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3 <title>MayaChemTools:Documentation:Fingerprints::AtomNeighborhoodsFingerprints.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="./FileUtil.html" title="FileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::AtomNeighborhoodsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/AtomNeighborhoodsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AtomNeighborhoodsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AtomNeighborhoodsFingerprints.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>AtomNeighborhoodsFingerprints</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::AtomNeighborhoodsFingerprints;</p>
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26 <p>use Fingerprints::AtomNeighborhoodsFingerprints 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>AtomNeighborhoodsFingerprints</strong> [ Ref 53-56, Ref 73 ] 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="#setmaxneighborhoodradius">SetMaxNeighborhoodRadius</a>
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33 , <a href="#setminneighborhoodradius">SetMinNeighborhoodRadius</a>, <a href="#stringifyatomneighborhoodsfingerprints">StringifyAtomNeighborhoodsFingerprints</a>
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34 </p><p><strong>AtomNeighborhoodsFingerprints</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>AtomNeighborhoodsFingerprints</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>AtomNeighborhoodsFingerprints</strong>
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43 corresponding to following <strong>AtomIdentifierTypes</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> along with other specified
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49 sucb as <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse</strong>, initial atom types are
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50 assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
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51 around each non-hydrogen central atom corresponding to radii between specified values
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52 <strong>MinNeighborhoodRadius</strong> and <strong>MaxNeighborhoodRadius</strong>, unique atom types at each radii
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53 level are counted and an atom neighborhood identifier is generated.</p>
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54 <p>The format of an atom neighborhood identifier around a central non-hydrogen atom at a
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55 specific radius is:</p>
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56 <div class="OptionsBox">
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57 NR<n>-<AtomType>-ATC<n></div>
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58 <div class="OptionsBox">
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59 NR: Neighborhood radius
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60 <br/> AtomType: Assigned atom type
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61 <br/> ATC: Atom type count</div>
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62 <p>The atom neighborhood identifier for non-hydrogen central atom corresponding to all specified radii
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63 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:</p>
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64 <div class="OptionsBox">
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65 NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...</div>
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66 <p>The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
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67 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.</p>
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68 <p>The current release of MayaChemTools generates the following types of atom neighborhoods
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69 fingerprints vector strings:</p>
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70 <div class="OptionsBox">
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71 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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72 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
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73 <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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74 <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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75 <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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76 <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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77 <div class="OptionsBox">
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78 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
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79 <br/> adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
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80 <br/> NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
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81 <br/> _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
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82 <br/> C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
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83 <br/> 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...</div>
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84 <div class="OptionsBox">
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85 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
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86 <br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
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87 <br/> NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
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88 <br/> 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
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89 <br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
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90 <br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...</div>
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91 <div class="OptionsBox">
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92 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
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93 <br/> s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
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94 <br/> ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
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95 <br/> C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
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96 <br/> R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
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97 <br/> TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...</div>
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98 <div class="OptionsBox">
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99 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
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100 <br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
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101 <br/> 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
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102 <br/> 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
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103 <br/> 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
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104 <br/> C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...</div>
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105 <div class="OptionsBox">
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106 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
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107 <br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
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108 <br/> CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
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109 <br/> NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
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110 <br/> ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
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111 <br/> 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...</div>
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112 <div class="OptionsBox">
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113 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
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114 <br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
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115 <br/> -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
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116 <br/> O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
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117 <br/> ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
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118 <br/> C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...</div>
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119 <div class="OptionsBox">
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120 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
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121 <br/> s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
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122 <br/> -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
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123 <br/> e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
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124 <br/> ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
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125 <br/> TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...</div>
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126 <div class="OptionsBox">
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127 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
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128 <br/> 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
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129 <br/> _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
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130 <br/> C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
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131 <br/> 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
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132 <br/> -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...</div>
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133 <p>
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134 </p>
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135 <h2>METHODS</h2>
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136 <dl>
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137 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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138 <dd>
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139 <div class="OptionsBox">
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140 $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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141 %NamesAndValues);</div>
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142 <p>Using specified <em>AtomNeighborhoodsFingerprints</em> property names and values hash, <strong>new</strong>
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143 method creates a new object and returns a reference to newly created <strong>AtomNeighborhoodsFingerprints</strong>
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144 object. By default, the following properties are initialized:</p>
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145 <div class="OptionsBox">
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146 Molecule = ''
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147 <br/> Type = 'AtomNeighborhoods'
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148 <br/> MinNeighborhoodRadius = 0
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149 <br/> MaxNeighborhoodRadius = 2
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150 <br/> AtomIdentifierType = ''
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151 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
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152 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
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153 <p>Examples:</p>
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154 <div class="OptionsBox">
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155 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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156 'Molecule' => $Molecule,
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157 'AtomIdentifierType' =>
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158 "AtomicInvariantsAtomTypes");</div>
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159 <div class="OptionsBox">
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160 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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161 'Molecule' => $Molecule,
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162 'MinNeighborhoodRadius' => 0,
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163 'MaxNeighborhoodRadius' => 2,
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164 'AtomIdentifierType' =>
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165 'AtomicInvariantsAtomTypes',
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166 'AtomicInvariantsToUse' =>
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167 ['AS', 'X', 'BO', 'H', 'FC'] );</div>
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168 <div class="OptionsBox">
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169 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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170 'Molecule' => $Molecule,
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171 'AtomIdentifierType' =>
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172 'SYBYLAtomTypes');</div>
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173 <div class="OptionsBox">
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174 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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175 'Molecule' => $Molecule,
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176 'AtomIdentifierType' =>
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177 'MMFF94AtomTypes');</div>
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178 <div class="OptionsBox">
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179 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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180 'Molecule' => $Molecule,
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181 'AtomIdentifierType' =>
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182 'AtomicInvariantsAtomTypes');</div>
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183 <div class="OptionsBox">
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184 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
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185 'Molecule' => $Molecule,
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186 'MinNeighborhoodRadius' => 0,
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187 'MaxNeighborhoodRadius' => 2,
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188 'AtomIdentifierType' =>
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189 'FunctionalClassAtomTypes',
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190 'FunctionalClassesToUse' =>
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191 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div>
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192 <div class="OptionsBox">
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193 $AtomNeighborhoodsFingerprints->GenerateFingerprints();
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194 <br/> print "$AtomNeighborhoodsFingerprints\n";</div>
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195 </dd>
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196 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
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197 <dd>
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198 <div class="OptionsBox">
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199 $AtomNeighborhoodsFingerprints->GenerateFingerprints();</div>
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200 <p>Generates atom neighborhood fingerprints and returns <em>AtomNeighborhoodsFingerprints</em>.</p>
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201 </dd>
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202 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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203 <dd>
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204 <div class="OptionsBox">
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205 $Description = $AtomNeighborhoodsFingerprints->GetDescription();</div>
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206 <p>Returns a string containing description of atom neighborhood fingerprints.</p>
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207 </dd>
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208 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
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209 <dd>
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210 <div class="OptionsBox">
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211 $AtomNeighborhoodsFingerprints->SetAtomIdentifierType($IdentifierType);</div>
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212 <p>Sets atom <em>IdentifierType</em> to use during atom neighborhood fingerprints generation and
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213 returns <em>AtomNeighborhoodsFingerprints</em>.</p>
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214 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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215 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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216 TPSAAtomTypes, UFFAtomTypes</em>.</p>
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217 </dd>
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218 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
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219 <dd>
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220 <div class="OptionsBox">
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221 $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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222 <br/> $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse(@Values);</div>
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223 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
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224 for atom neighborhood fingerprints generation and returns <em>AtomNeighborhoodsFingerprints</em>.</p>
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225 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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226 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
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227 <p>The atomic invariants abbreviations correspond to:</p>
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228 <div class="OptionsBox">
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229 AS = Atom symbol corresponding to element symbol</div>
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230 <div class="OptionsBox">
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231 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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232 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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233 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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234 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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235 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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236 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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237 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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238 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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239 <br/> RA = Ring atom annotation indicating whether atom is a ring
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240 <br/> FC<+n/-n> = Formal charge assigned to atom
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241 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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242 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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243 3 (triplet)</div>
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244 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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245 <div class="OptionsBox">
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246 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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247 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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248 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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249 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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250 are also allowed:</p>
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251 <div class="OptionsBox">
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252 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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253 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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254 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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255 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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256 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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257 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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258 <br/> H : NumOfImplicitAndExplicitHydrogens
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259 <br/> Ar : Aromatic
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260 <br/> RA : RingAtom
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261 <br/> FC : FormalCharge
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262 <br/> MN : MassNumber
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263 <br/> SM : SpinMultiplicity</div>
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264 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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265 atom types.</p>
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266 </dd>
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267 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
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268 <dd>
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269 <div class="OptionsBox">
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270 $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse($ValuesRef);
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271 <br/> $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse(@Values);</div>
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272 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
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273 for atom neighborhoods fingerprints generation and returns <em>AtomNeighborhoodsFingerprints</em>.</p>
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274 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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275 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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276 <p>The functional class abbreviations correspond to:</p>
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277 <div class="OptionsBox">
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278 HBD: HydrogenBondDonor
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279 <br/> HBA: HydrogenBondAcceptor
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280 <br/> PI : PositivelyIonizable
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281 <br/> NI : NegativelyIonizable
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282 <br/> Ar : Aromatic
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283 <br/> Hal : Halogen
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284 <br/> H : Hydrophobic
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285 <br/> RA : RingAtom
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286 <br/> CA : ChainAtom</div>
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287 <div class="OptionsBox">
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288 Functional class atom type specification for an atom corresponds to:</div>
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289 <div class="OptionsBox">
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290 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
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291 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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292 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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293 <div class="OptionsBox">
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294 HydrogenBondDonor: NH, NH2, OH
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295 <br/> HydrogenBondAcceptor: N[!H], O
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296 <br/> PositivelyIonizable: +, NH2
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297 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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298 </dd>
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299 <dt><strong><a name="setmaxneighborhoodradius" class="item"><strong>SetMaxNeighborhoodRadius</strong></a></strong></dt>
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300 <dd>
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301 <div class="OptionsBox">
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302 $AtomNeighborhoodsFingerprints->SetMaxNeighborhoodRadius($Radius);</div>
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303 <p>Sets maximum neighborhood radius to use during atom neighborhood fingerprints generation and
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304 returns <em>AtomNeighborhoodsFingerprints</em>.</p>
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305 </dd>
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306 <dt><strong><a name="setminneighborhoodradius" class="item"><strong>SetMinNeighborhoodRadius</strong></a></strong></dt>
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307 <dd>
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308 <div class="OptionsBox">
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309 $AtomNeighborhoodsFingerprints->SetMinNeighborhoodRadius($Radius);</div>
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310 <p>Sets minimum neighborhood radius to use during atom neighborhood fingerprints generation and
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311 returns <em>AtomNeighborhoodsFingerprints</em>.</p>
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312 </dd>
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313 <dt><strong><a name="stringifyatomneighborhoodsfingerprints" class="item"><strong>StringifyAtomNeighborhoodsFingerprints</strong></a></strong></dt>
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314 <dd>
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315 <div class="OptionsBox">
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316 $String = $Fingerprints->StringifyAtomNeighborhoodsFingerprints();</div>
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317 <p>Returns a string containing information about <em>AtomNeighborhoodsFingerprints</em> object.</p>
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318 </dd>
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319 </dl>
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320 <p>
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321 </p>
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322 <h2>AUTHOR</h2>
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323 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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324 <p>
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325 </p>
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326 <h2>SEE ALSO</h2>
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327 <p><a href="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, 
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328 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, 
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329 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, 
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330 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
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331 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
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332 </p>
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333 <p>
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334 </p>
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335 <h2>COPYRIGHT</h2>
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336 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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337 <p>This file is part of MayaChemTools.</p>
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338 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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339 the terms of the GNU Lesser General Public License as published by the Free
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340 Software Foundation; either version 3 of the License, or (at your option)
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341 any later version.</p>
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342 <p> </p><p> </p><div class="DocNav">
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343 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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344 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FileUtil.html" title="FileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::AtomNeighborhoodsFingerprints.pm</strong></td></tr>
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345 </table>
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346 </div>
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347 <br />
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348 <center>
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349 <img src="../../images/h2o2.png">
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350 </center>
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351 </body>
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352 </html>
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