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1 .\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
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29 . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
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51 .ie \nF \{\
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123 .rm #[ #] #H #V #F C
124 .\" ========================================================================
125 .\"
126 .IX Title "FINGERPRINTSSDFILEIO 1"
127 .TH FINGERPRINTSSDFILEIO 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 FingerprintsSDFileIO
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use FileIO::FingerprintsSDFileIO;
137 .PP
138 use FileIO::FingerprintsSDFileIO qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBFingerprintsSDFileIO\fR class provides the following methods:
142 .PP
143 new, GetCompoundString, GetFingerprints, GetFingerprintsString,
144 IsFingerprintsDataValid, IsFingerprintsFileDataValid, IsFingerprintsSDFile, Next,
145 Read, SetBitStringFormat, SetBitsOrder, SetCompoundIDMode, SetCompoundString,
146 SetDetailLevel, SetFingerprints, SetFingerprintsString, SetFingerprintsStringMode,
147 SetVectorStringFormat, WriteFingerprints, WriteFingerprintsString
148 .PP
149 The following methods can also be used as functions:
150 .PP
151 IsFingerprintsSDFile
152 .PP
153 \&\fBFingerprintsSDFileIO\fR class is derived from \fIFileIO\fR class and uses its methods to support
154 generic file related functionality.
155 .PP
156 The fingerprints \s-1SD\s0 file format with \fB.sdf\fR or \fB.sd\fR file extensions supports two types of
157 fingerprints string data: fingerprints bit-vectors and fingerprints vector strings. The fingerprints
158 string data is treated as value of a fingerprints data field label in a \s-1SD\s0 file.
159 .PP
160 Example of \s-1SD\s0 file format containing fingerprints string data:
161 .PP
162 .Vb 10
163 \& ... ...
164 \& ... ...
165 \& $$$$
166 \& ... ...
167 \& ... ...
168 \& ... ...
169 \& 41 44 0 0 0 0 0 0 0 0999 V2000
170 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
171 \& ... ...
172 \& 2 3 1 0 0 0 0
173 \& ... ...
174 \& M END
175 \& > <CmpdID>
176 \& Test
177 \&
178 \& > <PathLengthFingerprints>
179 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
180 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
181 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
182 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
183 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
184 \& aa0660a11014a011d46
185 \&
186 \& $$$$
187 \& ... ...
188 \& ... ...
189 .Ve
190 .PP
191 The current release of MayaChemTools supports the following types of fingerprint
192 bit-vector and vector strings:
193 .PP
194 .Vb 6
195 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
196 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
197 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
198 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
199 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
200 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
201 \&
202 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
203 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
204 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
205 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
206 \&
207 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
208 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
209 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
210 \&
211 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
212 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
213 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
214 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
215 \& 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
216 \& 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...
217 \&
218 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
219 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
220 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
221 \& .024 \-2.270
222 \&
223 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
224 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
225 \& 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
226 \& 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
227 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
228 \&
229 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
230 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
231 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
232 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
233 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
234 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
235 \&
236 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
237 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
238 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
239 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
240 \& 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
241 \& 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
242 \&
243 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
244 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
245 \& 0000000001010000000110000011000000000000100000000000000000000000100001
246 \& 1000000110000000000000000000000000010011000000000000000000000000010000
247 \& 0000000000000000000000000010000000000000000001000000000000000000000000
248 \& 0000000000010000100001000000000000101000000000000000100000000000000...
249 \&
250 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
251 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
252 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
253 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
254 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
255 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
256 \&
257 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
258 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
259 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
260 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
261 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
262 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
263 \&
264 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
265 \& 0000000000000000000000000000000001001000010010000000010010000000011100
266 \& 0100101010111100011011000100110110000011011110100110111111111111011111
267 \& 11111111111110111000
268 \&
269 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
270 \& 1110011111100101111111000111101100110000000000000011100010000000000000
271 \& 0000000000000000000000000000000000000000000000101000000000000000000000
272 \& 0000000000000000000000000000000000000000000000000000000000000000000000
273 \& 0000000000000000000000000000000000000011000000000000000000000000000000
274 \& 0000000000000000000000000000000000000000
275 \&
276 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
277 \& 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
278 \& 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
279 \& 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
280 \& 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
281 \& 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
282 \&
283 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
284 \& 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
285 \& 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
286 \& 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
287 \& 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
288 \& 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 ...
289 \&
290 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
291 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
292 \& 0100010101011000101001011100110001000010001001101000001001001001001000
293 \& 0010110100000111001001000001001010100100100000000011000000101001011100
294 \& 0010000001000101010100000100111100110111011011011000000010110111001101
295 \& 0101100011000000010001000011000010100011101100001000001000100000000...
296 \&
297 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
298 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
299 \& 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
300 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
301 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
302 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
303 \&
304 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
305 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
306 \& 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
307 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
308 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
309 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
310 \&
311 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
312 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
313 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
314 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
315 \& 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
316 \& 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...
317 \&
318 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
319 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
320 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
321 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
322 \& 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
323 \& 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 ...
324 \&
325 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
326 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
327 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
328 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
329 \& 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
330 \&
331 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
332 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
333 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
334 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
335 \& 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
336 \&
337 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
338 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
339 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
340 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
341 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
342 \& 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
343 \& 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...
344 \&
345 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
346 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
347 \& .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\-
348 \& 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
349 \& \-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.
350 \& 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...
351 \&
352 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
353 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
354 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
355 \& 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
356 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
357 \& 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
358 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
359 \&
360 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
361 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
362 \& 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
363 \& 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
364 \& 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
365 \& 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...
366 \&
367 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
368 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
369 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
370 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
371 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
372 \& 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
373 \& 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
374 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
375 \&
376 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
377 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
378 \& 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
379 \& 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
380 \& 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
381 \& 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 ...
382 .Ve
383 .SS "\s-1METHODS\s0"
384 .IX Subsection "METHODS"
385 .IP "\fBnew\fR" 4
386 .IX Item "new"
387 .Vb 1
388 \& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(%IOParameters);
389 .Ve
390 .Sp
391 Using specified \fIIOParameters\fR names and values hash, \fBnew\fR method creates a new
392 object and returns a reference to a newly created \fBFingerprintsSDFileIO\fR object. By default,
393 the following properties are initialized during \fIRead\fR mode:
394 .Sp
395 .Vb 10
396 \& Name = \*(Aq\*(Aq;
397 \& Mode = \*(AqRead\*(Aq;
398 \& Status = 0;
399 \& FingerprintsStringMode = \*(AqAutoDetect\*(Aq;
400 \& FingerprintsFieldLabel = \*(AqAutoDetect\*(Aq;
401 \& CompoundIDMode = \*(AqLabelPrefix\*(Aq;
402 \& CompoundIDFieldLabel = undef;
403 \& CompoundIDPrefix = \*(AqCmpd\*(Aq;
404 \& ValidateData = 1;
405 \& DetailLevel = 1;
406 .Ve
407 .Sp
408 During \fIWrite\fR mode, the following properties get initialize by default:
409 .Sp
410 .Vb 1
411 \& FingerprintsStringMode = undef;
412 \&
413 \& BitStringFormat = HexadecimalString;
414 \& BitsOrder = Ascending;
415 \&
416 \& VectorStringFormat = NumericalValuesString or ValuesString;
417 .Ve
418 .Sp
419 Examples:
420 .Sp
421 .Vb 3
422 \& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
423 \& \*(AqName\*(Aq => \*(AqSample.sdf\*(Aq,
424 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq);
425 \&
426 \& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
427 \& \*(AqName\*(Aq => \*(AqSample.sdf\*(Aq,
428 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq,;
429 \& \*(AqFingerprintsStringMode\*(Aq =>
430 \& \*(AqAutoDetect\*(Aq,
431 \& \*(AqFingerprintsFieldLabel\*(Aq =>
432 \& \*(AqFingerprints\*(Aq,
433 \& \*(AqCompoundIDMode\*(Aq =>
434 \& \*(AqDataField\*(Aq,
435 \& \*(AqCompoundIDFieldLabel\*(Aq =>
436 \& \*(AqCompoundID\*(Aq);
437 \&
438 \& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
439 \& \*(AqName\*(Aq => \*(AqSample.sdf\*(Aq,
440 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
441 \& \*(AqFingerprintsStringMode\*(Aq =>
442 \& \*(AqFingerprintsBitVectorString\*(Aq,
443 \& \*(AqOverwrite\*(Aq => 1,
444 \& \*(AqBitStringFormat\*(Aq => \*(AqHexadecimalString\*(Aq,
445 \& \*(AqBitsOrder\*(Aq => \*(AqAscending\*(Aq);
446 \&
447 \& $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
448 \& \*(AqName\*(Aq => \*(AqSample.sd\*(Aq,
449 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
450 \& \*(AqFingerprintsStringMode\*(Aq =>
451 \& \*(AqFingerprintsVectorString\*(Aq,
452 \& \*(AqOverwrite\*(Aq => 1,
453 \& \*(AqVectorStringFormat\*(Aq => \*(AqIDsAndValuesString\*(Aq,
454 \& \*(AqFingerprintsLabel\*(Aq => \*(AqFingerprints\*(Aq);
455 .Ve
456 .IP "\fBGetCompoundString\fR" 4
457 .IX Item "GetCompoundString"
458 .Vb 1
459 \& $CompoundString = $FingerprintsSDFileIO\->GetCompoundString();
460 .Ve
461 .Sp
462 Returns \fBCompoundString\fR for current compound.
463 .IP "\fBGetFingerprints\fR" 4
464 .IX Item "GetFingerprints"
465 .Vb 1
466 \& $FingerprintsObject = $FingerprintsSDFileIO\->GetFingerprints();
467 .Ve
468 .Sp
469 Returns \fBFingerprintsObject\fR generated for current compound using fingerprints bit-vector
470 or vector string data. The fingerprints object corresponds to any of the supported fingerprints
471 such as PathLengthFingerprints, ExtendedConnectivity, and so on.
472 .IP "\fBGetFingerprintsString\fR" 4
473 .IX Item "GetFingerprintsString"
474 .Vb 1
475 \& $FingerprintsString = $FingerprintsSDFileIO\->GetFingerprintsString();
476 .Ve
477 .Sp
478 Returns \fBFingerprintsString\fR for current compound.
479 .IP "\fBIsFingerprintsDataValid\fR" 4
480 .IX Item "IsFingerprintsDataValid"
481 .Vb 1
482 \& $Status = $FingerprintsSDFileIO\->IsFingerprintsDataValid();
483 .Ve
484 .Sp
485 Returns 1 or 0 based on whether \fBFingerprintsObject\fR is valid.
486 .IP "\fBIsFingerprintsFileDataValid\fR" 4
487 .IX Item "IsFingerprintsFileDataValid"
488 .Vb 1
489 \& $Status = $FingerprintsSDFileIO\->IsFingerprintsFileDataValid();
490 .Ve
491 .Sp
492 Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data.
493 .IP "\fBIsFingerprintsSDFile\fR" 4
494 .IX Item "IsFingerprintsSDFile"
495 .Vb 2
496 \& $Status = $FingerprintsSDFileIO\->IsFingerprintsSDFile($FileName);
497 \& $Status = FileIO::FingerprintsSDFileIO::IsFingerprintsSDFile($FileName);
498 .Ve
499 .Sp
500 Returns 1 or 0 based on whether \fIFileName\fR is a \s-1SD\s0 file.
501 .IP "\fBNext or Read\fR" 4
502 .IX Item "Next or Read"
503 .Vb 2
504 \& $FingerprintsSDFileIO = $FingerprintsSDFileIO\->Next();
505 \& $FingerprintsSDFileIO = $FingerprintsSDFileIO\->Read();
506 .Ve
507 .Sp
508 Reads next available compound fingerprints in \s-1SD\s0 file, processes the data, generates appropriate
509 fingerprints object, and returns \fBFingerprintsSDFileIO\fR. The generated fingerprints object is available
510 using method \fBGetFingerprints\fR.
511 .IP "\fBSetBitStringFormat\fR" 4
512 .IX Item "SetBitStringFormat"
513 .Vb 1
514 \& $FingerprintsSDFileIO\->SetBitStringFormat($Format);
515 .Ve
516 .Sp
517 Sets bit string \fIFormat\fR for fingerprints bit-vector string data in a \s-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR.
518 Possible values for \fBBitStringFormat\fR: \fIBinaryString or HexadecimalString\fR.
519 .IP "\fBSetBitsOrder\fR" 4
520 .IX Item "SetBitsOrder"
521 .Vb 1
522 \& $FingerprintsSDFileIO\->SetBitsOrder($BitsOrder);
523 .Ve
524 .Sp
525 Sets \fIBitsOrder\fR for fingerprints bit-vector string data in \s-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR.
526 Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR.
527 .IP "\fBSetCompoundIDMode\fR" 4
528 .IX Item "SetCompoundIDMode"
529 .Vb 1
530 \& $FingerprintsSDFileIO\->SetCompoundIDMode($Mode);
531 .Ve
532 .Sp
533 Sets compound \s-1ID\s0 \fIMode\fR for fingerprints bit-vector string data in a \s-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR.
534 Possible values for \fBCompoundIDMode\fR: \fIDataField, MolName, LabelPrefix, or MolNameOrLabelPrefix\fR.
535 .IP "\fBSetCompoundString\fR" 4
536 .IX Item "SetCompoundString"
537 .Vb 1
538 \& $FingerprintsSDFileIO\->SetCompoundString($CompoundString);
539 .Ve
540 .Sp
541 Sets \fICompoundString\fR and returns \fBFingerprintsSDFileIO\fR.
542 .IP "\fBSetDetailLevel\fR" 4
543 .IX Item "SetDetailLevel"
544 .Vb 1
545 \& $FingerprintsSDFileIO\->SetDetailLevel($Level);
546 .Ve
547 .Sp
548 Sets details \fILevel\fR for generating diagnostics messages during \s-1SD\s0 file processing and returns
549 \&\fBFingerprintsSDFileIO\fR. Possible values: \fIPositive integers\fR.
550 .IP "\fBSetFingerprints\fR" 4
551 .IX Item "SetFingerprints"
552 .Vb 1
553 \& $FingerprintsSDFileIO\->SetFingerprints($FingerprintsObject);
554 .Ve
555 .Sp
556 Sets \fIFingerprintsObject\fR for current data line and returns \fBFingerprintsSDFileIO\fR.
557 .IP "\fBSetFingerprintsString\fR" 4
558 .IX Item "SetFingerprintsString"
559 .Vb 1
560 \& $FingerprintsSDFileIO\->SetFingerprintsString($FingerprintsString);
561 .Ve
562 .Sp
563 Sets \fIFingerprintsString\fR for current data line and returns \fBFingerprintsSDFileIO\fR.
564 .IP "\fBSetFingerprintsStringMode\fR" 4
565 .IX Item "SetFingerprintsStringMode"
566 .Vb 1
567 \& $FingerprintsSDFileIO\->SetFingerprintsStringMode($Mode);
568 .Ve
569 .Sp
570 Sets \fIFingerprintsStringMode\fR for \s-1SD\s0 file and returns \fBFingerprintsFPFileIO\fR.
571 Possible values: \fIAutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString\fR
572 .IP "\fBSetVectorStringFormat\fR" 4
573 .IX Item "SetVectorStringFormat"
574 .Vb 1
575 \& $FingerprintsSDFileIO\->SetVectorStringFormat($Format);
576 .Ve
577 .Sp
578 Sets \fIVectorStringFormat\fR for \s-1SD\s0 file and returns \fBFingerprintsFPFileIO\fR. Possible values:
579 \&\fIIDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString\fR.
580 .IP "\fBWriteFingerprints\fR" 4
581 .IX Item "WriteFingerprints"
582 .Vb 2
583 \& $FingerprintsFPFileIO\->WriteFingerprints($FingerprintsObject,
584 \& $CompoundID);
585 .Ve
586 .Sp
587 Writes fingerprints string generated from \fIFingerprintsObject\fR object and other data including
588 \&\fICompoundID\fR to \s-1SD\s0 file and returns \fBFingerprintsSDFileIO\fR.
589 .IP "\fBWriteFingerprintsString\fR" 4
590 .IX Item "WriteFingerprintsString"
591 .Vb 2
592 \& $FingerprintsSDFileIO\->WriteFingerprints($FingerprintsString,
593 \& $CompoundID);
594 .Ve
595 .Sp
596 Writes \fIFingerprintsString\fR and other data including \fICompoundID\fR to \s-1SD\s0 file and returns
597 \&\fBFingerprintsSDFileIO\fR.
598 .Sp
599 Caveats:
600 .Sp
601 .Vb 4
602 \& o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
603 \& values are ignored during writing of fingerprints and it\*(Aqs written to the file
604 \& as it is.
605 \& o CompoundString is not checked to remove any existing fingerprints data
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 FingerprintsTextFileIO.pm, FingerprintsFPFileIO.pm, SDFileIO.pm
613 .SH "COPYRIGHT"
614 .IX Header "COPYRIGHT"
615 Copyright (C) 2015 Manish Sud. All rights reserved.
616 .PP
617 This file is part of MayaChemTools.
618 .PP
619 MayaChemTools is free software; you can redistribute it and/or modify it under
620 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
621 Software Foundation; either version 3 of the License, or (at your option)
622 any later version.