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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalPharmacophoreAtomPairsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomPairsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalPharmacophoreAtomPairsFingerprints.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>TopologicalPharmacophoreAtomPairsFingerprints.pl - Generate topological pharmacophore atom pairs fingerprints for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)...</p>
26 <p>TopologicalPharmacophoreAtomPairsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
27 [<strong>--AtomPairsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em>]
28 [<strong>-a, --AtomTypesToUse</strong> <em>&quot;AtomType1, AtomType2...&quot;</em>]
29 [<strong>--AtomTypesWeight</strong> <em>&quot;AtomType1, Weight1, AtomType2, Weight2...&quot;</em>]
30 [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>]
31 [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> <em>&quot;FieldLabel1, FieldLabel2,...&quot;</em>]
32 [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>]
33 [<strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>]
34 [<strong>--FuzzifyAtomPairsCount</strong> <em>Yes | No</em>] [<strong>--FuzzificationMode</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em>]
35 [<strong>--FuzzificationMethodology</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em>] [<strong>--FuzzFactor</strong> <em>number</em>]
36 [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] [<strong>--MinDistance</strong> <em>number</em>]
37 [<strong>--MaxDistance</strong> <em>number</em>] [<strong>-n, --NormalizationMethodology</strong> <em>None | ByHeavyAtomsCount | ByAtomTypesCount</em>]
38 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
39 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>--ValuesPrecision</strong> <em>number</em>]
40 [<strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
41 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
42 <p>
43 </p>
44 <h2>DESCRIPTION</h2>
45 <p>Generate topological pharmacophore atom pairs fingerprints [ Ref 60-62, Ref 65, Ref 68 ] for
46 <em>SDFile(s)</em> and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector
47 strings corresponding to molecular fingerprints.</p>
48 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
49 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
50 can be specified either by <em>*.sdf</em> or the current directory name.</p>
51 <p>Based on the values specified for <strong>--AtomTypesToUse</strong>, pharmacophore atom types are
52 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
53 A pharmacophore atom pairs basis set is initialized for all unique possible pairs within
54 <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> range.</p>
55 <div class="OptionsBox">
56 Let:</div>
57 <div class="OptionsBox">
58 P = Valid pharmacophore atom type</div>
59 <div class="OptionsBox">
60 Px = Pharmacophore atom type x
61 <br/> Py = Pharmacophore atom type y</div>
62 <div class="OptionsBox">
63 Dmin = Minimum distance corresponding to number of bonds between
64 two atoms
65 <br/> Dmax = Maximum distance corresponding to number of bonds between
66 two atoms
67 <br/> D = Distance corresponding to number of bonds between two atoms</div>
68 <div class="OptionsBox">
69 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
70 distance Dn</div>
71 <div class="OptionsBox">
72 P = Number of pharmacophore atom types to consider
73 <br/> PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</div>
74 <div class="OptionsBox">
75 PPT = Total number of possible pharmacophore atom pairs at all distances
76 between Dmin and Dmax</div>
77 <div class="OptionsBox">
78 Then:</div>
79 <div class="OptionsBox">
80 PPD = (P * (P - 1))/2 + P</div>
81 <div class="OptionsBox">
82 PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P)
83 <br/>&nbsp;&nbsp;&nbsp;&nbsp; = ((Dmax - Dmin) + 1) * PPD</div>
84 <div class="OptionsBox">
85 So for default values of Dmin = 1, Dmax = 10 and P = 5,</div>
86 <div class="OptionsBox">
87 PPD = (5 * (5 - 1))/2 + 5 = 15
88 <br/> PPT = ((10 - 1) + 1) * 15 = 150</div>
89 <div class="OptionsBox">
90 The pharmacophore atom pairs bais set includes 150 values.</div>
91 <div class="OptionsBox">
92 The atom pair IDs correspond to:</div>
93 <div class="OptionsBox">
94 Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at
95 distance Dn</div>
96 <div class="OptionsBox">
97 For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</div>
98 <p>Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom
99 pairs is counted. The contribution of each atom type to atom pair interaction is optionally
100 weighted by specified <strong>--AtomTypesWeight</strong> before assigning its count to appropriate distance
101 bin. Based on <strong>--NormalizationMethodology</strong> option, pharmacophore atom pairs count is optionally
102 normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after
103 the normalization controlled by values of <strong>--FuzzifyAtomPairsCount</strong>, <strong>--FuzzificationMode</strong>,
104 <strong>--FuzzificationMethodology</strong> and <strong>--FuzzFactor</strong> options.</p>
105 <p>The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen
106 atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs
107 fingerprints of the molecule.</p>
108 <p>For <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector correspond to
109 only those topological pharmacophore atom pairs which are present and have non-zero count. However,
110 for <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector contains all possible
111 valid topological pharmacophore atom pairs with both zero and non-zero count values.</p>
112 <p>Example of <em>SD</em> file containing topological pharmacophore atom pairs fingerprints string data:</p>
113 <div class="OptionsBox">
114 ... ...
115 <br/> ... ...
116 <br/> $$$$
117 <br/> ... ...
118 <br/> ... ...
119 <br/> ... ...
120 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
121 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
122 <br/> ... ...
123 <br/> 2 3 1 0 0 0 0
124 <br/> ... ...
125 <br/> M END
126 <br/> &gt; &lt;CmpdID&gt;
127 <br/> Cmpd1</div>
128 <div class="OptionsBox">
129 &gt; &lt;TopologicalPharmacophoreAtomPairsFingerprints&gt;
130 <br/> FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
131 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
132 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
133 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D...;
134 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
135 <br/> 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
136 <div class="OptionsBox">
137 $$$$
138 <br/> ... ...
139 <br/> ... ...</div>
140 <p>Example of <em>FP</em> file containing topological pharmacophore atom pairs fingerprints string data:</p>
141 <div class="OptionsBox">
142 #
143 <br/> # Package = MayaChemTools 7.4
144 <br/> # Release Date = Oct 21, 2010
145 <br/> #
146 <br/> # TimeStamp = Fri Mar 11 15:32:48 2011
147 <br/> #
148 <br/> # FingerprintsStringType = FingerprintsVector
149 <br/> #
150 <br/> # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10
151 <br/> # VectorStringFormat = IDsAndValuesString
152 <br/> # VectorValuesType = NumericalValues
153 <br/> #
154 <br/> Cmpd1 54;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;18 1 2...
155 <br/> Cmpd2 61;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;5 1 2 ...
156 <br/> ... ...
157 <br/> ... ..</div>
158 <p>Example of CSV <em>Text</em> file containing topological pharmacophore atom pairs fingerprints string data:</p>
159 <div class="OptionsBox">
160 &quot;CompoundID&quot;,&quot;TopologicalPharmacophoreAtomPairsFingerprints&quot;
161 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary
162 <br/> Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H
163 <br/> -D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA H
164 <br/> BA-D2-HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4...;
165 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3
166 <br/> 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1&quot;
167 <br/> ... ...
168 <br/> ... ...</div>
169 <p>The current release of MayaChemTools generates the following types of topological pharmacophore
170 atom pairs fingerprints vector strings:</p>
171 <div class="OptionsBox">
172 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
173 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
174 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
175 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
176 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
177 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
178 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
179 <div class="OptionsBox">
180 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
181 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
182 <br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
183 <br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
184 <br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
185 <br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div>
186 <div class="OptionsBox">
187 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
188 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
189 <br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
190 <br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
191 <br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
192 <br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
193 <br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
194 <br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</div>
195 <p>
196 </p>
197 <h2>OPTIONS</h2>
198 <dl>
199 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
200 <dd>
201 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
202 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
203 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
204 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
205 <p>The supported aromaticity model names along with model specific control parameters
206 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
207 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
208 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
209 for detecting aromaticity corresponding to a specific model.</p>
210 </dd>
211 <dt><strong><strong>--AtomPairsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt>
212 <dd>
213 <p>Atom pairs set size to use during generation of topological pharmacophore atom pairs
214 fingerprints.</p>
215 <p>Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p>
216 <p>For <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector
217 correspond to only those topological pharmacophore atom pairs which are present and
218 have non-zero count. However, for <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong>
219 option, the fingerprint vector contains all possible valid topological pharmacophore atom
220 pairs with both zero and non-zero count values.</p>
221 </dd>
222 <dt><strong><strong>-a, --AtomTypesToUse</strong> <em>&quot;AtomType1,AtomType2,...&quot;</em></strong></dt>
223 <dd>
224 <p>Pharmacophore atom types to use during generation of topological phramacophore
225 atom pairs. It's a list of comma separated valid pharmacophore atom types.</p>
226 <p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
227 Default value [ Ref 60-62 ] : <em>HBD,HBA,PI,NI,H</em>.</p>
228 <p>The pharmacophore atom types abbreviations correspond to:</p>
229 <div class="OptionsBox">
230 HBD: HydrogenBondDonor
231 <br/> HBA: HydrogenBondAcceptor
232 <br/> PI : PositivelyIonizable
233 <br/> NI : NegativelyIonizable
234 <br/> Ar : Aromatic
235 <br/> Hal : Halogen
236 <br/> H : Hydrophobic
237 <br/> RA : RingAtom
238 <br/> CA : ChainAtom</div>
239 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore atom
240 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
241 <div class="OptionsBox">
242 HydrogenBondDonor: NH, NH2, OH
243 <br/> HydrogenBondAcceptor: N[!H], O
244 <br/> PositivelyIonizable: +, NH2
245 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
246 </dd>
247 <dt><strong><strong>--AtomTypesWeight</strong> <em>&quot;AtomType1,Weight1,AtomType2,Weight2...&quot;</em></strong></dt>
248 <dd>
249 <p>Weights of specified pharmacophore atom types to use during calculation of their contribution
250 to atom pair count. Default value: <em>None</em>. Valid values: real numbers greater than 0. In general
251 it's comma delimited list of valid atom type and its weight.</p>
252 <p>The weight values allow to increase the importance of specific pharmacophore atom type
253 in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to
254 atom pair count where as weight value of 2 doubles its contribution.</p>
255 </dd>
256 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
257 <dd>
258 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
259 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
260 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
261 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
262 look like Cmpd&lt;Number&gt;.</p>
263 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
264 <div class="OptionsBox">
265 MolID
266 <br/> ExtReg</div>
267 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
268 <div class="OptionsBox">
269 Compound</div>
270 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
271 instead of default value of Cmpd&lt;Number&gt;.</p>
272 </dd>
273 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
274 <dd>
275 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
276 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
277 </dd>
278 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
279 <dd>
280 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
281 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
282 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
283 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
284 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
285 Default value: <em>LabelPrefix</em>.</p>
286 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
287 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
288 values are replaced with sequential compound IDs.</p>
289 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
290 </dd>
291 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
292 <dd>
293 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
294 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
295 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
296 <p>Examples:</p>
297 <div class="OptionsBox">
298 Extreg
299 <br/> MolID,CompoundName</div>
300 </dd>
301 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
302 <dd>
303 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
304 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
305 data field; transfer SD data files common to all compounds; extract specified data fields;
306 generate a compound ID using molname line, a compound prefix, or a combination of both.
307 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
308 </dd>
309 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
310 <dd>
311 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
312 Default value: <em>Yes</em>.</p>
313 <p>By default, compound data is checked before calculating fingerprints and compounds containing
314 atom data corresponding to non-element symbols or no atom data are ignored.</p>
315 </dd>
316 <dt><strong><strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt>
317 <dd>
318 <p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value:
319 use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append topological
320 atom pair count value IDs to <strong>--FingerprintsLabel</strong> option value.</p>
321 <p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value:
322 <em>FingerprintsLabelOnly</em>.</p>
323 <p>Topological atom pairs IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em>
324 values of <strong>--FingerprintsLabelMode</strong> correspond to atom pair count values in fingerprint vector string.</p>
325 <p><em>FingerprintsLabelWithIDs</em> value of <strong>--FingerprintsLabelMode</strong> is ignored during <em>ArbitrarySize</em> value
326 of <strong>--AtomPairsSetSizeToUse</strong> option and topological atom pairs IDs not appended to the label.</p>
327 </dd>
328 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
329 <dd>
330 <p>SD data label or text file column label to use for fingerprints string in output SD or
331 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalPharmacophoreAtomPairsFingerprints</em>.</p>
332 </dd>
333 <dt><strong><strong>--FuzzifyAtomPairsCount</strong> <em>Yes | No</em></strong></dt>
334 <dd>
335 <p>To fuzzify or not to fuzzify atom pairs count. Possible values: <em>Yes or No</em>. Default value:
336 <em>No</em>.</p>
337 </dd>
338 <dt><strong><strong>--FuzzificationMode</strong> <em>BeforeNormalization | AfterNormalization</em></strong></dt>
339 <dd>
340 <p>When to fuzzify atom pairs count. Possible values: <em>BeforeNormalization | AfterNormalizationYes</em>.
341 Default value: <em>AfterNormalization</em>.</p>
342 </dd>
343 <dt><strong><strong>--FuzzificationMethodology</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em></strong></dt>
344 <dd>
345 <p>How to fuzzify atom pairs count. Possible values: <em>FuzzyBinning | FuzzyBinSmoothing</em>.
346 Default value: <em>FuzzyBinning</em>.</p>
347 <p>In conjunction with values for options <strong>--FuzzifyAtomPairsCount</strong>, <strong>--FuzzificationMode</strong> and
348 <strong>--FuzzFactor</strong>, <strong>--FuzzificationMethodology</strong> option is used to fuzzify pharmacophore atom
349 pairs count.</p>
350 <p>Let:</p>
351 <div class="OptionsBox">
352 Px = Pharmacophore atom type x
353 <br/> Py = Pharmacophore atom type y
354 <br/> PPxy = Pharmacophore atom pair between atom type Px and Py</div>
355 <div class="OptionsBox">
356 PPxyDn = Pharmacophore atom pairs count between atom type Px and Py
357 at distance Dn
358 <br/> PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py
359 at distance Dn - 1
360 <br/> PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py
361 at distance Dn + 1</div>
362 <div class="OptionsBox">
363 FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</div>
364 <p>Then:</p>
365 <p>For <em>FuzzyBinning</em>:</p>
366 <div class="OptionsBox">
367 PPxyDn = PPxyDn (Unchanged)</div>
368 <div class="OptionsBox">
369 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
370 <br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div>
371 <p>For <em>FuzzyBinSmoothing</em>:</p>
372 <div class="OptionsBox">
373 PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin &lt; Dn &lt; Dmax
374 <br/> PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</div>
375 <div class="OptionsBox">
376 PPxyDn-1 = PPxyDn-1 + PPxyDn * FF
377 <br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div>
378 <p>In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurrence counts.
379 A value of 1 during <em>FuzzyBinning</em> corresponds to maximum fuzzification of occurrence counts;
380 however, a value of 1 during <em>FuzzyBinSmoothing</em> ends up completely distributing the value over
381 the previous and next distance bins.</p>
382 <p>So for default value of <strong>--FuzzFactor</strong> (FF) 0.15, the occurrence count of pharmacohore atom pairs
383 at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1
384 are incremented by PPxyDn * 0.15.</p>
385 <p>And during <em>FuzzyBinSmoothing</em> the occurrence counts at Distance Dn is scaled back using multiplicative
386 factor of (1 - 2*0.15) and the occurrence counts at distances Dn -1 and Dn + 1 are incremented by
387 PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out by distributing it over the
388 previous and next distance value.</p>
389 </dd>
390 <dt><strong><strong>--FuzzFactor</strong> <em>number</em></strong></dt>
391 <dd>
392 <p>Specify by how much to fuzzify atom pairs count. Default value: <em>0.15</em>. Valid values: For
393 <em>FuzzyBinning</em> value of <strong>--FuzzificationMethodology</strong> option: <em>between 0 and 1.0</em>; For
394 <em>FuzzyBinSmoothing</em> value of <strong>--FuzzificationMethodology</strong> option: <em>between 0 and 0.5</em>.</p>
395 </dd>
396 <dt><strong><strong>-h, --help</strong></strong></dt>
397 <dd>
398 <p>Print this help message.</p>
399 </dd>
400 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
401 <dd>
402 <p>Generate fingerprints for only the largest component in molecule. Possible values:
403 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
404 <p>For molecules containing multiple connected components, fingerprints can be generated
405 in two different ways: use all connected components or just the largest connected
406 component. By default, all atoms except for the largest connected component are
407 deleted before generation of fingerprints.</p>
408 </dd>
409 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
410 <dd>
411 <p>Minimum bond distance between atom pairs for generating topological pharmacophore atom
412 pairs. Default value: <em>1</em>. Valid values: positive integers including 0 and less than <strong>--MaxDistance</strong>.</p>
413 </dd>
414 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
415 <dd>
416 <p>Maximum bond distance between atom pairs for generating topological pharmacophore atom
417 pairs. Default value: <em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</p>
418 </dd>
419 <dt><strong><strong>-n, --NormalizationMethodology</strong> <em>None | ByHeavyAtomsCount | ByAtomTypesCount</em></strong></dt>
420 <dd>
421 <p>Normalization methodology to use for scaling the occurrence count of pharmacophore atom
422 pairs within specified distance range. Possible values: <em>None, ByHeavyAtomsCount or
423 ByAtomTypesCount</em>. Default value: <em>None</em>.</p>
424 </dd>
425 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
426 <dd>
427 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
428 Default value: <em>comma</em>.</p>
429 </dd>
430 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
431 <dd>
432 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
433 </dd>
434 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
435 <dd>
436 <p>Overwrite existing files.</p>
437 </dd>
438 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
439 <dd>
440 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
441 <em>Yes or No</em>. Default value: <em>Yes</em></p>
442 </dd>
443 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
444 <dd>
445 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file names:
446 &lt;SDFileName&gt;&lt;TopologicalPharmacophoreAtomPairsFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
447 The sdf, fpf, csv, and tsv &lt;Ext&gt; values are used for SD, FP, comma/semicolon, and tab
448 delimited text files, respectively.This option is ignored for multiple input files.</p>
449 </dd>
450 <dt><strong><strong>--ValuesPrecision</strong> <em>number</em></strong></dt>
451 <dd>
452 <p>Precision of atom pairs count real values which might be generated after normalization
453 or fuzzification. Default value: up to <em>2</em> decimal places. Valid values: positive integers.</p>
454 </dd>
455 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
456 <dd>
457 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
458 <strong>--output</strong> option. Possible values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString
459 | ValuesAndIDsString | ValuesAndIDsPairsString</em>.</p>
460 <p>Default value during <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option: <em>ValuesString</em>. Default
461 value during <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option: <em>IDsAndValuesString</em>.</p>
462 <p><em>ValuesString</em> option value is not allowed for <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong>
463 option.</p>
464 <p>Examples:</p>
465 <div class="OptionsBox">
466 FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
467 <br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H
468 <br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2-
469 <br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H
470 <br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...;
471 <br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
472 <br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div>
473 <div class="OptionsBox">
474 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
475 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
476 <br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
477 <br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
478 <br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
479 <br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div>
480 <div class="OptionsBox">
481 FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
482 <br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1
483 <br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H
484 <br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D
485 <br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...;
486 <br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3
487 <br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0
488 <br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</div>
489 </dd>
490 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
491 <dd>
492 <p>Location of working directory. Default value: current directory.</p>
493 </dd>
494 </dl>
495 <p>
496 </p>
497 <h2>EXAMPLES</h2>
498 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
499 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
500 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
501 with fingerprints vector strings data in ValuesString format, type:</p>
502 <div class="ExampleBox">
503 % TopologicalPharmacophoreAtomPairsFingerprints.pl -r SampleTPAPFP
504 -o Sample.sdf</div>
505 <p>To generate topological pharmacophore atom pairs fingerprints of fixed size corresponding to distances
506 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
507 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
508 with fingerprints vector strings data in ValuesString format, type:</p>
509 <div class="ExampleBox">
510 % TopologicalPharmacophoreAtomPairsFingerprints.pl
511 --AtomPairsSetSizeToUse FixedSize -r SampleTPAPFP-o Sample.sdf</div>
512 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
513 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
514 of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and SampleTPAPFP.csv files containing
515 sequential compound IDs in CSV file along with fingerprints vector strings data in ValuesString
516 format, type:</p>
517 <div class="ExampleBox">
518 % TopologicalPharmacophoreAtomPairsFingerprints.pl --output all
519 -r SampleTPAPFP -o Sample.sdf</div>
520 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
521 from 1 through 10 using default atom types with no weighting, normalization, and fuzzification
522 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
523 with fingerprints vector strings data in IDsAndValuesPairsString format, type:</p>
524 <div class="ExampleBox">
525 % TopologicalPharmacophoreAtomPairsFingerprints.pl --VectorStringFormat
526 IDsAndValuesPairsString -r SampleTPAPFP -o Sample.sdf</div>
527 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
528 from 1 through 6 using default atom types with no weighting, normalization, and fuzzification
529 of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along
530 with fingerprints vector strings data in ValuesString format, type:</p>
531 <div class="ExampleBox">
532 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
533 -MaxDistance 6 -r SampleTPAPFP -o Sample.sdf</div>
534 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
535 from 1 through 10 using &quot;HBD,HBA,PI,NI&quot; atom types with double the weighting for &quot;HBD,HBA&quot; and
536 normalization by HeavyAtomCount but no fuzzification of atom pairs count and create a
537 SampleTPAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
538 data in ValuesString format, type:</p>
539 <div class="ExampleBox">
540 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
541 -MaxDistance 10 --AtomTypesToUse &quot;HBD,HBA,PI, NI&quot; --AtomTypesWeight
542 &quot;HBD,2,HBA,2,PI,1,NI,1&quot; --NormalizationMethodology ByHeavyAtomsCount
543 --FuzzifyAtomPairsCount No -r SampleTPAPFP -o Sample.sdf</div>
544 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to
545 distances from 1 through 10 using &quot;HBD,HBA,PI,NI,H&quot; atom types with no weighting of atom types and
546 normalization but with fuzzification of atom pairs count using FuzzyBinning methodology
547 with FuzzFactor value 0.15 and create a SampleTPAPFP.csv file containing sequential compound
548 IDs along with fingerprints vector strings data in ValuesString format, type:</p>
549 <div class="ExampleBox">
550 % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1
551 --MaxDistance 10 --AtomTypesToUse &quot;HBD,HBA,PI, NI,H&quot; --AtomTypesWeight
552 &quot;HBD,1,HBA,1,PI,1,NI,1,H,1&quot; --NormalizationMethodology None
553 --FuzzifyAtomPairsCount Yes --FuzzificationMethodology FuzzyBinning
554 --FuzzFactor 0.5 -r SampleTPAPFP -o Sample.sdf</div>
555 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances
556 distances from 1 through 10 using default atom types with no weighting,
557 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
558 file containing compound ID from molecule name line along with fingerprints vector strings
559 data, type:</p>
560 <div class="ExampleBox">
561 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
562 CompoundID -CompoundIDMode MolName -r SampleTPAPFP -o Sample.sdf</div>
563 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
564 to distances from 1 through 10 using default atom types with no weighting,
565 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
566 file containing compound IDs using specified data field along with fingerprints vector strings
567 data, type:</p>
568 <div class="ExampleBox">
569 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
570 CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
571 -r SampleTPAPFP -o Sample.sdf</div>
572 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
573 to distances from 1 through 10 using default atom types with no weighting,
574 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
575 file containing compound ID using combination of molecule name line and an explicit compound
576 prefix along with fingerprints vector strings data, type:</p>
577 <div class="ExampleBox">
578 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
579 CompoundID -CompoundIDMode MolnameOrLabelPrefix
580 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTPAPFP -o Sample.sdf</div>
581 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
582 to distances from 1 through 10 using default atom types with no weighting,
583 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
584 file containing specific data fields columns along with fingerprints vector strings
585 data, type:</p>
586 <div class="ExampleBox">
587 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
588 Specify --DataFields Mol_ID -r SampleTPAPFP -o Sample.sdf</div>
589 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
590 to distances from 1 through 10 using default atom types with no weighting,
591 normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv
592 file containing common data fields columns along with fingerprints vector strings
593 data, type:</p>
594 <div class="ExampleBox">
595 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
596 Common -r SampleTPAPFP -o Sample.sdf</div>
597 <p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding
598 to distances from 1 through 10 using default atom types with no weighting,
599 normalization, and fuzzification of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf,
600 and SampleTPAPFP.csv files containing all data fields columns in CSV file along with fingerprints
601 data, type:</p>
602 <div class="ExampleBox">
603 % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode
604 All --output all -r SampleTPAPFP -o Sample.sdf</div>
605 <p>
606 </p>
607 <h2>AUTHOR</h2>
608 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
609 <p>
610 </p>
611 <h2>SEE ALSO</h2>
612 <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
613 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp
614 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
615 <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a>
616 </p>
617 <p>
618 </p>
619 <h2>COPYRIGHT</h2>
620 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
621 <p>This file is part of MayaChemTools.</p>
622 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
623 the terms of the GNU Lesser General Public License as published by the Free
624 Software Foundation; either version 3 of the License, or (at your option)
625 any later version.</p>
626 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
627 <table width="100%" border=0 cellpadding=0 cellspacing=2>
628 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalPharmacophoreAtomPairsFingerprints.pl</strong></td></tr>
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