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1 NAME
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2 TopologicalAtomTorsionsFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::TopologicalAtomTorsionsFingerprints;
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6
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7 use Fingerprints::TopologicalAtomTorsionsFingerprints qw(:all);
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8
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9 DESCRIPTION
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10 TopologicalAtomTorsionsFingerprints class provides the following
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11 methods:
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12
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13 new, GenerateFingerprints, GetAtomTorsionsIDs, GetDescription,
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14 SetAtomIdentifierType, SetAtomicInvariantsToUse,
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15 SetFunctionalClassesToUse, StringifyTopologicalAtomTorsionsFingerprints
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16
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17 TopologicalAtomTorsionsFingerprints is derived from Fingerprints class
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18 which in turn is derived from ObjectProperty base class that provides
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19 methods not explicitly defined in TopologicalAtomTorsionsFingerprints,
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20 Fingerprints or ObjectProperty classes using Perl's AUTOLOAD
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21 functionality. These methods are generated on-the-fly for a specified
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22 object property:
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23
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24 Set<PropertyName>(<PropertyValue>);
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25 $PropertyValue = Get<PropertyName>();
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26 Delete<PropertyName>();
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27
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28 The current release of MayaChemTools supports generation of
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29 TopologicalAtomTorsionsFingerprints corresponding to following
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30 AtomtomIdentifierTypes:
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31
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32 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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33 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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34 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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35
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36 Based on the values specified for AtomIdentifierType along with other
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37 specified parameters such as AtomicInvariantsToUse and
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38 FunctionalClassesToUse, initial atom types are assigned to all
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39 non-hydrogen in a molecule. All unique atom torsions are identified and
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40 an atom torsion identifier is generated; the format of atom torsion
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41 identifier is:
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42
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43 <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4>
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44
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45 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
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46
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47 where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
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48
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49 The atom torsion identifiers for all unique atom torsions corresponding
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50 to non-hydrogen atoms constitute topological atom torsions fingerprints
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51 of the molecule.
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52
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53 The current release of MayaChemTools generates the following types of
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54 topological atom torsions fingerprints vector strings:
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55
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56 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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57 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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58 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
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59 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
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60 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
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61
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62 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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63 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
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64 .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
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65 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
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66 O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
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67 O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
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68
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69 FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
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70 calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
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71 _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
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72 C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
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73 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1
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74
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75 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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76 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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77 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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78 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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79 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
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80
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81 FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
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82 ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
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83 Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
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84 -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
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85 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3
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86
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87 FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
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88 lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
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89 B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
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90 A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
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91 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
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92 1 1 2 1 1 3 1 3
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93
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94 FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
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95 Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
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96 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
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97 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
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98 C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
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99 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...
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100
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101 FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
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102 Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
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103 -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
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104 ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
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105 -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
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106 ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...
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107
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108 FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
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109 lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
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110 None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
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111 None-None 44 None-None-None-O3 3 None-None-None-O4 5
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112
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113 FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
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114 lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
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115 _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
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116 -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
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117 _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
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118 C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...
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119
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120 METHODS
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121 new
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122 $NewTopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
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123 %NamesAndValues);
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124
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125 Using specified *TopologicalAtomTorsionsFingerprints* property names
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126 and values hash, new method creates a new object and returns a
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127 reference to newly created TopologicalAtomTorsionsFingerprints
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128 object. By default, the following properties are initialized:
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129
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130 Molecule = ''
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131 Type = 'TopologicalAtomTorsions'
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132 AtomIdentifierType = ''
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133 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
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134 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
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135
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136 Examples:
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137
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138 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
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139 'Molecule' => $Molecule,
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140 'AtomIdentifierType' =>
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141 'AtomicInvariantsAtomTypes');
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142
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143 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
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144 'Molecule' => $Molecule,
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145 'AtomIdentifierType' =>
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146 'AtomicInvariantsAtomTypes',
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147 'AtomicInvariantsToUse' =>
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148 ['AS', 'X', 'BO', 'H', 'FC'] );
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149
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150 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
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151 'Molecule' => $Molecule,
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152 'AtomIdentifierType' =>
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153 'DREIDINGAtomTypes');
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154
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155 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
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156 'Molecule' => $Molecule,
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157 'AtomIdentifierType' =>
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158 'SYBYLAtomTypes');
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159
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160 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
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161 'Molecule' => $Molecule,
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162 'AtomIdentifierType' =>
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163 'SLogPAtomTypes');
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164
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165 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
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166 'Molecule' => $Molecule,
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167 'AtomIdentifierType' =>
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168 'FunctionalClassAtomTypes',
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169 'FunctionalClassesToUse' =>
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170 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );
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171
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172
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173 $TopologicalAtomTorsionsFingerprints->GenerateFingerprints();
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174 print "$TopologicalAtomTorsionsFingerprints\n";
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175
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176 GetDescription
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177 $Description = $TopologicalAtomTorsionsFingerprints->GetDescription();
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178
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179 Returns a string containing description of topological atom torsions
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180 fingerprints.
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181
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182 GenerateFingerprints
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183 $TopologicalAtomTorsionsFingerprints->GenerateFingerprints();
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184
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185 Generates topological atom torsions fingerprints and returns
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186 *TopologicalAtomTorsionsFingerprints*.
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187
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188 GetAtomTorsionsIDs
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189 $AtomPairIDsRef = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs();
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190 @AtomPairIDs = $TopologicalAtomTorsionsFingerprints->GetAtomTorsionsIDs();
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191
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192 Returns atom torsion IDs corresponding to atom torsion count values
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193 in topological atom torsions fingerprints vector as an array or
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194 reference to an array.
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195
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196 SetAtomIdentifierType
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197 $TopologicalAtomTorsionsFingerprints->SetAtomIdentifierType($IdentifierType);
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198
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199 Sets atom *IdentifierType* to use during atom torsions fingerprints
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200 generation and returns *TopologicalAtomTorsionsFingerprints*.
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201
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202 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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203 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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204 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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205
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206 SetAtomicInvariantsToUse
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207 $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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208 $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse(@Values);
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209
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210 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
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211 value of *AtomIdentifierType* for topological atom torsions
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212 fingerprints generation and returns
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213 *TopologicalAtomTorsionsFingerprints*.
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214
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215 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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216 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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217
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218 The atomic invariants abbreviations correspond to:
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219
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220 AS = Atom symbol corresponding to element symbol
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221
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222 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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223 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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224 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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225 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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226 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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227 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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228 H<n> = Number of implicit and explicit hydrogens for atom
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229 Ar = Aromatic annotation indicating whether atom is aromatic
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230 RA = Ring atom annotation indicating whether atom is a ring
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231 FC<+n/-n> = Formal charge assigned to atom
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232 MN<n> = Mass number indicating isotope other than most abundant isotope
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233 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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234 3 (triplet)
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235
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236 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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237 corresponds to:
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238
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239 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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240
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241 Except for AS which is a required atomic invariant in atom types,
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242 all other atomic invariants are optional. Atom type specification
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243 doesn't include atomic invariants with zero or undefined values.
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244
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245 In addition to usage of abbreviations for specifying atomic
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246 invariants, the following descriptive words are also allowed:
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247
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248 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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249 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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250 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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251 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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252 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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253 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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254 H : NumOfImplicitAndExplicitHydrogens
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255 Ar : Aromatic
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256 RA : RingAtom
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257 FC : FormalCharge
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258 MN : MassNumber
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259 SM : SpinMultiplicity
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260
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261 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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262 atomic invariant atom types.
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263
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264 SetFunctionalClassesToUse
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265 $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse($ValuesRef);
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266 $TopologicalTorsionsFingerprints->SetFunctionalClassesToUse(@Values);
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267
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268 Sets functional classes invariants to use during
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269 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
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270 topological atom torsions fingerprints generation and returns
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271 *TopologicalAtomTorsionsFingerprints*.
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272
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273 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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274 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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275 *HBD,HBA,PI,NI,Ar,Hal*.
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276
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277 The functional class abbreviations correspond to:
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278
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279 HBD: HydrogenBondDonor
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280 HBA: HydrogenBondAcceptor
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281 PI : PositivelyIonizable
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282 NI : NegativelyIonizable
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283 Ar : Aromatic
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284 Hal : Halogen
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285 H : Hydrophobic
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286 RA : RingAtom
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287 CA : ChainAtom
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288
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289 Functional class atom type specification for an atom corresponds to:
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290
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291 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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292
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293 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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294 functional class atom types. It uses following definitions [ Ref
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295 60-61, Ref 65-66 ]:
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296
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297 HydrogenBondDonor: NH, NH2, OH
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298 HydrogenBondAcceptor: N[!H], O
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299 PositivelyIonizable: +, NH2
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300 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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301
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302 StringifyTopologicalAtomTorsionsFingerprints
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303 $String = $TopologicalAtomTorsionsFingerprints->
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304 StringifyTopologicalAtomTorsionsFingerprints();
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305
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306 Returns a string containing information about
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307 *TopologicalAtomTorsionsFingerprints* object.
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308
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309 AUTHOR
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310 Manish Sud <msud@san.rr.com>
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311
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312 SEE ALSO
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313 Fingerprints.pm, FingerprintsStringUtil.pm,
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314 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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315 EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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316 MACCSKeys.pm, PathLengthFingerprints.pm,
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317 TopologicalAtomPairsFingerprints.pm,
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318 TopologicalAtomTripletsFingerprints.pm,
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319 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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320 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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321
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322 COPYRIGHT
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323 Copyright (C) 2015 Manish Sud. All rights reserved.
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324
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325 This file is part of MayaChemTools.
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326
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327 MayaChemTools is free software; you can redistribute it and/or modify it
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328 under the terms of the GNU Lesser General Public License as published by
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329 the Free Software Foundation; either version 3 of the License, or (at
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330 your option) any later version.
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331
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