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1 NAME
2 FingerprintsSDFileIO
3
4 SYNOPSIS
5 use FileIO::FingerprintsSDFileIO;
6
7 use FileIO::FingerprintsSDFileIO qw(:all);
8
9 DESCRIPTION
10 FingerprintsSDFileIO class provides the following methods:
11
12 new, GetCompoundString, GetFingerprints, GetFingerprintsString,
13 IsFingerprintsDataValid, IsFingerprintsFileDataValid,
14 IsFingerprintsSDFile, Next, Read, SetBitStringFormat, SetBitsOrder,
15 SetCompoundIDMode, SetCompoundString, SetDetailLevel, SetFingerprints,
16 SetFingerprintsString, SetFingerprintsStringMode, SetVectorStringFormat,
17 WriteFingerprints, WriteFingerprintsString
18
19 The following methods can also be used as functions:
20
21 IsFingerprintsSDFile
22
23 FingerprintsSDFileIO class is derived from *FileIO* class and uses its
24 methods to support generic file related functionality.
25
26 The fingerprints SD file format with .sdf or .sd file extensions
27 supports two types of fingerprints string data: fingerprints bit-vectors
28 and fingerprints vector strings. The fingerprints string data is treated
29 as value of a fingerprints data field label in a SD file.
30
31 Example of SD file format containing fingerprints string data:
32
33 ... ...
34 ... ...
35 $$$$
36 ... ...
37 ... ...
38 ... ...
39 41 44 0 0 0 0 0 0 0 0999 V2000
40 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
41 ... ...
42 2 3 1 0 0 0 0
43 ... ...
44 M END
45 > <CmpdID>
46 Test
47
48 > <PathLengthFingerprints>
49 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
50 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
51 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
52 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
53 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
54 aa0660a11014a011d46
55
56 $$$$
57 ... ...
58 ... ...
59
60 The current release of MayaChemTools supports the following types of
61 fingerprint bit-vector and vector strings:
62
63 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
64 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
65 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
66 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
67 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
68 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
69
70 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
71 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
72 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
73 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
74
75 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
76 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
77 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
78
79 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
80 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
81 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
82 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
83 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
84 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...
85
86 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
87 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
88 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
89 .024 -2.270
90
91 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
92 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
93 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
94 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
95 0 0 0 0 0 0 0 0 0 0 0 0 0 0
96
97 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
98 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
99 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
100 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
101 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
102 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
103
104 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
105 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
106 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
107 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
108 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
109 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
110
111 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
112 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
113 0000000001010000000110000011000000000000100000000000000000000000100001
114 1000000110000000000000000000000000010011000000000000000000000000010000
115 0000000000000000000000000010000000000000000001000000000000000000000000
116 0000000000010000100001000000000000101000000000000000100000000000000...
117
118 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
119 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
120 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
121 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
122 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
123 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
124
125 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
126 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
127 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
128 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
129 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
130 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
131
132 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
133 0000000000000000000000000000000001001000010010000000010010000000011100
134 0100101010111100011011000100110110000011011110100110111111111111011111
135 11111111111110111000
136
137 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
138 1110011111100101111111000111101100110000000000000011100010000000000000
139 0000000000000000000000000000000000000000000000101000000000000000000000
140 0000000000000000000000000000000000000000000000000000000000000000000000
141 0000000000000000000000000000000000000011000000000000000000000000000000
142 0000000000000000000000000000000000000000
143
144 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
145 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
146 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
147 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
148 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
149 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
150
151 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
152 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
153 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
154 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
155 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
156 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 ...
157
158 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
159 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
160 0100010101011000101001011100110001000010001001101000001001001001001000
161 0010110100000111001001000001001010100100100000000011000000101001011100
162 0010000001000101010100000100111100110111011011011000000010110111001101
163 0101100011000000010001000011000010100011101100001000001000100000000...
164
165 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
166 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
167 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
168 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
169 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
170 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
171
172 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
173 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
174 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
175 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
176 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
177 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
178
179 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
180 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
181 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
182 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
183 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
184 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...
185
186 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
187 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
188 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
189 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
190 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
191 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 ...
192
193 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
194 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
195 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
196 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
197 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
198
199 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
200 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
201 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
202 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
203 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
204
205 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
206 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
207 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
208 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
209 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
210 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
211 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...
212
213 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
214 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
215 .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-
216 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
217 -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.
218 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...
219
220 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
221 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
222 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
223 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
224 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
225 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
226 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
227
228 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
229 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
230 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
231 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
232 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
233 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...
234
235 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
236 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
237 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
238 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
239 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
240 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
241 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
242 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
243
244 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
245 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
246 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
247 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
248 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
249 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 ...
250
251 METHODS
252 new
253 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(%IOParameters);
254
255 Using specified *IOParameters* names and values hash, new method
256 creates a new object and returns a reference to a newly created
257 FingerprintsSDFileIO object. By default, the following properties
258 are initialized during *Read* mode:
259
260 Name = '';
261 Mode = 'Read';
262 Status = 0;
263 FingerprintsStringMode = 'AutoDetect';
264 FingerprintsFieldLabel = 'AutoDetect';
265 CompoundIDMode = 'LabelPrefix';
266 CompoundIDFieldLabel = undef;
267 CompoundIDPrefix = 'Cmpd';
268 ValidateData = 1;
269 DetailLevel = 1;
270
271 During *Write* mode, the following properties get initialize by
272 default:
273
274 FingerprintsStringMode = undef;
275
276 BitStringFormat = HexadecimalString;
277 BitsOrder = Ascending;
278
279 VectorStringFormat = NumericalValuesString or ValuesString;
280
281 Examples:
282
283 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
284 'Name' => 'Sample.sdf',
285 'Mode' => 'Read');
286
287 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
288 'Name' => 'Sample.sdf',
289 'Mode' => 'Read',;
290 'FingerprintsStringMode' =>
291 'AutoDetect',
292 'FingerprintsFieldLabel' =>
293 'Fingerprints',
294 'CompoundIDMode' =>
295 'DataField',
296 'CompoundIDFieldLabel' =>
297 'CompoundID');
298
299 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
300 'Name' => 'Sample.sdf',
301 'Mode' => 'Write',
302 'FingerprintsStringMode' =>
303 'FingerprintsBitVectorString',
304 'Overwrite' => 1,
305 'BitStringFormat' => 'HexadecimalString',
306 'BitsOrder' => 'Ascending');
307
308 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
309 'Name' => 'Sample.sd',
310 'Mode' => 'Write',
311 'FingerprintsStringMode' =>
312 'FingerprintsVectorString',
313 'Overwrite' => 1,
314 'VectorStringFormat' => 'IDsAndValuesString',
315 'FingerprintsLabel' => 'Fingerprints');
316
317 GetCompoundString
318 $CompoundString = $FingerprintsSDFileIO->GetCompoundString();
319
320 Returns CompoundString for current compound.
321
322 GetFingerprints
323 $FingerprintsObject = $FingerprintsSDFileIO->GetFingerprints();
324
325 Returns FingerprintsObject generated for current compound using
326 fingerprints bit-vector or vector string data. The fingerprints
327 object corresponds to any of the supported fingerprints such as
328 PathLengthFingerprints, ExtendedConnectivity, and so on.
329
330 GetFingerprintsString
331 $FingerprintsString = $FingerprintsSDFileIO->GetFingerprintsString();
332
333 Returns FingerprintsString for current compound.
334
335 IsFingerprintsDataValid
336 $Status = $FingerprintsSDFileIO->IsFingerprintsDataValid();
337
338 Returns 1 or 0 based on whether FingerprintsObject is valid.
339
340 IsFingerprintsFileDataValid
341 $Status = $FingerprintsSDFileIO->IsFingerprintsFileDataValid();
342
343 Returns 1 or 0 based on whether fingerprints file contains valid
344 fingerprints data.
345
346 IsFingerprintsSDFile
347 $Status = $FingerprintsSDFileIO->IsFingerprintsSDFile($FileName);
348 $Status = FileIO::FingerprintsSDFileIO::IsFingerprintsSDFile($FileName);
349
350 Returns 1 or 0 based on whether *FileName* is a SD file.
351
352 Next or Read
353 $FingerprintsSDFileIO = $FingerprintsSDFileIO->Next();
354 $FingerprintsSDFileIO = $FingerprintsSDFileIO->Read();
355
356 Reads next available compound fingerprints in SD file, processes the
357 data, generates appropriate fingerprints object, and returns
358 FingerprintsSDFileIO. The generated fingerprints object is available
359 using method GetFingerprints.
360
361 SetBitStringFormat
362 $FingerprintsSDFileIO->SetBitStringFormat($Format);
363
364 Sets bit string *Format* for fingerprints bit-vector string data in
365 a SD file and returns FingerprintsSDFileIO. Possible values for
366 BitStringFormat: *BinaryString or HexadecimalString*.
367
368 SetBitsOrder
369 $FingerprintsSDFileIO->SetBitsOrder($BitsOrder);
370
371 Sets *BitsOrder* for fingerprints bit-vector string data in SD file
372 and returns FingerprintsSDFileIO. Possible values for BitsOrder:
373 *Ascending or Descending*.
374
375 SetCompoundIDMode
376 $FingerprintsSDFileIO->SetCompoundIDMode($Mode);
377
378 Sets compound ID *Mode* for fingerprints bit-vector string data in a
379 SD file and returns FingerprintsSDFileIO. Possible values for
380 CompoundIDMode: *DataField, MolName, LabelPrefix, or
381 MolNameOrLabelPrefix*.
382
383 SetCompoundString
384 $FingerprintsSDFileIO->SetCompoundString($CompoundString);
385
386 Sets *CompoundString* and returns FingerprintsSDFileIO.
387
388 SetDetailLevel
389 $FingerprintsSDFileIO->SetDetailLevel($Level);
390
391 Sets details *Level* for generating diagnostics messages during SD
392 file processing and returns FingerprintsSDFileIO. Possible values:
393 *Positive integers*.
394
395 SetFingerprints
396 $FingerprintsSDFileIO->SetFingerprints($FingerprintsObject);
397
398 Sets *FingerprintsObject* for current data line and returns
399 FingerprintsSDFileIO.
400
401 SetFingerprintsString
402 $FingerprintsSDFileIO->SetFingerprintsString($FingerprintsString);
403
404 Sets *FingerprintsString* for current data line and returns
405 FingerprintsSDFileIO.
406
407 SetFingerprintsStringMode
408 $FingerprintsSDFileIO->SetFingerprintsStringMode($Mode);
409
410 Sets *FingerprintsStringMode* for SD file and returns
411 FingerprintsFPFileIO. Possible values: *AutoDetect,
412 FingerprintsBitVectorString, or FingerprintsVectorString*
413
414 SetVectorStringFormat
415 $FingerprintsSDFileIO->SetVectorStringFormat($Format);
416
417 Sets *VectorStringFormat* for SD file and returns
418 FingerprintsFPFileIO. Possible values: *IDsAndValuesString,
419 IDsAndValuesPairsString, ValuesAndIDsString,
420 ValuesAndIDsPairsString*.
421
422 WriteFingerprints
423 $FingerprintsFPFileIO->WriteFingerprints($FingerprintsObject,
424 $CompoundID);
425
426 Writes fingerprints string generated from *FingerprintsObject*
427 object and other data including *CompoundID* to SD file and returns
428 FingerprintsSDFileIO.
429
430 WriteFingerprintsString
431 $FingerprintsSDFileIO->WriteFingerprints($FingerprintsString,
432 $CompoundID);
433
434 Writes *FingerprintsString* and other data including *CompoundID* to
435 SD file and returns FingerprintsSDFileIO.
436
437 Caveats:
438
439 o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
440 values are ignored during writing of fingerprints and it's written to the file
441 as it is.
442 o CompoundString is not checked to remove any existing fingerprints data
443
444 AUTHOR
445 Manish Sud <msud@san.rr.com>
446
447 SEE ALSO
448 FingerprintsTextFileIO.pm, FingerprintsFPFileIO.pm, SDFileIO.pm
449
450 COPYRIGHT
451 Copyright (C) 2015 Manish Sud. All rights reserved.
452
453 This file is part of MayaChemTools.
454
455 MayaChemTools is free software; you can redistribute it and/or modify it
456 under the terms of the GNU Lesser General Public License as published by
457 the Free Software Foundation; either version 3 of the License, or (at
458 your option) any later version.
459