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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TOPOLOGICALPHARMACOPHOREATOMTRIPLETSFINGERPRINTS 1"
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127 .TH TOPOLOGICALPHARMACOPHOREATOMTRIPLETSFINGERPRINTS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 TopologicalPharmacophoreAtomTripletsFingerprints
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints;
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137 .PP
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138 use Fingerprints::TopologicalPharmacophoreAtomTripletsFingerprints qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBTopologicalPharmacophoreAtomTripletsFingerprints\fR [ Ref 66, Ref 68\-71 ] class provides
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142 the following methods:
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143 .PP
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144 new, GenerateFingerprints, , GetDescription, GetAtomTripletIDs,
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145 SetAtomTypesToUse, SetDistanceBinSize, SetMaxDistance, SetMinDistance,
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146 StringifyTopologicalPharmacophoreAtomTripletsFingerprints
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147 .PP
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148 \&\fBTopologicalPharmacophoreAtomTripletsFingerprints\fR is derived from \fBFingerprints\fR class
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149 which in turn is derived from \fBObjectProperty\fR base class that provides methods not explicitly
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150 defined in \fBTopologicalPharmacophoreAtomTripletsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR
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151 classes using Perl's \s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified
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152 object property:
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153 .PP
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154 .Vb 3
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155 \& Set<PropertyName>(<PropertyValue>);
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156 \& $PropertyValue = Get<PropertyName>();
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157 \& Delete<PropertyName>();
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158 .Ve
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159 .PP
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160 Based on the values specified for \fBAtomTypesToUse\fR, pharmacophore atom types are
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161 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
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162 Using \fBMinDistance\fR, \fBMaxDistance\fR, and \fBDistanceBinSize\fR values, a
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163 binned distance matrix is generated with lower bound on the distance bin as the distance
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164 in distance matrix; the lower bound on the distance bin is also used as the distance between
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165 atom pairs for generation of atom triplet identifiers.
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166 .PP
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167 A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting
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168 atom pairs binned distances between \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR. The value
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169 of \fB\-\-UseTriangleInequality\fR determines whether the triangle inequality test is applied during
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170 generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore
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171 types, is used during generation of atom triplet IDs.
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172 .PP
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173 .Vb 1
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174 \& Let:
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175 \&
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176 \& P = Valid pharmacophore atom type
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177 \&
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178 \& Px = Pharmacophore atom x
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179 \& Py = Pharmacophore atom y
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180 \& Pz = Pharmacophore atom z
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181 \&
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182 \& Dmin = Minimum distance corresponding to number of bonds between two atoms
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183 \& Dmax = Maximum distance corresponding to number of bonds between two atoms
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184 \& D = Distance corresponding to number of bonds between two atom
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185 \&
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186 \& Bsize = Distance bin size
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187 \& Nbins = Number of distance bins
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188 \&
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189 \& Dxy = Distance or lower bound of binned distance between Px and Py
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190 \& Dxz = Distance or lower bound of binned distance between Px and Pz
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191 \& Dyz = Distance or lower bound of binned distance between Py and Pz
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192 \&
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193 \& Then:
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194 \&
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195 \& PxDyz\-PyDxz\-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
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196 \& Py, and Pz
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197 \&
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198 \& For example: H1\-H1\-H1, H2\-HBA\-H2 and so on.
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199 \&
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200 \& For default values of Dmin = 1 , Dmax = 10 and Bsize = 2, the number of
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201 \& distance bins, Nbins = 5, are:
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202 \&
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203 \& [1, 2] [3, 4] [5, 6] [7, 8] [9 10]
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204 \&
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205 \& and atom triplet basis set size is 2692.
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206 \&
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207 \& Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
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208 \& conjunction with usage of triangle inequality is:
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209 \&
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210 \& Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize
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211 \& 1 10 2 No 4960
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212 \& 1 10 2 Yes 2692 [ Default ]
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213 \& 2 12 2 No 8436
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214 \& 2 12 2 Yes 4494
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215 .Ve
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216 .PP
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217 Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore
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218 atom triplets is counted.
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219 .PP
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220 The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen
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221 atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.
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222 .PP
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223 For \fIArbitrarySize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector correspond to
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224 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
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225 for \fIFixedSize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector contains all possible
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226 valid topological pharmacophore atom triplets with both zero and non-zero count values.
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227 .PP
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228 The current release of MayaChemTools generates the following types of topological pharmacophore
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229 atom triplets fingerprints vector strings:
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230 .PP
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231 .Vb 8
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232 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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233 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
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234 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
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235 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
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236 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
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237 \& 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
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238 \& 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
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239 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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240 \&
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241 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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242 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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243 \& 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
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244 \& 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
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245 \& 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
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246 \& 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 ...
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247 \&
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248 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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249 \& istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
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250 \& Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-Ar1\-NI1 Ar1\-Ar1\-P
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251 \& I1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1\-H1\-HBD1 Ar1\-H1\-NI1 Ar1\-H1\-PI1 Ar1\-HBA1\-HB
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252 \& A1 Ar1\-HBA1\-HBD1 Ar1\-HBA1\-NI1 Ar1\-HBA1\-PI1 Ar1\-HBD1\-HBD1 Ar1\-HBD1\-...;
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253 \& 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
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254 \& 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
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255 \& 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 ...
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256 .Ve
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257 .SS "\s-1METHODS\s0"
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258 .IX Subsection "METHODS"
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259 .IP "\fBnew\fR" 4
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260 .IX Item "new"
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261 .Vb 2
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262 \& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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263 \& %NamesAndValues);
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264 .Ve
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265 .Sp
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266 Using specified \fITopologicalPharmacophoreAtomTripletsFingerprints\fR property names and values hash, \fBnew\fR
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267 method creates a new object and returns a reference to newly created \fBTopologicalPharmacophoreAtomTripletsFingerprints\fR
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268 object. By default, the following properties are initialized:
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269 .Sp
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270 .Vb 7
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271 \& Molecule = \*(Aq\*(Aq
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272 \& Type = \*(AqTopologicalPharmacophoreAtomTriplets\*(Aq
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273 \& MinDistance = 1
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274 \& MaxDistance = 10
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275 \& DistanceBinSize = 2
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276 \& UseTriangleInequality = 1
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277 \& AtomTypesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq, \*(AqAr\*(Aq]
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278 .Ve
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279 .Sp
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280 Examples:
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281 .Sp
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282 .Vb 2
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283 \& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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284 \& \*(AqMolecule\*(Aq => $Molecule);
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285 \&
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286 \& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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287 \& \*(AqMolecule\*(Aq => $Molecule,
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288 \& \*(AqAtomTripletsSetSizeToUse\*(Aq => \*(AqArbitrarySize\*(Aq;
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289 \& \*(AqMinDistance\*(Aq => 1,
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290 \& \*(AqMaxDistance\*(Aq => 10,
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291 \& \*(AqDistanceBinSize\*(Aq => 2,
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292 \& \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq, \*(AqAr\*(Aq],
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293 \& \*(AqUseTriangleInequality\*(Aq => 1);
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294 \&
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295 \& $TPATFP = new TopologicalPharmacophoreAtomTripletsFingerprints(
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296 \& \*(AqMolecule\*(Aq => $Molecule,
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297 \& \*(AqAtomTripletsSetSizeToUse\*(Aq => \*(AqFixedSize\*(Aq;
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298 \& \*(AqMinDistance\*(Aq => 1,
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299 \& \*(AqMaxDistance\*(Aq => 10,
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300 \& \*(AqDistanceBinSize\*(Aq => 2,
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301 \& \*(AqAtomTypesToUse\*(Aq => [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqH\*(Aq, \*(AqAr\*(Aq],
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302 \& \*(AqUseTriangleInequality\*(Aq => 1);
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303 \&
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304 \& $TPATFP\->GenerateFingerprints();
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305 \& print "$TPATFP\en";
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306 .Ve
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307 .IP "\fBGetDescription\fR" 4
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308 .IX Item "GetDescription"
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309 .Vb 1
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310 \& $Description = $TopologicalPharmacophoreAtomTripletsFP\->GetDescription();
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311 .Ve
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312 .Sp
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313 Returns a string containing description of topological pharmacophore atom triplets fingerprints.
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314 .IP "\fBGenerateFingerprints\fR" 4
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315 .IX Item "GenerateFingerprints"
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316 .Vb 1
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317 \& $TopologicalPharmacophoreAtomTripletsFP\->GenerateFingerprints();
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318 .Ve
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319 .Sp
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320 Generates topological pharmacophore atom triplets fingerprints and returns
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321 \&\fITopologicalPharmacophoreAtomTripletsFP\fR.
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322 .IP "\fBGetAtomTripletIDs\fR" 4
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323 .IX Item "GetAtomTripletIDs"
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324 .Vb 2
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325 \& $AtomTripletsIDsRef = $TopologicalPharmacophoreATFP\->GetAtomTripletIDs();
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326 \& @AtomTripletIDs = $TopologicalPharmacophoreATFP\->GetAtomTripletIDs();
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327 .Ve
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328 .Sp
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329 Returns atom triplet IDs corresponding to atom pairs count values in topological pharmacophore
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330 atom triplet fingerprints vector as an array or reference to an array.
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331 .IP "\fBAtomTripletsSetSizeToUse\fR" 4
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332 .IX Item "AtomTripletsSetSizeToUse"
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333 .Vb 1
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334 \& $TPAFP\->AtomTripletsSetSizeToUse($Values);
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335 .Ve
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336 .Sp
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337 Sets pharmacophore atom triplets set size to use for topological pharmacophore fingerprints
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338 generation and returns \fITopologicalPharmacophoreAtomTripletsFingerprints\fR.
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339 .Sp
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340 Possible values for pharmacophore atom triplets set size are: \fIArbitrarySize, FizedSize\fR.
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341 Default value: \fIArbitrarySize\fR.
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342 .Sp
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343 For \fIArbitrarySize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector correspond to
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344 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
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345 for \fIFixedSize\fR value of \fBAtomTripletsSetSizeToUse\fR, the fingerprint vector contains all possible
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346 valid topological pharmacophore atom triplets with both zero and non-zero count values.
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347 .IP "\fBSetAtomTypesToUse\fR" 4
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348 .IX Item "SetAtomTypesToUse"
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349 .Vb 2
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350 \& $TopologicalPharmacophoreAtomTripletsFP\->SetAtomTypesToUse($ValuesRef);
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351 \& $TopologicalPharmacophoreAtomTripletsFP\->SetAtomTypesToUse(@Values);
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352 .Ve
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353 .Sp
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354 Sets pharmacophore atom types to use for topological pharmacophore fingerprints
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355 generation and returns \fITopologicalPharmacophoreAtomTripletsFingerprints\fR.
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356 .Sp
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357 Possible values for pharmacophore atom types are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
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358 Default value [ Ref 71 ] : \fI\s-1HBD\s0,HBA,PI,NI,H,Ar\fR.
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359 .Sp
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360 The pharmacophore atom types abbreviations correspond to:
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361 .Sp
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362 .Vb 9
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363 \& HBD: HydrogenBondDonor
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364 \& HBA: HydrogenBondAcceptor
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365 \& PI : PositivelyIonizable
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366 \& NI : NegativelyIonizable
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367 \& Ar : Aromatic
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368 \& Hal : Halogen
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369 \& H : Hydrophobic
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370 \& RA : RingAtom
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371 \& CA : ChainAtom
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372 .Ve
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373 .Sp
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374 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign pharmacophore atom
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375 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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376 .Sp
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377 .Vb 4
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378 \& HydrogenBondDonor: NH, NH2, OH
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379 \& HydrogenBondAcceptor: N[!H], O
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380 \& PositivelyIonizable: +, NH2
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381 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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382 .Ve
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383 .IP "\fBSetDistanceBinSize\fR" 4
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384 .IX Item "SetDistanceBinSize"
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385 .Vb 1
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386 \& $TopologicalPharmacophoreAtomTripletsFP\->SetDistanceBinSize($Value);
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387 .Ve
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388 .Sp
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389 Sets distance bin size used to bin distances between atom pairs in atom triplets and returns
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390 \&\fITopologicalPharmacophoreAtomTriplesFP\fR.
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391 .Sp
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392 For default \fBMinDistance\fR and \fBMaxDistance\fR values of 1 and 10 with \fBDistanceBinSize\fR
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393 of 2 [ Ref 70 ], the following 5 distance bins are generated:
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394 .Sp
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395 .Vb 1
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396 \& [1, 2] [3, 4] [5, 6] [7, 8] [9 10]
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397 .Ve
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398 .Sp
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399 The lower distance bound on the distance bin is uses to bin the distance between atom pairs in
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400 atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance
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401 bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.
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402 .Sp
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403 In order to distribute distance bins of equal size, the last bin is allowed to go past \fBMaxDistance\fR
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404 by up to distance bin size. For example, \fBMinDistance\fR and \fBMaxDistance\fR values of 2 and 10
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405 with \fBDistanceBinSize\fR of 2 generates the following 6 distance bins:
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406 .Sp
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407 .Vb 1
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408 \& [2, 3] [4, 5] [6, 7] [8, 9] [10 11]
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409 .Ve
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410 .IP "\fBSetMaxDistance\fR" 4
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411 .IX Item "SetMaxDistance"
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412 .Vb 1
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413 \& $TopologicalPharmacophoreAtomTriplesFP\->SetMaxDistance($Value);
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414 .Ve
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415 .Sp
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416 Sets maximum bond distance between atom pairs corresponding to atom triplets for
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417 generating topological pharmacophore atom triplets fingerprints and returns
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418 \&\fITopologicalPharmacophoreAtomTriplesFP\fR.
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419 .IP "\fBSetMinDistance\fR" 4
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420 .IX Item "SetMinDistance"
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421 .Vb 1
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422 \& $TopologicalPharmacophoreAtomTriplesFP\->SetMinDistance($Value);
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423 .Ve
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424 .Sp
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425 Sets minimum bond distance between atom pairs corresponding to atom triplets for
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426 generating topological pharmacophore atom triplets fingerprints and returns
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427 \&\fITopologicalPharmacophoreAtomTriplesFP\fR.
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428 .IP "\fBStringifyTopologicalPharmacophoreAtomTripletsFingerprints\fR" 4
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429 .IX Item "StringifyTopologicalPharmacophoreAtomTripletsFingerprints"
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430 .Vb 2
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431 \& $String = $TopologicalPharmacophoreAtomTripletsFingerprints\->
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432 \& StringifyTopologicalPharmacophoreAtomTripletsFingerprints();
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433 .Ve
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434 .Sp
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435 Returns a string containing information about \fITopologicalPharmacophoreAtomTripletsFingerprints\fR object.
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436 .SH "AUTHOR"
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437 .IX Header "AUTHOR"
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438 Manish Sud <msud@san.rr.com>
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439 .SH "SEE ALSO"
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440 .IX Header "SEE ALSO"
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441 Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm,
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442 AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
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443 MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
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444 TopologicalAtomTripletsFingerprints.pm, TopologicalAtomTorsionsFingerprints.pm,
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445 TopologicalPharmacophoreAtomPairsFingerprints.pm,
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446 .SH "COPYRIGHT"
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447 .IX Header "COPYRIGHT"
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448 Copyright (C) 2015 Manish Sud. All rights reserved.
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449 .PP
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450 This file is part of MayaChemTools.
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451 .PP
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452 MayaChemTools is free software; you can redistribute it and/or modify it under
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453 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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454 Software Foundation; either version 3 of the License, or (at your option)
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455 any later version.
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