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1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
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18 .\" Set up some character translations and predefined strings. \*(-- will
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21 .\" give a nicer C++. Capital omega is used to do unbreakable dashes and
22 .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff,
23 .\" nothing in troff, for use with C<>.
24 .tr \(*W-
25 .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
26 .ie n \{\
27 . ds -- \(*W-
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29 . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
30 . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch
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35 'br\}
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44 .ie \n(.g .ds Aq \(aq
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51 .ie \nF \{\
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91 . ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
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93 . ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
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99 .ds 8 \h'\*(#H'\(*b\h'-\*(#H'
100 .ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
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103 .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
104 .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
105 .ds ae a\h'-(\w'a'u*4/10)'e
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123 .rm #[ #] #H #V #F C
124 .\" ========================================================================
125 .\"
126 .IX Title "FINGERPRINTSFILEUTIL 1"
127 .TH FINGERPRINTSFILEUTIL 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
129 .\" way too many mistakes in technical documents.
130 .if n .ad l
131 .nh
132 .SH "NAME"
133 FingerprintsFileUtil
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use Fingerprints::FingerprintsFileUtil;
137 .PP
138 use Fingerprints::FingerprintsFileUtil qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBFingerprintsFileUtil\fR module provides the following functions:
142 .PP
143 GetFingerprintsFileType, NewFingerprintsFileIO, ReadAndProcessFingerpritsData
144 .PP
145 \&\fBFingerprintsFileUtil\fR module provides function to handle fingerprints data strings
146 in \s-1FP\s0, \s-1SD\s0 and \s-1CSV/TSV\s0 text files present in one of the following two types: fingerprints
147 bit-vectors and fingerprints vector strings
148 .PP
149 Example of \fB\s-1FP\s0\fR file format containing fingerprints bit-vector string data:
150 .PP
151 .Vb 10
152 \& #
153 \& # Package = MayaChemTools 7.4
154 \& # ReleaseDate = Oct 21, 2010
155 \& #
156 \& # TimeStamp = Mon Mar 7 15:14:01 2011
157 \& #
158 \& # FingerprintsStringType = FingerprintsBitVector
159 \& #
160 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
161 \& # Size = 1024
162 \& # BitStringFormat = HexadecimalString
163 \& # BitsOrder = Ascending
164 \& #
165 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
166 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
167 \& ... ...
168 \& ... ..
169 .Ve
170 .PP
171 Example of \fB\s-1FP\s0\fR file format containing fingerprints vector string data:
172 .PP
173 .Vb 10
174 \& #
175 \& # Package = MayaChemTools 7.4
176 \& # ReleaseDate = Oct 21, 2010
177 \& #
178 \& # TimeStamp = Mon Mar 7 15:14:01 2011
179 \& #
180 \& # FingerprintsStringType = FingerprintsVector
181 \& #
182 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
183 \& # VectorStringFormat = IDsAndValuesString
184 \& # VectorValuesType = NumericalValues
185 \& #
186 \& 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:
187 \& 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...;
188 \& 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
189 \& 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 ...
190 \& 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
191 \& O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
192 \& 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
193 \& 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 ...
194 \& ... ...
195 \& ... ...
196 .Ve
197 .PP
198 Example of \fB\s-1SD\s0\fR file format containing fingerprints vector string data:
199 .PP
200 .Vb 10
201 \& ... ...
202 \& ... ...
203 \& $$$$
204 \& ... ...
205 \& ... ...
206 \& ... ...
207 \& 41 44 0 0 0 0 0 0 0 0999 V2000
208 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
209 \& ... ...
210 \& 2 3 1 0 0 0 0
211 \& ... ...
212 \& M END
213 \& > <CmpdID>
214 \& Test
215 \&
216 \& > <PathLengthFingerprints>
217 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
218 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
219 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
220 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
221 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
222 \& aa0660a11014a011d46
223 \&
224 \& $$$$
225 \& ... ...
226 \& ... ...
227 .Ve
228 .PP
229 Example of \s-1CSV\s0 \fBtext\fR file format containing fingerprints bit-vector string data:
230 .PP
231 .Vb 7
232 \& "CompoundID","PathLengthFingerprints"
233 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
234 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
235 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
236 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
237 \& ... ...
238 \& ... ...
239 .Ve
240 .PP
241 The current release of MayaChemTools supports the following types of fingerprint
242 bit-vector and vector strings:
243 .PP
244 .Vb 6
245 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
246 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
247 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
248 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
249 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
250 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
251 \&
252 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
253 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
254 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
255 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
256 \&
257 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
258 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
259 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
260 \&
261 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
262 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
263 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
264 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
265 \& 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
266 \& 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...
267 \&
268 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
269 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
270 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
271 \& .024 \-2.270
272 \&
273 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
274 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
275 \& 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
276 \& 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
277 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
278 \&
279 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
280 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
281 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
282 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
283 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
284 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
285 \&
286 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
287 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
288 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
289 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
290 \& 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
291 \& 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
292 \&
293 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
294 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
295 \& 0000000001010000000110000011000000000000100000000000000000000000100001
296 \& 1000000110000000000000000000000000010011000000000000000000000000010000
297 \& 0000000000000000000000000010000000000000000001000000000000000000000000
298 \& 0000000000010000100001000000000000101000000000000000100000000000000...
299 \&
300 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
301 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
302 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
303 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
304 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
305 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
306 \&
307 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
308 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
309 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
310 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
311 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
312 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
313 \&
314 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
315 \& 0000000000000000000000000000000001001000010010000000010010000000011100
316 \& 0100101010111100011011000100110110000011011110100110111111111111011111
317 \& 11111111111110111000
318 \&
319 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
320 \& 1110011111100101111111000111101100110000000000000011100010000000000000
321 \& 0000000000000000000000000000000000000000000000101000000000000000000000
322 \& 0000000000000000000000000000000000000000000000000000000000000000000000
323 \& 0000000000000000000000000000000000000011000000000000000000000000000000
324 \& 0000000000000000000000000000000000000000
325 \&
326 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
327 \& 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
328 \& 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
329 \& 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
330 \& 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
331 \& 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
332 \&
333 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
334 \& 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
335 \& 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
336 \& 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
337 \& 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
338 \& 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 ...
339 \&
340 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
341 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
342 \& 0100010101011000101001011100110001000010001001101000001001001001001000
343 \& 0010110100000111001001000001001010100100100000000011000000101001011100
344 \& 0010000001000101010100000100111100110111011011011000000010110111001101
345 \& 0101100011000000010001000011000010100011101100001000001000100000000...
346 \&
347 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
348 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
349 \& 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
350 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
351 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
352 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
353 \&
354 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
355 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
356 \& 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
357 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
358 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
359 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
360 \&
361 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
362 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
363 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
364 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
365 \& 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
366 \& 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...
367 \&
368 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
369 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
370 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
371 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
372 \& 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
373 \& 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 ...
374 \&
375 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
376 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
377 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
378 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
379 \& 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
380 \&
381 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
382 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
383 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
384 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
385 \& 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
386 \&
387 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
388 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
389 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
390 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
391 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
392 \& 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
393 \& 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...
394 \&
395 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
396 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
397 \& .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\-
398 \& 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
399 \& \-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.
400 \& 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...
401 \&
402 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
403 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
404 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
405 \& 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
406 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
407 \& 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
408 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
409 \&
410 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
411 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
412 \& 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
413 \& 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
414 \& 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
415 \& 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...
416 \&
417 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
418 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
419 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
420 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
421 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
422 \& 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
423 \& 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
424 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
425 \&
426 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
427 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
428 \& 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
429 \& 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
430 \& 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
431 \& 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 ...
432 .Ve
433 .SH "FUNCTIONS"
434 .IX Header "FUNCTIONS"
435 .IP "\fBGetFingerprintsFileType\fR" 4
436 .IX Item "GetFingerprintsFileType"
437 .Vb 1
438 \& $FileType = GetFingerprintsFileType($FileName);
439 .Ve
440 .Sp
441 Returns fingerprints \fBFileType\fR of \fIFileName\fR determined using extension of file name.
442 Possible \fBFileType\fR values: \fI\s-1FP\s0, \s-1SD\s0, Text\fR. Supported file name extensions for various
443 file types are: \fB\s-1FP\s0\fR \- \fIfpf, fp\fR; \fB\s-1SD\s0\fR \- \fIsdf, sd\fR; \fBText\fR \- \fIcsv, tsv\fR.
444 .IP "\fBNewFingerprintsFileIO\fR" 4
445 .IX Item "NewFingerprintsFileIO"
446 .Vb 1
447 \& $FingerprintsFileIO = NewFingerprintsFileIO(%IOParameters);
448 .Ve
449 .Sp
450 Using specified \fIIOParameters\fR property names and values hash, \fBNewFingerprintsFileIO\fR
451 method creates a new object using appropriate fingerprints file \s-1IO\s0 class \- \fBFingerprintsFPFileIO,
452 FingerprintsSDFileIO, or FingerprintsTextFileIO\fR \- and returns a reference to a newly created
453 \&\fBFingerprintsFileIO\fR object.
454 .Sp
455 The \fIIOParameters\fR hash must contain \fIName\fR and \fIMode\fR as key/value pairs to create
456 a new \fBFingerprintsFileIO\fR object.
457 .Sp
458 Based on type of file \- \fB\s-1FP\s0, \s-1SD\s0 or Text\fR \- \fBNewFingerprintsFileIO\fR use \fBnew\fR method
459 from appropriate class \- \fBFingerprintsFPFileIO\fR \- along with \fIIOParameters\fR to create
460 \&\fBFingerprintsFileIO\fR object.
461 .IP "\fBReadAndProcessFingerpritsData\fR" 4
462 .IX Item "ReadAndProcessFingerpritsData"
463 .Vb 2
464 \& ($CompoundIDsRef, $FingerprintsObjectRef) =
465 \& ReadAndProcessFingerpritsData($FingerprintsFileIO);
466 .Ve
467 .Sp
468 Processes fingerprints bit-vector and vector string data in a file using \fIFingerprintsFileIO\fR
469 object and returns a references to arrays of \fBCompoundIDs\fR and \fIFingerprintsObjects\fR.
470 .Sp
471 The file open and close is automatically performed during processing.
472 .SH "AUTHOR"
473 .IX Header "AUTHOR"
474 Manish Sud <msud@san.rr.com>
475 .SH "SEE ALSO"
476 .IX Header "SEE ALSO"
477 FingerprintsFPFileIO.pm, FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm
478 .SH "COPYRIGHT"
479 .IX Header "COPYRIGHT"
480 Copyright (C) 2015 Manish Sud. All rights reserved.
481 .PP
482 This file is part of MayaChemTools.
483 .PP
484 MayaChemTools is free software; you can redistribute it and/or modify it under
485 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
486 Software Foundation; either version 3 of the License, or (at your option)
487 any later version.