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1
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1 NAME
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2 EStateIndiciesFingerprints.pl - Generate E-state indicies fingerprints
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3 for SD files
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4
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5 SYNOPSIS
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6 EStateIndiciesFingerprints.pl SDFile(s)...
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7
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8 EStateIndiciesFingerprints.pl [--AromaticityModel
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9 *AromaticityModelType*] [--CompoundID *DataFieldName or
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10 LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode
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11 *DataField | MolName | LabelPrefix | MolNameOrLabelPrefix*]
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12 [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
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13 *All | Common | Specify | CompoundID*] [-e, --EStateAtomTypesSetToUse
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14 *ArbitrarySize or FixedSize*] [-f, --Filter *Yes | No*]
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15 [--FingerprintsLabelMode *FingerprintsLabelOnly |
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16 FingerprintsLabelWithIDs*] [--FingerprintsLabel *text*] [-h, --help]
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17 [-k, --KeepLargestComponent *Yes | No*] [--OutDelim *comma | tab |
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18 semicolon*] [--output *SD | FP | text | all*] [-o, --overwrite] [-q,
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19 --quote *Yes | No*] [-r, --root *RootName*] [-s, --size *number*]
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20 [--ValuesPrecision *number*] [-v, --VectorStringFormat
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21 *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
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22 ValuesAndIDsPairsString*] [-w, --WorkingDir *DirName*]
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23
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24 DESCRIPTION
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25 Generate E-state indicies fingerprints [ Ref 75-78 ] for *SDFile(s)* and
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26 create appropriate SD, FP, or CSV/TSV text file(s) containing
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27 fingerprints bit-vector or vector strings corresponding to molecular
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28 fingerprints.
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29
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30 Multiple SDFile names are separated by spaces. The valid file extensions
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31 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
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32 in a current directory can be specified either by **.sdf* or the current
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33 directory name.
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34
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35 E-state atom types are assigned to all non-hydrogen atoms in a molecule
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36 using module AtomTypes::EStateAtomTypes.pm and E-state values are
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37 calculated using module AtomicDescriptors::EStateValues.pm. Using
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38 E-state atom types and E-state values, EStateIndiciesFingerprints
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39 constituting sum of E-state values for E-sate atom types is generated.
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40
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41 Two types of E-state atom types set size are allowed:
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42
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43 ArbitrarySize - Corresponds to only E-state atom types detected
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44 in molecule
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45 FixedSize - Corresponds to fixed number of E-state atom types previously
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46 defined
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47
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48 Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types
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49 to non-hydrogen atoms in the molecule, is able to assign atom types to
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50 any valid atom group. However, for *FixedSize* value of
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51 EStateAtomTypesSetToUse, only a fixed set of E-state atom types
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52 corresponding to specific atom groups [ Appendix III in Ref 77 ] are
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53 used for fingerprints.
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54
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55 The fixed size E-state atom type set size used during generation of
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56 fingerprints contains 87 E-state non-hydrogen atom types in
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57 EStateAtomTypes.csv data file distributed with MayaChemTools.
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58
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59 Combination of Type and EStateAtomTypesSetToUse allow generation of 2
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60 different types of E-state indicies fingerprints:
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61
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62 Type EStateAtomTypesSetToUse
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63
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64 EStateIndicies ArbitrarySize [ default fingerprints ]
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65 EStateIndicies FixedSize
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66
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67 Example of *SD* file containing E-state indicies fingerprints string
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68 data:
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69
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70 ... ...
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71 ... ...
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72 $$$$
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73 ... ...
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74 ... ...
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75 ... ...
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76 41 44 0 0 0 0 0 0 0 0999 V2000
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77 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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78 ... ...
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79 2 3 1 0 0 0 0
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80 ... ...
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81 M END
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82 > <CmpdID>
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83 Cmpd1
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84
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85 > <EStateIndiciesFingerprints>
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86 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDsA
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87 ndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssNH
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88 SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3.02
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89 4 -2.270
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90
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91 $$$$
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92 ... ...
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93 ... ...
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94
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95 Example of *FP* file containing E-state indicies fingerprints string
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96 data:
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97
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98 #
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99 # Package = MayaChemTools 7.4
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100 # Release Date = Oct 21, 2010
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101 #
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102 # TimeStamp = Fri Mar 11 14:35:11 2011
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103 #
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104 # FingerprintsStringType = FingerprintsVector
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105 #
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106 # Description = EStateIndicies:ArbitrarySize
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107 # VectorStringFormat = IDsAndValuesString
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108 # VectorValuesType = NumericalValues
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109 #
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110 Cmpd1 11;SaaCH SaasC SaasN SdO SdssC...;24.778 4.387 1.993 25.023 -1...
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111 Cmpd2 9;SdNH SdO SdssC SsCH3 SsNH...;7.418 22.984 -1.583 5.387 5.400...
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112 ... ...
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113 ... ..
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114
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115 Example of CSV *Text* file containing E-state indicies fingerprints
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116 string data:
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117
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118 "CompoundID","EStateIndiciesFingerprints"
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119 "Cmpd1","FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalVa
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120 lues;IDsAndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssC
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121 H2 SssNH SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0
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122 .073 3.024 -2.270"
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123 "Cmpd2","FingerprintsVector;EStateIndicies:ArbitrarySize;9;NumericalVal
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124 ues;IDsAndValuesString;SdNH SdO SdssC SsCH3 SsNH2 SsOH SssCH2 SssNH Sss
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125 sCH;7.418 22.984 -1.583 5.387 5.400 19.852 1.737 5.624 -3.319"
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126 ... ...
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127 ... ...
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128
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129 The current release of MayaChemTools generates the following types of
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130 E-state fingerprints vector strings:
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131
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132 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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133 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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134 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
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135 .024 -2.270
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136
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137 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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138 ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
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139 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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140 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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141 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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142
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143 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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144 IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
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145 SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
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146 C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
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147 0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0
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148 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
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149 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
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150
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151 OPTIONS
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152 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
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153 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
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154 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
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155 MayaChemToolsAromaticityModel*
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156 Specify aromaticity model to use during detection of aromaticity.
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157 Possible values in the current release are: *MDLAromaticityModel,
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158 TriposAromaticityModel, MMFFAromaticityModel,
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159 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
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160 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
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161 value: *MayaChemToolsAromaticityModel*.
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162
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163 The supported aromaticity model names along with model specific
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164 control parameters are defined in AromaticityModelsData.csv, which
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165 is distributed with the current release and is available under
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166 lib/data directory. Molecule.pm module retrieves data from this file
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167 during class instantiation and makes it available to method
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168 DetectAromaticity for detecting aromaticity corresponding to a
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169 specific model.
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170
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171 --CompoundID *DataFieldName or LabelPrefixString*
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172 This value is --CompoundIDMode specific and indicates how compound
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173 ID is generated.
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174
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175 For *DataField* value of --CompoundIDMode option, it corresponds to
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176 datafield label name whose value is used as compound ID; otherwise,
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177 it's a prefix string used for generating compound IDs like
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178 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
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179 IDs which look like Cmpd<Number>.
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180
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181 Examples for *DataField* value of --CompoundIDMode:
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182
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183 MolID
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184 ExtReg
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185
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186 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
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187 --CompoundIDMode:
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188
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189 Compound
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190
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191 The value specified above generates compound IDs which correspond to
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192 Compound<Number> instead of default value of Cmpd<Number>.
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193
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194 --CompoundIDLabel *text*
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195 Specify compound ID column label for FP or CSV/TSV text file(s) used
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196 during *CompoundID* value of --DataFieldsMode option. Default:
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197 *CompoundID*.
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198
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199 --CompoundIDMode *DataField | MolName | LabelPrefix |
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200 MolNameOrLabelPrefix*
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201 Specify how to generate compound IDs and write to FP or CSV/TSV text
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202 file(s) along with generated fingerprints for *FP | text | all*
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203 values of --output option: use a *SDFile(s)* datafield value; use
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204 molname line from *SDFile(s)*; generate a sequential ID with
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205 specific prefix; use combination of both MolName and LabelPrefix
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206 with usage of LabelPrefix values for empty molname lines.
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207
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208 Possible values: *DataField | MolName | LabelPrefix |
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209 MolNameOrLabelPrefix*. Default: *LabelPrefix*.
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210
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211 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
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212 in *SDFile(s)* takes precedence over sequential compound IDs
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213 generated using *LabelPrefix* and only empty molname values are
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214 replaced with sequential compound IDs.
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215
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216 This is only used for *CompoundID* value of --DataFieldsMode option.
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217
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218 --DataFields *"FieldLabel1,FieldLabel2,..."*
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219 Comma delimited list of *SDFiles(s)* data fields to extract and
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220 write to CSV/TSV text file(s) along with generated fingerprints for
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221 *text | all* values of --output option.
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222
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223 This is only used for *Specify* value of --DataFieldsMode option.
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224
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225 Examples:
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226
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227 Extreg
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228 MolID,CompoundName
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229
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230 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
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231 Specify how data fields in *SDFile(s)* are transferred to output
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232 CSV/TSV text file(s) along with generated fingerprints for *text |
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233 all* values of --output option: transfer all SD data field; transfer
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234 SD data files common to all compounds; extract specified data
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235 fields; generate a compound ID using molname line, a compound
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236 prefix, or a combination of both. Possible values: *All | Common |
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237 specify | CompoundID*. Default value: *CompoundID*.
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238
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239 -e, --EStateAtomTypesSetToUse *ArbitrarySize | FixedSize*
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240 E-state atom types set size to use during generation of E-state
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241 indicies fingerprints. Possible values: *ArbitrarySize | FixedSize*;
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242 Default value: *ArbitrarySize*.
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243
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244 *ArbitrarySize* corrresponds to only E-state atom types detected in
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245 molecule; *FixedSize* corresponds to fixed number of previously
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246 defined E-state atom types.
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247
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248 For *EStateIndicies*, a fingerprint vector string is generated. The
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249 vector string corresponding to *EStateIndicies* contains sum of
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250 E-state values for E-state atom types.
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251
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252 Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom
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253 types to non-hydrogen atoms in the molecule which is able to assign
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254 atom types to any valid atom group. However, for *FixedSize* value
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255 of EStateAtomTypesSetToUse, only a fixed set of E-state atom types
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256 corresponding to specific atom groups [ Appendix III in Ref 77 ] are
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257 used for fingerprints.
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258
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259 The fixed size E-state atom type set size used during generation of
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260 fingerprints contains 87 E-state non-hydrogen atom types in
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261 EStateAtomTypes.csv data file distributed with MayaChemTools.
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262
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263 -f, --Filter *Yes | No*
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264 Specify whether to check and filter compound data in SDFile(s).
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265 Possible values: *Yes or No*. Default value: *Yes*.
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266
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267 By default, compound data is checked before calculating fingerprints
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268 and compounds containing atom data corresponding to non-element
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269 symbols or no atom data are ignored.
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270
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271 --FingerprintsLabelMode *FingerprintsLabelOnly |
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272 FingerprintsLabelWithIDs*
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273 Specify how fingerprints label is generated in conjunction with
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274 --FingerprintsLabel option value: use fingerprints label generated
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275 only by --FingerprintsLabel option value or append E-state atom type
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276 value IDs to --FingerprintsLabel option value.
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277
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278 Possible values: *FingerprintsLabelOnly | FingerprintsLabelWithIDs*.
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279 Default value: *FingerprintsLabelOnly*.
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280
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281 This option is only used for *FixedSize* value of -e,
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282 --EStateAtomTypesSetToUse option during generation of
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283 *EStateIndicies* E-state fingerprints.
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284
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285 E-state atom type IDs appended to --FingerprintsLabel value during
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286 *FingerprintsLabelWithIDs* values of --FingerprintsLabelMode
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287 correspond to fixed number of previously defined E-state atom types.
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288
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289 --FingerprintsLabel *text*
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290 SD data label or text file column label to use for fingerprints
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291 string in output SD or CSV/TSV text file(s) specified by --output.
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292 Default value: *EStateIndiciesFingerprints*.
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293
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294 -h, --help
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295 Print this help message.
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296
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297 -k, --KeepLargestComponent *Yes | No*
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298 Generate fingerprints for only the largest component in molecule.
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299 Possible values: *Yes or No*. Default value: *Yes*.
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300
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301 For molecules containing multiple connected components, fingerprints
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302 can be generated in two different ways: use all connected components
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303 or just the largest connected component. By default, all atoms
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304 except for the largest connected component are deleted before
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305 generation of fingerprints.
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306
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307 --OutDelim *comma | tab | semicolon*
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308 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
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309 tab, or semicolon* Default value: *comma*.
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310
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311 --output *SD | FP | text | all*
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312 Type of output files to generate. Possible values: *SD, FP, text, or
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313 all*. Default value: *text*.
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314
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315 -o, --overwrite
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316 Overwrite existing files.
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317
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318 -q, --quote *Yes | No*
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319 Put quote around column values in output CSV/TSV text file(s).
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320 Possible values: *Yes or No*. Default value: *Yes*.
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321
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322 -r, --root *RootName*
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323 New file name is generated using the root: <Root>.<Ext>. Default for
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324 new file names: <SDFileName><EStateIndiciesFP>.<Ext>. The file type
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325 determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values are
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326 used for SD, FP, comma/semicolon, and tab delimited text files,
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327 respectively.This option is ignored for multiple input files.
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328
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329 --ValuesPrecision *number*
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330 Precision of values for E-state indicies option. Default value: up
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331 to *3* decimal places. Valid values: positive integers.
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332
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333 -v, --VectorStringFormat *ValuesString | IDsAndValuesString |
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334 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*
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335 Format of fingerprints vector string data in output SD, FP or
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336 CSV/TSV text file(s) specified by --output used for
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337 *EStateIndicies*. Possible values: *ValuesString,
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338 IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString,
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339 ValuesAndIDsPairsString*.
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340
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341 Default value during *ArbitrarySize* value of -e,
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342 --EStateAtomTypesSetToUse option: *IDsAndValuesString*. Default
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343 value during *FixedSize* value of -e, --EStateAtomTypesSetToUse
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344 option: *ValuesString*.
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345
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346 Examples:
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347
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348 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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349 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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350 H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
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351 .024 -2.270
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352
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353 -w, --WorkingDir *DirName*
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354 Location of working directory. Default: current directory.
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355
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356 EXAMPLES
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357 To generate E-state fingerprints of arbitrary size in vector string
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358 format and create a SampleESFP.csv file containing sequential compound
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359 IDs along with fingerprints vector strings data, type:
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360
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361 % EStateIndiciesFingerprints.pl -r SampleESFP -o Sample.sdf
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362
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363 To generate E-state fingerprints of fixed size in vector string format
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364 and create a SampleESFP.csv file containing sequential compound IDs
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365 along with fingerprints vector strings data, type:
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366
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367 % EStateIndiciesFingerprints.pl -e FixedSize -r SampleESFP
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368 -o Sample.sdf
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369
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370 To generate E-state fingerprints of fixed size in vector string with
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371 IDsAndValues format and create a SampleESFP.csv file containing
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372 sequential compound IDs along with fingerprints vector strings data,
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373 type:
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374
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375 % EStateIndiciesFingerprints.pl -e FixedSize -v IDsAndValuesString
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376 -r SampleESFP -o Sample.sdf
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377
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378 To generate E-state fingerprints of fixed size in vector string format
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379 and create a SampleESFP.csv file containing compound ID from molecule
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380 name line along with fingerprints vector strings data, type
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381
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382 % EStateIndiciesFingerprints.pl -e FixedSize
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383 --DataFieldsMode CompoundID --CompoundIDMode MolName
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384 -r SampleESFP -o Sample.sdf
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385
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386 To generate E-state fingerprints of fixed size in vector string format
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387 and create a SampleESFP.csv file containing compound IDs using specified
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388 data field along with fingerprints vector strings data, type:
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389
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390 % EStateIndiciesFingerprints.pl -e FixedSize
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391 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
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392 Mol_ID -r SampleESFP -o Sample.sdf
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393
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394 To generate E-state fingerprints of fixed size in vector string format
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395 and create a SampleESFP.csv file containing compound ID using
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396 combination of molecule name line and an explicit compound prefix along
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397 with fingerprints vector strings data, type:
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398
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399 % EStateIndiciesFingerprints.pl -e FixedSize
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400 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
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401 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleESFP -o Sample.sdf
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402
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403 To generate E-state fingerprints of fixed size in vector string format
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404 and create a SampleESFP.csv file containing specific data fields columns
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405 along with fingerprints vector strings data, type:
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406
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407 % EStateIndiciesFingerprints.pl -e FixedSize
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408 --DataFieldsMode Specify --DataFields Mol_ID -r SampleESFP
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409 -o Sample.sdf
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410
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411 To generate E-state fingerprints of fixed size in vector string format
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412 and create a SampleESFP.csv file containing common data fields columns
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413 along with fingerprints vector strings data, type:
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414
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415 % EStateIndiciesFingerprints.pl -e FixedSize
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416 --DataFieldsMode Common -r SampleESFP -o Sample.sdf
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417
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418 To generate E-state fingerprints of fixed size in vector string format
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419 and create SampleESFP.sdf, SampleESFP.fpf, and SampleESFP.csv files
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420 containing all data fields columns in CSV file along with fingerprints
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421 vector strings data, type:
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422
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423 % EStateIndiciesFingerprints.pl -e FixedSize
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424 --DataFieldsMode All --output all -r SampleESFP -o Sample.sdf
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425
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426 AUTHOR
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427 Manish Sud <msud@san.rr.com>
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428
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429 SEE ALSO
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430 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
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431 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
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432 MACCSKeysFingeprints.pl, PathLengthFingerprints.pl,
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433 TopologicalAtomPairsFingerprints.pl,
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434 TopologicalAtomTorsionsFingerprints.pl,
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435 TopologicalPharmacophoreAtomPairsFingerprints.pl,
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436 TopologicalPharmacophoreAtomTripletsFingerprints.pl
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437
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438 COPYRIGHT
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439 Copyright (C) 2015 Manish Sud. All rights reserved.
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440
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441 This file is part of MayaChemTools.
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442
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443 MayaChemTools is free software; you can redistribute it and/or modify it
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444 under the terms of the GNU Lesser General Public License as published by
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445 the Free Software Foundation; either version 3 of the License, or (at
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446 your option) any later version.
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447
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