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1 NAME
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2 TopologicalAtomTripletsFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::TopologicalAtomTripletsFingerprints;
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6
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7 use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all);
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8
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9 DESCRIPTION
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10 TopologicalAtomTripletsFingerprints [ Ref 57, Ref 59, Ref 72 ] class
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11 provides the following methods:
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12
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13 new, GenerateFingerprints, GetAtomTripletIDs, GetDescription,
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14 SetAtomIdentifierType, SetAtomicInvariantsToUse,
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15 SetFunctionalClassesToUse, SetMaxDistance, SetMinDistance,
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16 StringifyTopologicalAtomTripletsFingerprints
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17
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18 TopologicalAtomTripletsFingerprints is derived from Fingerprints class
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19 which in turn is derived from ObjectProperty base class that provides
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20 methods not explicitly defined in TopologicalAtomTripletsFingerprints,
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21 Fingerprints or ObjectProperty classes using Perl's AUTOLOAD
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22 functionality. These methods are generated on-the-fly for a specified
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23 object property:
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24
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25 Set<PropertyName>(<PropertyValue>);
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26 $PropertyValue = Get<PropertyName>();
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27 Delete<PropertyName>();
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28
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29 The current release of MayaChemTools supports generation of
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30 TopologicalAtomTripletsFingerprints corresponding to following
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31 AtomtomIdentifierTypes:
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32
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33 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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34 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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35 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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36
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37 Based on the values specified for AtomIdentifierType along with other
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38 specified parameters such as AtomicInvariantsToUse and
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39 FunctionalClassesToUse, initial atom types are assigned to all
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40 non-hydrogen atoms in a molecule. Using the distance matrix for the
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41 molecule and initial atom types assigned to non-hydrogen atoms, all
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42 unique atom triplets within MinDistance and MaxDistance are identified
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43 and counted. An atom triplet identifier is generated for each unique
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44 atom triplet; the format of atom triplet identifier is:
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45
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46 <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy
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47
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48 ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
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49 Dxy: Distance between atom x and atom y
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50 Dxz: Distance between atom x and atom z
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51 Dyz: Distance between atom y and atom z
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52
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53 where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12
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54
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55 The atom triplet identifiers for all unique atom triplets corresponding
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56 to non-hydrogen atoms constitute topological atom triplets fingerprints
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57 of the molecule.
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58
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59 The current release of MayaChemTools generates the following types of
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60 topological atom triplets fingerprints vector strings:
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61
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62 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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63 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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64 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
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65 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
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66 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
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67 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
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68 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...
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69
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70 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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71 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
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72 ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
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73 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
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74 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
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75 -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...
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76
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77 FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
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78 ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D
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79 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_
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80 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_
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81 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...;
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82 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
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83 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...
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84
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85 FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
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86 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D
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87 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC
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88 H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1-
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89 aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...;
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90 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
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91 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
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92 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...
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93
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94 FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
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95 nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1
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96 -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal
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97 -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar
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98 -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...;
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99 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
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100 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
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101 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...
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102
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103 FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
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104 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1-
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105 N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A
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106 -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B
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107 -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3-
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108 O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...
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109
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110 FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
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111 :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11
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112 -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D
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113 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C
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114 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1
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115 -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...
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116
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117 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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118 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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119 .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-
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120 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
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121 -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.
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122 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...
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123
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124 FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
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125 MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non
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126 e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D
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127 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5
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128 N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21-
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129 D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...
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130
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131 FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
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132 axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3
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133 -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9
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134 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1-
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135 C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5-
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136 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-C_3-...
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137
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138 METHODS
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139 new
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140 $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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141 %NamesAndValues);
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142
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143 Using specified *TopologicalAtomTripletsFingerprints* property names
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144 and values hash, new method creates a new object and returns a
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145 reference to newly created TopologicalAtomTripletsFingerprints
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146 object. By default, the following properties are initialized:
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147
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148 Molecule = ''
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149 Type = 'TopologicalAtomTriplets'
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150 MinDistance = 1
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151 MaxDistance = 10
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152 UseTriangleInequality = 1
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153 AtomIdentifierType = ''
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154 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
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155 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
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156
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157 Examples:
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158
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159 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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160 'Molecule' => $Molecule,
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161 'AtomIdentifierType' =>
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162 'AtomicInvariantsAtomTypes');
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163
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164 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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165 'Molecule' => $Molecule,
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166 'MinDistance' => 1,
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167 'MaxDistance' => 10,
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168 'AtomIdentifierType' =>
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169 'AtomicInvariantsAtomTypes',
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170 'AtomicInvariantsToUse' =>
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171 ['AS', 'X', 'BO', 'H', 'FC'] );
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172
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173 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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174 'Molecule' => $Molecule,
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175 'AtomIdentifierType' =>
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176 'DREIDINGAtomTypes');
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177
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178 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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179 'Molecule' => $Molecule,
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180 'AtomIdentifierType' =>
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181 'MMFF94AtomTypes');
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182
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183 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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184 'Molecule' => $Molecule,
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185 'AtomIdentifierType' =>
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186 'TPSAAtomTypes');
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187
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188 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
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189 'Molecule' => $Molecule,
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190 'MinDistance' => 1,
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191 'MaxDistance' => 10,
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192 'AtomIdentifierType' =>
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193 'FunctionalClassAtomTypes',
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194 'FunctionalClassesToUse' =>
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195 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);
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196
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197 $TopologicalAtomTripletsFingerprints->GenerateFingerprints();
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198 print "$TopologicalAtomTripletsFingerprints\n";
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199
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200 GetDescription
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201 $Return = $TopologicalAtomTripletsFingerprints->GetDescription();
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202
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203 Returns a string containing description of topological atom triplets
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204 fingerprints.
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205
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206 GenerateFingerprints
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207 $TopologicalAtomTripletsFingerprints->GenerateFingerprints();
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208
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209 Generates topological atom triplets fingerprints and returns
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210 *TopologicalAtomTripletsFingerprints*.
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211
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212 GetAtomTripletIDs
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213 $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs();
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214 @AtomTripletIDs = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs();
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215
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216 Returns atom triplet IDs corresponding to atom triplets count values
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217 in topological atom triplets fingerprints vector as an array or
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218 reference to an array.
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219
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220 SetAtomIdentifierType
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221 $TopologicalAtomTripletsFingerprints->SetAtomIdentifierType($IdentifierType);
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222
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223 Sets atom *IdentifierType* to use during atom triplets fingerprints
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224 generation and returns *TopologicalAtomTripletsFingerprints*.
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225
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226 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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227 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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228 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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229
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230 SetAtomicInvariantsToUse
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231 $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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232 $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse(@Values);
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233
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234 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
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235 value of *AtomIdentifierType* for topological atom triplets
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236 fingerprints generation and returns
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237 *TopologicalAtomTripletsFingerprints*.
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238
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239 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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240 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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241
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242 The atomic invariants abbreviations correspond to:
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243
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244 AS = Atom symbol corresponding to element symbol
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245
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246 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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247 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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248 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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249 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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250 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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251 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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252 H<n> = Number of implicit and explicit hydrogens for atom
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253 Ar = Aromatic annotation indicating whether atom is aromatic
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254 RA = Ring atom annotation indicating whether atom is a ring
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255 FC<+n/-n> = Formal charge assigned to atom
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256 MN<n> = Mass number indicating isotope other than most abundant isotope
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257 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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258 3 (triplet)
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259
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260 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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261 corresponds to:
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262
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263 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
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264
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265 Except for AS which is a required atomic invariant in atom types,
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266 all other atomic invariants are optional. Atom type specification
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267 doesn't include atomic invariants with zero or undefined values.
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268
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269 In addition to usage of abbreviations for specifying atomic
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270 invariants, the following descriptive words are also allowed:
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271
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272 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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273 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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274 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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275 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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276 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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277 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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278 H : NumOfImplicitAndExplicitHydrogens
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279 Ar : Aromatic
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280 RA : RingAtom
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281 FC : FormalCharge
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282 MN : MassNumber
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283 SM : SpinMultiplicity
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284
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285 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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286 atomic invariant atom types.
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287
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288 SetFunctionalClassesToUse
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289 $TopologicalTripletsFingerprints->SetFunctionalClassesToUse($ValuesRef);
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290 $TopologicalTripletsFingerprints->SetFunctionalClassesToUse(@Values);
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291
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292 Sets functional classes invariants to use during
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293 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
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294 topological atom triplets fingerprints generation and returns
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295 *TopologicalAtomTripletsFingerprints*.
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296
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297 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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298 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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299 *HBD,HBA,PI,NI,Ar,Hal*.
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300
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301 The functional class abbreviations correspond to:
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302
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303 HBD: HydrogenBondDonor
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304 HBA: HydrogenBondAcceptor
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305 PI : PositivelyIonizable
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306 NI : NegativelyIonizable
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307 Ar : Aromatic
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308 Hal : Halogen
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309 H : Hydrophobic
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310 RA : RingAtom
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311 CA : ChainAtom
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312
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313 Functional class atom type specification for an atom corresponds to:
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314
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315 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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316
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317 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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318 functional class atom types. It uses following definitions [ Ref
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319 60-61, Ref 65-66 ]:
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320
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321 HydrogenBondDonor: NH, NH2, OH
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322 HydrogenBondAcceptor: N[!H], O
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323 PositivelyIonizable: +, NH2
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324 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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325
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326 SetMaxDistance
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327 $TopologicalAtomTripletsFingerprints->SetMaxDistance($Distance);
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328
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329 Sets maximum distance to use during topological atom triplets
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330 fingerprints generation and returns
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331 *TopologicalAtomTripletsFingerprints*.
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332
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333 SetMinDistance
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334 $TopologicalAtomTripletsFingerprints->SetMinDistance($Distance);
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335
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336 Sets minimum distance to use during topological atom triplets
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337 fingerprints generation and returns
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338 *TopologicalAtomTripletsFingerprints*.
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339
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340 StringifyTopologicalAtomTripletsFingerprints
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341 $String = $TopologicalAtomTripletsFingerprints->
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342 StringifyTopologicalAtomTripletsFingerprints();
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343
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344 Returns a string containing information about
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345 *TopologicalAtomTripletsFingerprints* object.
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346
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347 AUTHOR
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348 Manish Sud <msud@san.rr.com>
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349
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350 SEE ALSO
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351 Fingerprints.pm, FingerprintsStringUtil.pm,
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352 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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353 EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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354 MACCSKeys.pm, PathLengthFingerprints.pm,
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355 TopologicalAtomPairsFingerprints.pm,
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356 TopologicalAtomTorsionsFingerprints.pm,
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357 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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358 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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359
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360 COPYRIGHT
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361 Copyright (C) 2015 Manish Sud. All rights reserved.
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362
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363 This file is part of MayaChemTools.
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364
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365 MayaChemTools is free software; you can redistribute it and/or modify it
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366 under the terms of the GNU Lesser General Public License as published by
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367 the Free Software Foundation; either version 3 of the License, or (at
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368 your option) any later version.
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369
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