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1 NAME
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2 FingerprintsSDFileIO
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3
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4 SYNOPSIS
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5 use FileIO::FingerprintsSDFileIO;
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6
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7 use FileIO::FingerprintsSDFileIO qw(:all);
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8
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9 DESCRIPTION
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10 FingerprintsSDFileIO class provides the following methods:
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11
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12 new, GetCompoundString, GetFingerprints, GetFingerprintsString,
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13 IsFingerprintsDataValid, IsFingerprintsFileDataValid,
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14 IsFingerprintsSDFile, Next, Read, SetBitStringFormat, SetBitsOrder,
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15 SetCompoundIDMode, SetCompoundString, SetDetailLevel, SetFingerprints,
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16 SetFingerprintsString, SetFingerprintsStringMode, SetVectorStringFormat,
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17 WriteFingerprints, WriteFingerprintsString
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18
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19 The following methods can also be used as functions:
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20
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21 IsFingerprintsSDFile
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22
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23 FingerprintsSDFileIO class is derived from *FileIO* class and uses its
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24 methods to support generic file related functionality.
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25
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26 The fingerprints SD file format with .sdf or .sd file extensions
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27 supports two types of fingerprints string data: fingerprints bit-vectors
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28 and fingerprints vector strings. The fingerprints string data is treated
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29 as value of a fingerprints data field label in a SD file.
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30
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31 Example of SD file format containing fingerprints string data:
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32
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33 ... ...
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34 ... ...
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35 $$$$
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36 ... ...
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37 ... ...
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38 ... ...
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39 41 44 0 0 0 0 0 0 0 0999 V2000
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40 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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41 ... ...
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42 2 3 1 0 0 0 0
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43 ... ...
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44 M END
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45 > <CmpdID>
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46 Test
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47
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48 > <PathLengthFingerprints>
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49 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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50 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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51 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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52 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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53 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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54 aa0660a11014a011d46
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55
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56 $$$$
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57 ... ...
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58 ... ...
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59
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60 The current release of MayaChemTools supports the following types of
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61 fingerprint bit-vector and vector strings:
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62
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63 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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64 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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65 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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66 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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67 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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68 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
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69
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70 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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71 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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72 .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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73 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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74
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75 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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76 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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77 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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78
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79 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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80 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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81 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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82 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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83 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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84 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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85
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86 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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87 AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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88 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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89 .024 -2.270
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90
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91 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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92 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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93 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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94 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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95 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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96
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97 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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98 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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99 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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100 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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101 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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102 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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103
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104 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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105 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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106 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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107 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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108 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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109 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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110
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111 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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112 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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113 0000000001010000000110000011000000000000100000000000000000000000100001
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114 1000000110000000000000000000000000010011000000000000000000000000010000
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115 0000000000000000000000000010000000000000000001000000000000000000000000
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116 0000000000010000100001000000000000101000000000000000100000000000000...
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117
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118 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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119 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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120 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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121 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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122 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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123 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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124
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125 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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126 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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127 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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128 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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129 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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130 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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131
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132 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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133 0000000000000000000000000000000001001000010010000000010010000000011100
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134 0100101010111100011011000100110110000011011110100110111111111111011111
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135 11111111111110111000
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136
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137 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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138 1110011111100101111111000111101100110000000000000011100010000000000000
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139 0000000000000000000000000000000000000000000000101000000000000000000000
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140 0000000000000000000000000000000000000000000000000000000000000000000000
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141 0000000000000000000000000000000000000011000000000000000000000000000000
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142 0000000000000000000000000000000000000000
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143
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144 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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145 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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146 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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147 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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148 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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149 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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150
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151 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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152 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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153 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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154 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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155 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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156 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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157
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158 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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159 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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160 0100010101011000101001011100110001000010001001101000001001001001001000
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161 0010110100000111001001000001001010100100100000000011000000101001011100
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162 0010000001000101010100000100111100110111011011011000000010110111001101
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163 0101100011000000010001000011000010100011101100001000001000100000000...
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164
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165 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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166 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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167 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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168 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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169 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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170 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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171
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172 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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173 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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174 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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175 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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176 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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177 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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178
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179 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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180 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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181 .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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182 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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183 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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184 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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185
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186 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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187 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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188 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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189 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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190 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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191 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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192
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193 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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194 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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195 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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196 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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197 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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198
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199 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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200 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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201 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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202 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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203 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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204
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205 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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206 inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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207 .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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208 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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209 -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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210 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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211 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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212
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213 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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214 :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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215 .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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216 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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217 -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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218 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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219
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220 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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221 Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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222 -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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223 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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224 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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225 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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226 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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227
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228 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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229 ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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230 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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231 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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232 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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233 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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234
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235 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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236 MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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237 Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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238 -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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239 HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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240 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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241 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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242 119 123 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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243
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244 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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245 istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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246 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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247 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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248 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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249 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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250
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251 METHODS
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252 new
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253 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(%IOParameters);
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254
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255 Using specified *IOParameters* names and values hash, new method
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256 creates a new object and returns a reference to a newly created
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257 FingerprintsSDFileIO object. By default, the following properties
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258 are initialized during *Read* mode:
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259
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260 Name = '';
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261 Mode = 'Read';
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262 Status = 0;
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263 FingerprintsStringMode = 'AutoDetect';
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264 FingerprintsFieldLabel = 'AutoDetect';
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265 CompoundIDMode = 'LabelPrefix';
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266 CompoundIDFieldLabel = undef;
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267 CompoundIDPrefix = 'Cmpd';
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268 ValidateData = 1;
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269 DetailLevel = 1;
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270
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271 During *Write* mode, the following properties get initialize by
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272 default:
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273
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274 FingerprintsStringMode = undef;
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275
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276 BitStringFormat = HexadecimalString;
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277 BitsOrder = Ascending;
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278
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279 VectorStringFormat = NumericalValuesString or ValuesString;
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280
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281 Examples:
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282
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283 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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284 'Name' => 'Sample.sdf',
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285 'Mode' => 'Read');
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286
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287 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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288 'Name' => 'Sample.sdf',
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289 'Mode' => 'Read',;
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290 'FingerprintsStringMode' =>
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291 'AutoDetect',
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292 'FingerprintsFieldLabel' =>
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293 'Fingerprints',
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294 'CompoundIDMode' =>
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295 'DataField',
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296 'CompoundIDFieldLabel' =>
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297 'CompoundID');
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298
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299 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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300 'Name' => 'Sample.sdf',
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301 'Mode' => 'Write',
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302 'FingerprintsStringMode' =>
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303 'FingerprintsBitVectorString',
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304 'Overwrite' => 1,
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305 'BitStringFormat' => 'HexadecimalString',
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306 'BitsOrder' => 'Ascending');
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307
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308 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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309 'Name' => 'Sample.sd',
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310 'Mode' => 'Write',
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311 'FingerprintsStringMode' =>
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312 'FingerprintsVectorString',
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313 'Overwrite' => 1,
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314 'VectorStringFormat' => 'IDsAndValuesString',
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315 'FingerprintsLabel' => 'Fingerprints');
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316
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317 GetCompoundString
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318 $CompoundString = $FingerprintsSDFileIO->GetCompoundString();
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319
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320 Returns CompoundString for current compound.
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321
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322 GetFingerprints
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323 $FingerprintsObject = $FingerprintsSDFileIO->GetFingerprints();
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324
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325 Returns FingerprintsObject generated for current compound using
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326 fingerprints bit-vector or vector string data. The fingerprints
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327 object corresponds to any of the supported fingerprints such as
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328 PathLengthFingerprints, ExtendedConnectivity, and so on.
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329
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330 GetFingerprintsString
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331 $FingerprintsString = $FingerprintsSDFileIO->GetFingerprintsString();
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332
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333 Returns FingerprintsString for current compound.
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334
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335 IsFingerprintsDataValid
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336 $Status = $FingerprintsSDFileIO->IsFingerprintsDataValid();
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337
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338 Returns 1 or 0 based on whether FingerprintsObject is valid.
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339
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340 IsFingerprintsFileDataValid
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341 $Status = $FingerprintsSDFileIO->IsFingerprintsFileDataValid();
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342
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343 Returns 1 or 0 based on whether fingerprints file contains valid
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344 fingerprints data.
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345
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346 IsFingerprintsSDFile
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347 $Status = $FingerprintsSDFileIO->IsFingerprintsSDFile($FileName);
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348 $Status = FileIO::FingerprintsSDFileIO::IsFingerprintsSDFile($FileName);
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349
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350 Returns 1 or 0 based on whether *FileName* is a SD file.
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351
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352 Next or Read
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353 $FingerprintsSDFileIO = $FingerprintsSDFileIO->Next();
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354 $FingerprintsSDFileIO = $FingerprintsSDFileIO->Read();
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355
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356 Reads next available compound fingerprints in SD file, processes the
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357 data, generates appropriate fingerprints object, and returns
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358 FingerprintsSDFileIO. The generated fingerprints object is available
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359 using method GetFingerprints.
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360
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361 SetBitStringFormat
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362 $FingerprintsSDFileIO->SetBitStringFormat($Format);
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363
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364 Sets bit string *Format* for fingerprints bit-vector string data in
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365 a SD file and returns FingerprintsSDFileIO. Possible values for
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366 BitStringFormat: *BinaryString or HexadecimalString*.
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367
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368 SetBitsOrder
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369 $FingerprintsSDFileIO->SetBitsOrder($BitsOrder);
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370
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371 Sets *BitsOrder* for fingerprints bit-vector string data in SD file
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372 and returns FingerprintsSDFileIO. Possible values for BitsOrder:
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373 *Ascending or Descending*.
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374
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375 SetCompoundIDMode
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376 $FingerprintsSDFileIO->SetCompoundIDMode($Mode);
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377
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378 Sets compound ID *Mode* for fingerprints bit-vector string data in a
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379 SD file and returns FingerprintsSDFileIO. Possible values for
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380 CompoundIDMode: *DataField, MolName, LabelPrefix, or
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381 MolNameOrLabelPrefix*.
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382
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383 SetCompoundString
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384 $FingerprintsSDFileIO->SetCompoundString($CompoundString);
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385
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386 Sets *CompoundString* and returns FingerprintsSDFileIO.
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387
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388 SetDetailLevel
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389 $FingerprintsSDFileIO->SetDetailLevel($Level);
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390
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391 Sets details *Level* for generating diagnostics messages during SD
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392 file processing and returns FingerprintsSDFileIO. Possible values:
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393 *Positive integers*.
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394
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395 SetFingerprints
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396 $FingerprintsSDFileIO->SetFingerprints($FingerprintsObject);
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397
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398 Sets *FingerprintsObject* for current data line and returns
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399 FingerprintsSDFileIO.
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400
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401 SetFingerprintsString
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402 $FingerprintsSDFileIO->SetFingerprintsString($FingerprintsString);
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403
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404 Sets *FingerprintsString* for current data line and returns
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405 FingerprintsSDFileIO.
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406
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407 SetFingerprintsStringMode
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408 $FingerprintsSDFileIO->SetFingerprintsStringMode($Mode);
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409
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410 Sets *FingerprintsStringMode* for SD file and returns
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411 FingerprintsFPFileIO. Possible values: *AutoDetect,
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412 FingerprintsBitVectorString, or FingerprintsVectorString*
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413
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414 SetVectorStringFormat
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415 $FingerprintsSDFileIO->SetVectorStringFormat($Format);
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416
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417 Sets *VectorStringFormat* for SD file and returns
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418 FingerprintsFPFileIO. Possible values: *IDsAndValuesString,
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419 IDsAndValuesPairsString, ValuesAndIDsString,
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|
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420 ValuesAndIDsPairsString*.
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421
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|
|
422 WriteFingerprints
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|
|
423 $FingerprintsFPFileIO->WriteFingerprints($FingerprintsObject,
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|
|
424 $CompoundID);
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|
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425
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|
426 Writes fingerprints string generated from *FingerprintsObject*
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|
|
427 object and other data including *CompoundID* to SD file and returns
|
|
|
428 FingerprintsSDFileIO.
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|
|
429
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|
|
430 WriteFingerprintsString
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|
|
431 $FingerprintsSDFileIO->WriteFingerprints($FingerprintsString,
|
|
|
432 $CompoundID);
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|
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433
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434 Writes *FingerprintsString* and other data including *CompoundID* to
|
|
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435 SD file and returns FingerprintsSDFileIO.
|
|
|
436
|
|
|
437 Caveats:
|
|
|
438
|
|
|
439 o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
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|
|
440 values are ignored during writing of fingerprints and it's written to the file
|
|
|
441 as it is.
|
|
|
442 o CompoundString is not checked to remove any existing fingerprints data
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|
|
443
|
|
|
444 AUTHOR
|
|
|
445 Manish Sud <msud@san.rr.com>
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|
|
446
|
|
|
447 SEE ALSO
|
|
|
448 FingerprintsTextFileIO.pm, FingerprintsFPFileIO.pm, SDFileIO.pm
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|
|
449
|
|
|
450 COPYRIGHT
|
|
|
451 Copyright (C) 2015 Manish Sud. All rights reserved.
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|
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452
|
|
|
453 This file is part of MayaChemTools.
|
|
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454
|
|
|
455 MayaChemTools is free software; you can redistribute it and/or modify it
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|
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456 under the terms of the GNU Lesser General Public License as published by
|
|
|
457 the Free Software Foundation; either version 3 of the License, or (at
|
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458 your option) any later version.
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459
|
