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1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:InfoFingerprintsFiles.pl</title>
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
6 </head>
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
8 <br/>
9 <center>
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
11 </center>
12 <br/>
13 <div class="DocNav">
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoAminoAcids.html" title="InfoAminoAcids.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Next</a></td><td width="34%" align="middle"><strong>InfoFingerprintsFiles.pl</strong></td><td width="33%" align="right"><a href="././code/InfoFingerprintsFiles.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/InfoFingerprintsFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/InfoFingerprintsFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/InfoFingerprintsFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/InfoFingerprintsFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
16 </table>
17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>InfoFingerprintsFiles.pl - List information about fingerprints data in SD, FP and CSV/TSV text file(s)</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>InfoFingerprintsFiles.pl SDFile(s) FPFile(s) TextFile(s)...</p>
26 <p>InfoFingerprintsFiles.pl [<strong>-a, --all</strong>] [<strong>--AverageBitDensity</strong>] [<strong>--BitDensity</strong>]
27 [<strong>-c, --count</strong>] [<strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em>] [<strong>--DataCheck</strong>]
28 [<strong>-d, --detail</strong> <em>InfoLevel</em>] [<strong>-e, --empty</strong>] [<strong>--FingerprintsCol</strong> <em>col number | col name</em>]
29 [<strong>--FingerprintsField</strong> <em>FieldLabel</em>] [<strong>--FingerprintsType</strong>] [<strong>--FingerprintsDescription</strong>]
30 [<strong>--FingerprintsSize</strong>] [<strong>--FingerprintsBitStringFormat</strong>] [<strong>--FingerprintsBitOrder</strong>]
31 [<strong>--FingerprintsVectorValuesType</strong>] [<strong>--FingerprintsVectorValuesFormat</strong>]
32 [<strong>-h, --help</strong>] [<strong>--InDelim</strong> <em>comma | semicolon</em>]
33 [<strong>--NumOfOnBits</strong>] [<strong>--NumOfNonZeroValues</strong>]
34 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s) FPFile(s) TextFile(s)...</p>
35 <p>
36 </p>
37 <h2>DESCRIPTION</h2>
38 <p>List information about fingerprints data in <em>SD, FP and CSV/TSV</em> text file(s): number of
39 rows containing fingerprints data, type of fingerprints vector, description and size of fingerprints,
40 bit density and average bit density for bit-vector fingerprints strings, and so on.</p>
41 <p>The scripts InfoFingerprintsSDFiles.pl and InfoFingerprintsTextFiles.pl have been removed from the
42 current release of MayaChemTools and their functionality merged with this script.</p>
43 <p>The valid <em>SDFile</em> extensions are <em>.sdf</em> and <em>.sd</em>. All SD files in a current directory
44 can be specified either by <em>*.sdf</em> or the current directory name.</p>
45 <p>The valid <em>FPFile</em> extensions are <em>.fpf</em> and <em>.fp</em>. All FP files in a current directory
46 can be specified either by <em>*.fpf</em> or the current directory name.</p>
47 <p>The valid <em>TextFile</em> extensions are <em>.csv</em> and <em>.tsv</em> for comma/semicolon and tab
48 delimited text files respectively. All other file names are ignored. All text files in a
49 current directory can be specified by <em>*.csv</em>, <em>*.tsv</em>, or the current directory
50 name. The <strong>--indelim</strong> option determines the format of <em>TextFile(s)</em>. Any file
51 which doesn't correspond to the format indicated by <strong>--indelim</strong> option is ignored.</p>
52 <p>Format of fingerprint strings data in <em>SDFile(s), FPFile(s) and TextFile(s)</em> is automatically
53 detected.</p>
54 <p>Example of <em>FP</em> file containing fingerprints bit-vector string data:</p>
55 <div class="OptionsBox">
56 #
57 <br/> # Package = MayaChemTools 7.4
58 <br/> # ReleaseDate = Oct 21, 2010
59 <br/> #
60 <br/> # TimeStamp = Mon Mar 7 15:14:01 2011
61 <br/> #
62 <br/> # FingerprintsStringType = FingerprintsBitVector
63 <br/> #
64 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
65 <br/> # Size = 1024
66 <br/> # BitStringFormat = HexadecimalString
67 <br/> # BitsOrder = Ascending
68 <br/> #
69 <br/> Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
70 <br/> Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
71 <br/> ... ...
72 <br/> ... ..</div>
73 <p>Example of <em>FP</em> file containing fingerprints vector string data:</p>
74 <div class="OptionsBox">
75 #
76 <br/> # Package = MayaChemTools 7.4
77 <br/> # ReleaseDate = Oct 21, 2010
78 <br/> #
79 <br/> # TimeStamp = Mon Mar 7 15:14:01 2011
80 <br/> #
81 <br/> # FingerprintsStringType = FingerprintsVector
82 <br/> #
83 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
84 <br/> # VectorStringFormat = IDsAndValuesString
85 <br/> # VectorValuesType = NumericalValues
86 <br/> #
87 <br/> Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C:
88 <br/> N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...;
89 <br/> 33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2
90 <br/> 6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ...
91 <br/> Cmpd2 103;C N O C=N C=O CC CN CO CC=O CCC CCN CCO CNC N=CN NC=O NCN O=C
92 <br/> O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
93 <br/> 15 4 4 1 2 13 5 2 2 15 5 3 2 2 1 1 1 2 17 7 6 5 1 1 1 2 15 8 5 7 2 2 2 2
94 <br/> 1 2 1 1 3 15 7 6 8 3 4 4 3 2 2 1 2 3 14 2 4 7 4 4 4 4 1 1 1 2 1 1 1 ...
95 <br/> ... ...
96 <br/> ... ...</div>
97 <p>Example of <em>SD</em> file containing fingerprints bit-vector string data:</p>
98 <div class="OptionsBox">
99 ... ...
100 <br/> ... ...
101 <br/> $$$$
102 <br/> ... ...
103 <br/> ... ...
104 <br/> ... ...
105 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
106 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
107 <br/> ... ...
108 <br/> 2 3 1 0 0 0 0
109 <br/> ... ...
110 <br/> M END
111 <br/> &gt; &lt;CmpdID&gt;
112 <br/> Cmpd1</div>
113 <div class="OptionsBox">
114 &gt; &lt;PathLengthFingerprints&gt;
115 <br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
116 <br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
117 <br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
118 <br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
119 <br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
120 <br/> aa0660a11014a011d46</div>
121 <div class="OptionsBox">
122 $$$$
123 <br/> ... ...
124 <br/> ... ...</div>
125 <p>Example of CSV <em>Text</em> file containing fingerprints bit-vector string data:</p>
126 <div class="OptionsBox">
127 &quot;CompoundID&quot;,&quot;PathLengthFingerprints&quot;
128 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
129 <br/> :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
130 <br/> 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
131 <br/> 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401...&quot;
132 <br/> ... ...
133 <br/> ... ...</div>
134 <p>The current release of MayaChemTools supports the following types of fingerprint
135 bit-vector and vector strings:</p>
136 <div class="OptionsBox">
137 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
138 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
139 <br/> C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
140 <br/> 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
141 <br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
142 <br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div>
143 <div class="OptionsBox">
144 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
145 <br/> ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
146 <br/> .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
147 <br/> O.X1.BO2;2 4 14 3 10 1 1 1 3 2</div>
148 <div class="OptionsBox">
149 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
150 <br/> ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
151 <br/> N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1</div>
152 <div class="OptionsBox">
153 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
154 <br/> umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
155 <br/> 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
156 <br/> 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
157 <br/> O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
158 <br/> 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...</div>
159 <div class="OptionsBox">
160 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
161 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
162 <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
163 <br/> .024 -2.270</div>
164 <div class="OptionsBox">
165 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
166 <br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
167 <br/> 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
168 <br/> 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
169 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
170 <div class="OptionsBox">
171 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
172 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
173 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
174 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
175 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
176 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
177 <div class="OptionsBox">
178 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
179 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
180 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
181 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
182 <br/> 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
183 <br/> 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1</div>
184 <div class="OptionsBox">
185 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
186 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
187 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
188 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
189 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
190 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
191 <div class="OptionsBox">
192 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
193 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
194 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
195 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
196 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
197 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
198 <div class="OptionsBox">
199 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
200 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
201 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
202 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
203 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
204 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
205 <div class="OptionsBox">
206 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
207 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
208 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
209 <br/> 11111111111110111000</div>
210 <div class="OptionsBox">
211 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
212 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
213 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
214 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
215 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
216 <br/> 0000000000000000000000000000000000000000</div>
217 <div class="OptionsBox">
218 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
219 <br/> ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
220 <br/> 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
221 <br/> 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
222 <br/> 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
223 <br/> 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1</div>
224 <div class="OptionsBox">
225 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
226 <br/> ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
227 <br/> 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
228 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
229 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
230 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...</div>
231 <div class="OptionsBox">
232 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
233 <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
234 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000
235 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100
236 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101
237 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div>
238 <div class="OptionsBox">
239 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
240 <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
241 <br/> C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
242 <br/> 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
243 <br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
244 <br/> 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....</div>
245 <div class="OptionsBox">
246 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
247 <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
248 <br/> 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
249 <br/> 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
250 <br/> CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
251 <br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div>
252 <div class="OptionsBox">
253 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
254 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
255 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
256 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
257 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
258 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div>
259 <div class="OptionsBox">
260 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
261 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
262 <br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
263 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
264 <br/> 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
265 <br/> 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...</div>
266 <div class="OptionsBox">
267 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
268 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
269 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
270 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
271 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
272 <div class="OptionsBox">
273 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
274 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
275 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
276 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
277 <br/> 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2</div>
278 <div class="OptionsBox">
279 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
280 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
281 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
282 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
283 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
284 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
285 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
286 <div class="OptionsBox">
287 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
288 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
289 <br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
290 <br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
291 <br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
292 <br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div>
293 <div class="OptionsBox">
294 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
295 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
296 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
297 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
298 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
299 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
300 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
301 <div class="OptionsBox">
302 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
303 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
304 <br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
305 <br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
306 <br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
307 <br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div>
308 <div class="OptionsBox">
309 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
310 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
311 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
312 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
313 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
314 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
315 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
316 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
317 <div class="OptionsBox">
318 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
319 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
320 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
321 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
322 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
323 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
324 <p>
325 </p>
326 <h2>OPTIONS</h2>
327 <dl>
328 <dt><strong><strong>-a, --all</strong></strong></dt>
329 <dd>
330 <p>List all the available information.</p>
331 </dd>
332 <dt><strong><strong>--AverageBitDensity</strong></strong></dt>
333 <dd>
334 <p>List average bit density of fingerprint bit-vector strings.</p>
335 </dd>
336 <dt><strong><strong>--BitDensity</strong></strong></dt>
337 <dd>
338 <p>List bit density of fingerprints bit-vector strings data in each row.</p>
339 </dd>
340 <dt><strong><strong>--count</strong></strong></dt>
341 <dd>
342 <p>List number of data entries containing fingerprints bit-vector or vector strings data. This
343 is <strong>default behavior</strong>.</p>
344 </dd>
345 <dt><strong><strong>-c, --ColMode</strong> <em>ColNum | ColLabel</em></strong></dt>
346 <dd>
347 <p>Specify how columns are identified in CSV/TSV <em>TextFile(s)</em>: using column number or column
348 label. Possible values: <em>ColNum or ColLabel</em>. Default value: <em>ColNum</em></p>
349 </dd>
350 <dt><strong><strong>-d, --detail</strong> <em>InfoLevel</em></strong></dt>
351 <dd>
352 <p>Level of information to print about lines being ignored. Default: <em>1</em>. Possible values:
353 <em>1, 2 or 3</em>.</p>
354 </dd>
355 <dt><strong><strong>--DataCheck</strong></strong></dt>
356 <dd>
357 <p>Validate fingerprints data specified using <strong>--FingerprintsCol</strong> and list information
358 about missing and invalid data.</p>
359 </dd>
360 <dt><strong><strong>-e, --empty</strong></strong></dt>
361 <dd>
362 <p>List number of rows containing no fingerprints data.</p>
363 </dd>
364 <dt><strong><strong>--FingerprintsCol</strong> <em>col number | col name</em></strong></dt>
365 <dd>
366 <p>This value is <strong>-c, --colmode</strong> specific. It corresponds to column in CSV/TSV <em>TextFile(s)</em>
367 containing fingerprints data. Possible values: <em>col number or col label</em>.
368 Default value: <em>first column containing the word Fingerprints in its column label</em>.</p>
369 </dd>
370 <dt><strong><strong>--FingerprintsField</strong> <em>FieldLabel</em></strong></dt>
371 <dd>
372 <p>Fingerprints field label to use during listing of fingerprints information for <em>SDFile(s)</em>.
373 Default value: <em>first data field label containing the word Fingerprints in its label</em>.</p>
374 </dd>
375 <dt><strong><strong>--FingerprintsType</strong></strong></dt>
376 <dd>
377 <p>List types of fingerprint strings: FingerprintsBitVector or FingerprintsVector.</p>
378 </dd>
379 <dt><strong><strong>--FingerprintsDescription</strong></strong></dt>
380 <dd>
381 <p>List types of fingerprints: PathLengthBits, PathLengthCount, MACCSKeyCount,
382 ExtendedConnectivity and so on.</p>
383 </dd>
384 <dt><strong><strong>--FingerprintsSize</strong></strong></dt>
385 <dd>
386 <p>List size of fingerprints.</p>
387 </dd>
388 <dt><strong><strong>--FingerprintsBitStringFormat</strong></strong></dt>
389 <dd>
390 <p>List format of fingerprint bit-vector strings: BinaryString or HexadecimalString.</p>
391 </dd>
392 <dt><strong><strong>--FingerprintsBitOrder</strong></strong></dt>
393 <dd>
394 <p>List order of bits data in fingerprint bit-vector bit strings: Ascending or Descending.</p>
395 </dd>
396 <dt><strong><strong>--FingerprintsVectorValuesType</strong></strong></dt>
397 <dd>
398 <p>List type of values in fingerprint vector strings: OrderedNumericalValues, NumericalValues or
399 AlphaNumericalValues.</p>
400 </dd>
401 <dt><strong><strong>--FingerprintsVectorValuesFormat</strong></strong></dt>
402 <dd>
403 <p>List format of values in fingerprint vector strings: ValuesString, IDsAndValuesString,
404 IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString.</p>
405 </dd>
406 <dt><strong><strong>-h, --help</strong></strong></dt>
407 <dd>
408 <p>Print this help message.</p>
409 </dd>
410 <dt><strong><strong>--InDelim</strong> <em>comma | semicolon</em></strong></dt>
411 <dd>
412 <p>Input delimiter for CSV <em>TextFile(s)</em>. Possible values: <em>comma or semicolon</em>.
413 Default value: <em>comma</em>. For TSV files, this option is ignored and <em>tab</em> is used as a
414 delimiter.</p>
415 </dd>
416 <dt><strong><strong>--NumOfOnBits</strong></strong></dt>
417 <dd>
418 <p>List number of on bits in fingerprints bit-vector strings data in each row.</p>
419 </dd>
420 <dt><strong><strong>--NumOfNonZeroValues</strong></strong></dt>
421 <dd>
422 <p>List number of non-zero values in fingerprints vector strings data in each row.</p>
423 </dd>
424 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
425 <dd>
426 <p>Location of working directory. Default: current directory.</p>
427 </dd>
428 </dl>
429 <p>
430 </p>
431 <h2>EXAMPLES</h2>
432 <p>To count number of lines containing fingerprints bit-vector or vector strings data present
433 in FP file, in a column name containing Fingerprint substring in text file, and in a data
434 field with Fingerprint substring in its label, type:</p>
435 <div class="ExampleBox">
436 % InfoFingerprintsFiles.pl SampleFPBin.csv</div>
437 <div class="ExampleBox">
438 % InfoFingerprintsFiles.pl SampleFPBin.sdf SampleFPBin.fpf
439 SampleFPBin.csv</div>
440 <div class="ExampleBox">
441 % InfoFingerprintsFiles.pl SampleFPHex.sdf SampleFPHex.fpf
442 SampleFPHex.csv</div>
443 <div class="ExampleBox">
444 % InfoFingerprintsFiles.pl SampleFPcount.sdf SampleFPcount.fpf
445 SampleFPcount.csv</div>
446 <p>To list all available information about fingerprints bit-vector or vector strings data present
447 in FP file, in a column name containing Fingerprint substring in text file, and in a data
448 field with Fingerprint substring in its label, type:</p>
449 <div class="ExampleBox">
450 % InfoFingerprintsFiles.pl -a SampleFPHex.sdf SampleFPHex.fpf
451 SampleFPHex.csv</div>
452 <div class="ExampleBox">
453 % InfoFingerprintsFiles.pl -a SampleFPcount.sdf SampleFPcount.fpf
454 SampleFPcount.csv</div>
455 <p>To list all available information about fingerprints bit-vector or vector strings data present in a
456 column named Fingerprints in text file, type:</p>
457 <div class="ExampleBox">
458 % InfoFingerprintsFiles.pl -a --ColMode ColLabel --FingerprintsCol
459 Fingerprints SampleFPHex.sdf</div>
460 <div class="ExampleBox">
461 % InfoFingerprintsFiles.pl -a --ColMode ColLabel --FingerprintsCol
462 Fingerprints SampleFPcount.csv</div>
463 <p>To list all available information about fingerprints bit-vector or vector strings data present in a
464 data field names Fingerprints in SD file, type:</p>
465 <div class="ExampleBox">
466 % InfoFingerprintsFiles.pl -a --FingerprintsField Fingerprints
467 SampleFPHex.sdf</div>
468 <div class="ExampleBox">
469 % InfoFingerprintsFiles.pl -a --FingerprintsField Fingerprints
470 SampleFPcount.sdf</div>
471 <p>To list bit density, average bit density, and number of on bits for fingerprints bit-vector strings data
472 present in FP file, in a column name containing Fingerprint substring in text file, and in a data
473 field with Fingerprint substring in its label, type:</p>
474 <div class="ExampleBox">
475 % InfoFingerprintsFiles.pl --BitDensity --AverageBitDensity
476 --NumOfOnBits SampleFPBin.csv SampleFPBin.sdf SampleFPBin.fpf</div>
477 <p>To list vector values type, format and number of non-zero values for fingerprints vector strings
478 data present in FP file, in a column name containing Fingerprint substring in text file, and in a data
479 field with Fingerprint substring in its label along with fingerprints type and description, type:</p>
480 <div class="ExampleBox">
481 % InfoFingerprintsFiles.pl --FingerprintsType --FingerprintsDescription
482 --FingerprintsVectorValuesType --FingerprintsVectorValuesFormat
483 --NumOfNonZeroValues SampleFPcount.csv SampleFPcount.sdf
484 SampleFPcount.fpf</div>
485 <p>
486 </p>
487 <h2>AUTHOR</h2>
488 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
489 <p>
490 </p>
491 <h2>SEE ALSO</h2>
492 <p><a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>,&nbsp<a href="./SimilaritySearchingFingerprints.html">SimilaritySearchingFingerprints.pl</a>,&nbsp<a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,&nbsp
493 <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,&nbsp<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,&nbsp
494 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
495 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
496 </p>
497 <p>
498 </p>
499 <h2>COPYRIGHT</h2>
500 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
501 <p>This file is part of MayaChemTools.</p>
502 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
503 the terms of the GNU Lesser General Public License as published by the Free
504 Software Foundation; either version 3 of the License, or (at your option)
505 any later version.</p>
506 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
507 <table width="100%" border=0 cellpadding=0 cellspacing=2>
508 <tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoAminoAcids.html" title="InfoAminoAcids.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoFingerprintsFiles.pl</strong></td></tr>
509 </table>
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