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1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:Fingerprints::FingerprintsFileUtil.pm</title>
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
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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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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsBitVector.html" title="FingerprintsBitVector.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FingerprintsStringUtil.html" title="FingerprintsStringUtil.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::FingerprintsFileUtil.pm</strong></td><td width="33%" align="right"><a href="././code/FingerprintsFileUtil.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/FingerprintsFileUtil.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/FingerprintsFileUtil.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/FingerprintsFileUtil.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/FingerprintsFileUtil.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>FingerprintsFileUtil</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::FingerprintsFileUtil;</p>
26 <p>use Fingerprints::FingerprintsFileUtil qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>FingerprintsFileUtil</strong> module provides the following functions:</p>
31 <p> <a href="#getfingerprintsfiletype">GetFingerprintsFileType</a>, <a href="#newfingerprintsfileio">NewFingerprintsFileIO</a>, <a href="#readandprocessfingerpritsdata">ReadAndProcessFingerpritsData</a>
32 </p><p><strong>FingerprintsFileUtil</strong> module provides function to handle fingerprints data strings
33 in FP, SD and CSV/TSV text files present in one of the following two types: fingerprints
34 bit-vectors and fingerprints vector strings</p>
35 <p>Example of <strong>FP</strong> file format containing fingerprints bit-vector string data:</p>
36 <div class="OptionsBox">
37 #
38 <br/> # Package = MayaChemTools 7.4
39 <br/> # ReleaseDate = Oct 21, 2010
40 <br/> #
41 <br/> # TimeStamp = Mon Mar 7 15:14:01 2011
42 <br/> #
43 <br/> # FingerprintsStringType = FingerprintsBitVector
44 <br/> #
45 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
46 <br/> # Size = 1024
47 <br/> # BitStringFormat = HexadecimalString
48 <br/> # BitsOrder = Ascending
49 <br/> #
50 <br/> Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
51 <br/> Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
52 <br/> ... ...
53 <br/> ... ..</div>
54 <p>Example of <strong>FP</strong> file format containing fingerprints 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 = FingerprintsVector
63 <br/> #
64 <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
65 <br/> # VectorStringFormat = IDsAndValuesString
66 <br/> # VectorValuesType = NumericalValues
67 <br/> #
68 <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:
69 <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...;
70 <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
71 <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 ...
72 <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
73 <br/> O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
74 <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
75 <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 ...
76 <br/> ... ...
77 <br/> ... ...</div>
78 <p>Example of <strong>SD</strong> file format containing fingerprints vector string data:</p>
79 <div class="OptionsBox">
80 ... ...
81 <br/> ... ...
82 <br/> $$$$
83 <br/> ... ...
84 <br/> ... ...
85 <br/> ... ...
86 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
87 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
88 <br/> ... ...
89 <br/> 2 3 1 0 0 0 0
90 <br/> ... ...
91 <br/> M END
92 <br/> &gt; &lt;CmpdID&gt;
93 <br/> Test</div>
94 <div class="OptionsBox">
95 &gt; &lt;PathLengthFingerprints&gt;
96 <br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
97 <br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
98 <br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
99 <br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
100 <br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
101 <br/> aa0660a11014a011d46</div>
102 <div class="OptionsBox">
103 $$$$
104 <br/> ... ...
105 <br/> ... ...</div>
106 <p>Example of CSV <strong>text</strong> file format containing fingerprints bit-vector string data:</p>
107 <div class="OptionsBox">
108 &quot;CompoundID&quot;,&quot;PathLengthFingerprints&quot;
109 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
110 <br/> :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
111 <br/> 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
112 <br/> 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401...&quot;
113 <br/> ... ...
114 <br/> ... ...</div>
115 <p>The current release of MayaChemTools supports the following types of fingerprint
116 bit-vector and vector strings:</p>
117 <div class="OptionsBox">
118 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
119 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
120 <br/> C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
121 <br/> 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
122 <br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
123 <br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div>
124 <div class="OptionsBox">
125 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
126 <br/> ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
127 <br/> .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
128 <br/> O.X1.BO2;2 4 14 3 10 1 1 1 3 2</div>
129 <div class="OptionsBox">
130 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
131 <br/> ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
132 <br/> N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1</div>
133 <div class="OptionsBox">
134 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
135 <br/> umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
136 <br/> 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
137 <br/> 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
138 <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
139 <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>
140 <div class="OptionsBox">
141 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
142 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
143 <br/> H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
144 <br/> .024 -2.270</div>
145 <div class="OptionsBox">
146 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
147 <br/> ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
148 <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
149 <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
150 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
151 <div class="OptionsBox">
152 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
153 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
154 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
155 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
156 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
157 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
158 <div class="OptionsBox">
159 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
160 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
161 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
162 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
163 <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
164 <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>
165 <div class="OptionsBox">
166 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
167 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
168 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
169 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
170 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
171 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
172 <div class="OptionsBox">
173 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
174 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
175 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
176 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
177 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
178 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
179 <div class="OptionsBox">
180 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
181 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
182 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
183 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
184 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
185 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
186 <div class="OptionsBox">
187 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
188 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
189 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
190 <br/> 11111111111110111000</div>
191 <div class="OptionsBox">
192 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
193 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
194 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
195 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
196 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
197 <br/> 0000000000000000000000000000000000000000</div>
198 <div class="OptionsBox">
199 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
200 <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
201 <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
202 <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
203 <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
204 <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>
205 <div class="OptionsBox">
206 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
207 <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
208 <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
209 <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
210 <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
211 <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>
212 <div class="OptionsBox">
213 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
214 <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
215 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000
216 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100
217 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101
218 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div>
219 <div class="OptionsBox">
220 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
221 <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
222 <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
223 <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
224 <br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
225 <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>
226 <div class="OptionsBox">
227 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
228 <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
229 <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
230 <br/> 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
231 <br/> CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
232 <br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div>
233 <div class="OptionsBox">
234 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
235 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
236 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
237 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
238 <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
239 <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>
240 <div class="OptionsBox">
241 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
242 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
243 <br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
244 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
245 <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
246 <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>
247 <div class="OptionsBox">
248 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
249 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
250 <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
251 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
252 <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>
253 <div class="OptionsBox">
254 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
255 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
256 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
257 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
258 <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>
259 <div class="OptionsBox">
260 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
261 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
262 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
263 <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
264 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
265 <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
266 <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>
267 <div class="OptionsBox">
268 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
269 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
270 <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-
271 <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
272 <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.
273 <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>
274 <div class="OptionsBox">
275 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
276 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
277 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
278 <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
279 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
280 <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
281 <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>
282 <div class="OptionsBox">
283 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
284 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
285 <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
286 <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
287 <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
288 <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>
289 <div class="OptionsBox">
290 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
291 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
292 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
293 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
294 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
295 <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
296 <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
297 <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>
298 <div class="OptionsBox">
299 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
300 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
301 <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
302 <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
303 <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
304 <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>
305 <p>
306 </p>
307 <h2>FUNCTIONS</h2>
308 <dl>
309 <dt><strong><a name="getfingerprintsfiletype" class="item"><strong>GetFingerprintsFileType</strong></a></strong></dt>
310 <dd>
311 <div class="OptionsBox">
312 $FileType = GetFingerprintsFileType($FileName);</div>
313 <p>Returns fingerprints <strong>FileType</strong> of <em>FileName</em> determined using extension of file name.
314 Possible <strong>FileType</strong> values: <em>FP, SD, Text</em>. Supported file name extensions for various
315 file types are: <strong>FP</strong> - <em>fpf, fp</em>; <strong>SD</strong> - <em>sdf, sd</em>; <strong>Text</strong> - <em>csv, tsv</em>.</p>
316 </dd>
317 <dt><strong><a name="newfingerprintsfileio" class="item"><strong>NewFingerprintsFileIO</strong></a></strong></dt>
318 <dd>
319 <div class="OptionsBox">
320 $FingerprintsFileIO = NewFingerprintsFileIO(%IOParameters);</div>
321 <p>Using specified <em>IOParameters</em> property names and values hash, <strong>NewFingerprintsFileIO</strong>
322 method creates a new object using appropriate fingerprints file IO class - <strong>FingerprintsFPFileIO,
323 FingerprintsSDFileIO, or FingerprintsTextFileIO</strong> - and returns a reference to a newly created
324 <strong>FingerprintsFileIO</strong> object.</p>
325 <p>The <em>IOParameters</em> hash must contain <em>Name</em> and <em>Mode</em> as key/value pairs to create
326 a new <strong>FingerprintsFileIO</strong> object.</p>
327 <p>Based on type of file - <strong>FP, SD or Text</strong> - <strong>NewFingerprintsFileIO</strong> use <strong>new</strong> method
328 from appropriate class - <strong>FingerprintsFPFileIO</strong> - along with <em>IOParameters</em> to create
329 <strong>FingerprintsFileIO</strong> object.</p>
330 </dd>
331 <dt><strong><a name="readandprocessfingerpritsdata" class="item"><strong>ReadAndProcessFingerpritsData</strong></a></strong></dt>
332 <dd>
333 <div class="OptionsBox">
334 ($CompoundIDsRef, $FingerprintsObjectRef) =
335 ReadAndProcessFingerpritsData($FingerprintsFileIO);</div>
336 <p>Processes fingerprints bit-vector and vector string data in a file using <em>FingerprintsFileIO</em>
337 object and returns a references to arrays of <strong>CompoundIDs</strong> and <em>FingerprintsObjects</em>.</p>
338 <p>The file open and close is automatically performed during processing.</p>
339 </dd>
340 </dl>
341 <p>
342 </p>
343 <h2>AUTHOR</h2>
344 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
345 <p>
346 </p>
347 <h2>SEE ALSO</h2>
348 <p><a href="./FingerprintsFPFileIO.html">FingerprintsFPFileIO.pm</a>,&nbsp<a href="./FingerprintsSDFileIO.html">FingerprintsSDFileIO.pm</a>,&nbsp<a href="./FingerprintsTextFileIO.html">FingerprintsTextFileIO.pm</a>
349 </p>
350 <p>
351 </p>
352 <h2>COPYRIGHT</h2>
353 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
354 <p>This file is part of MayaChemTools.</p>
355 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
356 the terms of the GNU Lesser General Public License as published by the Free
357 Software Foundation; either version 3 of the License, or (at your option)
358 any later version.</p>
359 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
360 <table width="100%" border=0 cellpadding=0 cellspacing=2>
361 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsBitVector.html" title="FingerprintsBitVector.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./FingerprintsStringUtil.html" title="FingerprintsStringUtil.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::FingerprintsFileUtil.pm</strong></td></tr>
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