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1 <html>
2 <head>
3 <title>MayaChemTools:Code:ExtendedConnectivityFingerprints.pl</title>
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css">
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8 <br/>
9 <center>
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
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12 <br/>
13 <pre>
14 1 #!/usr/bin/perl -w
15 2 <span class="c">#</span>
16 3 <span class="c"># $RCSfile: ExtendedConnectivityFingerprints.pl,v $</span>
17 4 <span class="c"># $Date: 2015/02/28 20:46:19 $</span>
18 5 <span class="c"># $Revision: 1.37 $</span>
19 6 <span class="c">#</span>
20 7 <span class="c"># Author: Manish Sud &lt;msud@san.rr.com&gt;</span>
21 8 <span class="c">#</span>
22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
23 10 <span class="c">#</span>
24 11 <span class="c"># This file is part of MayaChemTools.</span>
25 12 <span class="c">#</span>
26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
29 16 <span class="c"># later version.</span>
30 17 <span class="c">#</span>
31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
34 21 <span class="c"># details.</span>
35 22 <span class="c">#</span>
36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
37 24 <span class="c"># along with MayaChemTools; if not, see &lt;http://www.gnu.org/licenses/&gt; or</span>
38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
40 27 <span class="c">#</span>
41 28
42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
43 30 <span class="k">use</span> <span class="w">FindBin</span><span class="sc">;</span> <span class="k">use</span> <span class="w">lib</span> <span class="q">&quot;$FindBin::Bin/../lib&quot;</span><span class="sc">;</span>
44 31 <span class="k">use</span> <span class="w">Getopt::Long</span><span class="sc">;</span>
45 32 <span class="k">use</span> <span class="w">File::Basename</span><span class="sc">;</span>
46 33 <span class="k">use</span> <span class="w">Text::ParseWords</span><span class="sc">;</span>
47 34 <span class="k">use</span> <span class="w">Benchmark</span><span class="sc">;</span>
48 35 <span class="k">use</span> <span class="w">FileUtil</span><span class="sc">;</span>
49 36 <span class="k">use</span> <span class="w">TextUtil</span><span class="sc">;</span>
50 37 <span class="k">use</span> <span class="w">SDFileUtil</span><span class="sc">;</span>
51 38 <span class="k">use</span> <span class="w">MoleculeFileIO</span><span class="sc">;</span>
52 39 <span class="k">use</span> <span class="w">FileIO::FingerprintsSDFileIO</span><span class="sc">;</span>
53 40 <span class="k">use</span> <span class="w">FileIO::FingerprintsTextFileIO</span><span class="sc">;</span>
54 41 <span class="k">use</span> <span class="w">FileIO::FingerprintsFPFileIO</span><span class="sc">;</span>
55 42 <span class="k">use</span> <span class="w">AtomTypes::AtomicInvariantsAtomTypes</span><span class="sc">;</span>
56 43 <span class="k">use</span> <span class="w">AtomTypes::FunctionalClassAtomTypes</span><span class="sc">;</span>
57 44 <span class="k">use</span> <span class="w">Fingerprints::ExtendedConnectivityFingerprints</span><span class="sc">;</span>
58 45
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>
60 47
61 48 <span class="c"># Autoflush STDOUT</span>
62 49 <span class="i">$|</span> = <span class="n">1</span><span class="sc">;</span>
63 50
64 51 <span class="c"># Starting message...</span>
65 52 <span class="i">$ScriptName</span> = <span class="i">basename</span><span class="s">(</span><span class="i">$0</span><span class="s">)</span><span class="sc">;</span>
66 53 <span class="k">print</span> <span class="q">&quot;\n$ScriptName: Starting...\n\n&quot;</span><span class="sc">;</span>
67 54 <span class="i">$StartTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
68 55
69 56 <span class="c"># Get the options and setup script...</span>
70 57 <span class="i">SetupScriptUsage</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
71 58 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">help</span>} || <span class="i">@ARGV</span> &lt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
72 59 <span class="k">die</span> <span class="i">GetUsageFromPod</span><span class="s">(</span><span class="q">&quot;$FindBin::Bin/$ScriptName&quot;</span><span class="s">)</span><span class="sc">;</span>
73 60 <span class="s">}</span>
74 61
75 62 <span class="k">my</span><span class="s">(</span><span class="i">@SDFilesList</span><span class="s">)</span><span class="sc">;</span>
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">&quot;sdf sd&quot;</span><span class="s">)</span><span class="sc">;</span>
77 64
78 65 <span class="c"># Process options...</span>
79 66 <span class="k">print</span> <span class="q">&quot;Processing options...\n&quot;</span><span class="sc">;</span>
80 67 <span class="k">my</span><span class="s">(</span><span class="i">%OptionsInfo</span><span class="s">)</span><span class="sc">;</span>
81 68 <span class="i">ProcessOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
82 69
83 70 <span class="c"># Setup information about input files...</span>
84 71 <span class="k">print</span> <span class="q">&quot;Checking input SD file(s)...\n&quot;</span><span class="sc">;</span>
85 72 <span class="k">my</span><span class="s">(</span><span class="i">%SDFilesInfo</span><span class="s">)</span><span class="sc">;</span>
86 73 <span class="i">RetrieveSDFilesInfo</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
87 74
88 75 <span class="c"># Process input files..</span>
89 76 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
90 77 <span class="k">if</span> <span class="s">(</span><span class="i">@SDFilesList</span> &gt; <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
91 78 <span class="k">print</span> <span class="q">&quot;\nProcessing SD files...\n&quot;</span><span class="sc">;</span>
92 79 <span class="s">}</span>
93 80 <span class="k">for</span> <span class="i">$FileIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="i">$#SDFilesList</span><span class="s">)</span> <span class="s">{</span>
94 81 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$FileIndex</span>]<span class="s">)</span> <span class="s">{</span>
95 82 <span class="k">print</span> <span class="q">&quot;\nProcessing file $SDFilesList[$FileIndex]...\n&quot;</span><span class="sc">;</span>
96 83 <span class="i">GenerateExtendedConnectivityFingerprints</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
97 84 <span class="s">}</span>
98 85 <span class="s">}</span>
99 86 <span class="k">print</span> <span class="q">&quot;\n$ScriptName:Done...\n\n&quot;</span><span class="sc">;</span>
100 87
101 88 <span class="i">$EndTime</span> = <span class="w">new</span> <span class="w">Benchmark</span><span class="sc">;</span>
102 89 <span class="i">$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>
103 90 <span class="k">print</span> <span class="q">&quot;Total time: &quot;</span><span class="cm">,</span> <span class="i">timestr</span><span class="s">(</span><span class="i">$TotalTime</span><span class="s">)</span><span class="cm">,</span> <span class="q">&quot;\n&quot;</span><span class="sc">;</span>
104 91
105 92 <span class="c">###############################################################################</span>
106 93
107 94 <span class="c"># Generate fingerprints for a SD file...</span>
108 95 <span class="c">#</span>
109 <a name="GenerateExtendedConnectivityFingerprints-"></a> 96 <span class="k">sub </span><span class="m">GenerateExtendedConnectivityFingerprints</span> <span class="s">{</span>
110 97 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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">$Molecule</span><span class="cm">,</span> <span class="i">$ExtendedConnectivityFingerprints</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">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
112 99
113 100 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$FileIndex</span>]<span class="sc">;</span>
114 101
115 102 <span class="c"># Setup output files...</span>
116 103 <span class="c">#</span>
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>
118 105
119 106 <span class="i">$MoleculeFileIO</span> = <span class="w">new</span> <span class="i">MoleculeFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$SDFile</span><span class="s">)</span><span class="sc">;</span>
120 107 <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
121 108
122 109 <span class="i">$CmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
123 110 <span class="i">$IgnoredCmpdCount</span> = <span class="n">0</span><span class="sc">;</span>
124 111
125 112 <span class="j">COMPOUND:</span> <span class="k">while</span> <span class="s">(</span><span class="i">$Molecule</span> = <span class="i">$MoleculeFileIO</span><span class="i">-&gt;ReadMolecule</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
126 113 <span class="i">$CmpdCount</span>++<span class="sc">;</span>
127 114
128 115 <span class="c"># Filter compound data before calculating fingerprints...</span>
129 116 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Filter</span>}<span class="s">)</span> <span class="s">{</span>
130 117 <span class="k">if</span> <span class="s">(</span><span class="i">CheckAndFilterCompound</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
131 118 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
132 119 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
133 120 <span class="s">}</span>
134 121 <span class="s">}</span>
135 122
136 123 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="i">GenerateMoleculeFingerprints</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
137 124 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span> <span class="s">{</span>
138 125 <span class="i">$IgnoredCmpdCount</span>++<span class="sc">;</span>
139 126 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;FingerprintsGenerationFailed&#39;</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>
140 127 <span class="k">next</span> <span class="j">COMPOUND</span><span class="sc">;</span>
141 128 <span class="s">}</span>
142 129
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">$Molecule</span><span class="cm">,</span> <span class="i">$ExtendedConnectivityFingerprints</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">$NewFPFileIO</span><span class="s">)</span><span class="sc">;</span>
144 131 <span class="s">}</span>
145 132 <span class="i">$MoleculeFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
146 133
147 134 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
148 135 <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
149 136 <span class="s">}</span>
150 137 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
151 138 <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
152 139 <span class="s">}</span>
153 140 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
154 141 <span class="i">$NewFPFileIO</span><span class="i">-&gt;Close</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
155 142 <span class="s">}</span>
156 143
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>
158 145 <span class="s">}</span>
159 146
160 147 <span class="c"># Process compound being ignored due to problems in fingerprints geneation...</span>
161 148 <span class="c">#</span>
162 <a name="ProcessIgnoredCompound-"></a> 149 <span class="k">sub </span><span class="m">ProcessIgnoredCompound</span> <span class="s">{</span>
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">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
164 151 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="cm">,</span> <span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
165 152
166 153 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
167 154 <span class="i">$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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
168 155
169 156 <span class="j">MODE:</span> <span class="s">{</span>
170 157 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNonElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
171 158 <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n&quot;</span><span class="sc">;</span>
172 159 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
173 160 <span class="s">}</span>
174 161
175 162 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^ContainsNoElementalData$/i</span><span class="s">)</span> <span class="s">{</span>
176 163 <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n&quot;</span><span class="sc">;</span>
177 164 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
178 165 <span class="s">}</span>
179 166
180 167 <span class="k">if</span> <span class="s">(</span><span class="i">$Mode</span> =~ <span class="q">/^FingerprintsGenerationFailed$/i</span><span class="s">)</span> <span class="s">{</span>
181 168 <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
182 169 <span class="k">next</span> <span class="j">MODE</span><span class="sc">;</span>
183 170 <span class="s">}</span>
184 171 <span class="k">warn</span> <span class="q">&quot;\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn&#39;t succeed...\n\n&quot;</span><span class="sc">;</span>
185 172 <span class="s">}</span>
186 173 <span class="s">}</span>
187 174
188 175 <span class="c"># Check and filter compounds....</span>
189 176 <span class="c">#</span>
190 <a name="CheckAndFilterCompound-"></a> 177 <span class="k">sub </span><span class="m">CheckAndFilterCompound</span> <span class="s">{</span>
191 178 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
192 179 <span class="k">my</span><span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span><span class="sc">;</span>
193 180
194 181 <span class="s">(</span><span class="i">$ElementCount</span><span class="cm">,</span> <span class="i">$NonElementCount</span><span class="s">)</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetNumOfElementsAndNonElements</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
195 182
196 183 <span class="k">if</span> <span class="s">(</span><span class="i">$NonElementCount</span><span class="s">)</span> <span class="s">{</span>
197 184 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;ContainsNonElementalData&#39;</span><span class="cm">,</span> <span class="i">$CmpdCount</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span><span class="sc">;</span>
198 185 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
199 186 <span class="s">}</span>
200 187
201 188 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ElementCount</span><span class="s">)</span> <span class="s">{</span>
202 189 <span class="i">ProcessIgnoredCompound</span><span class="s">(</span><span class="q">&#39;ContainsNoElementalData&#39;</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>
203 190 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span>
204 191 <span class="s">}</span>
205 192
206 193 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span>
207 194 <span class="s">}</span>
208 195
209 196 <span class="c"># Write out compounds fingerprints generation summary statistics...</span>
210 197 <span class="c">#</span>
211 <a name="WriteFingerprintsGenerationSummaryStatistics-"></a> 198 <span class="k">sub </span><span class="m">WriteFingerprintsGenerationSummaryStatistics</span> <span class="s">{</span>
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>
213 200 <span class="k">my</span><span class="s">(</span><span class="i">$ProcessedCmpdCount</span><span class="s">)</span><span class="sc">;</span>
214 201
215 202 <span class="i">$ProcessedCmpdCount</span> = <span class="i">$CmpdCount</span> - <span class="i">$IgnoredCmpdCount</span><span class="sc">;</span>
216 203
217 204 <span class="k">print</span> <span class="q">&quot;\nNumber of compounds: $CmpdCount\n&quot;</span><span class="sc">;</span>
218 205 <span class="k">print</span> <span class="q">&quot;Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n&quot;</span><span class="sc">;</span>
219 206 <span class="k">print</span> <span class="q">&quot;Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n&quot;</span><span class="sc">;</span>
220 207 <span class="s">}</span>
221 208
222 209 <span class="c"># Open output files...</span>
223 210 <span class="c">#</span>
224 <a name="SetupAndOpenOutputFiles-"></a> 211 <span class="k">sub </span><span class="m">SetupAndOpenOutputFiles</span> <span class="s">{</span>
225 212 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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>
227 214
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">$NewFPFileIO</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="s">)</span> x <span class="n">3</span><span class="sc">;</span>
229 216
230 217 <span class="c"># Setup common parameters for fingerprints file IO objects...</span>
231 218 <span class="c">#</span>
232 219 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
233 220 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ExtendedConnectivity|ExtendedConnectivityCount)$/i</span><span class="s">)</span> <span class="s">{</span>
234 221 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Write&#39;</span><span class="cm">,</span> <span class="q">&#39;Overwrite&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;FingerprintsVectorString&#39;</span><span class="cm">,</span> <span class="q">&#39;VectorStringFormat&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>}<span class="s">)</span><span class="sc">;</span>
235 222 <span class="s">}</span>
236 223 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
237 224 <span class="i">%FingerprintsFileIOParams</span> = <span class="s">(</span><span class="q">&#39;Mode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;Write&#39;</span><span class="cm">,</span> <span class="q">&#39;Overwrite&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="cm">,</span> <span class="q">&#39;FingerprintsStringMode&#39;</span> <span class="cm">=&gt;</span> <span class="q">&#39;FingerprintsBitVectorString&#39;</span><span class="cm">,</span> <span class="q">&#39;BitStringFormat&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>}<span class="cm">,</span> <span class="q">&#39;BitsOrder&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>}<span class="s">)</span><span class="sc">;</span>
238 225 <span class="s">}</span>
239 226
240 227 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
241 228 <span class="i">$NewFPSDFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
242 229 <span class="k">print</span> <span class="q">&quot;Generating SD file $NewFPSDFile...\n&quot;</span><span class="sc">;</span>
243 230 <span class="i">$NewFPSDFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsSDFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPSDFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">&#39;FingerprintsFieldLabel&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="s">)</span><span class="sc">;</span>
244 231 <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
245 232 <span class="s">}</span>
246 233
247 234 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
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>
249 236 <span class="k">print</span> <span class="q">&quot;Generating FP file $NewFPFile...\n&quot;</span><span class="sc">;</span>
250 237 <span class="i">$NewFPFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsFPFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="s">)</span><span class="sc">;</span>
251 238 <span class="i">$NewFPFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
252 239 <span class="s">}</span>
253 240
254 241 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
255 242 <span class="k">my</span><span class="s">(</span><span class="i">$ColLabelsRef</span><span class="s">)</span><span class="sc">;</span>
256 243
257 244 <span class="i">$NewFPTextFile</span> = <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$FileIndex</span>]<span class="sc">;</span>
258 245 <span class="i">$ColLabelsRef</span> = <span class="i">SetupFPTextFileCoulmnLabels</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span><span class="sc">;</span>
259 246
260 247 <span class="k">print</span> <span class="q">&quot;Generating text file $NewFPTextFile...\n&quot;</span><span class="sc">;</span>
261 248 <span class="i">$NewFPTextFileIO</span> = <span class="w">new</span> <span class="i">FileIO::FingerprintsTextFileIO</span><span class="s">(</span><span class="q">&#39;Name&#39;</span> <span class="cm">=&gt;</span> <span class="i">$NewFPTextFile</span><span class="cm">,</span> <span class="i">%FingerprintsFileIOParams</span><span class="cm">,</span> <span class="q">&#39;DataColLabels&#39;</span> <span class="cm">=&gt;</span> <span class="i">$ColLabelsRef</span><span class="cm">,</span> <span class="q">&#39;OutDelim&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>}<span class="cm">,</span> <span class="q">&#39;OutQuote&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">OutQuote</span>}<span class="s">)</span><span class="sc">;</span>
262 249 <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;Open</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
263 250 <span class="s">}</span>
264 251
265 252 <span class="k">return</span> <span class="s">(</span><span class="i">$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>
266 253 <span class="s">}</span>
267 254
268 255 <span class="c"># Write fingerpritns and other data to appropriate output files...</span>
269 256 <span class="c">#</span>
270 <a name="WriteDataToOutputFiles-"></a> 257 <span class="k">sub </span><span class="m">WriteDataToOutputFiles</span> <span class="s">{</span>
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">$Molecule</span><span class="cm">,</span> <span class="i">$ExtendedConnectivityFingerprints</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">$NewFPFileIO</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
272 259 <span class="k">my</span><span class="s">(</span><span class="i">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
273 260
274 261 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="k">undef</span><span class="sc">;</span>
275 262 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span> || <span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
276 263 <span class="i">$DataFieldLabelAndValuesRef</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetDataFieldLabelAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
277 264 <span class="s">}</span>
278 265
279 266 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPSDFileIO</span><span class="s">)</span> <span class="s">{</span>
280 267 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
281 268
282 269 <span class="i">$CmpdString</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetInputMoleculeString</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
283 270 <span class="i">$NewFPSDFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="s">)</span><span class="sc">;</span>
284 271 <span class="s">}</span>
285 272
286 273 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPTextFileIO</span><span class="s">)</span> <span class="s">{</span>
287 274 <span class="k">my</span><span class="s">(</span><span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
288 275
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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
290 277 <span class="i">$NewFPTextFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="cm">,</span> <span class="i">$ColValuesRef</span><span class="s">)</span><span class="sc">;</span>
291 278 <span class="s">}</span>
292 279
293 280 <span class="k">if</span> <span class="s">(</span><span class="i">$NewFPFileIO</span><span class="s">)</span> <span class="s">{</span>
294 281 <span class="k">my</span><span class="s">(</span><span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
295 282
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>
297 284 <span class="i">$NewFPFileIO</span><span class="i">-&gt;WriteFingerprints</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="cm">,</span> <span class="i">$CompoundID</span><span class="s">)</span><span class="sc">;</span>
298 285 <span class="s">}</span>
299 286 <span class="s">}</span>
300 287
301 288 <span class="c"># Generate approriate column labels for FPText output file...</span>
302 289 <span class="c">#</span>
303 <a name="SetupFPTextFileCoulmnLabels-"></a> 290 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnLabels</span> <span class="s">{</span>
304 291 <span class="k">my</span><span class="s">(</span><span class="i">$FileIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
305 292 <span class="k">my</span><span class="s">(</span><span class="i">$Line</span><span class="cm">,</span> <span class="i">@ColLabels</span><span class="s">)</span><span class="sc">;</span>
306 293
307 294 <span class="i">@ColLabels</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
308 295 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
309 296 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
310 297 <span class="s">}</span>
311 298 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
312 299 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
313 300 <span class="s">}</span>
314 301 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
315 302 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
316 303 <span class="s">}</span>
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>
318 305 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>}<span class="sc">;</span>
319 306 <span class="s">}</span>
320 307 <span class="c"># Add fingerprints label...</span>
321 308 <span class="k">push</span> <span class="i">@ColLabels</span><span class="cm">,</span> <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>}<span class="sc">;</span>
322 309
323 310 <span class="k">return</span> \<span class="i">@ColLabels</span><span class="sc">;</span>
324 311 <span class="s">}</span>
325 312
326 313 <span class="c"># Generate column values FPText output file..</span>
327 314 <span class="c">#</span>
328 <a name="SetupFPTextFileCoulmnValues-"></a> 315 <span class="k">sub </span><span class="m">SetupFPTextFileCoulmnValues</span> <span class="s">{</span>
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>
330 317 <span class="k">my</span><span class="s">(</span><span class="i">@ColValues</span><span class="s">)</span><span class="sc">;</span>
331 318
332 319 <span class="i">@ColValues</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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>
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">$DataFieldLabelAndValuesRef</span><span class="s">)</span><span class="sc">;</span>
335 322 <span class="s">}</span>
336 323 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^All$/i</span><span class="s">)</span> <span class="s">{</span>
337 324 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
338 325 <span class="s">}</span>
339 326 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Common$/i</span><span class="s">)</span> <span class="s">{</span>
340 327 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$FileIndex</span>]}<span class="sc">;</span>
341 328 <span class="s">}</span>
342 329 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
343 330 <span class="i">@ColValues</span> = <span class="k">map</span> <span class="s">{</span> <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$_</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="s">}</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="sc">;</span>
344 331 <span class="s">}</span>
345 332
346 333 <span class="k">return</span> \<span class="i">@ColValues</span><span class="sc">;</span>
347 334 <span class="s">}</span>
348 335
349 336 <span class="c"># Generate compound ID for FP and FPText output files..</span>
350 337 <span class="c">#</span>
351 <a name="SetupCmpdIDForOutputFiles-"></a> 338 <span class="k">sub </span><span class="m">SetupCmpdIDForOutputFiles</span> <span class="s">{</span>
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">$DataFieldLabelAndValuesRef</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
353 340 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdID</span><span class="s">)</span><span class="sc">;</span>
354 341
355 342 <span class="i">$CmpdID</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
356 343 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^MolNameOrLabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
357 344 <span class="k">my</span><span class="s">(</span><span class="i">$MolName</span><span class="s">)</span><span class="sc">;</span>
358 345 <span class="i">$MolName</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
359 346 <span class="i">$CmpdID</span> = <span class="i">$MolName</span> ? <span class="i">$MolName</span> <span class="co">:</span> <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
360 347 <span class="s">}</span>
361 348 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} =~ <span class="q">/^LabelPrefix$/i</span><span class="s">)</span> <span class="s">{</span>
362 349 <span class="i">$CmpdID</span> = <span class="q">&quot;$OptionsInfo{CompoundID}${CmpdCount}&quot;</span><span class="sc">;</span>
363 350 <span class="s">}</span>
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>
365 352 <span class="k">my</span><span class="s">(</span><span class="i">$SpecifiedDataField</span><span class="s">)</span><span class="sc">;</span>
366 353 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
367 354 <span class="i">$CmpdID</span> = <span class="k">exists</span> <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$SpecifiedDataField</span>} ? <span class="i">$DataFieldLabelAndValuesRef</span>-&gt;{<span class="i">$SpecifiedDataField</span>} <span class="co">:</span> <span class="q">&#39;&#39;</span><span class="sc">;</span>
368 355 <span class="s">}</span>
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>
370 357 <span class="i">$CmpdID</span> = <span class="i">$Molecule</span><span class="i">-&gt;GetName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
371 358 <span class="s">}</span>
372 359 <span class="k">return</span> <span class="i">$CmpdID</span><span class="sc">;</span>
373 360 <span class="s">}</span>
374 361
375 362 <span class="c"># Generate fingerprints for molecule...</span>
376 363 <span class="c">#</span>
377 <a name="GenerateMoleculeFingerprints-"></a> 364 <span class="k">sub </span><span class="m">GenerateMoleculeFingerprints</span> <span class="s">{</span>
378 365 <span class="k">my</span><span class="s">(</span><span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
379 366 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span><span class="sc">;</span>
380 367
381 368 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">KeepLargestComponent</span>}<span class="s">)</span> <span class="s">{</span>
382 369 <span class="i">$Molecule</span><span class="i">-&gt;KeepLargestComponent</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
383 370 <span class="s">}</span>
384 371 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Molecule</span><span class="i">-&gt;DetectRings</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
385 372 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
386 373 <span class="s">}</span>
387 374 <span class="i">$Molecule</span><span class="i">-&gt;SetAromaticityModel</span><span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>}<span class="s">)</span><span class="sc">;</span>
388 375 <span class="i">$Molecule</span><span class="i">-&gt;DetectAromaticity</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
389 376
390 377 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="k">undef</span><span class="sc">;</span>
391 378 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^(ExtendedConnectivity|ExtendedConnectivityCount)$/i</span> <span class="s">)</span> <span class="s">{</span>
392 379 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">&#39;Type&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;NeighborhoodRadius&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">&#39;AtomIdentifierType&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="s">)</span><span class="sc">;</span>
393 380 <span class="s">}</span>
394 381 <span class="k">elsif</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} =~ <span class="q">/^ExtendedConnectivityBits$/i</span><span class="s">)</span> <span class="s">{</span>
395 382 <span class="i">$ExtendedConnectivityFingerprints</span> = <span class="w">new</span> <span class="i">Fingerprints::ExtendedConnectivityFingerprints</span><span class="s">(</span><span class="q">&#39;Type&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>}<span class="cm">,</span> <span class="q">&#39;Molecule&#39;</span> <span class="cm">=&gt;</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="q">&#39;NeighborhoodRadius&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">NeighborhoodRadius</span>}<span class="cm">,</span> <span class="q">&#39;AtomIdentifierType&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>}<span class="cm">,</span> <span class="q">&#39;Size&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">Size</span>}<span class="cm">,</span> <span class="q">&#39;UsePerlCoreRandom&#39;</span> <span class="cm">=&gt;</span> <span class="i">$OptionsInfo</span>{<span class="w">UsePerlCoreRandom</span>}<span class="s">)</span><span class="sc">;</span>
396 383 <span class="s">}</span>
397 384 <span class="k">else</span> <span class="s">{</span>
398 385 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits\n&quot;</span><span class="sc">;</span>
399 386 <span class="s">}</span>
400 387 <span class="i">SetAtomIdentifierTypeValuesToUse</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span><span class="sc">;</span>
401 388
402 389 <span class="c"># Generate fingerprints...</span>
403 390 <span class="i">$ExtendedConnectivityFingerprints</span><span class="i">-&gt;GenerateFingerprints</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
404 391
405 392 <span class="c"># Make sure fingerprints generation is successful...</span>
406 393 <span class="k">if</span> <span class="s">(</span>!<span class="i">$ExtendedConnectivityFingerprints</span><span class="i">-&gt;IsFingerprintsGenerationSuccessful</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
407 394 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
408 395 <span class="s">}</span>
409 396
410 397 <span class="k">return</span> <span class="i">$ExtendedConnectivityFingerprints</span><span class="sc">;</span>
411 398 <span class="s">}</span>
412 399
413 400 <span class="c"># Set atom identifier type to use for generating fingerprints...</span>
414 401 <span class="c">#</span>
415 <a name="SetAtomIdentifierTypeValuesToUse-"></a> 402 <span class="k">sub </span><span class="m">SetAtomIdentifierTypeValuesToUse</span> <span class="s">{</span>
416 403 <span class="k">my</span><span class="s">(</span><span class="i">$ExtendedConnectivityFingerprints</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
417 404
418 405 <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>
419 406 <span class="i">$ExtendedConnectivityFingerprints</span><span class="i">-&gt;SetAtomicInvariantsToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}}<span class="s">)</span><span class="sc">;</span>
420 407 <span class="s">}</span>
421 408 <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>
422 409 <span class="i">$ExtendedConnectivityFingerprints</span><span class="i">-&gt;SetFunctionalClassesToUse</span><span class="s">(</span>\<span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="s">)</span><span class="sc">;</span>
423 410 <span class="s">}</span>
424 411 <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>
425 412 <span class="c"># Nothing to do for now...</span>
426 413 <span class="s">}</span>
427 414 <span class="k">else</span> <span class="s">{</span>
428 415 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
429 416 <span class="s">}</span>
430 417 <span class="s">}</span>
431 418
432 419 <span class="c"># Retrieve information about SD files...</span>
433 420 <span class="c">#</span>
434 <a name="RetrieveSDFilesInfo-"></a> 421 <span class="k">sub </span><span class="m">RetrieveSDFilesInfo</span> <span class="s">{</span>
435 422 <span class="k">my</span><span class="s">(</span><span class="i">$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">$CommonDataFieldsRef</span><span class="s">)</span><span class="sc">;</span>
436 423
437 424 <span class="i">%SDFilesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
438 425 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
439 426 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
440 427 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
441 428 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
442 429 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
443 430 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
444 431 <span class="i">@</span>{<span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
445 432
446 433 <span class="i">$CheckDataField</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} &amp;&amp; <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> &amp;&amp; <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>
447 434 <span class="i">$CollectDataFields</span> = <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>} &amp;&amp; <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>
448 435
449 436 <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>
450 437 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
451 438
452 439 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">0</span><span class="sc">;</span>
453 440 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
454 441 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
455 442 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
456 443 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="q">&#39;&#39;</span><span class="sc">;</span>
457 444
458 445 <span class="i">$SDFile</span> = <span class="i">$SDFilesList</span>[<span class="i">$Index</span>]<span class="sc">;</span>
459 446 <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>
460 447 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
461 448 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
462 449 <span class="s">}</span>
463 450 <span class="k">if</span> <span class="s">(</span>!<span class="i">CheckFileType</span><span class="s">(</span><span class="i">$SDFile</span><span class="cm">,</span> <span class="q">&quot;sd sdf&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
464 451 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: It&#39;s not a SD file\n&quot;</span><span class="sc">;</span>
465 452 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
466 453 <span class="s">}</span>
467 454
468 455 <span class="k">if</span> <span class="s">(</span><span class="i">$CheckDataField</span><span class="s">)</span> <span class="s">{</span>
469 456 <span class="c"># Make sure data field exists in SD file..</span>
470 457 <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>
471 458
472 459 <span class="i">@CmpdLines</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
473 460 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
474 461 <span class="i">$CmpdString</span> = <span class="i">ReadCmpdString</span><span class="s">(</span>\<span class="i">*SDFILE</span><span class="s">)</span><span class="sc">;</span>
475 462 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
476 463 <span class="i">@CmpdLines</span> = <span class="k">split</span> <span class="q">&quot;\n&quot;</span><span class="cm">,</span> <span class="i">$CmpdString</span><span class="sc">;</span>
477 464 <span class="i">%DataFieldValues</span> = <span class="i">GetCmpdDataHeaderLabelsAndValues</span><span class="s">(</span>\<span class="i">@CmpdLines</span><span class="s">)</span><span class="sc">;</span>
478 465 <span class="i">$SpecifiedDataField</span> = <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>}<span class="sc">;</span>
479 466 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$DataFieldValues</span>{<span class="i">$SpecifiedDataField</span>}<span class="s">)</span> <span class="s">{</span>
480 467 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot; doesn&#39;t exist\n&quot;</span><span class="sc">;</span>
481 468 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
482 469 <span class="s">}</span>
483 470 <span class="s">}</span>
484 471
485 472 <span class="i">$AllDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
486 473 <span class="i">$CommonDataFieldsRef</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
487 474 <span class="k">if</span> <span class="s">(</span><span class="i">$CollectDataFields</span><span class="s">)</span> <span class="s">{</span>
488 475 <span class="k">my</span><span class="s">(</span><span class="i">$CmpdCount</span><span class="s">)</span><span class="sc">;</span>
489 476 <span class="k">open</span> <span class="w">SDFILE</span><span class="cm">,</span> <span class="q">&quot;$SDFile&quot;</span> <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t open $SDFile: $! \n&quot;</span><span class="sc">;</span>
490 477 <span class="s">(</span><span class="i">$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>
491 478 <span class="k">close</span> <span class="w">SDFILE</span><span class="sc">;</span>
492 479 <span class="s">}</span>
493 480
494 481 <span class="c"># Setup output file names...</span>
495 482 <span class="i">$FileDir</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileName</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span> <span class="i">$FileExt</span> = <span class="q">&quot;&quot;</span><span class="sc">;</span>
496 483 <span class="s">(</span><span class="i">$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">$SDFile</span><span class="s">)</span><span class="sc">;</span>
497 484
498 485 <span class="i">$TextOutFileExt</span> = <span class="q">&quot;csv&quot;</span><span class="sc">;</span>
499 486 <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>
500 487 <span class="i">$TextOutFileExt</span> = <span class="q">&quot;tsv&quot;</span><span class="sc">;</span>
501 488 <span class="s">}</span>
502 489 <span class="i">$SDOutFileExt</span> = <span class="i">$FileExt</span><span class="sc">;</span>
503 490 <span class="i">$FPOutFileExt</span> = <span class="q">&quot;fpf&quot;</span><span class="sc">;</span>
504 491
505 492 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} &amp;&amp; <span class="s">(</span><span class="i">@SDFilesList</span> == <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
506 493 <span class="k">my</span> <span class="s">(</span><span class="i">$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">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="s">)</span><span class="sc">;</span>
507 494 <span class="k">if</span> <span class="s">(</span><span class="i">$RootFileName</span> &amp;&amp; <span class="i">$RootFileExt</span><span class="s">)</span> <span class="s">{</span>
508 495 <span class="i">$FileName</span> = <span class="i">$RootFileName</span><span class="sc">;</span>
509 496 <span class="s">}</span>
510 497 <span class="k">else</span> <span class="s">{</span>
511 498 <span class="i">$FileName</span> = <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>}<span class="sc">;</span>
512 499 <span class="s">}</span>
513 500 <span class="i">$OutFileRoot</span> = <span class="i">$FileName</span><span class="sc">;</span>
514 501 <span class="s">}</span>
515 502 <span class="k">else</span> <span class="s">{</span>
516 503 <span class="i">$OutFileRoot</span> = <span class="q">&quot;${FileName}ExtendedConnectivityFP&quot;</span><span class="sc">;</span>
517 504 <span class="s">}</span>
518 505
519 506 <span class="i">$NewSDFileName</span> = <span class="q">&quot;${OutFileRoot}.${SDOutFileExt}&quot;</span><span class="sc">;</span>
520 507 <span class="i">$NewFPFileName</span> = <span class="q">&quot;${OutFileRoot}.${FPOutFileExt}&quot;</span><span class="sc">;</span>
521 508 <span class="i">$NewTextFileName</span> = <span class="q">&quot;${OutFileRoot}.${TextOutFileExt}&quot;</span><span class="sc">;</span>
522 509
523 510 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
524 511 <span class="k">if</span> <span class="s">(</span><span class="i">$SDFile</span> =~ <span class="q">/$NewSDFileName/i</span><span class="s">)</span> <span class="s">{</span>
525 512 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n&quot;</span><span class="sc">;</span>
526 513 <span class="k">print</span> <span class="q">&quot;Specify a different name using \&quot;-r --root\&quot; option or use default name.\n&quot;</span><span class="sc">;</span>
527 514 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
528 515 <span class="s">}</span>
529 516 <span class="s">}</span>
530 517
531 518 <span class="k">if</span> <span class="s">(</span>!<span class="i">$OptionsInfo</span>{<span class="w">OverwriteFiles</span>}<span class="s">)</span> <span class="s">{</span>
532 519 <span class="c"># Check SD and text outout files...</span>
533 520 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">SDOutput</span>}<span class="s">)</span> <span class="s">{</span>
534 521 <span class="k">if</span> <span class="s">(</span><span class="k">-e</span> <span class="i">$NewSDFileName</span><span class="s">)</span> <span class="s">{</span>
535 522 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n&quot;</span><span class="sc">;</span>
536 523 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
537 524 <span class="s">}</span>
538 525 <span class="s">}</span>
539 526 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">FPOutput</span>}<span class="s">)</span> <span class="s">{</span>
540 527 <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>
541 528 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n&quot;</span><span class="sc">;</span>
542 529 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
543 530 <span class="s">}</span>
544 531 <span class="s">}</span>
545 532 <span class="k">if</span> <span class="s">(</span><span class="i">$OptionsInfo</span>{<span class="w">TextOutput</span>}<span class="s">)</span> <span class="s">{</span>
546 533 <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>
547 534 <span class="k">warn</span> <span class="q">&quot;Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n&quot;</span><span class="sc">;</span>
548 535 <span class="k">next</span> <span class="j">FILELIST</span><span class="sc">;</span>
549 536 <span class="s">}</span>
550 537 <span class="s">}</span>
551 538 <span class="s">}</span>
552 539
553 540 <span class="i">$SDFilesInfo</span>{<span class="w">FileOkay</span>}[<span class="i">$Index</span>] = <span class="n">1</span><span class="sc">;</span>
554 541
555 542 <span class="i">$SDFilesInfo</span>{<span class="w">OutFileRoot</span>}[<span class="i">$Index</span>] = <span class="i">$OutFileRoot</span><span class="sc">;</span>
556 543 <span class="i">$SDFilesInfo</span>{<span class="w">SDOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewSDFileName</span><span class="sc">;</span>
557 544 <span class="i">$SDFilesInfo</span>{<span class="w">FPOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewFPFileName</span><span class="sc">;</span>
558 545 <span class="i">$SDFilesInfo</span>{<span class="w">TextOutFileNames</span>}[<span class="i">$Index</span>] = <span class="i">$NewTextFileName</span><span class="sc">;</span>
559 546
560 547 <span class="i">$SDFilesInfo</span>{<span class="w">AllDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$AllDataFieldsRef</span><span class="sc">;</span>
561 548 <span class="i">$SDFilesInfo</span>{<span class="w">CommonDataFieldsRef</span>}[<span class="i">$Index</span>] = <span class="i">$CommonDataFieldsRef</span><span class="sc">;</span>
562 549 <span class="s">}</span>
563 550 <span class="s">}</span>
564 551
565 552 <span class="c"># Process option values...</span>
566 <a name="ProcessOptions-"></a> 553 <span class="k">sub </span><span class="m">ProcessOptions</span> <span class="s">{</span>
567 554 <span class="i">%OptionsInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
568 555
569 556 <span class="i">ProcessAtomIdentifierTypeOptions</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
570 557
571 558 <span class="i">$OptionsInfo</span>{<span class="w">AromaticityModel</span>} = <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="sc">;</span>
572 559
573 560 <span class="i">$OptionsInfo</span>{<span class="w">BitsOrder</span>} = <span class="i">$Options</span>{<span class="w">bitsorder</span>}<span class="sc">;</span>
574 561 <span class="i">$OptionsInfo</span>{<span class="w">BitStringFormat</span>} = <span class="i">$Options</span>{<span class="w">bitstringformat</span>}<span class="sc">;</span>
575 562
576 563 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDMode</span>} = <span class="i">$Options</span>{<span class="w">compoundidmode</span>}<span class="sc">;</span>
577 564 <span class="i">$OptionsInfo</span>{<span class="w">CompoundIDLabel</span>} = <span class="i">$Options</span>{<span class="w">compoundidlabel</span>}<span class="sc">;</span>
578 565 <span class="i">$OptionsInfo</span>{<span class="w">DataFieldsMode</span>} = <span class="i">$Options</span>{<span class="w">datafieldsmode</span>}<span class="sc">;</span>
579 566
580 567 <span class="k">my</span><span class="s">(</span><span class="i">@SpecifiedDataFields</span><span class="s">)</span><span class="sc">;</span>
581 568 <span class="i">@SpecifiedDataFields</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
582 569
583 570 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
584 571 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
585 572
586 573 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^CompoundID$/i</span><span class="s">)</span> <span class="s">{</span>
587 574 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} =~ <span class="q">/^DataField$/i</span><span class="s">)</span> <span class="s">{</span>
588 575 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="s">)</span> <span class="s">{</span>
589 576 <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--CompoundID\&quot; option in \&quot;DataField\&quot; \&quot;--CompoundIDMode\&quot;. \n&quot;</span><span class="sc">;</span>
590 577 <span class="s">}</span>
591 578 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>}<span class="sc">;</span>
592 579 <span class="s">}</span>
593 580 <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>
594 581 <span class="i">$OptionsInfo</span>{<span class="w">CompoundID</span>} = <span class="i">$Options</span>{<span class="w">compoundid</span>} ? <span class="i">$Options</span>{<span class="w">compoundid</span>} <span class="co">:</span> <span class="q">&#39;Cmpd&#39;</span><span class="sc">;</span>
595 582 <span class="s">}</span>
596 583 <span class="s">}</span>
597 584 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} =~ <span class="q">/^Specify$/i</span><span class="s">)</span> <span class="s">{</span>
598 585 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Options</span>{<span class="w">datafields</span>}<span class="s">)</span> <span class="s">{</span>
599 586 <span class="k">die</span> <span class="q">&quot;Error: You must specify a value for \&quot;--DataFields\&quot; option in \&quot;Specify\&quot; \&quot;-d, --DataFieldsMode\&quot;. \n&quot;</span><span class="sc">;</span>
600 587 <span class="s">}</span>
601 588 <span class="i">@SpecifiedDataFields</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">datafields</span>}<span class="sc">;</span>
602 589 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">SpecifiedDataFields</span>}}<span class="cm">,</span> <span class="i">@SpecifiedDataFields</span><span class="sc">;</span>
603 590 <span class="s">}</span>
604 591
605 592 <span class="i">$OptionsInfo</span>{<span class="w">FingerprintsLabel</span>} = <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} ? <span class="i">$Options</span>{<span class="w">fingerprintslabel</span>} <span class="co">:</span> <span class="q">&#39;ExtendedConnectivityFingerprints&#39;</span><span class="sc">;</span>
606 593
607 594 <span class="i">$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>
608 595
609 596 <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$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
610 597
611 598 <span class="i">$OptionsInfo</span>{<span class="w">Mode</span>} = <span class="i">$Options</span>{<span class="w">mode</span>}<span class="sc">;</span>
612 599
613 600 <span class="i">$OptionsInfo</span>{<span class="w">NeighborhoodRadius</span>} = <span class="i">$Options</span>{<span class="w">neighborhoodradius</span>}<span class="sc">;</span>
614 601
615 602 <span class="i">$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>
616 603
617 604 <span class="i">$OptionsInfo</span>{<span class="w">Output</span>} = <span class="i">$Options</span>{<span class="w">output</span>}<span class="sc">;</span>
618 605 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
619 606 <span class="i">$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>
620 607 <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)$/i</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
621 608
622 609 <span class="i">$OptionsInfo</span>{<span class="w">OutDelim</span>} = <span class="i">$Options</span>{<span class="w">outdelim</span>}<span class="sc">;</span>
623 610 <span class="i">$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>
624 611
625 612 <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>
626 613 <span class="i">$OptionsInfo</span>{<span class="w">OutFileRoot</span>} = <span class="i">$Options</span>{<span class="w">root</span>} ? <span class="i">$Options</span>{<span class="w">root</span>} <span class="co">:</span> <span class="n">0</span><span class="sc">;</span>
627 614
628 615 <span class="k">my</span><span class="s">(</span><span class="i">$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>
629 616 <span class="i">$MinSize</span> = <span class="n">32</span><span class="sc">;</span>
630 617 <span class="i">$MaxSize</span> = <span class="n">2</span>**<span class="n">32</span><span class="sc">;</span>
631 618 <span class="i">$Size</span> = <span class="i">$Options</span>{<span class="w">size</span>}<span class="sc">;</span>
632 619 <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">$Size</span><span class="s">)</span> &amp;&amp; <span class="i">$Size</span> &gt;= <span class="i">$MinSize</span> &amp;&amp; <span class="i">$Size</span> &lt;= <span class="i">$MaxSize</span> &amp;&amp; <span class="i">IsNumberPowerOfNumber</span><span class="s">(</span><span class="i">$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>
633 620 <span class="k">die</span> <span class="q">&quot;Error: Invalid size value, $Size, for \&quot;-s, --size\&quot; option. Allowed values: power of 2, &gt;= minimum size of $MinSize, and &lt;= maximum size of $MaxSize.\n&quot;</span><span class="sc">;</span>
634 621 <span class="s">}</span>
635 622 <span class="i">$OptionsInfo</span>{<span class="w">Size</span>} = <span class="i">$Size</span><span class="sc">;</span>
636 623
637 624 <span class="c"># Setup default vector string format...</span>
638 625 <span class="c">#</span>
639 626 <span class="k">my</span><span class="s">(</span><span class="i">$VectorStringFormat</span><span class="s">)</span><span class="sc">;</span>
640 627 <span class="i">$VectorStringFormat</span> = <span class="q">&#39;&#39;</span><span class="sc">;</span>
641 628 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="s">)</span> <span class="s">{</span>
642 629 <span class="i">$VectorStringFormat</span> = <span class="i">$Options</span>{<span class="w">vectorstringformat</span>}<span class="sc">;</span>
643 630 <span class="s">}</span>
644 631 <span class="k">else</span> <span class="s">{</span>
645 632 <span class="i">$VectorStringFormat</span> = <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} =~ <span class="q">/^ExtendedConnectivity$/</span><span class="s">)</span> ? <span class="q">&quot;ValuesString&quot;</span> <span class="co">:</span> <span class="q">&quot;IDsAndValuesString&quot;</span><span class="sc">;</span>
646 633 <span class="s">}</span>
647 634 <span class="i">$OptionsInfo</span>{<span class="w">VectorStringFormat</span>} = <span class="i">$VectorStringFormat</span><span class="sc">;</span>
648 635 <span class="s">}</span>
649 636
650 637 <span class="c"># Process atom identifier type and related options...</span>
651 638 <span class="c">#</span>
652 <a name="ProcessAtomIdentifierTypeOptions-"></a> 639 <span class="k">sub </span><span class="m">ProcessAtomIdentifierTypeOptions</span> <span class="s">{</span>
653 640
654 641 <span class="i">$OptionsInfo</span>{<span class="w">AtomIdentifierType</span>} = <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>}<span class="sc">;</span>
655 642
656 643 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^AtomicInvariantsAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
657 644 <span class="i">ProcessAtomicInvariantsToUseOption</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
658 645 <span class="s">}</span>
659 646 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} =~ <span class="q">/^FunctionalClassAtomTypes$/i</span><span class="s">)</span> <span class="s">{</span>
660 647 <span class="i">ProcessFunctionalClassesToUse</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
661 648 <span class="s">}</span>
662 649 <span class="k">elsif</span> <span class="s">(</span><span class="i">$Options</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>
663 650 <span class="c"># Nothing to do for now...</span>
664 651 <span class="s">}</span>
665 652 <span class="k">else</span> <span class="s">{</span>
666 653 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
667 654 <span class="s">}</span>
668 655 <span class="s">}</span>
669 656
670 657 <span class="c"># Process specified atomic invariants to use...</span>
671 658 <span class="c">#</span>
672 <a name="ProcessAtomicInvariantsToUseOption-"></a> 659 <span class="k">sub </span><span class="m">ProcessAtomicInvariantsToUseOption</span> <span class="s">{</span>
673 660 <span class="k">my</span><span class="s">(</span><span class="i">$AtomicInvariant</span><span class="cm">,</span> <span class="i">$AtomSymbolSpecified</span><span class="cm">,</span> <span class="i">@AtomicInvariantsWords</span><span class="s">)</span><span class="sc">;</span>
674 661
675 662 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">AtomicInvariantsToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
676 663 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
677 664 <span class="k">die</span> <span class="q">&quot;Error: Atomic invariants value specified using \&quot;--AtomicInvariantsToUse\&quot; option is empty\n&quot;</span><span class="sc">;</span>
678 665 <span class="s">}</span>
679 666 <span class="i">$AtomSymbolSpecified</span> = <span class="n">0</span><span class="sc">;</span>
680 667 <span class="i">@AtomicInvariantsWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>}<span class="sc">;</span>
681 668 <span class="k">for</span> <span class="i">$AtomicInvariant</span> <span class="s">(</span><span class="i">@AtomicInvariantsWords</span><span class="s">)</span> <span class="s">{</span>
682 669 <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>
683 670 <span class="k">die</span> <span class="q">&quot;Error: Atomic invariant specified, $AtomicInvariant, using \&quot;--AtomicInvariantsToUse\&quot; option is not valid...\n &quot;</span><span class="sc">;</span>
684 671 <span class="s">}</span>
685 672 <span class="k">if</span> <span class="s">(</span><span class="i">$AtomicInvariant</span> =~ <span class="q">/^(AS|AtomSymbol)$/i</span><span class="s">)</span> <span class="s">{</span>
686 673 <span class="i">$AtomSymbolSpecified</span> = <span class="n">1</span><span class="sc">;</span>
687 674 <span class="s">}</span>
688 675 <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>
689 676 <span class="s">}</span>
690 677 <span class="k">if</span> <span class="s">(</span>!<span class="i">$AtomSymbolSpecified</span><span class="s">)</span> <span class="s">{</span>
691 678 <span class="k">die</span> <span class="q">&quot;Error: Atomic invariant, AS or AtomSymbol, must be specified as using \&quot;--AtomicInvariantsToUse\&quot; option...\n &quot;</span><span class="sc">;</span>
692 679 <span class="s">}</span>
693 680 <span class="s">}</span>
694 681
695 682 <span class="c"># Process specified functional classes invariants to use...</span>
696 683 <span class="c">#</span>
697 <a name="ProcessFunctionalClassesToUse-"></a> 684 <span class="k">sub </span><span class="m">ProcessFunctionalClassesToUse</span> <span class="s">{</span>
698 685 <span class="k">my</span><span class="s">(</span><span class="i">$FunctionalClass</span><span class="cm">,</span> <span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span><span class="sc">;</span>
699 686
700 687 <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
701 688 <span class="k">if</span> <span class="s">(</span><span class="i">IsEmpty</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
702 689 <span class="k">die</span> <span class="q">&quot;Error: Functional classes value specified using \&quot;--FunctionalClassesToUse\&quot; option is empty\n&quot;</span><span class="sc">;</span>
703 690 <span class="s">}</span>
704 691 <span class="i">@FunctionalClassesToUseWords</span> = <span class="k">split</span> <span class="q">/\,/</span><span class="cm">,</span> <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>}<span class="sc">;</span>
705 692 <span class="k">for</span> <span class="i">$FunctionalClass</span> <span class="s">(</span><span class="i">@FunctionalClassesToUseWords</span><span class="s">)</span> <span class="s">{</span>
706 693 <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>
707 694 <span class="k">die</span> <span class="q">&quot;Error: Functional class specified, $FunctionalClass, using \&quot;--FunctionalClassesToUse\&quot; option is not valid...\n &quot;</span><span class="sc">;</span>
708 695 <span class="s">}</span>
709 696 <span class="k">push</span> <span class="i">@</span>{<span class="i">$OptionsInfo</span>{<span class="w">FunctionalClassesToUse</span>}}<span class="cm">,</span> <span class="i">$FunctionalClass</span><span class="sc">;</span>
710 697 <span class="s">}</span>
711 698 <span class="s">}</span>
712 699
713 700 <span class="c"># Setup script usage and retrieve command line arguments specified using various options...</span>
714 <a name="SetupScriptUsage-"></a> 701 <span class="k">sub </span><span class="m">SetupScriptUsage</span> <span class="s">{</span>
715 702
716 703 <span class="c"># Retrieve all the options...</span>
717 704 <span class="i">%Options</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
718 705
719 706 <span class="i">$Options</span>{<span class="w">aromaticitymodel</span>} = <span class="q">&#39;MayaChemToolsAromaticityModel&#39;</span><span class="sc">;</span>
720 707
721 708 <span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} = <span class="q">&#39;AtomicInvariantsAtomTypes&#39;</span><span class="sc">;</span>
722 709 <span class="i">$Options</span>{<span class="w">atomicinvariantstouse</span>} = <span class="q">&#39;AS,X,BO,H,FC,MN&#39;</span><span class="sc">;</span>
723 710 <span class="i">$Options</span>{<span class="w">functionalclassestouse</span>} = <span class="q">&#39;HBD,HBA,PI,NI,Ar,Hal&#39;</span><span class="sc">;</span>
724 711
725 712 <span class="i">$Options</span>{<span class="w">bitsorder</span>} = <span class="q">&#39;Ascending&#39;</span><span class="sc">;</span>
726 713 <span class="i">$Options</span>{<span class="w">bitstringformat</span>} = <span class="q">&#39;HexadecimalString&#39;</span><span class="sc">;</span>
727 714
728 715 <span class="i">$Options</span>{<span class="w">compoundidmode</span>} = <span class="q">&#39;LabelPrefix&#39;</span><span class="sc">;</span>
729 716 <span class="i">$Options</span>{<span class="w">compoundidlabel</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
730 717 <span class="i">$Options</span>{<span class="w">datafieldsmode</span>} = <span class="q">&#39;CompoundID&#39;</span><span class="sc">;</span>
731 718
732 719 <span class="i">$Options</span>{<span class="w">filter</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
733 720
734 721 <span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} = <span class="q">&#39;Yes&#39;</span><span class="sc">;</span>
735 722
736 723 <span class="i">$Options</span>{<span class="w">mode</span>} = <span class="q">&#39;ExtendedConnectivity&#39;</span><span class="sc">;</span>
737 724
738 725 <span class="i">$Options</span>{<span class="w">neighborhoodradius</span>} = <span class="n">2</span><span class="sc">;</span>
739 726
740 727 <span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
741 728
742 729 <span class="i">$Options</span>{<span class="w">output</span>} = <span class="q">&#39;text&#39;</span><span class="sc">;</span>
743 730 <span class="i">$Options</span>{<span class="w">outdelim</span>} = <span class="q">&#39;comma&#39;</span><span class="sc">;</span>
744 731 <span class="i">$Options</span>{<span class="w">quote</span>} = <span class="q">&#39;yes&#39;</span><span class="sc">;</span>
745 732
746 733 <span class="i">$Options</span>{<span class="w">size</span>} = <span class="n">1024</span><span class="sc">;</span>
747 734
748 735 <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} = <span class="q">&#39;&#39;</span><span class="sc">;</span>
749 736
750 737 <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">&quot;aromaticitymodel=s&quot;</span><span class="cm">,</span> <span class="q">&quot;atomidentifiertype|a=s&quot;</span><span class="cm">,</span> <span class="q">&quot;atomicinvariantstouse=s&quot;</span><span class="cm">,</span> <span class="q">&quot;functionalclassestouse=s&quot;</span><span class="cm">,</span> <span class="q">&quot;bitsorder=s&quot;</span><span class="cm">,</span> <span class="q">&quot;bitstringformat|b=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundid=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidlabel=s&quot;</span><span class="cm">,</span> <span class="q">&quot;compoundidmode=s&quot;</span><span class="cm">,</span> <span class="q">&quot;datafields=s&quot;</span><span class="cm">,</span> <span class="q">&quot;datafieldsmode|d=s&quot;</span><span class="cm">,</span> <span class="q">&quot;filter|f=s&quot;</span><span class="cm">,</span> <span class="q">&quot;fingerprintslabel=s&quot;</span><span class="cm">,</span> <span class="q">&quot;help|h&quot;</span><span class="cm">,</span> <span class="q">&quot;keeplargestcomponent|k=s&quot;</span><span class="cm">,</span> <span class="q">&quot;mode|m=s&quot;</span><span class="cm">,</span> <span class="q">&quot;neighborhoodradius|n=s&quot;</span><span class="cm">,</span> <span class="q">&quot;outdelim=s&quot;</span><span class="cm">,</span> <span class="q">&quot;output=s&quot;</span><span class="cm">,</span> <span class="q">&quot;overwrite|o&quot;</span><span class="cm">,</span> <span class="q">&quot;quote|q=s&quot;</span><span class="cm">,</span> <span class="q">&quot;root|r=s&quot;</span><span class="cm">,</span> <span class="q">&quot;size|s=i&quot;</span><span class="cm">,</span> <span class="q">&quot;useperlcorerandom=s&quot;</span><span class="cm">,</span> <span class="q">&quot;vectorstringformat|v=s&quot;</span><span class="cm">,</span> <span class="q">&quot;workingdir|w=s&quot;</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
751 738 <span class="k">die</span> <span class="q">&quot;\nTo get a list of valid options and their values, use \&quot;$ScriptName -h\&quot; or\n\&quot;perl -S $ScriptName -h\&quot; command and try again...\n&quot;</span><span class="sc">;</span>
752 739 <span class="s">}</span>
753 740 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">workingdir</span>}<span class="s">)</span> <span class="s">{</span>
754 741 <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>
755 742 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{workingdir}, for option \&quot;-w --workingdir\&quot; is not a directory name.\n&quot;</span><span class="sc">;</span>
756 743 <span class="s">}</span>
757 744 <span class="k">chdir</span> <span class="i">$Options</span>{<span class="w">workingdir</span>} <span class="k">or</span> <span class="k">die</span> <span class="q">&quot;Error: Couldn&#39;t chdir $Options{workingdir}: $! \n&quot;</span><span class="sc">;</span>
758 745 <span class="s">}</span>
759 746 <span class="k">if</span> <span class="s">(</span>!<span class="i">Molecule::IsSupportedAromaticityModel</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">aromaticitymodel</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
760 747 <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>
761 748 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{aromaticitymodel}, for option \&quot;--AromaticityModel\&quot; is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n&quot;</span><span class="sc">;</span>
762 749 <span class="s">}</span>
763 750 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">atomidentifiertype</span>} !~ <span class="q">/^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i</span><span class="s">)</span> <span class="s">{</span>
764 751 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{atomidentifiertype}, for option \&quot;-a, --AtomIdentifierType\&quot; is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n&quot;</span><span class="sc">;</span>
765 752 <span class="s">}</span>
766 753 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitsorder</span>} !~ <span class="q">/^(Ascending|Descending)$/i</span><span class="s">)</span> <span class="s">{</span>
767 754 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{bitsorder}, for option \&quot;--BitsOrder\&quot; is not valid. Allowed values: Ascending or Descending\n&quot;</span><span class="sc">;</span>
768 755 <span class="s">}</span>
769 756 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">bitstringformat</span>} !~ <span class="q">/^(BinaryString|HexadecimalString)$/i</span><span class="s">)</span> <span class="s">{</span>
770 757 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{bitstringformat}, for option \&quot;-b, --bitstringformat\&quot; is not valid. Allowed values: BinaryString or HexadecimalString\n&quot;</span><span class="sc">;</span>
771 758 <span class="s">}</span>
772 759 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">compoundidmode</span>} !~ <span class="q">/^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i</span><span class="s">)</span> <span class="s">{</span>
773 760 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{compoundidmode}, for option \&quot;--CompoundIDMode\&quot; is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n&quot;</span><span class="sc">;</span>
774 761 <span class="s">}</span>
775 762 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">datafieldsmode</span>} !~ <span class="q">/^(All|Common|Specify|CompoundID)$/i</span><span class="s">)</span> <span class="s">{</span>
776 763 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{datafieldsmode}, for option \&quot;-d, --DataFieldsMode\&quot; is not valid. Allowed values: All, Common, Specify or CompoundID\n&quot;</span><span class="sc">;</span>
777 764 <span class="s">}</span>
778 765 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">filter</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
779 766 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{filter}, for option \&quot;-f, --Filter\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
780 767 <span class="s">}</span>
781 768 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">keeplargestcomponent</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
782 769 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{keeplargestcomponent}, for option \&quot;-k, --KeepLargestComponent\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
783 770 <span class="s">}</span>
784 771 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">mode</span>} !~ <span class="q">/^(ExtendedConnectivity|ExtendedConnectivityCount|ExtendedConnectivityBits)$/i</span><span class="s">)</span> <span class="s">{</span>
785 772 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{mode}, for option \&quot;-m, --mode\&quot; is not valid. Allowed values: ExtendedConnectivity, ExtendedConnecticityCount, or ExtendedConnectivityBits\n&quot;</span><span class="sc">;</span>
786 773 <span class="s">}</span>
787 774 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="i">IsInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">neighborhoodradius</span>}<span class="s">)</span> &amp;&amp; <span class="s">(</span><span class="i">$Options</span>{<span class="w">neighborhoodradius</span>} &gt;= <span class="n">0</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
788 775 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{neighborhoodradius}, for option \&quot;-n, --NeighborhoodRadius\&quot; is not valid. Allowed values: &gt;= 0 \n&quot;</span><span class="sc">;</span>
789 776 <span class="s">}</span>
790 777 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">output</span>} !~ <span class="q">/^(SD|FP|text|all)$/i</span><span class="s">)</span> <span class="s">{</span>
791 778 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{output}, for option \&quot;--output\&quot; is not valid. Allowed values: SD, FP, text, or all\n&quot;</span><span class="sc">;</span>
792 779 <span class="s">}</span>
793 780 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} !~ <span class="q">/^(comma|semicolon|tab)$/i</span><span class="s">)</span> <span class="s">{</span>
794 781 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{outdelim}, for option \&quot;--outdelim\&quot; is not valid. Allowed values: comma, tab, or semicolon\n&quot;</span><span class="sc">;</span>
795 782 <span class="s">}</span>
796 783 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">quote</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
797 784 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
798 785 <span class="s">}</span>
799 786 <span class="k">if</span> <span class="s">(</span>!<span class="i">IsPositiveInteger</span><span class="s">(</span><span class="i">$Options</span>{<span class="w">size</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span>
800 787 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{size}, for option \&quot;-s, --size\&quot; is not valid. Allowed values: &gt; 0 \n&quot;</span><span class="sc">;</span>
801 788 <span class="s">}</span>
802 789 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">outdelim</span>} =~ <span class="q">/semicolon/i</span> &amp;&amp; <span class="i">$Options</span>{<span class="w">quote</span>} =~ <span class="q">/^No$/i</span><span class="s">)</span> <span class="s">{</span>
803 790 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{quote}, for option \&quot;-q --quote\&quot; is not allowed with, semicolon value of \&quot;--outdelim\&quot; option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n&quot;</span><span class="sc">;</span>
804 791 <span class="s">}</span>
805 792 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">useperlcorerandom</span>} !~ <span class="q">/^(Yes|No)$/i</span><span class="s">)</span> <span class="s">{</span>
806 793 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{useperlcorerandom}, for option \&quot;--UsePerlCoreRandom\&quot; is not valid. Allowed values: Yes or No\n&quot;</span><span class="sc">;</span>
807 794 <span class="s">}</span>
808 795 <span class="k">if</span> <span class="s">(</span><span class="i">$Options</span>{<span class="w">vectorstringformat</span>} &amp;&amp; <span class="i">$Options</span>{<span class="w">vectorstringformat</span>} !~ <span class="q">/^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i</span><span class="s">)</span> <span class="s">{</span>
809 796 <span class="k">die</span> <span class="q">&quot;Error: The value specified, $Options{vectorstringformat}, for option \&quot;-v, --VectorStringFormat\&quot; is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n&quot;</span><span class="sc">;</span>
810 797 <span class="s">}</span>
811 798 <span class="s">}</span>
812 799
813 <a name="EOF-"></a></pre>
814 <p>&nbsp;</p>
815 <br />
816 <center>
817 <img src="../../../images/h2o2.png">
818 </center>
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