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3 <title>MayaChemTools:Documentation:Fingerprints::TopologicalAtomPairsFingerprints.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalAtomPairsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomPairsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalAtomPairsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>TopologicalAtomPairsFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::TopologicalAtomPairsFingerprints;</p>
26 <p>use Fingerprints::TopologicalAtomPairsFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>TopologicalAtomPairsFingerprints</strong> [ Ref 57, Ref 59, Ref 72 ] class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getatompairids">GetAtomPairIDs</a>, <a href="#getdescription">GetDescription</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a>
32 , <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>, <a href="#setmaxdistance">SetMaxDistance</a>
33 , <a href="#setmindistance">SetMinDistance</a>, <a href="#stringifytopologicalatompairsfingerprints">StringifyTopologicalAtomPairsFingerprints</a>
34 </p><p><strong>TopologicalAtomPairsFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn
35 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
36 in <strong>TopologicalAtomPairsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's
37 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
38 <div class="OptionsBox">
39 Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
40 <br/> $PropertyValue = Get&lt;PropertyName&gt;();
41 <br/> Delete&lt;PropertyName&gt;();</div>
42 <p>The current release of MayaChemTools supports generation of <strong>AtomTypesFingerpritns</strong>
43 corresponding to following <strong>AtomtomIdentifierTypes</strong>:</p>
44 <div class="OptionsBox">
45 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
46 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
47 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
48 <p>Based on the values specified for <strong>AtomIdentifierType</strong> along with other specified
49 parameters such as <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse</strong>, initial
50 atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
51 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
52 pairs within <strong>MinDistance</strong> and <strong>MaxDistance</strong> are identified and counted. An atom pair
53 identifier is generated for each unique atom pair; the format of atom pair identifier is:</p>
54 <div class="OptionsBox">
55 &lt;AtomType1&gt;-D&lt;n&gt;-&lt;AtomType2&gt;</div>
56 <div class="OptionsBox">
57 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
58 <br/> D: Distance between atom1 and atom2</div>
59 <div class="OptionsBox">
60 where AtomType1 &lt;= AtomType2</div>
61 <p>The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
62 topological atom pairs fingerprints of the molecule.</p>
63 <p>The current release of MayaChemTools generates the following types of topological atom pairs
64 fingerprints vector strings:</p>
65 <div class="OptionsBox">
66 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
67 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
68 <br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
69 <br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
70 <br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
71 <br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div>
72 <div class="OptionsBox">
73 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
74 <br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
75 <br/> 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
76 <br/> C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
77 <br/> .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
78 <br/> 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...</div>
79 <div class="OptionsBox">
80 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
81 <br/> :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
82 <br/> 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_
83 <br/> R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2
84 <br/> 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
85 <br/> 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...</div>
86 <div class="OptionsBox">
87 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
88 <br/> axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
89 <br/> D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
90 <br/> aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
91 <br/> 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
92 <br/> 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...</div>
93 <div class="OptionsBox">
94 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
95 <br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
96 <br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
97 <br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
98 <br/> 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
99 <br/> 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...</div>
100 <div class="OptionsBox">
101 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
102 <br/> axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
103 <br/> C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
104 <br/> CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1
105 <br/> COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR
106 <br/> 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...</div>
107 <div class="OptionsBox">
108 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
109 <br/> xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
110 <br/> -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
111 <br/> C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
112 <br/> 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
113 <br/> C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...</div>
114 <div class="OptionsBox">
115 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
116 <br/> xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
117 <br/> .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C.
118 <br/> 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a
119 <br/> r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3
120 <br/> -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...</div>
121 <div class="OptionsBox">
122 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
123 <br/> Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
124 <br/> -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
125 <br/> D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
126 <br/> 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
127 <br/> 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...</div>
128 <div class="OptionsBox">
129 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
130 <br/> istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
131 <br/> -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C
132 <br/> _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1
133 <br/> C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D
134 <br/> 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...</div>
135 <p>
136 </p>
137 <h2>METHODS</h2>
138 <dl>
139 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
140 <dd>
141 <div class="OptionsBox">
142 $NewTopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
143 %NamesAndValues);</div>
144 <p>Using specified <em>TopologicalAtomPairsFingerprints</em> property names and values hash, <strong>new</strong>
145 method creates a new object and returns a reference to newly created <strong>TopologicalAtomPairsFingerprints</strong>
146 object. By default, the following properties are initialized:</p>
147 <div class="OptionsBox">
148 Molecule = ''
149 <br/> Type = 'TopologicalAtomPairs'
150 <br/> MinDistance = 1
151 <br/> MaxDistance = 10
152 <br/> AtomIdentifierType = ''
153 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
154 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
155 <p>Examples:</p>
156 <div class="OptionsBox">
157 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
158 'Molecule' =&gt; $Molecule,
159 'AtomIdentifierType' =&gt;
160 'AtomicInvariantsAtomTypes');</div>
161 <div class="OptionsBox">
162 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
163 'Molecule' =&gt; $Molecule,
164 'MinDistance' =&gt; 1,
165 'MaxDistance' =&gt; 10,
166 'AtomIdentifierType' =&gt;
167 'AtomicInvariantsAtomTypes',
168 'AtomicInvariantsToUse' =&gt;
169 ['AS', 'X', 'BO', 'H', 'FC'] );</div>
170 <div class="OptionsBox">
171 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
172 'Molecule' =&gt; $Molecule,
173 'AtomIdentifierType' =&gt;
174 'EStateAtomTypes');</div>
175 <div class="OptionsBox">
176 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
177 'Molecule' =&gt; $Molecule,
178 'AtomIdentifierType' =&gt;
179 'SLogPAtomTypes');</div>
180 <div class="OptionsBox">
181 $TopologicalAtomPairsFingerprints = new TopologicalAtomPairsFingerprints(
182 'Molecule' =&gt; $Molecule,
183 'MinDistance' =&gt; 1,
184 'MaxDistance' =&gt; 10,
185 'AtomIdentifierType' =&gt;
186 'FunctionalClassAtomTypes',
187 'FunctionalClassesToUse' =&gt;
188 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);</div>
189 <div class="OptionsBox">
190 $TopologicalAtomPairsFingerprints-&gt;GenerateFingerprints();
191 <br/> print &quot;$TopologicalAtomPairsFingerprints\n&quot;;</div>
192 </dd>
193 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
194 <dd>
195 <div class="OptionsBox">
196 $Description = $TopologicalAtomPairsFingerprints-&gt;GetDescription();</div>
197 <p>Returns a string containing description of topological atom pairs fingerprints fingerprints.</p>
198 </dd>
199 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
200 <dd>
201 <div class="OptionsBox">
202 $TopologicalAtomPairsFingerprints-&gt;GenerateFingerprints();</div>
203 <p>Generates topological atom pairs fingerprints and returns <em>TopologicalAtomPairsFingerprints</em>.</p>
204 </dd>
205 <dt><strong><a name="getatompairids" class="item"><strong>GetAtomPairIDs</strong></a></strong></dt>
206 <dd>
207 <div class="OptionsBox">
208 $AtomPairIDsRef = $TopologicalAtomPairsFingerprints-&gt;GetAtomPairIDs();
209 <br/> @AtomPairIDs = $TopologicalAtomPairsFingerprints-&gt;GetAtomPairIDs();</div>
210 <p>Returns atom pair IDs corresponding to atom pairs count values in topological atom pairs
211 fingerprints vector as an array or reference to an array.</p>
212 </dd>
213 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
214 <dd>
215 <div class="OptionsBox">
216 $TopologicalAtomPairsFingerprints-&gt;SetAtomIdentifierType($IdentifierType);</div>
217 <p>Sets atom <em>IdentifierType</em> to use during atom pairs fingerprints generation and
218 returns <em>TopologicalAtomPairsFingerprints</em>.</p>
219 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
220 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
221 TPSAAtomTypes, UFFAtomTypes</em>.</p>
222 </dd>
223 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
224 <dd>
225 <div class="OptionsBox">
226 $TopologicalAtomPairsFingerprints-&gt;SetAtomicInvariantsToUse($ValuesRef);
227 <br/> $TopologicalAtomPairsFingerprints-&gt;SetAtomicInvariantsToUse(@Values);</div>
228 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
229 for topological atom pairs fingerprints generation and returns <em>TopologicalAtomPairsFingerprints</em>.</p>
230 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
231 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
232 <p>The atomic invariants abbreviations correspond to:</p>
233 <div class="OptionsBox">
234 AS = Atom symbol corresponding to element symbol</div>
235 <div class="OptionsBox">
236 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
237 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
238 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
239 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
240 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
241 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
242 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
243 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
244 <br/> RA = Ring atom annotation indicating whether atom is a ring
245 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
246 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
247 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
248 3 (triplet)</div>
249 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
250 <div class="OptionsBox">
251 AS.X&lt;n&gt;.BO&lt;n&gt;.LBO&lt;n&gt;.&lt;SB&gt;&lt;n&gt;.&lt;DB&gt;&lt;n&gt;.&lt;TB&gt;&lt;n&gt;.H&lt;n&gt;.Ar.RA.FC&lt;+n/-n&gt;.MN&lt;n&gt;.SM&lt;n&gt;</div>
252 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
253 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
254 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
255 are also allowed:</p>
256 <div class="OptionsBox">
257 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
258 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
259 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
260 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
261 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
262 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
263 <br/> H : NumOfImplicitAndExplicitHydrogens
264 <br/> Ar : Aromatic
265 <br/> RA : RingAtom
266 <br/> FC : FormalCharge
267 <br/> MN : MassNumber
268 <br/> SM : SpinMultiplicity</div>
269 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
270 atom types.</p>
271 </dd>
272 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
273 <dd>
274 <div class="OptionsBox">
275 $TopologicalAtomPairsFingerprints-&gt;SetFunctionalClassesToUse($ValuesRef);
276 <br/> $TopologicalAtomPairsFingerprints-&gt;SetFunctionalClassesToUse(@Values);</div>
277 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
278 for topological atom pairs fingerprints generation and returns <em>TopologicalAtomPairsFingerprints</em>.</p>
279 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
280 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
281 <p>The functional class abbreviations correspond to:</p>
282 <div class="OptionsBox">
283 HBD: HydrogenBondDonor
284 <br/> HBA: HydrogenBondAcceptor
285 <br/> PI : PositivelyIonizable
286 <br/> NI : NegativelyIonizable
287 <br/> Ar : Aromatic
288 <br/> Hal : Halogen
289 <br/> H : Hydrophobic
290 <br/> RA : RingAtom
291 <br/> CA : ChainAtom</div>
292 <div class="OptionsBox">
293 Functional class atom type specification for an atom corresponds to:</div>
294 <div class="OptionsBox">
295 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
296 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
297 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
298 <div class="OptionsBox">
299 HydrogenBondDonor: NH, NH2, OH
300 <br/> HydrogenBondAcceptor: N[!H], O
301 <br/> PositivelyIonizable: +, NH2
302 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
303 </dd>
304 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
305 <dd>
306 <div class="OptionsBox">
307 $TopologicalAtomPairsFingerprints-&gt;SetMaxDistance($Distance);</div>
308 <p>Sets maximum distance to use during topological atom pairs fingerprints generation and
309 returns <em>TopologicalAtomPairsFingerprints</em>.</p>
310 </dd>
311 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
312 <dd>
313 <div class="OptionsBox">
314 $TopologicalAtomPairsFingerprints-&gt;SetMinDistance($Distance);</div>
315 <p>Sets minimum distance to use during topological atom pairs fingerprints generation and
316 returns <em>TopologicalAtomPairsFingerprints</em>.</p>
317 </dd>
318 <dt><strong><a name="stringifytopologicalatompairsfingerprints" class="item"><strong>StringifyTopologicalAtomPairsFingerprints</strong></a></strong></dt>
319 <dd>
320 <div class="OptionsBox">
321 $String = $TopologicalAtomPairsFingerprints-&gt;
322 StringifyTopologicalAtomPairsFingerprints();</div>
323 <p>Returns a string containing information about <em>TopologicalAtomPairsFingerprints</em> object.</p>
324 </dd>
325 </dl>
326 <p>
327 </p>
328 <h2>AUTHOR</h2>
329 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
330 <p>
331 </p>
332 <h2>SEE ALSO</h2>
333 <p><a href="./Fingerprints.html">Fingerprints.pm</a>,&nbsp<a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>,&nbsp<a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>,&nbsp
334 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp
335 <a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp
336 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,&nbsp
337 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
338 </p>
339 <p>
340 </p>
341 <h2>COPYRIGHT</h2>
342 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
343 <p>This file is part of MayaChemTools.</p>
344 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
345 the terms of the GNU Lesser General Public License as published by the Free
346 Software Foundation; either version 3 of the License, or (at your option)
347 any later version.</p>
348 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
349 <table width="100%" border=0 cellpadding=0 cellspacing=2>
350 <tr align="left" valign="top"><td width="33%" align="left"><a href="./PathLengthFingerprints.html" title="PathLengthFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalAtomPairsFingerprints.pm</strong></td></tr>
351 </table>
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355 <img src="../../images/h2o2.png">
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