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3 <title>MayaChemTools:Documentation:Fingerprints::AtomNeighborhoodsFingerprints.pm</title>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FileUtil.html" title="FileUtil.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::AtomNeighborhoodsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/AtomNeighborhoodsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/AtomNeighborhoodsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/AtomNeighborhoodsFingerprints.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>AtomNeighborhoodsFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::AtomNeighborhoodsFingerprints;</p>
26 <p>use Fingerprints::AtomNeighborhoodsFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p><strong>AtomNeighborhoodsFingerprints</strong> [ Ref 53-56, Ref 73 ] class provides the following methods:</p>
31 <p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getdescription">GetDescription</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a>
32 , <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>, <a href="#setmaxneighborhoodradius">SetMaxNeighborhoodRadius</a>
33 , <a href="#setminneighborhoodradius">SetMinNeighborhoodRadius</a>, <a href="#stringifyatomneighborhoodsfingerprints">StringifyAtomNeighborhoodsFingerprints</a>
34 </p><p><strong>AtomNeighborhoodsFingerprints</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>AtomNeighborhoodsFingerprints</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>AtomNeighborhoodsFingerprints</strong>
43 corresponding to following <strong>AtomIdentifierTypes</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 sucb as <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse</strong>, initial atom types are
50 assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
51 around each non-hydrogen central atom corresponding to radii between specified values
52 <strong>MinNeighborhoodRadius</strong> and <strong>MaxNeighborhoodRadius</strong>, unique atom types at each radii
53 level are counted and an atom neighborhood identifier is generated.</p>
54 <p>The format of an atom neighborhood identifier around a central non-hydrogen atom at a
55 specific radius is:</p>
56 <div class="OptionsBox">
57 NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;</div>
58 <div class="OptionsBox">
59 NR: Neighborhood radius
60 <br/> AtomType: Assigned atom type
61 <br/> ATC: Atom type count</div>
62 <p>The atom neighborhood identifier for non-hydrogen central atom corresponding to all specified radii
63 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:</p>
64 <div class="OptionsBox">
65 NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;:NR&lt;n&gt;-&lt;AtomType&gt;-ATC&lt;n&gt;:...</div>
66 <p>The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
67 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.</p>
68 <p>The current release of MayaChemTools generates the following types of atom neighborhoods
69 fingerprints vector strings:</p>
70 <div class="OptionsBox">
71 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
72 <br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
73 <br/> C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
74 <br/> 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
75 <br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
76 <br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div>
77 <div class="OptionsBox">
78 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
79 <br/> adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
80 <br/> NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
81 <br/> _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
82 <br/> C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
83 <br/> 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...</div>
84 <div class="OptionsBox">
85 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
86 <br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
87 <br/> NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
88 <br/> 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
89 <br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
90 <br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...</div>
91 <div class="OptionsBox">
92 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
93 <br/> s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
94 <br/> ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
95 <br/> C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
96 <br/> R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
97 <br/> TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...</div>
98 <div class="OptionsBox">
99 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
100 <br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
101 <br/> 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
102 <br/> 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
103 <br/> 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
104 <br/> C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...</div>
105 <div class="OptionsBox">
106 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
107 <br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
108 <br/> CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
109 <br/> NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
110 <br/> ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
111 <br/> 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...</div>
112 <div class="OptionsBox">
113 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
114 <br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
115 <br/> -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
116 <br/> O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
117 <br/> ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
118 <br/> C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...</div>
119 <div class="OptionsBox">
120 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
121 <br/> s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
122 <br/> -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
123 <br/> e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
124 <br/> ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
125 <br/> TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...</div>
126 <div class="OptionsBox">
127 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
128 <br/> 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
129 <br/> _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
130 <br/> C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
131 <br/> 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
132 <br/> -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...</div>
133 <p>
134 </p>
135 <h2>METHODS</h2>
136 <dl>
137 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
138 <dd>
139 <div class="OptionsBox">
140 $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
141 %NamesAndValues);</div>
142 <p>Using specified <em>AtomNeighborhoodsFingerprints</em> property names and values hash, <strong>new</strong>
143 method creates a new object and returns a reference to newly created <strong>AtomNeighborhoodsFingerprints</strong>
144 object. By default, the following properties are initialized:</p>
145 <div class="OptionsBox">
146 Molecule = ''
147 <br/> Type = 'AtomNeighborhoods'
148 <br/> MinNeighborhoodRadius = 0
149 <br/> MaxNeighborhoodRadius = 2
150 <br/> AtomIdentifierType = ''
151 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
152 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
153 <p>Examples:</p>
154 <div class="OptionsBox">
155 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
156 'Molecule' =&gt; $Molecule,
157 'AtomIdentifierType' =&gt;
158 &quot;AtomicInvariantsAtomTypes&quot;);</div>
159 <div class="OptionsBox">
160 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
161 'Molecule' =&gt; $Molecule,
162 'MinNeighborhoodRadius' =&gt; 0,
163 'MaxNeighborhoodRadius' =&gt; 2,
164 'AtomIdentifierType' =&gt;
165 'AtomicInvariantsAtomTypes',
166 'AtomicInvariantsToUse' =&gt;
167 ['AS', 'X', 'BO', 'H', 'FC'] );</div>
168 <div class="OptionsBox">
169 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
170 'Molecule' =&gt; $Molecule,
171 'AtomIdentifierType' =&gt;
172 'SYBYLAtomTypes');</div>
173 <div class="OptionsBox">
174 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
175 'Molecule' =&gt; $Molecule,
176 'AtomIdentifierType' =&gt;
177 'MMFF94AtomTypes');</div>
178 <div class="OptionsBox">
179 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
180 'Molecule' =&gt; $Molecule,
181 'AtomIdentifierType' =&gt;
182 'AtomicInvariantsAtomTypes');</div>
183 <div class="OptionsBox">
184 $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
185 'Molecule' =&gt; $Molecule,
186 'MinNeighborhoodRadius' =&gt; 0,
187 'MaxNeighborhoodRadius' =&gt; 2,
188 'AtomIdentifierType' =&gt;
189 'FunctionalClassAtomTypes',
190 'FunctionalClassesToUse' =&gt;
191 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div>
192 <div class="OptionsBox">
193 $AtomNeighborhoodsFingerprints-&gt;GenerateFingerprints();
194 <br/> print &quot;$AtomNeighborhoodsFingerprints\n&quot;;</div>
195 </dd>
196 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
197 <dd>
198 <div class="OptionsBox">
199 $AtomNeighborhoodsFingerprints-&gt;GenerateFingerprints();</div>
200 <p>Generates atom neighborhood fingerprints and returns <em>AtomNeighborhoodsFingerprints</em>.</p>
201 </dd>
202 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
203 <dd>
204 <div class="OptionsBox">
205 $Description = $AtomNeighborhoodsFingerprints-&gt;GetDescription();</div>
206 <p>Returns a string containing description of atom neighborhood fingerprints.</p>
207 </dd>
208 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
209 <dd>
210 <div class="OptionsBox">
211 $AtomNeighborhoodsFingerprints-&gt;SetAtomIdentifierType($IdentifierType);</div>
212 <p>Sets atom <em>IdentifierType</em> to use during atom neighborhood fingerprints generation and
213 returns <em>AtomNeighborhoodsFingerprints</em>.</p>
214 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
215 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
216 TPSAAtomTypes, UFFAtomTypes</em>.</p>
217 </dd>
218 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
219 <dd>
220 <div class="OptionsBox">
221 $AtomNeighborhoodsFingerprints-&gt;SetAtomicInvariantsToUse($ValuesRef);
222 <br/> $AtomNeighborhoodsFingerprints-&gt;SetAtomicInvariantsToUse(@Values);</div>
223 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
224 for atom neighborhood fingerprints generation and returns <em>AtomNeighborhoodsFingerprints</em>.</p>
225 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
226 H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p>
227 <p>The atomic invariants abbreviations correspond to:</p>
228 <div class="OptionsBox">
229 AS = Atom symbol corresponding to element symbol</div>
230 <div class="OptionsBox">
231 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
232 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
233 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
234 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
235 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
236 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
237 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
238 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
239 <br/> RA = Ring atom annotation indicating whether atom is a ring
240 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
241 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
242 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
243 3 (triplet)</div>
244 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
245 <div class="OptionsBox">
246 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>
247 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
248 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
249 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
250 are also allowed:</p>
251 <div class="OptionsBox">
252 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
253 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
254 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
255 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
256 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
257 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
258 <br/> H : NumOfImplicitAndExplicitHydrogens
259 <br/> Ar : Aromatic
260 <br/> RA : RingAtom
261 <br/> FC : FormalCharge
262 <br/> MN : MassNumber
263 <br/> SM : SpinMultiplicity</div>
264 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
265 atom types.</p>
266 </dd>
267 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
268 <dd>
269 <div class="OptionsBox">
270 $AtomNeighborhoodsFingerprints-&gt;SetFunctionalClassesToUse($ValuesRef);
271 <br/> $AtomNeighborhoodsFingerprints-&gt;SetFunctionalClassesToUse(@Values);</div>
272 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
273 for atom neighborhoods fingerprints generation and returns <em>AtomNeighborhoodsFingerprints</em>.</p>
274 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
275 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
276 <p>The functional class abbreviations correspond to:</p>
277 <div class="OptionsBox">
278 HBD: HydrogenBondDonor
279 <br/> HBA: HydrogenBondAcceptor
280 <br/> PI : PositivelyIonizable
281 <br/> NI : NegativelyIonizable
282 <br/> Ar : Aromatic
283 <br/> Hal : Halogen
284 <br/> H : Hydrophobic
285 <br/> RA : RingAtom
286 <br/> CA : ChainAtom</div>
287 <div class="OptionsBox">
288 Functional class atom type specification for an atom corresponds to:</div>
289 <div class="OptionsBox">
290 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
291 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
292 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
293 <div class="OptionsBox">
294 HydrogenBondDonor: NH, NH2, OH
295 <br/> HydrogenBondAcceptor: N[!H], O
296 <br/> PositivelyIonizable: +, NH2
297 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
298 </dd>
299 <dt><strong><a name="setmaxneighborhoodradius" class="item"><strong>SetMaxNeighborhoodRadius</strong></a></strong></dt>
300 <dd>
301 <div class="OptionsBox">
302 $AtomNeighborhoodsFingerprints-&gt;SetMaxNeighborhoodRadius($Radius);</div>
303 <p>Sets maximum neighborhood radius to use during atom neighborhood fingerprints generation and
304 returns <em>AtomNeighborhoodsFingerprints</em>.</p>
305 </dd>
306 <dt><strong><a name="setminneighborhoodradius" class="item"><strong>SetMinNeighborhoodRadius</strong></a></strong></dt>
307 <dd>
308 <div class="OptionsBox">
309 $AtomNeighborhoodsFingerprints-&gt;SetMinNeighborhoodRadius($Radius);</div>
310 <p>Sets minimum neighborhood radius to use during atom neighborhood fingerprints generation and
311 returns <em>AtomNeighborhoodsFingerprints</em>.</p>
312 </dd>
313 <dt><strong><a name="stringifyatomneighborhoodsfingerprints" class="item"><strong>StringifyAtomNeighborhoodsFingerprints</strong></a></strong></dt>
314 <dd>
315 <div class="OptionsBox">
316 $String = $Fingerprints-&gt;StringifyAtomNeighborhoodsFingerprints();</div>
317 <p>Returns a string containing information about <em>AtomNeighborhoodsFingerprints</em> object.</p>
318 </dd>
319 </dl>
320 <p>
321 </p>
322 <h2>AUTHOR</h2>
323 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
324 <p>
325 </p>
326 <h2>SEE ALSO</h2>
327 <p><a href="./Fingerprints.html">Fingerprints.pm</a>,&nbsp<a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>,&nbsp<a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp
328 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,&nbsp<a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp
329 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp
330 <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,&nbsp
331 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
332 </p>
333 <p>
334 </p>
335 <h2>COPYRIGHT</h2>
336 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
337 <p>This file is part of MayaChemTools.</p>
338 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
339 the terms of the GNU Lesser General Public License as published by the Free
340 Software Foundation; either version 3 of the License, or (at your option)
341 any later version.</p>
342 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
343 <table width="100%" border=0 cellpadding=0 cellspacing=2>
344 <tr align="left" valign="top"><td width="33%" align="left"><a href="./FileUtil.html" title="FileUtil.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::AtomNeighborhoodsFingerprints.pm</strong></td></tr>
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