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3 <title>MayaChemTools:Documentation:FileIO::FingerprintsSDFileIO.pm</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsFPFileIO.html" title="FingerprintsFPFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Next</a></td><td width="34%" align="middle"><strong>FileIO::FingerprintsSDFileIO.pm</strong></td><td width="33%" align="right"><a href="././code/FingerprintsSDFileIO.html" title="View source code">Code</a> | <a href="./../pdf/FingerprintsSDFileIO.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/FingerprintsSDFileIO.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/FingerprintsSDFileIO.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/FingerprintsSDFileIO.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>FingerprintsSDFileIO</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use FileIO::FingerprintsSDFileIO;</p>
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26 <p>use FileIO::FingerprintsSDFileIO qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>FingerprintsSDFileIO</strong> class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#getcompoundstring">GetCompoundString</a>, <a href="#getfingerprints">GetFingerprints</a>, <a href="#getfingerprintsstring">GetFingerprintsString</a>
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32 , <a href="#isfingerprintsdatavalid">IsFingerprintsDataValid</a>, <a href="#isfingerprintsfiledatavalid">IsFingerprintsFileDataValid</a>, <a href="#isfingerprintssdfile">IsFingerprintsSDFile</a>, <a href="#next">Next</a>
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33 , <a href="#read">Read</a>, <a href="#setbitstringformat">SetBitStringFormat</a>, <a href="#setbitsorder">SetBitsOrder</a>, <a href="#setcompoundidmode">SetCompoundIDMode</a>, <a href="#setcompoundstring">SetCompoundString</a>
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34 , <a href="#setdetaillevel">SetDetailLevel</a>, <a href="#setfingerprints">SetFingerprints</a>, <a href="#setfingerprintsstring">SetFingerprintsString</a>, <a href="#setfingerprintsstringmode">SetFingerprintsStringMode</a>
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35 , <a href="#setvectorstringformat">SetVectorStringFormat</a>, <a href="#writefingerprints">WriteFingerprints</a>, <a href="#writefingerprintsstring">WriteFingerprintsString</a>
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36 </p><p>The following methods can also be used as functions:</p>
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37 <p>IsFingerprintsSDFile</p>
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38 <p><strong>FingerprintsSDFileIO</strong> class is derived from <em>FileIO</em> class and uses its methods to support
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39 generic file related functionality.</p>
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40 <p>The fingerprints SD file format with <strong>.sdf</strong> or <strong>.sd</strong> file extensions supports two types of
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41 fingerprints string data: fingerprints bit-vectors and fingerprints vector strings. The fingerprints
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42 string data is treated as value of a fingerprints data field label in a SD file.</p>
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43 <p>Example of SD file format containing fingerprints string data:</p>
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44 <div class="OptionsBox">
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45 ... ...
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46 <br/> ... ...
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47 <br/> $$$$
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48 <br/> ... ...
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49 <br/> ... ...
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50 <br/> ... ...
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51 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
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52 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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53 <br/> ... ...
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54 <br/> 2 3 1 0 0 0 0
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55 <br/> ... ...
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56 <br/> M END
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57 <br/> > <CmpdID>
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58 <br/> Test</div>
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59 <div class="OptionsBox">
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60 > <PathLengthFingerprints>
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61 <br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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62 <br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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63 <br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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64 <br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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65 <br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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66 <br/> aa0660a11014a011d46</div>
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67 <div class="OptionsBox">
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68 $$$$
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69 <br/> ... ...
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70 <br/> ... ...</div>
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71 <p>The current release of MayaChemTools supports the following types of fingerprint
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72 bit-vector and vector strings:</p>
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73 <div class="OptionsBox">
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74 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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75 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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76 <br/> 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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77 <br/> 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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78 <br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
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79 <br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div>
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80 <div class="OptionsBox">
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81 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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82 <br/> ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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83 <br/> .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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84 <br/> O.X1.BO2;2 4 14 3 10 1 1 1 3 2</div>
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85 <div class="OptionsBox">
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86 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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87 <br/> ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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88 <br/> N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1</div>
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89 <div class="OptionsBox">
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90 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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91 <br/> umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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92 <br/> 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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93 <br/> 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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94 <br/> 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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95 <br/> 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...</div>
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96 <div class="OptionsBox">
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97 FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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98 <br/> AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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99 <br/> 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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100 <br/> .024 -2.270</div>
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101 <div class="OptionsBox">
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102 FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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103 <br/> 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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104 <br/> 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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105 <br/> 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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106 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0</div>
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107 <div class="OptionsBox">
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108 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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109 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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110 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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111 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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112 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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113 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
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114 <div class="OptionsBox">
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115 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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116 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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117 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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118 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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119 <br/> 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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120 <br/> 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</div>
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121 <div class="OptionsBox">
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122 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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123 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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124 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
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125 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
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126 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
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127 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
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128 <div class="OptionsBox">
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129 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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130 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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131 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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132 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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133 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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134 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
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135 <div class="OptionsBox">
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136 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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137 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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138 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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139 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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140 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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141 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
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142 <div class="OptionsBox">
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143 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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144 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
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145 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
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146 <br/> 11111111111110111000</div>
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147 <div class="OptionsBox">
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148 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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149 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
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150 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
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151 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
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152 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
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153 <br/> 0000000000000000000000000000000000000000</div>
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154 <div class="OptionsBox">
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155 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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156 <br/> 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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157 <br/> 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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158 <br/> 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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159 <br/> 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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160 <br/> 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</div>
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161 <div class="OptionsBox">
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162 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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163 <br/> 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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164 <br/> 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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165 <br/> 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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166 <br/> 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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167 <br/> 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 ...</div>
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168 <div class="OptionsBox">
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169 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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170 <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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171 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000
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172 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100
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173 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101
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174 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div>
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175 <div class="OptionsBox">
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176 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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177 <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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178 <br/> 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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179 <br/> 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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180 <br/> 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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181 <br/> 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....</div>
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182 <div class="OptionsBox">
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183 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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184 <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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185 <br/> 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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186 <br/> 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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187 <br/> 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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188 <br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div>
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189 <div class="OptionsBox">
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190 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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191 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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192 <br/> .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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193 <br/> 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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194 <br/> 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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195 <br/> 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...</div>
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196 <div class="OptionsBox">
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197 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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198 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
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199 <br/> 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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200 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
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201 <br/> 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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202 <br/> 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 ...</div>
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203 <div class="OptionsBox">
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204 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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205 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
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206 <br/> 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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207 <br/> 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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208 <br/> 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</div>
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209 <div class="OptionsBox">
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210 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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211 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
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212 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
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213 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
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214 <br/> 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</div>
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215 <div class="OptionsBox">
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216 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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217 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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218 <br/> .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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219 <br/> 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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220 <br/> -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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221 <br/> 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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222 <br/> 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...</div>
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223 <div class="OptionsBox">
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224 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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225 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
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226 <br/> .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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227 <br/> 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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228 <br/> -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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229 <br/> 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...</div>
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230 <div class="OptionsBox">
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231 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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232 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
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233 <br/> -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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234 <br/> 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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235 <br/> 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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236 <br/> 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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237 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
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238 <div class="OptionsBox">
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239 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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240 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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241 <br/> 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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242 <br/> 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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243 <br/> 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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244 <br/> 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...</div>
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245 <div class="OptionsBox">
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246 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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247 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
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248 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
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249 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
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250 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
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251 <br/> 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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252 <br/> 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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253 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
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254 <div class="OptionsBox">
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255 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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256 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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257 <br/> 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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258 <br/> 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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259 <br/> 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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260 <br/> 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 ...</div>
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261 <p>
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262 </p>
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263 <h2>METHODS</h2>
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264 <dl>
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265 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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266 <dd>
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267 <div class="OptionsBox">
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268 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(%IOParameters);</div>
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269 <p>Using specified <em>IOParameters</em> names and values hash, <strong>new</strong> method creates a new
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270 object and returns a reference to a newly created <strong>FingerprintsSDFileIO</strong> object. By default,
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271 the following properties are initialized during <em>Read</em> mode:</p>
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272 <div class="OptionsBox">
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273 Name = '';
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274 <br/> Mode = 'Read';
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275 <br/> Status = 0;
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276 <br/> FingerprintsStringMode = 'AutoDetect';
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277 <br/> FingerprintsFieldLabel = 'AutoDetect';
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278 <br/> CompoundIDMode = 'LabelPrefix';
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279 <br/> CompoundIDFieldLabel = undef;
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280 <br/> CompoundIDPrefix = 'Cmpd';
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281 <br/> ValidateData = 1;
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282 <br/> DetailLevel = 1;</div>
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283 <p>During <em>Write</em> mode, the following properties get initialize by default:</p>
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284 <div class="OptionsBox">
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285 FingerprintsStringMode = undef;</div>
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286 <div class="OptionsBox">
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287 BitStringFormat = HexadecimalString;
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288 <br/> BitsOrder = Ascending;</div>
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289 <div class="OptionsBox">
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290 VectorStringFormat = NumericalValuesString or ValuesString;</div>
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291 <p>Examples:</p>
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292 <div class="OptionsBox">
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293 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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294 'Name' => 'Sample.sdf',
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295 'Mode' => 'Read');</div>
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296 <div class="OptionsBox">
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297 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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298 'Name' => 'Sample.sdf',
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299 'Mode' => 'Read',;
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300 'FingerprintsStringMode' =>
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301 'AutoDetect',
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302 'FingerprintsFieldLabel' =>
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303 'Fingerprints',
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304 'CompoundIDMode' =>
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305 'DataField',
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306 'CompoundIDFieldLabel' =>
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307 'CompoundID');</div>
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308 <div class="OptionsBox">
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309 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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310 'Name' => 'Sample.sdf',
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311 'Mode' => 'Write',
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312 'FingerprintsStringMode' =>
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313 'FingerprintsBitVectorString',
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314 'Overwrite' => 1,
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315 'BitStringFormat' => 'HexadecimalString',
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316 'BitsOrder' => 'Ascending');</div>
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317 <div class="OptionsBox">
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318 $NewFingerprintsSDFileIO = new FileIO::FingerprintsSDFileIO(
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319 'Name' => 'Sample.sd',
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320 'Mode' => 'Write',
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321 'FingerprintsStringMode' =>
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322 'FingerprintsVectorString',
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323 'Overwrite' => 1,
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324 'VectorStringFormat' => 'IDsAndValuesString',
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325 'FingerprintsLabel' => 'Fingerprints');</div>
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326 </dd>
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327 <dt><strong><a name="getcompoundstring" class="item"><strong>GetCompoundString</strong></a></strong></dt>
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328 <dd>
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329 <div class="OptionsBox">
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330 $CompoundString = $FingerprintsSDFileIO->GetCompoundString();</div>
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331 <p>Returns <strong>CompoundString</strong> for current compound.</p>
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332 </dd>
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333 <dt><strong><a name="getfingerprints" class="item"><strong>GetFingerprints</strong></a></strong></dt>
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334 <dd>
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335 <div class="OptionsBox">
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336 $FingerprintsObject = $FingerprintsSDFileIO->GetFingerprints();</div>
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337 <p>Returns <strong>FingerprintsObject</strong> generated for current compound using fingerprints bit-vector
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338 or vector string data. The fingerprints object corresponds to any of the supported fingerprints
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339 such as PathLengthFingerprints, ExtendedConnectivity, and so on.</p>
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340 </dd>
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341 <dt><strong><a name="getfingerprintsstring" class="item"><strong>GetFingerprintsString</strong></a></strong></dt>
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342 <dd>
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343 <div class="OptionsBox">
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344 $FingerprintsString = $FingerprintsSDFileIO->GetFingerprintsString();</div>
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345 <p>Returns <strong>FingerprintsString</strong> for current compound.</p>
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346 </dd>
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347 <dt><strong><a name="isfingerprintsdatavalid" class="item"><strong>IsFingerprintsDataValid</strong></a></strong></dt>
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348 <dd>
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349 <div class="OptionsBox">
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350 $Status = $FingerprintsSDFileIO->IsFingerprintsDataValid();</div>
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351 <p>Returns 1 or 0 based on whether <strong>FingerprintsObject</strong> is valid.</p>
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352 </dd>
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353 <dt><strong><a name="isfingerprintsfiledatavalid" class="item"><strong>IsFingerprintsFileDataValid</strong></a></strong></dt>
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354 <dd>
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355 <div class="OptionsBox">
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356 $Status = $FingerprintsSDFileIO->IsFingerprintsFileDataValid();</div>
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357 <p>Returns 1 or 0 based on whether fingerprints file contains valid fingerprints data.</p>
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358 </dd>
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359 <dt><strong><a name="isfingerprintssdfile" class="item"><strong>IsFingerprintsSDFile</strong></a></strong></dt>
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360 <dd>
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361 <div class="OptionsBox">
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362 $Status = $FingerprintsSDFileIO->IsFingerprintsSDFile($FileName);
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363 <br/> $Status = FileIO::FingerprintsSDFileIO::IsFingerprintsSDFile($FileName);</div>
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364 <p>Returns 1 or 0 based on whether <em>FileName</em> is a SD file.</p>
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365 </dd>
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366 <dt><strong><a name="next_or_read" class="item"><strong>Next or Read</strong></a></strong></dt>
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367 <dd>
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368 <div class="OptionsBox">
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369 $FingerprintsSDFileIO = $FingerprintsSDFileIO->Next();
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370 <br/> $FingerprintsSDFileIO = $FingerprintsSDFileIO->Read();</div>
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371 <p>Reads next available compound fingerprints in SD file, processes the data, generates appropriate
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372 fingerprints object, and returns <strong>FingerprintsSDFileIO</strong>. The generated fingerprints object is available
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373 using method <strong>GetFingerprints</strong>.</p>
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374 </dd>
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375 <dt><strong><a name="setbitstringformat" class="item"><strong>SetBitStringFormat</strong></a></strong></dt>
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376 <dd>
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377 <div class="OptionsBox">
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378 $FingerprintsSDFileIO->SetBitStringFormat($Format);</div>
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379 <p>Sets bit string <em>Format</em> for fingerprints bit-vector string data in a SD file and returns <strong>FingerprintsSDFileIO</strong>.
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380 Possible values for <strong>BitStringFormat</strong>: <em>BinaryString or HexadecimalString</em>.</p>
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381 </dd>
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382 <dt><strong><a name="setbitsorder" class="item"><strong>SetBitsOrder</strong></a></strong></dt>
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383 <dd>
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384 <div class="OptionsBox">
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385 $FingerprintsSDFileIO->SetBitsOrder($BitsOrder);</div>
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386 <p>Sets <em>BitsOrder</em> for fingerprints bit-vector string data in SD file and returns <strong>FingerprintsSDFileIO</strong>.
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387 Possible values for <strong>BitsOrder</strong>: <em>Ascending or Descending</em>.</p>
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388 </dd>
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389 <dt><strong><a name="setcompoundidmode" class="item"><strong>SetCompoundIDMode</strong></a></strong></dt>
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390 <dd>
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391 <div class="OptionsBox">
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392 $FingerprintsSDFileIO->SetCompoundIDMode($Mode);</div>
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393 <p>Sets compound ID <em>Mode</em> for fingerprints bit-vector string data in a SD file and returns <strong>FingerprintsSDFileIO</strong>.
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394 Possible values for <strong>CompoundIDMode</strong>: <em>DataField, MolName, LabelPrefix, or MolNameOrLabelPrefix</em>.</p>
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395 </dd>
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396 <dt><strong><a name="setcompoundstring" class="item"><strong>SetCompoundString</strong></a></strong></dt>
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397 <dd>
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398 <div class="OptionsBox">
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399 $FingerprintsSDFileIO->SetCompoundString($CompoundString);</div>
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400 <p>Sets <em>CompoundString</em> and returns <strong>FingerprintsSDFileIO</strong>.</p>
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401 </dd>
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402 <dt><strong><a name="setdetaillevel" class="item"><strong>SetDetailLevel</strong></a></strong></dt>
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403 <dd>
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404 <div class="OptionsBox">
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405 $FingerprintsSDFileIO->SetDetailLevel($Level);</div>
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406 <p>Sets details <em>Level</em> for generating diagnostics messages during SD file processing and returns
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407 <strong>FingerprintsSDFileIO</strong>. Possible values: <em>Positive integers</em>.</p>
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408 </dd>
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409 <dt><strong><a name="setfingerprints" class="item"><strong>SetFingerprints</strong></a></strong></dt>
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410 <dd>
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411 <div class="OptionsBox">
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412 $FingerprintsSDFileIO->SetFingerprints($FingerprintsObject);</div>
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413 <p>Sets <em>FingerprintsObject</em> for current data line and returns <strong>FingerprintsSDFileIO</strong>.</p>
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414 </dd>
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415 <dt><strong><a name="setfingerprintsstring" class="item"><strong>SetFingerprintsString</strong></a></strong></dt>
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416 <dd>
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417 <div class="OptionsBox">
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418 $FingerprintsSDFileIO->SetFingerprintsString($FingerprintsString);</div>
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419 <p>Sets <em>FingerprintsString</em> for current data line and returns <strong>FingerprintsSDFileIO</strong>.</p>
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420 </dd>
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421 <dt><strong><a name="setfingerprintsstringmode" class="item"><strong>SetFingerprintsStringMode</strong></a></strong></dt>
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422 <dd>
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423 <div class="OptionsBox">
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424 $FingerprintsSDFileIO->SetFingerprintsStringMode($Mode);</div>
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425 <p>Sets <em>FingerprintsStringMode</em> for SD file and returns <strong>FingerprintsFPFileIO</strong>.
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426 Possible values: <em>AutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString</em></p>
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427 </dd>
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428 <dt><strong><a name="setvectorstringformat" class="item"><strong>SetVectorStringFormat</strong></a></strong></dt>
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429 <dd>
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430 <div class="OptionsBox">
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431 $FingerprintsSDFileIO->SetVectorStringFormat($Format);</div>
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432 <p>Sets <em>VectorStringFormat</em> for SD file and returns <strong>FingerprintsFPFileIO</strong>. Possible values:
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433 <em>IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString</em>.</p>
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434 </dd>
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435 <dt><strong><a name="writefingerprints" class="item"><strong>WriteFingerprints</strong></a></strong></dt>
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436 <dd>
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437 <div class="OptionsBox">
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438 $FingerprintsFPFileIO->WriteFingerprints($FingerprintsObject,
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439 $CompoundID);</div>
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440 <p>Writes fingerprints string generated from <em>FingerprintsObject</em> object and other data including
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441 <em>CompoundID</em> to SD file and returns <strong>FingerprintsSDFileIO</strong>.</p>
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442 </dd>
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443 <dt><strong><a name="writefingerprintsstring" class="item"><strong>WriteFingerprintsString</strong></a></strong></dt>
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444 <dd>
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445 <div class="OptionsBox">
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446 $FingerprintsSDFileIO->WriteFingerprints($FingerprintsString,
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447 $CompoundID);</div>
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448 <p>Writes <em>FingerprintsString</em> and other data including <em>CompoundID</em> to SD file and returns
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449 <strong>FingerprintsSDFileIO</strong>.</p>
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450 <p>Caveats:</p>
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451 <div class="OptionsBox">
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452 o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
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453 values are ignored during writing of fingerprints and it's written to the file
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454 as it is.
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455 <br/> o CompoundString is not checked to remove any existing fingerprints data</div>
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456 </dd>
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457 </dl>
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458 <p>
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459 </p>
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460 <h2>AUTHOR</h2>
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461 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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462 <p>
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463 </p>
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464 <h2>SEE ALSO</h2>
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465 <p><a href="./FingerprintsTextFileIO.html">FingerprintsTextFileIO.pm</a>, <a href="./FingerprintsFPFileIO.html">FingerprintsFPFileIO.pm</a>, <a href="./SDFileIO.html">SDFileIO.pm</a>
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466 </p>
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467 <p>
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468 </p>
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469 <h2>COPYRIGHT</h2>
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470 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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471 <p>This file is part of MayaChemTools.</p>
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472 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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473 the terms of the GNU Lesser General Public License as published by the Free
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474 Software Foundation; either version 3 of the License, or (at your option)
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475 any later version.</p>
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476 <p> </p><p> </p><div class="DocNav">
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477 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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478 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FingerprintsFPFileIO.html" title="FingerprintsFPFileIO.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./FingerprintsTextFileIO.html" title="FingerprintsTextFileIO.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>FileIO::FingerprintsSDFileIO.pm</strong></td></tr>
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479 </table>
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480 </div>
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481 <br />
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482 <center>
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483 <img src="../../images/h2o2.png">
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484 </center>
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485 </body>
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486 </html>
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