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3 <title>MayaChemTools:Documentation:Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./CyclesDetection.html" title="CyclesDetection.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomTripletsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalPharmacophoreAtomTripletsFingerprints.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>TopologicalPharmacophoreAtomTripletsFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints;</p>
26 <p>use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong> [ Ref 66, Ref 68-71 ] class provides
31 the following methods:</p>
32 <p>new, GenerateFingerprints, , GetDescription, GetAtomTripletIDs,
33 SetAtomTypesToUse, SetDistanceBinSize, SetMaxDistance, SetMinDistance,
34 StringifyTopologicalPharmacophoreAtomTripletsFingerprints</p>
35 <p><strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong> is derived from <strong>Fingerprints</strong> class
36 which in turn is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly
37 defined in <strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong>
38 classes using Perl's AUTOLOAD functionality. These methods are generated on-the-fly for a specified
39 object property:</p>
40 <div class="OptionsBox">
41 Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
42 <br/> $PropertyValue = Get&lt;PropertyName&gt;();
43 <br/> Delete&lt;PropertyName&gt;();</div>
44 <p>Based on the values specified for <strong>AtomTypesToUse</strong>, pharmacophore atom types are
45 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
46 Using <strong>MinDistance</strong>, <strong>MaxDistance</strong>, and <strong>DistanceBinSize</strong> values, a
47 binned distance matrix is generated with lower bound on the distance bin as the distance
48 in distance matrix; the lower bound on the distance bin is also used as the distance between
49 atom pairs for generation of atom triplet identifiers.</p>
50 <p>A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting
51 atom pairs binned distances between <strong>--MinDistance</strong> and <strong>--MaxDistance</strong>. The value
52 of <strong>--UseTriangleInequality</strong> determines whether the triangle inequality test is applied during
53 generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore
54 types, is used during generation of atom triplet IDs.</p>
55 <div class="OptionsBox">
56 Let:</div>
57 <div class="OptionsBox">
58 P = Valid pharmacophore atom type</div>
59 <div class="OptionsBox">
60 Px = Pharmacophore atom x
61 <br/> Py = Pharmacophore atom y
62 <br/> Pz = Pharmacophore atom z</div>
63 <div class="OptionsBox">
64 Dmin = Minimum distance corresponding to number of bonds between two atoms
65 <br/> Dmax = Maximum distance corresponding to number of bonds between two atoms
66 <br/> D = Distance corresponding to number of bonds between two atom</div>
67 <div class="OptionsBox">
68 Bsize = Distance bin size
69 <br/> Nbins = Number of distance bins</div>
70 <div class="OptionsBox">
71 Dxy = Distance or lower bound of binned distance between Px and Py
72 <br/> Dxz = Distance or lower bound of binned distance between Px and Pz
73 <br/> Dyz = Distance or lower bound of binned distance between Py and Pz</div>
74 <div class="OptionsBox">
75 Then:</div>
76 <div class="OptionsBox">
77 PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
78 Py, and Pz</div>
79 <div class="OptionsBox">
80 For example: H1-H1-H1, H2-HBA-H2 and so on.</div>
81 <div class="OptionsBox">
82 For default values of Dmin = 1 , Dmax = 10 and Bsize = 2, the number of
83 <br/> distance bins, Nbins = 5, are:</div>
84 <div class="OptionsBox">
85 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
86 <div class="OptionsBox">
87 and atom triplet basis set size is 2692.</div>
88 <div class="OptionsBox">
89 Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
90 <br/> conjunction with usage of triangle inequality is:</div>
91 <div class="OptionsBox">
92 Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize
93 <br/> 1 10 2 No 4960
94 <br/> 1 10 2 Yes 2692 [ Default ]
95 <br/> 2 12 2 No 8436
96 <br/> 2 12 2 Yes 4494</div>
97 <p>Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore
98 atom triplets is counted.</p>
99 <p>The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen
100 atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.</p>
101 <p>For <em>ArbitrarySize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector correspond to
102 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
103 for <em>FixedSize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector contains all possible
104 valid topological pharmacophore atom triplets with both zero and non-zero count values.</p>
105 <p>The current release of MayaChemTools generates the following types of topological pharmacophore
106 atom triplets fingerprints vector strings:</p>
107 <div class="OptionsBox">
108 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
109 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
110 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
111 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
112 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
113 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
114 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
115 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
116 <div class="OptionsBox">
117 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
118 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
119 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
120 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
121 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
122 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
123 <div class="OptionsBox">
124 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
125 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
126 <br/> Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P
127 <br/> I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB
128 <br/> A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...;
129 <br/> 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1
130 <br/> 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145
131 <br/> 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ...</div>
132 <p>
133 </p>
134 <h2>METHODS</h2>
135 <dl>
136 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
137 <dd>
138 <div class="OptionsBox">
139 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
140 %NamesAndValues);</div>
141 <p>Using specified <em>TopologicalPharmacophoreAtomTripletsFingerprints</em> property names and values hash, <strong>new</strong>
142 method creates a new object and returns a reference to newly created <strong>TopologicalPharmacophoreAtomTripletsFingerprints</strong>
143 object. By default, the following properties are initialized:</p>
144 <div class="OptionsBox">
145 Molecule = ''
146 <br/> Type = 'TopologicalPharmacophoreAtomTriplets'
147 <br/> MinDistance = 1
148 <br/> MaxDistance = 10
149 <br/> DistanceBinSize = 2
150 <br/> UseTriangleInequality = 1
151 <br/> AtomTypesToUse = ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar']</div>
152 <p>Examples:</p>
153 <div class="OptionsBox">
154 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
155 'Molecule' =&gt; $Molecule);</div>
156 <div class="OptionsBox">
157 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
158 'Molecule' =&gt; $Molecule,
159 'AtomTripletsSetSizeToUse' =&gt; 'ArbitrarySize';
160 'MinDistance' =&gt; 1,
161 'MaxDistance' =&gt; 10,
162 'DistanceBinSize' =&gt; 2,
163 'AtomTypesToUse' =&gt; ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'],
164 'UseTriangleInequality' =&gt; 1);</div>
165 <div class="OptionsBox">
166 $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
167 'Molecule' =&gt; $Molecule,
168 'AtomTripletsSetSizeToUse' =&gt; 'FixedSize';
169 'MinDistance' =&gt; 1,
170 'MaxDistance' =&gt; 10,
171 'DistanceBinSize' =&gt; 2,
172 'AtomTypesToUse' =&gt; ['HBD', 'HBA', 'PI', 'NI', 'H', 'Ar'],
173 'UseTriangleInequality' =&gt; 1);</div>
174 <div class="OptionsBox">
175 $TPATFP-&gt;GenerateFingerprints();
176 <br/> print &quot;$TPATFP\n&quot;;</div>
177 </dd>
178 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
179 <dd>
180 <div class="OptionsBox">
181 $Description = $TopologicalPharmacophoreAtomTripletsFP-&gt;GetDescription();</div>
182 <p>Returns a string containing description of topological pharmacophore atom triplets fingerprints.</p>
183 </dd>
184 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
185 <dd>
186 <div class="OptionsBox">
187 $TopologicalPharmacophoreAtomTripletsFP-&gt;GenerateFingerprints();</div>
188 <p>Generates topological pharmacophore atom triplets fingerprints and returns
189 <em>TopologicalPharmacophoreAtomTripletsFP</em>.</p>
190 </dd>
191 <dt><strong><a name="getatomtripletids" class="item"><strong>GetAtomTripletIDs</strong></a></strong></dt>
192 <dd>
193 <div class="OptionsBox">
194 $AtomTripletsIDsRef = $TopologicalPharmacophoreATFP-&gt;GetAtomTripletIDs();
195 <br/> @AtomTripletIDs = $TopologicalPharmacophoreATFP-&gt;GetAtomTripletIDs();</div>
196 <p>Returns atom triplet IDs corresponding to atom pairs count values in topological pharmacophore
197 atom triplet fingerprints vector as an array or reference to an array.</p>
198 </dd>
199 <dt><strong><a name="atomtripletssetsizetouse" class="item"><strong>AtomTripletsSetSizeToUse</strong></a></strong></dt>
200 <dd>
201 <div class="OptionsBox">
202 $TPAFP-&gt;AtomTripletsSetSizeToUse($Values);</div>
203 <p>Sets pharmacophore atom triplets set size to use for topological pharmacophore fingerprints
204 generation and returns <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</p>
205 <p>Possible values for pharmacophore atom triplets set size are: <em>ArbitrarySize, FizedSize</em>.
206 Default value: <em>ArbitrarySize</em>.</p>
207 <p>For <em>ArbitrarySize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector correspond to
208 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
209 for <em>FixedSize</em> value of <strong>AtomTripletsSetSizeToUse</strong>, the fingerprint vector contains all possible
210 valid topological pharmacophore atom triplets with both zero and non-zero count values.</p>
211 </dd>
212 <dt><strong><a name="setatomtypestouse" class="item"><strong>SetAtomTypesToUse</strong></a></strong></dt>
213 <dd>
214 <div class="OptionsBox">
215 $TopologicalPharmacophoreAtomTripletsFP-&gt;SetAtomTypesToUse($ValuesRef);
216 <br/> $TopologicalPharmacophoreAtomTripletsFP-&gt;SetAtomTypesToUse(@Values);</div>
217 <p>Sets pharmacophore atom types to use for topological pharmacophore fingerprints
218 generation and returns <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</p>
219 <p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
220 Default value [ Ref 71 ] : <em>HBD,HBA,PI,NI,H,Ar</em>.</p>
221 <p>The pharmacophore atom types abbreviations correspond to:</p>
222 <div class="OptionsBox">
223 HBD: HydrogenBondDonor
224 <br/> HBA: HydrogenBondAcceptor
225 <br/> PI : PositivelyIonizable
226 <br/> NI : NegativelyIonizable
227 <br/> Ar : Aromatic
228 <br/> Hal : Halogen
229 <br/> H : Hydrophobic
230 <br/> RA : RingAtom
231 <br/> CA : ChainAtom</div>
232 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore atom
233 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
234 <div class="OptionsBox">
235 HydrogenBondDonor: NH, NH2, OH
236 <br/> HydrogenBondAcceptor: N[!H], O
237 <br/> PositivelyIonizable: +, NH2
238 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
239 </dd>
240 <dt><strong><a name="setdistancebinsize" class="item"><strong>SetDistanceBinSize</strong></a></strong></dt>
241 <dd>
242 <div class="OptionsBox">
243 $TopologicalPharmacophoreAtomTripletsFP-&gt;SetDistanceBinSize($Value);</div>
244 <p>Sets distance bin size used to bin distances between atom pairs in atom triplets and returns
245 <em>TopologicalPharmacophoreAtomTriplesFP</em>.</p>
246 <p>For default <strong>MinDistance</strong> and <strong>MaxDistance</strong> values of 1 and 10 with <strong>DistanceBinSize</strong>
247 of 2 [ Ref 70 ], the following 5 distance bins are generated:</p>
248 <div class="OptionsBox">
249 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
250 <p>The lower distance bound on the distance bin is uses to bin the distance between atom pairs in
251 atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance
252 bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.</p>
253 <p>In order to distribute distance bins of equal size, the last bin is allowed to go past <strong>MaxDistance</strong>
254 by up to distance bin size. For example, <strong>MinDistance</strong> and <strong>MaxDistance</strong> values of 2 and 10
255 with <strong>DistanceBinSize</strong> of 2 generates the following 6 distance bins:</p>
256 <div class="OptionsBox">
257 [2, 3] [4, 5] [6, 7] [8, 9] [10 11]</div>
258 </dd>
259 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
260 <dd>
261 <div class="OptionsBox">
262 $TopologicalPharmacophoreAtomTriplesFP-&gt;SetMaxDistance($Value);</div>
263 <p>Sets maximum bond distance between atom pairs corresponding to atom triplets for
264 generating topological pharmacophore atom triplets fingerprints and returns
265 <em>TopologicalPharmacophoreAtomTriplesFP</em>.</p>
266 </dd>
267 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
268 <dd>
269 <div class="OptionsBox">
270 $TopologicalPharmacophoreAtomTriplesFP-&gt;SetMinDistance($Value);</div>
271 <p>Sets minimum bond distance between atom pairs corresponding to atom triplets for
272 generating topological pharmacophore atom triplets fingerprints and returns
273 <em>TopologicalPharmacophoreAtomTriplesFP</em>.</p>
274 </dd>
275 <dt><strong><a name="stringifytopologicalpharmacophoreatomtripletsfingerprints" class="item"><strong>StringifyTopologicalPharmacophoreAtomTripletsFingerprints</strong></a></strong></dt>
276 <dd>
277 <div class="OptionsBox">
278 $String = $TopologicalPharmacophoreAtomTripletsFingerprints-&gt;
279 StringifyTopologicalPharmacophoreAtomTripletsFingerprints();</div>
280 <p>Returns a string containing information about <em>TopologicalPharmacophoreAtomTripletsFingerprints</em> object.</p>
281 </dd>
282 </dl>
283 <p>
284 </p>
285 <h2>AUTHOR</h2>
286 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
287 <p>
288 </p>
289 <h2>SEE ALSO</h2>
290 <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
291 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp
292 <a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp
293 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp
294 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>
295 </p>
296 <p>
297 </p>
298 <h2>COPYRIGHT</h2>
299 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
300 <p>This file is part of MayaChemTools.</p>
301 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
302 the terms of the GNU Lesser General Public License as published by the Free
303 Software Foundation; either version 3 of the License, or (at your option)
304 any later version.</p>
305 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
306 <table width="100%" border=0 cellpadding=0 cellspacing=2>
307 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./CyclesDetection.html" title="CyclesDetection.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints.pm</strong></td></tr>
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