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1 NAME
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2 TopologicalAtomPairsFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::TopologicalAtomPairsFingerprints;
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6
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7 use Fingerprints::TopologicalAtomPairsFingerprints qw(:all);
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8
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9 DESCRIPTION
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10 TopologicalAtomPairsFingerprints [ 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, GetAtomPairIDs, GetDescription,
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14 SetAtomIdentifierType, SetAtomicInvariantsToUse,
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15 SetFunctionalClassesToUse, SetMaxDistance, SetMinDistance,
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16 StringifyTopologicalAtomPairsFingerprints
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17
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18 TopologicalAtomPairsFingerprints 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 TopologicalAtomPairsFingerprints,
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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 AtomTypesFingerpritns corresponding to following 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 atoms in a molecule. Using the distance matrix for the
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40 molecule and initial atom types assigned to non-hydrogen atoms, all
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41 unique atom pairs within MinDistance and MaxDistance are identified and
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42 counted. An atom pair identifier is generated for each unique atom pair;
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43 the format of atom pair identifier is:
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44
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45 <AtomType1>-D<n>-<AtomType2>
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46
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47 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
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48 D: Distance between atom1 and atom2
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49
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50 where AtomType1 <= AtomType2
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51
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52 The atom pair identifiers for all unique atom pairs corresponding to
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53 non-hydrogen atoms constitute topological atom pairs fingerprints of the
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54 molecule.
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55
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56 The current release of MayaChemTools generates the following types of
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57 topological atom pairs fingerprints vector strings:
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58
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59 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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60 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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61 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
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62 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
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63 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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64 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
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65
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66 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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67 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
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68 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
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69 C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
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70 .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
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71 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...
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72
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73 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
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74 :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
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75 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_
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76 R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2
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77 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
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78 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...
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79
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80 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
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81 axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
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82 D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
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83 aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
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84 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
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85 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...
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86
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87 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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88 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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89 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
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90 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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91 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
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92 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
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93
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94 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
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95 axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
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96 C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
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97 CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1
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98 COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR
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99 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...
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100
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101 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
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102 xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
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103 -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
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104 C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
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105 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
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106 C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...
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107
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108 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
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109 xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
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110 .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C.
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111 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a
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112 r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3
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113 -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...
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114
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115 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
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116 Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
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117 -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
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118 D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
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119 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
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120 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...
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121
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122 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
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123 istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
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124 -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C
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125 _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1
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126 C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D
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127 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...
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128
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129 METHODS
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130 new
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131 $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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132 %NamesAndValues);
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133
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134 Using specified *TopologicalAtomPairsFingerprints* property names
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135 and values hash, new method creates a new object and returns a
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136 reference to newly created TopologicalAtomPairsFingerprints object.
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137 By default, the following properties are initialized:
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138
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139 Molecule = ''
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140 Type = 'TopologicalAtomPairs'
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141 MinDistance = 1
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142 MaxDistance = 10
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143 AtomIdentifierType = ''
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144 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
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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 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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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 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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155 'Molecule' => $Molecule,
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156 'MinDistance' => 1,
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157 'MaxDistance' => 10,
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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 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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164 'Molecule' => $Molecule,
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165 'AtomIdentifierType' =>
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166 'EStateAtomTypes');
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167
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168 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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169 'Molecule' => $Molecule,
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170 'AtomIdentifierType' =>
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171 'SLogPAtomTypes');
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172
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173 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
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174 'Molecule' => $Molecule,
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175 'MinDistance' => 1,
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176 'MaxDistance' => 10,
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177 'AtomIdentifierType' =>
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178 'FunctionalClassAtomTypes',
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179 'FunctionalClassesToUse' =>
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180 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);
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181
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182
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183 $TopologicalAtomPairsFingerprints->GenerateFingerprints();
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184 print "$TopologicalAtomPairsFingerprints\n";
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185
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186 GetDescription
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187 $Description = $TopologicalAtomPairsFingerprints->GetDescription();
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188
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189 Returns a string containing description of topological atom pairs
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190 fingerprints fingerprints.
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191
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192 GenerateFingerprints
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193 $TopologicalAtomPairsFingerprints->GenerateFingerprints();
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194
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195 Generates topological atom pairs fingerprints and returns
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196 *TopologicalAtomPairsFingerprints*.
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197
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198 GetAtomPairIDs
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199 $AtomPairIDsRef = $TopologicalAtomPairsFingerprints->GetAtomPairIDs();
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200 @AtomPairIDs = $TopologicalAtomPairsFingerprints->GetAtomPairIDs();
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201
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202 Returns atom pair IDs corresponding to atom pairs count values in
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203 topological atom pairs fingerprints vector as an array or reference
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204 to an array.
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205
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206 SetAtomIdentifierType
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207 $TopologicalAtomPairsFingerprints->SetAtomIdentifierType($IdentifierType);
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208
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209 Sets atom *IdentifierType* to use during atom pairs fingerprints
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210 generation and returns *TopologicalAtomPairsFingerprints*.
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211
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212 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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213 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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214 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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215
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216 SetAtomicInvariantsToUse
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217 $TopologicalAtomPairsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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218 $TopologicalAtomPairsFingerprints->SetAtomicInvariantsToUse(@Values);
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219
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220 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
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221 value of *AtomIdentifierType* for topological atom pairs
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222 fingerprints generation and returns
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223 *TopologicalAtomPairsFingerprints*.
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224
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225 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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226 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
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227
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228 The atomic invariants abbreviations correspond to:
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229
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230 AS = Atom symbol corresponding to element symbol
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231
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232 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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233 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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234 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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235 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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236 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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237 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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238 H<n> = Number of implicit and explicit hydrogens for atom
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239 Ar = Aromatic annotation indicating whether atom is aromatic
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240 RA = Ring atom annotation indicating whether atom is a ring
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241 FC<+n/-n> = Formal charge assigned to atom
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242 MN<n> = Mass number indicating isotope other than most abundant isotope
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243 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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244 3 (triplet)
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245
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246 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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247 corresponds to:
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248
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249 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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250
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251 Except for AS which is a required atomic invariant in atom types,
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252 all other atomic invariants are optional. Atom type specification
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253 doesn't include atomic invariants with zero or undefined values.
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254
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255 In addition to usage of abbreviations for specifying atomic
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256 invariants, the following descriptive words are also allowed:
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257
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258 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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259 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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260 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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261 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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262 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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263 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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264 H : NumOfImplicitAndExplicitHydrogens
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265 Ar : Aromatic
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266 RA : RingAtom
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267 FC : FormalCharge
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268 MN : MassNumber
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269 SM : SpinMultiplicity
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270
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271 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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272 atomic invariant atom types.
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273
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274 SetFunctionalClassesToUse
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275 $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse($ValuesRef);
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276 $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse(@Values);
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277
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278 Sets functional classes invariants to use during
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279 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
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280 topological atom pairs fingerprints generation and returns
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281 *TopologicalAtomPairsFingerprints*.
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282
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283 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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284 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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285 *HBD,HBA,PI,NI,Ar,Hal*.
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286
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287 The functional class abbreviations correspond to:
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288
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289 HBD: HydrogenBondDonor
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290 HBA: HydrogenBondAcceptor
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291 PI : PositivelyIonizable
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292 NI : NegativelyIonizable
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293 Ar : Aromatic
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294 Hal : Halogen
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295 H : Hydrophobic
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296 RA : RingAtom
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297 CA : ChainAtom
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298
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299 Functional class atom type specification for an atom corresponds to:
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300
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301 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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302
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303 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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304 functional class atom types. It uses following definitions [ Ref
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305 60-61, Ref 65-66 ]:
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306
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307 HydrogenBondDonor: NH, NH2, OH
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308 HydrogenBondAcceptor: N[!H], O
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309 PositivelyIonizable: +, NH2
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310 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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311
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312 SetMaxDistance
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313 $TopologicalAtomPairsFingerprints->SetMaxDistance($Distance);
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314
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315 Sets maximum distance to use during topological atom pairs
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316 fingerprints generation and returns
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317 *TopologicalAtomPairsFingerprints*.
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318
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319 SetMinDistance
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320 $TopologicalAtomPairsFingerprints->SetMinDistance($Distance);
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321
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322 Sets minimum distance to use during topological atom pairs
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323 fingerprints generation and returns
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324 *TopologicalAtomPairsFingerprints*.
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325
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326 StringifyTopologicalAtomPairsFingerprints
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327 $String = $TopologicalAtomPairsFingerprints->
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328 StringifyTopologicalAtomPairsFingerprints();
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329
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330 Returns a string containing information about
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331 *TopologicalAtomPairsFingerprints* object.
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332
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333 AUTHOR
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334 Manish Sud <msud@san.rr.com>
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335
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336 SEE ALSO
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337 Fingerprints.pm, FingerprintsStringUtil.pm,
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338 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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339 EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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340 MACCSKeys.pm, PathLengthFingerprints.pm,
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341 TopologicalAtomTripletsFingerprints.pm,
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342 TopologicalAtomTorsionsFingerprints.pm,
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343 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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344 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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345
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346 COPYRIGHT
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347 Copyright (C) 2015 Manish Sud. All rights reserved.
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348
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349 This file is part of MayaChemTools.
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350
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351 MayaChemTools is free software; you can redistribute it and/or modify it
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352 under the terms of the GNU Lesser General Public License as published by
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353 the Free Software Foundation; either version 3 of the License, or (at
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354 your option) any later version.
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355
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