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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./JoinTextFiles.html" title="JoinTextFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./MergeTextFiles.html" title="MergeTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>MACCSKeysFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/MACCSKeysFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/MACCSKeysFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/MACCSKeysFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/MACCSKeysFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/MACCSKeysFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>MACCSKeysFingerprints.pl - Generate MACCS key fingerprints for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>MACCSKeysFingerprints.pl SDFile(s)...</p>
26 <p>MACCSKeysFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
27 [<strong>--BitsOrder</strong> <em>Ascending | Descending</em>]
28 [<strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em>]
29 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>]
30 [<strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>]
31 [<strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em>] [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>]
32 [<strong>-f, --Filter</strong> <em>Yes | No</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>]
33 [<strong>-m, --mode</strong> <em>MACCSKeyBits | MACCSKeyCount</em>] [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>]
34 [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
35 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-s, --size</strong> <em>number</em>]
36 [<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
37 [<strong>-w, --WorkingDir</strong> <em>DirName</em>]</p>
38 <p>
39 </p>
40 <h2>DESCRIPTION</h2>
41 <p>Generate MACCS (Molecular ACCess System) keys fingerprints [ Ref 45-47 ] for <em>SDFile(s)</em>
42 and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints bit-vector or
43 vector strings corresponding to molecular fingerprints.</p>
44 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
45 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
46 can be specified either by <em>*.sdf</em> or the current directory name.</p>
47 <p>For each MACCS keys definition, atoms are processed to determine their membership to the key
48 and the appropriate molecular fingerprints strings are generated. An atom can belong to multiple
49 MACCS keys.</p>
50 <p>For <em>MACCSKeyBits</em> value of <strong>-m, --mode</strong> option, a fingerprint bit-vector string containing
51 zeros and ones is generated and for <em>MACCSKeyCount</em> value, a fingerprint vector string
52 corresponding to number of MACCS keys [ Ref 45-47 ] is generated.</p>
53 <p><em>MACCSKeyBits | MACCSKeyCount</em> values for <strong>-m, --mode</strong> option along with two possible
54 <em>166 | 322</em> values of <strong>-s, --size</strong> supports generation of four different types of MACCS
55 keys fingerprint: <em>MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount</em>.</p>
56 <p>Example of <em>SD</em> file containing MAACS keys fingerprints string data:</p>
57 <div class="OptionsBox">
58 ... ...
59 <br/> ... ...
60 <br/> $$$$
61 <br/> ... ...
62 <br/> ... ...
63 <br/> ... ...
64 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
65 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
66 <br/> ... ...
67 <br/> 2 3 1 0 0 0 0
68 <br/> ... ...
69 <br/> M END
70 <br/> &gt; &lt;CmpdID&gt;
71 <br/> Cmpd1</div>
72 <div class="OptionsBox">
73 &gt; &lt;MACCSKeysFingerprints&gt;
74 <br/> FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;000000000
75 <br/> 00000000000000000000000000000000100100001001000000001001000000001110001
76 <br/> 00101010111100011011000100110110000011011110100110111111111111011111111
77 <br/> 11111111110111000</div>
78 <div class="OptionsBox">
79 $$$$
80 <br/> ... ...
81 <br/> ... ...</div>
82 <p>Example of <em>FP</em> file containing MAACS keys fingerprints string data:</p>
83 <div class="OptionsBox">
84 #
85 <br/> # Package = MayaChemTools 7.4
86 <br/> # Release Date = Oct 21, 2010
87 <br/> #
88 <br/> # TimeStamp = Fri Mar 11 14:57:24 2011
89 <br/> #
90 <br/> # FingerprintsStringType = FingerprintsBitVector
91 <br/> #
92 <br/> # Description = MACCSKeyBits
93 <br/> # Size = 166
94 <br/> # BitStringFormat = BinaryString
95 <br/> # BitsOrder = Ascending
96 <br/> #
97 <br/> Cmpd1 00000000000000000000000000000000000000000100100001001000000001...
98 <br/> Cmpd2 00000000000000000000000010000000001000000010000000001000000000...
99 <br/> ... ...
100 <br/> ... ..</div>
101 <p>Example of CSV <em>Text</em> file containing MAACS keys fingerprints string data:</p>
102 <div class="OptionsBox">
103 &quot;CompoundID&quot;,&quot;MACCSKeysFingerprints&quot;
104 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;
105 <br/> 00000000000000000000000000000000000000000100100001001000000001001000000
106 <br/> 00111000100101010111100011011000100110110000011011110100110111111111111
107 <br/> 01111111111111111110111000&quot;
108 <br/> ... ...
109 <br/> ... ...</div>
110 <p>The current release of MayaChemTools generates the following types of MACCS keys
111 fingerprints bit-vector and vector strings:</p>
112 <div class="OptionsBox">
113 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
114 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
115 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
116 <br/> 11111111111110111000</div>
117 <div class="OptionsBox">
118 FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000
119 <br/> 000000021210210e845f8d8c60b79dffbffffd1</div>
120 <div class="OptionsBox">
121 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
122 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
123 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
124 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
125 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
126 <br/> 0000000000000000000000000000000000000000</div>
127 <div class="OptionsBox">
128 FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7
129 <br/> e7af3edc000c1100000000000000500000000000000000000000000000000300000000
130 <br/> 000000000</div>
131 <div class="OptionsBox">
132 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
133 <br/> ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
134 <br/> 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
135 <br/> 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
136 <br/> 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
137 <br/> 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1</div>
138 <div class="OptionsBox">
139 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
140 <br/> ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
141 <br/> 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
142 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
143 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
144 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...</div>
145 <p>
146 </p>
147 <h2>OPTIONS</h2>
148 <dl>
149 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
150 <dd>
151 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
152 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
153 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
154 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
155 <p>The supported aromaticity model names along with model specific control parameters
156 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
157 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
158 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
159 for detecting aromaticity corresponding to a specific model.</p>
160 </dd>
161 <dt><strong><strong>--BitsOrder</strong> <em>Ascending | Descending</em></strong></dt>
162 <dd>
163 <p>Bits order to use during generation of fingerprints bit-vector string for <em>MACCSKeyBits</em> value of
164 <strong>-m, --mode</strong> option. Possible values: <em>Ascending, Descending</em>. Default: <em>Ascending</em>.</p>
165 <p><em>Ascending</em> bit order which corresponds to first bit in each byte as the lowest bit as
166 opposed to the highest bit.</p>
167 <p>Internally, bits are stored in <em>Ascending</em> order using Perl vec function. Regardless
168 of machine order, big-endian or little-endian, vec function always considers first
169 string byte as the lowest byte and first bit within each byte as the lowest bit.</p>
170 </dd>
171 <dt><strong><strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em></strong></dt>
172 <dd>
173 <p>Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by
174 <strong>--output</strong> used during <em>MACCSKeyBits</em> value of <strong>-m, --mode</strong> option. Possible
175 values: <em>BinaryString, HexadecimalString</em>. Default value: <em>BinaryString</em>.</p>
176 <p><em>BinaryString</em> corresponds to an ASCII string containing 1s and 0s. <em>HexadecimalString</em>
177 contains bit values in ASCII hexadecimal format.</p>
178 <p>Examples:</p>
179 <div class="OptionsBox">
180 FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
181 <br/> 0000000000000000000000000000000001001000010010000000010010000000011100
182 <br/> 0100101010111100011011000100110110000011011110100110111111111111011111
183 <br/> 11111111111110111000</div>
184 <div class="OptionsBox">
185 FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000
186 <br/> 000000021210210e845f8d8c60b79dffbffffd1</div>
187 <div class="OptionsBox">
188 FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
189 <br/> 1110011111100101111111000111101100110000000000000011100010000000000000
190 <br/> 0000000000000000000000000000000000000000000000101000000000000000000000
191 <br/> 0000000000000000000000000000000000000000000000000000000000000000000000
192 <br/> 0000000000000000000000000000000000000011000000000000000000000000000000
193 <br/> 0000000000000000000000000000000000000000</div>
194 <div class="OptionsBox">
195 FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7
196 <br/> e7af3edc000c1100000000000000500000000000000000000000000000000300000000
197 <br/> 000000000</div>
198 </dd>
199 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
200 <dd>
201 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
202 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
203 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
204 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
205 look like Cmpd&lt;Number&gt;.</p>
206 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
207 <div class="OptionsBox">
208 MolID
209 <br/> ExtReg</div>
210 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
211 <div class="OptionsBox">
212 Compound</div>
213 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
214 instead of default value of Cmpd&lt;Number&gt;.</p>
215 </dd>
216 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
217 <dd>
218 <p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value
219 of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p>
220 </dd>
221 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
222 <dd>
223 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
224 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
225 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
226 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
227 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
228 Default: <em>LabelPrefix</em>.</p>
229 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
230 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
231 values are replaced with sequential compound IDs.</p>
232 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
233 </dd>
234 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
235 <dd>
236 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
237 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
238 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
239 <p>Examples:</p>
240 <div class="OptionsBox">
241 Extreg
242 <br/> MolID,CompoundName</div>
243 </dd>
244 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
245 <dd>
246 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
247 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
248 data field; transfer SD data files common to all compounds; extract specified data fields;
249 generate a compound ID using molname line, a compound prefix, or a combination of both.
250 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
251 </dd>
252 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
253 <dd>
254 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
255 Default value: <em>Yes</em>.</p>
256 <p>By default, compound data is checked before calculating fingerprints and compounds containing
257 atom data corresponding to non-element symbols or no atom data are ignored.</p>
258 </dd>
259 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
260 <dd>
261 <p>SD data label or text file column label to use for fingerprints string in output SD or
262 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>MACCSKeyFingerprints</em>.</p>
263 </dd>
264 <dt><strong><strong>-h, --help</strong></strong></dt>
265 <dd>
266 <p>Print this help message.</p>
267 </dd>
268 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
269 <dd>
270 <p>Generate fingerprints for only the largest component in molecule. Possible values:
271 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
272 <p>For molecules containing multiple connected components, fingerprints can be generated
273 in two different ways: use all connected components or just the largest connected
274 component. By default, all atoms except for the largest connected component are
275 deleted before generation of fingerprints.</p>
276 </dd>
277 <dt><strong><strong>-m, --mode</strong> <em>MACCSKeyBits | MACCSKeyCount</em></strong></dt>
278 <dd>
279 <p>Specify type of MACCS keys [ Ref 45-47 ] fingerprints to generate for molecules in <em>SDFile(s)</em>.
280 Possible values: <em>MACCSKeyBits, MACCSKeyCount</em>. Default value: <em>MACCSKeyBits</em>.</p>
281 <p>For <em>MACCSKeyBits</em> value of <strong>-m, --mode</strong> option, a fingerprint bit-vector string containing
282 zeros and ones is generated and for <em>MACCSKeyCount</em> value, a fingerprint vector string
283 corresponding to number of MACCS keys is generated.</p>
284 <p><em>MACCSKeyBits | MACCSKeyCount</em> values for <strong>-m, --mode</strong> option along with two possible
285 <em>166 | 322</em> values of <strong>-s, --size</strong> supports generation of four different types of MACCS
286 keys fingerprint: <em>MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount</em>.</p>
287 <p>Definition of MACCS keys uses the following atom and bond symbols to define atom and
288 bond environments:</p>
289 <div class="OptionsBox">
290 Atom symbols for 166 keys [ Ref 47 ]:</div>
291 <div class="OptionsBox">
292 A : Any valid periodic table element symbol
293 <br/> Q : Hetro atoms; any non-C or non-H atom
294 <br/> X : Halogens; F, Cl, Br, I
295 <br/> Z : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I</div>
296 <div class="OptionsBox">
297 Atom symbols for 322 keys [ Ref 46 ]:</div>
298 <div class="OptionsBox">
299 A : Any valid periodic table element symbol
300 <br/> Q : Hetro atoms; any non-C or non-H atom
301 <br/> X : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I
302 <br/> Z is neither defined nor used</div>
303 <div class="OptionsBox">
304 Bond types:</div>
305 <div class="OptionsBox">
306 - : Single
307 <br/> = : Double
308 <br/> T : Triple
309 <br/> # : Triple
310 <br/> ~ : Single or double query bond
311 <br/> % : An aromatic query bond</div>
312 <div class="OptionsBox">
313 None : Any bond type; no explicit bond specified</div>
314 <div class="OptionsBox">
315 $ : Ring bond; $ before a bond type specifies ring bond
316 <br/> ! : Chain or non-ring bond; ! before a bond type specifies chain bond</div>
317 <div class="OptionsBox">
318 @ : A ring linkage and the number following it specifies the
319 atoms position in the line, thus @1 means linked back to the first
320 atom in the list.</div>
321 <div class="OptionsBox">
322 Aromatic: Kekule or Arom5</div>
323 <div class="OptionsBox">
324 Kekule: Bonds in 6-membered rings with alternate single/double bonds
325 or perimeter bonds
326 <br/> Arom5: Bonds in 5-membered rings with two double bonds and a hetro
327 atom at the apex of the ring.</div>
328 <p>MACCS 166 keys [ Ref 45-47 ] are defined as follows:</p>
329 <div class="OptionsBox">
330 Key Description</div>
331 <div class="OptionsBox">
332 1 ISOTOPE
333 <br/> 2 103 &lt; ATOMIC NO. &lt; 256
334 <br/> 3 GROUP IVA,VA,VIA PERIODS 4-6 (Ge...)
335 <br/> 4 ACTINIDE
336 <br/> 5 GROUP IIIB,IVB (Sc...)
337 <br/> 6 LANTHANIDE
338 <br/> 7 GROUP VB,VIB,VIIB (V...)
339 <br/> 8 QAAA@1
340 <br/> 9 GROUP VIII (Fe...)
341 <br/> 10 GROUP IIA (ALKALINE EARTH)
342 <br/> 11 4M RING
343 <br/> 12 GROUP IB,IIB (Cu...)
344 <br/> 13 ON(C)C
345 <br/> 14 S-S
346 <br/> 15 OC(O)O
347 <br/> 16 QAA@1
348 <br/> 17 CTC
349 <br/> 18 GROUP IIIA (B...)
350 <br/> 19 7M RING
351 <br/> 20 SI
352 <br/> 21 C=C(Q)Q
353 <br/> 22 3M RING
354 <br/> 23 NC(O)O
355 <br/> 24 N-O
356 <br/> 25 NC(N)N
357 <br/> 26 C$=C($A)$A
358 <br/> 27 I
359 <br/> 28 QCH2Q
360 <br/> 29 P
361 <br/> 30 CQ(C)(C)A
362 <br/> 31 QX
363 <br/> 32 CSN
364 <br/> 33 NS
365 <br/> 34 CH2=A
366 <br/> 35 GROUP IA (ALKALI METAL)
367 <br/> 36 S HETEROCYCLE
368 <br/> 37 NC(O)N
369 <br/> 38 NC(C)N
370 <br/> 39 OS(O)O
371 <br/> 40 S-O
372 <br/> 41 CTN
373 <br/> 42 F
374 <br/> 43 QHAQH
375 <br/> 44 OTHER
376 <br/> 45 C=CN
377 <br/> 46 BR
378 <br/> 47 SAN
379 <br/> 48 OQ(O)O
380 <br/> 49 CHARGE
381 <br/> 50 C=C(C)C
382 <br/> 51 CSO
383 <br/> 52 NN
384 <br/> 53 QHAAAQH
385 <br/> 54 QHAAQH
386 <br/> 55 OSO
387 <br/> 56 ON(O)C
388 <br/> 57 O HETEROCYCLE
389 <br/> 58 QSQ
390 <br/> 59 Snot%A%A
391 <br/> 60 S=O
392 <br/> 61 AS(A)A
393 <br/> 62 A$A!A$A
394 <br/> 63 N=O
395 <br/> 64 A$A!S
396 <br/> 65 C%N
397 <br/> 66 CC(C)(C)A
398 <br/> 67 QS
399 <br/> 68 QHQH (&amp;...)
400 <br/> 69 QQH
401 <br/> 70 QNQ
402 <br/> 71 NO
403 <br/> 72 OAAO
404 <br/> 73 S=A
405 <br/> 74 CH3ACH3
406 <br/> 75 A!N$A
407 <br/> 76 C=C(A)A
408 <br/> 77 NAN
409 <br/> 78 C=N
410 <br/> 79 NAAN
411 <br/> 80 NAAAN
412 <br/> 81 SA(A)A
413 <br/> 82 ACH2QH
414 <br/> 83 QAAAA@1
415 <br/> 84 NH2
416 <br/> 85 CN(C)C
417 <br/> 86 CH2QCH2
418 <br/> 87 X!A$A
419 <br/> 88 S
420 <br/> 89 OAAAO
421 <br/> 90 QHAACH2A
422 <br/> 91 QHAAACH2A
423 <br/> 92 OC(N)C
424 <br/> 93 QCH3
425 <br/> 94 QN
426 <br/> 95 NAAO
427 <br/> 96 5M RING
428 <br/> 97 NAAAO
429 <br/> 98 QAAAAA@1
430 <br/> 99 C=C
431 <br/> 100 ACH2N
432 <br/> 101 8M RING
433 <br/> 102 QO
434 <br/> 103 CL
435 <br/> 104 QHACH2A
436 <br/> 105 A$A($A)$A
437 <br/> 106 QA(Q)Q
438 <br/> 107 XA(A)A
439 <br/> 108 CH3AAACH2A
440 <br/> 109 ACH2O
441 <br/> 110 NCO
442 <br/> 111 NACH2A
443 <br/> 112 AA(A)(A)A
444 <br/> 113 Onot%A%A
445 <br/> 114 CH3CH2A
446 <br/> 115 CH3ACH2A
447 <br/> 116 CH3AACH2A
448 <br/> 117 NAO
449 <br/> 118 ACH2CH2A &gt; 1
450 <br/> 119 N=A
451 <br/> 120 HETEROCYCLIC ATOM &gt; 1 (&amp;...)
452 <br/> 121 N HETEROCYCLE
453 <br/> 122 AN(A)A
454 <br/> 123 OCO
455 <br/> 124 QQ
456 <br/> 125 AROMATIC RING &gt; 1
457 <br/> 126 A!O!A
458 <br/> 127 A$A!O &gt; 1 (&amp;...)
459 <br/> 128 ACH2AAACH2A
460 <br/> 129 ACH2AACH2A
461 <br/> 130 QQ &gt; 1 (&amp;...)
462 <br/> 131 QH &gt; 1
463 <br/> 132 OACH2A
464 <br/> 133 A$A!N
465 <br/> 134 X (HALOGEN)
466 <br/> 135 Nnot%A%A
467 <br/> 136 O=A &gt; 1
468 <br/> 137 HETEROCYCLE
469 <br/> 138 QCH2A &gt; 1 (&amp;...)
470 <br/> 139 OH
471 <br/> 140 O &gt; 3 (&amp;...)
472 <br/> 141 CH3 &gt; 2 (&amp;...)
473 <br/> 142 N &gt; 1
474 <br/> 143 A$A!O
475 <br/> 144 Anot%A%Anot%A
476 <br/> 145 6M RING &gt; 1
477 <br/> 146 O &gt; 2
478 <br/> 147 ACH2CH2A
479 <br/> 148 AQ(A)A
480 <br/> 149 CH3 &gt; 1
481 <br/> 150 A!A$A!A
482 <br/> 151 NH
483 <br/> 152 OC(C)C
484 <br/> 153 QCH2A
485 <br/> 154 C=O
486 <br/> 155 A!CH2!A
487 <br/> 156 NA(A)A
488 <br/> 157 C-O
489 <br/> 158 C-N
490 <br/> 159 O &gt; 1
491 <br/> 160 CH3
492 <br/> 161 N
493 <br/> 162 AROMATIC
494 <br/> 163 6M RING
495 <br/> 164 O
496 <br/> 165 RING
497 <br/> 166 FRAGMENTS</div>
498 <p>MACCS 322 keys set as defined in tables 1, 2 and 3 [ Ref 46 ] include:</p>
499 <div class="OptionsBox">
500 . 26 atom properties of type P, as listed in Table 1
501 <br/> . 32 one-atom environments, as listed in Table 3
502 <br/> . 264 atom-bond-atom combinations listed in Table 4</div>
503 <p>Total number of keys in three tables is : 322</p>
504 <p>Atom symbol, X, used for 322 keys [ Ref 46 ] doesn't refer to Halogens as it does for 166 keys. In
505 order to keep the definition of 322 keys consistent with the published definitions, the symbol X is
506 used to imply &quot;others&quot; atoms, but it's internally mapped to symbol X as defined for 166 keys
507 during the generation of key values.</p>
508 <p>Atom properties-based keys (26):</p>
509 <div class="OptionsBox">
510 Key Description
511 <br/> 1 A(AAA) or AA(A)A - atom with at least three neighbors
512 <br/> 2 Q - heteroatom
513 <br/> 3 Anot%not-A - atom involved in one or more multiple bonds, not aromatic
514 <br/> 4 A(AAAA) or AA(A)(A)A - atom with at least four neighbors
515 <br/> 5 A(QQ) or QA(Q) - atom with at least two heteroatom neighbors
516 <br/> 6 A(QQQ) or QA(Q)Q - atom with at least three heteroatom neighbors
517 <br/> 7 QH - heteroatom with at least one hydrogen attached
518 <br/> 8 CH2(AA) or ACH2A - carbon with at least two single bonds and at least
519 two hydrogens attached
520 <br/> 9 CH3(A) or ACH3 - carbon with at least one single bond and at least three
521 hydrogens attached
522 <br/> 10 Halogen
523 <br/> 11 A(-A-A-A) or A-A(-A)-A - atom has at least three single bonds
524 <br/> 12 AAAAAA@1 &gt; 2 - atom is in at least two different six-membered rings
525 <br/> 13 A($A$A$A) or A$A($A)$A - atom has more than two ring bonds
526 <br/> 14 A$A!A$A - atom is at a ring/chain boundary. When a comparison is done
527 with another atom the path passes through the chain bond.
528 <br/> 15 Anot%A%Anot%A - atom is at an aromatic/nonaromatic boundary. When a
529 comparison is done with another atom the path
530 passes through the aromatic bond.
531 <br/> 16 A!A!A - atom with more than one chain bond
532 <br/> 17 A!A$A!A - atom is at a ring/chain boundary. When a comparison is done
533 with another atom the path passes through the ring bond.
534 <br/> 18 A%Anot%A%A - atom is at an aromatic/nonaromatic boundary. When a
535 comparison is done with another atom the
536 path passes through the nonaromatic bond.
537 <br/> 19 HETEROCYCLE - atom is a heteroatom in a ring.
538 <br/> 20 rare properties: atom with five or more neighbors, atom in
539 four or more rings, or atom types other than
540 H, C, N, O, S, F, Cl, Br, or I
541 <br/> 21 rare properties: atom has a charge, is an isotope, has two or
542 more multiple bonds, or has a triple bond.
543 <br/> 22 N - nitrogen
544 <br/> 23 S - sulfur
545 <br/> 24 O - oxygen
546 <br/> 25 A(AA)A(A)A(AA) - atom has two neighbors, each with three or
547 more neighbors (including the central atom).
548 <br/> 26 CHACH2 - atom has two hydrocarbon (CH2) neighbors</div>
549 <p>Atomic environments properties-based keys (32):</p>
550 <div class="OptionsBox">
551 Key Description
552 <br/> 27 C(CC)
553 <br/> 28 C(CCC)
554 <br/> 29 C(CN)
555 <br/> 30 C(CCN)
556 <br/> 31 C(NN)
557 <br/> 32 C(NNC)
558 <br/> 33 C(NNN)
559 <br/> 34 C(CO)
560 <br/> 35 C(CCO)
561 <br/> 36 C(NO)
562 <br/> 37 C(NCO)
563 <br/> 38 C(NNO)
564 <br/> 39 C(OO)
565 <br/> 40 C(COO)
566 <br/> 41 C(NOO)
567 <br/> 42 C(OOO)
568 <br/> 43 Q(CC)
569 <br/> 44 Q(CCC)
570 <br/> 45 Q(CN)
571 <br/> 46 Q(CCN)
572 <br/> 47 Q(NN)
573 <br/> 48 Q(CNN)
574 <br/> 49 Q(NNN)
575 <br/> 50 Q(CO)
576 <br/> 51 Q(CCO)
577 <br/> 52 Q(NO)
578 <br/> 53 Q(CNO)
579 <br/> 54 Q(NNO)
580 <br/> 55 Q(OO)
581 <br/> 56 Q(COO)
582 <br/> 57 Q(NOO)
583 <br/> 58 Q(OOO)</div>
584 <p>Note: The first symbol is the central atom, with atoms bonded to the central atom listed in
585 parentheses. Q is any non-C, non-H atom. If only two atoms are in parentheses, there is
586 no implication concerning the other atoms bonded to the central atom.</p>
587 <p>Atom-Bond-Atom properties-based keys: (264)</p>
588 <div class="OptionsBox">
589 Key Description
590 <br/> 59 C-C
591 <br/> 60 C-N
592 <br/> 61 C-O
593 <br/> 62 C-S
594 <br/> 63 C-Cl
595 <br/> 64 C-P
596 <br/> 65 C-F
597 <br/> 66 C-Br
598 <br/> 67 C-Si
599 <br/> 68 C-I
600 <br/> 69 C-X
601 <br/> 70 N-N
602 <br/> 71 N-O
603 <br/> 72 N-S
604 <br/> 73 N-Cl
605 <br/> 74 N-P
606 <br/> 75 N-F
607 <br/> 76 N-Br
608 <br/> 77 N-Si
609 <br/> 78 N-I
610 <br/> 79 N-X
611 <br/> 80 O-O
612 <br/> 81 O-S
613 <br/> 82 O-Cl
614 <br/> 83 O-P
615 <br/> 84 O-F
616 <br/> 85 O-Br
617 <br/> 86 O-Si
618 <br/> 87 O-I
619 <br/> 88 O-X
620 <br/> 89 S-S
621 <br/> 90 S-Cl
622 <br/> 91 S-P
623 <br/> 92 S-F
624 <br/> 93 S-Br
625 <br/> 94 S-Si
626 <br/> 95 S-I
627 <br/> 96 S-X
628 <br/> 97 Cl-Cl
629 <br/> 98 Cl-P
630 <br/> 99 Cl-F
631 <br/> 100 Cl-Br
632 <br/> 101 Cl-Si
633 <br/> 102 Cl-I
634 <br/> 103 Cl-X
635 <br/> 104 P-P
636 <br/> 105 P-F
637 <br/> 106 P-Br
638 <br/> 107 P-Si
639 <br/> 108 P-I
640 <br/> 109 P-X
641 <br/> 110 F-F
642 <br/> 111 F-Br
643 <br/> 112 F-Si
644 <br/> 113 F-I
645 <br/> 114 F-X
646 <br/> 115 Br-Br
647 <br/> 116 Br-Si
648 <br/> 117 Br-I
649 <br/> 118 Br-X
650 <br/> 119 Si-Si
651 <br/> 120 Si-I
652 <br/> 121 Si-X
653 <br/> 122 I-I
654 <br/> 123 I-X
655 <br/> 124 X-X
656 <br/> 125 C=C
657 <br/> 126 C=N
658 <br/> 127 C=O
659 <br/> 128 C=S
660 <br/> 129 C=Cl
661 <br/> 130 C=P
662 <br/> 131 C=F
663 <br/> 132 C=Br
664 <br/> 133 C=Si
665 <br/> 134 C=I
666 <br/> 135 C=X
667 <br/> 136 N=N
668 <br/> 137 N=O
669 <br/> 138 N=S
670 <br/> 139 N=Cl
671 <br/> 140 N=P
672 <br/> 141 N=F
673 <br/> 142 N=Br
674 <br/> 143 N=Si
675 <br/> 144 N=I
676 <br/> 145 N=X
677 <br/> 146 O=O
678 <br/> 147 O=S
679 <br/> 148 O=Cl
680 <br/> 149 O=P
681 <br/> 150 O=F
682 <br/> 151 O=Br
683 <br/> 152 O=Si
684 <br/> 153 O=I
685 <br/> 154 O=X
686 <br/> 155 S=S
687 <br/> 156 S=Cl
688 <br/> 157 S=P
689 <br/> 158 S=F
690 <br/> 159 S=Br
691 <br/> 160 S=Si
692 <br/> 161 S=I
693 <br/> 162 S=X
694 <br/> 163 Cl=Cl
695 <br/> 164 Cl=P
696 <br/> 165 Cl=F
697 <br/> 166 Cl=Br
698 <br/> 167 Cl=Si
699 <br/> 168 Cl=I
700 <br/> 169 Cl=X
701 <br/> 170 P=P
702 <br/> 171 P=F
703 <br/> 172 P=Br
704 <br/> 173 P=Si
705 <br/> 174 P=I
706 <br/> 175 P=X
707 <br/> 176 F=F
708 <br/> 177 F=Br
709 <br/> 178 F=Si
710 <br/> 179 F=I
711 <br/> 180 F=X
712 <br/> 181 Br=Br
713 <br/> 182 Br=Si
714 <br/> 183 Br=I
715 <br/> 184 Br=X
716 <br/> 185 Si=Si
717 <br/> 186 Si=I
718 <br/> 187 Si=X
719 <br/> 188 I=I
720 <br/> 189 I=X
721 <br/> 190 X=X
722 <br/> 191 C#C
723 <br/> 192 C#N
724 <br/> 193 C#O
725 <br/> 194 C#S
726 <br/> 195 C#Cl
727 <br/> 196 C#P
728 <br/> 197 C#F
729 <br/> 198 C#Br
730 <br/> 199 C#Si
731 <br/> 200 C#I
732 <br/> 201 C#X
733 <br/> 202 N#N
734 <br/> 203 N#O
735 <br/> 204 N#S
736 <br/> 205 N#Cl
737 <br/> 206 N#P
738 <br/> 207 N#F
739 <br/> 208 N#Br
740 <br/> 209 N#Si
741 <br/> 210 N#I
742 <br/> 211 N#X
743 <br/> 212 O#O
744 <br/> 213 O#S
745 <br/> 214 O#Cl
746 <br/> 215 O#P
747 <br/> 216 O#F
748 <br/> 217 O#Br
749 <br/> 218 O#Si
750 <br/> 219 O#I
751 <br/> 220 O#X
752 <br/> 221 S#S
753 <br/> 222 S#Cl
754 <br/> 223 S#P
755 <br/> 224 S#F
756 <br/> 225 S#Br
757 <br/> 226 S#Si
758 <br/> 227 S#I
759 <br/> 228 S#X
760 <br/> 229 Cl#Cl
761 <br/> 230 Cl#P
762 <br/> 231 Cl#F
763 <br/> 232 Cl#Br
764 <br/> 233 Cl#Si
765 <br/> 234 Cl#I
766 <br/> 235 Cl#X
767 <br/> 236 P#P
768 <br/> 237 P#F
769 <br/> 238 P#Br
770 <br/> 239 P#Si
771 <br/> 240 P#I
772 <br/> 241 P#X
773 <br/> 242 F#F
774 <br/> 243 F#Br
775 <br/> 244 F#Si
776 <br/> 245 F#I
777 <br/> 246 F#X
778 <br/> 247 Br#Br
779 <br/> 248 Br#Si
780 <br/> 249 Br#I
781 <br/> 250 Br#X
782 <br/> 251 Si#Si
783 <br/> 252 Si#I
784 <br/> 253 Si#X
785 <br/> 254 I#I
786 <br/> 255 I#X
787 <br/> 256 X#X
788 <br/> 257 C$C
789 <br/> 258 C$N
790 <br/> 259 C$O
791 <br/> 260 C$S
792 <br/> 261 C$Cl
793 <br/> 262 C$P
794 <br/> 263 C$F
795 <br/> 264 C$Br
796 <br/> 265 C$Si
797 <br/> 266 C$I
798 <br/> 267 C$X
799 <br/> 268 N$N
800 <br/> 269 N$O
801 <br/> 270 N$S
802 <br/> 271 N$Cl
803 <br/> 272 N$P
804 <br/> 273 N$F
805 <br/> 274 N$Br
806 <br/> 275 N$Si
807 <br/> 276 N$I
808 <br/> 277 N$X
809 <br/> 278 O$O
810 <br/> 279 O$S
811 <br/> 280 O$Cl
812 <br/> 281 O$P
813 <br/> 282 O$F
814 <br/> 283 O$Br
815 <br/> 284 O$Si
816 <br/> 285 O$I
817 <br/> 286 O$X
818 <br/> 287 S$S
819 <br/> 288 S$Cl
820 <br/> 289 S$P
821 <br/> 290 S$F
822 <br/> 291 S$Br
823 <br/> 292 S$Si
824 <br/> 293 S$I
825 <br/> 294 S$X
826 <br/> 295 Cl$Cl
827 <br/> 296 Cl$P
828 <br/> 297 Cl$F
829 <br/> 298 Cl$Br
830 <br/> 299 Cl$Si
831 <br/> 300 Cl$I
832 <br/> 301 Cl$X
833 <br/> 302 P$P
834 <br/> 303 P$F
835 <br/> 304 P$Br
836 <br/> 305 P$Si
837 <br/> 306 P$I
838 <br/> 307 P$X
839 <br/> 308 F$F
840 <br/> 309 F$Br
841 <br/> 310 F$Si
842 <br/> 311 F$I
843 <br/> 312 F$X
844 <br/> 313 Br$Br
845 <br/> 314 Br$Si
846 <br/> 315 Br$I
847 <br/> 316 Br$X
848 <br/> 317 Si$Si
849 <br/> 318 Si$I
850 <br/> 319 Si$X
851 <br/> 320 I$I
852 <br/> 321 I$X
853 <br/> 322 X$X</div>
854 </dd>
855 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
856 <dd>
857 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
858 Default value: <em>comma</em>.</p>
859 </dd>
860 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
861 <dd>
862 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
863 </dd>
864 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
865 <dd>
866 <p>Overwrite existing files.</p>
867 </dd>
868 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
869 <dd>
870 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
871 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
872 </dd>
873 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
874 <dd>
875 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file
876 names: &lt;SDFileName&gt;&lt;MACCSKeysFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
877 The sdf, fpf, csv, and tsv &lt;Ext&gt; values are used for SD, FP, comma/semicolon, and tab
878 delimited text files, respectively.This option is ignored for multiple input files.</p>
879 </dd>
880 <dt><strong><strong>-s, --size</strong> <em>number</em></strong></dt>
881 <dd>
882 <p>Size of MACCS keys [ Ref 45-47 ] set to use during fingerprints generation. Possible values: <em>166 or 322</em>.
883 Default value: <em>166</em>.</p>
884 </dd>
885 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
886 <dd>
887 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
888 <strong>--output</strong> used during <em>MACCSKeyCount</em> value of <strong>-m, --mode</strong> option. Possible
889 values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
890 ValuesAndIDsPairsString</em>. Defaultvalue: <em>ValuesString</em>.</p>
891 <p>Examples:</p>
892 <div class="OptionsBox">
893 FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
894 <br/> ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
895 <br/> 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
896 <br/> 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
897 <br/> 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
898 <br/> 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1</div>
899 <div class="OptionsBox">
900 FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
901 <br/> ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
902 <br/> 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
903 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
904 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
905 <br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...</div>
906 </dd>
907 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
908 <dd>
909 <p>Location of working directory. Default: current directory.</p>
910 </dd>
911 </dl>
912 <p>
913 </p>
914 <h2>EXAMPLES</h2>
915 <p>To generate MACCS keys fingerprints of size 166 in binary bit-vector string format
916 and create a SampleMACCS166FPBin.csv file containing sequential compound IDs along with
917 fingerprints bit-vector strings data, type:</p>
918 <div class="ExampleBox">
919 % MACCSKeysFingerprints.pl -r SampleMACCS166FPBin -o Sample.sdf</div>
920 <p>To generate MACCS keys fingerprints of size 166 in binary bit-vector string format
921 and create SampleMACCS166FPBin.sdf, SampleMACCS166FPBin.csv and SampleMACCS166FPBin.csv
922 files containing sequential compound IDs in CSV file along with fingerprints bit-vector strings data, type:</p>
923 <div class="ExampleBox">
924 % MACCSKeysFingerprints.pl --output all -r SampleMACCS166FPBin
925 -o Sample.sdf</div>
926 <p>To generate MACCS keys fingerprints of size 322 in binary bit-vector string format
927 and create a SampleMACCS322FPBin.csv file containing sequential compound IDs along with
928 fingerprints bit-vector strings data, type:</p>
929 <div class="ExampleBox">
930 % MACCSKeysFingerprints.pl -size 322 -r SampleMACCS322FPBin -o Sample.sdf</div>
931 <p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in
932 ValuesString format and create a SampleMACCS166FPCount.csv file containing sequential
933 compound IDs along with fingerprints vector strings data, type:</p>
934 <div class="ExampleBox">
935 % MACCSKeysFingerprints.pl -m MACCSKeyCount -r SampleMACCS166FPCount
936 -o Sample.sdf</div>
937 <p>To generate MACCS keys fingerprints of size 322 corresponding to count of keys in
938 ValuesString format and create a SampleMACCS322FPCount.csv file containing sequential
939 compound IDs along with fingerprints vector strings data, type:</p>
940 <div class="ExampleBox">
941 % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322
942 -r SampleMACCS322FPCount -o Sample.sdf</div>
943 <p>To generate MACCS keys fingerprints of size 166 in hexadecimal bit-vector string format with
944 ascending bits order and create a SampleMACCS166FPHex.csv file containing compound IDs
945 from MolName along with fingerprints bit-vector strings data, type:</p>
946 <div class="ExampleBox">
947 % MACCSKeysFingerprints.pl -m MACCSKeyBits --size 166 --BitStringFormat
948 HexadecimalString --BitsOrder Ascending --DataFieldsMode CompoundID
949 --CompoundIDMode MolName -r SampleMACCS166FPBin -o Sample.sdf</div>
950 <p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in
951 IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing
952 compound IDs from MolName line along with fingerprints vector strings data, type:</p>
953 <div class="ExampleBox">
954 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166
955 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID
956 --CompoundIDMode MolName -r SampleMACCS166FPCount -o Sample.sdf</div>
957 <p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in
958 IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing
959 compound IDs using specified data field along with fingerprints vector strings data, type:</p>
960 <div class="ExampleBox">
961 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166
962 --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID
963 --CompoundIDMode DataField --CompoundID Mol_ID -r
964 SampleMACCS166FPCount -o Sample.sdf</div>
965 <p>To generate MACCS keys fingerprints of size 322 corresponding to count of keys in
966 ValuesString format and create a SampleMACCS322FPCount.tsv file containing compound
967 IDs derived from combination of molecule name line and an explicit compound prefix
968 along with fingerprints vector strings data in a column labels MACCSKeyCountFP, type:</p>
969 <div class="ExampleBox">
970 % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 --DataFieldsMode
971 CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd
972 --CompoundIDLabel MolID --FingerprintsLabel MACCSKeyCountFP --OutDelim
973 Tab -r SampleMACCS322FPCount -o Sample.sdf</div>
974 <p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in
975 ValuesString format and create a SampleMACCS166FPCount.csv file containing
976 specific data fields columns along with fingerprints vector strings data, type:</p>
977 <div class="ExampleBox">
978 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166
979 --VectorStringFormat ValuesString --DataFieldsMode Specify --DataFields
980 Mol_ID -r SampleMACCS166FPCount -o Sample.sdf</div>
981 <p>To generate MACCS keys fingerprints of size 322 corresponding to count of keys in
982 ValuesString format and create a SampleMACCS322FPCount.csv file containing
983 common data fields columns along with fingerprints vector strings data, type:</p>
984 <div class="ExampleBox">
985 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 322
986 --VectorStringFormat ValuesString --DataFieldsMode Common -r
987 SampleMACCS322FPCount -o Sample.sdf</div>
988 <p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in
989 ValuesString format and create SampleMACCS166FPCount.sdf, SampleMACCS166FPCount.fpf and
990 SampleMACCS166FPCount.csv files containing all data fields columns in CSV file
991 along with fingerprints vector strings data, type:</p>
992 <div class="ExampleBox">
993 % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --output all
994 --VectorStringFormat ValuesString --DataFieldsMode All -r
995 SampleMACCS166FPCount -o Sample.sdf</div>
996 <p>
997 </p>
998 <h2>AUTHOR</h2>
999 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
1000 <p>
1001 </p>
1002 <h2>SEE ALSO</h2>
1003 <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
1004 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp
1005 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
1006 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
1007 </p>
1008 <p>
1009 </p>
1010 <h2>COPYRIGHT</h2>
1011 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
1012 <p>This file is part of MayaChemTools.</p>
1013 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
1014 the terms of the GNU Lesser General Public License as published by the Free
1015 Software Foundation; either version 3 of the License, or (at your option)
1016 any later version.</p>
1017 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
1018 <table width="100%" border=0 cellpadding=0 cellspacing=2>
1019 <tr align="left" valign="top"><td width="33%" align="left"><a href="./JoinTextFiles.html" title="JoinTextFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./MergeTextFiles.html" title="MergeTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MACCSKeysFingerprints.pl</strong></td></tr>
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