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1 NAME
2 Fingerprints - Fingerprints class
3
4 SYNOPSIS
5 use Fingerprints::Fingerprints;
6
7 use Fingerprints::Fingerprints qw(:all);
8
9 DESCRIPTION
10 Fingerprints class provides the following methods:
11
12 new, FoldFingerprintsByBitDensity, FoldFingerprintsBySize,
13 GetFingerprintBitsAsBinaryString, GetFingerprintBitsAsHexadecimalString,
14 GetFingerprintBitsAsRawBinaryString, GetFingerprintsVectorValueIDs,
15 GetFingerprintsVectorValues, IsFingerprintsGenerationSuccessful,
16 SetFingerprintsBitVector, SetFingerprintsVector,
17 SetFingerprintsVectorType, SetMolecule, SetSize, SetType, SetVectorType
18
19 Fingerprints class is used as a base class for various specific
20 fingerprint classes such as AtomNeighborhoodsFingerprints,
21 AtomTypesFingerprints, EStateIndiciesFingerprints,
22 PathLengthFingerprints, ExtendedConnectivityFingerprints, MACCSKeys and
23 so on. It implements functionality common to fingerprint classes.
24
25 Fingerprints class is derived from ObjectProperty base class which
26 provides methods not explicitly defined in Fingerprints or
27 ObjectProperty classes using Perl's AUTOLOAD functionality. These
28 methods are generated on-the-fly for a specified object property:
29
30 Set<PropertyName>(<PropertyValue>);
31 $PropertyValue = Get<PropertyName>();
32 Delete<PropertyName>();
33
34 Fingerprints class uses FingerprintsBitVector class to provide bits
35 manipulation functionality.
36
37 METHODS
38 new
39 $NewFingerprints = new Fingerprints(%NamesAndValues);
40
41 Using specified *Fingerprints* property names and values hash, new
42 method creates a new object and returns a reference to newly created
43 Fingerprints object. By default, following properties are
44 initialized:
45
46 Molecule = '';
47 Type = '';
48 VectorType = '';
49 Size = '';
50 MinSize = '';
51 MaxSize = '';
52 FingerprintsBitVector = '';
53 FingerprintsVectorType = '';
54 FingerprintsVector = '';
55
56 FoldFingerprintsByBitDensity
57 $Fingerprints->FoldFingerprintsByBitDensity($BitDensity);
58
59 Folds fingerprints by recursively reducing its size by half until
60 bit density is greater than or equal to specified *BitDensity* and
61 returns *Fingerprints*.
62
63 FoldFingerprintsBySize
64 $Fingerprints->FoldFingerprintsBySize($Size, [$CheckSizeValue]);
65
66 Fold fingerprints by recursively reducing its size by half until
67 size is less than or equal to specified *Size* and returns
68 *Fingerprints*. By default, value *Size* is checked to make sure
69 it's:
70
71 >= MinSize and < Size and IsPowerOfTwo
72
73 GetFingerprintBitsAsBinaryString
74 $BinaryASCIIString =
75 $Fingerprints->GetFingerprintBitsAsBinaryString();
76
77 Returns fingerprints as a binary ASCII string containing 0s and 1s.
78
79 GetFingerprintBitsAsHexadecimalString
80 $HexadecimalString =
81 $Fingerprints->GetFingerprintBitsAsHexadecimalString();
82
83 Returns fingerprints as a hexadecimal string
84
85 GetFingerprintBitsAsRawBinaryString
86 $RawBinaryString =
87 $Fingerprints->GetFingerprintBitsAsRawBinaryString();
88
89 Returns fingerprints as a raw binary string containing packed bit
90 values for each byte.
91
92 GetFingerprintsVectorValueIDs
93 $ValueIDsRef = $Fingerprints->GetFingerprintsVectorValueIDs();
94 @ValueIDs = $Fingerprints->GetFingerprintsVectorValueIDs();
95
96 Returns fingerprints vector value IDs as an array or reference to an
97 array.
98
99 GetFingerprintsVectorValues
100 $ValuesRef = $Fingerprints->GetFingerprintsVectorValues();
101 @Values = $Fingerprints->GetFingerprintsVectorValues();
102
103 Returns fingerprints vector values as an array or reference to an
104 array.
105
106 IsFingerprintsGenerationSuccessful
107 $Return = $Fingerprints->IsFingerprintsGenerationSuccessful();
108
109 Returns 1 or 0 based on whether fingerprints were successfully
110 generated.
111
112 SetFingerprintsBitVector
113 $Fingerprints->SetFingerprintsBitVector($FingerprintsBitVector);
114
115 Sets *FingerprintsBitVector* object for *Fingerprints* and returns
116 *Fingerprints*.
117
118 SetFingerprintsVector
119 $Fingerprints->SetFingerprintsVector();
120
121 Sets *FingerprintsVector* object for *Fingerprints* and returns
122 *Fingerprints*.
123
124 SetFingerprintsVectorType
125 $Fingerprints->SetFingerprintsVectorType($VectorType);
126
127 Sets *FingerprintsVector* type for *Fingerprints* and returns
128 *Fingerprints*. Possible *VectorType* values:
129 *OrderedNumericalValues, NumericalValues or AlphaNumericalValues*.
130
131 SetMolecule
132 $Fingerprints->SetMolecule($Molecule);
133
134 Sets *Molecule* object for *Fingerprints* and returns
135 *Fingerprints*.
136
137 SetSize
138 $Fingerprints->SetSize($Size);
139
140 Sets *Size* of fingerprints and returns *Fingerprints*.
141
142 SetType
143 $Fingerprints->SetType($Type);
144
145 Sets *Type* of fingerprints and returns *Fingerprints*.
146
147 SetVectorType
148 $Fingerprints->SetVectorType($Type);
149
150 Sets *Type* of fingerprints vector and returns *Fingerprints*.
151 Possible *Type* values: *FingerprintsBitVector or
152 FingerprintsVector*.
153
154 AUTHOR
155 Manish Sud <msud@san.rr.com>
156
157 SEE ALSO
158 FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
159 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm,
160 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm,
161 PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
162 TopologicalAtomTripletsFingerprints.pm,
163 TopologicalAtomTorsionsFingerprints.pm,
164 TopologicalPharmacophoreAtomPairsFingerprints.pm,
165 TopologicalPharmacophoreAtomTripletsFingerprints.pm
166
167 COPYRIGHT
168 Copyright (C) 2015 Manish Sud. All rights reserved.
169
170 This file is part of MayaChemTools.
171
172 MayaChemTools is free software; you can redistribute it and/or modify it
173 under the terms of the GNU Lesser General Public License as published by
174 the Free Software Foundation; either version 3 of the License, or (at
175 your option) any later version.
176