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1
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1 NAME
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2 PathLengthFingerprints
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3
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4 SYNOPSIS
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5 use Fingerprints::PathLengthFingerprints;
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6
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7 use Fingerprints::PathLengthFingerprints qw(:all);
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8
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9 DESCRIPTION
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10 PathLengthFingerprints class provides the following methods:
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11
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12 new, GenerateFingerprints, , GetDescription, SetAtomIdentifierType,
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13 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxLength,
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14 SetMinLength, SetNumOfBitsToSetPerPath, SetType,
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15 StringifyPathLengthFingerprints
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16
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17 PathLengthFingerprints is derived from Fingerprints class which in turn
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18 is derived from ObjectProperty base class that provides methods not
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19 explicitly defined in PathLengthFingerprints, Fingerprints or
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20 ObjectProperty classes using Perl's AUTOLOAD functionality. These
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21 methods are generated on-the-fly for a specified object property:
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22
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23 Set<PropertyName>(<PropertyValue>);
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24 $PropertyValue = Get<PropertyName>();
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25 Delete<PropertyName>();
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26
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27 The current release of MayaChemTools supports generation of
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28 AtomTypesFingerpritns corresponding to following AtomtomIdentifierTypes:
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29
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30 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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31 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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32 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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33
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34 Based on the values specified for Type, AtomtomIdentifierTypes,
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35 MinPathLength and MaxPathLength, all appropriate atom paths are
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36 generated for each atom in the molecule and collected in a list and the
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37 list is filtered to remove any structurally duplicate paths as indicated
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38 by the value of UseUniquePaths.
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39
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40 For molecules containing rings, atom paths starting from each atom can
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41 be traversed in four different ways:
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42
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43 o Atom paths without any rings and sharing of bonds in traversed paths.
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44 o Atom paths containing rings and without any sharing of bonds in
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45 traversed paths
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46 o All possible atom paths without any rings and sharing of bonds in
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47 traversed paths
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48 o All possible atom paths containing rings and with sharing of bonds in
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49 traversed paths.
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50
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51 Atom path traversal is terminated at the last ring atom. For molecules
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52 containing no rings, first two and last two types described above are
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53 equivalent.
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54
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55 AllowSharedBonds and AllowRings allow generation of different types of
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56 paths to be used for fingerprints generation.
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57
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58 The combination of AllowSharedBonds, AllowRings, and UseBondSymbols
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59 allows generation of 8 different types of path length fingerprints:
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60
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61 AllowSharedBonds AllowRings UseBondSymbols
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62
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63 0 0 1 - AtomPathsNoCyclesWithBondSymbols
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64 0 1 1 - AtomPathsWithCyclesWithBondSymbols
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65
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66 1 0 1 - AllAtomPathsNoCyclesWithBondSymbols
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67 1 1 1 - AllAtomPathsWithCyclesWithBondSymbols
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68 [ DEFAULT ]
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69
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70 0 0 0 - AtomPathsNoCyclesNoBondSymbols
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71 0 1 0 - AtomPathsWithCyclesNoBondSymbols
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72
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73 1 0 0 - AllAtomPathsNoCyclesNoBondSymbols
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74 1 1 0 - AllAtomPathsWithCyclesNoWithBondSymbols
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75
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76 Additionally, possible values for option --AtomIdentifierType in
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77 conjunction with corresponding specified values for
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78 AtomicInvariantsToUse and FunctionalClassesToUse changes the nature of
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79 atom path length strings and the fingerprints.
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80
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81 For each atom path in the filtered atom paths list, an atom path string
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82 is created using value of AtomIdentifierType and specified values to use
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83 for a particular atom identifier type. Value of UseBondSymbols controls
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84 whether bond order symbols are used during generation of atom path
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85 string. Atom symbol corresponds to element symbol and characters used to
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86 represent bond order are: *1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic -
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87 ':'; others: bond order value*. By default, bond symbols are included in
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88 atom path strings. Exclusion of bond symbols in atom path strings
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89 results in fingerprints which correspond purely to atom paths without
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90 considering bonds.
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91
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92 UseUniquePaths controls the removal of structurally duplicate atom path
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93 strings are removed from the list.
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94
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95 For *PathLengthBits* value of Type, each atom path is hashed to a 32 bit
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96 unsigned integer key using TextUtil::HashCode function. Using the hash
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97 key as a seed for a random number generator, a random integer value
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98 between 0 and Size is used to set corresponding bits in the fingerprint
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99 bit-vector string. Value of NumOfBitsToSetPerPaths option controls the
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100 number of time a random number is generated to set corresponding bits.
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101
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102 For * PathLengthCount* value of Typen, the number of times an atom path
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103 appears is tracked and a fingerprints count-string corresponding to
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104 count of atom paths is generated.
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105
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106 The current release of MayaChemTools generates the following types of
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107 path length fingerprints bit-vector and vector strings:
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108
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109 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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110 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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111 0100010101011000101001011100110001000010001001101000001001001001001000
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112 0010110100000111001001000001001010100100100000000011000000101001011100
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113 0010000001000101010100000100111100110111011011011000000010110111001101
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114 0101100011000000010001000011000010100011101100001000001000100000000...
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115
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116 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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117 th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
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118 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
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119 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
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120 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
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121 6ea05280140069c780290c43
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122
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123 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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124 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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125 C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
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126 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
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127 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
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128 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
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129
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130 FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen
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131 gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_
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132 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3
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133 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C
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134 _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C
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135 _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ...
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136
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137 FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
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138 h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
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139 O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
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140 aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
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141 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
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142 sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
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143
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144 FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1
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145 :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1
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146 HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar:
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147 Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI
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148 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr
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149 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...
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150
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151 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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152 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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153 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
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154 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
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155 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
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156 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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157
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158 FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength
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159 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C
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160 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1
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161 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18
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162 :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1
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163 C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...
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164
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165 FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength
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166 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1
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167 N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C.
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168 ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C
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169 .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C
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170 .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3...
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171
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172 FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8
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173 ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O
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174 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N
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175 oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N
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176 one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20
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177 None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...
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178
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179 FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8;
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180 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_
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181 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_
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182 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_
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183 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3
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184 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3...
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185
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186 METHODS
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187 new
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188 $NewPathLengthFingerprints = new PathLengthFingerprints(
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189 %NamesAndValues);
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190
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191 Using specified *PathLengthFingerprints* property names and values
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192 hash, new method creates a new object and returns a reference to
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193 newly created PathLengthFingerprints object. By default, the
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194 following properties are initialized:
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195
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196 Molecule = '';
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197 Type = ''
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198 Size = 1024
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199 MinSize = 32
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200 MaxSize = 2**32
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201 NumOfBitsToSetPerPath = 1
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202 MinLength = 1
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203 MaxLength = 8
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204 AllowSharedBonds = 1
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205 AllowRings = 1
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206 UseBondSymbols = 1
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207 UseUniquePaths = ''
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208 AtomIdentifierType = ''
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209 SetAtomicInvariantsToUse = ['AS']
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210 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
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211
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212 Examples:
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213
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214 $PathLengthFingerprints = new PathLengthFingerprints(
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215 'Molecule' => $Molecule,
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216 'Type' => 'PathLengthBits',
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217 'AtomIdentifierType' =
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218 'AtomicInvariantsAtomTypes');
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219
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220 $PathLengthFingerprints = new PathLengthFingerprints(
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221 'Molecule' => $Molecule,
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222 'Type' => 'PathLengthBits',
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223 'Size' => 1024,
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224 'MinLength' => 1,
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225 'MaxLength' => 8,
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226 'AllowRings' => 1,
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227 'AllowSharedBonds' => 1,
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228 'UseBondSymbols' => 1,
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229 'UseUniquePaths' => 1,
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230 'AtomIdentifierType' =
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231 'AtomicInvariantsAtomTypes',
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232 'AtomicInvariantsToUse' => ['AS']);
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233
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234 $PathLengthFingerprints = new PathLengthFingerprints(
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235 'Molecule' => $Molecule,
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236 'Type' => 'PathLengthCount',
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237 'MinLength' => 1,
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238 'MaxLength' => 8,
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239 'AllowRings' => 1,
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240 'AllowSharedBonds' => 1,
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241 'UseBondSymbols' => 1,
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242 'UseUniquePaths' => 1,
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243 'AtomIdentifierType' =>
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244 'AtomicInvariantsAtomTypes',
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245 'AtomicInvariantsToUse' => ['AS']);
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246
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247 $PathLengthFingerprints = new PathLengthFingerprints(
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248 'Molecule' => $Molecule,
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249 'Type' => 'PathLengthBits',
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250 'AtomIdentifierType' =
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251 'SLogPAtomTypes');
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252
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253 $PathLengthFingerprints = new PathLengthFingerprints(
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254 'Molecule' => $Molecule,
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255 'Type' => 'PathLengthCount',
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256 'AtomIdentifierType' =
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257 'SYBYLAtomTypes');
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258
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259 $PathLengthFingerprints = new PathLengthFingerprints(
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260 'Molecule' => $Molecule,
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261 'Type' => 'PathLengthBits',
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262 'AtomIdentifierType' =
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263 'FunctionalClassAtomTypes',
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264 'FunctionalClassesToUse' => ['HBD', 'HBA', 'Ar']);
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265
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266 $PathLengthFingerprints->GenerateFingerprints();
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267 print "$PathLengthFingerprints\n";
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268
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269 GetDescription
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270 $Description = $PathLengthFingerprints->GetDescription();
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271
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272 Returns a string containing description of path length fingerprints.
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273
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274 GenerateFingerprints
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275 $PathLengthFingerprints->GenerateFingerprints();
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276
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277 Generates path length fingerprints and returns
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278 *PathLengthFingerprints*.
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279
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280 SetMaxLength
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281 $PathLengthFingerprints->SetMaxLength($Length);
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282
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283 Sets maximum value of atom path length to be used during atom path
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284 length fingerprints generation and returns *PathLengthFingerprints*
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285
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286 SetAtomIdentifierType
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287 $PathLengthFingerprints->SetAtomIdentifierType();
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288
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289 Sets atom *IdentifierType* to use during path length fingerprints
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290 generation and returns *PathLengthFingerprints*.
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291
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292 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
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293 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
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294 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
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295
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296 SetAtomicInvariantsToUse
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297 $PathLengthFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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298 $PathLengthFingerprints->SetAtomicInvariantsToUse(@Values);
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299
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300 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
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301 value of *AtomIdentifierType* for path length fingerprints
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302 generation and returns *PathLengthFingerprints*.
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303
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304 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
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305 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS*.
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306
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307 The atomic invariants abbreviations correspond to:
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308
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309 AS = Atom symbol corresponding to element symbol
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310
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311 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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312 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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313 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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314 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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315 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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316 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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317 H<n> = Number of implicit and explicit hydrogens for atom
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318 Ar = Aromatic annotation indicating whether atom is aromatic
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319 RA = Ring atom annotation indicating whether atom is a ring
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320 FC<+n/-n> = Formal charge assigned to atom
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321 MN<n> = Mass number indicating isotope other than most abundant isotope
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322 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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323 3 (triplet)
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324
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325 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
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326 corresponds to:
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327
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328 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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329
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330 Except for AS which is a required atomic invariant in atom types,
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331 all other atomic invariants are optional. Atom type specification
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332 doesn't include atomic invariants with zero or undefined values.
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333
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334 In addition to usage of abbreviations for specifying atomic
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335 invariants, the following descriptive words are also allowed:
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336
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337 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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338 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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339 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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340 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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341 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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342 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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343 H : NumOfImplicitAndExplicitHydrogens
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344 Ar : Aromatic
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345 RA : RingAtom
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346 FC : FormalCharge
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347 MN : MassNumber
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348 SM : SpinMultiplicity
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349
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350 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
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351 atomic invariant atom types.
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352
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353 SetFunctionalClassesToUse
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354 $PathLengthFingerprints->SetFunctionalClassesToUse($ValuesRef);
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355 $PathLengthFingerprints->SetFunctionalClassesToUse(@Values);
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356
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357 Sets functional classes invariants to use during
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358 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for path
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359 length fingerprints generation and returns *PathLengthFingerprints*.
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360
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361 Possible values for atom functional classes are: *Ar, CA, H, HBA,
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362 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
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363 *HBD,HBA,PI,NI,Ar,Hal*.
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364
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365 The functional class abbreviations correspond to:
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366
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367 HBD: HydrogenBondDonor
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368 HBA: HydrogenBondAcceptor
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369 PI : PositivelyIonizable
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370 NI : NegativelyIonizable
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371 Ar : Aromatic
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372 Hal : Halogen
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373 H : Hydrophobic
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374 RA : RingAtom
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375 CA : ChainAtom
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376
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377 Functional class atom type specification for an atom corresponds to:
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378
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379 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
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380
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381 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
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382 functional class atom types. It uses following definitions [ Ref
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383 60-61, Ref 65-66 ]:
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384
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385 HydrogenBondDonor: NH, NH2, OH
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386 HydrogenBondAcceptor: N[!H], O
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387 PositivelyIonizable: +, NH2
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388 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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389
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390 SetMinLength
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391 $PathLengthFingerprints->SetMinLength($Length);
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392
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393 Sets minimum value of atom path length to be used during atom path
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394 length fingerprints generation and returns *PathLengthFingerprints*.
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395
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396 SetMaxLength
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397 $PathLengthFingerprints->SetMaxLength($Length);
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398
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399 Sets maximum value of atom path length to be used during atom path
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400 length fingerprints generation and returns *PathLengthFingerprints*.
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401
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402 SetNumOfBitsToSetPerPath
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403 $PathLengthFingerprints->SetNumOfBitsToSetPerPath($NumOfBits);
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404
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405 Sets number of bits to set for each path during *PathLengthBits*
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406 Type during path length fingerprints generation and returns
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407 *PathLengthFingerprints*.
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408
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409 SetType
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410 $PathLengthFingerprints->SetType($Type);
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411
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412 Sets type of path length fingerprints and returns
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413 *PathLengthFingerprints*. Possible values: *PathLengthBits or
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414 PathLengthCount*.
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415
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416 StringifyPathLengthFingerprints
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417 $String = $PathLengthFingerprints->StringifyPathLengthFingerprints();
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418
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419 Returns a string containing information about
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420 *PathLengthFingerprints* object.
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421
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422 AUTHOR
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423 Manish Sud <msud@san.rr.com>
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424
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425 SEE ALSO
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426 Fingerprints.pm, FingerprintsStringUtil.pm,
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427 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
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428 EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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429 MACCSKeys.pm, TopologicalAtomPairsFingerprints.pm,
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430 TopologicalAtomTripletsFingerprints.pm,
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431 TopologicalAtomTorsionsFingerprints.pm,
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432 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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433 TopologicalPharmacophoreAtomTripletsFingerprints.pm
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434
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435 COPYRIGHT
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436 Copyright (C) 2015 Manish Sud. All rights reserved.
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437
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438 This file is part of MayaChemTools.
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439
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440 MayaChemTools is free software; you can redistribute it and/or modify it
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441 under the terms of the GNU Lesser General Public License as published by
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442 the Free Software Foundation; either version 3 of the License, or (at
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443 your option) any later version.
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444
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