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1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
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123 .rm #[ #] #H #V #F C
124 .\" ========================================================================
125 .\"
126 .IX Title "FINGERPRINTSTEXTFILEIO 1"
127 .TH FINGERPRINTSTEXTFILEIO 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 FingerprintsTextFileIO
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use FileIO::FingerprintsTextFileIO;
137 .PP
138 use FileIO::FingerprintsTextFileIO qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBFingerprintsTextFileIO\fR class provides the following methods:
142 .PP
143 new, GetDataColLabels, GetDataLineWords, GetFingerprints, GetFingerprintsString,
144 IsFingerprintsDataValid, IsFingerprintsFileDataValid, IsFingerprintsTextFile,
145 Next, Read, SetBitStringFormat, SetBitsOrder, SetColMode, SetDataColLabels,
146 SetDataLineWords, SetDetailLevel, SetFingerprints, SetFingerprintsString,
147 SetFingerprintsStringMode, SetInDelim, SetOutDelim, SetVectorStringFormat,
148 WriteFingerprints, WriteFingerprintsString
149 .PP
150 The following methods can also be used as functions:
151 .PP
152 IsFingerprintsTextFile
153 .PP
154 \&\fBFingerprintsTextFileIO\fR class is derived from \fIFileIO\fR class and uses its methods to support
155 generic file related functionality.
156 .PP
157 The fingerprints \s-1CSV/TSV\s0 text file format with \fB.csv\fR or \fB.tsv\fR file extensions supports two
158 types of fingerprints string data: fingerprints bit-vectors and fingerprints vector strings. The
159 fingerprints string data is treated as column value in a text file.
160 .PP
161 Example of text file format containing fingerprints string data:
162 .PP
163 .Vb 7
164 \& "CompoundID","PathLengthFingerprints"
165 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
166 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
167 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
168 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
169 \& ... ...
170 \& ... ...
171 .Ve
172 .PP
173 The current release of MayaChemTools supports the following types of fingerprint
174 bit-vector and vector strings:
175 .PP
176 .Vb 6
177 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
178 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
179 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
180 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
181 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
182 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
183 \&
184 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
185 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
186 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
187 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
188 \&
189 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
190 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
191 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
192 \&
193 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
194 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
195 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
196 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
197 \& 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
198 \& 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...
199 \&
200 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
201 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
202 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
203 \& .024 \-2.270
204 \&
205 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
206 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
207 \& 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
208 \& 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
209 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
210 \&
211 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
212 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
213 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
214 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
215 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
216 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
217 \&
218 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
219 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
220 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
221 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
222 \& 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
223 \& 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
224 \&
225 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
226 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
227 \& 0000000001010000000110000011000000000000100000000000000000000000100001
228 \& 1000000110000000000000000000000000010011000000000000000000000000010000
229 \& 0000000000000000000000000010000000000000000001000000000000000000000000
230 \& 0000000000010000100001000000000000101000000000000000100000000000000...
231 \&
232 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
233 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
234 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
235 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
236 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
237 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
238 \&
239 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
240 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
241 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
242 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
243 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
244 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
245 \&
246 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
247 \& 0000000000000000000000000000000001001000010010000000010010000000011100
248 \& 0100101010111100011011000100110110000011011110100110111111111111011111
249 \& 11111111111110111000
250 \&
251 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
252 \& 1110011111100101111111000111101100110000000000000011100010000000000000
253 \& 0000000000000000000000000000000000000000000000101000000000000000000000
254 \& 0000000000000000000000000000000000000000000000000000000000000000000000
255 \& 0000000000000000000000000000000000000011000000000000000000000000000000
256 \& 0000000000000000000000000000000000000000
257 \&
258 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
259 \& 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
260 \& 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
261 \& 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
262 \& 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
263 \& 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
264 \&
265 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
266 \& 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
267 \& 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
268 \& 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
269 \& 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
270 \& 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 ...
271 \&
272 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
273 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
274 \& 0100010101011000101001011100110001000010001001101000001001001001001000
275 \& 0010110100000111001001000001001010100100100000000011000000101001011100
276 \& 0010000001000101010100000100111100110111011011011000000010110111001101
277 \& 0101100011000000010001000011000010100011101100001000001000100000000...
278 \&
279 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
280 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
281 \& 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
282 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
283 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
284 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
285 \&
286 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
287 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
288 \& 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
289 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
290 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
291 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
292 \&
293 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
294 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
295 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
296 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
297 \& 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
298 \& 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...
299 \&
300 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
301 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
302 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
303 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
304 \& 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
305 \& 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 ...
306 \&
307 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
308 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
309 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
310 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
311 \& 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
312 \&
313 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
314 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
315 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
316 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
317 \& 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
318 \&
319 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
320 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
321 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
322 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
323 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
324 \& 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
325 \& 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...
326 \&
327 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
328 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
329 \& .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\-
330 \& 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
331 \& \-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.
332 \& 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...
333 \&
334 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
335 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
336 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
337 \& 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
338 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
339 \& 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
340 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
341 \&
342 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
343 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
344 \& 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
345 \& 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
346 \& 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
347 \& 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...
348 \&
349 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
350 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
351 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
352 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
353 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
354 \& 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
355 \& 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
356 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
357 \&
358 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
359 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
360 \& 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
361 \& 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
362 \& 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
363 \& 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 ...
364 .Ve
365 .SS "\s-1METHODS\s0"
366 .IX Subsection "METHODS"
367 .IP "\fBnew\fR" 4
368 .IX Item "new"
369 .Vb 1
370 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(%IOParameters);
371 .Ve
372 .Sp
373 Using specified \fIIOParameters\fR names and values hash, \fBnew\fR method creates a new
374 object and returns a reference to a newly created \fBFingerprintsTextFileIO\fR object. By default,
375 the following properties are initialized during \fIRead\fR mode:
376 .Sp
377 .Vb 11
378 \& Name = \*(Aq\*(Aq;
379 \& Mode = \*(AqRead\*(Aq;
380 \& Status = 0;
381 \& FingerprintsStringMode = \*(AqAutoDetect\*(Aq;
382 \& FingerprintsCol = \*(AqAutoDetect\*(Aq;
383 \& ColMode = \*(AqColNum\*(Aq;
384 \& CompoundIDCol = \*(AqAutoDetect\*(Aq;
385 \& CompoundIDPrefix = \*(AqCmpd\*(Aq;
386 \& InDelim = \*(AqComma\*(Aq;
387 \& ValidateData = 1;
388 \& DetailLevel = 1;
389 .Ve
390 .Sp
391 During \fIWrite\fR mode, the following properties get initialize by default:
392 .Sp
393 .Vb 1
394 \& FingerprintsStringMode = undef;
395 \&
396 \& BitStringFormat = HexadecimalString;
397 \& BitsOrder = Ascending;
398 \&
399 \& VectorStringFormat = NumericalValuesString or ValuesString;
400 \& OutDelim = \*(AqComma\*(Aq;
401 \& OutQuote = 1;
402 .Ve
403 .Sp
404 Examples:
405 .Sp
406 .Vb 3
407 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
408 \& \*(AqName\*(Aq => \*(AqSample.csv\*(Aq,
409 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq);
410 \&
411 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
412 \& \*(AqName\*(Aq => \*(AqSample.csv\*(Aq,
413 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq,;
414 \& \*(AqFingerprintsStringMode\*(Aq =>
415 \& \*(AqAutoDetect\*(Aq,
416 \& \*(AqColMode\*(Aq => \*(AqColLabel\*(Aq,
417 \& \*(AqFingerprintsCol\*(Aq => \*(AqFingerprints\*(Aq,
418 \& \*(AqCompoundIDCol\*(Aq => \*(AqCompoundID\*(Aq,
419 \& \*(AqInDelim\*(Aq => \*(AqComma\*(Aq);
420 \&
421 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
422 \& \*(AqName\*(Aq => \*(AqSample.csv\*(Aq,
423 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
424 \& \*(AqFingerprintsStringMode\*(Aq =>
425 \& \*(AqFingerprintsBitVectorString\*(Aq,
426 \& \*(AqOverwrite\*(Aq => 1,
427 \& \*(AqBitStringFormat\*(Aq => \*(AqHexadecimalString\*(Aq,
428 \& \*(AqBitsOrder\*(Aq => \*(AqAscending\*(Aq);
429 \&
430 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
431 \& \*(AqName\*(Aq => \*(AqSample.tsv\*(Aq,
432 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
433 \& \*(AqFingerprintsStringMode\*(Aq =>
434 \& \*(AqFingerprintsVectorString\*(Aq,
435 \& \*(AqOverwrite\*(Aq => 1,
436 \& \*(AqVectorStringFormat\*(Aq => \*(AqIDsAndValuesString\*(Aq,
437 \& \*(AqOutDelim\*(Aq => \*(AqTab\*(Aq,
438 \& \*(AqOutQuote\*(Aq => 0);
439 .Ve
440 .IP "\fBGetDataColLabels\fR" 4
441 .IX Item "GetDataColLabels"
442 .Vb 2
443 \& @ColLabels = $FingerprintsTextFileIO\->GetDataColLabels();
444 \& $NumOfColLabels = $FingerprintsTextFileIO\->GetDataColLabels();
445 .Ve
446 .Sp
447 Returns an array of \fBColLabels\fR from first line in text file. In scalar context, it returns
448 number of column labels.
449 .IP "\fBGetDataLineWords\fR" 4
450 .IX Item "GetDataLineWords"
451 .Vb 2
452 \& @DataWords = $FingerprintsTextFileIO\->GetDataLineWords();
453 \& $NumOfDataWords = $FingerprintsTextFileIO\->GetDataLineWords();
454 .Ve
455 .Sp
456 Returns an array of \fBDataWords\fR in current data line. In scalar context, it returns
457 number of data words.
458 .IP "\fBGetFingerprints\fR" 4
459 .IX Item "GetFingerprints"
460 .Vb 1
461 \& $FingerprintsObject = $FingerprintsTextFileIO\->GetFingerprints();
462 .Ve
463 .Sp
464 Returns \fBFingerprintsObject\fR generated for current data line using fingerprints bit-vector
465 or vector string data. The fingerprints object corresponds to any of the supported fingerprints
466 such as PathLengthFingerprints, ExtendedConnectivity, and so on.
467 .IP "\fBGetFingerprintsString\fR" 4
468 .IX Item "GetFingerprintsString"
469 .Vb 1
470 \& $FingerprintsString = $FingerprintsTextFileIO\->GetFingerprintsString();
471 .Ve
472 .Sp
473 Returns \fBFingerprintsString\fR for current data line.
474 .IP "\fBIsFingerprintsDataValid\fR" 4
475 .IX Item "IsFingerprintsDataValid"
476 .Vb 1
477 \& $Status = $FingerprintsTextFileIO\->IsFingerprintsDataValid();
478 .Ve
479 .Sp
480 Returns 1 or 0 based on whether \fBFingerprintsObject\fR is valid.
481 .IP "\fBIsFingerprintsFileDataValid\fR" 4
482 .IX Item "IsFingerprintsFileDataValid"
483 .Vb 1
484 \& $Status = $FingerprintsTextFileIO\->IsFingerprintsFileDataValid();
485 .Ve
486 .Sp
487 Returns 1 or 0 based on whether text file contains valid fingerprints data.
488 .IP "\fBIsFingerprintsTextFile\fR" 4
489 .IX Item "IsFingerprintsTextFile"
490 .Vb 2
491 \& $Status = $FingerprintsTextFileIO\->IsFingerprintsTextFile($FileName);
492 \& $Status = FileIO::FingerprintsTextFileIO::IsFingerprintsTextFile($FileName);
493 .Ve
494 .Sp
495 Returns 1 or 0 based on whether \fIFileName\fR is a fingerprints text file.
496 .IP "\fBNext or Read\fR" 4
497 .IX Item "Next or Read"
498 .Vb 2
499 \& $FingerprintsTextFileIO = $FingerprintsTextFileIO\->Next();
500 \& $FingerprintsTextFileIO = $FingerprintsTextFileIO\->Read();
501 .Ve
502 .Sp
503 Reads next available fingerprints line in text file, processes the data, generates appropriate
504 fingerprints object, and returns \fBFingerprintsTextFileIO\fR. The generated fingerprints object
505 is available using method \fBGetFingerprints\fR.
506 .IP "\fBSetBitStringFormat\fR" 4
507 .IX Item "SetBitStringFormat"
508 .Vb 1
509 \& $FingerprintsTextFileIO\->SetBitStringFormat($Format);
510 .Ve
511 .Sp
512 Sets bit string \fIFormat\fR for fingerprints bit-vector string data in a text file and returns
513 \&\fBFingerprintsTextFileIO\fR. Possible values for \fBBitStringFormat\fR: \fIBinaryString or HexadecimalString\fR.
514 .IP "\fBSetBitsOrder\fR" 4
515 .IX Item "SetBitsOrder"
516 .Vb 1
517 \& $FingerprintsTextFileIO\->SetBitsOrder($BitsOrder);
518 .Ve
519 .Sp
520 Sets \fIBitsOrder\fR for fingerprints bit-vector string data in a text file and returns \fBFingerprintsTextFileIO\fR.
521 Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR.
522 .IP "\fBSetColMode\fR" 4
523 .IX Item "SetColMode"
524 .Vb 1
525 \& $FingerprintsTextFileIO\->SetColMode($ColMode);
526 .Ve
527 .Sp
528 Sets \fIColMode\fR for a text file and returns \fBFingerprintsTextFileIO\fR. Possible values for \fBColMode\fR:
529 \&\fIColNum or ColLabel\fR.
530 .IP "\fBSetDataColLabels\fR" 4
531 .IX Item "SetDataColLabels"
532 .Vb 2
533 \& $FingerprintsTextFileIO\->SetDataColLabels(@ColLabels);
534 \& $FingerprintsTextFileIO\->SetDataColLabels(\e@ColLabels);
535 .Ve
536 .Sp
537 Sets \fIColLabels\fR for a text file using an array or a reference to an array containing column labels
538 and returns \fBFingerprintsTextFileIO\fR.
539 .IP "\fBSetDataLineWords\fR" 4
540 .IX Item "SetDataLineWords"
541 .Vb 2
542 \& $FingerprintsTextFileIO\->SetDataLineWords(@LineWords);
543 \& $FingerprintsTextFileIO\->SetDataLineWords(\e@LineWords);
544 .Ve
545 .Sp
546 Sets \fIDataLineWords\fR for a text file using an array or a reference to an array containing data words
547 and returns \fBFingerprintsTextFileIO\fR.
548 .IP "\fBSetDetailLevel\fR" 4
549 .IX Item "SetDetailLevel"
550 .Vb 1
551 \& $FingerprintsTextFileIO\->SetDetailLevel($Level);
552 .Ve
553 .Sp
554 Sets details \fILevel\fR for generating diagnostics messages during text file processing and returns
555 \&\fBFingerprintsTextFileIO\fR. Possible values: \fIPositive integers\fR.
556 .IP "\fBSetFingerprints\fR" 4
557 .IX Item "SetFingerprints"
558 .Vb 1
559 \& $FingerprintsTextFileIO\->SetFingerprints($FingerprintsObject);
560 .Ve
561 .Sp
562 Sets \fIFingerprintsObject\fR for current data line and returns \fBFingerprintsTextFileIO\fR.
563 .IP "\fBSetFingerprintsString\fR" 4
564 .IX Item "SetFingerprintsString"
565 .Vb 1
566 \& $FingerprintsTextFileIO\->SetFingerprintsString($FingerprintsString);
567 .Ve
568 .Sp
569 Sets \fIFingerprintsString\fR for current data line and returns \fBFingerprintsTextFileIO\fR.
570 .IP "\fBSetFingerprintsStringMode\fR" 4
571 .IX Item "SetFingerprintsStringMode"
572 .Vb 1
573 \& $FingerprintsTextFileIO\->SetFingerprintsStringMode($Mode);
574 .Ve
575 .Sp
576 Sets \fIFingerprintsStringMode\fR for text file and returns \fBFingerprintsTextFileIO\fR.
577 Possible values: \fIAutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString\fR
578 .IP "\fBSetInDelim\fR" 4
579 .IX Item "SetInDelim"
580 .Vb 1
581 \& $FingerprintsTextFileIO\->SetInDelim($InDelim);
582 .Ve
583 .Sp
584 Sets \fIInDelim\fR for text file and returns \fBFingerprintsTextFileIO\fR. Possible values: \fIcomma,
585 semicolon, tab\fR.
586 .IP "\fBSetOutDelim\fR" 4
587 .IX Item "SetOutDelim"
588 .Vb 1
589 \& $FingerprintsTextFileIO\->SetOutDelim($OutDelim);
590 .Ve
591 .Sp
592 Sets \fIOutDelim\fR for text file and returns \fBFingerprintsTextFileIO\fR. Possible values: \fIcomma,
593 semicolon, tab\fR.
594 .IP "\fBSetVectorStringFormat\fR" 4
595 .IX Item "SetVectorStringFormat"
596 .Vb 1
597 \& $FingerprintsTextFileIO\->SetVectorStringFormat($Format);
598 .Ve
599 .Sp
600 Sets \fIVectorStringFormat\fR for text file and returns \fBFingerprintsTextFileIO\fR. Possible values:
601 \&\fIIDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString\fR.
602 .IP "\fBWriteFingerprints\fR" 4
603 .IX Item "WriteFingerprints"
604 .Vb 2
605 \& $FingerprintsTextFileIO\->WriteFingerprints($FingerprintsObject,
606 \& @DataColValues);
607 .Ve
608 .Sp
609 Writes fingerprints string generated from \fIFingerprintsObject\fR object and other data including
610 \&\fIDataColValues\fR to text file and returns \fBFingerprintsTextFileIO\fR.
611 .IP "\fBWriteFingerprintsString\fR" 4
612 .IX Item "WriteFingerprintsString"
613 .Vb 2
614 \& $FingerprintsSDFileIO\->WriteFingerprints($FingerprintsString,
615 \& @DataColValues);
616 .Ve
617 .Sp
618 Writes \fIFingerprintsString\fR and other data including \fIDataColValues\fR to text file and returns
619 \&\fBFingerprintsTextFileIO\fR.
620 .Sp
621 Caveats:
622 .Sp
623 .Vb 3
624 \& o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
625 \& values are ignored during writing of fingerprints and it\*(Aqs written to the file
626 \& as it is.
627 .Ve
628 .SH "AUTHOR"
629 .IX Header "AUTHOR"
630 Manish Sud <msud@san.rr.com>
631 .SH "SEE ALSO"
632 .IX Header "SEE ALSO"
633 FingerprintsSDFileIO.pm, FingerprintsFPFileIO.pm
634 .SH "COPYRIGHT"
635 .IX Header "COPYRIGHT"
636 Copyright (C) 2015 Manish Sud. All rights reserved.
637 .PP
638 This file is part of MayaChemTools.
639 .PP
640 MayaChemTools is free software; you can redistribute it and/or modify it under
641 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
642 Software Foundation; either version 3 of the License, or (at your option)
643 any later version.