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3 <title>MayaChemTools:Documentation:Fingerprints::TopologicalAtomTorsionsFingerprints.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalAtomTorsionsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTorsionsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalAtomTorsionsFingerprints.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>TopologicalAtomTorsionsFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::TopologicalAtomTorsionsFingerprints;</p>
26 <p>use Fingerprints::TopologicalAtomTorsionsFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>TopologicalAtomTorsionsFingerprints</strong> class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getatomtorsionsids">GetAtomTorsionsIDs</a>, <a href="#getdescription">GetDescription</a>
32 , <a href="#setatomidentifiertype">SetAtomIdentifierType</a>, <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>
33 , <a href="#stringifytopologicalatomtorsionsfingerprints">StringifyTopologicalAtomTorsionsFingerprints</a>
34 </p><p><strong>TopologicalAtomTorsionsFingerprints</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>TopologicalAtomTorsionsFingerprints</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>TopologicalAtomTorsionsFingerprints</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 in a molecule. All unique atom torsions
51 are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:</p>
52 <div class="OptionsBox">
53 &lt;AtomType1&gt;-&lt;AtomType2&gt;-&lt;AtomType3&gt;-&lt;AtomType4&gt;</div>
54 <div class="OptionsBox">
55 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types</div>
56 <div class="OptionsBox">
57 where AtomType1 &lt;= AtomType2 &lt;= AtomType3 &lt;= AtomType4</div>
58 <p>The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute
59 topological atom torsions fingerprints of the molecule.</p>
60 <p>The current release of MayaChemTools generates the following types of topological atom torsions
61 fingerprints vector strings:</p>
62 <div class="OptionsBox">
63 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
64 <br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
65 <br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
66 <br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
67 <br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div>
68 <div class="OptionsBox">
69 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
70 <br/> 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
71 <br/> .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
72 <br/> 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
73 <br/> O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
74 <br/> O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...</div>
75 <div class="OptionsBox">
76 FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
77 <br/> calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
78 <br/> _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
79 <br/> C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
80 <br/> 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1</div>
81 <div class="OptionsBox">
82 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
83 <br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
84 <br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
85 <br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
86 <br/> 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2</div>
87 <div class="OptionsBox">
88 FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
89 <br/> ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
90 <br/> Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
91 <br/> -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
92 <br/> 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3</div>
93 <div class="OptionsBox">
94 FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
95 <br/> lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
96 <br/> B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
97 <br/> A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
98 <br/> 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
99 <br/> 1 1 2 1 1 3 1 3</div>
100 <div class="OptionsBox">
101 FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
102 <br/> Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
103 <br/> 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
104 <br/> 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
105 <br/> C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
106 <br/> 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...</div>
107 <div class="OptionsBox">
108 FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
109 <br/> Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
110 <br/> -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
111 <br/> ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
112 <br/> -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
113 <br/> ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...</div>
114 <div class="OptionsBox">
115 FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
116 <br/> lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
117 <br/> None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
118 <br/> None-None 44 None-None-None-O3 3 None-None-None-O4 5</div>
119 <div class="OptionsBox">
120 FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
121 <br/> lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
122 <br/> _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
123 <br/> -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
124 <br/> _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
125 C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...</div>
126 <p>
127 </p>
128 <h2>METHODS</h2>
129 <dl>
130 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
131 <dd>
132 <div class="OptionsBox">
133 $NewTopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
134 %NamesAndValues);</div>
135 <p>Using specified <em>TopologicalAtomTorsionsFingerprints</em> property names and values hash, <strong>new</strong>
136 method creates a new object and returns a reference to newly created <strong>TopologicalAtomTorsionsFingerprints</strong>
137 object. By default, the following properties are initialized:</p>
138 <div class="OptionsBox">
139 Molecule = ''
140 <br/> Type = 'TopologicalAtomTorsions'
141 <br/> AtomIdentifierType = ''
142 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
143 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
144 <p>Examples:</p>
145 <div class="OptionsBox">
146 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
147 'Molecule' =&gt; $Molecule,
148 'AtomIdentifierType' =&gt;
149 'AtomicInvariantsAtomTypes');</div>
150 <div class="OptionsBox">
151 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
152 'Molecule' =&gt; $Molecule,
153 'AtomIdentifierType' =&gt;
154 'AtomicInvariantsAtomTypes',
155 'AtomicInvariantsToUse' =&gt;
156 ['AS', 'X', 'BO', 'H', 'FC'] );</div>
157 <div class="OptionsBox">
158 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
159 'Molecule' =&gt; $Molecule,
160 'AtomIdentifierType' =&gt;
161 'DREIDINGAtomTypes');</div>
162 <div class="OptionsBox">
163 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
164 'Molecule' =&gt; $Molecule,
165 'AtomIdentifierType' =&gt;
166 'SYBYLAtomTypes');</div>
167 <div class="OptionsBox">
168 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
169 'Molecule' =&gt; $Molecule,
170 'AtomIdentifierType' =&gt;
171 'SLogPAtomTypes');</div>
172 <div class="OptionsBox">
173 $TopologicalAtomTorsionsFingerprints = new TopologicalAtomTorsionsFingerprints(
174 'Molecule' =&gt; $Molecule,
175 'AtomIdentifierType' =&gt;
176 'FunctionalClassAtomTypes',
177 'FunctionalClassesToUse' =&gt;
178 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div>
179 <div class="OptionsBox">
180 $TopologicalAtomTorsionsFingerprints-&gt;GenerateFingerprints();
181 <br/> print &quot;$TopologicalAtomTorsionsFingerprints\n&quot;;</div>
182 </dd>
183 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
184 <dd>
185 <div class="OptionsBox">
186 $Description = $TopologicalAtomTorsionsFingerprints-&gt;GetDescription();</div>
187 <p>Returns a string containing description of topological atom torsions fingerprints.</p>
188 </dd>
189 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
190 <dd>
191 <div class="OptionsBox">
192 $TopologicalAtomTorsionsFingerprints-&gt;GenerateFingerprints();</div>
193 <p>Generates topological atom torsions fingerprints and returns <em>TopologicalAtomTorsionsFingerprints</em>.</p>
194 </dd>
195 <dt><strong><a name="getatomtorsionsids" class="item"><strong>GetAtomTorsionsIDs</strong></a></strong></dt>
196 <dd>
197 <div class="OptionsBox">
198 $AtomPairIDsRef = $TopologicalAtomTorsionsFingerprints-&gt;GetAtomTorsionsIDs();
199 <br/> @AtomPairIDs = $TopologicalAtomTorsionsFingerprints-&gt;GetAtomTorsionsIDs();</div>
200 <p>Returns atom torsion IDs corresponding to atom torsion count values in topological atom torsions
201 fingerprints vector as an array or reference to an array.</p>
202 </dd>
203 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
204 <dd>
205 <div class="OptionsBox">
206 $TopologicalAtomTorsionsFingerprints-&gt;SetAtomIdentifierType($IdentifierType);</div>
207 <p>Sets atom <em>IdentifierType</em> to use during atom torsions fingerprints generation and
208 returns <em>TopologicalAtomTorsionsFingerprints</em>.</p>
209 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
210 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
211 TPSAAtomTypes, UFFAtomTypes</em>.</p>
212 </dd>
213 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
214 <dd>
215 <div class="OptionsBox">
216 $TopologicalAtomTorsionsFingerprints-&gt;SetAtomicInvariantsToUse($ValuesRef);
217 <br/> $TopologicalAtomTorsionsFingerprints-&gt;SetAtomicInvariantsToUse(@Values);</div>
218 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
219 for topological atom torsions fingerprints generation and returns <em>TopologicalAtomTorsionsFingerprints</em>.</p>
220 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
221 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
222 <p>The atomic invariants abbreviations correspond to:</p>
223 <div class="OptionsBox">
224 AS = Atom symbol corresponding to element symbol</div>
225 <div class="OptionsBox">
226 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
227 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
228 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
229 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
230 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
231 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
232 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
233 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
234 <br/> RA = Ring atom annotation indicating whether atom is a ring
235 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
236 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
237 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
238 3 (triplet)</div>
239 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
240 <div class="OptionsBox">
241 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>
242 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
243 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
244 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
245 are also allowed:</p>
246 <div class="OptionsBox">
247 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
248 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
249 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
250 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
251 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
252 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
253 <br/> H : NumOfImplicitAndExplicitHydrogens
254 <br/> Ar : Aromatic
255 <br/> RA : RingAtom
256 <br/> FC : FormalCharge
257 <br/> MN : MassNumber
258 <br/> SM : SpinMultiplicity</div>
259 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
260 atom types.</p>
261 </dd>
262 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
263 <dd>
264 <div class="OptionsBox">
265 $TopologicalTorsionsFingerprints-&gt;SetFunctionalClassesToUse($ValuesRef);
266 <br/> $TopologicalTorsionsFingerprints-&gt;SetFunctionalClassesToUse(@Values);</div>
267 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
268 for topological atom torsions fingerprints generation and returns <em>TopologicalAtomTorsionsFingerprints</em>.</p>
269 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
270 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
271 <p>The functional class abbreviations correspond to:</p>
272 <div class="OptionsBox">
273 HBD: HydrogenBondDonor
274 <br/> HBA: HydrogenBondAcceptor
275 <br/> PI : PositivelyIonizable
276 <br/> NI : NegativelyIonizable
277 <br/> Ar : Aromatic
278 <br/> Hal : Halogen
279 <br/> H : Hydrophobic
280 <br/> RA : RingAtom
281 <br/> CA : ChainAtom</div>
282 <div class="OptionsBox">
283 Functional class atom type specification for an atom corresponds to:</div>
284 <div class="OptionsBox">
285 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
286 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
287 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
288 <div class="OptionsBox">
289 HydrogenBondDonor: NH, NH2, OH
290 <br/> HydrogenBondAcceptor: N[!H], O
291 <br/> PositivelyIonizable: +, NH2
292 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
293 </dd>
294 <dt><strong><a name="stringifytopologicalatomtorsionsfingerprints" class="item"><strong>StringifyTopologicalAtomTorsionsFingerprints</strong></a></strong></dt>
295 <dd>
296 <div class="OptionsBox">
297 $String = $TopologicalAtomTorsionsFingerprints-&gt;
298 StringifyTopologicalAtomTorsionsFingerprints();</div>
299 <p>Returns a string containing information about <em>TopologicalAtomTorsionsFingerprints</em> object.</p>
300 </dd>
301 </dl>
302 <p>
303 </p>
304 <h2>AUTHOR</h2>
305 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
306 <p>
307 </p>
308 <h2>SEE ALSO</h2>
309 <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
310 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp
311 <a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp
312 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,&nbsp
313 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
314 </p>
315 <p>
316 </p>
317 <h2>COPYRIGHT</h2>
318 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
319 <p>This file is part of MayaChemTools.</p>
320 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
321 the terms of the GNU Lesser General Public License as published by the Free
322 Software Foundation; either version 3 of the License, or (at your option)
323 any later version.</p>
324 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
325 <table width="100%" border=0 cellpadding=0 cellspacing=2>
326 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalAtomTorsionsFingerprints.pm</strong></td></tr>
327 </table>
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