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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.pl \- Generate topological pharmacophore atom triplets fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)...
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137 .PP
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138 TopologicalPharmacophoreAtomTripletsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
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139 [\fB\-\-AtomTripletsSetSizeToUse\fR \fIArbitrarySize | FixedSize\fR]
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140 [\fB\-a, \-\-AtomTypesToUse\fR \fI\*(L"AtomType1, AtomType2...\*(R"\fR]
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141 [\fB\-\-AtomTypesWeight\fR \fI\*(L"AtomType1, Weight1, AtomType2, Weight2...\*(R"\fR]
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142 [\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR]
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143 [\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1, FieldLabel2,...\*(R"\fR]
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144 [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] [\fB\-\-DistanceBinSize\fR \fInumber\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR]
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145 [\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR]
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146 [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] [\fB\-\-MinDistance\fR \fInumber\fR] [\fB\-\-MaxDistance\fR \fInumber\fR]
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147 [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-o, \-\-overwrite\fR]
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148 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR]
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149 [\fB\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
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150 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
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151 .SH "DESCRIPTION"
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152 .IX Header "DESCRIPTION"
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153 Generate topological pharmacophore atom triplets fingerprints [ Ref 66, Ref 68\-71 ] for
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154 \&\fISDFile(s)\fR and create appropriate \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector
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155 strings corresponding to molecular fingerprints.
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156 .PP
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157 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
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158 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
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159 can be specified either by \fI*.sdf\fR or the current directory name.
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160 .PP
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161 Based on the values specified for \fB\-\-AtomTypesToUse\fR, pharmacophore atom types are
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162 assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated.
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163 Using \fB\-\-MinDistance\fR, \fB\-\-MaxDistance\fR, and \fB\-\-DistanceBinSize\fR values, a
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164 binned distance matrix is generated with lower bound on the distance bin as the distance
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165 in distance matrix; the lower bound on the distance bin is also used as the distance between
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166 atom pairs for generation of atom triplet identifiers.
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167 .PP
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168 A pharmacophore atom triplets basis set is generated for all unique atom triplets constituting
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169 atom pairs binned distances between \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR. The value
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170 of \fB\-\-UseTriangleInequality\fR determines whether the triangle inequality test is applied during
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171 generation of atom triplets basis set. The lower distance bound, along with specified pharmacophore
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172 types, is used during generation of atom triplet IDs.
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173 .PP
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174 .Vb 1
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175 \& Let:
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176 \&
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177 \& P = Valid pharmacophore atom type
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178 \&
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179 \& Px = Pharmacophore atom x
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180 \& Py = Pharmacophore atom y
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181 \& Pz = Pharmacophore atom z
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182 \&
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183 \& Dmin = Minimum distance corresponding to number of bonds between two atoms
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184 \& Dmax = Maximum distance corresponding to number of bonds between two atoms
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185 \& D = Distance corresponding to number of bonds between two atom
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186 \&
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187 \& Bsize = Distance bin size
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188 \& Nbins = Number of distance bins
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189 \&
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190 \& Dxy = Distance or lower bound of binned distance between Px and Py
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191 \& Dxz = Distance or lower bound of binned distance between Px and Pz
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192 \& Dyz = Distance or lower bound of binned distance between Py and Pz
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193 \&
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194 \& Then:
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195 \&
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196 \& PxDyz\-PyDxz\-PzDxy = Pharmacophore atom triplet IDs for atom types Px,
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197 \& Py, and Pz
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198 \&
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199 \& For example: H1\-H1\-H1, H2\-HBA\-H2 and so on
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200 \&
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201 \& For default values of Dmin = 1 , Dmax = 10 and Bsize = 2:
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202 \&
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203 \& the number of distance bins, Nbins = 5, are:
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204 \&
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205 \& [1, 2] [3, 4] [5, 6] [7, 8] [9 10]
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206 \&
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207 \& and atom triplet basis set size is 2692.
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208 \&
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209 \& Atom triplet basis set size for various values of Dmin, Dmax and Bsize in
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210 \& conjunction with usage of triangle inequality is:
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211 \&
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212 \& Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize
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213 \& 1 10 2 No 4960
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214 \& 1 10 2 Yes 2692 [ Default ]
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215 \& 2 12 2 No 8436
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216 \& 2 12 2 Yes 4494
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217 .Ve
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218 .PP
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219 Using binned distance matrix and pharmacohore atom types, occurrence of unique pharmacohore
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220 atom triplets is counted.
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221 .PP
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222 The final pharmacophore atom triples count along with atom pair identifiers involving all non-hydrogen
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223 atoms constitute pharmacophore topological atom triplets fingerprints of the molecule.
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224 .PP
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225 For \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option, the fingerprint vector correspond to
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226 only those topological pharmacophore atom triplets which are present and have non-zero count. However,
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227 for \fIFixedSize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option, the fingerprint vector contains all possible
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228 valid topological pharmacophore atom triplets with both zero and non-zero count values.
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229 .PP
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230 Example of \fI\s-1SD\s0\fR file containing topological pharmacophore atom triplets fingerprints string data:
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231 .PP
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232 .Vb 10
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233 \& ... ...
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234 \& ... ...
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235 \& $$$$
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236 \& ... ...
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237 \& ... ...
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238 \& ... ...
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239 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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240 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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241 \& ... ...
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242 \& 2 3 1 0 0 0 0
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243 \& ... ...
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244 \& M END
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245 \& > <CmpdID>
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246 \& Cmpd1
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247 \&
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248 \& > <TopologicalPharmacophoreAtomTripletsFingerprints>
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249 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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250 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
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251 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
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252 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
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253 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
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254 \& 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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255 \& 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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256 \& 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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257 \&
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258 \& $$$$
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259 \& ... ...
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260 \& ... ...
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261 .Ve
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262 .PP
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263 Example of \fI\s-1FP\s0\fR file containing topological pharmacophore atom triplets fingerprints string data:
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264 .PP
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265 .Vb 10
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266 \& #
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267 \& # Package = MayaChemTools 7.4
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268 \& # Release Date = Oct 21, 2010
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269 \& #
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270 \& # TimeStamp = Fri Mar 11 15:38:58 2011
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271 \& #
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272 \& # FingerprintsStringType = FingerprintsVector
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273 \& #
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274 \& # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M...
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275 \& # VectorStringFormat = IDsAndValuesString
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276 \& # VectorValuesType = NumericalValues
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277 \& #
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278 \& Cmpd1 696;Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1...;;46 106...
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279 \& Cmpd2 251;H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-H1\-NI1...;4 1 3 1 1 2 2...
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280 \& ... ...
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281 \& ... ..
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282 .Ve
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283 .PP
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284 Example of \s-1CSV\s0 \fIText\fR file containing topological pharmacophore atom triplets fingerprints string data:
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285 .PP
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286 .Vb 11
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287 \& "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints"
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288 \& "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr
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289 \& arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri
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290 \& ng;Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HB
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291 \& A1 Ar1\-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA
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292 \& 1 H1\-HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 A...;
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293 \& 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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294 \& 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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295 \& 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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296 \& ... ...
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297 \& ... ...
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298 .Ve
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299 .PP
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300 The current release of MayaChemTools generates the following types of topological pharmacophore
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301 atom triplets fingerprints vector strings:
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302 .PP
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303 .Vb 8
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304 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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305 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
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306 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
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307 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
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308 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
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309 \& 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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310 \& 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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311 \& 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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312 \&
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313 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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314 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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315 \& 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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316 \& 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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317 \& 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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318 \& 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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319 \&
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320 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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321 \& istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString;
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322 \& Ar1\-Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-Ar1\-NI1 Ar1\-Ar1\-P
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323 \& I1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1\-H1\-HBD1 Ar1\-H1\-NI1 Ar1\-H1\-PI1 Ar1\-HBA1\-HB
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324 \& A1 Ar1\-HBA1\-HBD1 Ar1\-HBA1\-NI1 Ar1\-HBA1\-PI1 Ar1\-HBD1\-HBD1 Ar1\-HBD1\-...;
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325 \& 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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326 \& 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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327 \& 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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328 .Ve
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329 .SH "OPTIONS"
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330 .IX Header "OPTIONS"
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331 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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332 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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333 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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334 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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335 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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336 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
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337 .Sp
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338 The supported aromaticity model names along with model specific control parameters
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339 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
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340 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
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341 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
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342 for detecting aromaticity corresponding to a specific model.
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343 .IP "\fB\-\-AtomTripletsSetSizeToUse\fR \fIArbitrarySize | FixedSize\fR" 4
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344 .IX Item "--AtomTripletsSetSizeToUse ArbitrarySize | FixedSize"
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345 Atom triplets set size to use during generation of topological pharmacophore atom triplets
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346 fingerprints.
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347 .Sp
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348 Possible values: \fIArbitrarySize | FixedSize\fR; Default value: \fIArbitrarySize\fR.
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349 .Sp
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350 For \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option, the fingerprint vector
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351 correspond to only those topological pharmacophore atom triplets which are present and
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352 have non-zero count. However, for \fIFixedSize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR
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353 option, the fingerprint vector contains all possible valid topological pharmacophore atom
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354 triplets with both zero and non-zero count values.
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355 .ie n .IP "\fB\-a, \-\-AtomTypesToUse\fR \fI""AtomType1,AtomType2,...""\fR" 4
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356 .el .IP "\fB\-a, \-\-AtomTypesToUse\fR \fI``AtomType1,AtomType2,...''\fR" 4
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357 .IX Item "-a, --AtomTypesToUse AtomType1,AtomType2,..."
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358 Pharmacophore atom types to use during generation of topological phramacophore
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359 atom triplets. It's a list of comma separated valid pharmacophore atom types.
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360 .Sp
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361 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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362 Default value [ Ref 71 ] : \fI\s-1HBD\s0,HBA,PI,NI,H,Ar\fR.
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363 .Sp
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364 The pharmacophore atom types abbreviations correspond to:
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365 .Sp
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366 .Vb 9
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367 \& HBD: HydrogenBondDonor
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368 \& HBA: HydrogenBondAcceptor
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369 \& PI : PositivelyIonizable
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370 \& NI : NegativelyIonizable
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371 \& Ar : Aromatic
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372 \& Hal : Halogen
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373 \& H : Hydrophobic
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374 \& RA : RingAtom
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375 \& CA : ChainAtom
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376 .Ve
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377 .Sp
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378 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign pharmacophore atom
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379 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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380 .Sp
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381 .Vb 4
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382 \& HydrogenBondDonor: NH, NH2, OH
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383 \& HydrogenBondAcceptor: N[!H], O
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384 \& PositivelyIonizable: +, NH2
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385 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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386 .Ve
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387 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
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388 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
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389 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
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390 .Sp
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391 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
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392 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
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393 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
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394 look like Cmpd<Number>.
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395 .Sp
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396 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
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397 .Sp
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398 .Vb 2
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399 \& MolID
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400 \& ExtReg
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401 .Ve
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402 .Sp
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403 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
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404 .Sp
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405 .Vb 1
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406 \& Compound
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407 .Ve
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408 .Sp
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409 The value specified above generates compound IDs which correspond to Compound<Number>
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410 instead of default value of Cmpd<Number>.
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411 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
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412 .IX Item "--CompoundIDLabel text"
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413 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
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414 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
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415 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
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416 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
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417 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
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418 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
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419 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
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420 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
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421 .Sp
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422 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
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423 Default value: \fILabelPrefix\fR.
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424 .Sp
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425 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
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426 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
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427 values are replaced with sequential compound IDs.
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428 .Sp
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429 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
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430 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
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431 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
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432 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
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433 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
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434 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
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435 .Sp
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436 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
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437 .Sp
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438 Examples:
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439 .Sp
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440 .Vb 2
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441 \& Extreg
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442 \& MolID,CompoundName
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443 .Ve
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444 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
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445 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
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446 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
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447 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
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448 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
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449 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
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450 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
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451 .IP "\fB\-\-DistanceBinSize\fR \fInumber\fR" 4
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452 .IX Item "--DistanceBinSize number"
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453 Distance bin size used to bin distances between atom pairs in atom triplets. Default value: \fI2\fR.
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454 Valid values: positive integers.
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455 .Sp
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456 For default \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR values of 1 and 10 with \fB\-\-DistanceBinSize\fR
|
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457 of 2 [ Ref 70 ], the following 5 distance bins are generated:
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458 .Sp
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459 .Vb 1
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460 \& [1, 2] [3, 4] [5, 6] [7, 8] [9 10]
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461 .Ve
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462 .Sp
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463 The lower distance bound on the distance bin is uses to bin the distance between atom pairs in
|
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464 atom triplets. So in the previous example, atom pairs with distances 1 and 2 fall in first distance
|
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465 bin, atom pairs with distances 3 and 4 fall in second distance bin and so on.
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466 .Sp
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467 In order to distribute distance bins of equal size, the last bin is allowed to go past \fB\-\-MaxDistance\fR
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468 by up to distance bin size. For example, \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR values of 2 and 10
|
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469 with \fB\-\-DistanceBinSize\fR of 2 generates the following 6 distance bins:
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|
470 .Sp
|
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|
471 .Vb 1
|
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472 \& [2, 3] [4, 5] [6, 7] [8, 9] [10 11]
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473 .Ve
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|
474 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
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|
475 .IX Item "-f, --Filter Yes | No"
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|
476 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
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477 Default value: \fIYes\fR.
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|
478 .Sp
|
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|
479 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
480 atom data corresponding to non-element symbols or no atom data are ignored.
|
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|
481 .IP "\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR" 4
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|
|
482 .IX Item "--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs"
|
|
|
483 Specify how fingerprints label is generated in conjunction with \fB\-\-FingerprintsLabel\fR option value:
|
|
|
484 use fingerprints label generated only by \fB\-\-FingerprintsLabel\fR option value or append topological
|
|
|
485 atom pair count value IDs to \fB\-\-FingerprintsLabel\fR option value.
|
|
|
486 .Sp
|
|
|
487 Possible values: \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR. Default value:
|
|
|
488 \&\fIFingerprintsLabelOnly\fR.
|
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|
489 .Sp
|
|
|
490 Topological atom pairs IDs appended to \fB\-\-FingerprintsLabel\fR value during \fIFingerprintsLabelWithIDs\fR
|
|
|
491 values of \fB\-\-FingerprintsLabelMode\fR correspond to atom pair count values in fingerprint vector string.
|
|
|
492 .Sp
|
|
|
493 \&\fIFingerprintsLabelWithIDs\fR value of \fB\-\-FingerprintsLabelMode\fR is ignored during \fIArbitrarySize\fR value
|
|
|
494 of \fB\-\-AtomTripletsSetSizeToUse\fR option and topological atom triplets IDs not appended to the label.
|
|
|
495 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
496 .IX Item "--FingerprintsLabel text"
|
|
|
497 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
498 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalPharmacophoreAtomTripletsFingerprints\fR.
|
|
|
499 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
500 .IX Item "-h, --help"
|
|
|
501 Print this help message.
|
|
|
502 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
|
|
503 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
504 Generate fingerprints for only the largest component in molecule. Possible values:
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|
505 \&\fIYes or No\fR. Default value: \fIYes\fR.
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|
506 .Sp
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|
|
507 For molecules containing multiple connected components, fingerprints can be generated
|
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|
508 in two different ways: use all connected components or just the largest connected
|
|
|
509 component. By default, all atoms except for the largest connected component are
|
|
|
510 deleted before generation of fingerprints.
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|
|
511 .IP "\fB\-\-MinDistance\fR \fInumber\fR" 4
|
|
|
512 .IX Item "--MinDistance number"
|
|
|
513 Minimum bond distance between atom pairs corresponding to atom triplets for generating
|
|
|
514 topological pharmacophore atom triplets. Default value: \fI1\fR. Valid values: positive integers and
|
|
|
515 less than \fB\-\-MaxDistance\fR.
|
|
|
516 .IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4
|
|
|
517 .IX Item "--MaxDistance number"
|
|
|
518 Maximum bond distance between atom pairs corresponding to atom triplets for generating
|
|
|
519 topological pharmacophore atom triplets. Default value: \fI10\fR. Valid values: positive integers and
|
|
|
520 greater than \fB\-\-MinDistance\fR.
|
|
|
521 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
522 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
523 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
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|
524 Default value: \fIcomma\fR.
|
|
|
525 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
|
|
|
526 .IX Item "--output SD | FP | text | all"
|
|
|
527 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
|
|
|
528 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
529 .IX Item "-o, --overwrite"
|
|
|
530 Overwrite existing files.
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|
531 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
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|
|
532 .IX Item "-q, --quote Yes | No"
|
|
|
533 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
|
|
|
534 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
535 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
|
|
|
536 .IX Item "-r, --root RootName"
|
|
|
537 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
538 <SDFileName><TopologicalPharmacophoreAtomTripletsFP>.<Ext>. The file type determines <Ext> value.
|
|
|
539 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
|
|
|
540 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
541 .IP "\fB\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR" 4
|
|
|
542 .IX Item "-u, --UseTriangleInequality Yes | No"
|
|
|
543 Specify whether to imply triangle distance inequality test to distances between atom pairs in
|
|
|
544 atom triplets during generation of atom triplets basis set generation. Possible values:
|
|
|
545 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
546 .Sp
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|
|
547 Triangle distance inequality test implies that distance or binned distance between any two atom
|
|
|
548 pairs in an atom triplet must be less than the sum of distances or binned distances between other
|
|
|
549 two atoms pairs and greater than the difference of their distances.
|
|
|
550 .Sp
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|
|
551 .Vb 1
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|
|
552 \& For atom triplet PxDyz\-PyDxz\-PzDxy to satisfy triangle inequality:
|
|
|
553 \&
|
|
|
554 \& Dyz > |Dxz \- Dxy| and Dyz < Dxz + Dxy
|
|
|
555 \& Dxz > |Dyz \- Dxy| and Dyz < Dyz + Dxy
|
|
|
556 \& Dxy > |Dyz \- Dxz| and Dxy < Dyz + Dxz
|
|
|
557 .Ve
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|
|
558 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
|
|
|
559 .IX Item "-v, --VectorStringFormat ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
|
|
|
560 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
|
|
|
561 \&\fB\-\-output\fR option. Possible values: \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString |
|
|
|
562 ValuesAndIDsString | ValuesAndIDsPairsString\fR. Defaultvalue: \fIValuesString\fR.
|
|
|
563 .Sp
|
|
|
564 Default value during \fIFixedSize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option: \fIValuesString\fR. Default
|
|
|
565 value during \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR option: \fIIDsAndValuesString\fR.
|
|
|
566 .Sp
|
|
|
567 \&\fIValuesString\fR option value is not allowed for \fIArbitrarySize\fR value of \fB\-\-AtomTripletsSetSizeToUse\fR
|
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568 option.
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569 .Sp
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570 Examples:
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571 .Sp
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572 .Vb 8
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573 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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574 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
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575 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
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576 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
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577 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
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578 \& 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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579 \& 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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580 \& 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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581 \&
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582 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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583 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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584 \& 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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585 \& 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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586 \& 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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587 \& 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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588 \&
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589 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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590 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt
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591 \& ring;46 Ar1\-Ar1\-Ar1 106 Ar1\-Ar1\-H1 8 Ar1\-Ar1\-HBA1 3 Ar1\-Ar1\-HBD1 0 Ar1
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592 \& \-Ar1\-NI1 0 Ar1\-Ar1\-PI1 83 Ar1\-H1\-H1 11 Ar1\-H1\-HBA1 4 Ar1\-H1\-HBD1 0 Ar1
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593 \& \-H1\-NI1 0 Ar1\-H1\-PI1 0 Ar1\-HBA1\-HBA1 1 Ar1\-HBA1\-HBD1 0 Ar1\-HBA1\-NI1 0
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594 \& Ar1\-HBA1\-PI1 0 Ar1\-HBD1\-HBD1 0 Ar1\-HBD1\-NI1 0 Ar1\-HBD1\-PI1 0 Ar1\-NI...
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595 .Ve
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596 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
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597 .IX Item "-w, --WorkingDir DirName"
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598 Location of working directory. Default value: current directory.
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599 .SH "EXAMPLES"
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600 .IX Header "EXAMPLES"
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601 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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602 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
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603 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
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604 with fingerprints vector strings data in ValuesString format, type:
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605 .PP
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606 .Vb 2
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607 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-r SampleTPATFP
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608 \& \-o Sample.sdf
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609 .Ve
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610 .PP
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611 To generate topological pharmacophore atom triplets fingerprints of fixed size corresponding to 5
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612 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
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613 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
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614 with fingerprints vector strings data in ValuesString format, type:
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615 .PP
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616 .Vb 2
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617 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl
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618 \& \-\-AtomTripletsSetSizeToUse FixedSize \-r SampleTPATFP \-o Sample.sdf
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619 .Ve
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620 .PP
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621 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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622 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
623 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files with \s-1CSV\s0 file containing
|
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624 sequential compound IDs along with fingerprints vector strings data in ValuesString format, type:
|
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|
625 .PP
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626 .Vb 2
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627 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-output all
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628 \& \-r SampleTPATFP \-o Sample.sdf
|
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629 .Ve
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630 .PP
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631 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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632 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
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|
633 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
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634 with fingerprints vector strings data in ValuesString format and atom triplets IDs in the
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635 fingerprint data column label starting with Fingerprints, type:
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636 .PP
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637 .Vb 3
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638 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl
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639 \& \-\-FingerprintsLabelMode FingerprintsLabelWithIDs \-\-FingerprintsLabel
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|
|
640 \& Fingerprints \-r SampleTPATFP \-o Sample.sdf
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|
641 .Ve
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642 .PP
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643 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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|
644 distance bins spanning distances from 1 through 10 using default atoms with distances not satisfying triangle
|
|
|
645 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
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|
|
646 with fingerprints vector strings data in ValuesString format, type:
|
|
|
647 .PP
|
|
|
648 .Vb 2
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649 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl
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650 \& \-\-UseTriangleInequality No \-r SampleTPATFP \-o Sample.sdf
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651 .Ve
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652 .PP
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|
653 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6
|
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654 distance bins spanning distances from 1 through 12 using default atoms with distances satisfying triangle
|
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|
655 inequality and create a SampleTPATFP.csv file containing sequential compound IDs along
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656 with fingerprints vector strings data in ValuesString format, type:
|
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|
657 .PP
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|
658 .Vb 3
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659 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl
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660 \& \-\-UseTriangleInequality Yes \-\-MinDistance 1 \-\-MaxDistance 12
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661 \& \-\-DistanceBinSIze 2 \-r SampleTPATFP \-o Sample.sdf
|
|
|
662 .Ve
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663 .PP
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|
664 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 6
|
|
|
665 distance bins spanning distances from 1 through 12 using \*(L"\s-1HBD\s0,HBA,PI, \s-1NI\s0, H, Ar\*(R" atoms with distances
|
|
|
666 satisfying triangle inequality and create a SampleTPATFP.csv file containing sequential compound
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|
|
667 IDs along with fingerprints vector strings data in ValuesString format, type:
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|
668 .PP
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|
669 .Vb 4
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670 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl
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|
671 \& \-\-AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" \-\-UseTriangleInequality Yes
|
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|
672 \& \-\-MinDistance 1 \-\-MaxDistance 12 \-\-DistanceBinSIze 2
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|
|
673 \& \-\-VectorStringFormat ValuesString \-r SampleTPATFP \-o Sample.sdf
|
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|
674 .Ve
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|
675 .PP
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676 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
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|
677 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
678 inequality and create a SampleTPATFP.csv file containing sequential compound IDs from
|
|
|
679 molecule name line along with fingerprints vector strings data in ValuesString format, type:
|
|
|
680 .PP
|
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|
681 .Vb 2
|
|
|
682 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode
|
|
|
683 \& CompoundID \-CompoundIDMode MolName \-r SampleTPATFP \-o Sample.sdf
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|
684 .Ve
|
|
|
685 .PP
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|
686 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
687 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
688 inequality and create a SampleTPATFP.csv file containing sequential compound IDs using
|
|
|
689 specified data field along with fingerprints vector strings data in ValuesString format, type:
|
|
|
690 .PP
|
|
|
691 .Vb 3
|
|
|
692 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode
|
|
|
693 \& CompoundID \-CompoundIDMode DataField \-\-CompoundID Mol_ID
|
|
|
694 \& \-r SampleTPATFP \-o Sample.sdf
|
|
|
695 .Ve
|
|
|
696 .PP
|
|
|
697 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
698 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
699 inequality and create a SampleTPATFP.csv file containing sequential compound IDs using
|
|
|
700 combination of molecule name line and an explicit compound prefix along with fingerprints vector
|
|
|
701 strings data, type:
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|
|
702 .PP
|
|
|
703 .Vb 4
|
|
|
704 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode
|
|
|
705 \& CompoundID \-CompoundIDMode MolnameOrLabelPrefix
|
|
|
706 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleSampleTPATFP
|
|
|
707 \& \-o Sample.sdf
|
|
|
708 .Ve
|
|
|
709 .PP
|
|
|
710 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
711 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
712 inequality and create a SampleTPATFP.csv file containing specific data fields columns along
|
|
|
713 with fingerprints vector strings data, type:
|
|
|
714 .PP
|
|
|
715 .Vb 2
|
|
|
716 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode
|
|
|
717 \& Specify \-\-DataFields Mol_ID \-r SampleTPATFP \-o Sample.sdf
|
|
|
718 .Ve
|
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|
719 .PP
|
|
|
720 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
721 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
722 inequality and create a SampleTPATFP.csv file containing common data fields columns along
|
|
|
723 with fingerprints vector strings data, type:
|
|
|
724 .PP
|
|
|
725 .Vb 2
|
|
|
726 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode
|
|
|
727 \& Common \-r SampleTPATFP \-o Sample.sdf
|
|
|
728 .Ve
|
|
|
729 .PP
|
|
|
730 To generate topological pharmacophore atom triplets fingerprints of arbitrary size corresponding to 5
|
|
|
731 distance bins spanning distances from 1 through 10 using default atoms with distances satisfying triangle
|
|
|
732 inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and SampleTPATFP.csv files containing all
|
|
|
733 data fields columns in \s-1CSV\s0 file along with fingerprints data, type:
|
|
|
734 .PP
|
|
|
735 .Vb 2
|
|
|
736 \& % TopologicalPharmacophoreAtomTripletsFingerprints.pl \-\-DataFieldsMode
|
|
|
737 \& All \-\-output all \-r SampleTPATFP \-o Sample.sdf
|
|
|
738 .Ve
|
|
|
739 .SH "AUTHOR"
|
|
|
740 .IX Header "AUTHOR"
|
|
|
741 Manish Sud <msud@san.rr.com>
|
|
|
742 .SH "SEE ALSO"
|
|
|
743 .IX Header "SEE ALSO"
|
|
|
744 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
745 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
746 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
747 TopologicalPharmacophoreAtomPairsFingerprints.pl
|
|
|
748 .SH "COPYRIGHT"
|
|
|
749 .IX Header "COPYRIGHT"
|
|
|
750 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
751 .PP
|
|
|
752 This file is part of MayaChemTools.
|
|
|
753 .PP
|
|
|
754 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
755 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
756 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
757 any later version.
|
