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1 NAME
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2 AtomNeighborhoodsFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::AtomNeighborhoodsFingerprints;
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6
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7 use Fingerprints::AtomNeighborhoodsFingerprints qw(:all);
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8
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9 DESCRIPTION
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10 AtomNeighborhoodsFingerprints [ Ref 53-56, Ref 73 ] class provides the
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11 following methods:
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12
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13 new, GenerateFingerprints, GetDescription, SetAtomIdentifierType,
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14 SetAtomicInvariantsToUse, SetFunctionalClassesToUse,
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15 SetMaxNeighborhoodRadius, SetMinNeighborhoodRadius,
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16 StringifyAtomNeighborhoodsFingerprints
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17
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18 AtomNeighborhoodsFingerprints is derived from Fingerprints class which
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19 in turn is derived from ObjectProperty base class that provides methods
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20 not explicitly defined in AtomNeighborhoodsFingerprints, Fingerprints or
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21 ObjectProperty classes using Perl's AUTOLOAD functionality. These
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22 methods are generated on-the-fly for a specified 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 AtomNeighborhoodsFingerprints corresponding to following
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30 AtomIdentifierTypes:
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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 sucb as AtomicInvariantsToUse and FunctionalClassesToUse,
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38 initial atom types are assigned to all non-hydrogen atoms in a molecule.
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39 Using atom neighborhoods around each non-hydrogen central atom
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40 corresponding to radii between specified values MinNeighborhoodRadius
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41 and MaxNeighborhoodRadius, unique atom types at each radii level are
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42 counted and an atom neighborhood identifier is generated.
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43
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44 The format of an atom neighborhood identifier around a central
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45 non-hydrogen atom at a specific radius is:
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46
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47 NR<n>-<AtomType>-ATC<n>
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48
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49 NR: Neighborhood radius
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50 AtomType: Assigned atom type
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51 ATC: Atom type count
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52
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53 The atom neighborhood identifier for non-hydrogen central atom
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54 corresponding to all specified radii is generated by concatenating
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55 neighborhood identifiers at each radii by colon as a delimiter:
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56
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57 NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...
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58
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59 The atom neighborhood identifiers for all non-hydrogen central atoms at
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60 all specified radii are concatenated using space as a delimiter and
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61 constitute atom neighborhood fingerprint of the molecule.
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62
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63 The current release of MayaChemTools generates the following types of
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64 atom neighborhoods fingerprints vector strings:
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65
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66 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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67 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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68 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
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69 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
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70 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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71 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
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72
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73 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
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74 adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
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75 NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
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76 _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
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77 C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
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78 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...
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79
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80 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
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81 ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
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82 NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
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83 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
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84 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
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85 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...
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86
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87 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
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88 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
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89 ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
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90 C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
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91 R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
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92 TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...
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93
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94 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
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95 ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
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96 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
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97 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
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98 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
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99 C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...
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100
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101 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
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102 us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
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103 CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
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104 NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
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105 ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
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106 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...
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107
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108 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
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109 us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
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110 -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
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111 O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
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112 ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
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113 C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...
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114
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115 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
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116 s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
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117 -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
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118 e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
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119 ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
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120 TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...
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121
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122 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
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123 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
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124 _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
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125 C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
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126 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
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127 -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...
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128
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129 METHODS
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130 new
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131 $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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132 %NamesAndValues);
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133
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134 Using specified *AtomNeighborhoodsFingerprints* property names and
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135 values hash, new method creates a new object and returns a reference
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136 to newly created AtomNeighborhoodsFingerprints object. By default,
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137 the following properties are initialized:
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138
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139 Molecule = ''
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140 Type = 'AtomNeighborhoods'
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141 MinNeighborhoodRadius = 0
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142 MaxNeighborhoodRadius = 2
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143 AtomIdentifierType = ''
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144 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
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145 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
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146
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147 Examples:
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148
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149 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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150 'Molecule' => $Molecule,
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151 'AtomIdentifierType' =>
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152 "AtomicInvariantsAtomTypes");
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153
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154 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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155 'Molecule' => $Molecule,
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156 'MinNeighborhoodRadius' => 0,
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157 'MaxNeighborhoodRadius' => 2,
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158 'AtomIdentifierType' =>
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159 'AtomicInvariantsAtomTypes',
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160 'AtomicInvariantsToUse' =>
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161 ['AS', 'X', 'BO', 'H', 'FC'] );
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162
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163 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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164 'Molecule' => $Molecule,
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165 'AtomIdentifierType' =>
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166 'SYBYLAtomTypes');
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167
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168 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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169 'Molecule' => $Molecule,
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170 'AtomIdentifierType' =>
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171 'MMFF94AtomTypes');
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172
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173 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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174 'Molecule' => $Molecule,
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175 'AtomIdentifierType' =>
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176 'AtomicInvariantsAtomTypes');
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177
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178 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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179 'Molecule' => $Molecule,
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180 'MinNeighborhoodRadius' => 0,
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181 'MaxNeighborhoodRadius' => 2,
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182 'AtomIdentifierType' =>
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183 'FunctionalClassAtomTypes',
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184 'FunctionalClassesToUse' =>
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185 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );
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186
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187 $AtomNeighborhoodsFingerprints->GenerateFingerprints();
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188 print "$AtomNeighborhoodsFingerprints\n";
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189
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190 GenerateFingerprints
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191 $AtomNeighborhoodsFingerprints->GenerateFingerprints();
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192
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193 Generates atom neighborhood fingerprints and returns
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194 *AtomNeighborhoodsFingerprints*.
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195
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196 GetDescription
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197 $Description = $AtomNeighborhoodsFingerprints->GetDescription();
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198
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199 Returns a string containing description of atom neighborhood
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200 fingerprints.
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201
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202 SetAtomIdentifierType
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203 $AtomNeighborhoodsFingerprints->SetAtomIdentifierType($IdentifierType);
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204
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205 Sets atom *IdentifierType* to use during atom neighborhood
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206 fingerprints generation and returns *AtomNeighborhoodsFingerprints*.
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207
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208 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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209 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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210 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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211
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212 SetAtomicInvariantsToUse
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213 $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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214 $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse(@Values);
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215
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216 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
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217 value of *AtomIdentifierType* for atom neighborhood fingerprints
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218 generation and returns *AtomNeighborhoodsFingerprints*.
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219
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220 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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221 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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222
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223 The atomic invariants abbreviations correspond to:
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224
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225 AS = Atom symbol corresponding to element symbol
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226
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227 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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228 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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229 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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230 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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231 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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232 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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233 H<n> = Number of implicit and explicit hydrogens for atom
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234 Ar = Aromatic annotation indicating whether atom is aromatic
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235 RA = Ring atom annotation indicating whether atom is a ring
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236 FC<+n/-n> = Formal charge assigned to atom
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237 MN<n> = Mass number indicating isotope other than most abundant isotope
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238 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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239 3 (triplet)
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240
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241 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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242 corresponds to:
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243
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244 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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245
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246 Except for AS which is a required atomic invariant in atom types,
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247 all other atomic invariants are optional. Atom type specification
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248 doesn't include atomic invariants with zero or undefined values.
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249
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250 In addition to usage of abbreviations for specifying atomic
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251 invariants, the following descriptive words are also allowed:
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252
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253 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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254 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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255 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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256 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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257 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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258 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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259 H : NumOfImplicitAndExplicitHydrogens
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260 Ar : Aromatic
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261 RA : RingAtom
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262 FC : FormalCharge
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263 MN : MassNumber
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264 SM : SpinMultiplicity
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265
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266 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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267 atomic invariant atom types.
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268
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269 SetFunctionalClassesToUse
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270 $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse($ValuesRef);
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271 $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse(@Values);
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272
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273 Sets functional classes invariants to use during
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274 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for atom
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275 neighborhoods fingerprints generation and returns
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276 *AtomNeighborhoodsFingerprints*.
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277
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278 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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279 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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280 *HBD,HBA,PI,NI,Ar,Hal*.
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281
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282 The functional class abbreviations correspond to:
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283
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284 HBD: HydrogenBondDonor
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285 HBA: HydrogenBondAcceptor
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286 PI : PositivelyIonizable
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287 NI : NegativelyIonizable
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288 Ar : Aromatic
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289 Hal : Halogen
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290 H : Hydrophobic
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291 RA : RingAtom
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292 CA : ChainAtom
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293
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294 Functional class atom type specification for an atom corresponds to:
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295
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296 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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297
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298 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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299 functional class atom types. It uses following definitions [ Ref
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300 60-61, Ref 65-66 ]:
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301
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302 HydrogenBondDonor: NH, NH2, OH
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303 HydrogenBondAcceptor: N[!H], O
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304 PositivelyIonizable: +, NH2
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305 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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306
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307 SetMaxNeighborhoodRadius
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308 $AtomNeighborhoodsFingerprints->SetMaxNeighborhoodRadius($Radius);
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309
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310 Sets maximum neighborhood radius to use during atom neighborhood
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311 fingerprints generation and returns *AtomNeighborhoodsFingerprints*.
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312
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313 SetMinNeighborhoodRadius
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314 $AtomNeighborhoodsFingerprints->SetMinNeighborhoodRadius($Radius);
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315
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316 Sets minimum neighborhood radius to use during atom neighborhood
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317 fingerprints generation and returns *AtomNeighborhoodsFingerprints*.
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318
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319 StringifyAtomNeighborhoodsFingerprints
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320 $String = $Fingerprints->StringifyAtomNeighborhoodsFingerprints();
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321
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322 Returns a string containing information about
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323 *AtomNeighborhoodsFingerprints* object.
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324
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325 AUTHOR
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326 Manish Sud <msud@san.rr.com>
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327
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328 SEE ALSO
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329 Fingerprints.pm, FingerprintsStringUtil.pm, AtomTypesFingerprints.pm,
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330 EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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331 MACCSKeys.pm, PathLengthFingerprints.pm,
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332 TopologicalAtomPairsFingerprints.pm,
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333 TopologicalAtomTripletsFingerprints.pm,
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334 TopologicalAtomTorsionsFingerprints.pm,
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335 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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336 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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337
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338 COPYRIGHT
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339 Copyright (C) 2015 Manish Sud. All rights reserved.
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340
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341 This file is part of MayaChemTools.
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342
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343 MayaChemTools is free software; you can redistribute it and/or modify it
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344 under the terms of the GNU Lesser General Public License as published by
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345 the Free Software Foundation; either version 3 of the License, or (at
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346 your option) any later version.
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347
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