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3 <title>MayaChemTools:Documentation:Fingerprints::ExtendedConnectivityFingerprints.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="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./Fingerprints.html" title="Fingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::ExtendedConnectivityFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/ExtendedConnectivityFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtendedConnectivityFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtendedConnectivityFingerprints.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>ExtendedConnectivityFingerprints</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 Fingerprints::ExtendedConnectivityFingerprints;</p>
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26 <p>use Fingerprints::ExtendedConnectivityFingerprints 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>ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getdescription">GetDescription</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a>
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32 , <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>, <a href="#setneighborhoodradius">SetNeighborhoodRadius</a>
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33 , <a href="#stringifyextendedconnectivityfingerprints">StringifyExtendedConnectivityFingerprints</a>
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34 </p><p><strong>ExtendedConnectivityFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn
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35 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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36 in <strong>ExtendedConnectivityFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's
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37 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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38 <div class="OptionsBox">
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39 Set<PropertyName>(<PropertyValue>);
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40 <br/> $PropertyValue = Get<PropertyName>();
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41 <br/> Delete<PropertyName>();</div>
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42 <p>The current release of MayaChemTools supports generation of <strong>ExtendedConnectivityFingerprints</strong>
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43 corresponding to following <strong>AtomtomIdentifierTypes</strong>:</p>
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44 <div class="OptionsBox">
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45 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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46 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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47 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
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48 <p>Based on the values specified for <strong>AtomIdentifierType</strong>, <strong>AtomicInvariantsToUse</strong>
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49 and <strong>FunctionalClassesToUse</strong>, initial atom types are assigned to all non-hydrogen atoms in
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50 a molecule and these atom types strings are converted into initial atom identifier integers using
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51 <strong>TextUtil::HashCode</strong> function. The duplicate atom identifiers are removed.</p>
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52 <p>For <strong>NeighborhoodRadius</strong> value of <em>0</em>, the initial set of unique atom identifiers comprises
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53 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
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54 atom up-to specified <strong>NeighborhoodRadius</strong> value. For each non-hydrogen central atom
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55 at a specific radius, its neighbors at next radius level along with their bond orders and previously
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56 calculated atom identifiers are collected which in turn are used to generate a new integer
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57 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
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58 followed by atom identifiers to make these values graph invariant.</p>
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59 <p>After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
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60 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
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61 value generated using <strong>TextUtil::HashCode</strong> are tracked by keeping the atom identifiers at
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62 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
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63 radius are also tracked by identifying equivalent atom and bonds corresponding to substructures
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64 used for generating atom identifier and keeping integer atom identifier with lowest value.</p>
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65 <p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>Type</strong>, the duplicate identifiers are
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66 removed from the list and the unique atom identifiers constitute the extended connectivity
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67 fingerprints of a molecule.</p>
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68 <p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>Type</strong>, the occurrence of each
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69 unique atom identifiers appears is counted and the unique atom identifiers along with their
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70 count constitute the extended connectivity fingerprints of a molecule.</p>
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71 <p>For <em>ExtendedConnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, the unique atom identifiers
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72 are used as a random number seed to generate a random integer value between 0 and <strong>--Size</strong> which
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73 in turn is used to set corresponding bits in the fingerprint bit-vector string.</p>
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74 <p>The current release of MayaChemTools generates the following types of extended connectivity
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75 fingerprints vector strings:</p>
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76 <div class="OptionsBox">
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77 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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78 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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79 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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80 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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81 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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82 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
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83 <div class="OptionsBox">
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84 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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85 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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86 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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87 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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88 <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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89 <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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90 <div class="OptionsBox">
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91 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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92 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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93 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
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94 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
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95 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
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96 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
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97 <div class="OptionsBox">
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98 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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99 <br/> es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
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100 <br/> 0300000091000004000000020000100000000124008200020000000040020000000000
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101 <br/> 2080000000820040010020000000008040000000000080001000000000400000000000
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102 <br/> 4040000090000061010000000800200000000000001400000000020080000000000020
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103 <br/> 00008020200000408000</div>
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104 <div class="OptionsBox">
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105 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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106 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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107 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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108 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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109 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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110 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
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111 <div class="OptionsBox">
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112 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
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113 <br/> Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
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114 <br/> 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
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115 <br/> 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
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116 <br/> 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
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117 <br/> 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1</div>
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118 <div class="OptionsBox">
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119 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
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120 <br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
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121 <br/> 0000000001000100000000001000000000000000000000000000000000101000000010
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122 <br/> 0000001000000000010000000000000000000000000000000000000000000000000100
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123 <br/> 0000000000001000000000000001000000000001001000000000000000000000000000
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124 <br/> 0000000000000000100000000000001000000000000000000000000000000000000...</div>
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125 <div class="OptionsBox">
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126 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
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127 <br/> lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
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128 <br/> 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
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129 <br/> 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
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130 <br/> 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
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131 <br/> 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...</div>
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132 <div class="OptionsBox">
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133 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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134 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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135 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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136 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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137 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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138 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
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139 <div class="OptionsBox">
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140 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
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141 <br/> haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
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142 <br/> 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
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143 <br/> 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
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144 <br/> 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
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145 <br/> 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...</div>
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146 <div class="OptionsBox">
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147 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
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148 <br/> aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
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149 <br/> 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
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150 <br/> 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
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151 <br/> 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
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152 <br/> 41915747 679881756 721736571 794256218 908276640 992898760 10987549...</div>
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153 <div class="OptionsBox">
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154 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
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155 <br/> aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
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156 <br/> 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
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157 <br/> 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
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158 <br/> 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
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159 <br/> 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...</div>
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160 <div class="OptionsBox">
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161 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
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162 <br/> NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
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163 <br/> 700688206 265614156 363161397 681332588 810600886 885767127 950172500
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164 <br/> 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
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165 <br/> 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
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166 <br/> 654 256360355 279492740 291251259 317592700 333763396 972105960 101...</div>
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167 <div class="OptionsBox">
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168 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
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169 <br/> umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
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170 <br/> 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
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171 <br/> 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
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172 <br/> 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
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173 <br/> 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...</div>
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174 <p>
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175 </p>
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176 <h2>METHODS</h2>
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177 <dl>
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178 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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179 <dd>
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180 <div class="OptionsBox">
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181 $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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182 %NamesAndValues);</div>
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183 <p>Using specified <em>ExtendedConnectivityFingerprints</em> property names and values hash, <strong>new</strong>
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184 method creates a new object and returns a reference to newly created <strong>ExtendedConnectivityFingerprints</strong>
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185 object. By default, the following properties are initialized:</p>
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186 <div class="OptionsBox">
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187 Molecule = ''
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188 <br/> Type = 'ExtendedConnectivity'
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189 <br/> NeighborhoodRadius = 2
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190 <br/> AtomIdentifierType = ''
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191 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
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192 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
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193 <p>Examples:</p>
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194 <div class="OptionsBox">
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195 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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196 'Molecule' => $Molecule,
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197 'AtomIdentifierType' =>
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198 'AtomicInvariantsAtomTypes');</div>
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199 <div class="OptionsBox">
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200 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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201 'Type' => 'ExtendedConnectivityCount',
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202 'Molecule' => $Molecule,
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203 'AtomIdentifierType' =>
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204 'AtomicInvariantsAtomTypes');</div>
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205 <div class="OptionsBox">
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206 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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207 'Type' => 'ExtendedConnectivityBits',
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208 'Molecule' => $Molecule,
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209 'Size' => 1024,
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210 'AtomIdentifierType' =>
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211 'AtomicInvariantsAtomTypes');</div>
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212 <div class="OptionsBox">
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213 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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214 'Type' => 'ExtendedConnectivity',
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215 'Molecule' => $Molecule,
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216 'NeighborhoodRadius' => 2,
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217 'AtomIdentifierType' =>
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218 'AtomicInvariantsAtomTypes',
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219 'AtomicInvariantsToUse' =>
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220 ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );</div>
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221 <div class="OptionsBox">
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222 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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223 'Type' => 'ExtendedConnectivity',
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224 'Molecule' => $Molecule,
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225 'NeighborhoodRadius' => 2,
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226 'AtomIdentifierType' =>
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227 'FunctionalClassAtomTypes',
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228 'FunctionalClassesToUse' =>
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229 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div>
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230 <div class="OptionsBox">
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231 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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232 'Type' => 'ExtendedConnectivity',
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233 'Molecule' => $Molecule,;
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234 'AtomIdentifierType' =>
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235 'MMFF94AtomTypes');</div>
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236 <div class="OptionsBox">
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237 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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238 'Type' => 'ExtendedConnectivityCount',
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239 'Molecule' => $Molecule,;
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240 'AtomIdentifierType' =>
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241 'MMFF94AtomTypes');</div>
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242 <div class="OptionsBox">
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243 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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244 'Type' => 'ExtendedConnectivityCount',
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245 'Molecule' => $Molecule,;
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246 'AtomIdentifierType' =>
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247 'SLogPAtomTypes');</div>
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248 <div class="OptionsBox">
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249 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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250 'Type' => 'ExtendedConnectivity',
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251 'Molecule' => $Molecule,;
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252 'AtomIdentifierType' =>
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253 'SLogPAtomTypes');</div>
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254 <div class="OptionsBox">
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255 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
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256 'Type' => 'ExtendedConnectivity',
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257 'Molecule' => $Molecule,;
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258 'AtomIdentifierType' =>
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259 'SYBYLAtomTypes');</div>
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260 <div class="OptionsBox">
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261 $ExtendedConnectivityFingerprints->GenerateFingerprints();
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262 <br/> print "$ExtendedConnectivityFingerprints\n";</div>
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263 </dd>
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264 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
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265 <dd>
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266 <div class="OptionsBox">
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267 $ExtendedConnectivityFingerprints->GenerateFingerprints();</div>
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268 <p>Generates extended connectivity fingerprints and returns <em>ExtendedConnectivityFingerprints</em>.</p>
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269 </dd>
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270 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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271 <dd>
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272 <div class="OptionsBox">
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273 $Description = $ExtendedConnectivityFingerprints->GetDescription();</div>
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274 <p>Returns a string containing description of extended connectivity fingerprints
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275 fingerprints.</p>
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276 </dd>
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277 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
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278 <dd>
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279 <div class="OptionsBox">
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280 $ExtendedConnectivityFingerprints->SetAtomIdentifierType($IdentifierType);</div>
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281 <p>Sets atom <em>IdentifierType</em> to use during extended connectivity fingerprints generation and
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282 returns <em>ExtendedConnectivityFingerprints</em>.</p>
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283 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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284 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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285 TPSAAtomTypes, UFFAtomTypes</em>.</p>
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286 </dd>
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287 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
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288 <dd>
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289 <div class="OptionsBox">
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290 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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291 <br/> $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(@Values);</div>
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292 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
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293 for extended connectivity fingerprints generation and returns <em>ExtendedConnectivityFingerprints</em>.</p>
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294 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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295 H, Ar, RA, FC, MN, SM</em>. Default value [ Ref 24 ]: <em>AS,X,BO,H,FC,MN</em>.</p>
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296 <p>The atomic invariants abbreviations correspond to:</p>
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297 <div class="OptionsBox">
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298 AS = Atom symbol corresponding to element symbol</div>
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299 <div class="OptionsBox">
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300 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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301 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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302 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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303 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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304 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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305 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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306 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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307 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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308 <br/> RA = Ring atom annotation indicating whether atom is a ring
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309 <br/> FC<+n/-n> = Formal charge assigned to atom
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310 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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311 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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312 3 (triplet)</div>
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313 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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314 <div class="OptionsBox">
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315 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div>
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316 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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317 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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318 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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319 are also allowed:</p>
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320 <div class="OptionsBox">
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321 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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322 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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323 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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324 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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325 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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326 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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327 <br/> H : NumOfImplicitAndExplicitHydrogens
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328 <br/> Ar : Aromatic
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329 <br/> RA : RingAtom
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330 <br/> FC : FormalCharge
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331 <br/> MN : MassNumber
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332 <br/> SM : SpinMultiplicity</div>
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333 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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334 atom types.</p>
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335 </dd>
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336 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
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337 <dd>
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338 <div class="OptionsBox">
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339 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse($ValuesRef);
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340 <br/> $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(@Values);</div>
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341 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
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342 for extended connectivity fingerprints generation and returns <em>ExtendedConnectivityFingerprints</em>.</p>
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343 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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344 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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345 <p>The functional class abbreviations correspond to:</p>
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346 <div class="OptionsBox">
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347 HBD: HydrogenBondDonor
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348 <br/> HBA: HydrogenBondAcceptor
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349 <br/> PI : PositivelyIonizable
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350 <br/> NI : NegativelyIonizable
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351 <br/> Ar : Aromatic
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352 <br/> Hal : Halogen
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353 <br/> H : Hydrophobic
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354 <br/> RA : RingAtom
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355 <br/> CA : ChainAtom</div>
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356 <div class="OptionsBox">
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357 Functional class atom type specification for an atom corresponds to:</div>
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358 <div class="OptionsBox">
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359 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
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360 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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361 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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362 <div class="OptionsBox">
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363 HydrogenBondDonor: NH, NH2, OH
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364 <br/> HydrogenBondAcceptor: N[!H], O
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365 <br/> PositivelyIonizable: +, NH2
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366 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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367 </dd>
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368 <dt><strong><a name="setneighborhoodradius" class="item"><strong>SetNeighborhoodRadius</strong></a></strong></dt>
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369 <dd>
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370 <div class="OptionsBox">
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371 $ExtendedConnectivityFingerprints->SetNeighborhoodRadius($Radius);</div>
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372 <p>Sets neighborhood radius to use during extended connectivity fingerprints generation and
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373 returns <em>ExtendedConnectivityFingerprints</em>.</p>
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374 </dd>
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375 <dt><strong><a name="stringifyextendedconnectivityfingerprints" class="item"><strong>StringifyExtendedConnectivityFingerprints</strong></a></strong></dt>
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376 <dd>
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377 <div class="OptionsBox">
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378 $String = $Fingerprints->StringifyExtendedConnectivityFingerprints();</div>
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379 <p>Returns a string containing information about <em>ExtendedConnectivityFingerprints</em> object.</p>
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380 </dd>
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381 </dl>
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382 <p>
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383 </p>
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384 <h2>AUTHOR</h2>
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385 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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386 <p>
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387 </p>
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388 <h2>SEE ALSO</h2>
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389 <p><a href="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, 
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390 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>, 
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391 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, 
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392 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, 
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393 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
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394 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
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395 </p>
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396 <p>
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397 </p>
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398 <h2>COPYRIGHT</h2>
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399 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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400 <p>This file is part of MayaChemTools.</p>
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401 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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402 the terms of the GNU Lesser General Public License as published by the Free
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403 Software Foundation; either version 3 of the License, or (at your option)
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404 any later version.</p>
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405 <p> </p><p> </p><div class="DocNav">
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406 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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407 <tr align="left" valign="top"><td width="33%" align="left"><a href="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./Fingerprints.html" title="Fingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::ExtendedConnectivityFingerprints.pm</strong></td></tr>
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408 </table>
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409 </div>
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410 <br />
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411 <center>
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412 <img src="../../images/h2o2.png">
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413 </center>
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414 </body>
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415 </html>
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