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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomPairsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalPharmacophoreAtomPairsFingerprints.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>TopologicalPharmacophoreAtomPairsFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints;</p>
26 <p>use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>TopologicalPharmacophoreAtomPairsFingerprints</strong> [ Ref 60-62, Ref 65, Ref 68 ] class provides
31 the following methods:</p>
32 <p>new, GenerateFingerprints, GetDescription, GetAtomPairIDs, SetAtomTypesToUse,
33 SetAtomTypesWeight, SetFuzzFactor, SetFuzzificationMethodology,
34 SetFuzzificationMode, SetMaxDistance, SetMinDistance,
35 SetNormalizationMethodology, SetValuesPrecision,
36 StringifyTopologicalPharmacophoreAtomPairsFingerprints</p>
37 <p><strong>TopologicalPharmacophoreAtomPairsFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn
38 is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined
39 in <strong>TopologicalPharmacophoreAtomPairsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's
40 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p>
41 <div class="OptionsBox">
42 Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
43 <br/> $PropertyValue = Get&lt;PropertyName&gt;();
44 <br/> Delete&lt;PropertyName&gt;();</div>
45 <p>Based on the values specified for <strong>AtomTypesToUse</strong>, pharmacophore atom types are
46 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
47 A pharmacophore atom pairs basis set is initialized for all unique possible pairs within
48 <strong>MinDistance</strong> and <strong>MaxDistance</strong> range.</p>
49 <div class="OptionsBox">
50 Let:</div>
51 <div class="OptionsBox">
52 P = Valid pharmacophore atom type</div>
53 <div class="OptionsBox">
54 Px = Pharmacophore atom type x
55 <br/> Py = Pharmacophore atom type y</div>
56 <div class="OptionsBox">
57 Dmin = Minimum distance corresponding to number of bonds between two atoms
58 <br/> Dmax = Maximum distance corresponding to number of bonds between two atoms
59 <br/> D = Distance corresponding to number of bonds between two atoms</div>
60 <div class="OptionsBox">
61 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</div>
62 <div class="OptionsBox">
63 P = Number of pharmacophore atom types to consider
64 <br/> PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</div>
65 <div class="OptionsBox">
66 PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax</div>
67 <div class="OptionsBox">
68 Then:</div>
69 <div class="OptionsBox">
70 PPD = (P * (P - 1))/2 + P</div>
71 <div class="OptionsBox">
72 PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)
73 <br/>&nbsp;&nbsp;&nbsp;&nbsp; = ((Dmax - Dmin) + 1) * PPD</div>
74 <div class="OptionsBox">
75 So for default values of Dmin = 1, Dmax = 10 and P = 5,</div>
76 <div class="OptionsBox">
77 PPD = (5 * (5 - 1))/2 + 5 = 15
78 <br/> PPT = ((10 - 1) + 1) * 15 = 150</div>
79 <div class="OptionsBox">
80 The pharmacophore atom pairs bais set includes 150 values.</div>
81 <div class="OptionsBox">
82 The atom pair IDs correspond to:</div>
83 <div class="OptionsBox">
84 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</div>
85 <div class="OptionsBox">
86 For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</div>
87 <p>Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom
88 pairs is counted. The contribution of each atom type to atom pair interaction is optionally
89 weighted by specified <strong>AtomTypesWeight</strong> before assigning its count to appropriate distance
90 bin. Based on <strong>NormalizationMethodology</strong> option, pharmacophore atom pairs count is optionally
91 normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after
92 the normalization controlled by values of <strong>FuzzifyAtomPairsCount</strong>, <strong>FuzzificationMode</strong>,
93 <strong>FuzzificationMethodology</strong> and <strong>FuzzFactor</strong>.</p>
94 <p>The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen
95 atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs
96 fingerprints of the molecule.</p>
97 <p>For <em>ArbitrarySize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector correspond to
98 only those topological pharmacophore atom pairs which are present and have non-zero count. However,
99 for <em>FixedSize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector contains all possible
100 valid topological pharmacophore atom pairs with both zero and non-zero count values.</p>
101 <p>The current release of MayaChemTools generates the following types of topological pharmacophore
102 atom pairs fingerprints vector strings:</p>
103 <div class="OptionsBox">
104 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
105 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
106 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
107 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
108 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
109 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
110 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
111 <div class="OptionsBox">
112 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
113 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
114 <br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
115 <br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
116 <br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
117 <br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div>
118 <div class="OptionsBox">
119 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
120 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
121 <br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
122 <br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
123 <br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
124 <br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
125 <br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
126 <br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</div>
127 <p>
128 </p>
129 <h2>METHODS</h2>
130 <dl>
131 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
132 <dd>
133 <div class="OptionsBox">
134 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
135 %NamesAndValues);</div>
136 <p>Using specified <em>TopologicalPharmacophoreAtomPairsFingerprints</em> property names and
137 values hash, <strong>new</strong> method creates a new object and returns a reference to newly created
138 <strong>TopologicalPharmacophoreAtomPairsFingerprints</strong> object. By default, the following properties
139 are initialized:</p>
140 <div class="OptionsBox">
141 Molecule = ''
142 <br/> Type = 'TopologicalPharmacophoreAtomPairs'
143 <br/> MinDistance = 1
144 <br/> MaxDistance = 10
145 <br/> NormalizationMethodology = 'None'
146 <br/> AtomTypesToUse = ['HBD', 'HBA', 'PI', 'NI', 'H']</div>
147 <div class="OptionsBox">
148 FuzzifyAtomPairsCount = 0
149 <br/> FuzzificationMode = 'AfterNormalization'
150 <br/> FuzzificationMethodology = 'FuzzyBinning'
151 <br/> FuzzFactor = 0.15</div>
152 <div class="OptionsBox">
153 ValuesPrecision = 2</div>
154 <p>Examples:</p>
155 <div class="OptionsBox">
156 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
157 'Molecule' =&gt; $Molecule);</div>
158 <div class="OptionsBox">
159 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
160 'Molecule' =&gt; $Molecule,
161 'AtomPairsSetSizeToUse' =&gt; 'ArbitrarySize',
162 'MinDistance' =&gt; 1,
163 'MaxDistance' =&gt; 10,
164 'NormalizationMethodology' =&gt; 'None',
165 'AtomTypesToUse' =&gt; ['HBD', 'HBA', 'PI', 'NI', 'H'],
166 'FuzzifyAtomPairsCount' =&gt; 0);</div>
167 <div class="OptionsBox">
168 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
169 'Molecule' =&gt; $Molecule,
170 'AtomPairsSetSizeToUse' =&gt; 'FizedSize',
171 'MinDistance' =&gt; 1,
172 'MaxDistance' =&gt; 10,
173 'NormalizationMethodology' =&gt; 'None',
174 'AtomTypesToUse' =&gt; ['HBD', 'HBA', 'PI', 'NI', 'H'],
175 'FuzzifyAtomPairsCount' =&gt; 1,
176 'FuzzificationMethodology' =&gt; 'FuzzyBinning',
177 'FuzzFactor' =&gt; 0.15,
178 'ValuesPrecision' =&gt; 2);</div>
179 <div class="OptionsBox">
180 $TPAPFP-&gt;GenerateFingerprints();
181 <br/> print &quot;$TPAPFP\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 = $TopologicalPharmacophoreAtomPairsFP-&gt;GetDescription();</div>
187 <p>Returns a string containing description of topological pharmacophore atom pairs 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 $TopologicalPharmacophoreAtomPairsFP-&gt;GenerateFingerprints();</div>
193 <p>Generates topological pharmacophore atom pairs fingerprints and returns
194 <em>TopologicalPharmacophoreAtomPairsFP</em>.</p>
195 </dd>
196 <dt><strong><a name="getatompairids" class="item"><strong>GetAtomPairIDs</strong></a></strong></dt>
197 <dd>
198 <div class="OptionsBox">
199 $AtomPairIDsRef = $TopologicalPharmacophoreAtomPairsFP-&gt;GetAtomPairIDs();
200 <br/> @AtomPairIDs = $TopologicalPharmacophoreAtomPairsFP-&gt;GetAtomPairIDs();</div>
201 <p>Returns atom pair IDs corresponding to atom pairs count values in topological pharmacophore
202 atom pairs fingerprints vector as an array or reference to an array.</p>
203 </dd>
204 <dt><strong><a name="setatompairssetsizetouse" class="item"><strong>SetAtomPairsSetSizeToUse</strong></a></strong></dt>
205 <dd>
206 <div class="OptionsBox">
207 $TopologicalPharmacophoreAtomPairsFP-&gt;SetAtomPairsSetSizeToUse($Values);</div>
208 <p>Sets pharmacophore atom pairs set size to use for topological pharmacophore fingerprints
209 generation and returns <em>TopologicalPharmacophoreAtomPairsFingerprints</em>.</p>
210 <p>Possible values for pharmacophore atom pairs set size are: <em>ArbitrarySize, FizedSize</em>.
211 Default value: <em>ArbitrarySize</em>.</p>
212 <p>For <em>ArbitrarySize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector correspond to
213 only those topological pharmacophore atom pairs which are present and have non-zero count. However,
214 for <em>FixedSize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector contains all possible
215 valid topological pharmacophore atom pairs with both zero and non-zero count values.</p>
216 </dd>
217 <dt><strong><a name="setatomtypestouse" class="item"><strong>SetAtomTypesToUse</strong></a></strong></dt>
218 <dd>
219 <div class="OptionsBox">
220 $TopologicalPharmacophoreAtomPairsFP-&gt;SetAtomTypesToUse($ValuesRef);
221 <br/> $TopologicalPharmacophoreAtomPairsFP-&gt;SetAtomTypesToUse(@Values);</div>
222 <p>Sets pharmacophore atom types to use for topological pharmacophore fingerprints
223 generation and returns <em>TopologicalPharmacophoreAtomPairsFingerprints</em>.</p>
224 <p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
225 Default value [ Ref 60-62 ] : <em>HBD,HBA,PI,NI,H</em>.</p>
226 <p>The pharmacophore atom types abbreviations correspond to:</p>
227 <div class="OptionsBox">
228 HBD: HydrogenBondDonor
229 <br/> HBA: HydrogenBondAcceptor
230 <br/> PI : PositivelyIonizable
231 <br/> NI : NegativelyIonizable
232 <br/> Ar : Aromatic
233 <br/> Hal : Halogen
234 <br/> H : Hydrophobic
235 <br/> RA : RingAtom
236 <br/> CA : ChainAtom</div>
237 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore atom
238 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
239 <div class="OptionsBox">
240 HydrogenBondDonor: NH, NH2, OH
241 <br/> HydrogenBondAcceptor: N[!H], O
242 <br/> PositivelyIonizable: +, NH2
243 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
244 </dd>
245 <dt><strong><a name="setatomtypesweight" class="item"><strong>SetAtomTypesWeight</strong></a></strong></dt>
246 <dd>
247 <div class="OptionsBox">
248 $TopologicalPharmacophoreAtomPairsFP-&gt;SetAtomTypesWeight(
249 <br/>&nbsp;&nbsp;&nbsp;&nbsp; %AtomTypesToWeight);</div>
250 <p>Sets weights of specified pharmacophore atom types to use during calculation of their contribution
251 to atom pair count and returns <em>TopologicalPharmacophoreAtomPairsFP</em>. Default values: <em>1 for
252 each atom type</em>.</p>
253 <p>The weight values allow to increase the importance of specific pharmacophore atom type
254 in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to
255 atom pair count where as weight value of 2 doubles its contribution.</p>
256 </dd>
257 <dt><strong><a name="setfuzzfactor" class="item"><strong>SetFuzzFactor</strong></a></strong></dt>
258 <dd>
259 <div class="OptionsBox">
260 $TopologicalPharmacophoreAtomPairsFP-&gt;SetFuzzFactor($Value);</div>
261 <p>Sets fuzz factor value to use during fuzzification of atom pairs count and returns
262 <em>TopologicalPharmacophoreAtomPairsFP</em>. Default value: <em>0.15</em>.</p>
263 <p>Valid values: For <em>FuzzyBinning</em> value of <strong>FuzzificationMethodology</strong>: <em>between 0 and 1.0</em>; For
264 <em>FuzzyBinSmoothing</em> value of <strong>FuzzificationMethodology</strong>: <em>between 0 and 0.5</em>.</p>
265 </dd>
266 <dt><strong><a name="setfuzzificationmethodology" class="item"><strong>SetFuzzificationMethodology</strong></a></strong></dt>
267 <dd>
268 <div class="OptionsBox">
269 $TopologicalPharmacophoreAtomPairsFP-&gt;SetFuzzificationMethodology($Value);</div>
270 <p>Sets fuzzification methodology to use for fuzzification of atom pairs count and returns
271 <em>TopologicalPharmacophoreAtomPairsFP</em>. Default value: <em>FuzzyBinning</em>. Possible values:
272 <em>FuzzyBinning | FuzzyBinSmoothing</em>.</p>
273 <p>In conjunction with values for options <strong>FuzzifyAtomPairsCount</strong>, <strong>FuzzificationMode</strong> and
274 <strong>FuzzFactor</strong>, <strong>FuzzificationMethodology</strong> option is used to fuzzify pharmacophore atom
275 pairs count.</p>
276 <p>Let:</p>
277 <div class="OptionsBox">
278 Px = Pharmacophore atom type x
279 <br/> Py = Pharmacophore atom type y
280 <br/> PPxy = Pharmacophore atom pair between atom type Px and Py</div>
281 <div class="OptionsBox">
282 PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
283 at distance Dn
284 <br/> PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py
285 at distance Dn - 1
286 <br/> PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
287 at distance Dn + 1</div>
288 <div class="OptionsBox">
289 FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</div>
290 <p>Then:</p>
291 <p>For <em>FuzzyBinning</em>:</p>
292 <div class="OptionsBox">
293 PPxyDn = PPxyDn (Unchanged)</div>
294 <div class="OptionsBox">
295 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
296 <br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div>
297 <p>For <em>FuzzyBinSmoothing</em>:</p>
298 <div class="OptionsBox">
299 PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin &lt; Dn &lt; Dmax
300 <br/> PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</div>
301 <div class="OptionsBox">
302 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
303 <br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div>
304 <p>In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurrence counts.
305 A value of 1 during <em>FuzzyBinning</em> corresponds to maximum fuzzification of occurrence counts;
306 however, a value of 1 during <em>FuzzyBinSmoothing</em> ends up completely distributing the value over
307 the previous and next distance bins.</p>
308 <p>So for default value of <strong>FuzzFactor</strong> (FF) 0.15, the occurrence count of pharmacohore atom pairs
309 at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1
310 are incremented by PPxyDn * 0.15.</p>
311 <p>And during <em>FuzzyBinSmoothing</em> the occurrence counts at Distance Dn is scaled back using multiplicative
312 factor of (1 - 2*0.15) and the occurrence counts at distances Dn -1 and Dn + 1 are incremented by
313 PPxyDn * 0.15. In other words, occurrence bin count is smoothed out by distributing it over the
314 previous and next distance value.</p>
315 </dd>
316 <dt><strong><a name="setfuzzificationmode" class="item"><strong>SetFuzzificationMode</strong></a></strong></dt>
317 <dd>
318 <div class="OptionsBox">
319 $TopologicalPharmacophoreAtomPairsFP-&gt;SetFuzzificationMode($Value);</div>
320 <p>Sets fuzzification mode to use for fuzzification of atom pairs count and returns
321 <em>TopologicalPharmacophoreAtomPairsFP</em>. Default value: <em>AfterNormalization</em>. Possible values:
322 <em>BeforeNormalization | AfterNormalization</em>.</p>
323 </dd>
324 <dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt>
325 <dd>
326 <div class="OptionsBox">
327 $TopologicalPharmacophoreAtomPairsFP-&gt;SetMaxDistance($Value);</div>
328 <p>Sets maximum bond distance between atom pairs for generating topological pharmacophore atom
329 pairs fingerprints and returns <em>TopologicalPharmacophoreAtomPairsFP</em>.</p>
330 </dd>
331 <dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt>
332 <dd>
333 <div class="OptionsBox">
334 $TopologicalPharmacophoreAtomPairsFP-&gt;SetMinDistance($Value);</div>
335 <p>Sets minimum bond distance between atom pairs for generating topological pharmacophore atom
336 pairs fingerprints and returns <em>TopologicalPharmacophoreAtomPairsFP</em>.</p>
337 </dd>
338 <dt><strong><a name="setnormalizationmethodology" class="item"><strong>SetNormalizationMethodology</strong></a></strong></dt>
339 <dd>
340 <div class="OptionsBox">
341 $TopologicalPharmacophoreAtomPairsFP-&gt;SetNormalizationMethodology($Value);</div>
342 <p>Sets normalization methodology to use for scaling the occurrence count of pharmacophore atom
343 pairs within specified distance range and returns <em>TopologicalPharmacophoreAtomPairsFP</em>.
344 Default value: <em>None</em>. Possible values: <em>None, ByHeavyAtomsCount or ByAtomTypesCount</em>.</p>
345 </dd>
346 <dt><strong><a name="setvaluesprecision" class="item"><strong>SetValuesPrecision</strong></a></strong></dt>
347 <dd>
348 <div class="OptionsBox">
349 $TopologicalPharmacophoreAtomPairsFP-&gt;SetValuesPrecision($Value);</div>
350 <p>Sets precision of atom pairs count real values which might be generated after normalization
351 or fuzzification and returns <em>TopologicalPharmacophoreAtomPairsFP</em>. Default: up to <em>2</em> decimal
352 places.</p>
353 </dd>
354 <dt><strong><a name="stringifytopologicalpharmacophoreatompairsfingerprints" class="item"><strong>StringifyTopologicalPharmacophoreAtomPairsFingerprints</strong></a></strong></dt>
355 <dd>
356 <div class="OptionsBox">
357 $String = $TopologicalPharmacophoreAtomPairsFP-&gt;
358 StringifyTopologicalPharmacophoreAtomPairsFingerprints();</div>
359 <p>Returns a string containing information about <em>TopologicalPharmacophoreAtomPairsFingerprints</em> object.</p>
360 </dd>
361 </dl>
362 <p>
363 </p>
364 <h2>AUTHOR</h2>
365 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
366 <p>
367 </p>
368 <h2>SEE ALSO</h2>
369 <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
370 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp
371 <a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp
372 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp
373 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
374 </p>
375 <p>
376 </p>
377 <h2>COPYRIGHT</h2>
378 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
379 <p>This file is part of MayaChemTools.</p>
380 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
381 the terms of the GNU Lesser General Public License as published by the Free
382 Software Foundation; either version 3 of the License, or (at your option)
383 any later version.</p>
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