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1 NAME
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2 FingerprintsFPFileIO
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3
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4 SYNOPSIS
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5 use FileIO::FingerprintsFPFileIO;
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6
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7 use FileIO::FingerprintsFPFileIO qw(:all);
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8
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9 DESCRIPTION
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10 FingerprintsFPFileIO class provides the following methods:
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11
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12 new, GetFingerprints, GetFingerprintsString, GetHeaderDataKeyValue,
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13 GetHeaderDataKeys, GetHeaderDataKeysAndValues,
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14 GetPartialFingerprintsString, GetRequiredHeaderDataKeys,
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15 GetRequiredHeaderDataKeysAndValues, IsFingerprintsDataValid,
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16 IsFingerprintsFPFile, IsFingerprintsFileDataValid,
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17 IsHeaderDataKeyPresent, Next, Read, SetBitStringFormat, SetBitsOrder,
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18 SetCompoundID, SetDetailLevel, SetFingerprints, SetFingerprintsString,
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19 SetFingerprintsStringMode, SetPartialFingerprintsString,
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20 SetVectorStringFormat, WriteFingerprints, WriteFingerprintsString
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21
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22 The following methods can also be used as functions:
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23
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24 IsFingerprintsFPFile
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25
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26 FingerprintsFPFileIO class is derived from *FileIO* class and uses its
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27 methods to support generic file related functionality.
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28
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29 The MayaChemTools fingerprints file (FP) format with .fpf or .fp file
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30 extensions supports two types of fingerprints data: fingerprints
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31 bit-vectors and fingerprints vectors.
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32
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33 Example of FP file format containing fingerprints bit-vector string
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34 data:
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35
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36 #
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37 # Package = MayaChemTools 7.4
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38 # ReleaseDate = Oct 21, 2010
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39 #
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40 # TimeStamp = Mon Mar 7 15:14:01 2011
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41 #
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42 # FingerprintsStringType = FingerprintsBitVector
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43 #
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44 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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45 # Size = 1024
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46 # BitStringFormat = HexadecimalString
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47 # BitsOrder = Ascending
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48 #
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49 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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50 Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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51 ... ...
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52 ... ..
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53
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54 Example of FP file format containing fingerprints vector string data:
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55
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56 #
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57 # Package = MayaChemTools 7.4
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58 # ReleaseDate = Oct 21, 2010
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59 #
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60 # TimeStamp = Mon Mar 7 15:14:01 2011
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61 #
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62 # FingerprintsStringType = FingerprintsVector
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63 #
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64 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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65 # VectorStringFormat = IDsAndValuesString
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66 # VectorValuesType = NumericalValues
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67 #
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68 Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C:
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69 N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...;
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70 33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2
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71 6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ...
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72 Cmpd2 103;C N O C=N C=O CC CN CO CC=O CCC CCN CCO CNC N=CN NC=O NCN O=C
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73 O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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74 15 4 4 1 2 13 5 2 2 15 5 3 2 2 1 1 1 2 17 7 6 5 1 1 1 2 15 8 5 7 2 2 2 2
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75 1 2 1 1 3 15 7 6 8 3 4 4 3 2 2 1 2 3 14 2 4 7 4 4 4 4 1 1 1 2 1 1 1 ...
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76 ... ...
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77 ... ...
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78
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79 FP file data format consists of two main sections: header section and
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80 fingerprints string data section. The header section lines start with #
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81 and the first line not starting with # represents the start of
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82 fingerprints string data section. The header section contains both the
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83 required and optional information which is specified as key = value
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84 pairs. The required information describes fingerprints bit-vector and
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85 vector strings and used to generate fingerprints objects; the optional
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86 information is ignored during generation of fingerpints objects.
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87
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88 The key = value data specification in the header section and its
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89 processing follows these rules:
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90
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91 o Leading and trailing spaces for key = value pairs are ignored
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92 o Key and value strings may contain spaces
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93 o Multiple key = value pairs on a single are delimited by semicolon
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94
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95 The default optional header data section key = value pairs are:
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96
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97 # Package = MayaChemTools 7.4
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98 # ReleaseDate = Oct 21, 2010
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99
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100 The FingerprintsStringType key is required data header key for both
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101 fingerprints bit-vector and vector strings. Possible key values:
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102 *FingerprintsBitVector or FingerprintsVector*. For example:
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103
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104 # FingerprintsStringType = FingerprintsBitVector
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105
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106 The required data header keys for fingerprints bit-vector string are:
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107 Description, Size, BitStringFormat, and BitsOrder. Possible values for
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108 BitStringFormat: *HexadecimalString or BinaryString*. Possible values
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109 for BitsOrder: *Ascending or Descending*. The Description key contains
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110 information about various parameters used to generate fingerprints
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111 bit-vector string. The Size corresponds to number of fingerprints bits
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112 and is always less than or equal to number of bits in bit-vetor string
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113 which might contain extra bits at the end to round off the size to make
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114 it multiple of 8. For example:
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115
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116 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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117 # Size = 1024
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118 # BitStringFormat = HexadecimalString
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119 # BitsOrder = Ascending
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120
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121 The required data header keys for fingerprints vector string are:
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122 Description, VectorStringFormat, and VectorValuesType. Possible values
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123 for VectorStringFormat: *DsAndValuesString, IDsAndValuesPairsString,
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124 ValuesAndIDsString, ValuesAndIDsPairsString or ValuesString*. Possible
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125 values for VectorValuesType: *NumericalValues, OrderedNumericalValues or
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126 AlphaNumericalValues*. The Description keys contains information various
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127 parameters used to generate fingerprints vector string. For example:
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128
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129 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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130 # VectorStringFormat = IDsAndValuesString
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131 # VectorValuesType = NumericalValues
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132
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133 The fingerprints data section for fingerprints bit-vector string
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134 contains data in the following format:
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135
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136 ... ...
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137 CmpdID FingerprintsPartialBitVectorString
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138 ... ...
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139
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140 For example:
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141
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142 ... ...
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143 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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144 ... ...
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145
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146 The fingerprints data section for fingerprints vector string contains
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147 data in the following format:
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148
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149 ... ...
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150 CmpdID Size;FingerprintsPartialVectorString
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151 ... ...
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152
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153 For example:
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154
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155 ... ...
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156 Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C:
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157 N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...;
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158 33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2
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159 6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ...
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160 ... ...
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161
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162 Unlike fingerprints bit-vector string, *Size* is specified for each
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163 partial fingerprints vector string: It may change from molecule to
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164 molecule for same type of fingerprints.
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165
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166 Values IDs are optional for fingerprints vector string containing
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167 *OrderedNumericalValues or AlphaNumericalValues*; however, they must be
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168 present for for *NumericalValues*. Due to various possible values for
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169 VectorStringFormat, the fingerprints data section for fingerprints
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170 vector string supports following type of data formats:
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171
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172 CmpdID Size;ID1 ID2 ID3...;Value1 Value2 Value3...
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173 CmpdID Size;ID1 Value1 ID2 Value2 ID3 Value3... ...
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174 CmpdID Size;ValuesAndIDsString: Value1 Value2 Value3...;ID1 ID2 ID3...
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175 CmpdID Size;ValuesAndIDsPairsString: Value1 ID1 Value2 ID2 Value3 ID3... ...
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176 CmpdID Size;Value1 Value2 Value3 ...
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177
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178 However, all the fingerprints vector string data present in FP file must
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179 correspond to only one of the formats shown above; multiple data formats
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180 in the same file are not allowed.
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181
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182 The current release of MayaChemTools supports the following types of
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183 fingerprint bit-vector and vector strings:
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184
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185 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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186 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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187 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
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188 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
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189 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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190 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
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191
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192 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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193 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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194 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
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195 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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196
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197 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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198 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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199 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
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200
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201 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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202 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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203 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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204 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
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205 O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
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206 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...
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207
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208 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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209 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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210 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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211 .024 -2.270
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212
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213 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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214 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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215 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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216 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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217 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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218
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219 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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220 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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221 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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222 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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223 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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224 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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225
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226 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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227 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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228 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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229 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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230 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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231 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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232
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233 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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234 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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235 0000000001010000000110000011000000000000100000000000000000000000100001
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236 1000000110000000000000000000000000010011000000000000000000000000010000
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237 0000000000000000000000000010000000000000000001000000000000000000000000
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238 0000000000010000100001000000000000101000000000000000100000000000000...
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239
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240 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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241 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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242 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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243 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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244 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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245 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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246
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247 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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248 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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249 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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250 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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251 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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252 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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253
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254 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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255 0000000000000000000000000000000001001000010010000000010010000000011100
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256 0100101010111100011011000100110110000011011110100110111111111111011111
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257 11111111111110111000
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258
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259 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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260 1110011111100101111111000111101100110000000000000011100010000000000000
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261 0000000000000000000000000000000000000000000000101000000000000000000000
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262 0000000000000000000000000000000000000000000000000000000000000000000000
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263 0000000000000000000000000000000000000011000000000000000000000000000000
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264 0000000000000000000000000000000000000000
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265
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266 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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267 ng;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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268 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
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269 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
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270 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
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271 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1
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272
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273 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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274 ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
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275 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
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276 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 0
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277 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
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278 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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279
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280 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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281 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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282 0100010101011000101001011100110001000010001001101000001001001001001000
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283 0010110100000111001001000001001010100100100000000011000000101001011100
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284 0010000001000101010100000100111100110111011011011000000010110111001101
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285 0101100011000000010001000011000010100011101100001000001000100000000...
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286
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287 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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288 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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289 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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290 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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291 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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292 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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293
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294 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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295 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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296 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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297 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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298 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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299 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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300
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301 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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302 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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303 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
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304 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
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305 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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306 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
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307
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308 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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309 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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310 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
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311 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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312 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
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313 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
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314
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315 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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316 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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317 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
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|
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318 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
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319 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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320
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321 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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322 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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323 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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324 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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325 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
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326
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327 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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328 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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329 .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
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330 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
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331 -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
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332 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
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333 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
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334
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335 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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336 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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337 .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
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338 D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
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339 -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
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340 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...
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341
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342 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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343 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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344 -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
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345 HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
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346 BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
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347 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
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348 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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349
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350 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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351 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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352 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
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353 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
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354 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
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355 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
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356
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357 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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358 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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359 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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|
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360 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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|
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361 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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362 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
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|
|
363 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
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364 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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365
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366 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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367 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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|
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368 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
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|
|
369 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
|
|
|
370 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
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|
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371 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...
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372
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373 METHODS
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374 new
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375 $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(%IOParameters);
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376
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377 Using specified *IOParameters* names and values hash, new method
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378 creates a new object and returns a reference to a newly created
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379 FingerprintsFPFileIO object. By default, the following properties
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380 are initialized during *Read* mode:
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381
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382 Name = '';
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383 Mode = 'Read';
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384 Status = 0;
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385 FingerprintsStringMode = 'AutoDetect';
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|
386 ValidateData = 1;
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387 DetailLevel = 1;
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388
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|
|
389 During *Write* mode, the following properties get initialize by
|
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390 default:
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391
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392 FingerprintsStringMode = undef;
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393
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394 BitStringFormat = HexadecimalString;
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395 BitsOrder = Ascending;
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396
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397 VectorStringFormat = NumericalValuesString or ValuesString;
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398
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399 Examples:
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400
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401 $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
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402 'Name' => 'Sample.fpf',
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403 'Mode' => 'Read',
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404 'FingerprintsStringMode' =>
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|
405 'AutoDetect');
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406
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|
407 $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
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|
408 'Name' => 'Sample.fpf',
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|
409 'Mode' => 'Write',
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|
410 'FingerprintsStringMode' =>
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411 'FingerprintsBitVectorString',
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412 'Overwrite' => 1,
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413 'BitStringFormat' => 'HexadecimalString',
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414 'BitsOrder' => 'Ascending');
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415
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416 $NewFingerprintsFPFileIO = new FileIO::FingerprintsFPFileIO(
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417 'Name' => 'Sample.fp',
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418 'Mode' => 'Write',
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419 'FingerprintsStringMode' =>
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420 'FingerprintsVectorString',
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421 'Overwrite' => 1,
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422 'VectorStringFormat' => 'IDsAndValuesString');
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423
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424 GetFingerprints
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425 $FingerprintsObject = $FingerprintsFPFileIO->GetFingerprints();
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426
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427 Returns FingerprintsObject generated for current data line using
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428 fingerprints bit-vector or vector string data. The fingerprints
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|
|
429 object corresponds to any of the supported fingerprints such as
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430 PathLengthFingerprints, ExtendedConnectivity, and so on.
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431
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432 GetFingerprintsString
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433 $FingerprintsString = $FingerprintsFPFileIO->GetFingerprintsString();
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434
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|
435 Returns FingerprintsString for current data line.
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436
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|
437 GetHeaderDataKeyValue
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|
|
438 $KeyValue = $FingerprintsFPFileIO->GetHeaderDataKeyValue($Key);
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439
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440 Returns KeyValue of a data header *Key*.
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441
|
|
|
442 GetHeaderDataKeys
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|
|
443 @Keys = $FingerprintsFPFileIO->GetHeaderDataKeys();
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|
|
444 $NumOfKeys = $FingerprintsFPFileIO->GetHeaderDataKeys();
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|
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445
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|
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446 Returns an array of data header Keys retrieved from data header
|
|
|
447 section of fingerprints file. In scalar context, it returns number
|
|
|
448 of keys.
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449
|
|
|
450 GetHeaderDataKeysAndValues
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|
|
451 %KeysAndValues = $FingerprintsFPFileIO->GetHeaderDataKeysAndValues();
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|
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452
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|
453 Returns a hash of data header keys and values retrieved from data
|
|
|
454 header section of fingerprints file.
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455
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|
456 GetPartialFingerprintsString
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|
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457 $FingerprintsString = $FingerprintsFPFileIO->GetPartialFingerprintsString();
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458
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459 Returns partial FingerprintsString for current data line. It
|
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460 corresponds to fingerprints string specified present in a line.
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461
|
|
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462 GetRequiredHeaderDataKeys
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|
|
463 @Keys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys();
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|
|
464 $NumOfKeys = $FingerprintsFPFileIO->GetRequiredHeaderDataKeys();
|
|
|
465
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|
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466 Returns an array of required data header Keys for a fingerprints
|
|
|
467 file containing bit-vector or vector strings data. In scalar
|
|
|
468 context, it returns number of keys.
|
|
|
469
|
|
|
470 GetRequiredHeaderDataKeysAndValues
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|
|
471 %KeysAndValues = $FingerprintsFPFileIO->
|
|
|
472 GetRequiredHeaderDataKeysAndValues();
|
|
|
473
|
|
|
474 Returns a hash of required data header keys and values for a
|
|
|
475 fingerprints file containing bit-vector or vector strings data
|
|
|
476
|
|
|
477 IsFingerprintsDataValid
|
|
|
478 $Status = $FingerprintsFPFileIO->IsFingerprintsDataValid();
|
|
|
479
|
|
|
480 Returns 1 or 0 based on whether FingerprintsObject is valid.
|
|
|
481
|
|
|
482 IsFingerprintsFPFile
|
|
|
483 $Status = $FingerprintsFPFileIO->IsFingerprintsFPFile($FileName);
|
|
|
484 $Status = FileIO::FingerprintsFPFileIO::IsFingerprintsFPFile($FileName);
|
|
|
485
|
|
|
486 Returns 1 or 0 based on whether *FileName* is a FP file.
|
|
|
487
|
|
|
488 IsFingerprintsFileDataValid
|
|
|
489 $Status = $FingerprintsFPFileIO->IsFingerprintsFileDataValid();
|
|
|
490
|
|
|
491 Returns 1 or 0 based on whether fingerprints file contains valid
|
|
|
492 fingerprints data.
|
|
|
493
|
|
|
494 IsHeaderDataKeyPresent
|
|
|
495 $Status = $FingerprintsFPFileIO->IsHeaderDataKeyPresent($Key);
|
|
|
496
|
|
|
497 Returns 1 or 0 based on whether data header *Key* is present in data
|
|
|
498 header section of a FP file.
|
|
|
499
|
|
|
500 Next or Read
|
|
|
501 $FingerprintsFPFileIO = $FingerprintsFPFileIO->Next();
|
|
|
502 $FingerprintsFPFileIO = $FingerprintsFPFileIO->Read();
|
|
|
503
|
|
|
504 Reads next available fingerprints line in FP file, processes the
|
|
|
505 data, generates appropriate fingerprints object, and returns
|
|
|
506 FingerprintsFPFileIO. The generated fingerprints object is available
|
|
|
507 using method GetFingerprints.
|
|
|
508
|
|
|
509 SetBitStringFormat
|
|
|
510 $FingerprintsFPFileIO->SetBitStringFormat($Format);
|
|
|
511
|
|
|
512 Sets bit string *Format* for fingerprints bit-vector string data in
|
|
|
513 a FP file and returns FingerprintsFPFileIO. Possible values for
|
|
|
514 BitStringFormat: *BinaryString or HexadecimalString*.
|
|
|
515
|
|
|
516 SetBitsOrder
|
|
|
517 $FingerprintsFPFileIO->SetBitsOrder($BitsOrder);
|
|
|
518
|
|
|
519 Sets *BitsOrder* for fingerprints bit-vector string data in a FP
|
|
|
520 file and returns FingerprintsFPFileIO. Possible values for
|
|
|
521 BitsOrder: *Ascending or Descending*.
|
|
|
522
|
|
|
523 SetCompoundID
|
|
|
524 $FingerprintsFPFileIO->SetCompoundID($ID);
|
|
|
525
|
|
|
526 Sets compound ID for current data line and returns
|
|
|
527 FingerprintsFPFileIO. Spaces are not allowed in compound IDs.
|
|
|
528
|
|
|
529 SetDetailLevel
|
|
|
530 $FingerprintsFPFileIO->SetDetailLevel($Level);
|
|
|
531
|
|
|
532 Sets details *Level* for generating diagnostics messages during FP
|
|
|
533 file processing and returns FingerprintsFPFileIO. Possible values:
|
|
|
534 *Positive integers*.
|
|
|
535
|
|
|
536 SetFingerprints
|
|
|
537 $FingerprintsFPFileIO->SetFingerprints($FingerprintsObject);
|
|
|
538
|
|
|
539 Sets *FingerprintsObject* for current data line and returns
|
|
|
540 FingerprintsFPFileIO.
|
|
|
541
|
|
|
542 SetFingerprintsString
|
|
|
543 $FingerprintsFPFileIO->SetFingerprintsString($FingerprintsString);
|
|
|
544
|
|
|
545 Sets *FingerprintsString* for current data line and returns
|
|
|
546 FingerprintsFPFileIO.
|
|
|
547
|
|
|
548 SetFingerprintsStringMode
|
|
|
549 $FingerprintsFPFileIO->SetFingerprintsStringMode($Mode);
|
|
|
550
|
|
|
551 Sets *FingerprintsStringMode* for FP file and returns
|
|
|
552 FingerprintsFPFileIO. Possible values: *AutoDetect,
|
|
|
553 FingerprintsBitVectorString, or FingerprintsVectorString*
|
|
|
554
|
|
|
555 SetPartialFingerprintsString
|
|
|
556 $FingerprintsFPFileIO->SetPartialFingerprintsString($PartialString);
|
|
|
557
|
|
|
558 Sets *PartialFingerprintsString* for current data line and returns
|
|
|
559 FingerprintsFPFileIO.
|
|
|
560
|
|
|
561 SetVectorStringFormat
|
|
|
562 $FingerprintsFPFileIO->SetVectorStringFormat($Format);
|
|
|
563
|
|
|
564 Sets *VectorStringFormat* for FP file and returns
|
|
|
565 FingerprintsFPFileIO. Possible values: *IDsAndValuesString,
|
|
|
566 IDsAndValuesPairsString, ValuesAndIDsString,
|
|
|
567 ValuesAndIDsPairsString*.
|
|
|
568
|
|
|
569 WriteFingerprints
|
|
|
570 $FingerprintsFPFileIO->WriteFingerprints($FingerprintsObject,
|
|
|
571 $CompoundID);
|
|
|
572
|
|
|
573 Writes fingerprints string generated from *FingerprintsObject*
|
|
|
574 object and other data including *CompoundID* to FP file and returns
|
|
|
575 FingerprintsFPFileIO.
|
|
|
576
|
|
|
577 WriteFingerprintsString
|
|
|
578 $FingerprintsFPFileIO->WriteFingerprints($FingerprintsString,
|
|
|
579 $CompoundID);
|
|
|
580
|
|
|
581 Writes *FingerprintsString* and other data including *CompoundID* to
|
|
|
582 FP file and returns FingerprintsFPFileIO.
|
|
|
583
|
|
|
584 Caveats:
|
|
|
585
|
|
|
586 o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
|
|
|
587 values are ignored during writing of fingerprints and it's written to
|
|
|
588 the file as it is.
|
|
|
589 o FingerprintsString is a regular fingerprints string as oppose to a
|
|
|
590 partial fingerprints string.
|
|
|
591
|
|
|
592 AUTHOR
|
|
|
593 Manish Sud <msud@san.rr.com>
|
|
|
594
|
|
|
595 SEE ALSO
|
|
|
596 FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm
|
|
|
597
|
|
|
598 COPYRIGHT
|
|
|
599 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
600
|
|
|
601 This file is part of MayaChemTools.
|
|
|
602
|
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|
603 MayaChemTools is free software; you can redistribute it and/or modify it
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|
604 under the terms of the GNU Lesser General Public License as published by
|
|
|
605 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
606 your option) any later version.
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607
|
