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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TOPOLOGICALATOMTRIPLETSFINGERPRINTS 1"
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127 .TH TOPOLOGICALATOMTRIPLETSFINGERPRINTS 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 TopologicalAtomTripletsFingerprints.pl \- Generate topological 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 TopologicalAtomTripletsFingerprints.pl SDFile(s)...
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137 .PP
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138 TopologicalAtomTripletsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
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139 [\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes\fR]
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140 [\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR]
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141 [\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(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\-f, \-\-Filter\fR \fIYes | No\fR]
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145 [\fB\-\-FingerprintsLabel\fR \fItext\fR] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR]
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146 [\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 atom triplets fingerprints for \fISDFile(s)\fR and create
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154 appropriate \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector strings corresponding to
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155 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 The current release of MayaChemTools supports generation of topological atom triplets
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162 fingerprints corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
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163 .PP
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164 .Vb 3
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165 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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166 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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167 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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168 .Ve
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169 .PP
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170 Based on the values specified for \fB\-a, \-\-AtomIdentifierType\fR and \fB\-\-AtomicInvariantsToUse\fR,
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171 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
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172 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
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173 pairs within \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR are identified and counted. An atom triplet
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174 identifier is generated for each unique atom triplet; the format of the atom triplet identifier is:
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175 .PP
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176 .Vb 1
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177 \& <ATx>\-Dyz\-<ATy>\-Dxz\-<ATz>\-Dxy
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178 \&
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179 \& ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
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180 \& Dxy: Distance between atom x and atom y
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181 \& Dxz: Distance between atom x and atom z
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182 \& Dyz: Distance between atom y and atom z
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183 \&
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184 \& where <AT1>\-D23 <= <AT2>\-D13 <= <AT3>\-D12
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185 .Ve
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186 .PP
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187 The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
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188 topological atom triplets fingerprints of the molecule.
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189 .PP
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190 Example of \fI\s-1SD\s0\fR file containing topological atom triplets fingerprints string data:
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191 .PP
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192 .Vb 10
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193 \& ... ...
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194 \& ... ...
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195 \& $$$$
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196 \& ... ...
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197 \& ... ...
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198 \& ... ...
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199 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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200 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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201 \& ... ...
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202 \& 2 3 1 0 0 0 0
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203 \& ... ...
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204 \& M END
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205 \& > <CmpdID>
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206 \& Cmpd1
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207 \&
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208 \& > <TopologicalAtomTripletsFingerprints>
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209 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi
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210 \& nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B
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211 \& O1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D10\-C
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212 \& .X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1...;
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213 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
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214 \& 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
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215 \&
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216 \& $$$$
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217 \& ... ...
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218 \& ... ...
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219 .Ve
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220 .PP
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221 Example of \fI\s-1FP\s0\fR file containing topological atom triplets fingerprints string data:
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222 .PP
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223 .Vb 10
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224 \& #
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225 \& # Package = MayaChemTools 7.4
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226 \& # Release Date = Oct 21, 2010
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227 \& #
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228 \& # TimeStamp = Fri Mar 11 15:24:01 2011
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229 \& #
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230 \& # FingerprintsStringType = FingerprintsVector
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231 \& #
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232 \& # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi...
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233 \& # VectorStringFormat = IDsAndValuesString
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234 \& # VectorValuesType = NumericalValues
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235 \& #
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236 \& Cmpd1 3096;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2...;1 2 2 2 2...
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237 \& Cmpd2 1093;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D3\-C.X2.BO2.H2\-D4...;2 2 2 2 2...
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238 \& ... ...
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239 \& ... ..
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240 .Ve
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241 .PP
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242 Example of \s-1CSV\s0 \fIText\fR file containing topological atom triplets fingerprints string data:
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243 .PP
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244 .Vb 9
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245 \& "CompoundID","TopologicalAtomTripletsFingerprints"
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246 \& "Cmpd1","FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto
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247 \& mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri
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248 \& ng;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2
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249 \& .H2\-D10\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1....;
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250 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
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251 \& 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
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252 \& ... ...
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253 \& ... ...
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254 .Ve
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255 .PP
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256 The current release of MayaChemTools generates the following types of topological atom triplets
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257 fingerprints vector strings:
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258 .PP
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259 .Vb 7
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260 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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261 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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262 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
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263 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
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264 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
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265 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
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266 \& 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
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267 \&
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268 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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269 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
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270 \& ;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 1 C.X1.BO1.H3\-D1\-C.X2.BO
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271 \& 2.H2\-D10\-C.X3.BO4\-D9 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 2 C.X
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272 \& 1.BO1.H3\-D1\-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2
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273 \& \-D6\-C.X3.BO3.H1\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3.BO3.H1\-D7 2...
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274 \&
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275 \& FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
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276 \& ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D
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277 \& 9\-C_3\-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_
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278 \& 3\-D9 C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_
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279 \& 2\-D1\-C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D...;
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280 \& 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
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281 \& 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...
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282 \&
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283 \& FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
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284 \& 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH\-D
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285 \& 1\-aaCH\-D2 aaCH\-D1\-aaCH\-D1\-aasC\-D2 aaCH\-D1\-aaCH\-D10\-aaCH\-D9 aaCH\-D1\-aaC
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286 \& H\-D10\-aasC\-D9 aaCH\-D1\-aaCH\-D2\-aaCH\-D3 aaCH\-D1\-aaCH\-D2\-aasC\-D1 aaCH\-D1\-
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287 \& aaCH\-D2\-aasC\-D3 aaCH\-D1\-aaCH\-D3\-aasC\-D2 aaCH\-D1\-aaCH\-D4\-aasC\-D5 aa...;
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288 \& 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
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289 \& 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
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290 \& 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...
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291 \&
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292 \& FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
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293 \& nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar\-D1
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294 \& \-Ar\-D1\-Ar\-D2 Ar\-D1\-Ar\-D1\-Ar.HBA\-D2 Ar\-D1\-Ar\-D10\-Ar\-D9 Ar\-D1\-Ar\-D10\-Hal
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295 \& \-D9 Ar\-D1\-Ar\-D2\-Ar\-D2 Ar\-D1\-Ar\-D2\-Ar\-D3 Ar\-D1\-Ar\-D2\-Ar.HBA\-D1 Ar\-D1\-Ar
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296 \& \-D2\-Ar.HBA\-D2 Ar\-D1\-Ar\-D2\-Ar.HBA\-D3 Ar\-D1\-Ar\-D2\-HBD\-D1 Ar\-D1\-Ar\-D2...;
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297 \& 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
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298 \& 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
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299 \& 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...
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300 \&
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301 \& FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
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302 \& 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A\-D1\-C5A\-D1\-
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303 \& N5\-D2 C5A\-D1\-C5A\-D2\-C5B\-D2 C5A\-D1\-C5A\-D3\-CB\-D2 C5A\-D1\-C5A\-D3\-CR\-D2 C5A
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304 \& \-D1\-C5B\-D1\-C5B\-D2 C5A\-D1\-C5B\-D2\-C=ON\-D1 C5A\-D1\-C5B\-D2\-CB\-D1 C5A\-D1\-C5B
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305 \& \-D3\-C=ON\-D2 C5A\-D1\-C5B\-D3\-CB\-D2 C5A\-D1\-C=ON\-D3\-NC=O\-D2 C5A\-D1\-C=ON\-D3\-
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306 \& O=CN\-D2 C5A\-D1\-C=ON\-D4\-NC=O\-D3 C5A\-D1\-C=ON\-D4\-O=CN\-D3 C5A\-D1\-CB\-D1\-...
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307 \&
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308 \& FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
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309 \& :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1\-D1\-C1\-D1\-C11
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310 \& \-D2 C1\-D1\-C1\-D1\-CS\-D2 C1\-D1\-C1\-D10\-C5\-D9 C1\-D1\-C1\-D3\-C10\-D2 C1\-D1\-C1\-D
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311 \& 3\-C5\-D2 C1\-D1\-C1\-D3\-CS\-D2 C1\-D1\-C1\-D3\-CS\-D4 C1\-D1\-C1\-D4\-C10\-D5 C1\-D1\-C
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312 \& 1\-D4\-C11\-D5 C1\-D1\-C1\-D5\-C10\-D4 C1\-D1\-C1\-D5\-C5\-D4 C1\-D1\-C1\-D6\-C11\-D7 C1
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313 \& \-D1\-C1\-D6\-CS\-D5 C1\-D1\-C1\-D6\-CS\-D7 C1\-D1\-C1\-D8\-C11\-D9 C1\-D1\-C1\-D8\-CS...
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314 \&
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315 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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316 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
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317 \& .3\-D10 C.2\-D1\-C.2\-D9\-C.ar\-D10 C.2\-D1\-C.3\-D1\-C.3\-D2 C.2\-D1\-C.3\-D10\-C.3\-
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318 \& D9 C.2\-D1\-C.3\-D2\-C.3\-D3 C.2\-D1\-C.3\-D2\-C.ar\-D3 C.2\-D1\-C.3\-D3\-C.3\-D4 C.2
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319 \& \-D1\-C.3\-D3\-N.ar\-D4 C.2\-D1\-C.3\-D3\-O.3\-D2 C.2\-D1\-C.3\-D4\-C.3\-D5 C.2\-D1\-C.
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320 \& 3\-D5\-C.3\-D6 C.2\-D1\-C.3\-D5\-O.3\-D4 C.2\-D1\-C.3\-D6\-C.3\-D7 C.2\-D1\-C.3\-D7...
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321 \&
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322 \& FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
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323 \& MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21\-D1\-N7\-D3\-Non
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324 \& e\-D4 N21\-D1\-N7\-D5\-None\-D4 N21\-D1\-None\-D1\-None\-D2 N21\-D1\-None\-D2\-None\-D
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325 \& 2 N21\-D1\-None\-D2\-None\-D3 N21\-D1\-None\-D3\-None\-D4 N21\-D1\-None\-D4\-None\-D5
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326 \& N21\-D1\-None\-D4\-O3\-D3 N21\-D1\-None\-D4\-O4\-D3 N21\-D1\-None\-D5\-None\-D6 N21\-
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327 \& D1\-None\-D6\-None\-D7 N21\-D1\-None\-D6\-O4\-D5 N21\-D1\-None\-D7\-None\-D8 N21\-...
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328 \&
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329 \& FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
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330 \& axDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D9\-C_3
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331 \& \-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_3\-D9
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332 \& C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_2\-D1\-
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333 \& C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D1\-C_3\-D5\-
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334 \& C_3\-D6 C_2\-D1\-C_3\-D5\-O_3\-D4 C_2\-D1\-C_3\-D6\-C_3\-D7 C_2\-D1\-C_3\-D7\-C_3\-...
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335 .Ve
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336 .SH "OPTIONS"
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337 .IX Header "OPTIONS"
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338 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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339 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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340 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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341 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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342 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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343 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
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344 .Sp
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345 The supported aromaticity model names along with model specific control parameters
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346 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
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347 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
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348 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
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349 for detecting aromaticity corresponding to a specific model.
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350 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
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351 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
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352 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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353 atoms during calculation of topological atom triplets fingerprints. Possible values in the current
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354 release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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355 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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356 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
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357 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
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358 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
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359 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
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360 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
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361 option. It's a list of comma separated valid atomic invariant atom types.
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362 .Sp
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363 Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0,
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364 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0,X,BO,H,FC\fR.
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365 .Sp
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366 The atomic invariants abbreviations correspond to:
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367 .Sp
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368 .Vb 1
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369 \& AS = Atom symbol corresponding to element symbol
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370 \&
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371 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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372 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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373 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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374 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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375 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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376 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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377 \& H<n> = Number of implicit and explicit hydrogens for atom
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378 \& Ar = Aromatic annotation indicating whether atom is aromatic
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379 \& RA = Ring atom annotation indicating whether atom is a ring
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380 \& FC<+n/\-n> = Formal charge assigned to atom
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381 \& MN<n> = Mass number indicating isotope other than most abundant isotope
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382 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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383 \& 3 (triplet)
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384 .Ve
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385 .Sp
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386 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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387 .Sp
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388 .Vb 1
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389 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
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390 .Ve
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391 .Sp
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392 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
|
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393 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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394 .Sp
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395 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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396 are also allowed:
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397 .Sp
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398 .Vb 12
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399 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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400 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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401 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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402 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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403 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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404 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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405 \& H : NumOfImplicitAndExplicitHydrogens
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406 \& Ar : Aromatic
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407 \& RA : RingAtom
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408 \& FC : FormalCharge
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409 \& MN : MassNumber
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410 \& SM : SpinMultiplicity
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411 .Ve
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412 .Sp
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413 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
|
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414 atom types.
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415 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
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416 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
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417 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
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418 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
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419 option. It's a list of comma separated valid functional classes.
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|
420 .Sp
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|
421 Possible values for atom functional classes 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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422 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
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423 .Sp
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424 The functional class abbreviations correspond to:
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425 .Sp
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426 .Vb 9
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427 \& HBD: HydrogenBondDonor
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428 \& HBA: HydrogenBondAcceptor
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429 \& PI : PositivelyIonizable
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430 \& NI : NegativelyIonizable
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431 \& Ar : Aromatic
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432 \& Hal : Halogen
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433 \& H : Hydrophobic
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434 \& RA : RingAtom
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435 \& CA : ChainAtom
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436 \&
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|
437 \& Functional class atom type specification for an atom corresponds to:
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|
438 \&
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|
439 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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|
440 .Ve
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441 .Sp
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442 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
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443 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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444 .Sp
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|
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445 .Vb 4
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|
446 \& HydrogenBondDonor: NH, NH2, OH
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447 \& HydrogenBondAcceptor: N[!H], O
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448 \& PositivelyIonizable: +, NH2
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449 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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450 .Ve
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451 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
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452 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
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453 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
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454 .Sp
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455 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
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456 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
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457 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
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458 look like Cmpd<Number>.
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459 .Sp
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460 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
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461 .Sp
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462 .Vb 2
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463 \& MolID
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464 \& ExtReg
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465 .Ve
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466 .Sp
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467 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
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468 .Sp
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469 .Vb 1
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470 \& Compound
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471 .Ve
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472 .Sp
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473 The value specified above generates compound IDs which correspond to Compound<Number>
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474 instead of default value of Cmpd<Number>.
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475 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
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|
476 .IX Item "--CompoundIDLabel text"
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|
477 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
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478 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
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479 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
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480 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
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481 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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|
482 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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|
483 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
|
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|
484 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
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485 .Sp
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486 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
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487 Default value: \fILabelPrefix\fR.
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488 .Sp
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489 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
|
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|
490 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
|
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|
491 values are replaced with sequential compound IDs.
|
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492 .Sp
|
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|
493 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
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|
494 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
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|
495 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
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|
496 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
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|
497 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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|
498 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
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499 .Sp
|
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|
500 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
|
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|
501 .Sp
|
|
|
502 Examples:
|
|
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503 .Sp
|
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|
504 .Vb 2
|
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|
505 \& Extreg
|
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|
506 \& MolID,CompoundName
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507 .Ve
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|
508 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
|
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|
509 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
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510 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
|
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|
511 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
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512 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
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513 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
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|
|
514 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
|
|
|
515 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
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|
|
516 .IX Item "-f, --Filter Yes | No"
|
|
|
517 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
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|
|
518 Default value: \fIYes\fR.
|
|
|
519 .Sp
|
|
|
520 By default, compound data is checked before calculating fingerprints and compounds containing
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|
|
521 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
522 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
523 .IX Item "--FingerprintsLabel text"
|
|
|
524 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
525 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalAtomTripletsFingerprints\fR.
|
|
|
526 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
527 .IX Item "-h, --help"
|
|
|
528 Print this help message.
|
|
|
529 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
|
|
530 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
531 Generate fingerprints for only the largest component in molecule. Possible values:
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|
532 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
533 .Sp
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|
|
534 For molecules containing multiple connected components, fingerprints can be generated
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|
|
535 in two different ways: use all connected components or just the largest connected
|
|
|
536 component. By default, all atoms except for the largest connected component are
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|
|
537 deleted before generation of fingerprints.
|
|
|
538 .IP "\fB\-\-MinDistance\fR \fInumber\fR" 4
|
|
|
539 .IX Item "--MinDistance number"
|
|
|
540 Minimum bond distance between atom triplets for generating topological atom triplets. Default value:
|
|
|
541 \&\fI1\fR. Valid values: positive integers and less than \fB\-\-MaxDistance\fR.
|
|
|
542 .IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4
|
|
|
543 .IX Item "--MaxDistance number"
|
|
|
544 Maximum bond distance between atom triplets for generating topological atom triplets. Default value:
|
|
|
545 \&\fI10\fR. Valid values: positive integers and greater than \fB\-\-MinDistance\fR.
|
|
|
546 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
547 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
548 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
|
|
549 Default value: \fIcomma\fR
|
|
|
550 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
|
|
|
551 .IX Item "--output SD | FP | text | all"
|
|
|
552 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
|
|
|
553 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
554 .IX Item "-o, --overwrite"
|
|
|
555 Overwrite existing files.
|
|
|
556 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
|
|
|
557 .IX Item "-q, --quote Yes | No"
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|
|
558 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
|
|
|
559 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
560 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
|
|
|
561 .IX Item "-r, --root RootName"
|
|
|
562 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
563 <SDFileName><TopologicalAtomTripletsFP>.<Ext>. The file type determines <Ext> value.
|
|
|
564 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
|
|
|
565 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
566 .IP "\fB\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR" 4
|
|
|
567 .IX Item "-u, --UseTriangleInequality Yes | No"
|
|
|
568 Specify whether to imply triangle distance inequality test to distances between atom pairs in
|
|
|
569 atom triplets during generation of atom triplets generation. Possible values: \fIYes or No\fR.
|
|
|
570 Default value: \fINo\fR.
|
|
|
571 .Sp
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|
|
572 Triangle distance inequality test implies that distance or binned distance between any two atom
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|
|
573 pairs in an atom triplet must be less than the sum of distances or binned distances between other
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|
|
574 two atoms pairs and greater than the difference of their distances.
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|
|
575 .Sp
|
|
|
576 .Vb 1
|
|
|
577 \& For atom triplet ATx\-Dyz\-ATy\-Dxz\-ATz\-Dxy to satisfy triangle inequality:
|
|
|
578 \&
|
|
|
579 \& Dyz > |Dxz \- Dxy| and Dyz < Dxz + Dxy
|
|
|
580 \& Dxz > |Dyz \- Dxy| and Dyz < Dyz + Dxy
|
|
|
581 \& Dxy > |Dyz \- Dxz| and Dxy < Dyz + Dxz
|
|
|
582 .Ve
|
|
|
583 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
|
|
|
584 .IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
|
|
|
585 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
|
|
|
586 \&\fB\-\-output\fR option. Possible values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
587 ValuesAndIDsPairsString\fR. Default value: \fIIDsAndValuesString\fR.
|
|
|
588 .Sp
|
|
|
589 Examples:
|
|
|
590 .Sp
|
|
|
591 .Vb 7
|
|
|
592 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
593 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
594 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
|
|
|
595 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
|
|
|
596 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
|
|
|
597 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
|
|
|
598 \& 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
|
|
|
599 \&
|
|
|
600 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
601 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
|
|
|
602 \& ;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 1 C.X1.BO1.H3\-D1\-C.X2.BO
|
|
|
603 \& 2.H2\-D10\-C.X3.BO4\-D9 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 2 C.X
|
|
|
604 \& 1.BO1.H3\-D1\-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2
|
|
|
605 \& \-D6\-C.X3.BO3.H1\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3.BO3.H1\-D7 2...
|
|
|
606 .Ve
|
|
|
607 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
|
|
|
608 .IX Item "-w, --WorkingDir DirName"
|
|
|
609 Location of working directory. Default value: current directory.
|
|
|
610 .SH "EXAMPLES"
|
|
|
611 .IX Header "EXAMPLES"
|
|
|
612 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
613 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
614 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
615 .PP
|
|
|
616 .Vb 1
|
|
|
617 \& % TopologicalAtomTripletsFingerprints.pl \-r SampleTATFP \-o Sample.sdf
|
|
|
618 .Ve
|
|
|
619 .PP
|
|
|
620 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
621 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
|
|
|
622 SampleTATFP.fpf and SampleTATFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along
|
|
|
623 with fingerprints vector strings data, type:
|
|
|
624 .PP
|
|
|
625 .Vb 2
|
|
|
626 \& % TopologicalAtomTripletsFingerprints.pl \-\-output all \-r SampleTATFP
|
|
|
627 \& \-o Sample.sdf
|
|
|
628 .Ve
|
|
|
629 .PP
|
|
|
630 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
631 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTATFP.csv
|
|
|
632 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
633 .PP
|
|
|
634 .Vb 2
|
|
|
635 \& % TopologicalAtomTripletsFingerprints.pl \-\-VectorStringFormat
|
|
|
636 \& IDsAndValuesPairsString \-r SampleTATFP \-o Sample.sdf
|
|
|
637 .Ve
|
|
|
638 .PP
|
|
|
639 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
640 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
641 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
642 .PP
|
|
|
643 .Vb 2
|
|
|
644 \& % TopologicalAtomTripletsFingerprints.pl \-a DREIDINGAtomTypes
|
|
|
645 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
646 .Ve
|
|
|
647 .PP
|
|
|
648 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
649 10 using E\-state atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
650 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
651 .PP
|
|
|
652 .Vb 2
|
|
|
653 \& % TopologicalAtomTripletsFingerprints.pl \-a EStateAtomTypes
|
|
|
654 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
655 .Ve
|
|
|
656 .PP
|
|
|
657 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
658 10 using functional class atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
659 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
660 .PP
|
|
|
661 .Vb 2
|
|
|
662 \& % TopologicalAtomTripletsFingerprints.pl \-a FunctionalClassAtomTypes
|
|
|
663 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
664 .Ve
|
|
|
665 .PP
|
|
|
666 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
667 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
668 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
669 .PP
|
|
|
670 .Vb 2
|
|
|
671 \& % TopologicalAtomTripletsFingerprints.pl \-a DREIDINGAtomTypes
|
|
|
672 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
673 .Ve
|
|
|
674 .PP
|
|
|
675 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
676 10 using \s-1MM94\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
677 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
678 .PP
|
|
|
679 .Vb 2
|
|
|
680 \& % TopologicalAtomTripletsFingerprints.pl \-a MMFF94AtomTypes
|
|
|
681 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
682 .Ve
|
|
|
683 .PP
|
|
|
684 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
685 10 using SLogP atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
686 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
687 .PP
|
|
|
688 .Vb 2
|
|
|
689 \& % TopologicalAtomTripletsFingerprints.pl \-a SLogPAtomTypes
|
|
|
690 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
691 .Ve
|
|
|
692 .PP
|
|
|
693 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
694 10 using \s-1SYBYL\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
695 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
696 .PP
|
|
|
697 .Vb 2
|
|
|
698 \& % TopologicalAtomTripletsFingerprints.pl \-a SYBYLAtomTypes
|
|
|
699 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
700 .Ve
|
|
|
701 .PP
|
|
|
702 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
703 10 using \s-1TPSA\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
704 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
705 .PP
|
|
|
706 .Vb 2
|
|
|
707 \& % TopologicalAtomTripletsFingerprints.pl \-a TPSAAtomTypes
|
|
|
708 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
709 .Ve
|
|
|
710 .PP
|
|
|
711 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
712 10 using \s-1UFF\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
713 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
714 .PP
|
|
|
715 .Vb 2
|
|
|
716 \& % TopologicalAtomTripletsFingerprints.pl \-a UFFAtomTypes
|
|
|
717 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
718 .Ve
|
|
|
719 .PP
|
|
|
720 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
721 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
722 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
723 .PP
|
|
|
724 .Vb 2
|
|
|
725 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
726 \& \-\-MinDistance 1 \-\-MaxDistance 6 \-r SampleTATFP \-o Sample.sdf
|
|
|
727 .Ve
|
|
|
728 .PP
|
|
|
729 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
730 10 using only \s-1AS\s0,X atomic invariants atom types in IDsAndValuesString format and create a
|
|
|
731 SampleTATFP.csv file containing sequential compound IDs along with fingerprints vector strings
|
|
|
732 data, type:
|
|
|
733 .PP
|
|
|
734 .Vb 3
|
|
|
735 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
736 \& \-\-AtomicInvariantsToUse "AS,X" \-\-MinDistance 1 \-\-MaxDistance 6
|
|
|
737 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
738 .Ve
|
|
|
739 .PP
|
|
|
740 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
741 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
742 file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings
|
|
|
743 data, type:
|
|
|
744 .PP
|
|
|
745 .Vb 3
|
|
|
746 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
747 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
|
|
|
748 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
749 .Ve
|
|
|
750 .PP
|
|
|
751 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
752 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
753 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
754 data, type:
|
|
|
755 .PP
|
|
|
756 .Vb 3
|
|
|
757 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
758 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID
|
|
|
759 \& Mol_ID \-r SampleTATFP \-o Sample.sdf
|
|
|
760 .Ve
|
|
|
761 .PP
|
|
|
762 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
763 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
764 file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
|
|
|
765 prefix along with fingerprints vector strings data, type:
|
|
|
766 .PP
|
|
|
767 .Vb 3
|
|
|
768 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
769 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
|
|
|
770 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTATFP \-o Sample.sdf
|
|
|
771 .Ve
|
|
|
772 .PP
|
|
|
773 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
774 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
775 file containing specific data fields columns along with fingerprints vector strings
|
|
|
776 data, type:
|
|
|
777 .PP
|
|
|
778 .Vb 3
|
|
|
779 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
780 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTATFP
|
|
|
781 \& \-o Sample.sdf
|
|
|
782 .Ve
|
|
|
783 .PP
|
|
|
784 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
785 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
|
|
|
786 file containing common data fields columns along with fingerprints vector strings
|
|
|
787 data, type:
|
|
|
788 .PP
|
|
|
789 .Vb 2
|
|
|
790 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
791 \& \-\-DataFieldsMode Common \-r SampleTATFP \-o Sample.sdf
|
|
|
792 .Ve
|
|
|
793 .PP
|
|
|
794 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
|
|
|
795 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
|
|
|
796 SampleTATFP.fpf and SampleTATFP.csv files containing all data fields columns in \s-1CSV\s0 file along with
|
|
|
797 fingerprints data, type:
|
|
|
798 .PP
|
|
|
799 .Vb 3
|
|
|
800 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
801 \& \-\-DataFieldsMode All \-\-output all \-r SampleTATFP
|
|
|
802 \& \-o Sample.sdf
|
|
|
803 .Ve
|
|
|
804 .SH "AUTHOR"
|
|
|
805 .IX Header "AUTHOR"
|
|
|
806 Manish Sud <msud@san.rr.com>
|
|
|
807 .SH "SEE ALSO"
|
|
|
808 .IX Header "SEE ALSO"
|
|
|
809 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
810 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
|
|
|
811 PathLengthFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
812 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
813 .SH "COPYRIGHT"
|
|
|
814 .IX Header "COPYRIGHT"
|
|
|
815 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
816 .PP
|
|
|
817 This file is part of MayaChemTools.
|
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818 .PP
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819 MayaChemTools is free software; you can redistribute it and/or modify it under
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820 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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821 Software Foundation; either version 3 of the License, or (at your option)
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822 any later version.
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