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123 .rm #[ #] #H #V #F C
124 .\" ========================================================================
125 .\"
126 .IX Title "FINGERPRINTSFPFILEIO 1"
127 .TH FINGERPRINTSFPFILEIO 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 FingerprintsFPFileIO
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use FileIO::FingerprintsFPFileIO;
137 .PP
138 use FileIO::FingerprintsFPFileIO qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBFingerprintsFPFileIO\fR class provides the following methods:
142 .PP
143 new, GetFingerprints, GetFingerprintsString, GetHeaderDataKeyValue,
144 GetHeaderDataKeys, GetHeaderDataKeysAndValues, GetPartialFingerprintsString,
145 GetRequiredHeaderDataKeys, GetRequiredHeaderDataKeysAndValues,
146 IsFingerprintsDataValid, IsFingerprintsFPFile, IsFingerprintsFileDataValid,
147 IsHeaderDataKeyPresent, Next, Read, SetBitStringFormat, SetBitsOrder,
148 SetCompoundID, SetDetailLevel, SetFingerprints, SetFingerprintsString,
149 SetFingerprintsStringMode, SetPartialFingerprintsString, SetVectorStringFormat,
150 WriteFingerprints, WriteFingerprintsString
151 .PP
152 The following methods can also be used as functions:
153 .PP
154 IsFingerprintsFPFile
155 .PP
156 \&\fBFingerprintsFPFileIO\fR class is derived from \fIFileIO\fR class and uses its methods to support
157 generic file related functionality.
158 .PP
159 The MayaChemTools fingerprints file (\s-1FP\s0) format with \fB.fpf\fR or \fB.fp\fR file extensions supports
160 two types of fingerprints data: fingerprints bit-vectors and fingerprints vectors.
161 .PP
162 Example of \s-1FP\s0 file format containing fingerprints bit-vector string data:
163 .PP
164 .Vb 10
165 \& #
166 \& # Package = MayaChemTools 7.4
167 \& # ReleaseDate = Oct 21, 2010
168 \& #
169 \& # TimeStamp = Mon Mar 7 15:14:01 2011
170 \& #
171 \& # FingerprintsStringType = FingerprintsBitVector
172 \& #
173 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
174 \& # Size = 1024
175 \& # BitStringFormat = HexadecimalString
176 \& # BitsOrder = Ascending
177 \& #
178 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
179 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
180 \& ... ...
181 \& ... ..
182 .Ve
183 .PP
184 Example of \s-1FP\s0 file format containing fingerprints vector string data:
185 .PP
186 .Vb 10
187 \& #
188 \& # Package = MayaChemTools 7.4
189 \& # ReleaseDate = Oct 21, 2010
190 \& #
191 \& # TimeStamp = Mon Mar 7 15:14:01 2011
192 \& #
193 \& # FingerprintsStringType = FingerprintsVector
194 \& #
195 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
196 \& # VectorStringFormat = IDsAndValuesString
197 \& # VectorValuesType = NumericalValues
198 \& #
199 \& 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:
200 \& 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...;
201 \& 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
202 \& 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 ...
203 \& 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
204 \& O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
205 \& 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
206 \& 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 ...
207 \& ... ...
208 \& ... ...
209 .Ve
210 .PP
211 \&\fB\s-1FP\s0\fR file data format consists of two main sections: header section and fingerprints string
212 data section. The header section lines start with # and the first line not starting with # represents
213 the start of fingerprints string data section. The header section contains both the required and
214 optional information which is specified as key = value pairs. The required information
215 describes fingerprints bit-vector and vector strings and used to generate fingerprints objects;
216 the optional information is ignored during generation of fingerpints objects.
217 .PP
218 The key = value data specification in the header section and its processing follows these
219 rules:
220 .PP
221 .Vb 3
222 \& o Leading and trailing spaces for key = value pairs are ignored
223 \& o Key and value strings may contain spaces
224 \& o Multiple key = value pairs on a single are delimited by semicolon
225 .Ve
226 .PP
227 The default optional header data section key = value pairs are:
228 .PP
229 .Vb 2
230 \& # Package = MayaChemTools 7.4
231 \& # ReleaseDate = Oct 21, 2010
232 .Ve
233 .PP
234 The \fBFingerprintsStringType\fR key is required data header key for both fingerprints bit-vector
235 and vector strings. Possible key values: \fIFingerprintsBitVector or FingerprintsVector\fR.
236 For example:
237 .PP
238 .Vb 1
239 \& # FingerprintsStringType = FingerprintsBitVector
240 .Ve
241 .PP
242 The required data header keys for fingerprints bit-vector string are: \fBDescription, Size,
243 BitStringFormat, and BitsOrder\fR. Possible values for \fBBitStringFormat\fR: \fIHexadecimalString
244 or BinaryString\fR. Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR. The \fBDescription\fR
245 key contains information about various parameters used to generate fingerprints bit-vector
246 string. The \fBSize\fR corresponds to number of fingerprints bits and is always less than or equal
247 to number of bits in bit-vetor string which might contain extra bits at the end to round off the
248 size to make it multiple of 8. For example:
249 .PP
250 .Vb 4
251 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
252 \& # Size = 1024
253 \& # BitStringFormat = HexadecimalString
254 \& # BitsOrder = Ascending
255 .Ve
256 .PP
257 The required data header keys for fingerprints vector string are: \fBDescription, VectorStringFormat,
258 and VectorValuesType\fR. Possible values for \fBVectorStringFormat\fR: \fIDsAndValuesString,
259 IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString or ValuesString\fR.
260 Possible values for \fBVectorValuesType\fR: \fINumericalValues, OrderedNumericalValues or
261 AlphaNumericalValues\fR. The \fBDescription\fR keys contains information various parameters used
262 to generate fingerprints vector string. For example:
263 .PP
264 .Vb 3
265 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
266 \& # VectorStringFormat = IDsAndValuesString
267 \& # VectorValuesType = NumericalValues
268 .Ve
269 .PP
270 The fingerprints data section for fingerprints bit-vector string contains data in the following
271 format:
272 .PP
273 .Vb 3
274 \& ... ...
275 \& CmpdID FingerprintsPartialBitVectorString
276 \& ... ...
277 .Ve
278 .PP
279 For example:
280 .PP
281 .Vb 3
282 \& ... ...
283 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
284 \& ... ...
285 .Ve
286 .PP
287 The fingerprints data section for fingerprints vector string contains data in the following
288 format:
289 .PP
290 .Vb 3
291 \& ... ...
292 \& CmpdID Size;FingerprintsPartialVectorString
293 \& ... ...
294 .Ve
295 .PP
296 For example:
297 .PP
298 .Vb 6
299 \& ... ...
300 \& 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:
301 \& 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...;
302 \& 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
303 \& 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 ...
304 \& ... ...
305 .Ve
306 .PP
307 Unlike fingerprints bit-vector string, \fISize\fR is specified for each partial fingerprints vector string:
308 It may change from molecule to molecule for same type of fingerprints.
309 .PP
310 Values IDs are optional for fingerprints vector string containing \fIOrderedNumericalValues or
311 AlphaNumericalValues\fR; however, they must be present for for \fINumericalValues\fR. Due to
312 various possible values for \fBVectorStringFormat\fR, the fingerprints data section for fingerprints
313 vector string supports following type of data formats:
314 .PP
315 .Vb 5
316 \& CmpdID Size;ID1 ID2 ID3...;Value1 Value2 Value3...
317 \& CmpdID Size;ID1 Value1 ID2 Value2 ID3 Value3... ...
318 \& CmpdID Size;ValuesAndIDsString: Value1 Value2 Value3...;ID1 ID2 ID3...
319 \& CmpdID Size;ValuesAndIDsPairsString: Value1 ID1 Value2 ID2 Value3 ID3... ...
320 \& CmpdID Size;Value1 Value2 Value3 ...
321 .Ve
322 .PP
323 However, all the fingerprints vector string data present in \s-1FP\s0 file must correspond to only
324 one of the formats shown above; multiple data formats in the same file are not allowed.
325 .PP
326 The current release of MayaChemTools supports the following types of fingerprint
327 bit-vector and vector strings:
328 .PP
329 .Vb 6
330 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
331 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
332 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
333 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
334 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
335 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
336 \&
337 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
338 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
339 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
340 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
341 \&
342 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
343 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
344 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
345 \&
346 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
347 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
348 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
349 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
350 \& 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
351 \& 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...
352 \&
353 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
354 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
355 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
356 \& .024 \-2.270
357 \&
358 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
359 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
360 \& 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
361 \& 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
362 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
363 \&
364 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
365 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
366 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
367 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
368 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
369 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
370 \&
371 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
372 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
373 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
374 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
375 \& 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
376 \& 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
377 \&
378 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
379 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
380 \& 0000000001010000000110000011000000000000100000000000000000000000100001
381 \& 1000000110000000000000000000000000010011000000000000000000000000010000
382 \& 0000000000000000000000000010000000000000000001000000000000000000000000
383 \& 0000000000010000100001000000000000101000000000000000100000000000000...
384 \&
385 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
386 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
387 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
388 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
389 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
390 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
391 \&
392 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
393 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
394 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
395 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
396 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
397 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
398 \&
399 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
400 \& 0000000000000000000000000000000001001000010010000000010010000000011100
401 \& 0100101010111100011011000100110110000011011110100110111111111111011111
402 \& 11111111111110111000
403 \&
404 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
405 \& 1110011111100101111111000111101100110000000000000011100010000000000000
406 \& 0000000000000000000000000000000000000000000000101000000000000000000000
407 \& 0000000000000000000000000000000000000000000000000000000000000000000000
408 \& 0000000000000000000000000000000000000011000000000000000000000000000000
409 \& 0000000000000000000000000000000000000000
410 \&
411 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
412 \& 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
413 \& 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
414 \& 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
415 \& 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
416 \& 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
417 \&
418 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
419 \& 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
420 \& 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
421 \& 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
422 \& 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
423 \& 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 ...
424 \&
425 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
426 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
427 \& 0100010101011000101001011100110001000010001001101000001001001001001000
428 \& 0010110100000111001001000001001010100100100000000011000000101001011100
429 \& 0010000001000101010100000100111100110111011011011000000010110111001101
430 \& 0101100011000000010001000011000010100011101100001000001000100000000...
431 \&
432 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
433 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
434 \& 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
435 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
436 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
437 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
438 \&
439 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
440 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
441 \& 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
442 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
443 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
444 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
445 \&
446 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
447 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
448 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
449 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
450 \& 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
451 \& 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...
452 \&
453 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
454 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
455 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
456 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
457 \& 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
458 \& 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 ...
459 \&
460 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
461 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
462 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
463 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
464 \& 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
465 \&
466 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
467 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
468 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
469 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
470 \& 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
471 \&
472 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
473 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
474 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
475 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
476 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
477 \& 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
478 \& 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...
479 \&
480 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
481 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
482 \& .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\-
483 \& 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
484 \& \-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.
485 \& 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...
486 \&
487 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
488 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
489 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
490 \& 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
491 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
492 \& 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
493 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
494 \&
495 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
496 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
497 \& 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
498 \& 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
499 \& 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
500 \& 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...
501 \&
502 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
503 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
504 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
505 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
506 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
507 \& 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
508 \& 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
509 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
510 \&
511 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
512 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
513 \& 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
514 \& 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
515 \& 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
516 \& 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 ...
517 .Ve
518 .SS "\s-1METHODS\s0"
519 .IX Subsection "METHODS"
520 .IP "\fBnew\fR" 4
521 .IX Item "new"
522 .Vb 1
523 \& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(%IOParameters);
524 .Ve
525 .Sp
526 Using specified \fIIOParameters\fR names and values hash, \fBnew\fR method creates a new
527 object and returns a reference to a newly created \fBFingerprintsFPFileIO\fR object. By default,
528 the following properties are initialized during \fIRead\fR mode:
529 .Sp
530 .Vb 6
531 \& Name = \*(Aq\*(Aq;
532 \& Mode = \*(AqRead\*(Aq;
533 \& Status = 0;
534 \& FingerprintsStringMode = \*(AqAutoDetect\*(Aq;
535 \& ValidateData = 1;
536 \& DetailLevel = 1;
537 .Ve
538 .Sp
539 During \fIWrite\fR mode, the following properties get initialize by default:
540 .Sp
541 .Vb 1
542 \& FingerprintsStringMode = undef;
543 \&
544 \& BitStringFormat = HexadecimalString;
545 \& BitsOrder = Ascending;
546 \&
547 \& VectorStringFormat = NumericalValuesString or ValuesString;
548 .Ve
549 .Sp
550 Examples:
551 .Sp
552 .Vb 5
553 \& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
554 \& \*(AqName\*(Aq => \*(AqSample.fpf\*(Aq,
555 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq,
556 \& \*(AqFingerprintsStringMode\*(Aq =>
557 \& \*(AqAutoDetect\*(Aq);
558 \&
559 \& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
560 \& \*(AqName\*(Aq => \*(AqSample.fpf\*(Aq,
561 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
562 \& \*(AqFingerprintsStringMode\*(Aq =>
563 \& \*(AqFingerprintsBitVectorString\*(Aq,
564 \& \*(AqOverwrite\*(Aq => 1,
565 \& \*(AqBitStringFormat\*(Aq => \*(AqHexadecimalString\*(Aq,
566 \& \*(AqBitsOrder\*(Aq => \*(AqAscending\*(Aq);
567 \&
568 \& $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
569 \& \*(AqName\*(Aq => \*(AqSample.fp\*(Aq,
570 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
571 \& \*(AqFingerprintsStringMode\*(Aq =>
572 \& \*(AqFingerprintsVectorString\*(Aq,
573 \& \*(AqOverwrite\*(Aq => 1,
574 \& \*(AqVectorStringFormat\*(Aq => \*(AqIDsAndValuesString\*(Aq);
575 .Ve
576 .IP "\fBGetFingerprints\fR" 4
577 .IX Item "GetFingerprints"
578 .Vb 1
579 \& $FingerprintsObject = $FingerprintsFPFileIO\->GetFingerprints();
580 .Ve
581 .Sp
582 Returns \fBFingerprintsObject\fR generated for current data line using fingerprints bit-vector
583 or vector string data. The fingerprints object corresponds to any of the supported fingerprints
584 such as PathLengthFingerprints, ExtendedConnectivity, and so on.
585 .IP "\fBGetFingerprintsString\fR" 4
586 .IX Item "GetFingerprintsString"
587 .Vb 1
588 \& $FingerprintsString = $FingerprintsFPFileIO\->GetFingerprintsString();
589 .Ve
590 .Sp
591 Returns \fBFingerprintsString\fR for current data line.
592 .IP "\fBGetHeaderDataKeyValue\fR" 4
593 .IX Item "GetHeaderDataKeyValue"
594 .Vb 1
595 \& $KeyValue = $FingerprintsFPFileIO\->GetHeaderDataKeyValue($Key);
596 .Ve
597 .Sp
598 Returns \fBKeyValue\fR of a data header \fIKey\fR.
599 .IP "\fBGetHeaderDataKeys\fR" 4
600 .IX Item "GetHeaderDataKeys"
601 .Vb 2
602 \& @Keys = $FingerprintsFPFileIO\->GetHeaderDataKeys();
603 \& $NumOfKeys = $FingerprintsFPFileIO\->GetHeaderDataKeys();
604 .Ve
605 .Sp
606 Returns an array of data header \fBKeys\fR retrieved from data header section of fingerprints
607 file. In scalar context, it returns number of keys.
608 .IP "\fBGetHeaderDataKeysAndValues\fR" 4
609 .IX Item "GetHeaderDataKeysAndValues"
610 .Vb 1
611 \& %KeysAndValues = $FingerprintsFPFileIO\->GetHeaderDataKeysAndValues();
612 .Ve
613 .Sp
614 Returns a hash of data header keys and values retrieved from data header section of fingerprints
615 file.
616 .IP "\fBGetPartialFingerprintsString\fR" 4
617 .IX Item "GetPartialFingerprintsString"
618 .Vb 1
619 \& $FingerprintsString = $FingerprintsFPFileIO\->GetPartialFingerprintsString();
620 .Ve
621 .Sp
622 Returns partial \fBFingerprintsString\fR for current data line. It corresponds to fingerprints string
623 specified present in a line.
624 .IP "\fBGetRequiredHeaderDataKeys\fR" 4
625 .IX Item "GetRequiredHeaderDataKeys"
626 .Vb 2
627 \& @Keys = $FingerprintsFPFileIO\->GetRequiredHeaderDataKeys();
628 \& $NumOfKeys = $FingerprintsFPFileIO\->GetRequiredHeaderDataKeys();
629 .Ve
630 .Sp
631 Returns an array of required data header \fBKeys\fR for a fingerprints file containing bit-vector or
632 vector strings data. In scalar context, it returns number of keys.
633 .IP "\fBGetRequiredHeaderDataKeysAndValues\fR" 4
634 .IX Item "GetRequiredHeaderDataKeysAndValues"
635 .Vb 2
636 \& %KeysAndValues = $FingerprintsFPFileIO\->
637 \& GetRequiredHeaderDataKeysAndValues();
638 .Ve
639 .Sp
640 Returns a hash of required data header keys and values for a fingerprints file containing bit-vector or
641 vector strings data
642 .IP "\fBIsFingerprintsDataValid\fR" 4
643 .IX Item "IsFingerprintsDataValid"
644 .Vb 1
645 \& $Status = $FingerprintsFPFileIO\->IsFingerprintsDataValid();
646 .Ve
647 .Sp
648 Returns 1 or 0 based on whether \fBFingerprintsObject\fR is valid.
649 .IP "\fBIsFingerprintsFPFile\fR" 4
650 .IX Item "IsFingerprintsFPFile"
651 .Vb 2
652 \& $Status = $FingerprintsFPFileIO\->IsFingerprintsFPFile($FileName);
653 \& $Status = FileIO::FingerprintsFPFileIO::IsFingerprintsFPFile($FileName);
654 .Ve
655 .Sp
656 Returns 1 or 0 based on whether \fIFileName\fR is a \s-1FP\s0 file.
657 .IP "\fBIsFingerprintsFileDataValid\fR" 4
658 .IX Item "IsFingerprintsFileDataValid"
659 .Vb 1
660 \& $Status = $FingerprintsFPFileIO\->IsFingerprintsFileDataValid();
661 .Ve
662 .Sp
663 Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data.
664 .IP "\fBIsHeaderDataKeyPresent\fR" 4
665 .IX Item "IsHeaderDataKeyPresent"
666 .Vb 1
667 \& $Status = $FingerprintsFPFileIO\->IsHeaderDataKeyPresent($Key);
668 .Ve
669 .Sp
670 Returns 1 or 0 based on whether data header \fIKey\fR is present in data header
671 section of a \s-1FP\s0 file.
672 .IP "\fBNext or Read\fR" 4
673 .IX Item "Next or Read"
674 .Vb 2
675 \& $FingerprintsFPFileIO = $FingerprintsFPFileIO\->Next();
676 \& $FingerprintsFPFileIO = $FingerprintsFPFileIO\->Read();
677 .Ve
678 .Sp
679 Reads next available fingerprints line in \s-1FP\s0 file, processes the data, generates appropriate fingerprints
680 object, and returns \fBFingerprintsFPFileIO\fR. The generated fingerprints object is available using
681 method \fBGetFingerprints\fR.
682 .IP "\fBSetBitStringFormat\fR" 4
683 .IX Item "SetBitStringFormat"
684 .Vb 1
685 \& $FingerprintsFPFileIO\->SetBitStringFormat($Format);
686 .Ve
687 .Sp
688 Sets bit string \fIFormat\fR for fingerprints bit-vector string data in a \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR.
689 Possible values for \fBBitStringFormat\fR: \fIBinaryString or HexadecimalString\fR.
690 .IP "\fBSetBitsOrder\fR" 4
691 .IX Item "SetBitsOrder"
692 .Vb 1
693 \& $FingerprintsFPFileIO\->SetBitsOrder($BitsOrder);
694 .Ve
695 .Sp
696 Sets \fIBitsOrder\fR for fingerprints bit-vector string data in a \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR.
697 Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR.
698 .IP "\fBSetCompoundID\fR" 4
699 .IX Item "SetCompoundID"
700 .Vb 1
701 \& $FingerprintsFPFileIO\->SetCompoundID($ID);
702 .Ve
703 .Sp
704 Sets compound \s-1ID\s0 for current data line and returns \fBFingerprintsFPFileIO\fR. Spaces are not allowed
705 in compound IDs.
706 .IP "\fBSetDetailLevel\fR" 4
707 .IX Item "SetDetailLevel"
708 .Vb 1
709 \& $FingerprintsFPFileIO\->SetDetailLevel($Level);
710 .Ve
711 .Sp
712 Sets details \fILevel\fR for generating diagnostics messages during \s-1FP\s0 file processing and returns
713 \&\fBFingerprintsFPFileIO\fR. Possible values: \fIPositive integers\fR.
714 .IP "\fBSetFingerprints\fR" 4
715 .IX Item "SetFingerprints"
716 .Vb 1
717 \& $FingerprintsFPFileIO\->SetFingerprints($FingerprintsObject);
718 .Ve
719 .Sp
720 Sets \fIFingerprintsObject\fR for current data line and returns \fBFingerprintsFPFileIO\fR.
721 .IP "\fBSetFingerprintsString\fR" 4
722 .IX Item "SetFingerprintsString"
723 .Vb 1
724 \& $FingerprintsFPFileIO\->SetFingerprintsString($FingerprintsString);
725 .Ve
726 .Sp
727 Sets \fIFingerprintsString\fR for current data line and returns \fBFingerprintsFPFileIO\fR.
728 .IP "\fBSetFingerprintsStringMode\fR" 4
729 .IX Item "SetFingerprintsStringMode"
730 .Vb 1
731 \& $FingerprintsFPFileIO\->SetFingerprintsStringMode($Mode);
732 .Ve
733 .Sp
734 Sets \fIFingerprintsStringMode\fR for \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR.
735 Possible values: \fIAutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString\fR
736 .IP "\fBSetPartialFingerprintsString\fR" 4
737 .IX Item "SetPartialFingerprintsString"
738 .Vb 1
739 \& $FingerprintsFPFileIO\->SetPartialFingerprintsString($PartialString);
740 .Ve
741 .Sp
742 Sets \fIPartialFingerprintsString\fR for current data line and returns \fBFingerprintsFPFileIO\fR.
743 .IP "\fBSetVectorStringFormat\fR" 4
744 .IX Item "SetVectorStringFormat"
745 .Vb 1
746 \& $FingerprintsFPFileIO\->SetVectorStringFormat($Format);
747 .Ve
748 .Sp
749 Sets \fIVectorStringFormat\fR for \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR. Possible values:
750 \&\fIIDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString\fR.
751 .IP "\fBWriteFingerprints\fR" 4
752 .IX Item "WriteFingerprints"
753 .Vb 2
754 \& $FingerprintsFPFileIO\->WriteFingerprints($FingerprintsObject,
755 \& $CompoundID);
756 .Ve
757 .Sp
758 Writes fingerprints string generated from \fIFingerprintsObject\fR object and other data including
759 \&\fICompoundID\fR to \s-1FP\s0 file and returns \fBFingerprintsFPFileIO\fR.
760 .IP "\fBWriteFingerprintsString\fR" 4
761 .IX Item "WriteFingerprintsString"
762 .Vb 2
763 \& $FingerprintsFPFileIO\->WriteFingerprints($FingerprintsString,
764 \& $CompoundID);
765 .Ve
766 .Sp
767 Writes \fIFingerprintsString\fR and other data including \fICompoundID\fR to \s-1FP\s0 file and returns
768 \&\fBFingerprintsFPFileIO\fR.
769 .Sp
770 Caveats:
771 .Sp
772 .Vb 5
773 \& o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
774 \& values are ignored during writing of fingerprints and it\*(Aqs written to
775 \& the file as it is.
776 \& o FingerprintsString is a regular fingerprints string as oppose to a
777 \& partial fingerprints string.
778 .Ve
779 .SH "AUTHOR"
780 .IX Header "AUTHOR"
781 Manish Sud <msud@san.rr.com>
782 .SH "SEE ALSO"
783 .IX Header "SEE ALSO"
784 FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm
785 .SH "COPYRIGHT"
786 .IX Header "COPYRIGHT"
787 Copyright (C) 2015 Manish Sud. All rights reserved.
788 .PP
789 This file is part of MayaChemTools.
790 .PP
791 MayaChemTools is free software; you can redistribute it and/or modify it under
792 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
793 Software Foundation; either version 3 of the License, or (at your option)
794 any later version.