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author	deepakjadmin
date	Wed, 20 Jan 2016 12:15:15 -0500
parents	73ae111cf86f
children

rev	line source
0 73ae111cf86f Uploaded deepakjadmin parents: diff changeset	1 <html>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	2 <head>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	3 <title>MayaChemTools:Code:PathLengthFingerprints.pl</title>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	6 </head>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	8 <br/>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	9 <center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	11 </center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	12 <br/>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	13 <pre>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	14 1 #!/usr/bin/perl -w
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	15 2 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	16 3 <span class="c"># $RCSfile: PathLengthFingerprints.pl,v $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	17 4 <span class="c"># $Date: 2015/02/28 20:46:20 $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	18 5 <span class="c"># $Revision: 1.50 $</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	19 6 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	21 8 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	23 10 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	24 11 <span class="c"># This file is part of MayaChemTools.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	25 12 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	29 16 <span class="c"># later version.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	30 17 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	34 21 <span class="c"># details.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	35 22 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	40 27 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	41 28
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	43 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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	50 37 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	51 38 <span class="k">use</span> <span class="w">MoleculeFileIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	52 39 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	53 40 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	54 41 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	55 42 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	56 43 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	57 44 <span class="k">use</span> <span class="w">Fingerprints::PathLengthFingerprints</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	58 45
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	59 46 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	60 47
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	61 48 <span class="c"># Autoflush STDOUT</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	62 49 <span class="i">$\|</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	63 50
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	64 51 <span class="c"># Starting message...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	65 52 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	66 53 <span class="k">print</span> <span class="q">"\n$ScriptName: Starting...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	67 54 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	68 55
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	69 56 <span class="c"># Get the options and setup script...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	70 57 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	71 58 <span class="k">if</span> <span class="s">(</span><span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	72 59 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	73 60 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	74 61
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	75 62 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	76 63 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	77 64
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	78 65 <span class="c"># Process options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	79 66 <span class="k">print</span> <span class="q">"Processing options...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	80 67 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	81 68 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	82 69
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	83 70 <span class="c"># Setup information about input files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	84 71 <span class="k">print</span> <span class="q">"Checking input SD file(s)...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	85 72 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	86 73 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	87 74
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	88 75 <span class="c"># Process input files..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	89 76 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	90 77 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> > <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	91 78 <span class="k">print</span> <span class="q">"\nProcessing SD files...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	92 79 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	93 80 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	94 81 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	95 82 <span class="k">print</span> <span class="q">"\nProcessing file $SDFilesList[$FileIndex]...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	96 83 <span class="i">GeneratePathLengthFingerprints</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	97 84 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	98 85 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	99 86 <span class="k">print</span> <span class="q">"\n$ScriptName:Done...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	100 87
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	101 88 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	102 89 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	103 90 <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">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">"\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	104 91
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	105 92 <span class="c">###############################################################################</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	106 93
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	107 94 <span class="c"># Generate fingerprints for a SD file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	108 95 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	109 <a name="GeneratePathLengthFingerprints-"></a> 96 <span class="k">sub </span><span class="m">GeneratePathLengthFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	110 97 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	111 98 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="cm">,</span> <span class="i">$SDFile</span><span class="cm">,</span> <span class="i">$MoleculeFileIO</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	112 99
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	113 100 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	114 101
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	115 102 <span class="c"># Setup output files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	116 103 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	117 104 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">SetupAndOpenOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	118 105
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	119 106 <span class="i">$MoleculeFileIO</span> = <span class="w">new</span> <span class="i">MoleculeFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	120 107 <span class="i">$MoleculeFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	121 108
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	122 109 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	123 110 <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	124 111
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	125 112 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">->ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	126 113 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	127 114
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	128 115 <span class="c"># Filter compound data before calculating fingerprints...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	129 116 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	130 117 <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	131 118 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	132 119 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	133 120 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	134 121 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	135 122
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	136 123 <span class="i">$PathLengthFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	137 124 <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathLengthFingerprints</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	138 125 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	139 126 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'FingerprintsGenerationFailed'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	140 127 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	141 128 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	142 129
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	143 130 <span class="i">WriteDataToOutputFiles</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	144 131 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	145 132 <span class="i">$MoleculeFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	146 133
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	147 134 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	148 135 <span class="i">$NewFPSDFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	149 136 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	150 137 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	151 138 <span class="i">$NewFPTextFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	152 139 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	153 140 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	154 141 <span class="i">$NewFPFileIO</span><span class="i">->Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	155 142 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	156 143
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	157 144 <span class="i">WriteFingerprintsGenerationSummaryStatistics</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	158 145 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	159 146
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	160 147 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	161 148 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	162 <a name="ProcessIgnoredCompound-"></a> 149 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	163 150 <span class="k">my</span><span class="s">(</span><span class="i">$Mode</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	164 151 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	165 152
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	166 153 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	167 154 <span class="i">$CmpdID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	168 155
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	169 156 <span class="j">MODE:</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	170 157 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	171 158 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	172 159 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	173 160 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	174 161
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	175 162 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	176 163 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	177 164 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	178 165 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	179 166
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	180 167 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	181 168 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	182 169 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	183 170 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	184 171 <span class="k">warn</span> <span class="q">"\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	185 172 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	186 173 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	187 174
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	188 175 <span class="c"># Check and filter compounds....</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	189 176 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	190 <a name="CheckAndFilterCompound-"></a> 177 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	191 178 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	192 179 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	193 180
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	194 181 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfElementsAndNonElements</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	195 182
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	196 183 <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	197 184 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNonElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	198 185 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	199 186 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	200 187
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	201 188 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	202 189 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">'ContainsNoElementalData'</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	203 190 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	204 191 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	205 192
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	206 193 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	207 194 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	208 195
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	209 196 <span class="c"># Write out compounds fingerprints generation summary statistics...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	210 197 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	211 <a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 198 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	212 199 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$IgnoredCmpdCount</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	213 200 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	214 201
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	215 202 <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	216 203
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	217 204 <span class="k">print</span> <span class="q">"\nNumber of compounds: $CmpdCount\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	218 205 <span class="k">print</span> <span class="q">"Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	219 206 <span class="k">print</span> <span class="q">"Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	220 207 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	221 208
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	222 209 <span class="c"># Open output files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	223 210 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	224 <a name="SetupAndOpenOutputFiles-"></a> 211 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	225 212 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	226 213 <span class="k">my</span><span class="s">(</span><span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	227 214
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	228 215 <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	229 216
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	230 217 <span class="c"># Setup common parameters for fingerprints file IO objects...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	231 218 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	232 219 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	233 220 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	234 221 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Write'</span><span class="cm">,</span> <span class="q">'Overwrite'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="q">'FingerprintsBitVectorString'</span><span class="cm">,</span> <span class="q">'BitStringFormat'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>}<span class="cm">,</span> <span class="q">'BitsOrder'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	235 222 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	236 223 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	237 224 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">'Mode'</span> <span class="cm">=></span> <span class="q">'Write'</span><span class="cm">,</span> <span class="q">'Overwrite'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">'FingerprintsStringMode'</span> <span class="cm">=></span> <span class="q">'FingerprintsVectorString'</span><span class="cm">,</span> <span class="q">'VectorStringFormat'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	238 225 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	239 226
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	241 228 <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	242 229 <span class="k">print</span> <span class="q">"Generating SD file $NewFPSDFile...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	243 230 <span class="i">$NewFPSDFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">'FingerprintsFieldLabel'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	244 231 <span class="i">$NewFPSDFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	245 232 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	246 233
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	247 234 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	248 235 <span class="i">$NewFPFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	249 236 <span class="k">print</span> <span class="q">"Generating FP file $NewFPFile...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	250 237 <span class="i">$NewFPFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	251 238 <span class="i">$NewFPFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	252 239 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	253 240
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	254 241 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	255 242 <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	256 243
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	257 244 <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	258 245 <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	259 246
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	260 247 <span class="k">print</span> <span class="q">"Generating text file $NewFPTextFile...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	261 248 <span class="i">$NewFPTextFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="q">'Name'</span> <span class="cm">=></span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">'DataColLabels'</span> <span class="cm">=></span> <span class="i">$ColLabelsRef</span><span class="cm">,</span> <span class="q">'OutDelim'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="q">'OutQuote'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	262 249 <span class="i">$NewFPTextFileIO</span><span class="i">->Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	263 250 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	264 251
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	265 252 <span class="k">return</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	266 253 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	267 254
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	268 255 <span class="c"># Write fingerpritns and other data to appropriate output files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	269 256 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	270 <a name="WriteDataToOutputFiles-"></a> 257 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	271 258 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$NewFPSDFileIO</span><span class="cm">,</span> <span class="i">$NewFPTextFileIO</span><span class="cm">,</span> <span class="i">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	272 259 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	273 260
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	274 261 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	275 262 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> \|\| <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	276 263 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">->GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	277 264 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	278 265
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	279 266 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	280 267 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	281 268
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	282 269 <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">->GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	283 270 <span class="i">$NewFPSDFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	284 271 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	285 272
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	286 273 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	287 274 <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	288 275
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	289 276 <span class="i">$ColValuesRef</span> = <span class="i">SetupFPTextFileCoulmnValues</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	290 277 <span class="i">$NewFPTextFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	291 278 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	292 279
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	293 280 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	294 281 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	295 282
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	296 283 <span class="i">$CompoundID</span> = <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	297 284 <span class="i">$NewFPFileIO</span><span class="i">->WriteFingerprints</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	298 285 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	299 286 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	300 287
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	301 288 <span class="c"># Generate approriate column labels for FPText output file...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	302 289 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	303 <a name="SetupFPTextFileCoulmnLabels-"></a> 290 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	304 291 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	305 292 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	306 293
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	307 294 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	308 295 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	309 296 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	310 297 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	311 298 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	312 299 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	313 300 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	314 301 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	315 302 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	316 303 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	317 304 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	318 305 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	319 306 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	320 307 <span class="c"># Add fingerprints label...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	321 308 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	322 309
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	323 310 <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	324 311 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	325 312
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	326 313 <span class="c"># Generate column values FPText output file..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	327 314 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	328 <a name="SetupFPTextFileCoulmnValues-"></a> 315 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	329 316 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	330 317 <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	331 318
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	332 319 <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	333 320 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	334 321 <span class="k">push</span> <span class="i">@ColValues</span><span class="cm">,</span> <span class="i">SetupCmpdIDForOutputFiles</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	335 322 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	336 323 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	337 324 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	338 325 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	339 326 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	340 327 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	341 328 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	342 329 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	343 330 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$_</span>} <span class="co">:</span> <span class="q">''</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	344 331 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	345 332
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	346 333 <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	347 334 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	348 335
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	349 336 <span class="c"># Generate compound ID for FP and FPText output files..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	350 337 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	351 <a name="SetupCmpdIDForOutputFiles-"></a> 338 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	352 339 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	353 340 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	354 341
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	355 342 <span class="i">$CmpdID</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	356 343 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	357 344 <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	358 345 <span class="i">$MolName</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	359 346 <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	360 347 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	361 348 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	362 349 <span class="i">$CmpdID</span> = <span class="q">"$OptionsInfo{CompoundID}${CmpdCount}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	363 350 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	364 351 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	365 352 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	366 353 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	367 354 <span class="i">$CmpdID</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>->{<span class="i">$SpecifiedDataField</span>} <span class="co">:</span> <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	368 355 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	369 356 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolName$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	370 357 <span class="i">$CmpdID</span> = <span class="i">$Molecule</span><span class="i">->GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	371 358 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	372 359 <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	373 360 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	374 361
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	375 362 <span class="c"># Generate fingerprints for molecule...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	376 363 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	377 <a name="GenerateMoleculeFingerprints-"></a> 364 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	378 365 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	379 366 <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	380 367
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	382 369 <span class="i">$Molecule</span><span class="i">->KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	383 370 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	384 371 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">IgnoreHydrogens</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	385 372 <span class="i">$Molecule</span><span class="i">->DeleteHydrogens</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	386 373 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	387 374
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	388 375 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DetectAromaticity</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	389 376 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">->DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	390 377 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	391 378 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	392 379 <span class="i">$Molecule</span><span class="i">->SetAromaticityModel</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	393 380 <span class="i">$Molecule</span><span class="i">->DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	394 381 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	395 382
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	396 383 <span class="i">$PathLengthFingerprints</span> = <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	397 384 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthBits$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	398 385 <span class="i">$PathLengthFingerprints</span> = <span class="i">GeneratePathLengthBitsFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	399 386 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	400 387 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^PathLengthCount$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	401 388 <span class="i">$PathLengthFingerprints</span> = <span class="i">GeneratePathLengthCountFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	402 389 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	403 390 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	404 391 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	405 392 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	406 393
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	407 394 <span class="k">return</span> <span class="i">$PathLengthFingerprints</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	408 395 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	409 396
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	410 397 <span class="c"># Generate pathlength bits finerprints for molecule...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	411 398 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	412 <a name="GeneratePathLengthBitsFingerprints-"></a> 399 <span class="k">sub </span><span class="m">GeneratePathLengthBitsFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	413 400 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	414 401 <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	415 402
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	416 403 <span class="i">$PathLengthFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'PathLengthBits'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'NumOfBitsToSetPerPath'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">NumOfBitsToSetPerPath</span>}<span class="cm">,</span> <span class="q">'Size'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="q">'MinLength'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">'MaxLength'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">'AllowRings'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AllowRings</span>}<span class="cm">,</span> <span class="q">'AllowSharedBonds'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AllowSharedBonds</span>}<span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">UseUniquePaths</span>}<span class="cm">,</span> <span class="q">'UsePerlCoreRandom'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	417 404
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	418 405 <span class="c"># Set atom identifier type...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	419 406 <span class="i">SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	420 407
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	421 408 <span class="c"># Generate fingerprints...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	422 409 <span class="i">$PathLengthFingerprints</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	423 410
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	424 411 <span class="c"># Make sure fingerprints generation is successful...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	425 412 <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathLengthFingerprints</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	426 413 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	427 414 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	428 415
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	429 416 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Fold</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	430 417 <span class="k">my</span><span class="s">(</span><span class="i">$CheckSizeValue</span><span class="s">)</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	431 418 <span class="i">$PathLengthFingerprints</span><span class="i">->FoldFingerprintsBySize</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FoldedSize</span>}<span class="cm">,</span> <span class="i">$CheckSizeValue</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	432 419 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	433 420
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	434 421 <span class="k">return</span> <span class="i">$PathLengthFingerprints</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	435 422 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	436 423
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	437 424 <span class="c"># Generate pathlength count finerprints for molecule...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	438 425 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	439 <a name="GeneratePathLengthCountFingerprints-"></a> 426 <span class="k">sub </span><span class="m">GeneratePathLengthCountFingerprints</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	440 427 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	441 428 <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	442 429
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	443 430 <span class="i">$PathLengthFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::PathLengthFingerprints</span><span class="s">(</span><span class="q">'Molecule'</span> <span class="cm">=></span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">'Type'</span> <span class="cm">=></span> <span class="q">'PathLengthCount'</span><span class="cm">,</span> <span class="q">'AtomIdentifierType'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">'MinLength'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MinPathLength</span>}<span class="cm">,</span> <span class="q">'MaxLength'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">MaxPathLength</span>}<span class="cm">,</span> <span class="q">'AllowRings'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AllowRings</span>}<span class="cm">,</span> <span class="q">'AllowSharedBonds'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">AllowSharedBonds</span>}<span class="cm">,</span> <span class="q">'UseBondSymbols'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">UseBondSymbols</span>}<span class="cm">,</span> <span class="q">'UseUniquePaths'</span> <span class="cm">=></span> <span class="i">$OptionsInfo</span>{<span class="w">UseUniquePaths</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	444 431
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	445 432 <span class="c"># Set atom identifier type...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	446 433 <span class="i">SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	447 434
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	448 435 <span class="c"># Generate fingerprints...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	449 436 <span class="i">$PathLengthFingerprints</span><span class="i">->GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	450 437
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	451 438 <span class="c"># Make sure fingerprints generation is successful...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	452 439 <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathLengthFingerprints</span><span class="i">->IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	453 440 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	454 441 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	455 442 <span class="k">return</span> <span class="i">$PathLengthFingerprints</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	456 443 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	457 444
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	458 445 <span class="c"># Set atom identifier type to use for generating path strings...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	459 446 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	460 <a name="SetAtomIdentifierTypeValuesToUse-"></a> 447 <span class="k">sub </span><span class="m">SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	461 448 <span class="k">my</span><span class="s">(</span><span class="i">$PathLengthFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	462 449
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	463 450 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	464 451 <span class="i">$PathLengthFingerprints</span><span class="i">->SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	465 452 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	466 453 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	467 454 <span class="i">$PathLengthFingerprints</span><span class="i">->SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	468 455 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	469 456 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes\|EStateAtomTypes\|MMFF94AtomTypes\|SLogPAtomTypes\|SYBYLAtomTypes\|TPSAAtomTypes\|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	470 457 <span class="c"># Nothing to do for now...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	471 458 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	472 459 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	473 460 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	474 461 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	475 462 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	476 463
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	477 464 <span class="c"># Retrieve information about SD files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	478 465 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	479 <a name="RetrieveSDFilesInfo-"></a> 466 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	480 467 <span class="k">my</span><span class="s">(</span><span class="i">$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">$FileExt</span><span class="cm">,</span> <span class="i">$FileName</span><span class="cm">,</span> <span class="i">$OutFileRoot</span><span class="cm">,</span> <span class="i">$TextOutFileExt</span><span class="cm">,</span> <span class="i">$SDOutFileExt</span><span class="cm">,</span> <span class="i">$FPOutFileExt</span><span class="cm">,</span> <span class="i">$NewSDFileName</span><span class="cm">,</span> <span class="i">$NewFPFileName</span><span class="cm">,</span> <span class="i">$NewTextFileName</span><span class="cm">,</span> <span class="i">$CheckDataField</span><span class="cm">,</span> <span class="i">$CollectDataFields</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	481 468
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	482 469 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	483 470 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	484 471 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	485 472 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	486 473 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	487 474 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	488 475 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	489 476 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	490 477
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	491 478 <span class="i">$CheckDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	492 479 <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} && <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^(All\|Common)$/i</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	493 480
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	494 481 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	495 482 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	496 483
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	497 484 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	498 485 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	499 486 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	500 487 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	501 488 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	502 489
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	503 490 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	504 491 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	505 492 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It doesn't exist\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	506 493 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	507 494 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	508 495 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">"sd sdf"</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	509 496 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: It's not a SD file\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	510 497 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	511 498 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	512 499
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	513 500 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	514 501 <span class="c"># Make sure data field exists in SD file..</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	515 502 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="cm">,</span> <span class="i">$SpecifiedDataField</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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	516 503
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	517 504 <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	518 505 <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: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	519 506 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	520 507 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	521 508 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">"\n"</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	522 509 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	523 510 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	524 511 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	525 512 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	526 513 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	527 514 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	528 515 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	529 516
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	530 517 <span class="i">$AllDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	531 518 <span class="i">$CommonDataFieldsRef</span> = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	532 519 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	533 520 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	534 521 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">"$SDFile"</span> <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't open $SDFile: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	535 522 <span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$AllDataFieldsRef</span><span class="cm">,</span> <span class="i">$CommonDataFieldsRef</span><span class="s">)</span> = <span class="i">GetAllAndCommonCmpdDataHeaderLabels</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	536 523 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	537 524 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	538 525
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	539 526 <span class="c"># Setup output file names...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	540 527 <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">$FileExt</span> = <span class="q">""</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	541 528 <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	542 529
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	543 530 <span class="i">$TextOutFileExt</span> = <span class="q">"csv"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	544 531 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/^tab$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	545 532 <span class="i">$TextOutFileExt</span> = <span class="q">"tsv"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	546 533 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	547 534 <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	548 535 <span class="i">$FPOutFileExt</span> = <span class="q">"fpf"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	549 536
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	550 537 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} && <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	551 538 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	552 539 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> && <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	553 540 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	554 541 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	555 542 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	556 543 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	557 544 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	558 545 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	559 546 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	560 547 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	561 548 <span class="i">$OutFileRoot</span> = <span class="q">"${FileName}PathLengthFP"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	562 549 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	563 550
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	564 551 <span class="i">$NewSDFileName</span> = <span class="q">"${OutFileRoot}.${SDOutFileExt}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	565 552 <span class="i">$NewFPFileName</span> = <span class="q">"${OutFileRoot}.${FPOutFileExt}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	566 553 <span class="i">$NewTextFileName</span> = <span class="q">"${OutFileRoot}.${TextOutFileExt}"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	567 554
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	568 555 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	569 556 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	570 557 <span class="k">warn</span> <span class="q">"Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	571 558 <span class="k">print</span> <span class="q">"Specify a different name using \"-r --root\" option or use default name.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	572 559 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	573 560 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	574 561 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	575 562
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	576 563 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	577 564 <span class="c"># Check SD, FP and text outout files...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	578 565 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	579 566 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	580 567 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	581 568 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	582 569 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	583 570 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	584 571 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	585 572 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewFPFileName</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	586 573 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	587 574 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	588 575 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	589 576 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	590 577 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	591 578 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewTextFileName</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	592 579 <span class="k">warn</span> <span class="q">"Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	593 580 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	594 581 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	595 582 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	596 583 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	597 584
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	598 585 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	599 586
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	600 587 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	601 588 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	602 589 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	603 590 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	604 591
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	605 592 <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	606 593 <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	607 594 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	608 595 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	609 596
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	610 597 <span class="c"># Process option values...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	611 <a name="ProcessOptions-"></a> 598 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	612 599 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	613 600
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	614 601 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	615 602 <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	616 603 <span class="i">$OptionsInfo</span>{<span class="w">PathMode</span>} = <span class="i">$Options</span>{<span class="w">pathmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	617 604
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	618 605 <span class="i">ProcessAtomIdentifierTypeOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	619 606
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	620 607 <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>} = <span class="i">$Options</span>{<span class="w">bitsorder</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	621 608 <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>} = <span class="i">$Options</span>{<span class="w">bitstringformat</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	622 609
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	623 610 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	624 611 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	625 612 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	626 613
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	627 614 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	628 615 <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	629 616
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	630 617 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	631 618 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">''</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	632 619
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	633 620 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	634 621 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	635 622 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	636 623 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	637 624 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	638 625 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	639 626 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	640 627 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^(LabelPrefix\|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	641 628 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">'Cmpd'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	642 629 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	643 630 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	644 631 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	645 632 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	646 633 <span class="k">die</span> <span class="q">"Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	647 634 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	648 635 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	649 636 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	650 637 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	651 638
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	652 639 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} !~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	653 640 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detectaromaticity</span>} =~ <span class="q">/^No$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	654 641 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. No value is only allowed during AtomicInvariantsAtomTypes value for \"-a, --AtomIdentifierType\" \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	655 642 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	656 643 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	657 644 <span class="i">$OptionsInfo</span>{<span class="w">DetectAromaticity</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">detectaromaticity</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	658 645
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	659 646 <span class="i">$OptionsInfo</span>{<span class="w">Filter</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	660 647
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	661 648 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} ? <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} <span class="co">:</span> <span class="q">'PathLengthFingerprints'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	662 649
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	663 650 <span class="k">my</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="i">$MinSize</span><span class="cm">,</span> <span class="i">$MaxSize</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	664 651 <span class="i">$MinSize</span> = <span class="n">32</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	665 652 <span class="i">$MaxSize</span> = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	666 653 <span class="i">$Size</span> = <span class="i">$Options</span>{<span class="w">size</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	667 654 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Size</span><span class="s">)</span> && <span class="i">$Size</span> >= <span class="i">$MinSize</span> && <span class="i">$Size</span> <= <span class="i">$MaxSize</span> && <span class="i">IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$Size</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	668 655 <span class="k">die</span> <span class="q">"Error: Invalid size value, $Size, for \"-s, --size\" option. Allowed values: power of 2, >= minimum size of $MinSize, and <= maximum size of $MaxSize.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	669 656 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	670 657 <span class="i">$OptionsInfo</span>{<span class="w">Size</span>} = <span class="i">$Size</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	671 658
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	672 659 <span class="i">$OptionsInfo</span>{<span class="w">Fold</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">fold</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	673 660 <span class="k">my</span><span class="s">(</span><span class="i">$FoldedSize</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	674 661 <span class="i">$FoldedSize</span> = <span class="i">$Options</span>{<span class="w">foldedsize</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	675 662 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fold</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	676 663 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$FoldedSize</span><span class="s">)</span> && <span class="i">$FoldedSize</span> < <span class="i">$Size</span> && <span class="i">IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$FoldedSize</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	677 664 <span class="k">die</span> <span class="q">"Error: Invalid folded size value, $FoldedSize, for \"--FoldedSize\" option. Allowed values: power of 2, >= minimum size of $MinSize, and < size value of $Size.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	678 665 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	679 666 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	680 667 <span class="i">$OptionsInfo</span>{<span class="w">FoldedSize</span>} = <span class="i">$FoldedSize</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	681 668
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	682 669 <span class="i">$OptionsInfo</span>{<span class="w">IgnoreHydrogens</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignorehydrogens</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	683 670 <span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	684 671
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	685 672 <span class="k">my</span><span class="s">(</span><span class="i">$MinPathLength</span><span class="cm">,</span> <span class="i">$MaxPathLength</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	686 673 <span class="i">$MinPathLength</span> = <span class="i">$Options</span>{<span class="w">minpathlength</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	687 674 <span class="i">$MaxPathLength</span> = <span class="i">$Options</span>{<span class="w">maxpathlength</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	688 675 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$MinPathLength</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	689 676 <span class="k">die</span> <span class="q">"Error: Invalid path length value, $MinPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	690 677 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	691 678 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$MaxPathLength</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	692 679 <span class="k">die</span> <span class="q">"Error: Invalid path length value, $MaxPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	693 680 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	694 681 <span class="k">if</span> <span class="s">(</span><span class="i">$MinPathLength</span> >= <span class="i">$MaxPathLength</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	695 682 <span class="k">die</span> <span class="q">"Error: Invalid minimum and maximum path length values, $MinPathLength and $MaxPathLength, for \"--MinPathLength\" and \"--MaxPathLength\"options. Allowed values: minimum path length value must be smaller than maximum path length value.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	696 683 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	697 684 <span class="i">$OptionsInfo</span>{<span class="w">MinPathLength</span>} = <span class="i">$MinPathLength</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	698 685 <span class="i">$OptionsInfo</span>{<span class="w">MaxPathLength</span>} = <span class="i">$MaxPathLength</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	699 686
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	700 687 <span class="k">my</span><span class="s">(</span><span class="i">$NumOfBitsToSetPerPath</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	701 688 <span class="i">$NumOfBitsToSetPerPath</span> = <span class="i">$Options</span>{<span class="w">numofbitstosetperpath</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	702 689 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$MaxPathLength</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	703 690 <span class="k">die</span> <span class="q">"Error: Invalid value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: > 0\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	704 691 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	705 692 <span class="k">if</span> <span class="s">(</span><span class="i">$NumOfBitsToSetPerPath</span> >= <span class="i">$Size</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	706 693 <span class="k">die</span> <span class="q">"Error: Invalid value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: It must be less than the size, $Size, of the fingerprint bit-string.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	707 694 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	708 695 <span class="i">$OptionsInfo</span>{<span class="w">NumOfBitsToSetPerPath</span>} = <span class="i">$NumOfBitsToSetPerPath</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	709 696
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	710 697 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	711 698 <span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(SD\|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	712 699 <span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(FP\|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	713 700 <span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} =~ <span class="q">/^(Text\|All)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	714 701
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	715 702 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	716 703 <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	717 704
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	718 705 <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>} = <span class="i">$Options</span>{<span class="w">overwrite</span>} ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	719 706 <span class="i">$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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	720 707
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	721 708 <span class="i">$OptionsInfo</span>{<span class="w">UseBondSymbols</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">usebondsymbols</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	722 709
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	723 710 <span class="i">$OptionsInfo</span>{<span class="w">UsePerlCoreRandom</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	724 711
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	725 712 <span class="i">$OptionsInfo</span>{<span class="w">UseUniquePaths</span>} = <span class="s">(</span><span class="i">$Options</span>{<span class="w">useuniquepaths</span>} =~ <span class="q">/^Yes$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	726 713
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	727 714 <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	728 715
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	729 716 <span class="c"># Setup parameters used during generation of fingerprints by PathLengthFingerprints class...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	730 717 <span class="k">my</span><span class="s">(</span><span class="i">$AllowRings</span><span class="cm">,</span> <span class="i">$AllowSharedBonds</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	731 718 <span class="i">$AllowRings</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	732 719 <span class="i">$AllowSharedBonds</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	733 720 <span class="j">MODE:</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	734 721 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AtomPathsWithoutRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	735 722 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AtomPathsWithRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	736 723 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AllAtomPathsWithoutRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">0</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	737 724 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} =~ <span class="q">/^AllAtomPathsWithRings$/i</span><span class="s">)</span> <span class="s">{</span> <span class="i">$AllowSharedBonds</span> = <span class="n">1</span><span class="sc">;</span> <span class="i">$AllowRings</span> = <span class="n">1</span><span class="sc">;</span> <span class="k">last</span> <span class="j">MODE</span><span class="sc">;</span><span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	738 725 <span class="k">die</span> <span class="q">"Error: ProcessOptions: mode value, $Options{pathmode}, is not supported.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	739 726 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	740 727 <span class="i">$OptionsInfo</span>{<span class="w">AllowRings</span>} = <span class="i">$AllowRings</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	741 728 <span class="i">$OptionsInfo</span>{<span class="w">AllowSharedBonds</span>} = <span class="i">$AllowSharedBonds</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	742 729 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	743 730
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	744 731 <span class="c"># Process atom identifier type and related options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	745 732 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	746 <a name="ProcessAtomIdentifierTypeOptions-"></a> 733 <span class="k">sub </span><span class="m">ProcessAtomIdentifierTypeOptions</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	747 734
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	748 735 <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} = <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	749 736
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	750 737 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	751 738 <span class="i">ProcessAtomicInvariantsToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	752 739 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	753 740 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	754 741 <span class="i">ProcessFunctionalClassesToUse</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	755 742 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	756 743 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} =~ <span class="q">/^(DREIDINGAtomTypes\|EStateAtomTypes\|MMFF94AtomTypes\|SLogPAtomTypes\|SYBYLAtomTypes\|TPSAAtomTypes\|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	757 744 <span class="c"># Nothing to do for now...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	758 745 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	759 746 <span class="k">else</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	760 747 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	761 748 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	762 749 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	763 750
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	764 751 <span class="c"># Process specified atomic invariants to use...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	765 752 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	766 <a name="ProcessAtomicInvariantsToUseOption-"></a> 753 <span class="k">sub </span><span class="m">ProcessAtomicInvariantsToUseOption</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	767 754 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSymbolSpecified</span><span class="cm">,</span> <span class="i">@AtomicInvariantsWords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	768 755
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	769 756 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	770 757 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	771 758 <span class="k">die</span> <span class="q">"Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	772 759 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	773 760 <span class="i">$AtomSymbolSpecified</span> = <span class="n">0</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	774 761 <span class="i">@AtomicInvariantsWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	775 762 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsWords</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	776 763 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	777 764 <span class="k">die</span> <span class="q">"Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n "</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	778 765 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	779 766 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS\|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	780 767 <span class="i">$AtomSymbolSpecified</span> = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	781 768 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	782 769 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="cm">,</span> <span class="i">$AtomicInvariant</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	783 770 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	784 771 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolSpecified</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	785 772 <span class="k">die</span> <span class="q">"Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n "</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	786 773 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	787 774 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	788 775
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	789 776 <span class="c"># Process specified functional classes invariants to use...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	790 777 <span class="c">#</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	791 <a name="ProcessFunctionalClassesToUse-"></a> 778 <span class="k">sub </span><span class="m">ProcessFunctionalClassesToUse</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	792 779 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	793 780
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	794 781 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	795 782 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	796 783 <span class="k">die</span> <span class="q">"Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	797 784 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	798 785 <span class="i">@FunctionalClassesToUseWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	799 786 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	800 787 <span class="k">if</span> <span class="s">(</span>!<span class="i">AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	801 788 <span class="k">die</span> <span class="q">"Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n "</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	802 789 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	803 790 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	804 791 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	805 792 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	806 793
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	807 794 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	808 <a name="SetupScriptUsage-"></a> 795 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	809 796
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	810 797 <span class="c"># Retrieve all the options...</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	811 798 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	812 799
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	813 800 <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">'MayaChemToolsAromaticityModel'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	814 801
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	815 802 <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} = <span class="q">'AtomicInvariantsAtomTypes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	816 803 <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>} = <span class="q">'AS'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	817 804
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	818 805 <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>} = <span class="q">'HBD,HBA,PI,NI,Ar,Hal'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	819 806
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	820 807 <span class="i">$Options</span>{<span class="w">bitsorder</span>} = <span class="q">'Ascending'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	821 808 <span class="i">$Options</span>{<span class="w">bitstringformat</span>} = <span class="q">'HexadecimalString'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	822 809
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	823 810 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">'LabelPrefix'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	824 811 <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	825 812 <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">'CompoundID'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	826 813 <span class="i">$Options</span>{<span class="w">detectaromaticity</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	827 814
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	828 815 <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	829 816
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	830 817 <span class="i">$Options</span>{<span class="w">fold</span>} = <span class="q">'No'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	831 818 <span class="i">$Options</span>{<span class="w">foldedsize</span>} = <span class="n">256</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	832 819
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	833 820 <span class="i">$Options</span>{<span class="w">ignorehydrogens</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	834 821 <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">'Yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	835 822
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	836 823 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">'PathLengthBits'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	837 824 <span class="i">$Options</span>{<span class="w">pathmode</span>} = <span class="q">'AllAtomPathsWithRings'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	838 825
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	839 826 <span class="i">$Options</span>{<span class="w">minpathlength</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	840 827 <span class="i">$Options</span>{<span class="w">maxpathlength</span>} = <span class="n">8</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	841 828
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	842 829 <span class="i">$Options</span>{<span class="w">numofbitstosetperpath</span>} = <span class="n">1</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	843 830
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	844 831 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">'text'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	845 832 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">'comma'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	846 833 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">'yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	847 834
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	848 835 <span class="i">$Options</span>{<span class="w">size</span>} = <span class="n">1024</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	849 836
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	850 837 <span class="i">$Options</span>{<span class="w">usebondsymbols</span>} = <span class="q">'yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	851 838 <span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} = <span class="q">'yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	852 839 <span class="i">$Options</span>{<span class="w">useuniquepaths</span>} = <span class="q">'yes'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	853 840
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	854 841 <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">'IDsAndValuesString'</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	855 842
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	856 843 <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">"aromaticitymodel=s"</span><span class="cm">,</span> <span class="q">"atomidentifiertype\|a=s"</span><span class="cm">,</span> <span class="q">"atomicinvariantstouse=s"</span><span class="cm">,</span> <span class="q">"functionalclassestouse=s"</span><span class="cm">,</span> <span class="q">"bitsorder=s"</span><span class="cm">,</span> <span class="q">"bitstringformat\|b=s"</span><span class="cm">,</span> <span class="q">"compoundid=s"</span><span class="cm">,</span> <span class="q">"compoundidlabel=s"</span><span class="cm">,</span> <span class="q">"compoundidmode=s"</span><span class="cm">,</span> <span class="q">"datafields=s"</span><span class="cm">,</span> <span class="q">"datafieldsmode\|d=s"</span><span class="cm">,</span> <span class="q">"detectaromaticity=s"</span><span class="cm">,</span> <span class="q">"filter\|f=s"</span><span class="cm">,</span> <span class="q">"fingerprintslabel=s"</span><span class="cm">,</span> <span class="q">"fold=s"</span><span class="cm">,</span> <span class="q">"foldedsize=i"</span><span class="cm">,</span> <span class="q">"help\|h"</span><span class="cm">,</span> <span class="q">"ignorehydrogens\|i=s"</span><span class="cm">,</span> <span class="q">"keeplargestcomponent\|k=s"</span><span class="cm">,</span> <span class="q">"mode\|m=s"</span><span class="cm">,</span> <span class="q">"minpathlength=i"</span><span class="cm">,</span> <span class="q">"maxpathlength=i"</span><span class="cm">,</span> <span class="q">"numofbitstosetperpath\|n=i"</span><span class="cm">,</span> <span class="q">"outdelim=s"</span><span class="cm">,</span> <span class="q">"output=s"</span><span class="cm">,</span> <span class="q">"overwrite\|o"</span><span class="cm">,</span> <span class="q">"pathmode\|p=s"</span><span class="cm">,</span> <span class="q">"quote\|q=s"</span><span class="cm">,</span> <span class="q">"root\|r=s"</span><span class="cm">,</span> <span class="q">"size\|s=i"</span><span class="cm">,</span> <span class="q">"usebondsymbols\|u=s"</span><span class="cm">,</span> <span class="q">"useperlcorerandom=s"</span><span class="cm">,</span> <span class="q">"useuniquepaths=s"</span><span class="cm">,</span> <span class="q">"vectorstringformat\|v=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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	857 844 <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 $ScriptName -h\" command and try again...\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	858 845 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	859 846 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	860 847 <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>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	861 848 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	862 849 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	863 850 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">"Error: Couldn't chdir $Options{workingdir}: $! \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	864 851 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	865 852 <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	866 853 <span class="k">my</span><span class="s">(</span><span class="i">@SupportedModels</span><span class="s">)</span> = <span class="i">Molecule::GetSupportedAromaticityModels</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	867 854 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	868 855 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	869 856 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} !~ <span class="q">/^(AtomicInvariantsAtomTypes\|DREIDINGAtomTypes\|EStateAtomTypes\|FunctionalClassAtomTypes\|MMFF94AtomTypes\|SLogPAtomTypes\|SYBYLAtomTypes\|TPSAAtomTypes\|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	870 857 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	871 858 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	872 859 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitsorder</span>} !~ <span class="q">/^(Ascending\|Descending)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	873 860 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	874 861 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	875 862 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitstringformat</span>} !~ <span class="q">/^(BinaryString\|HexadecimalString)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	876 863 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	877 864 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	878 865 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField\|MolName\|LabelPrefix\|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	879 866 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	880 867 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	881 868 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All\|Common\|Specify\|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	882 869 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	883 870 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	884 871 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">detectaromaticity</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	885 872 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	886 873 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	887 874 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	888 875 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	889 876 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	890 877 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">fold</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	891 878 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{fold}, for option \"--fold\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	892 879 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	893 880 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">foldedsize</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	894 881 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{foldedsize}, for option \"--FoldedSize\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	895 882 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	896 883 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">ignorehydrogens</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	897 884 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{ignorehydrogens}, for option \"-i, --IgnoreHydrogens\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	898 885 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	899 886 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	900 887 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	901 888 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	902 889 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(PathLengthBits\|PathLengthCount)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	903 890 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	904 891 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	905 892 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">minpathlength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	906 893 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{minpathlength}, for option \"--MinPathLength\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	907 894 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	908 895 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">numofbitstosetperpath</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	909 896 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{NumOfBitsToSetPerPath}, for option \"--NumOfBitsToSetPerPath\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	910 897 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	911 898 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">maxpathlength</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	912 899 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{maxpathlength}, for option \"--MaxPathLength\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	913 900 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	914 901 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD\|FP\|text\|all)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	915 902 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	916 903 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	917 904 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma\|semicolon\|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	918 905 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	919 906 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	920 907 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">pathmode</span>} !~ <span class="q">/^(AtomPathsWithoutRings\|AtomPathsWithRings\|AllAtomPathsWithoutRings\|AllAtomPathsWithRings)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	921 908 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{pathmode}, for option \"-m, --PathMode\" is not valid. Allowed values: AtomPathsWithoutRings, AtomPathsWithRings, AllAtomPathsWithoutRings or AllAtomPathsWithRings\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	922 909 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	923 910 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	924 911 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	925 912 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	926 913 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span> && <span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^No$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	927 914 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	928 915 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	929 916
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	930 917 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">size</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	931 918 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	932 919 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	933 920 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">usebondsymbols</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	934 921 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{usebondsymbols}, for option \"-u, --UseBondSymbols\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	935 922 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	936 923 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	937 924 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	938 925 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	939 926 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">useuniquepaths</span>} !~ <span class="q">/^(Yes\|No)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	940 927 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{useuniquepaths}, for option \"--UseUniquePaths\" is not valid. Allowed values: Yes or No\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	941 928 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	942 929 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>} !~ <span class="q">/^(IDsAndValuesString\|IDsAndValuesPairsString\|ValuesAndIDsString\|ValuesAndIDsPairsString)$/i</span><span class="s">)</span> <span class="s">{</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	943 930 <span class="k">die</span> <span class="q">"Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n"</span><span class="sc">;</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	944 931 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	945 932 <span class="s">}</span>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	946 933
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	947 <a name="EOF-"></a></pre>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	948 <p> </p>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	949 <br />
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	950 <center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	951 <img src="../../../images/h2o2.png">
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	952 </center>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	953 </body>
73ae111cf86f Uploaded deepakjadmin parents: diff changeset	954 </html>

Mercurial > repos > deepakjadmin > mayatool3_test3

annotate mayachemtools/docs/scripts/html/code/PathLengthFingerprints.html @ 2:dfff2614510e draft