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1 NAME
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2 InfoFingerprintsFiles.pl - List information about fingerprints data in
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3 SD, FP and CSV/TSV text file(s)
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4
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5 SYNOPSIS
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6 InfoFingerprintsFiles.pl SDFile(s) FPFile(s) TextFile(s)...
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7
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8 InfoFingerprintsFiles.pl [-a, --all] [--AverageBitDensity]
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9 [--BitDensity] [-c, --count] [-c, --ColMode *ColNum | ColLabel*]
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10 [--DataCheck] [-d, --detail *InfoLevel*] [-e, --empty]
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11 [--FingerprintsCol *col number | col name*] [--FingerprintsField
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12 *FieldLabel*] [--FingerprintsType] [--FingerprintsDescription]
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13 [--FingerprintsSize] [--FingerprintsBitStringFormat]
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14 [--FingerprintsBitOrder] [--FingerprintsVectorValuesType]
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15 [--FingerprintsVectorValuesFormat] [-h, --help] [--InDelim *comma |
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16 semicolon*] [--NumOfOnBits] [--NumOfNonZeroValues] [-w, --WorkingDir
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17 dirname] SDFile(s) FPFile(s) TextFile(s)...
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18
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19 DESCRIPTION
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20 List information about fingerprints data in *SD, FP and CSV/TSV* text
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21 file(s): number of rows containing fingerprints data, type of
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22 fingerprints vector, description and size of fingerprints, bit density
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23 and average bit density for bit-vector fingerprints strings, and so on.
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24
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25 The scripts InfoFingerprintsSDFiles.pl and InfoFingerprintsTextFiles.pl
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26 have been removed from the current release of MayaChemTools and their
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27 functionality merged with this script.
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28
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29 The valid *SDFile* extensions are *.sdf* and *.sd*. All SD files in a
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30 current directory can be specified either by **.sdf* or the current
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31 directory name.
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32
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33 The valid *FPFile* extensions are *.fpf* and *.fp*. All FP files in a
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34 current directory can be specified either by **.fpf* or the current
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35 directory name.
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36
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37 The valid *TextFile* extensions are *.csv* and *.tsv* for
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38 comma/semicolon and tab delimited text files respectively. All other
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39 file names are ignored. All text files in a current directory can be
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40 specified by **.csv*, **.tsv*, or the current directory name. The
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41 --indelim option determines the format of *TextFile(s)*. Any file which
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42 doesn't correspond to the format indicated by --indelim option is
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43 ignored.
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44
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45 Format of fingerprint strings data in *SDFile(s), FPFile(s) and
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46 TextFile(s)* is automatically detected.
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47
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48 Example of *FP* file containing fingerprints bit-vector string data:
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49
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50 #
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51 # Package = MayaChemTools 7.4
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52 # ReleaseDate = Oct 21, 2010
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53 #
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54 # TimeStamp = Mon Mar 7 15:14:01 2011
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55 #
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56 # FingerprintsStringType = FingerprintsBitVector
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57 #
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58 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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59 # Size = 1024
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60 # BitStringFormat = HexadecimalString
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61 # BitsOrder = Ascending
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62 #
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63 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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64 Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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65 ... ...
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66 ... ..
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67
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68 Example of *FP* file containing fingerprints vector string data:
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69
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70 #
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71 # Package = MayaChemTools 7.4
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72 # ReleaseDate = Oct 21, 2010
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73 #
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74 # TimeStamp = Mon Mar 7 15:14:01 2011
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75 #
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76 # FingerprintsStringType = FingerprintsVector
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77 #
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78 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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79 # VectorStringFormat = IDsAndValuesString
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80 # VectorValuesType = NumericalValues
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81 #
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82 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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83 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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84 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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85 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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86 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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87 O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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88 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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89 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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90 ... ...
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91 ... ...
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92
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93 Example of *SD* file containing fingerprints bit-vector string data:
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94
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95 ... ...
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96 ... ...
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97 $$$$
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98 ... ...
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99 ... ...
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100 ... ...
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101 41 44 0 0 0 0 0 0 0 0999 V2000
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102 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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103 ... ...
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104 2 3 1 0 0 0 0
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105 ... ...
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106 M END
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107 > <CmpdID>
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108 Cmpd1
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109
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110 > <PathLengthFingerprints>
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111 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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112 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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113 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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114 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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115 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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116 aa0660a11014a011d46
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117
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118 $$$$
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119 ... ...
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120 ... ...
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121
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122 Example of CSV *Text* file containing fingerprints bit-vector string
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123 data:
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124
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125 "CompoundID","PathLengthFingerprints"
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126 "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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127 :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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128 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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129 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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130 ... ...
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131 ... ...
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132
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133 The current release of MayaChemTools supports the following types of
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134 fingerprint bit-vector and vector strings:
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135
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136 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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137 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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138 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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139 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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140 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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141 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
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142
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143 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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144 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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145 .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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146 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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147
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148 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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149 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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150 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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151
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152 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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153 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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154 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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155 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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156 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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157 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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158
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159 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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160 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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161 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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162 .024 -2.270
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163
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164 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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165 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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166 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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167 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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168 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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169
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170 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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171 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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172 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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173 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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174 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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175 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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176
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177 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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178 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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179 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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180 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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181 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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182 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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183
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184 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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185 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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186 0000000001010000000110000011000000000000100000000000000000000000100001
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187 1000000110000000000000000000000000010011000000000000000000000000010000
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188 0000000000000000000000000010000000000000000001000000000000000000000000
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189 0000000000010000100001000000000000101000000000000000100000000000000...
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190
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191 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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192 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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193 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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194 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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195 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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196 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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197
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198 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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199 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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200 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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201 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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202 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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203 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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204
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205 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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206 0000000000000000000000000000000001001000010010000000010010000000011100
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207 0100101010111100011011000100110110000011011110100110111111111111011111
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208 11111111111110111000
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209
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210 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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211 1110011111100101111111000111101100110000000000000011100010000000000000
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212 0000000000000000000000000000000000000000000000101000000000000000000000
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213 0000000000000000000000000000000000000000000000000000000000000000000000
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214 0000000000000000000000000000000000000011000000000000000000000000000000
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215 0000000000000000000000000000000000000000
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216
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217 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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218 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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219 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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220 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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221 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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222 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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223
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224 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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225 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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226 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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227 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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228 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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229 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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230
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231 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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232 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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233 0100010101011000101001011100110001000010001001101000001001001001001000
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234 0010110100000111001001000001001010100100100000000011000000101001011100
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235 0010000001000101010100000100111100110111011011011000000010110111001101
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236 0101100011000000010001000011000010100011101100001000001000100000000...
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237
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238 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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239 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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240 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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241 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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242 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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243 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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244
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245 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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246 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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247 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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248 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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249 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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250 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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251
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252 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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253 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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254 .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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255 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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256 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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257 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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258
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259 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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260 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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261 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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262 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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263 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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264 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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265
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266 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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267 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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268 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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269 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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270 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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271
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272 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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273 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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274 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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275 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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276 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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277
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278 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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279 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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280 .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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281 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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282 -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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283 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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284 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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285
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286 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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287 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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288 .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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289 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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290 -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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291 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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292
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293 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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294 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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295 -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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296 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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297 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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298 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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299 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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300
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301 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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302 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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303 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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304 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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305 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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306 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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307
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308 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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309 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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310 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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311 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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312 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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313 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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314 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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315 119 123 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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316
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317 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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318 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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319 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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320 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
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321 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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322 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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323
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324 OPTIONS
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325 -a, --all
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326 List all the available information.
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327
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328 --AverageBitDensity
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329 List average bit density of fingerprint bit-vector strings.
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330
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331 --BitDensity
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332 List bit density of fingerprints bit-vector strings data in each
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333 row.
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334
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335 --count
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336 List number of data entries containing fingerprints bit-vector or
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337 vector strings data. This is default behavior.
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338
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339 -c, --ColMode *ColNum | ColLabel*
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340 Specify how columns are identified in CSV/TSV *TextFile(s)*: using
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341 column number or column label. Possible values: *ColNum or
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342 ColLabel*. Default value: *ColNum*
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343
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344 -d, --detail *InfoLevel*
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345 Level of information to print about lines being ignored. Default:
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346 *1*. Possible values: *1, 2 or 3*.
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347
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348 --DataCheck
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349 Validate fingerprints data specified using --FingerprintsCol and
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350 list information about missing and invalid data.
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351
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352 -e, --empty
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353 List number of rows containing no fingerprints data.
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354
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355 --FingerprintsCol *col number | col name*
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356 This value is -c, --colmode specific. It corresponds to column in
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357 CSV/TSV *TextFile(s)* containing fingerprints data. Possible values:
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358 *col number or col label*. Default value: *first column containing
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359 the word Fingerprints in its column label*.
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360
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361 --FingerprintsField *FieldLabel*
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362 Fingerprints field label to use during listing of fingerprints
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363 information for *SDFile(s)*. Default value: *first data field label
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364 containing the word Fingerprints in its label*.
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365
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366 --FingerprintsType
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367 List types of fingerprint strings: FingerprintsBitVector or
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368 FingerprintsVector.
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369
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370 --FingerprintsDescription
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371 List types of fingerprints: PathLengthBits, PathLengthCount,
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372 MACCSKeyCount, ExtendedConnectivity and so on.
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373
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374 --FingerprintsSize
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375 List size of fingerprints.
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376
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377 --FingerprintsBitStringFormat
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378 List format of fingerprint bit-vector strings: BinaryString or
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379 HexadecimalString.
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380
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381 --FingerprintsBitOrder
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382 List order of bits data in fingerprint bit-vector bit strings:
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383 Ascending or Descending.
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384
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385 --FingerprintsVectorValuesType
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386 List type of values in fingerprint vector strings:
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387 OrderedNumericalValues, NumericalValues or AlphaNumericalValues.
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388
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389 --FingerprintsVectorValuesFormat
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390 List format of values in fingerprint vector strings: ValuesString,
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391 IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or
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392 ValuesAndIDsPairsString.
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393
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394 -h, --help
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395 Print this help message.
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396
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397 --InDelim *comma | semicolon*
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398 Input delimiter for CSV *TextFile(s)*. Possible values: *comma or
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399 semicolon*. Default value: *comma*. For TSV files, this option is
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400 ignored and *tab* is used as a delimiter.
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401
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402 --NumOfOnBits
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403 List number of on bits in fingerprints bit-vector strings data in
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404 each row.
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405
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406 --NumOfNonZeroValues
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407 List number of non-zero values in fingerprints vector strings data
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408 in each row.
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409
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410 -w, --WorkingDir *DirName*
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411 Location of working directory. Default: current directory.
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412
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413 EXAMPLES
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414 To count number of lines containing fingerprints bit-vector or vector
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415 strings data present in FP file, in a column name containing Fingerprint
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416 substring in text file, and in a data field with Fingerprint substring
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417 in its label, type:
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418
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419 % InfoFingerprintsFiles.pl SampleFPBin.csv
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420
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421 % InfoFingerprintsFiles.pl SampleFPBin.sdf SampleFPBin.fpf
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422 SampleFPBin.csv
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423
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424 % InfoFingerprintsFiles.pl SampleFPHex.sdf SampleFPHex.fpf
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425 SampleFPHex.csv
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426
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427 % InfoFingerprintsFiles.pl SampleFPcount.sdf SampleFPcount.fpf
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428 SampleFPcount.csv
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429
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430 To list all available information about fingerprints bit-vector or
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431 vector strings data present in FP file, in a column name containing
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432 Fingerprint substring in text file, and in a data field with Fingerprint
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433 substring in its label, type:
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434
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435 % InfoFingerprintsFiles.pl -a SampleFPHex.sdf SampleFPHex.fpf
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436 SampleFPHex.csv
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437
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438 % InfoFingerprintsFiles.pl -a SampleFPcount.sdf SampleFPcount.fpf
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439 SampleFPcount.csv
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440
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441 To list all available information about fingerprints bit-vector or
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442 vector strings data present in a column named Fingerprints in text file,
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443 type:
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444
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445 % InfoFingerprintsFiles.pl -a --ColMode ColLabel --FingerprintsCol
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446 Fingerprints SampleFPHex.sdf
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447
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448 % InfoFingerprintsFiles.pl -a --ColMode ColLabel --FingerprintsCol
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449 Fingerprints SampleFPcount.csv
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450
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451 To list all available information about fingerprints bit-vector or
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452 vector strings data present in a data field names Fingerprints in SD
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453 file, type:
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454
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455 % InfoFingerprintsFiles.pl -a --FingerprintsField Fingerprints
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456 SampleFPHex.sdf
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457
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458 % InfoFingerprintsFiles.pl -a --FingerprintsField Fingerprints
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459 SampleFPcount.sdf
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460
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461 To list bit density, average bit density, and number of on bits for
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462 fingerprints bit-vector strings data present in FP file, in a column
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463 name containing Fingerprint substring in text file, and in a data field
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464 with Fingerprint substring in its label, type:
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465
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466 % InfoFingerprintsFiles.pl --BitDensity --AverageBitDensity
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467 --NumOfOnBits SampleFPBin.csv SampleFPBin.sdf SampleFPBin.fpf
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468
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469 To list vector values type, format and number of non-zero values for
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470 fingerprints vector strings data present in FP file, in a column name
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471 containing Fingerprint substring in text file, and in a data field with
|
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472 Fingerprint substring in its label along with fingerprints type and
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473 description, type:
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474
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475 % InfoFingerprintsFiles.pl --FingerprintsType --FingerprintsDescription
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476 --FingerprintsVectorValuesType --FingerprintsVectorValuesFormat
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477 --NumOfNonZeroValues SampleFPcount.csv SampleFPcount.sdf
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478 SampleFPcount.fpf
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479
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480 AUTHOR
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481 Manish Sud <msud@san.rr.com>
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482
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483 SEE ALSO
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484 SimilarityMatricesFingerprints.pl, SimilaritySearchingFingerprints.pl,
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485 AtomNeighborhoodsFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
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486 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
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487 PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl,
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488 TopologicalAtomTorsionsFingerprints.pl,
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489 TopologicalPharmacophoreAtomPairsFingerprints.pl,
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490 TopologicalPharmacophoreAtomTripletsFingerprints.pl
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491
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492 COPYRIGHT
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493 Copyright (C) 2015 Manish Sud. All rights reserved.
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494
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495 This file is part of MayaChemTools.
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496
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497 MayaChemTools is free software; you can redistribute it and/or modify it
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498 under the terms of the GNU Lesser General Public License as published by
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499 the Free Software Foundation; either version 3 of the License, or (at
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500 your option) any later version.
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501
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