|
1
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:Fingerprints::ExtendedConnectivityFingerprints.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="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <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> | <a href="./../pdf/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtendedConnectivityFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <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<PropertyName>(<PropertyValue>);
|
|
|
40 <br/> $PropertyValue = Get<PropertyName>();
|
|
|
41 <br/> Delete<PropertyName>();</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' => $Molecule,
|
|
|
197 'AtomIdentifierType' =>
|
|
|
198 'AtomicInvariantsAtomTypes');</div>
|
|
|
199 <div class="OptionsBox">
|
|
|
200 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
201 'Type' => 'ExtendedConnectivityCount',
|
|
|
202 'Molecule' => $Molecule,
|
|
|
203 'AtomIdentifierType' =>
|
|
|
204 'AtomicInvariantsAtomTypes');</div>
|
|
|
205 <div class="OptionsBox">
|
|
|
206 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
207 'Type' => 'ExtendedConnectivityBits',
|
|
|
208 'Molecule' => $Molecule,
|
|
|
209 'Size' => 1024,
|
|
|
210 'AtomIdentifierType' =>
|
|
|
211 'AtomicInvariantsAtomTypes');</div>
|
|
|
212 <div class="OptionsBox">
|
|
|
213 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
214 'Type' => 'ExtendedConnectivity',
|
|
|
215 'Molecule' => $Molecule,
|
|
|
216 'NeighborhoodRadius' => 2,
|
|
|
217 'AtomIdentifierType' =>
|
|
|
218 'AtomicInvariantsAtomTypes',
|
|
|
219 'AtomicInvariantsToUse' =>
|
|
|
220 ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );</div>
|
|
|
221 <div class="OptionsBox">
|
|
|
222 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
223 'Type' => 'ExtendedConnectivity',
|
|
|
224 'Molecule' => $Molecule,
|
|
|
225 'NeighborhoodRadius' => 2,
|
|
|
226 'AtomIdentifierType' =>
|
|
|
227 'FunctionalClassAtomTypes',
|
|
|
228 'FunctionalClassesToUse' =>
|
|
|
229 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div>
|
|
|
230 <div class="OptionsBox">
|
|
|
231 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
232 'Type' => 'ExtendedConnectivity',
|
|
|
233 'Molecule' => $Molecule,;
|
|
|
234 'AtomIdentifierType' =>
|
|
|
235 'MMFF94AtomTypes');</div>
|
|
|
236 <div class="OptionsBox">
|
|
|
237 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
238 'Type' => 'ExtendedConnectivityCount',
|
|
|
239 'Molecule' => $Molecule,;
|
|
|
240 'AtomIdentifierType' =>
|
|
|
241 'MMFF94AtomTypes');</div>
|
|
|
242 <div class="OptionsBox">
|
|
|
243 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
244 'Type' => 'ExtendedConnectivityCount',
|
|
|
245 'Molecule' => $Molecule,;
|
|
|
246 'AtomIdentifierType' =>
|
|
|
247 'SLogPAtomTypes');</div>
|
|
|
248 <div class="OptionsBox">
|
|
|
249 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
250 'Type' => 'ExtendedConnectivity',
|
|
|
251 'Molecule' => $Molecule,;
|
|
|
252 'AtomIdentifierType' =>
|
|
|
253 'SLogPAtomTypes');</div>
|
|
|
254 <div class="OptionsBox">
|
|
|
255 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
256 'Type' => 'ExtendedConnectivity',
|
|
|
257 'Molecule' => $Molecule,;
|
|
|
258 'AtomIdentifierType' =>
|
|
|
259 'SYBYLAtomTypes');</div>
|
|
|
260 <div class="OptionsBox">
|
|
|
261 $ExtendedConnectivityFingerprints->GenerateFingerprints();
|
|
|
262 <br/> print "$ExtendedConnectivityFingerprints\n";</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->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->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 $ExtendedConnectivityFingerprints->SetAtomIdentifierType($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 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse($ValuesRef);
|
|
|
291 <br/> $ExtendedConnectivityFingerprints->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<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
301 <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
302 <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
303 <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
304 <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
305 <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
306 <br/> H<n> = 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<+n/-n> = Formal charge assigned to atom
|
|
|
310 <br/> MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
311 <br/> SM<n> = 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<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></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 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse($ValuesRef);
|
|
|
340 <br/> $ExtendedConnectivityFingerprints->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 $ExtendedConnectivityFingerprints->SetNeighborhoodRadius($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->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>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>, 
|
|
|
390 <a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>, 
|
|
|
391 <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>, 
|
|
|
392 <a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, 
|
|
|
393 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>, 
|
|
|
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> </p><p> </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> <a href="./index.html" title="Table of Contents">TOC</a> <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>
|
|
|
410 <br />
|
|
|
411 <center>
|
|
|
412 <img src="../../images/h2o2.png">
|
|
|
413 </center>
|
|
|
414 </body>
|
|
|
415 </html>
|
