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290 To generate NewSample.sdf file from Sample*.mol files, type:
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291
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292 % MolFilesToSD.pl -r NewSample -o Sample*.mol
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293
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294 To generate NewSample.sdf with Cmpd1, Cmpd2 and so on as compound ID in
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295 MolName line and Cmpd_ID datafield from Sample*.mol files, type:
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296
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297 % MolFilesToSD.pl -r NewSample -m both -o Sample*.mol
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298
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299 =head1 AUTHOR
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300
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301 Manish Sud <msud@san.rr.com>
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302
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303 =head1 SEE ALSO
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304
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305 InfoSDFiles.pl, SDToMolFiles.pl
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306
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307 =head1 COPYRIGHT
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308
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309 Copyright (C) 2015 Manish Sud. All rights reserved.
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310
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311 This file is part of MayaChemTools.
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312
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313 MayaChemTools is free software; you can redistribute it and/or modify it under
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314 the terms of the GNU Lesser General Public License as published by the Free
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315 Software Foundation; either version 3 of the License, or (at your option)
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316 any later version.
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317
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318 =cut
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