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1 <html>
2 <head>
3 <title>MayaChemTools:Documentation:Fingerprints::ExtendedConnectivityFingerprints.pm</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./Fingerprints.html" title="Fingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::ExtendedConnectivityFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/ExtendedConnectivityFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/ExtendedConnectivityFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/ExtendedConnectivityFingerprints.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>ExtendedConnectivityFingerprints</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>use Fingerprints::ExtendedConnectivityFingerprints;</p>
26 <p>use Fingerprints::ExtendedConnectivityFingerprints qw(:all);</p>
27 <p>
28 </p>
29 <h2>DESCRIPTION</h2>
30 <p>ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] 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="#setneighborhoodradius">SetNeighborhoodRadius</a>
33 , <a href="#stringifyextendedconnectivityfingerprints">StringifyExtendedConnectivityFingerprints</a>
34 </p><p><strong>ExtendedConnectivityFingerprints</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>ExtendedConnectivityFingerprints</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>ExtendedConnectivityFingerprints</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>, <strong>AtomicInvariantsToUse</strong>
49 and <strong>FunctionalClassesToUse</strong>, initial atom types are assigned to all non-hydrogen atoms in
50 a molecule and these atom types strings are converted into initial atom identifier integers using
51 <strong>TextUtil::HashCode</strong> function. The duplicate atom identifiers are removed.</p>
52 <p>For <strong>NeighborhoodRadius</strong> value of <em>0</em>, the initial set of unique atom identifiers comprises
53 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
54 atom up-to specified <strong>NeighborhoodRadius</strong> value. For each non-hydrogen central atom
55 at a specific radius, its neighbors at next radius level along with their bond orders and previously
56 calculated atom identifiers are collected which in turn are used to generate a new integer
57 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
58 followed by atom identifiers to make these values graph invariant.</p>
59 <p>After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
60 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
61 value generated using <strong>TextUtil::HashCode</strong> are tracked by keeping the atom identifiers at
62 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
63 radius are also tracked by identifying equivalent atom and bonds corresponding to substructures
64 used for generating atom identifier and keeping integer atom identifier with lowest value.</p>
65 <p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>Type</strong>, the duplicate identifiers are
66 removed from the list and the unique atom identifiers constitute the extended connectivity
67 fingerprints of a molecule.</p>
68 <p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>Type</strong>, the occurrence of each
69 unique atom identifiers appears is counted and the unique atom identifiers along with their
70 count constitute the extended connectivity fingerprints of a molecule.</p>
71 <p>For <em>ExtendedConnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, the unique atom identifiers
72 are used as a random number seed to generate a random integer value between 0 and <strong>--Size</strong> which
73 in turn is used to set corresponding bits in the fingerprint bit-vector string.</p>
74 <p>The current release of MayaChemTools generates the following types of extended connectivity
75 fingerprints vector strings:</p>
76 <div class="OptionsBox">
77 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
78 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
79 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
80 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
81 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
82 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
83 <div class="OptionsBox">
84 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
85 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
86 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
87 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
88 <br/> 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
89 <br/> 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1</div>
90 <div class="OptionsBox">
91 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
92 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
93 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
94 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
95 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
96 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
97 <div class="OptionsBox">
98 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
99 <br/> es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
100 <br/> 0300000091000004000000020000100000000124008200020000000040020000000000
101 <br/> 2080000000820040010020000000008040000000000080001000000000400000000000
102 <br/> 4040000090000061010000000800200000000000001400000000020080000000000020
103 <br/> 00008020200000408000</div>
104 <div class="OptionsBox">
105 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
106 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
107 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
108 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
109 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
110 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
111 <div class="OptionsBox">
112 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
113 <br/> Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
114 <br/> 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
115 <br/> 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
116 <br/> 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
117 <br/> 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1</div>
118 <div class="OptionsBox">
119 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
120 <br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
121 <br/> 0000000001000100000000001000000000000000000000000000000000101000000010
122 <br/> 0000001000000000010000000000000000000000000000000000000000000000000100
123 <br/> 0000000000001000000000000001000000000001001000000000000000000000000000
124 <br/> 0000000000000000100000000000001000000000000000000000000000000000000...</div>
125 <div class="OptionsBox">
126 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
127 <br/> lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
128 <br/> 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
129 <br/> 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
130 <br/> 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
131 <br/> 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...</div>
132 <div class="OptionsBox">
133 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
134 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
135 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
136 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
137 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
138 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
139 <div class="OptionsBox">
140 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
141 <br/> haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
142 <br/> 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
143 <br/> 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
144 <br/> 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
145 <br/> 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...</div>
146 <div class="OptionsBox">
147 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
148 <br/> aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
149 <br/> 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
150 <br/> 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
151 <br/> 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
152 <br/> 41915747 679881756 721736571 794256218 908276640 992898760 10987549...</div>
153 <div class="OptionsBox">
154 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
155 <br/> aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
156 <br/> 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
157 <br/> 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
158 <br/> 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
159 <br/> 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...</div>
160 <div class="OptionsBox">
161 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
162 <br/> NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
163 <br/> 700688206 265614156 363161397 681332588 810600886 885767127 950172500
164 <br/> 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
165 <br/> 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
166 <br/> 654 256360355 279492740 291251259 317592700 333763396 972105960 101...</div>
167 <div class="OptionsBox">
168 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
169 <br/> umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
170 <br/> 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
171 <br/> 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
172 <br/> 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
173 <br/> 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...</div>
174 <p>
175 </p>
176 <h2>METHODS</h2>
177 <dl>
178 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
179 <dd>
180 <div class="OptionsBox">
181 $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
182 %NamesAndValues);</div>
183 <p>Using specified <em>ExtendedConnectivityFingerprints</em> property names and values hash, <strong>new</strong>
184 method creates a new object and returns a reference to newly created <strong>ExtendedConnectivityFingerprints</strong>
185 object. By default, the following properties are initialized:</p>
186 <div class="OptionsBox">
187 Molecule = ''
188 <br/> Type = 'ExtendedConnectivity'
189 <br/> NeighborhoodRadius = 2
190 <br/> AtomIdentifierType = ''
191 <br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
192 <br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div>
193 <p>Examples:</p>
194 <div class="OptionsBox">
195 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
196 'Molecule' =&gt; $Molecule,
197 'AtomIdentifierType' =&gt;
198 'AtomicInvariantsAtomTypes');</div>
199 <div class="OptionsBox">
200 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
201 'Type' =&gt; 'ExtendedConnectivityCount',
202 'Molecule' =&gt; $Molecule,
203 'AtomIdentifierType' =&gt;
204 'AtomicInvariantsAtomTypes');</div>
205 <div class="OptionsBox">
206 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
207 'Type' =&gt; 'ExtendedConnectivityBits',
208 'Molecule' =&gt; $Molecule,
209 'Size' =&gt; 1024,
210 'AtomIdentifierType' =&gt;
211 'AtomicInvariantsAtomTypes');</div>
212 <div class="OptionsBox">
213 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
214 'Type' =&gt; 'ExtendedConnectivity',
215 'Molecule' =&gt; $Molecule,
216 'NeighborhoodRadius' =&gt; 2,
217 'AtomIdentifierType' =&gt;
218 'AtomicInvariantsAtomTypes',
219 'AtomicInvariantsToUse' =&gt;
220 ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );</div>
221 <div class="OptionsBox">
222 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
223 'Type' =&gt; 'ExtendedConnectivity',
224 'Molecule' =&gt; $Molecule,
225 'NeighborhoodRadius' =&gt; 2,
226 'AtomIdentifierType' =&gt;
227 'FunctionalClassAtomTypes',
228 'FunctionalClassesToUse' =&gt;
229 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div>
230 <div class="OptionsBox">
231 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
232 'Type' =&gt; 'ExtendedConnectivity',
233 'Molecule' =&gt; $Molecule,;
234 'AtomIdentifierType' =&gt;
235 'MMFF94AtomTypes');</div>
236 <div class="OptionsBox">
237 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
238 'Type' =&gt; 'ExtendedConnectivityCount',
239 'Molecule' =&gt; $Molecule,;
240 'AtomIdentifierType' =&gt;
241 'MMFF94AtomTypes');</div>
242 <div class="OptionsBox">
243 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
244 'Type' =&gt; 'ExtendedConnectivityCount',
245 'Molecule' =&gt; $Molecule,;
246 'AtomIdentifierType' =&gt;
247 'SLogPAtomTypes');</div>
248 <div class="OptionsBox">
249 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
250 'Type' =&gt; 'ExtendedConnectivity',
251 'Molecule' =&gt; $Molecule,;
252 'AtomIdentifierType' =&gt;
253 'SLogPAtomTypes');</div>
254 <div class="OptionsBox">
255 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
256 'Type' =&gt; 'ExtendedConnectivity',
257 'Molecule' =&gt; $Molecule,;
258 'AtomIdentifierType' =&gt;
259 'SYBYLAtomTypes');</div>
260 <div class="OptionsBox">
261 $ExtendedConnectivityFingerprints-&gt;GenerateFingerprints();
262 <br/> print &quot;$ExtendedConnectivityFingerprints\n&quot;;</div>
263 </dd>
264 <dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt>
265 <dd>
266 <div class="OptionsBox">
267 $ExtendedConnectivityFingerprints-&gt;GenerateFingerprints();</div>
268 <p>Generates extended connectivity fingerprints and returns <em>ExtendedConnectivityFingerprints</em>.</p>
269 </dd>
270 <dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt>
271 <dd>
272 <div class="OptionsBox">
273 $Description = $ExtendedConnectivityFingerprints-&gt;GetDescription();</div>
274 <p>Returns a string containing description of extended connectivity fingerprints
275 fingerprints.</p>
276 </dd>
277 <dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt>
278 <dd>
279 <div class="OptionsBox">
280 $ExtendedConnectivityFingerprints-&gt;SetAtomIdentifierType($IdentifierType);</div>
281 <p>Sets atom <em>IdentifierType</em> to use during extended connectivity fingerprints generation and
282 returns <em>ExtendedConnectivityFingerprints</em>.</p>
283 <p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
284 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
285 TPSAAtomTypes, UFFAtomTypes</em>.</p>
286 </dd>
287 <dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt>
288 <dd>
289 <div class="OptionsBox">
290 $ExtendedConnectivityFingerprints-&gt;SetAtomicInvariantsToUse($ValuesRef);
291 <br/> $ExtendedConnectivityFingerprints-&gt;SetAtomicInvariantsToUse(@Values);</div>
292 <p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em>
293 for extended connectivity fingerprints generation and returns <em>ExtendedConnectivityFingerprints</em>.</p>
294 <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB,
295 H, Ar, RA, FC, MN, SM</em>. Default value [ Ref 24 ]: <em>AS,X,BO,H,FC,MN</em>.</p>
296 <p>The atomic invariants abbreviations correspond to:</p>
297 <div class="OptionsBox">
298 AS = Atom symbol corresponding to element symbol</div>
299 <div class="OptionsBox">
300 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
301 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
302 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
303 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
304 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
305 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
306 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
307 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
308 <br/> RA = Ring atom annotation indicating whether atom is a ring
309 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
310 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
311 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
312 3 (triplet)</div>
313 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
314 <div class="OptionsBox">
315 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>
316 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
317 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
318 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
319 are also allowed:</p>
320 <div class="OptionsBox">
321 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
322 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
323 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
324 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
325 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
326 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
327 <br/> H : NumOfImplicitAndExplicitHydrogens
328 <br/> Ar : Aromatic
329 <br/> RA : RingAtom
330 <br/> FC : FormalCharge
331 <br/> MN : MassNumber
332 <br/> SM : SpinMultiplicity</div>
333 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
334 atom types.</p>
335 </dd>
336 <dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt>
337 <dd>
338 <div class="OptionsBox">
339 $ExtendedConnectivityFingerprints-&gt;SetFunctionalClassesToUse($ValuesRef);
340 <br/> $ExtendedConnectivityFingerprints-&gt;SetFunctionalClassesToUse(@Values);</div>
341 <p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em>
342 for extended connectivity fingerprints generation and returns <em>ExtendedConnectivityFingerprints</em>.</p>
343 <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
344 Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p>
345 <p>The functional class abbreviations correspond to:</p>
346 <div class="OptionsBox">
347 HBD: HydrogenBondDonor
348 <br/> HBA: HydrogenBondAcceptor
349 <br/> PI : PositivelyIonizable
350 <br/> NI : NegativelyIonizable
351 <br/> Ar : Aromatic
352 <br/> Hal : Halogen
353 <br/> H : Hydrophobic
354 <br/> RA : RingAtom
355 <br/> CA : ChainAtom</div>
356 <div class="OptionsBox">
357 Functional class atom type specification for an atom corresponds to:</div>
358 <div class="OptionsBox">
359 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div>
360 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom
361 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
362 <div class="OptionsBox">
363 HydrogenBondDonor: NH, NH2, OH
364 <br/> HydrogenBondAcceptor: N[!H], O
365 <br/> PositivelyIonizable: +, NH2
366 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
367 </dd>
368 <dt><strong><a name="setneighborhoodradius" class="item"><strong>SetNeighborhoodRadius</strong></a></strong></dt>
369 <dd>
370 <div class="OptionsBox">
371 $ExtendedConnectivityFingerprints-&gt;SetNeighborhoodRadius($Radius);</div>
372 <p>Sets neighborhood radius to use during extended connectivity fingerprints generation and
373 returns <em>ExtendedConnectivityFingerprints</em>.</p>
374 </dd>
375 <dt><strong><a name="stringifyextendedconnectivityfingerprints" class="item"><strong>StringifyExtendedConnectivityFingerprints</strong></a></strong></dt>
376 <dd>
377 <div class="OptionsBox">
378 $String = $Fingerprints-&gt;StringifyExtendedConnectivityFingerprints();</div>
379 <p>Returns a string containing information about <em>ExtendedConnectivityFingerprints</em> object.</p>
380 </dd>
381 </dl>
382 <p>
383 </p>
384 <h2>AUTHOR</h2>
385 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
386 <p>
387 </p>
388 <h2>SEE ALSO</h2>
389 <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
390 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>,&nbsp<a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>,&nbsp<a href="./MACCSKeys.html">MACCSKeys.pm</a>,&nbsp
391 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,&nbsp
392 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,&nbsp
393 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,&nbsp
394 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</a>
395 </p>
396 <p>
397 </p>
398 <h2>COPYRIGHT</h2>
399 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
400 <p>This file is part of MayaChemTools.</p>
401 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
402 the terms of the GNU Lesser General Public License as published by the Free
403 Software Foundation; either version 3 of the License, or (at your option)
404 any later version.</p>
405 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
406 <table width="100%" border=0 cellpadding=0 cellspacing=2>
407 <tr align="left" valign="top"><td width="33%" align="left"><a href="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./Fingerprints.html" title="Fingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::ExtendedConnectivityFingerprints.pm</strong></td></tr>
408 </table>
409 </div>
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412 <img src="../../images/h2o2.png">
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