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3 <title>MayaChemTools:Documentation:Fingerprints::PathLengthFingerprints.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="./MACCSKeys.html" title="MACCSKeys.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::PathLengthFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/PathLengthFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/PathLengthFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/PathLengthFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/PathLengthFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/PathLengthFingerprints.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>PathLengthFingerprints</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::PathLengthFingerprints;</p>
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26 <p>use Fingerprints::PathLengthFingerprints 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>PathLengthFingerprints</strong> 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="#setmaxlength">SetMaxLength</a>
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33 , <a href="#setminlength">SetMinLength</a>, <a href="#setnumofbitstosetperpath">SetNumOfBitsToSetPerPath</a>, <a href="#settype">SetType</a>
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34 , <a href="#stringifypathlengthfingerprints">StringifyPathLengthFingerprints</a>
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35 </p><p><strong>PathLengthFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn
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36 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
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37 in <strong>PathLengthFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's
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38 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
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39 <div class="OptionsBox">
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40 Set<PropertyName>(<PropertyValue>);
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41 <br/> $PropertyValue = Get<PropertyName>();
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42 <br/> Delete<PropertyName>();</div>
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43 <p>The current release of MayaChemTools supports generation of <strong>AtomTypesFingerpritns</strong>
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44 corresponding to following <strong>AtomtomIdentifierTypes</strong>:</p>
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45 <div class="OptionsBox">
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46 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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47 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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48 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
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49 <p>Based on the values specified for <strong>Type</strong>, <strong>AtomtomIdentifierTypes</strong>, <strong>MinPathLength</strong> and
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50 <strong>MaxPathLength</strong>, all appropriate atom paths are generated for each atom in the molecule
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51 and collected in a list and the list is filtered to remove any structurally duplicate paths as
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52 indicated by the value of <strong>UseUniquePaths</strong>.</p>
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53 <p>For molecules containing rings, atom paths starting from each atom can be traversed in four
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54 different ways:</p>
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55 <div class="OptionsBox">
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56 o Atom paths without any rings and sharing of bonds in traversed paths.
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57 <br/> o Atom paths containing rings and without any sharing of bonds in
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58 traversed paths
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59 <br/> o All possible atom paths without any rings and sharing of bonds in
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60 traversed paths
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61 <br/> o All possible atom paths containing rings and with sharing of bonds in
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62 traversed paths.</div>
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63 <p>Atom path traversal is terminated at the last ring atom. For molecules containing no rings,
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64 first two and last two types described above are equivalent.</p>
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65 <p><strong>AllowSharedBonds</strong> and <strong>AllowRings</strong> allow generation of different types of paths
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66 to be used for fingerprints generation.</p>
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67 <p>The combination of <strong>AllowSharedBonds</strong>, <strong>AllowRings</strong>, and <strong>UseBondSymbols</strong> allows generation of
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68 8 different types of path length fingerprints:</p>
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69 <div class="OptionsBox">
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70 AllowSharedBonds AllowRings UseBondSymbols</div>
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71 <div class="OptionsBox">
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72 0 0 1 - AtomPathsNoCyclesWithBondSymbols
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73 <br/> 0 1 1 - AtomPathsWithCyclesWithBondSymbols</div>
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74 <div class="OptionsBox">
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75 1 0 1 - AllAtomPathsNoCyclesWithBondSymbols
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76 <br/> 1 1 1 - AllAtomPathsWithCyclesWithBondSymbols
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77 [ DEFAULT ]</div>
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78 <div class="OptionsBox">
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79 0 0 0 - AtomPathsNoCyclesNoBondSymbols
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80 <br/> 0 1 0 - AtomPathsWithCyclesNoBondSymbols</div>
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81 <div class="OptionsBox">
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82 1 0 0 - AllAtomPathsNoCyclesNoBondSymbols
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83 <br/> 1 1 0 - AllAtomPathsWithCyclesNoWithBondSymbols</div>
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84 <p>Additionally, possible values for option <strong>--AtomIdentifierType</strong> in conjunction with corresponding
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85 specified values for <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse </strong> changes the nature
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86 of atom path length strings and the fingerprints.</p>
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87 <p>For each atom path in the filtered atom paths list, an atom path string is created using value of
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88 <strong>AtomIdentifierType</strong> and specified values to use for a particular atom identifier type.
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89 Value of <strong>UseBondSymbols</strong> controls whether bond order symbols are used during generation
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90 of atom path string. Atom symbol corresponds to element symbol and characters used to represent
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91 bond order are: <em>1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order value</em>. By default,
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92 bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings
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93 results in fingerprints which correspond purely to atom paths without considering bonds.</p>
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94 <p><strong>UseUniquePaths</strong> controls the removal of structurally duplicate atom path strings are removed
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95 from the list.</p>
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96 <p>For <em>PathLengthBits</em> value of <strong>Type</strong>, each atom path is hashed to a 32 bit unsigned
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97 integer key using <strong>TextUtil::HashCode</strong> function. Using the hash key as a seed for a random number
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98 generator, a random integer value between 0 and <strong>Size</strong> is used to set corresponding bits
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99 in the fingerprint bit-vector string. Value of <strong>NumOfBitsToSetPerPaths</strong> option controls the number
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100 of time a random number is generated to set corresponding bits.</p>
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101 <p>For <em> PathLengthCount</em> value of <strong>Type</strong>n, the number of times an atom path appears
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102 is tracked and a fingerprints count-string corresponding to count of atom paths is generated.</p>
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103 <p>The current release of MayaChemTools generates the following types of path length
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104 fingerprints bit-vector and vector strings:</p>
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105 <div class="OptionsBox">
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106 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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107 <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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108 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000
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109 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100
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110 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101
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111 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div>
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112 <div class="OptionsBox">
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113 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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114 <br/> th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
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115 <br/> 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
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116 <br/> 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
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117 <br/> 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
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118 <br/> 6ea05280140069c780290c43</div>
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119 <div class="OptionsBox">
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120 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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121 <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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122 <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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123 <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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124 <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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125 <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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126 <div class="OptionsBox">
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127 FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen
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128 <br/> gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_
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129 <br/> 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3
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130 <br/> 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C
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131 <br/> _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C
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132 <br/> _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ...</div>
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133 <div class="OptionsBox">
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134 FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
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135 <br/> h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
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136 <br/> O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
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137 <br/> aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
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138 <br/> 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
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139 <br/> sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...</div>
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140 <div class="OptionsBox">
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141 FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1
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142 <br/> :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1
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143 <br/> HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar:
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144 <br/> Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI
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145 <br/> 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr
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146 <br/> 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...</div>
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147 <div class="OptionsBox">
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148 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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149 <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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150 <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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151 <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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152 <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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153 <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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154 <div class="OptionsBox">
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155 FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength
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156 <br/> 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C
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157 <br/> 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1
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158 <br/> 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18
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159 <br/> :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1
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160 <br/> C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...</div>
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161 <div class="OptionsBox">
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162 FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength
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163 <br/> 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1
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164 <br/> N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C.
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165 <br/> ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C
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166 <br/> .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C
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167 <br/> .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3...</div>
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168 <div class="OptionsBox">
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169 FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8
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170 <br/> ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O
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171 <br/> 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N
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172 <br/> oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N
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173 <br/> one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20
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174 <br/> None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...</div>
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175 <div class="OptionsBox">
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176 FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8;
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177 <br/> 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_
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178 <br/> 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_
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179 <br/> 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_
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180 <br/> 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3
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181 <br/> 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3...</div>
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182 <p>
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183 </p>
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184 <h2>METHODS</h2>
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185 <dl>
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186 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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187 <dd>
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188 <div class="OptionsBox">
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189 $NewPathLengthFingerprints = new PathLengthFingerprints(
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190 %NamesAndValues);</div>
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191 <p>Using specified <em>PathLengthFingerprints</em> property names and values hash, <strong>new</strong> method creates a new object
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192 and returns a reference to newly created <strong>PathLengthFingerprints</strong> object. By default, the following properties are
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193 initialized:</p>
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194 <div class="OptionsBox">
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195 Molecule = '';
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196 <br/> Type = ''
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197 <br/> Size = 1024
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198 <br/> MinSize = 32
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199 <br/> MaxSize = 2**32
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200 <br/> NumOfBitsToSetPerPath = 1
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201 <br/> MinLength = 1
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202 <br/> MaxLength = 8
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203 <br/> AllowSharedBonds = 1
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204 <br/> AllowRings = 1
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205 <br/> UseBondSymbols = 1
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206 <br/> UseUniquePaths = ''
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207 <br/> AtomIdentifierType = ''
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208 <br/> SetAtomicInvariantsToUse = ['AS']
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209 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
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210 <p>Examples:</p>
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211 <div class="OptionsBox">
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212 $PathLengthFingerprints = new PathLengthFingerprints(
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213 'Molecule' => $Molecule,
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214 'Type' => 'PathLengthBits',
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215 'AtomIdentifierType' =
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216 'AtomicInvariantsAtomTypes');</div>
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217 <div class="OptionsBox">
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218 $PathLengthFingerprints = new PathLengthFingerprints(
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219 'Molecule' => $Molecule,
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220 'Type' => 'PathLengthBits',
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221 'Size' => 1024,
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222 'MinLength' => 1,
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223 'MaxLength' => 8,
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224 'AllowRings' => 1,
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225 'AllowSharedBonds' => 1,
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226 'UseBondSymbols' => 1,
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227 'UseUniquePaths' => 1,
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228 'AtomIdentifierType' =
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229 'AtomicInvariantsAtomTypes',
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230 'AtomicInvariantsToUse' => ['AS']);</div>
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231 <div class="OptionsBox">
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232 $PathLengthFingerprints = new PathLengthFingerprints(
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233 'Molecule' => $Molecule,
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234 'Type' => 'PathLengthCount',
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235 'MinLength' => 1,
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236 'MaxLength' => 8,
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237 'AllowRings' => 1,
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238 'AllowSharedBonds' => 1,
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239 'UseBondSymbols' => 1,
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240 'UseUniquePaths' => 1,
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241 'AtomIdentifierType' =>
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242 'AtomicInvariantsAtomTypes',
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243 'AtomicInvariantsToUse' => ['AS']);</div>
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244 <div class="OptionsBox">
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245 $PathLengthFingerprints = new PathLengthFingerprints(
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246 'Molecule' => $Molecule,
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247 'Type' => 'PathLengthBits',
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248 'AtomIdentifierType' =
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249 'SLogPAtomTypes');</div>
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250 <div class="OptionsBox">
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251 $PathLengthFingerprints = new PathLengthFingerprints(
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252 'Molecule' => $Molecule,
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253 'Type' => 'PathLengthCount',
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254 'AtomIdentifierType' =
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255 'SYBYLAtomTypes');</div>
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256 <div class="OptionsBox">
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257 $PathLengthFingerprints = new PathLengthFingerprints(
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258 'Molecule' => $Molecule,
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259 'Type' => 'PathLengthBits',
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260 'AtomIdentifierType' =
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261 'FunctionalClassAtomTypes',
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262 'FunctionalClassesToUse' => ['HBD', 'HBA', 'Ar']);</div>
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263 <div class="OptionsBox">
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264 $PathLengthFingerprints->GenerateFingerprints();
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265 <br/> print "$PathLengthFingerprints\n";</div>
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266 </dd>
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267 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
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268 <dd>
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269 <div class="OptionsBox">
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270 $Description = $PathLengthFingerprints->GetDescription();</div>
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271 <p>Returns a string containing description of path length fingerprints.</p>
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272 </dd>
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273 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
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274 <dd>
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275 <div class="OptionsBox">
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276 $PathLengthFingerprints->GenerateFingerprints();</div>
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277 <p>Generates path length fingerprints and returns <em>PathLengthFingerprints</em>.</p>
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278 </dd>
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279 <dt><strong><a name="setmaxlength" class="item"><strong>SetMaxLength</strong></a></strong></dt>
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280 <dd>
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281 <div class="OptionsBox">
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282 $PathLengthFingerprints->SetMaxLength($Length);</div>
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283 <p>Sets maximum value of atom path length to be used during atom path length fingerprints
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284 generation and returns <em>PathLengthFingerprints</em></p>
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285 </dd>
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286 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
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287 <dd>
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288 <div class="OptionsBox">
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289 $PathLengthFingerprints->SetAtomIdentifierType();</div>
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290 <p>Sets atom <em>IdentifierType</em> to use during path length fingerprints generation and
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291 returns <em>PathLengthFingerprints</em>.</p>
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292 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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293 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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294 TPSAAtomTypes, UFFAtomTypes</em>.</p>
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295 </dd>
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296 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
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297 <dd>
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298 <div class="OptionsBox">
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299 $PathLengthFingerprints->SetAtomicInvariantsToUse($ValuesRef);
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300 <br/> $PathLengthFingerprints->SetAtomicInvariantsToUse(@Values);</div>
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301 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
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302 for path length fingerprints generation and returns <em>PathLengthFingerprints</em>.</p>
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303 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
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304 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS</em>.</p>
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305 <p>The atomic invariants abbreviations correspond to:</p>
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306 <div class="OptionsBox">
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307 AS = Atom symbol corresponding to element symbol</div>
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308 <div class="OptionsBox">
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309 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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310 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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311 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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312 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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313 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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314 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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315 <br/> H<n> = Number of implicit and explicit hydrogens for atom
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316 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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317 <br/> RA = Ring atom annotation indicating whether atom is a ring
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318 <br/> FC<+n/-n> = Formal charge assigned to atom
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319 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
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320 <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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321 3 (triplet)</div>
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322 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
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323 <div class="OptionsBox">
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324 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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325 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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326 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
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327 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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328 are also allowed:</p>
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329 <div class="OptionsBox">
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330 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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331 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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332 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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333 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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334 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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335 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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336 <br/> H : NumOfImplicitAndExplicitHydrogens
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337 <br/> Ar : Aromatic
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338 <br/> RA : RingAtom
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339 <br/> FC : FormalCharge
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340 <br/> MN : MassNumber
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341 <br/> SM : SpinMultiplicity</div>
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342 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
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343 atom types.</p>
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344 </dd>
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345 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
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346 <dd>
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347 <div class="OptionsBox">
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348 $PathLengthFingerprints->SetFunctionalClassesToUse($ValuesRef);
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349 <br/> $PathLengthFingerprints->SetFunctionalClassesToUse(@Values);</div>
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350 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
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351 for path length fingerprints generation and returns <em>PathLengthFingerprints</em>.</p>
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352 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
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353 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
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354 <p>The functional class abbreviations correspond to:</p>
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355 <div class="OptionsBox">
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356 HBD: HydrogenBondDonor
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357 <br/> HBA: HydrogenBondAcceptor
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358 <br/> PI : PositivelyIonizable
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359 <br/> NI : NegativelyIonizable
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360 <br/> Ar : Aromatic
|
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361 <br/> Hal : Halogen
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362 <br/> H : Hydrophobic
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363 <br/> RA : RingAtom
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364 <br/> CA : ChainAtom</div>
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365 <div class="OptionsBox">
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366 Functional class atom type specification for an atom corresponds to:</div>
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367 <div class="OptionsBox">
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368 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
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369 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
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370 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
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371 <div class="OptionsBox">
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372 HydrogenBondDonor: NH, NH2, OH
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373 <br/> HydrogenBondAcceptor: N[!H], O
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374 <br/> PositivelyIonizable: +, NH2
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375 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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376 </dd>
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377 <dt><strong><a name="setminlength" class="item"><strong>SetMinLength</strong></a></strong></dt>
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378 <dd>
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379 <div class="OptionsBox">
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380 $PathLengthFingerprints->SetMinLength($Length);</div>
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381 <p>Sets minimum value of atom path length to be used during atom path length fingerprints
|
|
|
382 generation and returns <em>PathLengthFingerprints</em>.</p>
|
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383 </dd>
|
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384 <dt><strong><a name="setmaxlength2" class="item"><strong>SetMaxLength</strong></a></strong></dt>
|
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385 <dd>
|
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386 <div class="OptionsBox">
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387 $PathLengthFingerprints->SetMaxLength($Length);</div>
|
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388 <p>Sets maximum value of atom path length to be used during atom path length fingerprints
|
|
|
389 generation and returns <em>PathLengthFingerprints</em>.</p>
|
|
|
390 </dd>
|
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|
391 <dt><strong><a name="setnumofbitstosetperpath" class="item"><strong>SetNumOfBitsToSetPerPath</strong></a></strong></dt>
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392 <dd>
|
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393 <div class="OptionsBox">
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394 $PathLengthFingerprints->SetNumOfBitsToSetPerPath($NumOfBits);</div>
|
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395 <p>Sets number of bits to set for each path during <em>PathLengthBits</em> <strong>Type </strong> during path length fingerprints
|
|
|
396 generation and returns <em>PathLengthFingerprints</em>.</p>
|
|
|
397 </dd>
|
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398 <dt><strong><a name="settype" class="item"><strong>SetType</strong></a></strong></dt>
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399 <dd>
|
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400 <div class="OptionsBox">
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401 $PathLengthFingerprints->SetType($Type);</div>
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402 <p>Sets type of path length fingerprints and returns <em>PathLengthFingerprints</em>. Possible values:
|
|
|
403 <em>PathLengthBits or PathLengthCount</em>.</p>
|
|
|
404 </dd>
|
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405 <dt><strong><a name="stringifypathlengthfingerprints" class="item"><strong>StringifyPathLengthFingerprints</strong></a></strong></dt>
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406 <dd>
|
|
|
407 <div class="OptionsBox">
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|
408 $String = $PathLengthFingerprints->StringifyPathLengthFingerprints();</div>
|
|
|
409 <p>Returns a string containing information about <em>PathLengthFingerprints</em> object.</p>
|
|
|
410 </dd>
|
|
|
411 </dl>
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412 <p>
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413 </p>
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414 <h2>AUTHOR</h2>
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415 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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416 <p>
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417 </p>
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418 <h2>SEE ALSO</h2>
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419 <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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420 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, 
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421 <a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, 
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422 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
|
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423 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
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424 </p>
|
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|
425 <p>
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426 </p>
|
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427 <h2>COPYRIGHT</h2>
|
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428 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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429 <p>This file is part of MayaChemTools.</p>
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430 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
|
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431 the terms of the GNU Lesser General Public License as published by the Free
|
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432 Software Foundation; either version 3 of the License, or (at your option)
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433 any later version.</p>
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434 <p> </p><p> </p><div class="DocNav">
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435 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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436 <tr align="left" valign="top"><td width="33%" align="left"><a href="./MACCSKeys.html" title="MACCSKeys.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::PathLengthFingerprints.pm</strong></td></tr>
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437 </table>
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438 </div>
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439 <br />
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440 <center>
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441 <img src="../../images/h2o2.png">
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442 </center>
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443 </body>
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444 </html>
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