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1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
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96 .\}
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99 .ds 8 \h'\*(#H'\(*b\h'-\*(#H'
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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\*(#]
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123 .rm #[ #] #H #V #F C
124 .\" ========================================================================
125 .\"
126 .IX Title "INFOFINGERPRINTSFILES 1"
127 .TH INFOFINGERPRINTSFILES 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 InfoFingerprintsFiles.pl \- List information about fingerprints data in SD, FP and CSV/TSV text file(s)
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 InfoFingerprintsFiles.pl SDFile(s) FPFile(s) TextFile(s)...
137 .PP
138 InfoFingerprintsFiles.pl [\fB\-a, \-\-all\fR] [\fB\-\-AverageBitDensity\fR] [\fB\-\-BitDensity\fR]
139 [\fB\-c, \-\-count\fR] [\fB\-c, \-\-ColMode\fR \fIColNum | ColLabel\fR] [\fB\-\-DataCheck\fR]
140 [\fB\-d, \-\-detail\fR \fIInfoLevel\fR] [\fB\-e, \-\-empty\fR] [\fB\-\-FingerprintsCol\fR \fIcol number | col name\fR]
141 [\fB\-\-FingerprintsField\fR \fIFieldLabel\fR] [\fB\-\-FingerprintsType\fR] [\fB\-\-FingerprintsDescription\fR]
142 [\fB\-\-FingerprintsSize\fR] [\fB\-\-FingerprintsBitStringFormat\fR] [\fB\-\-FingerprintsBitOrder\fR]
143 [\fB\-\-FingerprintsVectorValuesType\fR] [\fB\-\-FingerprintsVectorValuesFormat\fR]
144 [\fB\-h, \-\-help\fR] [\fB\-\-InDelim\fR \fIcomma | semicolon\fR]
145 [\fB\-\-NumOfOnBits\fR] [\fB\-\-NumOfNonZeroValues\fR]
146 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s) FPFile(s) TextFile(s)...
147 .SH "DESCRIPTION"
148 .IX Header "DESCRIPTION"
149 List information about fingerprints data in \fI\s-1SD\s0, \s-1FP\s0 and \s-1CSV/TSV\s0\fR text file(s): number of
150 rows containing fingerprints data, type of fingerprints vector, description and size of fingerprints,
151 bit density and average bit density for bit-vector fingerprints strings, and so on.
152 .PP
153 The scripts InfoFingerprintsSDFiles.pl and InfoFingerprintsTextFiles.pl have been removed from the
154 current release of MayaChemTools and their functionality merged with this script.
155 .PP
156 The valid \fISDFile\fR extensions are \fI.sdf\fR and \fI.sd\fR. All \s-1SD\s0 files in a current directory
157 can be specified either by \fI*.sdf\fR or the current directory name.
158 .PP
159 The valid \fIFPFile\fR extensions are \fI.fpf\fR and \fI.fp\fR. All \s-1FP\s0 files in a current directory
160 can be specified either by \fI*.fpf\fR or the current directory name.
161 .PP
162 The valid \fITextFile\fR extensions are \fI.csv\fR and \fI.tsv\fR for comma/semicolon and tab
163 delimited text files respectively. All other file names are ignored. All text files in a
164 current directory can be specified by \fI*.csv\fR, \fI*.tsv\fR, or the current directory
165 name. The \fB\-\-indelim\fR option determines the format of \fITextFile(s)\fR. Any file
166 which doesn't correspond to the format indicated by \fB\-\-indelim\fR option is ignored.
167 .PP
168 Format of fingerprint strings data in \fISDFile(s), FPFile(s) and TextFile(s)\fR is automatically
169 detected.
170 .PP
171 Example of \fI\s-1FP\s0\fR file containing fingerprints bit-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 = FingerprintsBitVector
181 \& #
182 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
183 \& # Size = 1024
184 \& # BitStringFormat = HexadecimalString
185 \& # BitsOrder = Ascending
186 \& #
187 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
188 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
189 \& ... ...
190 \& ... ..
191 .Ve
192 .PP
193 Example of \fI\s-1FP\s0\fR file containing fingerprints vector string data:
194 .PP
195 .Vb 10
196 \& #
197 \& # Package = MayaChemTools 7.4
198 \& # ReleaseDate = Oct 21, 2010
199 \& #
200 \& # TimeStamp = Mon Mar 7 15:14:01 2011
201 \& #
202 \& # FingerprintsStringType = FingerprintsVector
203 \& #
204 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
205 \& # VectorStringFormat = IDsAndValuesString
206 \& # VectorValuesType = NumericalValues
207 \& #
208 \& 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:
209 \& 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...;
210 \& 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
211 \& 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 ...
212 \& 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
213 \& O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
214 \& 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
215 \& 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 ...
216 \& ... ...
217 \& ... ...
218 .Ve
219 .PP
220 Example of \fI\s-1SD\s0\fR file containing fingerprints bit-vector string data:
221 .PP
222 .Vb 10
223 \& ... ...
224 \& ... ...
225 \& $$$$
226 \& ... ...
227 \& ... ...
228 \& ... ...
229 \& 41 44 0 0 0 0 0 0 0 0999 V2000
230 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
231 \& ... ...
232 \& 2 3 1 0 0 0 0
233 \& ... ...
234 \& M END
235 \& > <CmpdID>
236 \& Cmpd1
237 \&
238 \& > <PathLengthFingerprints>
239 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
240 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
241 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
242 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
243 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
244 \& aa0660a11014a011d46
245 \&
246 \& $$$$
247 \& ... ...
248 \& ... ...
249 .Ve
250 .PP
251 Example of \s-1CSV\s0 \fIText\fR file containing fingerprints bit-vector string data:
252 .PP
253 .Vb 7
254 \& "CompoundID","PathLengthFingerprints"
255 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
256 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
257 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
258 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
259 \& ... ...
260 \& ... ...
261 .Ve
262 .PP
263 The current release of MayaChemTools supports the following types of fingerprint
264 bit-vector and vector strings:
265 .PP
266 .Vb 6
267 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
268 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
269 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
270 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
271 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
272 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
273 \&
274 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
275 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
276 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
277 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
278 \&
279 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
280 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
281 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
282 \&
283 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
284 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
285 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
286 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
287 \& 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
288 \& 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...
289 \&
290 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
291 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
292 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
293 \& .024 \-2.270
294 \&
295 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
296 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
297 \& 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
298 \& 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
299 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
300 \&
301 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
302 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
303 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
304 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
305 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
306 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
307 \&
308 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
309 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
310 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
311 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
312 \& 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
313 \& 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
314 \&
315 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
316 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
317 \& 0000000001010000000110000011000000000000100000000000000000000000100001
318 \& 1000000110000000000000000000000000010011000000000000000000000000010000
319 \& 0000000000000000000000000010000000000000000001000000000000000000000000
320 \& 0000000000010000100001000000000000101000000000000000100000000000000...
321 \&
322 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
323 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
324 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
325 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
326 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
327 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
328 \&
329 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
330 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
331 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
332 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
333 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
334 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
335 \&
336 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
337 \& 0000000000000000000000000000000001001000010010000000010010000000011100
338 \& 0100101010111100011011000100110110000011011110100110111111111111011111
339 \& 11111111111110111000
340 \&
341 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
342 \& 1110011111100101111111000111101100110000000000000011100010000000000000
343 \& 0000000000000000000000000000000000000000000000101000000000000000000000
344 \& 0000000000000000000000000000000000000000000000000000000000000000000000
345 \& 0000000000000000000000000000000000000011000000000000000000000000000000
346 \& 0000000000000000000000000000000000000000
347 \&
348 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
349 \& 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
350 \& 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
351 \& 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
352 \& 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
353 \& 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
354 \&
355 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
356 \& 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
357 \& 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
358 \& 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
359 \& 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
360 \& 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 ...
361 \&
362 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
363 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
364 \& 0100010101011000101001011100110001000010001001101000001001001001001000
365 \& 0010110100000111001001000001001010100100100000000011000000101001011100
366 \& 0010000001000101010100000100111100110111011011011000000010110111001101
367 \& 0101100011000000010001000011000010100011101100001000001000100000000...
368 \&
369 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
370 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
371 \& 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
372 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
373 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
374 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
375 \&
376 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
377 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
378 \& 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
379 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
380 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
381 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
382 \&
383 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
384 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
385 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
386 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
387 \& 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
388 \& 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...
389 \&
390 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
391 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
392 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
393 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
394 \& 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
395 \& 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 ...
396 \&
397 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
398 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
399 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
400 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
401 \& 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
402 \&
403 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
404 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
405 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
406 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
407 \& 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
408 \&
409 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
410 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
411 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
412 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
413 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
414 \& 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
415 \& 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...
416 \&
417 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
418 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
419 \& .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\-
420 \& 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
421 \& \-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.
422 \& 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...
423 \&
424 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
425 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
426 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
427 \& 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
428 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
429 \& 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
430 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
431 \&
432 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
433 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
434 \& 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
435 \& 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
436 \& 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
437 \& 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...
438 \&
439 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
440 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
441 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
442 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
443 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
444 \& 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
445 \& 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
446 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
447 \&
448 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
449 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
450 \& 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
451 \& 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
452 \& 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
453 \& 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 ...
454 .Ve
455 .SH "OPTIONS"
456 .IX Header "OPTIONS"
457 .IP "\fB\-a, \-\-all\fR" 4
458 .IX Item "-a, --all"
459 List all the available information.
460 .IP "\fB\-\-AverageBitDensity\fR" 4
461 .IX Item "--AverageBitDensity"
462 List average bit density of fingerprint bit-vector strings.
463 .IP "\fB\-\-BitDensity\fR" 4
464 .IX Item "--BitDensity"
465 List bit density of fingerprints bit-vector strings data in each row.
466 .IP "\fB\-\-count\fR" 4
467 .IX Item "--count"
468 List number of data entries containing fingerprints bit-vector or vector strings data. This
469 is \fBdefault behavior\fR.
470 .IP "\fB\-c, \-\-ColMode\fR \fIColNum | ColLabel\fR" 4
471 .IX Item "-c, --ColMode ColNum | ColLabel"
472 Specify how columns are identified in \s-1CSV/TSV\s0 \fITextFile(s)\fR: using column number or column
473 label. Possible values: \fIColNum or ColLabel\fR. Default value: \fIColNum\fR
474 .IP "\fB\-d, \-\-detail\fR \fIInfoLevel\fR" 4
475 .IX Item "-d, --detail InfoLevel"
476 Level of information to print about lines being ignored. Default: \fI1\fR. Possible values:
477 \&\fI1, 2 or 3\fR.
478 .IP "\fB\-\-DataCheck\fR" 4
479 .IX Item "--DataCheck"
480 Validate fingerprints data specified using \fB\-\-FingerprintsCol\fR and list information
481 about missing and invalid data.
482 .IP "\fB\-e, \-\-empty\fR" 4
483 .IX Item "-e, --empty"
484 List number of rows containing no fingerprints data.
485 .IP "\fB\-\-FingerprintsCol\fR \fIcol number | col name\fR" 4
486 .IX Item "--FingerprintsCol col number | col name"
487 This value is \fB\-c, \-\-colmode\fR specific. It corresponds to column in \s-1CSV/TSV\s0 \fITextFile(s)\fR
488 containing fingerprints data. Possible values: \fIcol number or col label\fR.
489 Default value: \fIfirst column containing the word Fingerprints in its column label\fR.
490 .IP "\fB\-\-FingerprintsField\fR \fIFieldLabel\fR" 4
491 .IX Item "--FingerprintsField FieldLabel"
492 Fingerprints field label to use during listing of fingerprints information for \fISDFile(s)\fR.
493 Default value: \fIfirst data field label containing the word Fingerprints in its label\fR.
494 .IP "\fB\-\-FingerprintsType\fR" 4
495 .IX Item "--FingerprintsType"
496 List types of fingerprint strings: FingerprintsBitVector or FingerprintsVector.
497 .IP "\fB\-\-FingerprintsDescription\fR" 4
498 .IX Item "--FingerprintsDescription"
499 List types of fingerprints: PathLengthBits, PathLengthCount, MACCSKeyCount,
500 ExtendedConnectivity and so on.
501 .IP "\fB\-\-FingerprintsSize\fR" 4
502 .IX Item "--FingerprintsSize"
503 List size of fingerprints.
504 .IP "\fB\-\-FingerprintsBitStringFormat\fR" 4
505 .IX Item "--FingerprintsBitStringFormat"
506 List format of fingerprint bit-vector strings: BinaryString or HexadecimalString.
507 .IP "\fB\-\-FingerprintsBitOrder\fR" 4
508 .IX Item "--FingerprintsBitOrder"
509 List order of bits data in fingerprint bit-vector bit strings: Ascending or Descending.
510 .IP "\fB\-\-FingerprintsVectorValuesType\fR" 4
511 .IX Item "--FingerprintsVectorValuesType"
512 List type of values in fingerprint vector strings: OrderedNumericalValues, NumericalValues or
513 AlphaNumericalValues.
514 .IP "\fB\-\-FingerprintsVectorValuesFormat\fR" 4
515 .IX Item "--FingerprintsVectorValuesFormat"
516 List format of values in fingerprint vector strings: ValuesString, IDsAndValuesString,
517 IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString.
518 .IP "\fB\-h, \-\-help\fR" 4
519 .IX Item "-h, --help"
520 Print this help message.
521 .IP "\fB\-\-InDelim\fR \fIcomma | semicolon\fR" 4
522 .IX Item "--InDelim comma | semicolon"
523 Input delimiter for \s-1CSV\s0 \fITextFile(s)\fR. Possible values: \fIcomma or semicolon\fR.
524 Default value: \fIcomma\fR. For \s-1TSV\s0 files, this option is ignored and \fItab\fR is used as a
525 delimiter.
526 .IP "\fB\-\-NumOfOnBits\fR" 4
527 .IX Item "--NumOfOnBits"
528 List number of on bits in fingerprints bit-vector strings data in each row.
529 .IP "\fB\-\-NumOfNonZeroValues\fR" 4
530 .IX Item "--NumOfNonZeroValues"
531 List number of non-zero values in fingerprints vector strings data in each row.
532 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
533 .IX Item "-w, --WorkingDir DirName"
534 Location of working directory. Default: current directory.
535 .SH "EXAMPLES"
536 .IX Header "EXAMPLES"
537 To count number of lines containing fingerprints bit-vector or vector strings data present
538 in \s-1FP\s0 file, in a column name containing Fingerprint substring in text file, and in a data
539 field with Fingerprint substring in its label, type:
540 .PP
541 .Vb 1
542 \& % InfoFingerprintsFiles.pl SampleFPBin.csv
543 \&
544 \& % InfoFingerprintsFiles.pl SampleFPBin.sdf SampleFPBin.fpf
545 \& SampleFPBin.csv
546 \&
547 \& % InfoFingerprintsFiles.pl SampleFPHex.sdf SampleFPHex.fpf
548 \& SampleFPHex.csv
549 \&
550 \& % InfoFingerprintsFiles.pl SampleFPcount.sdf SampleFPcount.fpf
551 \& SampleFPcount.csv
552 .Ve
553 .PP
554 To list all available information about fingerprints bit-vector or vector strings data present
555 in \s-1FP\s0 file, in a column name containing Fingerprint substring in text file, and in a data
556 field with Fingerprint substring in its label, type:
557 .PP
558 .Vb 2
559 \& % InfoFingerprintsFiles.pl \-a SampleFPHex.sdf SampleFPHex.fpf
560 \& SampleFPHex.csv
561 \&
562 \& % InfoFingerprintsFiles.pl \-a SampleFPcount.sdf SampleFPcount.fpf
563 \& SampleFPcount.csv
564 .Ve
565 .PP
566 To list all available information about fingerprints bit-vector or vector strings data present in a
567 column named Fingerprints in text file, type:
568 .PP
569 .Vb 2
570 \& % InfoFingerprintsFiles.pl \-a \-\-ColMode ColLabel \-\-FingerprintsCol
571 \& Fingerprints SampleFPHex.sdf
572 \&
573 \& % InfoFingerprintsFiles.pl \-a \-\-ColMode ColLabel \-\-FingerprintsCol
574 \& Fingerprints SampleFPcount.csv
575 .Ve
576 .PP
577 To list all available information about fingerprints bit-vector or vector strings data present in a
578 data field names Fingerprints in \s-1SD\s0 file, type:
579 .PP
580 .Vb 2
581 \& % InfoFingerprintsFiles.pl \-a \-\-FingerprintsField Fingerprints
582 \& SampleFPHex.sdf
583 \&
584 \& % InfoFingerprintsFiles.pl \-a \-\-FingerprintsField Fingerprints
585 \& SampleFPcount.sdf
586 .Ve
587 .PP
588 To list bit density, average bit density, and number of on bits for fingerprints bit-vector strings data
589 present in \s-1FP\s0 file, in a column name containing Fingerprint substring in text file, and in a data
590 field with Fingerprint substring in its label, type:
591 .PP
592 .Vb 2
593 \& % InfoFingerprintsFiles.pl \-\-BitDensity \-\-AverageBitDensity
594 \& \-\-NumOfOnBits SampleFPBin.csv SampleFPBin.sdf SampleFPBin.fpf
595 .Ve
596 .PP
597 To list vector values type, format and number of non-zero values for fingerprints vector strings
598 data present in \s-1FP\s0 file, in a column name containing Fingerprint substring in text file, and in a data
599 field with Fingerprint substring in its label along with fingerprints type and description, type:
600 .PP
601 .Vb 4
602 \& % InfoFingerprintsFiles.pl \-\-FingerprintsType \-\-FingerprintsDescription
603 \& \-\-FingerprintsVectorValuesType \-\-FingerprintsVectorValuesFormat
604 \& \-\-NumOfNonZeroValues SampleFPcount.csv SampleFPcount.sdf
605 \& SampleFPcount.fpf
606 .Ve
607 .SH "AUTHOR"
608 .IX Header "AUTHOR"
609 Manish Sud <msud@san.rr.com>
610 .SH "SEE ALSO"
611 .IX Header "SEE ALSO"
612 SimilarityMatricesFingerprints.pl, SimilaritySearchingFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
613 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
614 PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
615 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
616 .SH "COPYRIGHT"
617 .IX Header "COPYRIGHT"
618 Copyright (C) 2015 Manish Sud. All rights reserved.
619 .PP
620 This file is part of MayaChemTools.
621 .PP
622 MayaChemTools is free software; you can redistribute it and/or modify it under
623 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
624 Software Foundation; either version 3 of the License, or (at your option)
625 any later version.