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3 <title>MayaChemTools:Documentation:Fingerprints::TopologicalAtomTripletsFingerprints.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalAtomTripletsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTripletsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>TopologicalAtomTripletsFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::TopologicalAtomTripletsFingerprints;</p>
26 <p>use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>TopologicalAtomTripletsFingerprints</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="#getatomtripletids">GetAtomTripletIDs</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="#setmaxdistance">SetMaxDistance</a>, <a href="#setmindistance">SetMinDistance</a>, <a href="#stringifytopologicalatomtripletsfingerprints">StringifyTopologicalAtomTripletsFingerprints</a>
34 </p><p><strong>TopologicalAtomTripletsFingerprints</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>TopologicalAtomTripletsFingerprints</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>TopologicalAtomTripletsFingerprints</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 triplets within <strong>MinDistance</strong> and <strong>MaxDistance</strong> are identified and counted. An atom triplet
53 identifier is generated for each unique atom triplet; the format of atom triplet identifier is:</p>
54 <div class="OptionsBox">
55 &lt;ATx&gt;-Dyz-&lt;ATy&gt;-Dxz-&lt;ATz&gt;-Dxy</div>
56 <div class="OptionsBox">
57 ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
58 <br/> Dxy: Distance between atom x and atom y
59 <br/> Dxz: Distance between atom x and atom z
60 <br/> Dyz: Distance between atom y and atom z</div>
61 <div class="OptionsBox">
62 where &lt;AT1&gt;-D23 &lt;= &lt;AT2&gt;-D13 &lt;= &lt;AT3&gt;-D12</div>
63 <p>The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
64 topological atom triplets fingerprints of the molecule.</p>
65 <p>The current release of MayaChemTools generates the following types of topological atom triplets
66 fingerprints vector strings:</p>
67 <div class="OptionsBox">
68 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
69 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
70 <br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1
71 <br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1
72 <br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....;
73 <br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
74 <br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div>
75 <div class="OptionsBox">
76 FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
77 <br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
78 <br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO
79 <br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X
80 <br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2
81 <br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div>
82 <div class="OptionsBox">
83 FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
84 <br/> ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D
85 <br/> 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_
86 <br/> 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_
87 <br/> 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...;
88 <br/> 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
89 <br/> 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...</div>
90 <div class="OptionsBox">
91 FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
92 <br/> 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D
93 <br/> 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC
94 <br/> H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1-
95 <br/> aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...;
96 <br/> 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
97 <br/> 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
98 <br/> 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...</div>
99 <div class="OptionsBox">
100 FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
101 <br/> nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1
102 <br/> -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal
103 <br/> -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar
104 <br/> -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...;
105 <br/> 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
106 <br/> 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
107 <br/> 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...</div>
108 <div class="OptionsBox">
109 FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
110 <br/> 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1-
111 <br/> N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A
112 <br/> -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B
113 <br/> -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3-
114 <br/> O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...</div>
115 <div class="OptionsBox">
116 FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
117 <br/> :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11
118 <br/> -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D
119 <br/> 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C
120 <br/> 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1
121 <br/> -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...</div>
122 <div class="OptionsBox">
123 FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
124 <br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C
125 <br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3-
126 <br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2
127 <br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C.
128 <br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div>
129 <div class="OptionsBox">
130 FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
131 <br/> MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non
132 <br/> e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D
133 <br/> 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5
134 N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21-
135 <br/> D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...</div>
136 <div class="OptionsBox">
137 FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
138 <br/> axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3
139 <br/> -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9
140 <br/> C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1-
141 <br/> C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5-
142 <br/> C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-...</div>
143 <p>
144 </p>
145 <h2>METHODS</h2>
146 <dl>
147 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
148 <dd>
149 <div class="OptionsBox">
150 $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
151 %NamesAndValues);</div>
152 <p>Using specified <em>TopologicalAtomTripletsFingerprints</em> property names and values hash, <strong>new</strong>
153 method creates a new object and returns a reference to newly created <strong>TopologicalAtomTripletsFingerprints</strong>
154 object. By default, the following properties are initialized:</p>
155 <div class="OptionsBox">
156 Molecule = ''
157 <br/> Type = 'TopologicalAtomTriplets'
158 <br/> MinDistance = 1
159 <br/> MaxDistance = 10
160 <br/> UseTriangleInequality = 1
161 <br/> AtomIdentifierType = ''
162 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC']
163 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
164 <p>Examples:</p>
165 <div class="OptionsBox">
166 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
167 'Molecule' =&gt; $Molecule,
168 'AtomIdentifierType' =&gt;
169 'AtomicInvariantsAtomTypes');</div>
170 <div class="OptionsBox">
171 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
172 'Molecule' =&gt; $Molecule,
173 'MinDistance' =&gt; 1,
174 'MaxDistance' =&gt; 10,
175 'AtomIdentifierType' =&gt;
176 'AtomicInvariantsAtomTypes',
177 'AtomicInvariantsToUse' =&gt;
178 ['AS', 'X', 'BO', 'H', 'FC'] );</div>
179 <div class="OptionsBox">
180 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
181 'Molecule' =&gt; $Molecule,
182 'AtomIdentifierType' =&gt;
183 'DREIDINGAtomTypes');</div>
184 <div class="OptionsBox">
185 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
186 'Molecule' =&gt; $Molecule,
187 'AtomIdentifierType' =&gt;
188 'MMFF94AtomTypes');</div>
189 <div class="OptionsBox">
190 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
191 'Molecule' =&gt; $Molecule,
192 'AtomIdentifierType' =&gt;
193 'TPSAAtomTypes');</div>
194 <div class="OptionsBox">
195 $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints(
196 'Molecule' =&gt; $Molecule,
197 'MinDistance' =&gt; 1,
198 'MaxDistance' =&gt; 10,
199 'AtomIdentifierType' =&gt;
200 'FunctionalClassAtomTypes',
201 'FunctionalClassesToUse' =&gt;
202 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);</div>
203 <div class="OptionsBox">
204 $TopologicalAtomTripletsFingerprints-&gt;GenerateFingerprints();
205 <br/> print &quot;$TopologicalAtomTripletsFingerprints\n&quot;;</div>
206 </dd>
207 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
208 <dd>
209 <div class="OptionsBox">
210 $Return = $TopologicalAtomTripletsFingerprints-&gt;GetDescription();</div>
211 <p>Returns a string containing description of topological atom triplets fingerprints.</p>
212 </dd>
213 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
214 <dd>
215 <div class="OptionsBox">
216 $TopologicalAtomTripletsFingerprints-&gt;GenerateFingerprints();</div>
217 <p>Generates topological atom triplets fingerprints and returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
218 </dd>
219 <dt><strong><a name="getatomtripletids" class="item"><strong>GetAtomTripletIDs</strong></a></strong></dt>
220 <dd>
221 <div class="OptionsBox">
222 $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints-&gt;GetAtomTripletIDs();
223 <br/> @AtomTripletIDs = $TopologicalAtomTripletsFingerprints-&gt;GetAtomTripletIDs();</div>
224 <p>Returns atom triplet IDs corresponding to atom triplets count values in topological atom triplets
225 fingerprints vector as an array or reference to an array.</p>
226 </dd>
227 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
228 <dd>
229 <div class="OptionsBox">
230 $TopologicalAtomTripletsFingerprints-&gt;SetAtomIdentifierType($IdentifierType);</div>
231 <p>Sets atom <em>IdentifierType</em> to use during atom triplets fingerprints generation and
232 returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
233 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
234 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
235 TPSAAtomTypes, UFFAtomTypes</em>.</p>
236 </dd>
237 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
238 <dd>
239 <div class="OptionsBox">
240 $TopologicalAtomTripletsFingerprints-&gt;SetAtomicInvariantsToUse($ValuesRef);
241 <br/> $TopologicalAtomTripletsFingerprints-&gt;SetAtomicInvariantsToUse(@Values);</div>
242 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
243 for topological atom triplets fingerprints generation and returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
244 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
245 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
246 <p>The atomic invariants abbreviations correspond to:</p>
247 <div class="OptionsBox">
248 AS = Atom symbol corresponding to element symbol</div>
249 <div class="OptionsBox">
250 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
251 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
252 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
253 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
254 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
255 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
256 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
257 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
258 <br/> RA = Ring atom annotation indicating whether atom is a ring
259 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
260 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
261 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
262 3 (triplet)</div>
263 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
264 <div class="OptionsBox">
265 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>
266 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
267 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
268 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
269 are also allowed:</p>
270 <div class="OptionsBox">
271 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
272 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
273 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
274 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
275 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
276 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
277 <br/> H : NumOfImplicitAndExplicitHydrogens
278 <br/> Ar : Aromatic
279 <br/> RA : RingAtom
280 <br/> FC : FormalCharge
281 <br/> MN : MassNumber
282 <br/> SM : SpinMultiplicity</div>
283 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
284 atom types.</p>
285 </dd>
286 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
287 <dd>
288 <div class="OptionsBox">
289 $TopologicalTripletsFingerprints-&gt;SetFunctionalClassesToUse($ValuesRef);
290 <br/> $TopologicalTripletsFingerprints-&gt;SetFunctionalClassesToUse(@Values);</div>
291 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
292 for topological atom triplets fingerprints generation and returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
293 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
294 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
295 <p>The functional class abbreviations correspond to:</p>
296 <div class="OptionsBox">
297 HBD: HydrogenBondDonor
298 <br/> HBA: HydrogenBondAcceptor
299 <br/> PI : PositivelyIonizable
300 <br/> NI : NegativelyIonizable
301 <br/> Ar : Aromatic
302 <br/> Hal : Halogen
303 <br/> H : Hydrophobic
304 <br/> RA : RingAtom
305 <br/> CA : ChainAtom</div>
306 <div class="OptionsBox">
307 Functional class atom type specification for an atom corresponds to:</div>
308 <div class="OptionsBox">
309 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
310 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
311 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
312 <div class="OptionsBox">
313 HydrogenBondDonor: NH, NH2, OH
314 <br/> HydrogenBondAcceptor: N[!H], O
315 <br/> PositivelyIonizable: +, NH2
316 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
317 </dd>
318 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
319 <dd>
320 <div class="OptionsBox">
321 $TopologicalAtomTripletsFingerprints-&gt;SetMaxDistance($Distance);</div>
322 <p>Sets maximum distance to use during topological atom triplets fingerprints generation and
323 returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
324 </dd>
325 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
326 <dd>
327 <div class="OptionsBox">
328 $TopologicalAtomTripletsFingerprints-&gt;SetMinDistance($Distance);</div>
329 <p>Sets minimum distance to use during topological atom triplets fingerprints generation and
330 returns <em>TopologicalAtomTripletsFingerprints</em>.</p>
331 </dd>
332 <dt><strong><a name="stringifytopologicalatomtripletsfingerprints" class="item"><strong>StringifyTopologicalAtomTripletsFingerprints</strong></a></strong></dt>
333 <dd>
334 <div class="OptionsBox">
335 $String = $TopologicalAtomTripletsFingerprints-&gt;
336 StringifyTopologicalAtomTripletsFingerprints();</div>
337 <p>Returns a string containing information about <em>TopologicalAtomTripletsFingerprints</em> object.</p>
338 </dd>
339 </dl>
340 <p>
341 </p>
342 <h2>AUTHOR</h2>
343 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
344 <p>
345 </p>
346 <h2>SEE ALSO</h2>
347 <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
348 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp
349 <a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp
350 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,&nbsp
351 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
352 </p>
353 <p>
354 </p>
355 <h2>COPYRIGHT</h2>
356 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
357 <p>This file is part of MayaChemTools.</p>
358 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
359 the terms of the GNU Lesser General Public License as published by the Free
360 Software Foundation; either version 3 of the License, or (at your option)
361 any later version.</p>
362 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
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364 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalAtomTripletsFingerprints.pm</strong></td></tr>
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