|
0
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.pm</title>
|
|
|
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
|
|
|
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
|
|
|
6 </head>
|
|
|
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
|
|
|
8 <br/>
|
|
|
9 <center>
|
|
|
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
|
|
|
11 </center>
|
|
|
12 <br/>
|
|
|
13 <div class="DocNav">
|
|
|
14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
|
|
|
16 </table>
|
|
|
17 </div>
|
|
|
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<PropertyName>(<PropertyValue>);
|
|
|
43 <br/> $PropertyValue = Get<PropertyName>();
|
|
|
44 <br/> Delete<PropertyName>();</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/> = ((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' => $Molecule);</div>
|
|
|
158 <div class="OptionsBox">
|
|
|
159 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
|
|
|
160 'Molecule' => $Molecule,
|
|
|
161 'AtomPairsSetSizeToUse' => 'ArbitrarySize',
|
|
|
162 'MinDistance' => 1,
|
|
|
163 'MaxDistance' => 10,
|
|
|
164 'NormalizationMethodology' => 'None',
|
|
|
165 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H'],
|
|
|
166 'FuzzifyAtomPairsCount' => 0);</div>
|
|
|
167 <div class="OptionsBox">
|
|
|
168 $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints(
|
|
|
169 'Molecule' => $Molecule,
|
|
|
170 'AtomPairsSetSizeToUse' => 'FizedSize',
|
|
|
171 'MinDistance' => 1,
|
|
|
172 'MaxDistance' => 10,
|
|
|
173 'NormalizationMethodology' => 'None',
|
|
|
174 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H'],
|
|
|
175 'FuzzifyAtomPairsCount' => 1,
|
|
|
176 'FuzzificationMethodology' => 'FuzzyBinning',
|
|
|
177 'FuzzFactor' => 0.15,
|
|
|
178 'ValuesPrecision' => 2);</div>
|
|
|
179 <div class="OptionsBox">
|
|
|
180 $TPAPFP->GenerateFingerprints();
|
|
|
181 <br/> print "$TPAPFP\n";</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->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->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->GetAtomPairIDs();
|
|
|
200 <br/> @AtomPairIDs = $TopologicalPharmacophoreAtomPairsFP->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 $TopologicalPharmacophoreAtomPairsFP->SetAtomPairsSetSizeToUse($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 $TopologicalPharmacophoreAtomPairsFP->SetAtomTypesToUse($ValuesRef);
|
|
|
221 <br/> $TopologicalPharmacophoreAtomPairsFP->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->SetAtomTypesWeight(
|
|
|
249 <br/> %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 $TopologicalPharmacophoreAtomPairsFP->SetFuzzFactor($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 $TopologicalPharmacophoreAtomPairsFP->SetFuzzificationMethodology($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 < Dn < 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 $TopologicalPharmacophoreAtomPairsFP->SetFuzzificationMode($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 $TopologicalPharmacophoreAtomPairsFP->SetMaxDistance($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 $TopologicalPharmacophoreAtomPairsFP->SetMinDistance($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 $TopologicalPharmacophoreAtomPairsFP->SetNormalizationMethodology($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 $TopologicalPharmacophoreAtomPairsFP->SetValuesPrecision($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->
|
|
|
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>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, 
|
|
|
370 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>, 
|
|
|
371 <a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, 
|
|
|
372 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, 
|
|
|
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>
|
|
|
384 <p> </p><p> </p><div class="DocNav">
|
|
|
385 <table width="100%" border=0 cellpadding=0 cellspacing=2>
|
|
|
386 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.pm</strong></td></tr>
|
|
|
387 </table>
|
|
|
388 </div>
|
|
|
389 <br />
|
|
|
390 <center>
|
|
|
391 <img src="../../images/h2o2.png">
|
|
|
392 </center>
|
|
|
393 </body>
|
|
|
394 </html>
|
