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1 NAME
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2 ExtendedConnectivityFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::ExtendedConnectivityFingerprints;
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6
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7 use Fingerprints::ExtendedConnectivityFingerprints qw(:all);
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8
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9 DESCRIPTION
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10 ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] 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 SetNeighborhoodRadius, StringifyExtendedConnectivityFingerprints
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16
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17 ExtendedConnectivityFingerprints 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 ExtendedConnectivityFingerprints,
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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 ExtendedConnectivityFingerprints 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,
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37 AtomicInvariantsToUse and FunctionalClassesToUse, initial atom types are
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38 assigned to all non-hydrogen atoms in a molecule and these atom types
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39 strings are converted into initial atom identifier integers using
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40 TextUtil::HashCode function. The duplicate atom identifiers are removed.
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41
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42 For NeighborhoodRadius value of *0*, the initial set of unique atom
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43 identifiers comprises the molecule fingerprints. Otherwise, atom
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44 neighborhoods are generated for each non-hydrogen atom up-to specified
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45 NeighborhoodRadius value. For each non-hydrogen central atom at a
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46 specific radius, its neighbors at next radius level along with their
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47 bond orders and previously calculated atom identifiers are collected
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48 which in turn are used to generate a new integer atom identifier; the
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49 bond orders and atom identifier pairs list is first sorted by bond order
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50 followed by atom identifiers to make these values graph invariant.
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51
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52 After integer atom identifiers have been generated for all non-hydrogen
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53 atoms at all specified neighborhood radii, the duplicate integer atom
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54 identifiers corresponding to same hash code value generated using
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55 TextUtil::HashCode are tracked by keeping the atom identifiers at lower
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56 radius. Additionally, all structurally duplicate integer atom
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57 identifiers at each specified radius are also tracked by identifying
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58 equivalent atom and bonds corresponding to substructures used for
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59 generating atom identifier and keeping integer atom identifier with
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60 lowest value.
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61
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62 For *ExtendedConnnectivity* value of fingerprints Type, the duplicate
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63 identifiers are removed from the list and the unique atom identifiers
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64 constitute the extended connectivity fingerprints of a molecule.
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65
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66 For *ExtendedConnnectivityCount* value of fingerprints Type, the
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67 occurrence of each unique atom identifiers appears is counted and the
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68 unique atom identifiers along with their count constitute the extended
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69 connectivity fingerprints of a molecule.
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70
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71 For *ExtendedConnectivityBits* value of fingerprints -m, --mode, the
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72 unique atom identifiers are used as a random number seed to generate a
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73 random integer value between 0 and --Size which in turn is used to set
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74 corresponding bits in the fingerprint bit-vector string.
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75
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76 The current release of MayaChemTools generates the following types of
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77 extended connectivity fingerprints vector strings:
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78
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79 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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80 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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81 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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82 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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83 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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84 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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85
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86 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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87 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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88 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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89 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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90 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
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91 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
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92
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93 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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94 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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95 0000000001010000000110000011000000000000100000000000000000000000100001
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96 1000000110000000000000000000000000010011000000000000000000000000010000
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97 0000000000000000000000000010000000000000000001000000000000000000000000
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98 0000000000010000100001000000000000101000000000000000100000000000000...
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99
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100 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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101 es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
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102 0300000091000004000000020000100000000124008200020000000040020000000000
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103 2080000000820040010020000000008040000000000080001000000000400000000000
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104 4040000090000061010000000800200000000000001400000000020080000000000020
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105 00008020200000408000
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106
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107 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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108 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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109 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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110 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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111 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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112 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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113
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114 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
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115 Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
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116 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
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117 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
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118 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
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119 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1
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120
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121 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
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122 s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
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123 0000000001000100000000001000000000000000000000000000000000101000000010
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124 0000001000000000010000000000000000000000000000000000000000000000000100
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125 0000000000001000000000000001000000000001001000000000000000000000000000
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126 0000000000000000100000000000001000000000000000000000000000000000000...
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127
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128 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
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129 lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
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130 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
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131 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
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132 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
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133 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...
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134
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135 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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136 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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137 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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138 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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139 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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140 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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141
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142 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
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143 haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
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144 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
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145 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
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146 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
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147 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...
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148
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149 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
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150 aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
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151 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
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152 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
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153 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
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154 41915747 679881756 721736571 794256218 908276640 992898760 10987549...
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155
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156 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
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157 aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
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158 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
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159 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
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160 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
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161 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...
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162
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163 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
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164 NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
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165 700688206 265614156 363161397 681332588 810600886 885767127 950172500
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166 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
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167 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
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168 654 256360355 279492740 291251259 317592700 333763396 972105960 101...
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169
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170 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
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171 umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
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172 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
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173 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
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174 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
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175 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...
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176
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177 METHODS
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178 new
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179 $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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180 %NamesAndValues);
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181
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182 Using specified *ExtendedConnectivityFingerprints* property names
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183 and values hash, new method creates a new object and returns a
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184 reference to newly created ExtendedConnectivityFingerprints object.
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185 By default, the following properties are initialized:
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186
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187 Molecule = ''
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188 Type = 'ExtendedConnectivity'
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189 NeighborhoodRadius = 2
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190 AtomIdentifierType = ''
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191 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
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192 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
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193
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194 Examples:
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195
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196 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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197 'Molecule' => $Molecule,
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198 'AtomIdentifierType' =>
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199 'AtomicInvariantsAtomTypes');
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200
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201 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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202 'Type' => 'ExtendedConnectivityCount',
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203 'Molecule' => $Molecule,
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204 'AtomIdentifierType' =>
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205 'AtomicInvariantsAtomTypes');
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206
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207 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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208 'Type' => 'ExtendedConnectivityBits',
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209 'Molecule' => $Molecule,
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210 'Size' => 1024,
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211 'AtomIdentifierType' =>
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212 'AtomicInvariantsAtomTypes');
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213
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214 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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215 'Type' => 'ExtendedConnectivity',
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216 'Molecule' => $Molecule,
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217 'NeighborhoodRadius' => 2,
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218 'AtomIdentifierType' =>
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219 'AtomicInvariantsAtomTypes',
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220 'AtomicInvariantsToUse' =>
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221 ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );
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222
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223 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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224 'Type' => 'ExtendedConnectivity',
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225 'Molecule' => $Molecule,
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226 'NeighborhoodRadius' => 2,
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227 'AtomIdentifierType' =>
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228 'FunctionalClassAtomTypes',
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229 'FunctionalClassesToUse' =>
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230 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );
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231
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232 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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233 'Type' => 'ExtendedConnectivity',
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234 'Molecule' => $Molecule,;
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235 'AtomIdentifierType' =>
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236 'MMFF94AtomTypes');
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237
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238 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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239 'Type' => 'ExtendedConnectivityCount',
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240 'Molecule' => $Molecule,;
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241 'AtomIdentifierType' =>
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242 'MMFF94AtomTypes');
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243
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244 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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245 'Type' => 'ExtendedConnectivityCount',
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246 'Molecule' => $Molecule,;
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247 'AtomIdentifierType' =>
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248 'SLogPAtomTypes');
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249
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250 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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251 'Type' => 'ExtendedConnectivity',
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252 'Molecule' => $Molecule,;
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253 'AtomIdentifierType' =>
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254 'SLogPAtomTypes');
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255
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256 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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257 'Type' => 'ExtendedConnectivity',
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258 'Molecule' => $Molecule,;
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259 'AtomIdentifierType' =>
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260 'SYBYLAtomTypes');
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261
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262 $ExtendedConnectivityFingerprints->GenerateFingerprints();
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263 print "$ExtendedConnectivityFingerprints\n";
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264
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265 GenerateFingerprints
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266 $ExtendedConnectivityFingerprints->GenerateFingerprints();
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267
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268 Generates extended connectivity fingerprints and returns
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269 *ExtendedConnectivityFingerprints*.
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270
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271 GetDescription
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272 $Description = $ExtendedConnectivityFingerprints->GetDescription();
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273
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274 Returns a string containing description of extended connectivity
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275 fingerprints fingerprints.
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276
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277 SetAtomIdentifierType
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278 $ExtendedConnectivityFingerprints->SetAtomIdentifierType($IdentifierType);
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279
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280 Sets atom *IdentifierType* to use during extended connectivity
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281 fingerprints generation and returns
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282 *ExtendedConnectivityFingerprints*.
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283
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284 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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285 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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286 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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287
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288 SetAtomicInvariantsToUse
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289 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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290 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(@Values);
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291
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292 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
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293 value of *AtomIdentifierType* for extended connectivity fingerprints
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294 generation and returns *ExtendedConnectivityFingerprints*.
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295
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296 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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297 TB, H, Ar, RA, FC, MN, SM*. Default value [ Ref 24 ]:
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298 *AS,X,BO,H,FC,MN*.
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299
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300 The atomic invariants abbreviations correspond to:
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301
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302 AS = Atom symbol corresponding to element symbol
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303
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304 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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305 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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306 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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307 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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308 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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309 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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310 H<n> = Number of implicit and explicit hydrogens for atom
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311 Ar = Aromatic annotation indicating whether atom is aromatic
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312 RA = Ring atom annotation indicating whether atom is a ring
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313 FC<+n/-n> = Formal charge assigned to atom
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314 MN<n> = Mass number indicating isotope other than most abundant isotope
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315 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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316 3 (triplet)
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317
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318 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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319 corresponds to:
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320
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321 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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322
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323 Except for AS which is a required atomic invariant in atom types,
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324 all other atomic invariants are optional. Atom type specification
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325 doesn't include atomic invariants with zero or undefined values.
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326
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327 In addition to usage of abbreviations for specifying atomic
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328 invariants, the following descriptive words are also allowed:
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329
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330 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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331 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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332 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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333 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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334 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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335 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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336 H : NumOfImplicitAndExplicitHydrogens
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337 Ar : Aromatic
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338 RA : RingAtom
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339 FC : FormalCharge
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340 MN : MassNumber
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341 SM : SpinMultiplicity
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342
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343 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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344 atomic invariant atom types.
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345
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346 SetFunctionalClassesToUse
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347 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse($ValuesRef);
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348 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(@Values);
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349
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350 Sets functional classes invariants to use during
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351 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
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352 extended connectivity fingerprints generation and returns
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353 *ExtendedConnectivityFingerprints*.
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354
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355 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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356 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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357 *HBD,HBA,PI,NI,Ar,Hal*.
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358
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359 The functional class abbreviations correspond to:
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360
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361 HBD: HydrogenBondDonor
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362 HBA: HydrogenBondAcceptor
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363 PI : PositivelyIonizable
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364 NI : NegativelyIonizable
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365 Ar : Aromatic
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366 Hal : Halogen
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367 H : Hydrophobic
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368 RA : RingAtom
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369 CA : ChainAtom
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370
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371 Functional class atom type specification for an atom corresponds to:
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372
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373 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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374
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375 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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376 functional class atom types. It uses following definitions [ Ref
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377 60-61, Ref 65-66 ]:
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378
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379 HydrogenBondDonor: NH, NH2, OH
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380 HydrogenBondAcceptor: N[!H], O
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381 PositivelyIonizable: +, NH2
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382 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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383
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384 SetNeighborhoodRadius
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385 $ExtendedConnectivityFingerprints->SetNeighborhoodRadius($Radius);
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386
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387 Sets neighborhood radius to use during extended connectivity
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388 fingerprints generation and returns
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389 *ExtendedConnectivityFingerprints*.
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390
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391 StringifyExtendedConnectivityFingerprints
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392 $String = $Fingerprints->StringifyExtendedConnectivityFingerprints();
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393
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394 Returns a string containing information about
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395 *ExtendedConnectivityFingerprints* object.
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396
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397 AUTHOR
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398 Manish Sud <msud@san.rr.com>
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399
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400 SEE ALSO
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401 Fingerprints.pm, FingerprintsStringUtil.pm,
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402 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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403 EStateIndiciesFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
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404 TopologicalAtomPairsFingerprints.pm,
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405 TopologicalAtomTripletsFingerprints.pm,
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406 TopologicalAtomTorsionsFingerprints.pm,
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407 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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408 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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409
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410 COPYRIGHT
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411 Copyright (C) 2015 Manish Sud. All rights reserved.
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412
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413 This file is part of MayaChemTools.
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414
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415 MayaChemTools is free software; you can redistribute it and/or modify it
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416 under the terms of the GNU Lesser General Public License as published by
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417 the Free Software Foundation; either version 3 of the License, or (at
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418 your option) any later version.
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419
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