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3 <title>MayaChemTools:Documentation:ExtendedConnectivityFingerprints.pl</title>
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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="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtendedConnectivityFingerprints.pl</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>
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17 </div>
18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>ExtendedConnectivityFingerprints.pl - Generate extended connectivity fingerprints for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>ExtendedConnectivityFingerprints.pl SDFile(s)...</p>
26 <p>ExtendedConnectivityFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
27 [<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>]
28 [<strong>--AtomicInvariantsToUse</strong> <em>&quot;AtomicInvariant,AtomicInvariant...&quot;</em>]
29 [<strong>--FunctionalClassesToUse</strong> <em>&quot;FunctionalClass1,FunctionalClass2...&quot;</em>]
30 [<strong>--BitsOrder</strong> <em>Ascending | Descending</em>] [<strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em>]
31 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>]
32 [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em>]
33 [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
34 [<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>]
35 [<strong>-m, --mode</strong> <em>ExtendedConnectivity | ExtendedConnecticityCount | ExtendedConnecticityBits</em>]
36 [<strong>-n, --NeighborhoodRadius</strong> <em>number</em>] [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>]
37 [<strong>-o, --overwrite</strong>] [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-s, --size</strong> <em>number</em>]
38 [<strong>--UsePerlCoreRandom</strong> <em>Yes | No</em>]
39 [<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
40 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
41 <p>
42 </p>
43 <h2>DESCRIPTION</h2>
44 <p>Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for <em>SDFile(s)</em> and create appropriate
45 SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to molecular fingerprints.</p>
46 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
47 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
48 can be specified either by <em>*.sdf</em> or the current directory name.</p>
49 <p>The current release of MayaChemTools supports generation of extended connectivity fingerprints
50 corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p>
51 <div class="OptionsBox">
52 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
53 <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
54 <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div>
55 <p>Based on values specified for <strong>-a, --AtomIdentifierType</strong>, <strong>--AtomicInvariantsToUse</strong>
56 and <strong>--FunctionalClassesToUse</strong>, initial atom types are assigned to all non-hydrogen atoms in
57 a molecule and these atom types strings are converted into initial atom identifier integers using
58 <strong>TextUtil::HashCode</strong> function. The duplicate atom identifiers are removed.</p>
59 <p>For <strong>-n, --NeighborhoodRadius</strong> value of <em>0</em>, the initial set of unique atom identifiers comprises
60 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
61 atom up to specified <strong>-n, --NeighborhoodRadius</strong> value. For each non-hydrogen central atom
62 at a specific radius, its neighbors at next radius level along with their bond orders and previously
63 calculated atom identifiers are collected which in turn are used to generate a new integer
64 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
65 followed by atom identifiers to make these values graph invariant.</p>
66 <p>After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
67 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
68 value generated using <strong>TextUtil::HashCode</strong> are tracked by keeping the atom identifiers at
69 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
70 radius are also tracked by identifying equivalent atoms and bonds corresponding to substructures
71 used for generating atom identifier and keeping integer atom identifier with lowest value.</p>
72 <p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>-m, --mode</strong>, the duplicate identifiers are
73 removed from the list and the unique atom identifiers constitute the extended connectivity
74 fingerprints of a molecule.</p>
75 <p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>-m, --mode</strong>, the occurrence of each
76 unique atom identifiers appears is counted and the unique atom identifiers along with their
77 count constitute the extended connectivity fingerprints of a molecule.</p>
78 <p>For <em>ExtendedConnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, the unique atom identifiers
79 are used as a random number seed to generate a random integer value between 0 and <strong>--Size</strong> which
80 in turn is used to set corresponding bits in the fingerprint bit-vector string.</p>
81 <p>Example of <em>SD</em> file containing extended connectivity fingerprints string data:</p>
82 <div class="OptionsBox">
83 ... ...
84 <br/> ... ...
85 <br/> $$$$
86 <br/> ... ...
87 <br/> ... ...
88 <br/> ... ...
89 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
90 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
91 <br/> ... ...
92 <br/> 2 3 1 0 0 0 0
93 <br/> ... ...
94 <br/> M END
95 <br/> &gt; &lt;CmpdID&gt;
96 <br/> Cmpd1</div>
97 <div class="OptionsBox">
98 &gt; &lt;ExtendedConnectivityFingerprints&gt;
99 <br/> FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu
100 <br/> s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66
101 <br/> 6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087
102 <br/> 99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90
103 <br/> 6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853...</div>
104 <div class="OptionsBox">
105 $$$$
106 <br/> ... ...
107 <br/> ... ...</div>
108 <p>Example of <em>FP</em> file containing extended connectivity fingerprints string data:</p>
109 <div class="OptionsBox">
110 #
111 <br/> # Package = MayaChemTools 7.4
112 <br/> # Release Date = Oct 21, 2010
113 <br/> #
114 <br/> # TimeStamp = Fri Mar 11 14:43:57 2011
115 <br/> #
116 <br/> # FingerprintsStringType = FingerprintsVector
117 <br/> #
118 <br/> # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2
119 <br/> # VectorStringFormat = ValuesString
120 <br/> # VectorValuesType = AlphaNumericalValues
121 <br/> #
122 <br/> Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432...
123 <br/> Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699...
124 <br/> ... ...
125 <br/> ... ..</div>
126 <p>Example of CSV <em>Text</em> file containing extended connectivity fingerprints string data:</p>
127 <div class="OptionsBox">
128 &quot;CompoundID&quot;,&quot;ExtendedConnectivityFingerprints&quot;
129 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy
130 <br/> pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352
131 <br/> 413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
132 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551
133 <br/> 41035 906706094 988546669 1018231313 1032696425 1197507444 13312500...&quot;
134 <br/> ... ...
135 <br/> ... ...</div>
136 <p>The current release of MayaChemTools generates the following types of extended connectivity
137 fingerprints vector strings:</p>
138 <div class="OptionsBox">
139 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
140 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
141 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
142 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
143 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
144 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
145 <div class="OptionsBox">
146 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
147 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
148 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
149 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
150 <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
151 <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>
152 <div class="OptionsBox">
153 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
154 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
155 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
156 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
157 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
158 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
159 <div class="OptionsBox">
160 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
161 <br/> es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
162 <br/> 0300000091000004000000020000100000000124008200020000000040020000000000
163 <br/> 2080000000820040010020000000008040000000000080001000000000400000000000
164 <br/> 4040000090000061010000000800200000000000001400000000020080000000000020
165 <br/> 00008020200000408000</div>
166 <div class="OptionsBox">
167 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
168 <br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
169 <br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
170 <br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
171 <br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
172 <br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div>
173 <div class="OptionsBox">
174 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
175 <br/> Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
176 <br/> 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
177 <br/> 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
178 <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
179 <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>
180 <div class="OptionsBox">
181 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
182 <br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
183 <br/> 0000000001000100000000001000000000000000000000000000000000101000000010
184 <br/> 0000001000000000010000000000000000000000000000000000000000000000000100
185 <br/> 0000000000001000000000000001000000000001001000000000000000000000000000
186 <br/> 0000000000000000100000000000001000000000000000000000000000000000000...</div>
187 <div class="OptionsBox">
188 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
189 <br/> lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
190 <br/> 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
191 <br/> 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
192 <br/> 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
193 <br/> 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...</div>
194 <div class="OptionsBox">
195 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
196 <br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
197 <br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
198 <br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
199 <br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
200 <br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div>
201 <div class="OptionsBox">
202 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
203 <br/> haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
204 <br/> 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
205 <br/> 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
206 <br/> 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
207 <br/> 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...</div>
208 <div class="OptionsBox">
209 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
210 <br/> aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
211 <br/> 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
212 <br/> 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
213 <br/> 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
214 <br/> 41915747 679881756 721736571 794256218 908276640 992898760 10987549...</div>
215 <div class="OptionsBox">
216 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
217 <br/> aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
218 <br/> 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
219 <br/> 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
220 <br/> 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
221 <br/> 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...</div>
222 <div class="OptionsBox">
223 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
224 <br/> NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
225 <br/> 700688206 265614156 363161397 681332588 810600886 885767127 950172500
226 <br/> 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
227 <br/> 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
228 <br/> 654 256360355 279492740 291251259 317592700 333763396 972105960 101...</div>
229 <div class="OptionsBox">
230 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
231 <br/> umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
232 <br/> 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
233 <br/> 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
234 <br/> 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
235 <br/> 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...</div>
236 <p>
237 </p>
238 <h2>OPTIONS</h2>
239 <dl>
240 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
241 <dd>
242 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
243 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
244 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
245 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
246 <p>The supported aromaticity model names along with model specific control parameters
247 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
248 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
249 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
250 for detecting aromaticity corresponding to a specific model.</p>
251 </dd>
252 <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt>
253 <dd>
254 <p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
255 atoms during calculation of extended connectivity fingerprints [ Ref 48, Ref 52]. Possible values
256 in the current release are: <em>AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,
257 DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
258 TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p>
259 </dd>
260 <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>&quot;AtomicInvariant,AtomicInvariant...&quot;</em></strong></dt>
261 <dd>
262 <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
263 option. It's a list of comma separated valid atomic invariant atom types.</p>
264 <p>Possible values for atomic invarians are: <em>AS, X, BO, LBO, SB, DB, TB,
265 H, Ar, RA, FC, MN, SM</em>. Default value [ Ref 24 ]: <em>AS,X,BO,H,FC,MN</em>.</p>
266 <p>The atomic invariants abbreviations correspond to:</p>
267 <div class="OptionsBox">
268 AS = Atom symbol corresponding to element symbol</div>
269 <div class="OptionsBox">
270 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
271 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
272 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy atoms
273 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
274 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
275 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
276 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
277 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
278 <br/> RA = Ring atom annotation indicating whether atom is a ring
279 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
280 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
281 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
282 3 (triplet)</div>
283 <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p>
284 <div class="OptionsBox">
285 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>
286 <p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
287 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p>
288 <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
289 are also allowed:</p>
290 <div class="OptionsBox">
291 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
292 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
293 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
294 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
295 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
296 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
297 <br/> H : NumOfImplicitAndExplicitHydrogens
298 <br/> Ar : Aromatic
299 <br/> RA : RingAtom
300 <br/> FC : FormalCharge
301 <br/> MN : MassNumber
302 <br/> SM : SpinMultiplicity</div>
303 <p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant
304 atom types.</p>
305 </dd>
306 <dt><strong><strong>--BitsOrder</strong> <em>Ascending | Descending</em></strong></dt>
307 <dd>
308 <p>Bits order to use during generation of fingerprints bit-vector string for <em>ExtendedConnectivityBits</em>
309 value of <strong>-m, --mode</strong> option. Possible values: <em>Ascending, Descending</em>. Default: <em>Ascending</em>.</p>
310 <p><em>Ascending</em> bit order which corresponds to first bit in each byte as the lowest bit as
311 opposed to the highest bit.</p>
312 <p>Internally, bits are stored in <em>Ascending</em> order using Perl vec function. Regardless
313 of machine order, big-endian or little-endian, vec function always considers first
314 string byte as the lowest byte and first bit within each byte as the lowest bit.</p>
315 </dd>
316 <dt><strong><strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em></strong></dt>
317 <dd>
318 <p>Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by
319 <strong>--output</strong> used during <em>ExtendedConnectivityBits</em> value of <strong>-m, --mode</strong> option. Possible
320 values: <em>BinaryString, HexadecimalString</em>. Default value: <em>BinaryString</em>.</p>
321 <p><em>BinaryString</em> corresponds to an ASCII string containing 1s and 0s. <em>HexadecimalString</em>
322 contains bit values in ASCII hexadecimal format.</p>
323 <p>Examples:</p>
324 <div class="OptionsBox">
325 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
326 <br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
327 <br/> 0000000001010000000110000011000000000000100000000000000000000000100001
328 <br/> 1000000110000000000000000000000000010011000000000000000000000000010000
329 <br/> 0000000000000000000000000010000000000000000001000000000000000000000000
330 <br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div>
331 <div class="OptionsBox">
332 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
333 <br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
334 <br/> 0000000001000100000000001000000000000000000000000000000000101000000010
335 <br/> 0000001000000000010000000000000000000000000000000000000000000000000100
336 <br/> 0000000000001000000000000001000000000001001000000000000000000000000000
337 <br/> 0000000000000000100000000000001000000000000000000000000000000000000...</div>
338 </dd>
339 <dt><strong><strong>--FunctionalClassesToUse</strong> <em>&quot;FunctionalClass1,FunctionalClass2...&quot;</em></strong></dt>
340 <dd>
341 <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong>
342 option. It's a list of comma separated valid functional classes.</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</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><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
369 <dd>
370 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
371 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
372 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
373 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
374 look like Cmpd&lt;Number&gt;.</p>
375 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
376 <div class="OptionsBox">
377 MolID
378 <br/> ExtReg</div>
379 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
380 <div class="OptionsBox">
381 Compound</div>
382 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
383 instead of default value of Cmpd&lt;Number&gt;.</p>
384 </dd>
385 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
386 <dd>
387 <p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value
388 of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p>
389 </dd>
390 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
391 <dd>
392 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
393 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
394 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
395 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
396 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
397 Default: <em>LabelPrefix</em>.</p>
398 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
399 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
400 values are replaced with sequential compound IDs.</p>
401 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
402 </dd>
403 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
404 <dd>
405 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
406 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
407 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
408 <p>Examples:</p>
409 <div class="OptionsBox">
410 Extreg
411 <br/> MolID,CompoundName</div>
412 </dd>
413 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
414 <dd>
415 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
416 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
417 data field; transfer SD data files common to all compounds; extract specified data fields;
418 generate a compound ID using molname line, a compound prefix, or a combination of both.
419 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
420 </dd>
421 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
422 <dd>
423 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
424 Default value: <em>Yes</em>.</p>
425 <p>By default, compound data is checked before calculating fingerprints and compounds containing
426 atom data corresponding to non-element symbols or no atom data are ignored.</p>
427 </dd>
428 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
429 <dd>
430 <p>SD data label or text file column label to use for fingerprints string in output SD or
431 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>ExtendedConnectivityFingerprints</em>.</p>
432 </dd>
433 <dt><strong><strong>-h, --help</strong></strong></dt>
434 <dd>
435 <p>Print this help message.</p>
436 </dd>
437 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
438 <dd>
439 <p>Generate fingerprints for only the largest component in molecule. Possible values:
440 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
441 <p>For molecules containing multiple connected components, fingerprints can be generated
442 in two different ways: use all connected components or just the largest connected
443 component. By default, all atoms except for the largest connected component are
444 deleted before generation of fingerprints.</p>
445 </dd>
446 <dt><strong><strong>-m, --mode</strong> <em>ExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits</em></strong></dt>
447 <dd>
448 <p>Specify type of extended connectivity fingerprints to generate for molecules in <em>SDFile(s)</em>.
449 Possible values: <em>ExtendedConnectivity, ExtendedConnecticityCount or
450 ExtendedConnectivityBits</em>. Default value: <em>ExtendedConnectivity</em>.</p>
451 <p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint vector
452 containing unique atom identifiers constitute the extended connectivity fingerprints
453 of a molecule.</p>
454 <p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint vector
455 containing unique atom identifiers along with their count constitute the extended connectivity
456 fingerprints of a molecule.</p>
457 <p>For <em>ExtendedConnnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint bit vector
458 indicating presence/absence of structurally unique atom identifiers constitute the extended
459 connectivity fingerprints of a molecule.</p>
460 </dd>
461 <dt><strong><strong>-n, --NeighborhoodRadius</strong> <em>number</em></strong></dt>
462 <dd>
463 <p>Atomic neighborhood radius for generating extended connectivity neighborhoods. Default
464 value: <em>2</em>. Valid values: &gt;= 0. Neighborhood radius of zero correspond to just the list
465 of non-hydrogen atoms.</p>
466 <p>Default value of <em>2</em> for atomic neighborhood radius generates extended connectivity
467 fingerprints corresponding to path length or diameter value of <em>4</em> [ Ref 52b ].</p>
468 </dd>
469 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
470 <dd>
471 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
472 Default value: <em>comma</em>.</p>
473 </dd>
474 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
475 <dd>
476 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
477 </dd>
478 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
479 <dd>
480 <p>Overwrite existing files.</p>
481 </dd>
482 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
483 <dd>
484 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
485 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
486 </dd>
487 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
488 <dd>
489 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file names:
490 &lt;SDFileName&gt;&lt;ExtendedConnectivityFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt;
491 value. The sdf, fpf, csv, and tsv &lt;Ext&gt; values are used for SD, FP, comma/semicolon, and tab
492 delimited text files, respectively.This option is ignored for multiple input files.</p>
493 </dd>
494 <dt><strong><strong>-s, --size</strong> <em>number</em></strong></dt>
495 <dd>
496 <p>Size of bit-vector to use during generation of fingerprints bit-vector string for
497 <em>ExtendedConnectivityBits</em> value of <strong>-m, --mode</strong>. Default value: <em>1024</em>.
498 Valid values correspond to any positive integer which satisfies the following criteria:
499 power of 2, &gt;= 32 and &lt;= 2 ** 32.</p>
500 <p>Examples:</p>
501 <div class="OptionsBox">
502 512
503 1024
504 2048</div>
505 </dd>
506 <dt><strong><strong>--UsePerlCoreRandom</strong> <em>Yes | No</em></strong></dt>
507 <dd>
508 <p>Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function
509 during random number generation for setting bits in fingerprints bit-vector strings. Possible
510 values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
511 <p><em>No</em> value option for <strong>--UsePerlCoreRandom</strong> allows the generation of fingerprints
512 bit-vector strings which are same across different platforms.</p>
513 <p>The random number generator implemented in MayaChemTools is a variant of
514 linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].
515 It is also referred to as Lehmer random number generator or Park-Miller
516 random number generator.</p>
517 <p>Unlike Perl's core random number generator function rand, the random number
518 generator implemented in MayaChemTools, MathUtil::random, generates consistent
519 random values across different platforms for a specific random seed and leads
520 to generation of portable fingerprints bit-vector strings.</p>
521 </dd>
522 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
523 <dd>
524 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
525 <strong>--output</strong> used during &lt;ExtendedConnectivityCount&gt; value of <strong>-m, --mode</strong> option. Possible
526 values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
527 ValuesAndIDsPairsString</em>.</p>
528 <p>Default value during &lt;ExtendedConnectivityCount&gt; value of <strong>-m, --mode</strong> option:
529 <em>IDsAndValuesString</em>.</p>
530 <p>Default value during &lt;ExtendedConnectivity&gt; value of <strong>-m, --mode</strong> option: <em>ValuesString</em>.</p>
531 <p>Examples:</p>
532 <div class="OptionsBox">
533 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
534 <br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
535 <br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
536 <br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
537 <br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
538 <br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div>
539 <div class="OptionsBox">
540 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
541 <br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
542 <br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
543 <br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
544 <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
545 <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>
546 </dd>
547 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
548 <dd>
549 <p>Location of working directory. Default: current directory.</p>
550 </dd>
551 </dl>
552 <p>
553 </p>
554 <h2>EXAMPLES</h2>
555 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
556 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
557 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
558 <div class="ExampleBox">
559 % ExtendedConnectivityFingerprints.pl -r SampleECAIFP -o Sample.sdf</div>
560 <p>To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
561 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
562 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
563 <div class="ExampleBox">
564 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
565 -r SampleECAIFP -o Sample.sdf</div>
566 <p>To generate extended connectivity bits fingerprints as hexadecimal bit-string corresponding to
567 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
568 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
569 vector strings data, type:</p>
570 <div class="ExampleBox">
571 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
572 -r SampleECAIFP -o Sample.sdf</div>
573 <p>To generate extended connectivity bits fingerprints as binary bit-string corresponding to
574 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
575 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
576 vector strings data, type:</p>
577 <div class="ExampleBox">
578 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
579 --BitStringFormat BinaryString -r SampleECAIFP -o Sample.sdf</div>
580 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
581 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
582 and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints
583 vector strings data, type:</p>
584 <div class="ExampleBox">
585 % ExtendedConnectivityFingerprints.pl --output all -r SampleECAIFP
586 -o Sample.sdf</div>
587 <p>To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
588 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
589 and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints
590 vector strings data, type:</p>
591 <div class="ExampleBox">
592 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
593 --output all -r SampleECAIFP -o Sample.sdf</div>
594 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
595 2 using functional class atom types in vector string format and create a SampleECFCFP.csv file
596 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
597 <div class="ExampleBox">
598 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
599 -r SampleECFCFP -o Sample.sdf</div>
600 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
601 2 using DREIDING atom types in vector string format and create a SampleECFP.csv file
602 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
603 <div class="ExampleBox">
604 % ExtendedConnectivityFingerprints.pl -a DREIDINGAtomTypes
605 -r SampleECFP -o Sample.sdf</div>
606 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
607 2 using E-state atom types in vector string format and create a SampleECFP.csv file
608 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
609 <div class="ExampleBox">
610 % ExtendedConnectivityFingerprints.pl -a EStateAtomTypes
611 -r SampleECFP -o Sample.sdf</div>
612 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
613 2 using MMFF94 atom types in vector string format and create a SampleECFP.csv file
614 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
615 <div class="ExampleBox">
616 % ExtendedConnectivityFingerprints.pl -a MMFF94AtomTypes
617 -r SampleECFP -o Sample.sdf</div>
618 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
619 2 using SLogP atom types in vector string format and create a SampleECFP.csv file
620 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
621 <div class="ExampleBox">
622 % ExtendedConnectivityFingerprints.pl -a SLogPAtomTypes
623 -r SampleECFP -o Sample.sdf</div>
624 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
625 2 using SYBYL atom types in vector string format and create a SampleECFP.csv file
626 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
627 <div class="ExampleBox">
628 % ExtendedConnectivityFingerprints.pl -a SYBYLAtomTypes
629 -r SampleECFP -o Sample.sdf</div>
630 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
631 2 using TPSA atom types in vector string format and create a SampleECFP.csv file
632 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
633 <div class="ExampleBox">
634 % ExtendedConnectivityFingerprints.pl -a TPSAAtomTypes
635 -r SampleECFP -o Sample.sdf</div>
636 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
637 2 using UFF atom types in vector string format and create a SampleECFP.csv file
638 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
639 <div class="ExampleBox">
640 % ExtendedConnectivityFingerprints.pl -a UFFAtomTypes
641 -r SampleECFP -o Sample.sdf</div>
642 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
643 3 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
644 file containing sequential compound IDs along with fingerprints vector strings data, type:</p>
645 <div class="ExampleBox">
646 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes -n 3
647 -r SampleECAIFP -o Sample.sdf</div>
648 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
649 3 using functional class atom types in vector string format and create a SampleECFCFP.csv file
650 containing sequential compound IDs along with fingerprints vector strings data, type:</p>
651 <div class="ExampleBox">
652 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes -n 3
653 -r SampleECFCFP -o Sample.sdf</div>
654 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
655 2 using only AS,X atomic invariants atom types in vector string format and create a
656 SampleECAIFP.csv file containing sequential compound IDs along with fingerprints vector
657 strings data, type:</p>
658 <div class="ExampleBox">
659 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
660 --AtomicInvariantsToUse &quot;AS,X&quot; -r SampleECAIFP -o Sample.sdf</div>
661 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
662 2 using only HBD,HBA functional class atom types in vector string format and create a
663 SampleECFCFP.csv file containing sequential compound IDs along with fingerprints vector
664 strings data, type:</p>
665 <div class="ExampleBox">
666 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
667 --FunctionalClassesToUse &quot;HBD,HBA&quot; -r SampleECFCFP -o Sample.sdf</div>
668 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
669 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
670 file containing compound ID from molecule name line along with fingerprints vector strings
671 data, type:</p>
672 <div class="ExampleBox">
673 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
674 --DataFieldsMode CompoundID -CompoundIDMode MolName
675 -r SampleECAIFP -o Sample.sdf</div>
676 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
677 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
678 file containing compound IDs using specified data field along with fingerprints vector strings
679 data, type:</p>
680 <div class="ExampleBox">
681 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
682 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
683 -r SampleECFCFP -o Sample.sdf</div>
684 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
685 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
686 file containing compound ID using combination of molecule name line and an explicit compound
687 prefix along with fingerprints vector strings data, type:</p>
688 <div class="ExampleBox">
689 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
690 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
691 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleECAIFP -o Sample.sdf</div>
692 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
693 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
694 file containing specific data fields columns along with fingerprints vector strings
695 data, type:</p>
696 <div class="ExampleBox">
697 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
698 --DataFieldsMode Specify --DataFields Mol_ID -r SampleECFCFP
699 -o Sample.sdf</div>
700 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
701 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
702 file containing common data fields columns along with fingerprints vector strings data, type:</p>
703 <div class="ExampleBox">
704 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
705 --DataFieldsMode Common -r SampleECAIFP -o Sample.sdf</div>
706 <p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to
707 2 using functional class atom types in vector string format and create SampleECFCFP.sdf, SampleECFCFP.fpf
708 and SampleECFCFP.csv files containing all data fields columns in CSV file along with fingerprints
709 vector strings data, type:</p>
710 <div class="ExampleBox">
711 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
712 --DataFieldsMode All --output all -r SampleECFCFP
713 -o Sample.sdf</div>
714 <p>
715 </p>
716 <h2>AUTHOR</h2>
717 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
718 <p>
719 </p>
720 <h2>SEE ALSO</h2>
721 <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>,&nbsp<a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>,&nbsp<a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,&nbsp
722 <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp
723 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
724 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
725 </p>
726 <p>
727 </p>
728 <h2>COPYRIGHT</h2>
729 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
730 <p>This file is part of MayaChemTools.</p>
731 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
732 the terms of the GNU Lesser General Public License as published by the Free
733 Software Foundation; either version 3 of the License, or (at your option)
734 any later version.</p>
735 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
736 <table width="100%" border=0 cellpadding=0 cellspacing=2>
737 <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="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtendedConnectivityFingerprints.pl</strong></td></tr>
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