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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./EndPage.html" title="EndPage.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalPharmacophoreAtomTripletsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomTripletsFingerprints.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/TopologicalPharmacophoreAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/TopologicalPharmacophoreAtomTripletsFingerprints.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>TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate topological pharmacophore atom triplets fingerprints for SD files</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)...</p>
26 <p>TopologicalPharmacophoreAtomTripletsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>]
27 [<strong>--AtomTripletsSetSizeToUse</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>--DistanceBinSize</strong> <em>number</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>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] [<strong>--MinDistance</strong> <em>number</em>] [<strong>--MaxDistance</strong> <em>number</em>]
35 [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>]
36 [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-u, --UseTriangleInequality</strong> <em>Yes | No</em>]
37 [<strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>]
38 [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p>
39 <p>
40 </p>
41 <h2>DESCRIPTION</h2>
42 <p>Generate topological pharmacophore atom triplets fingerprints [ Ref 66, Ref 68-71 ] for
43 <em>SDFile(s)</em> and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector
44 strings corresponding to molecular fingerprints.</p>
45 <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
46 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
47 can be specified either by <em>*.sdf</em> or the current directory name.</p>
48 <p>Based on the values specified for <strong>--AtomTypesToUse</strong>, pharmacophore atom types are
49 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
50 Using <strong>--MinDistance</strong>, <strong>--MaxDistance</strong>, and <strong>--DistanceBinSize</strong> values, a
51 binned distance matrix is generated with lower bound on the distance bin as the distance
52 in distance matrix; the lower bound on the distance bin is also used as the distance between
53 atom pairs for generation of atom triplet identifiers.</p>
54 <p>A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting
55 atom pairs binned distances between <strong>--MinDistance</strong> and <strong>--MaxDistance</strong>. The value
56 of <strong>--UseTriangleInequality</strong> determines whether the triangle inequality test is applied during
57 generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore
58 types, is used during generation of atom triplet IDs.</p>
59 <div class="OptionsBox">
60 Let:</div>
61 <div class="OptionsBox">
62 P = Valid pharmacophore atom type</div>
63 <div class="OptionsBox">
64 Px = Pharmacophore atom x
65 <br/> Py = Pharmacophore atom y
66 <br/> Pz = Pharmacophore atom z</div>
67 <div class="OptionsBox">
68 Dmin = Minimum distance corresponding to number of bonds between two atoms
69 <br/> Dmax = Maximum distance corresponding to number of bonds between two atoms
70 <br/> D = Distance corresponding to number of bonds between two atom</div>
71 <div class="OptionsBox">
72 Bsize = Distance bin size
73 <br/> Nbins = Number of distance bins</div>
74 <div class="OptionsBox">
75 Dxy = Distance or lower bound of binned distance between Px and Py
76 <br/> Dxz = Distance or lower bound of binned distance between Px and Pz
77 <br/> Dyz = Distance or lower bound of binned distance between Py and Pz</div>
78 <div class="OptionsBox">
79 Then:</div>
80 <div class="OptionsBox">
81 PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
82 Py, and Pz</div>
83 <div class="OptionsBox">
84 For example: H1-H1-H1, H2-HBA-H2 and so on</div>
85 <div class="OptionsBox">
86 For default values of Dmin = 1 , Dmax = 10 and Bsize = 2:</div>
87 <div class="OptionsBox">
88 the number of distance bins, Nbins = 5, are:</div>
89 <div class="OptionsBox">
90 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
91 <div class="OptionsBox">
92 and atom triplet basis set size is 2692.</div>
93 <div class="OptionsBox">
94 Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
95 <br/> conjunction with usage of triangle inequality is:</div>
96 <div class="OptionsBox">
97 Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize
98 <br/> 1 10 2 No 4960
99 <br/> 1 10 2 Yes 2692 [ Default ]
100 <br/> 2 12 2 No 8436
101 <br/> 2 12 2 Yes 4494</div>
102 <p>Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore
103 atom triplets is counted.</p>
104 <p>The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen
105 atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.</p>
106 <p>For <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector correspond to
107 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
108 for <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector contains all possible
109 valid topological pharmacophore atom triplets with both zero and non-zero count values.</p>
110 <p>Example of <em>SD</em> file containing topological pharmacophore atom triplets fingerprints string data:</p>
111 <div class="OptionsBox">
112 ... ...
113 <br/> ... ...
114 <br/> $$$$
115 <br/> ... ...
116 <br/> ... ...
117 <br/> ... ...
118 <br/> 41 44 0 0 0 0 0 0 0 0999 V2000
119 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
120 <br/> ... ...
121 <br/> 2 3 1 0 0 0 0
122 <br/> ... ...
123 <br/> M END
124 <br/> &gt; &lt;CmpdID&gt;
125 <br/> Cmpd1</div>
126 <div class="OptionsBox">
127 &gt; &lt;TopologicalPharmacophoreAtomTripletsFingerprints&gt;
128 <br/> FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
129 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
130 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
131 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
132 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
133 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
134 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
135 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
136 <div class="OptionsBox">
137 $$$$
138 <br/> ... ...
139 <br/> ... ...</div>
140 <p>Example of <em>FP</em> file containing topological pharmacophore atom triplets 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 15:38:58 2011
147 <br/> #
148 <br/> # FingerprintsStringType = FingerprintsVector
149 <br/> #
150 <br/> # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M...
151 <br/> # VectorStringFormat = IDsAndValuesString
152 <br/> # VectorValuesType = NumericalValues
153 <br/> #
154 <br/> Cmpd1 696;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1...;;46 106...
155 <br/> Cmpd2 251;H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-H1-NI1...;4 1 3 1 1 2 2...
156 <br/> ... ...
157 <br/> ... ..</div>
158 <p>Example of CSV <em>Text</em> file containing topological pharmacophore atom triplets fingerprints string data:</p>
159 <div class="OptionsBox">
160 &quot;CompoundID&quot;,&quot;TopologicalPharmacophoreAtomTripletsFingerprints&quot;
161 <br/> &quot;Cmpd1&quot;,&quot;FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr
162 <br/> arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri
163 <br/> ng;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HB
164 <br/> A1 Ar1-H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA
165 <br/> 1 H1-HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 A...;
166 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
167 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
168 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
169 <br/> ... ...
170 <br/> ... ...</div>
171 <p>The current release of MayaChemTools generates the following types of topological pharmacophore
172 atom triplets fingerprints vector strings:</p>
173 <div class="OptionsBox">
174 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
175 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
176 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
177 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
178 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
179 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
180 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
181 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
182 <div class="OptionsBox">
183 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
184 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
185 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
186 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
187 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
188 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
189 <div class="OptionsBox">
190 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
191 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
192 <br/> Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P
193 <br/> I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB
194 <br/> A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...;
195 <br/> 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1
196 <br/> 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145
197 <br/> 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ...</div>
198 <p>
199 </p>
200 <h2>OPTIONS</h2>
201 <dl>
202 <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt>
203 <dd>
204 <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current
205 release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
206 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
207 or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p>
208 <p>The supported aromaticity model names along with model specific control parameters
209 are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release
210 and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from
211 this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong>
212 for detecting aromaticity corresponding to a specific model.</p>
213 </dd>
214 <dt><strong><strong>--AtomTripletsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt>
215 <dd>
216 <p>Atom triplets set size to use during generation of topological pharmacophore atom triplets
217 fingerprints.</p>
218 <p>Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p>
219 <p>For <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option, the fingerprint vector
220 correspond to only those topological pharmacophore atom triplets which are present and
221 have non-zero count. However, for <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong>
222 option, the fingerprint vector contains all possible valid topological pharmacophore atom
223 triplets with both zero and non-zero count values.</p>
224 </dd>
225 <dt><strong><strong>-a, --AtomTypesToUse</strong> <em>&quot;AtomType1,AtomType2,...&quot;</em></strong></dt>
226 <dd>
227 <p>Pharmacophore atom types to use during generation of topological phramacophore
228 atom triplets. It's a list of comma separated valid pharmacophore atom types.</p>
229 <p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.
230 Default value [ Ref 71 ] : <em>HBD,HBA,PI,NI,H,Ar</em>.</p>
231 <p>The pharmacophore atom types abbreviations correspond to:</p>
232 <div class="OptionsBox">
233 HBD: HydrogenBondDonor
234 <br/> HBA: HydrogenBondAcceptor
235 <br/> PI : PositivelyIonizable
236 <br/> NI : NegativelyIonizable
237 <br/> Ar : Aromatic
238 <br/> Hal : Halogen
239 <br/> H : Hydrophobic
240 <br/> RA : RingAtom
241 <br/> CA : ChainAtom</div>
242 <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore atom
243 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p>
244 <div class="OptionsBox">
245 HydrogenBondDonor: NH, NH2, OH
246 <br/> HydrogenBondAcceptor: N[!H], O
247 <br/> PositivelyIonizable: +, NH2
248 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
249 </dd>
250 <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt>
251 <dd>
252 <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p>
253 <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> option, it corresponds to datafield label name
254 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
255 IDs like LabelPrefixString&lt;Number&gt;. Default value, <em>Cmpd</em>, generates compound IDs which
256 look like Cmpd&lt;Number&gt;.</p>
257 <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p>
258 <div class="OptionsBox">
259 MolID
260 <br/> ExtReg</div>
261 <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p>
262 <div class="OptionsBox">
263 Compound</div>
264 <p>The value specified above generates compound IDs which correspond to Compound&lt;Number&gt;
265 instead of default value of Cmpd&lt;Number&gt;.</p>
266 </dd>
267 <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt>
268 <dd>
269 <p>Specify compound ID column label for CSV/TSV text file(s) used during <em>CompoundID</em> value
270 of <strong>--DataFieldsMode</strong> option. Default value: <em>CompoundID</em>.</p>
271 </dd>
272 <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt>
273 <dd>
274 <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
275 fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value;
276 use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination
277 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p>
278 <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>.
279 Default value: <em>LabelPrefix</em>.</p>
280 <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes
281 precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname
282 values are replaced with sequential compound IDs.</p>
283 <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p>
284 </dd>
285 <dt><strong><strong>--DataFields</strong> <em>&quot;FieldLabel1,FieldLabel2,...&quot;</em></strong></dt>
286 <dd>
287 <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along
288 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p>
289 <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p>
290 <p>Examples:</p>
291 <div class="OptionsBox">
292 Extreg
293 <br/> MolID,CompoundName</div>
294 </dd>
295 <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt>
296 <dd>
297 <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along
298 with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option: transfer all SD
299 data field; transfer SD data files common to all compounds; extract specified data fields;
300 generate a compound ID using molname line, a compound prefix, or a combination of both.
301 Possible values: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p>
302 </dd>
303 <dt><strong><strong>--DistanceBinSize</strong> <em>number</em></strong></dt>
304 <dd>
305 <p>Distance bin size used to bin distances between atom pairs in atom triplets. Default value: <em>2</em>.
306 Valid values: positive integers.</p>
307 <p>For default <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> values of 1 and 10 with <strong>--DistanceBinSize</strong>
308 of 2 [ Ref 70 ], the following 5 distance bins are generated:</p>
309 <div class="OptionsBox">
310 [1, 2] [3, 4] [5, 6] [7, 8] [9 10]</div>
311 <p>The lower distance bound on the distance bin is uses to bin the distance between atom pairs in
312 atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance
313 bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.</p>
314 <p>In order to distribute distance bins of equal size, the last bin is allowed to go past <strong>--MaxDistance</strong>
315 by up to distance bin size. For example, <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> values of 2 and 10
316 with <strong>--DistanceBinSize</strong> of 2 generates the following 6 distance bins:</p>
317 <div class="OptionsBox">
318 [2, 3] [4, 5] [6, 7] [8, 9] [10 11]</div>
319 </dd>
320 <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt>
321 <dd>
322 <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>.
323 Default value: <em>Yes</em>.</p>
324 <p>By default, compound data is checked before calculating fingerprints and compounds containing
325 atom data corresponding to non-element symbols or no atom data are ignored.</p>
326 </dd>
327 <dt><strong><strong>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt>
328 <dd>
329 <p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value:
330 use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append topological
331 atom pair count value IDs to <strong>--FingerprintsLabel</strong> option value.</p>
332 <p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value:
333 <em>FingerprintsLabelOnly</em>.</p>
334 <p>Topological atom pairs IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em>
335 values of <strong>--FingerprintsLabelMode</strong> correspond to atom pair count values in fingerprint vector string.</p>
336 <p><em>FingerprintsLabelWithIDs</em> value of <strong>--FingerprintsLabelMode</strong> is ignored during <em>ArbitrarySize</em> value
337 of <strong>--AtomTripletsSetSizeToUse</strong> option and topological atom triplets IDs not appended to the label.</p>
338 </dd>
339 <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt>
340 <dd>
341 <p>SD data label or text file column label to use for fingerprints string in output SD or
342 CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>.</p>
343 </dd>
344 <dt><strong><strong>-h, --help</strong></strong></dt>
345 <dd>
346 <p>Print this help message.</p>
347 </dd>
348 <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt>
349 <dd>
350 <p>Generate fingerprints for only the largest component in molecule. Possible values:
351 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
352 <p>For molecules containing multiple connected components, fingerprints can be generated
353 in two different ways: use all connected components or just the largest connected
354 component. By default, all atoms except for the largest connected component are
355 deleted before generation of fingerprints.</p>
356 </dd>
357 <dt><strong><strong>--MinDistance</strong> <em>number</em></strong></dt>
358 <dd>
359 <p>Minimum bond distance between atom pairs corresponding to atom triplets for generating
360 topological pharmacophore atom triplets. Default value: <em>1</em>. Valid values: positive integers and
361 less than <strong>--MaxDistance</strong>.</p>
362 </dd>
363 <dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt>
364 <dd>
365 <p>Maximum bond distance between atom pairs corresponding to atom triplets for generating
366 topological pharmacophore atom triplets. Default value: <em>10</em>. Valid values: positive integers and
367 greater than <strong>--MinDistance</strong>.</p>
368 </dd>
369 <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt>
370 <dd>
371 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
372 Default value: <em>comma</em>.</p>
373 </dd>
374 <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt>
375 <dd>
376 <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p>
377 </dd>
378 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
379 <dd>
380 <p>Overwrite existing files.</p>
381 </dd>
382 <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt>
383 <dd>
384 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
385 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
386 </dd>
387 <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt>
388 <dd>
389 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file names:
390 &lt;SDFileName&gt;&lt;TopologicalPharmacophoreAtomTripletsFP&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
391 The sdf, fpf, csv, and tsv &lt;Ext&gt; values are used for SD, FP, comma/semicolon, and tab
392 delimited text files, respectively.This option is ignored for multiple input files.</p>
393 </dd>
394 <dt><strong><strong>-u, --UseTriangleInequality</strong> <em>Yes | No</em></strong></dt>
395 <dd>
396 <p>Specify whether to imply triangle distance inequality test to distances between atom pairs in
397 atom triplets during generation of atom triplets basis set generation. Possible values:
398 <em>Yes or No</em>. Default value: <em>Yes</em>.</p>
399 <p>Triangle distance inequality test implies that distance or binned distance between any two atom
400 pairs in an atom triplet must be less than the sum of distances or binned distances between other
401 two atoms pairs and greater than the difference of their distances.</p>
402 <div class="OptionsBox">
403 For atom triplet PxDyz-PyDxz-PzDxy to satisfy triangle inequality:</div>
404 <div class="OptionsBox">
405 Dyz &gt; |Dxz - Dxy| and Dyz &lt; Dxz + Dxy
406 <br/> Dxz &gt; |Dyz - Dxy| and Dyz &lt; Dyz + Dxy
407 <br/> Dxy &gt; |Dyz - Dxz| and Dxy &lt; Dyz + Dxz</div>
408 </dd>
409 <dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt>
410 <dd>
411 <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
412 <strong>--output</strong> option. Possible values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
413 ValuesAndIDsString | ValuesAndIDsPairsString</em>. Defaultvalue: <em>ValuesString</em>.</p>
414 <p>Default value during <em>FixedSize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option: <em>ValuesString</em>. Default
415 value during <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong> option: <em>IDsAndValuesString</em>.</p>
416 <p><em>ValuesString</em> option value is not allowed for <em>ArbitrarySize</em> value of <strong>--AtomTripletsSetSizeToUse</strong>
417 option.</p>
418 <p>Examples:</p>
419 <div class="OptionsBox">
420 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
421 <br/> MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1-
422 <br/> Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1
423 <br/> -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1-
424 <br/> HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...;
425 <br/> 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
426 <br/> 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
427 <br/> 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...</div>
428 <div class="OptionsBox">
429 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
430 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
431 <br/> 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
432 <br/> 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
433 <br/> 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
434 <br/> 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...</div>
435 <div class="OptionsBox">
436 FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
437 <br/> istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt
438 <br/> ring;46 Ar1-Ar1-Ar1 106 Ar1-Ar1-H1 8 Ar1-Ar1-HBA1 3 Ar1-Ar1-HBD1 0 Ar1
439 <br/> -Ar1-NI1 0 Ar1-Ar1-PI1 83 Ar1-H1-H1 11 Ar1-H1-HBA1 4 Ar1-H1-HBD1 0 Ar1
440 <br/> -H1-NI1 0 Ar1-H1-PI1 0 Ar1-HBA1-HBA1 1 Ar1-HBA1-HBD1 0 Ar1-HBA1-NI1 0
441 <br/> Ar1-HBA1-PI1 0 Ar1-HBD1-HBD1 0 Ar1-HBD1-NI1 0 Ar1-HBD1-PI1 0 Ar1-NI...</div>
442 </dd>
443 <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt>
444 <dd>
445 <p>Location of working directory. Default value: current directory.</p>
446 </dd>
447 </dl>
448 <p>
449 </p>
450 <h2>EXAMPLES</h2>
451 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
452 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
453 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
454 with fingerprints vector strings data in ValuesString format, type:</p>
455 <div class="ExampleBox">
456 % TopologicalPharmacophoreAtomTripletsFingerprints.pl -r SampleTPATFP
457 -o Sample.sdf</div>
458 <p>To generate topological pharmacophore atom triplets fingerprints of fixed size corresponding to 5
459 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
460 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
461 with fingerprints vector strings data in ValuesString format, type:</p>
462 <div class="ExampleBox">
463 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
464 --AtomTripletsSetSizeToUse FixedSize -r SampleTPATFP -o Sample.sdf</div>
465 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
466 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
467 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files with CSV file containing
468 sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:</p>
469 <div class="ExampleBox">
470 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --output all
471 -r SampleTPATFP -o Sample.sdf</div>
472 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
473 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
474 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
475 with fingerprints vector strings data in ValuesString format and atom triplets IDs in the
476 fingerprint data column label starting with Fingerprints, type:</p>
477 <div class="ExampleBox">
478 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
479 --FingerprintsLabelMode FingerprintsLabelWithIDs --FingerprintsLabel
480 Fingerprints -r SampleTPATFP -o Sample.sdf</div>
481 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
482 distance bins spanning distances from 1 through 10 using default atoms with distances not satisfying triangle
483 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
484 with fingerprints vector strings data in ValuesString format, type:</p>
485 <div class="ExampleBox">
486 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
487 --UseTriangleInequality No -r SampleTPATFP -o Sample.sdf</div>
488 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6
489 distance bins spanning distances from 1 through 12 using default atoms with distances satisfying triangle
490 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
491 with fingerprints vector strings data in ValuesString format, type:</p>
492 <div class="ExampleBox">
493 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
494 --UseTriangleInequality Yes --MinDistance 1 --MaxDistance 12
495 --DistanceBinSIze 2 -r SampleTPATFP -o Sample.sdf</div>
496 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6
497 distance bins spanning distances from 1 through 12 using &quot;HBD,HBA,PI, NI, H, Ar&quot; atoms with distances
498 satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound
499 IDs along with fingerprints vector strings data in ValuesString format, type:</p>
500 <div class="ExampleBox">
501 % TopologicalPharmacophoreAtomTripletsFingerprints.pl
502 --AtomTypesToUse &quot;HBD,HBA,PI,NI,H,Ar&quot; --UseTriangleInequality Yes
503 --MinDistance 1 --MaxDistance 12 --DistanceBinSIze 2
504 --VectorStringFormat ValuesString -r SampleTPATFP -o Sample.sdf</div>
505 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
506 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
507 inequality and create a SampleTPATFP.csv file containing sequential compound IDs from
508 molecule name line along with fingerprints vector strings data in ValuesString format, type:</p>
509 <div class="ExampleBox">
510 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
511 CompoundID -CompoundIDMode MolName -r SampleTPATFP -o Sample.sdf</div>
512 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
513 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
514 inequality and create a SampleTPATFP.csv file containing sequential compound IDs using
515 specified data field along with fingerprints vector strings data in ValuesString format, type:</p>
516 <div class="ExampleBox">
517 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
518 CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
519 -r SampleTPATFP -o Sample.sdf</div>
520 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
521 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
522 inequality and create a SampleTPATFP.csv file containing sequential compound IDs using
523 combination of molecule name line and an explicit compound prefix along with fingerprints vector
524 strings data, type:</p>
525 <div class="ExampleBox">
526 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
527 CompoundID -CompoundIDMode MolnameOrLabelPrefix
528 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleSampleTPATFP
529 -o Sample.sdf</div>
530 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
531 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
532 inequality and create a SampleTPATFP.csv file containing specific data fields columns along
533 with fingerprints vector strings data, type:</p>
534 <div class="ExampleBox">
535 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
536 Specify --DataFields Mol_ID -r SampleTPATFP -o Sample.sdf</div>
537 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
538 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
539 inequality and create a SampleTPATFP.csv file containing common data fields columns along
540 with fingerprints vector strings data, type:</p>
541 <div class="ExampleBox">
542 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
543 Common -r SampleTPATFP -o Sample.sdf</div>
544 <p>To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
545 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
546 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files containing all
547 data fields columns in CSV file along with fingerprints data, type:</p>
548 <div class="ExampleBox">
549 % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode
550 All --output all -r SampleTPATFP -o Sample.sdf</div>
551 <p>
552 </p>
553 <h2>AUTHOR</h2>
554 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
555 <p>
556 </p>
557 <h2>SEE ALSO</h2>
558 <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
559 <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>,&nbsp<a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,&nbsp<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pl</a>,&nbsp
560 <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>,&nbsp<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,&nbsp
561 <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>
562 </p>
563 <p>
564 </p>
565 <h2>COPYRIGHT</h2>
566 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
567 <p>This file is part of MayaChemTools.</p>
568 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
569 the terms of the GNU Lesser General Public License as published by the Free
570 Software Foundation; either version 3 of the License, or (at your option)
571 any later version.</p>
572 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
573 <table width="100%" border=0 cellpadding=0 cellspacing=2>
574 <tr align="left" valign="top"><td width="33%" align="left"><a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./EndPage.html" title="EndPage.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalPharmacophoreAtomTripletsFingerprints.pl</strong></td></tr>
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