Mercurial > repos > deepakjadmin > mayatool3_test3

comparison mayachemtools/docs/modules/txt/FingerprintsTextFileIO.txt @ 0:73ae111cf86f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 11:55:01 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:73ae111cf86f
1 NAME
2 FingerprintsTextFileIO
3
4 SYNOPSIS
5 use FileIO::FingerprintsTextFileIO;
6
7 use FileIO::FingerprintsTextFileIO qw(:all);
8
9 DESCRIPTION
10 FingerprintsTextFileIO class provides the following methods:
11
12 new, GetDataColLabels, GetDataLineWords, GetFingerprints,
13 GetFingerprintsString, IsFingerprintsDataValid,
14 IsFingerprintsFileDataValid, IsFingerprintsTextFile, Next, Read,
15 SetBitStringFormat, SetBitsOrder, SetColMode, SetDataColLabels,
16 SetDataLineWords, SetDetailLevel, SetFingerprints,
17 SetFingerprintsString, SetFingerprintsStringMode, SetInDelim,
18 SetOutDelim, SetVectorStringFormat, WriteFingerprints,
19 WriteFingerprintsString
20
21 The following methods can also be used as functions:
22
23 IsFingerprintsTextFile
24
25 FingerprintsTextFileIO class is derived from *FileIO* class and uses its
26 methods to support generic file related functionality.
27
28 The fingerprints CSV/TSV text file format with .csv or .tsv file
29 extensions supports two types of fingerprints string data: fingerprints
30 bit-vectors and fingerprints vector strings. The fingerprints string
31 data is treated as column value in a text file.
32
33 Example of text file format containing fingerprints string data:
34
35 "CompoundID","PathLengthFingerprints"
36 "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
37 :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
38 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
39 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
40 ... ...
41 ... ...
42
43 The current release of MayaChemTools supports the following types of
44 fingerprint bit-vector and vector strings:
45
46 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
47 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
48 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
49 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
50 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
51 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
52
53 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
54 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
55 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
56 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
57
58 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
59 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
60 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
61
62 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
63 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
64 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
65 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
66 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
67 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...
68
69 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
70 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
71 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
72 .024 -2.270
73
74 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
75 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
76 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
77 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
78 0 0 0 0 0 0 0 0 0 0 0 0 0 0
79
80 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
81 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
82 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
83 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
84 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
85 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
86
87 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
88 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
89 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
90 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
91 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
92 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
93
94 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
95 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
96 0000000001010000000110000011000000000000100000000000000000000000100001
97 1000000110000000000000000000000000010011000000000000000000000000010000
98 0000000000000000000000000010000000000000000001000000000000000000000000
99 0000000000010000100001000000000000101000000000000000100000000000000...
100
101 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
102 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
103 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
104 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
105 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
106 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
107
108 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
109 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
110 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
111 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
112 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
113 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
114
115 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
116 0000000000000000000000000000000001001000010010000000010010000000011100
117 0100101010111100011011000100110110000011011110100110111111111111011111
118 11111111111110111000
119
120 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
121 1110011111100101111111000111101100110000000000000011100010000000000000
122 0000000000000000000000000000000000000000000000101000000000000000000000
123 0000000000000000000000000000000000000000000000000000000000000000000000
124 0000000000000000000000000000000000000011000000000000000000000000000000
125 0000000000000000000000000000000000000000
126
127 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
128 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
129 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
130 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
131 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
132 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
133
134 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
135 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
136 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
137 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
138 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
139 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 ...
140
141 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
142 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
143 0100010101011000101001011100110001000010001001101000001001001001001000
144 0010110100000111001001000001001010100100100000000011000000101001011100
145 0010000001000101010100000100111100110111011011011000000010110111001101
146 0101100011000000010001000011000010100011101100001000001000100000000...
147
148 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
149 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
150 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
151 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
152 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
153 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
154
155 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
156 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
157 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
158 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
159 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
160 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
161
162 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
163 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
164 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
165 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
166 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
167 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...
168
169 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
170 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
171 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
172 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
173 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
174 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 ...
175
176 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
177 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
178 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
179 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
180 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
181
182 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
183 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
184 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
185 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
186 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
187
188 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
189 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
190 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
191 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
192 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
193 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
194 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...
195
196 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
197 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
198 .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-
199 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
200 -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.
201 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...
202
203 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
204 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
205 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
206 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
207 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
208 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
209 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
210
211 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
212 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
213 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
214 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
215 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
216 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...
217
218 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
219 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
220 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
221 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
222 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
223 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
224 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
225 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
226
227 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
228 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
229 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
230 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
231 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
232 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 ...
233
234 METHODS
235 new
236 $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(%IOParameters);
237
238 Using specified *IOParameters* names and values hash, new method
239 creates a new object and returns a reference to a newly created
240 FingerprintsTextFileIO object. By default, the following properties
241 are initialized during *Read* mode:
242
243 Name = '';
244 Mode = 'Read';
245 Status = 0;
246 FingerprintsStringMode = 'AutoDetect';
247 FingerprintsCol = 'AutoDetect';
248 ColMode = 'ColNum';
249 CompoundIDCol = 'AutoDetect';
250 CompoundIDPrefix = 'Cmpd';
251 InDelim = 'Comma';
252 ValidateData = 1;
253 DetailLevel = 1;
254
255 During *Write* mode, the following properties get initialize by
256 default:
257
258 FingerprintsStringMode = undef;
259
260 BitStringFormat = HexadecimalString;
261 BitsOrder = Ascending;
262
263 VectorStringFormat = NumericalValuesString or ValuesString;
264 OutDelim = 'Comma';
265 OutQuote = 1;
266
267 Examples:
268
269 $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
270 'Name' => 'Sample.csv',
271 'Mode' => 'Read');
272
273 $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
274 'Name' => 'Sample.csv',
275 'Mode' => 'Read',;
276 'FingerprintsStringMode' =>
277 'AutoDetect',
278 'ColMode' => 'ColLabel',
279 'FingerprintsCol' => 'Fingerprints',
280 'CompoundIDCol' => 'CompoundID',
281 'InDelim' => 'Comma');
282
283 $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
284 'Name' => 'Sample.csv',
285 'Mode' => 'Write',
286 'FingerprintsStringMode' =>
287 'FingerprintsBitVectorString',
288 'Overwrite' => 1,
289 'BitStringFormat' => 'HexadecimalString',
290 'BitsOrder' => 'Ascending');
291
292 $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
293 'Name' => 'Sample.tsv',
294 'Mode' => 'Write',
295 'FingerprintsStringMode' =>
296 'FingerprintsVectorString',
297 'Overwrite' => 1,
298 'VectorStringFormat' => 'IDsAndValuesString',
299 'OutDelim' => 'Tab',
300 'OutQuote' => 0);
301
302 GetDataColLabels
303 @ColLabels = $FingerprintsTextFileIO->GetDataColLabels();
304 $NumOfColLabels = $FingerprintsTextFileIO->GetDataColLabels();
305
306 Returns an array of ColLabels from first line in text file. In
307 scalar context, it returns number of column labels.
308
309 GetDataLineWords
310 @DataWords = $FingerprintsTextFileIO->GetDataLineWords();
311 $NumOfDataWords = $FingerprintsTextFileIO->GetDataLineWords();
312
313 Returns an array of DataWords in current data line. In scalar
314 context, it returns number of data words.
315
316 GetFingerprints
317 $FingerprintsObject = $FingerprintsTextFileIO->GetFingerprints();
318
319 Returns FingerprintsObject generated for current data line using
320 fingerprints bit-vector or vector string data. The fingerprints
321 object corresponds to any of the supported fingerprints such as
322 PathLengthFingerprints, ExtendedConnectivity, and so on.
323
324 GetFingerprintsString
325 $FingerprintsString = $FingerprintsTextFileIO->GetFingerprintsString();
326
327 Returns FingerprintsString for current data line.
328
329 IsFingerprintsDataValid
330 $Status = $FingerprintsTextFileIO->IsFingerprintsDataValid();
331
332 Returns 1 or 0 based on whether FingerprintsObject is valid.
333
334 IsFingerprintsFileDataValid
335 $Status = $FingerprintsTextFileIO->IsFingerprintsFileDataValid();
336
337 Returns 1 or 0 based on whether text file contains valid
338 fingerprints data.
339
340 IsFingerprintsTextFile
341 $Status = $FingerprintsTextFileIO->IsFingerprintsTextFile($FileName);
342 $Status = FileIO::FingerprintsTextFileIO::IsFingerprintsTextFile($FileName);
343
344 Returns 1 or 0 based on whether *FileName* is a fingerprints text
345 file.
346
347 Next or Read
348 $FingerprintsTextFileIO = $FingerprintsTextFileIO->Next();
349 $FingerprintsTextFileIO = $FingerprintsTextFileIO->Read();
350
351 Reads next available fingerprints line in text file, processes the
352 data, generates appropriate fingerprints object, and returns
353 FingerprintsTextFileIO. The generated fingerprints object is
354 available using method GetFingerprints.
355
356 SetBitStringFormat
357 $FingerprintsTextFileIO->SetBitStringFormat($Format);
358
359 Sets bit string *Format* for fingerprints bit-vector string data in
360 a text file and returns FingerprintsTextFileIO. Possible values for
361 BitStringFormat: *BinaryString or HexadecimalString*.
362
363 SetBitsOrder
364 $FingerprintsTextFileIO->SetBitsOrder($BitsOrder);
365
366 Sets *BitsOrder* for fingerprints bit-vector string data in a text
367 file and returns FingerprintsTextFileIO. Possible values for
368 BitsOrder: *Ascending or Descending*.
369
370 SetColMode
371 $FingerprintsTextFileIO->SetColMode($ColMode);
372
373 Sets *ColMode* for a text file and returns FingerprintsTextFileIO.
374 Possible values for ColMode: *ColNum or ColLabel*.
375
376 SetDataColLabels
377 $FingerprintsTextFileIO->SetDataColLabels(@ColLabels);
378 $FingerprintsTextFileIO->SetDataColLabels(\@ColLabels);
379
380 Sets *ColLabels* for a text file using an array or a reference to an
381 array containing column labels and returns FingerprintsTextFileIO.
382
383 SetDataLineWords
384 $FingerprintsTextFileIO->SetDataLineWords(@LineWords);
385 $FingerprintsTextFileIO->SetDataLineWords(\@LineWords);
386
387 Sets *DataLineWords* for a text file using an array or a reference
388 to an array containing data words and returns
389 FingerprintsTextFileIO.
390
391 SetDetailLevel
392 $FingerprintsTextFileIO->SetDetailLevel($Level);
393
394 Sets details *Level* for generating diagnostics messages during text
395 file processing and returns FingerprintsTextFileIO. Possible values:
396 *Positive integers*.
397
398 SetFingerprints
399 $FingerprintsTextFileIO->SetFingerprints($FingerprintsObject);
400
401 Sets *FingerprintsObject* for current data line and returns
402 FingerprintsTextFileIO.
403
404 SetFingerprintsString
405 $FingerprintsTextFileIO->SetFingerprintsString($FingerprintsString);
406
407 Sets *FingerprintsString* for current data line and returns
408 FingerprintsTextFileIO.
409
410 SetFingerprintsStringMode
411 $FingerprintsTextFileIO->SetFingerprintsStringMode($Mode);
412
413 Sets *FingerprintsStringMode* for text file and returns
414 FingerprintsTextFileIO. Possible values: *AutoDetect,
415 FingerprintsBitVectorString, or FingerprintsVectorString*
416
417 SetInDelim
418 $FingerprintsTextFileIO->SetInDelim($InDelim);
419
420 Sets *InDelim* for text file and returns FingerprintsTextFileIO.
421 Possible values: *comma, semicolon, tab*.
422
423 SetOutDelim
424 $FingerprintsTextFileIO->SetOutDelim($OutDelim);
425
426 Sets *OutDelim* for text file and returns FingerprintsTextFileIO.
427 Possible values: *comma, semicolon, tab*.
428
429 SetVectorStringFormat
430 $FingerprintsTextFileIO->SetVectorStringFormat($Format);
431
432 Sets *VectorStringFormat* for text file and returns
433 FingerprintsTextFileIO. Possible values: *IDsAndValuesString,
434 IDsAndValuesPairsString, ValuesAndIDsString,
435 ValuesAndIDsPairsString*.
436
437 WriteFingerprints
438 $FingerprintsTextFileIO->WriteFingerprints($FingerprintsObject,
439 @DataColValues);
440
441 Writes fingerprints string generated from *FingerprintsObject*
442 object and other data including *DataColValues* to text file and
443 returns FingerprintsTextFileIO.
444
445 WriteFingerprintsString
446 $FingerprintsSDFileIO->WriteFingerprints($FingerprintsString,
447 @DataColValues);
448
449 Writes *FingerprintsString* and other data including *DataColValues*
450 to text file and returns FingerprintsTextFileIO.
451
452 Caveats:
453
454 o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
455 values are ignored during writing of fingerprints and it's written to the file
456 as it is.
457
458 AUTHOR
459 Manish Sud <msud@san.rr.com>
460
461 SEE ALSO
462 FingerprintsSDFileIO.pm, FingerprintsFPFileIO.pm
463
464 COPYRIGHT
465 Copyright (C) 2015 Manish Sud. All rights reserved.
466
467 This file is part of MayaChemTools.
468
469 MayaChemTools is free software; you can redistribute it and/or modify it
470 under the terms of the GNU Lesser General Public License as published by
471 the Free Software Foundation; either version 3 of the License, or (at
472 your option) any later version.
473