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<html> <head> <title>MayaChemTools:Code:SplitSDFiles.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> 1 #!/usr/bin/perl -w 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: SplitSDFiles.pl,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:46:21 $</span> 5 <span class="c"># $Revision: 1.36 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">"$FindBin::Bin/../lib"</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span> 36 37 <span class="k">my</span><span class="s">(</span><span class="i">$ScriptName</span><span class="cm">,</span> <span class="i">%Options</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="cm">,</span> <span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$TotalTime</span><span class="s">)</span><span class="sc">;</span> 38 39 <span class="c"># Autoflush STDOUT</span> 40 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span> 41 42 <span class="c"># Starting message...</span> 43 <span class="i">$ScriptName</span> = <span class="w">basename</span> <span class="i">$0</span><span class="sc">;</span> 44 <span class="k">print</span> <span class="q">"\n$ScriptName:Starting...\n\n"</span><span class="sc">;</span> 45 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 46 47 <span class="c"># Get the options and setup script...</span> 48 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 49 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 50 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">"$FindBin::Bin/$ScriptName"</span><span class="s">)</span><span class="sc">;</span> 51 <span class="s">}</span> 52 53 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span> 54 <span class="i">@SDFilesList</span> = <span class="i">ExpandFileNames</span><span class="s">(</span>\<span class="i">@ARGV</span><span class="cm">,</span> <span class="q">"sdf sd"</span><span class="s">)</span><span class="sc">;</span> 55 56 <span class="c"># Process options...</span> 57 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span> 58 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span> 59 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 60 61 <span class="c"># Setup information about input files...</span> 62 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span> 63 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span> 64 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 65 66 <span class="c"># Process input files..</span> 67 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 68 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 69 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span> 70 <span class="s">}</span> 71 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 72 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span> 73 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span> 74 <span class="i">SplitSDFile</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 75 <span class="s">}</span> 76 <span class="s">}</span> 77 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span> 78 79 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span> 80 <span class="i">$TotalTime</span> = <span class="w">timediff</span> <span class="s">(</span><span class="i">$EndTime</span><span class="cm">,</span> <span class="i">$StartTime</span><span class="s">)</span><span class="sc">;</span> 81 <span class="k">print</span> <span class="q">"Total time: "</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span> 82 83 <span class="c">###############################################################################</span> 84 85 <span class="c"># Split a SD file...</span> 86 <span class="c">#</span> <a name="SplitSDFile-"></a> 87 <span class="k">sub </span><span class="m">SplitSDFile</span> <span class="s">{</span> 88 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 89 90 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Files$/i</span><span class="s">)</span> <span class="s">{</span> 91 <span class="i">SplitSDFileByNumOfFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 92 <span class="s">}</span> 93 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^Cmpds$/i</span><span class="s">)</span> <span class="s">{</span> 94 <span class="i">SplitSDFileByNumOfCmpds</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 95 <span class="s">}</span> 96 <span class="s">}</span> 97 98 <span class="c"># Split SD into specified number of files...</span> 99 <span class="c">#</span> <a name="SplitSDFileByNumOfFiles-"></a> 100 <span class="k">sub </span><span class="m">SplitSDFileByNumOfFiles</span> <span class="s">{</span> 101 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 102 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="s">)</span><span class="sc">;</span> 103 104 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 105 106 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span><span class="s">)</span> <span class="s">{</span> 107 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 108 <span class="k">return</span><span class="sc">;</span> 109 <span class="s">}</span> 110 111 <span class="i">$MaxNumOfFiles</span> = <span class="i">$OptionsInfo</span>{<span class="w">NumOfFiles</span>}<span class="sc">;</span> 112 113 <span class="c"># Count number of compounds to figure out maximum number of compound per file...</span> 114 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 115 <span class="k">while</span> <span class="s">(</span><span class="q"><SDFILE></span><span class="s">)</span> <span class="s">{</span> 116 <span class="k">if</span> <span class="s">(</span><span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span> 117 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 118 <span class="s">}</span> 119 <span class="s">}</span> 120 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 121 122 <span class="k">if</span> <span class="s">(</span><span class="i">$CmpdCount</span> < <span class="i">$MaxNumOfFiles</span><span class="s">)</span> <span class="s">{</span> 123 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Total number of compounds, $CmpdCount, is smaller than number of new files, $MaxNumOfFiles\n"</span><span class="sc">;</span> 124 <span class="k">return</span><span class="sc">;</span> 125 <span class="s">}</span> 126 127 <span class="i">$MaxCmpdsPerFile</span> = <span class="k">int</span> <span class="i">$CmpdCount</span> / <span class="i">$MaxNumOfFiles</span><span class="sc">;</span> 128 129 <span class="i">SplitSDFileByNumOfFilesAndCmpds</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span><span class="sc">;</span> 130 <span class="s">}</span> 131 132 <span class="c"># Split SD into files containing specified number of compounds...</span> 133 <span class="c">#</span> <a name="SplitSDFileByNumOfCmpds-"></a> 134 <span class="k">sub </span><span class="m">SplitSDFileByNumOfCmpds</span> <span class="s">{</span> 135 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 136 137 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">NumOfCmpds</span>} == <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 138 <span class="i">SplitSDFileByOneCmpdPerFile</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 139 <span class="s">}</span> 140 <span class="k">else</span> <span class="s">{</span> 141 <span class="i">SplitSDFileByNumOfCmpdsPerFile</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span> 142 <span class="s">}</span> 143 <span class="s">}</span> 144 145 <span class="c"># Split SD into files containing one compound per file...</span> 146 <span class="c">#</span> <a name="SplitSDFileByOneCmpdPerFile-"></a> 147 <span class="k">sub </span><span class="m">SplitSDFileByOneCmpdPerFile</span> <span class="s">{</span> 148 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 149 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$NewSDFile</span><span class="cm">,</span> <span class="i">$NewSDFileRoot</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$OverwriteFiles</span><span class="cm">,</span> <span class="i">$UseDataField</span><span class="cm">,</span> <span class="i">$DataFieldName</span><span class="cm">,</span> <span class="i">$UseMolName</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">@CmpdLines</span><span class="cm">,</span> <span class="i">%DataFieldValues</span><span class="s">)</span><span class="sc">;</span> 150 151 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 152 153 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span><span class="s">)</span> <span class="s">{</span> 154 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 155 <span class="k">return</span><span class="sc">;</span> 156 <span class="s">}</span> 157 158 <span class="k">print</span> <span class="q">"\n"</span><span class="sc">;</span> 159 160 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 161 162 <span class="i">$FileExt</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 163 164 <span class="i">$OutFileRoot</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 165 <span class="i">$OverwriteFiles</span> = <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="sc">;</span> 166 167 <span class="i">$UseDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CmpdsMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 168 <span class="i">$DataFieldName</span> = <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>}<span class="sc">;</span> 169 170 <span class="i">$UseMolName</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CmpdsMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 171 172 <span class="j">CMPDSTRING:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 173 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 174 175 <span class="c"># Setup SD file name...</span> 176 <span class="i">$NewSDFileRoot</span> = <span class="q">''</span><span class="sc">;</span> 177 <span class="k">if</span> <span class="s">(</span><span class="i">$UseDataField</span><span class="s">)</span> <span class="s">{</span> 178 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 179 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span> 180 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="s">)</span> <span class="s">{</span> 181 <span class="i">$NewSDFileRoot</span> = <span class="i">$DataFieldValues</span>{<span class="i">$DataFieldName</span>}<span class="sc">;</span> 182 <span class="s">}</span> 183 <span class="s">}</span> 184 <span class="k">elsif</span> <span class="s">(</span><span class="i">$UseMolName</span><span class="s">)</span> <span class="s">{</span> 185 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span> 186 <span class="i">$NewSDFileRoot</span> = <span class="i">$CmpdLines</span>[<span class="n">0</span>]<span class="sc">;</span> 187 <span class="s">}</span> 188 189 <span class="c"># Check for any invalid file name characters in data field or molname values...</span> 190 <span class="k">if</span> <span class="s">(</span><span class="i">$NewSDFileRoot</span> && <span class="i">$NewSDFileRoot</span> =~ <span class="q">/[^a-zA-Z0-9_]/</span><span class="s">)</span> <span class="s">{</span> 191 <span class="i">$NewSDFileRoot</span> =~ <span class="q">s/[^a-zA-Z0-9_]//g</span><span class="sc">;</span> 192 <span class="s">}</span> 193 194 <span class="c"># Fall back plan for SD file name...</span> 195 <span class="k">if</span> <span class="s">(</span>!<span class="i">$NewSDFileRoot</span><span class="s">)</span> <span class="s">{</span> 196 <span class="i">$NewSDFileRoot</span> = <span class="q">"${OutFileRoot}Cmpd${CmpdCount}"</span><span class="sc">;</span> 197 <span class="s">}</span> 198 199 <span class="i">$NewSDFile</span> = <span class="q">"${NewSDFileRoot}.${FileExt}"</span><span class="sc">;</span> 200 201 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OverwriteFiles</span><span class="s">)</span> <span class="s">{</span> 202 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFile</span><span class="s">)</span> <span class="s">{</span> 203 <span class="k">warn</span> <span class="q">"Warning: Ignoring compound number, $CmpdCount, in $SDFile: New SD file, $NewSDFile, already exists\n"</span><span class="sc">;</span> 204 <span class="k">next</span> <span class="j">CMPDSTRING</span><span class="sc">;</span> 205 <span class="s">}</span> 206 <span class="s">}</span> 207 208 <span class="c"># Write out new SD file...</span> 209 210 <span class="k">print</span> <span class="q">"Generating $NewSDFile file\n"</span><span class="sc">;</span> 211 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $NewSDFile: $! \n"</span><span class="sc">;</span> 212 <span class="k">print</span> <span class="i">NEWSDFILE</span> <span class="q">"$CmpdString\n"</span><span class="sc">;</span> 213 <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span> 214 215 <span class="s">}</span> 216 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 217 <span class="s">}</span> 218 219 <span class="c"># Split SD into files containing specified number of compounds per file...</span> 220 <span class="c">#</span> <a name="SplitSDFileByNumOfCmpdsPerFile-"></a> 221 <span class="k">sub </span><span class="m">SplitSDFileByNumOfCmpdsPerFile</span> <span class="s">{</span> 222 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 223 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="s">)</span><span class="sc">;</span> 224 225 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 226 227 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span><span class="s">)</span> <span class="s">{</span> 228 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 229 <span class="k">return</span><span class="sc">;</span> 230 <span class="s">}</span> 231 232 <span class="i">$MaxCmpdsPerFile</span> = <span class="i">$OptionsInfo</span>{<span class="w">NumOfCmpds</span>}<span class="sc">;</span> 233 234 <span class="c"># Count number of compounds to figure out maximum number of files...</span> 235 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 236 <span class="k">while</span> <span class="s">(</span><span class="q"><SDFILE></span><span class="s">)</span> <span class="s">{</span> 237 <span class="k">if</span> <span class="s">(</span><span class="q">/^\$\$\$\$/</span><span class="s">)</span> <span class="s">{</span> 238 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 239 <span class="s">}</span> 240 <span class="s">}</span> 241 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span> 242 243 <span class="i">$MaxNumOfFiles</span> = <span class="k">int</span> <span class="i">$CmpdCount</span> / <span class="i">$MaxCmpdsPerFile</span><span class="sc">;</span> 244 245 <span class="k">if</span> <span class="s">(</span><span class="s">(</span><span class="i">$MaxNumOfFiles</span> * <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span> < <span class="i">$CmpdCount</span><span class="s">)</span> <span class="s">{</span> 246 <span class="i">$MaxNumOfFiles</span>++<span class="sc">;</span> 247 <span class="s">}</span> 248 249 <span class="k">if</span> <span class="s">(</span><span class="i">$CmpdCount</span> <= <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span> <span class="s">{</span> 250 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Total number of compounds, $CmpdCount, is <= specified number of compunds per file, $MaxCmpdsPerFile\n"</span><span class="sc">;</span> 251 <span class="k">return</span><span class="sc">;</span> 252 <span class="s">}</span> 253 254 <span class="i">SplitSDFileByNumOfFilesAndCmpds</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$MaxNumOfFiles</span><span class="cm">,</span> <span class="i">$MaxCmpdsPerFile</span><span class="s">)</span><span class="sc">;</span> 255 <span class="s">}</span> 256 257 <span class="c"># Split SD files into specified number of files with specified number of compounds</span> 258 <span class="c"># in each file...</span> 259 <span class="c">#</span> <a name="SplitSDFileByNumOfFilesAndCmpds-"></a> 260 <span class="k">sub </span><span class="m">SplitSDFileByNumOfFilesAndCmpds</span> <span class="s">{</span> 261 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$NumOfFiles</span><span class="cm">,</span> <span class="i">$NumOfCmpdsPerFile</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 262 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$NewFileIndex</span><span class="cm">,</span> <span class="i">$NewFileName</span><span class="cm">,</span> <span class="i">$MaxCmpdsCount</span><span class="cm">,</span> <span class="i">@NewSDFilesList</span><span class="s">)</span><span class="sc">;</span> 263 264 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span> 265 266 <span class="k">if</span> <span class="s">(</span>!<span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span><span class="s">)</span> <span class="s">{</span> 267 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Couldn't open it: $! \n"</span><span class="sc">;</span> 268 <span class="k">return</span><span class="sc">;</span> 269 <span class="s">}</span> 270 271 <span class="c"># Setup new file names list...</span> 272 <span class="i">@NewSDFilesList</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 273 <span class="k">for</span> <span class="i">$NewFileIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span> 274 <span class="i">$NewFileName</span> = <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$FileIndex</span>] . <span class="q">"Part${NewFileIndex}."</span> . <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span> 275 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span> 276 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewFileName</span><span class="s">)</span> <span class="s">{</span> 277 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: New SD file, $NewFileName, already exists\n"</span><span class="sc">;</span> 278 <span class="k">return</span><span class="sc">;</span> 279 <span class="s">}</span> 280 <span class="s">}</span> 281 <span class="k">push</span> <span class="i">@NewSDFilesList</span><span class="cm">,</span> <span class="i">$NewFileName</span><span class="sc">;</span> 282 <span class="s">}</span> 283 284 <span class="i">$MaxCmpdsCount</span> = <span class="i">$NumOfCmpdsPerFile</span><span class="sc">;</span> 285 286 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span> 287 <span class="i">$NewFileIndex</span> = <span class="n">1</span><span class="sc">;</span> 288 289 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFilesList[$NewFileIndex - 1]"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $NewSDFilesList[$NewFileIndex -1]: $! \n"</span><span class="sc">;</span> 290 <span class="k">print</span> <span class="q">"\nGenerating $NewSDFilesList[$NewFileIndex - 1] file\n"</span><span class="sc">;</span> 291 292 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $SDFile: $! \n"</span><span class="sc">;</span> 293 294 <span class="k">while</span> <span class="s">(</span><span class="q"><SDFILE></span><span class="s">)</span> <span class="s">{</span> 295 <span class="q">s/(\r\n)|(\r)/\n/g</span><span class="sc">;</span> 296 <span class="k">print</span> <span class="i">NEWSDFILE</span><span class="sc">;</span> 297 298 <span class="k">if</span> <span class="s">(</span> <span class="q">/^\$\$\$\$/</span> <span class="s">)</span> <span class="s">{</span> 299 <span class="i">$CmpdCount</span>++<span class="sc">;</span> 300 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFileIndex</span> <= <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span> 301 <span class="k">if</span> <span class="s">(</span><span class="i">$CmpdCount</span> >= <span class="i">$MaxCmpdsCount</span><span class="s">)</span> <span class="s">{</span> 302 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFileIndex</span> < <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span> 303 <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span> 304 <span class="s">}</span> 305 <span class="i">$NewFileIndex</span>++<span class="sc">;</span> 306 <span class="i">$MaxCmpdsCount</span> = <span class="i">$NumOfCmpdsPerFile</span> * <span class="i">$NewFileIndex</span><span class="sc">;</span> 307 308 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFileIndex</span> <= <span class="i">$NumOfFiles</span><span class="s">)</span> <span class="s">{</span> 309 <span class="k">open</span> <span class="w">NEWSDFILE</span><span class="cm">,</span> <span class="q">">$NewSDFilesList[$NewFileIndex - 1]"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Can't open $NewSDFilesList[$NewFileIndex - 1]: $! \n"</span><span class="sc">;</span> 310 <span class="k">print</span> <span class="q">"Generating $NewSDFilesList[$NewFileIndex - 1] file...\n"</span><span class="sc">;</span> 311 <span class="s">}</span> 312 <span class="s">}</span> 313 <span class="s">}</span> 314 <span class="s">}</span> 315 <span class="s">}</span> 316 <span class="k">close</span> <span class="w">NEWSDFILE</span><span class="sc">;</span> 317 <span class="s">}</span> 318 319 <span class="c"># Retrieve information about SD files...</span> 320 <span class="c">#</span> <a name="RetrieveSDFilesInfo-"></a> 321 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span> 322 <span class="k">my</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$Index</span><span class="cm">,</span> <span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="s">)</span><span class="sc">;</span> 323 324 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 325 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 326 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 327 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 328 329 <span class="j">FILELIST:</span> <span class="k">for</span> <span class="i">$Index</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span> 330 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 331 332 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span> 333 <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 334 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span> 335 336 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span> 337 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">-e</span> <span class="i">$SDFile</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 338 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span> 339 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 340 <span class="s">}</span> 341 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 342 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span> 343 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span> 344 <span class="s">}</span> 345 346 <span class="c"># Setup output file root...</span> 347 <span class="i">$FileDir</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">""</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">""</span><span class="sc">;</span> 348 <span class="s">(</span><span class="i">$FileDir</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$FileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span> 349 350 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 351 <span class="k">my</span> <span class="s">(</span><span class="i">$RootFileDir</span><span class="cm">,</span> <span class="i">$RootFileName</span><span class="cm">,</span> <span class="i">$RootFileExt</span><span class="s">)</span> = <span class="i">ParseFileName</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span> 352 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span> 353 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span> 354 <span class="s">}</span> 355 <span class="k">else</span> <span class="s">{</span> 356 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span> 357 <span class="s">}</span> 358 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span> 359 <span class="s">}</span> 360 <span class="k">else</span> <span class="s">{</span> 361 <span class="i">$OutFileRoot</span> = <span class="q">"$FileName"</span><span class="sc">;</span> 362 <span class="s">}</span> 363 364 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span> 365 <span class="i">$SDFilesInfo</span>{<span class="w">FileExt</span>}[<span class="i">$Index</span>] = <span class="i">$FileExt</span><span class="sc">;</span> 366 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span> 367 <span class="s">}</span> 368 <span class="s">}</span> 369 370 <span class="c"># Process option values...</span> <a name="ProcessOptions-"></a> 371 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span> 372 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 373 374 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span> 375 376 <span class="i">$OptionsInfo</span>{<span class="w">CmpdsMode</span>} = <span class="i">$Options</span>{<span class="w">cmpdsmode</span>}<span class="sc">;</span> 377 378 <span class="i">$OptionsInfo</span>{<span class="w">NumOfFiles</span>} = <span class="i">$Options</span>{<span class="w">numfiles</span>}<span class="sc">;</span> 379 <span class="i">$OptionsInfo</span>{<span class="w">NumOfCmpds</span>} = <span class="i">$Options</span>{<span class="w">numcmpds</span>}<span class="sc">;</span> 380 381 <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="q">''</span><span class="sc">;</span> 382 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^Cmpds$/i</span> && <span class="i">$Options</span>{<span class="w">cmpdsmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span> 383 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafield</span>}<span class="s">)</span> <span class="s">{</span> 384 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"-d, --DataField\" option in \"DataField\" value of \"-c, --CmpdsMode\" during \"Cmpds\" \"-m, --mode\" value. \n"</span><span class="sc">;</span> 385 <span class="s">}</span> 386 <span class="i">$OptionsInfo</span>{<span class="w">DataField</span>} = <span class="i">$Options</span>{<span class="w">datafield</span>}<span class="sc">;</span> 387 <span class="s">}</span> 388 389 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 390 391 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 392 <span class="s">}</span> 393 394 395 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span> <a name="SetupScriptUsage-"></a> 396 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span> 397 398 <span class="c"># Retrieve all the options...</span> 399 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 400 401 <span class="i">$Options</span>{<span class="w">cmpdsmode</span>} = <span class="q">'RootPrefix'</span><span class="sc">;</span> 402 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'Files'</span><span class="sc">;</span> 403 404 <span class="i">$Options</span>{<span class="w">numfiles</span>} = <span class="n">2</span><span class="sc">;</span> 405 <span class="i">$Options</span>{<span class="w">numcmpds</span>} = <span class="n">1</span><span class="sc">;</span> 406 407 408 <span class="k">if</span> <span class="s">(</span>!<span class="i">GetOptions</span><span class="s">(</span>\<span class="i">%Options</span><span class="cm">,</span> <span class="q">"cmpdsmode|c=s"</span><span class="cm">,</span> <span class="q">"datafield|d=s"</span><span class="cm">,</span> <span class="q">"help|h"</span><span class="cm">,</span> <span class="q">"mode|m=s"</span><span class="cm">,</span> <span class="q">"numfiles|n=i"</span><span class="cm">,</span> <span class="q">"numcmpds=i"</span><span class="cm">,</span> <span class="q">"overwrite|o"</span><span class="cm">,</span> <span class="q">"root|r=s"</span><span class="cm">,</span> <span class="q">"workingdir|w=s"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 409 <span class="k">die</span> <span class="q">"\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span> 410 <span class="s">}</span> 411 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 412 <span class="k">if</span> <span class="s">(</span>! <span class="k">-d</span> <span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span> 413 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span> 414 <span class="s">}</span> 415 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span> 416 <span class="s">}</span> 417 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">cmpdsmode</span>} !~ <span class="q">/^(DataField|MolName|RootPrefix)$/i</span><span class="s">)</span> <span class="s">{</span> 418 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{cmpdsmode}, for option \"-c, --CmpdsMode\" is not valid. Allowed values: DataField, MolName, RootPrefix\n"</span><span class="sc">;</span> 419 <span class="s">}</span> 420 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(Cmpds|Files)$/i</span><span class="s">)</span> <span class="s">{</span> 421 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: Cmpds, Files\n"</span><span class="sc">;</span> 422 <span class="s">}</span> 423 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">numfiles</span>} < <span class="n">2</span><span class="s">)</span> <span class="s">{</span> 424 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{numfiles}, for option \"-n --numfiles\" is not valid. Allowed values: >= 2 \n"</span><span class="sc">;</span> 425 <span class="s">}</span> 426 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">numcmpds</span>} < <span class="n">1</span><span class="s">)</span> <span class="s">{</span> 427 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{numcmpds}, for option \"-n --numcmpds\" is not valid. Allowed values: >= 1 \n"</span><span class="sc">;</span> 428 <span class="s">}</span> 429 <span class="s">}</span> 430 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>