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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TOPOLOGICALATOMTORSIONSFINGERPRINTS 1"
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127 .TH TOPOLOGICALATOMTORSIONSFINGERPRINTS 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 TopologicalAtomTorsionsFingerprints.pl \- Generate topological atom torsions fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 TopologicalAtomTorsionsFingerprints.pl SDFile(s)...
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137 .PP
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138 TopologicalAtomTorsionsFingerprints.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\-\-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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147 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-v, \-\-VectorStringFormat\fR]
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148 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
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149 .SH "DESCRIPTION"
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150 .IX Header "DESCRIPTION"
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151 Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for \fISDFile(s)\fR and create
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152 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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153 molecular fingerprints.
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154 .PP
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155 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
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156 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
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157 can be specified either by \fI*.sdf\fR or the current directory name.
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158 .PP
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159 The current release of MayaChemTools supports generation of topological atom torsions
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160 fingerprints corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
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161 .PP
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162 .Vb 3
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163 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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164 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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165 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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166 .Ve
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167 .PP
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168 Based on the values specified for \fB\-a, \-\-AtomIdentifierType\fR and \fB\-\-AtomicInvariantsToUse\fR,
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169 initial atom types are assigned to all non-hydrogen atoms in a molecule. All unique atom torsions
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170 are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:
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171 .PP
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172 .Vb 1
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173 \& <AtomType1>\-<AtomType2>\-<AtomType3>\-<AtomType4>
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174 \&
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175 \& AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
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176 \&
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177 \& where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
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178 .Ve
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179 .PP
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180 The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute
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181 topological atom torsions fingerprints of the molecule.
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182 .PP
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183 Example of \fI\s-1SD\s0\fR file containing topological atom torsions fingerprints string data:
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184 .PP
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185 .Vb 10
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186 \& ... ...
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187 \& ... ...
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188 \& $$$$
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189 \& ... ...
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190 \& ... ...
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191 \& ... ...
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192 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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193 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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194 \& ... ...
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195 \& 2 3 1 0 0 0 0
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196 \& ... ...
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197 \& M END
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198 \& > <CmpdID>
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199 \& Cmpd1
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200 \&
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201 \& > <TopologicalAtomTorsionsFingerprints>
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202 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
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203 \& ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-C.
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204 \& X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO2.H
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205 \& 2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O.X1....;
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206 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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207 \&
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208 \& $$$$
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209 \& ... ...
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210 \& ... ...
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211 .Ve
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212 .PP
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213 Example of \fI\s-1FP\s0\fR file containing topological atom torsions fingerprints string data:
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214 .PP
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215 .Vb 10
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216 \& #
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217 \& # Package = MayaChemTools 7.4
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218 \& # Release Date = Oct 21, 2010
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219 \& #
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220 \& # TimeStamp = Fri Mar 11 15:17:20 2011
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221 \& #
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222 \& # FingerprintsStringType = FingerprintsVector
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223 \& #
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224 \& # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
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225 \& # VectorStringFormat = IDsAndValuesString
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226 \& # VectorValuesType = NumericalValues
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227 \& #
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228 \& Cmpd1 33;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-C.X3.BO4...;2 2 1 1 2 2 ...
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229 \& Cmpd2 23;C.X1.BO1.H3\-C.X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2...;2 2 1 5 ...
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230 \& ... ...
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231 \& ... ..
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232 .Ve
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233 .PP
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234 Example of \s-1CSV\s0 \fIText\fR file containing topological atom torsions fingerprints string data:
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235 .PP
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236 .Vb 8
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237 \& "CompoundID","TopologicalAtomTorsionsFingerprints"
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238 \& "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
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239 \& mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.
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240 \& X3.BO4\-C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C
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241 \& .X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3....;
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242 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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243 \& ... ...
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244 \& ... ...
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245 .Ve
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246 .PP
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247 The current release of MayaChemTools generates the following types of topological atom torsions
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248 fingerprints vector strings:
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249 .PP
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250 .Vb 5
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251 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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252 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
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253 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
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254 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
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255 \& ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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256 \&
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257 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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258 \& 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3
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259 \& .BO4\-C.X3.BO4 2 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 2 C.X2.BO2.H
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260 \& 2\-C.X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.B
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261 \& O3.H1\-O.X1.BO1.H1 1 C.X2.BO2.H2\-C.X2.BO2.H2\-N.X3.BO3\-C.X3.BO4 2 C.X2.B
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262 \& O2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2\-C.X3.BO3.H1 2 C.X2.BO2.H2\-C.X3.BO3.H1...
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263 \&
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264 \& FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
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265 \& calValues;IDsAndValuesString;C_2\-C_3\-C_3\-C_3 C_2\-C_3\-C_3\-O_3 C_2\-C_R\-C
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266 \& _R\-C_3 C_2\-C_R\-C_R\-C_R C_2\-C_R\-C_R\-N_R C_2\-N_3\-C_R\-C_R C_3\-C_3\-C_2\-O_2
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267 \& C_3\-C_3\-C_2\-O_3 C_3\-C_3\-C_3\-C_3 C_3\-C_3\-C_3\-N_R C_3\-C_3\-C_3\-O_3 C_...;
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268 \& 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1
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269 \&
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270 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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271 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
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272 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
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273 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
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274 \& 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
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275 \&
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276 \& FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
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277 \& ;NumericalValues;IDsAndValuesString;Ar\-Ar\-Ar\-Ar Ar\-Ar\-Ar\-Ar.HBA Ar\-Ar\-
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278 \& Ar\-HBD Ar\-Ar\-Ar\-Hal Ar\-Ar\-Ar\-None Ar\-Ar\-Ar.HBA\-Ar Ar\-Ar\-Ar.HBA\-None Ar
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279 \& \-Ar\-HBD\-None Ar\-Ar\-None\-HBA Ar\-Ar\-None\-HBD Ar\-Ar\-None\-None Ar\-Ar.H...;
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280 \& 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3
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281 \&
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282 \& FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
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283 \& lValues;IDsAndValuesString;C5A\-C5B\-C5B\-C5A C5A\-C5B\-C5B\-C=ON C5A\-C5B\-C5
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284 \& B\-CB C5A\-C5B\-C=ON\-NC=O C5A\-C5B\-C=ON\-O=CN C5A\-C5B\-CB\-CB C5A\-CB\-CB\-CB C5
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285 \& A\-N5\-C5A\-C5B C5A\-N5\-C5A\-CB C5A\-N5\-C5A\-CR C5A\-N5\-CR\-CR C5B\-C5A\-CB\-C...;
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286 \& 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
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287 \& 1 1 2 1 1 3 1 3
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288 \&
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289 \& FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
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290 \& Values;IDsAndValuesPairsString;C1\-C10\-N11\-C20 1 C1\-C10\-N11\-C21 1 C1\-C1
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291 \& 1\-C21\-C21 2 C1\-C11\-C21\-N11 2 C1\-CS\-C1\-C10 1 C1\-CS\-C1\-C5 1 C1\-CS\-C1\-CS
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292 \& 2 C10\-C1\-CS\-O2 1 C10\-N11\-C20\-C20 2 C10\-N11\-C21\-C11 1 C10\-N11\-C21\-C21 1
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293 \& C11\-C21\-C21\-C20 1 C11\-C21\-C21\-C5 1 C11\-C21\-N11\-C20 1 C14\-C18\-C18\-C20
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294 \& 2 C18\-C14\-C18\-C18 2 C18\-C18\-C14\-F 2 C18\-C18\-C18\-C18 4 C18\-C18\-C18\-C...
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295 \&
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296 \& FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
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297 \& Values;IDsAndValuesPairsString;C.2\-C.3\-C.3\-C.3 1 C.2\-C.3\-C.3\-O.3 1 C.2
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298 \& \-C.ar\-C.ar\-C.3 1 C.2\-C.ar\-C.ar\-C.ar 2 C.2\-C.ar\-C.ar\-N.ar 1 C.2\-N.am\-C.
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299 \& ar\-C.ar 2 C.3\-C.3\-C.2\-O.co2 2 C.3\-C.3\-C.3\-C.3 3 C.3\-C.3\-C.3\-N.ar 1 C.3
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300 \& \-C.3\-C.3\-O.3 3 C.3\-C.3\-C.ar\-C.ar 2 C.3\-C.3\-C.ar\-N.ar 2 C.3\-C.3\-N.ar\-C.
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301 \& ar 2 C.3\-C.ar\-C.ar\-C.ar 1 C.3\-C.ar\-N.ar\-C.3 1 C.3\-C.ar\-N.ar\-C.ar 1 ...
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302 \&
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303 \& FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
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304 \& lues;IDsAndValuesPairsString;N21\-None\-None\-None 9 N7\-None\-None\-None 4
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305 \& None\-N21\-None\-None 10 None\-N7\-None\-None 3 None\-N7\-None\-O3 1 None\-None\-
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306 \& None\-None 44 None\-None\-None\-O3 3 None\-None\-None\-O4 5
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307 \&
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308 \& FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
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309 \& lues;IDsAndValuesPairsString;C_2\-C_3\-C_3\-C_3 1 C_2\-C_3\-C_3\-O_3 1 C_2\-C
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310 \& _R\-C_R\-C_3 1 C_2\-C_R\-C_R\-C_R 2 C_2\-C_R\-C_R\-N_R 1 C_2\-N_3\-C_R\-C_R 2 C_3
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311 \& \-C_3\-C_2\-O_2 1 C_3\-C_3\-C_2\-O_3 1 C_3\-C_3\-C_3\-C_3 3 C_3\-C_3\-C_3\-N_R 1 C
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312 \& _3\-C_3\-C_3\-O_3 3 C_3\-C_3\-C_R\-C_R 2 C_3\-C_3\-C_R\-N_R 2 C_3\-C_3\-N_R\-C_R 2
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313 \& C_3\-C_R\-C_R\-C_R 1 C_3\-C_R\-N_R\-C_3 1 C_3\-C_R\-N_R\-C_R 1 C_3\-N_R\-C_R\-...
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314 .Ve
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315 .SH "OPTIONS"
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316 .IX Header "OPTIONS"
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317 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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318 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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319 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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320 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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321 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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322 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
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323 .Sp
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324 The supported aromaticity model names along with model specific control parameters
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325 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
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326 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
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327 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
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328 for detecting aromaticity corresponding to a specific model.
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329 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
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330 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
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331 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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332 atoms during calculation of topological atom torsions fingerprints. Possible values in the current
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333 release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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334 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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335 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
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336 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
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337 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
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338 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
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339 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
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340 option. It's a list of comma separated valid atomic invariant atom types.
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341 .Sp
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342 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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343 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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344 .Sp
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345 The atomic invariants abbreviations correspond to:
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346 .Sp
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347 .Vb 1
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348 \& AS = Atom symbol corresponding to element symbol
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349 \&
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350 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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351 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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352 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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353 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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354 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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355 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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356 \& H<n> = Number of implicit and explicit hydrogens for atom
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357 \& Ar = Aromatic annotation indicating whether atom is aromatic
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358 \& RA = Ring atom annotation indicating whether atom is a ring
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359 \& FC<+n/\-n> = Formal charge assigned to atom
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360 \& MN<n> = Mass number indicating isotope other than most abundant isotope
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361 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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362 \& 3 (triplet)
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363 .Ve
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364 .Sp
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365 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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366 .Sp
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367 .Vb 1
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368 \& 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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369 .Ve
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370 .Sp
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371 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
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372 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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373 .Sp
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374 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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375 are also allowed:
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376 .Sp
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377 .Vb 12
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378 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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379 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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380 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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381 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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382 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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383 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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384 \& H : NumOfImplicitAndExplicitHydrogens
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385 \& Ar : Aromatic
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386 \& RA : RingAtom
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387 \& FC : FormalCharge
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388 \& MN : MassNumber
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389 \& SM : SpinMultiplicity
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390 .Ve
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391 .Sp
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392 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
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393 atom types.
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394 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
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395 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
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396 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
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397 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
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398 option. It's a list of comma separated valid functional classes.
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399 .Sp
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400 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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401 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
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402 .Sp
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403 The functional class abbreviations correspond to:
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404 .Sp
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405 .Vb 9
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406 \& HBD: HydrogenBondDonor
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407 \& HBA: HydrogenBondAcceptor
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408 \& PI : PositivelyIonizable
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409 \& NI : NegativelyIonizable
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410 \& Ar : Aromatic
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411 \& Hal : Halogen
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412 \& H : Hydrophobic
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413 \& RA : RingAtom
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414 \& CA : ChainAtom
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415 \&
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416 \& Functional class atom type specification for an atom corresponds to:
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417 \&
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418 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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419 .Ve
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420 .Sp
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421 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
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422 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
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423 .Sp
|
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424 .Vb 4
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425 \& HydrogenBondDonor: NH, NH2, OH
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426 \& HydrogenBondAcceptor: N[!H], O
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427 \& PositivelyIonizable: +, NH2
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428 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
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429 .Ve
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430 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
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431 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
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432 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
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433 .Sp
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434 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
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435 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
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436 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
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437 look like Cmpd<Number>.
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438 .Sp
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439 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
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440 .Sp
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441 .Vb 2
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442 \& MolID
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443 \& ExtReg
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444 .Ve
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445 .Sp
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446 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
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447 .Sp
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|
448 .Vb 1
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|
449 \& Compound
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450 .Ve
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451 .Sp
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|
452 The value specified above generates compound IDs which correspond to Compound<Number>
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453 instead of default value of Cmpd<Number>.
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|
454 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
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|
455 .IX Item "--CompoundIDLabel text"
|
|
|
456 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
|
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457 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
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|
458 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
|
|
|
459 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
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|
|
460 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
|
|
|
461 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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|
|
462 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
|
|
|
463 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
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|
464 .Sp
|
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|
465 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
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466 Default value: \fILabelPrefix\fR.
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|
|
467 .Sp
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|
|
468 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
|
|
|
469 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
|
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|
470 values are replaced with sequential compound IDs.
|
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|
471 .Sp
|
|
|
472 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
473 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
|
|
|
474 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
|
|
|
475 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
|
|
|
476 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
|
|
|
477 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
|
|
|
478 .Sp
|
|
|
479 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
480 .Sp
|
|
|
481 Examples:
|
|
|
482 .Sp
|
|
|
483 .Vb 2
|
|
|
484 \& Extreg
|
|
|
485 \& MolID,CompoundName
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|
486 .Ve
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|
|
487 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
|
|
|
488 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
|
|
|
489 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
|
|
|
490 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
|
|
|
491 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
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|
492 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
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|
493 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
|
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|
494 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
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|
495 .IX Item "-f, --Filter Yes | No"
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|
496 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
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|
|
497 Default value: \fIYes\fR.
|
|
|
498 .Sp
|
|
|
499 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
500 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
501 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
502 .IX Item "--FingerprintsLabel text"
|
|
|
503 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
504 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalAtomTorsionsFingerprints\fR.
|
|
|
505 .IP "\fB\-h, \-\-help\fR" 4
|
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|
506 .IX Item "-h, --help"
|
|
|
507 Print this help message.
|
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|
508 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
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|
509 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
510 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
511 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
512 .Sp
|
|
|
513 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
514 in two different ways: use all connected components or just the largest connected
|
|
|
515 component. By default, all atoms except for the largest connected component are
|
|
|
516 deleted before generation of fingerprints.
|
|
|
517 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
518 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
519 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
|
|
520 Default value: \fIcomma\fR.
|
|
|
521 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
|
|
|
522 .IX Item "--output SD | FP | text | all"
|
|
|
523 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
|
|
|
524 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
525 .IX Item "-o, --overwrite"
|
|
|
526 Overwrite existing files.
|
|
|
527 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
|
|
|
528 .IX Item "-q, --quote Yes | No"
|
|
|
529 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
|
|
|
530 \&\fIYes or No\fR. Default value: \fIYes\fR
|
|
|
531 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
|
|
|
532 .IX Item "-r, --root RootName"
|
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533 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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534 <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The file type determines <Ext> value.
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535 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
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536 delimited text files, respectively.This option is ignored for multiple input files.
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537 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
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538 .IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
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539 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
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540 \&\fB\-\-output\fR option. Possible values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
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541 ValuesAndIDsPairsString\fR. Defaultvalue: \fIIDsAndValuesString\fR.
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542 .Sp
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543 Examples:
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544 .Sp
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545 .Vb 5
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546 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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547 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
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548 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
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549 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
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550 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
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551 \&
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552 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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553 \& 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3
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554 \& .BO4\-C.X3.BO4 2 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 2 C.X2.BO2.H
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555 \& 2\-C.X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.B
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556 \& O3.H1\-O.X1.BO1.H1 1 C.X2.BO2.H2\-C.X2.BO2.H2\-N.X3.BO3\-C.X3.BO4 2 C.X2.B
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557 \& O2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2\-C.X3.BO3.H1 2 C.X2.BO2.H2\-C.X3.BO3.H1...
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558 .Ve
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559 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
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560 .IX Item "-w, --WorkingDir DirName"
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561 Location of working directory. Default value: current directory.
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562 .SH "EXAMPLES"
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563 .IX Header "EXAMPLES"
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564 To generate topological atom torsions fingerprints using atomic invariants atom types in
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565 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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566 compound IDs along with fingerprints vector strings data, type:
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567 .PP
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568 .Vb 1
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569 \& % TopologicalAtomTorsionsFingerprints.pl \-r SampleTATFP \-o Sample.sdf
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570 .Ve
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571 .PP
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572 To generate topological atom torsions fingerprints using atomic invariants atom types in
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573 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
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574 files containing sequential compound IDs in \s-1CSV\s0 file along with fingerprints vector strings
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575 data, type:
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576 .PP
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577 .Vb 2
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578 \& % TopologicalAtomTorsionsFingerprints.pl \-\-output all \-r SampleTATFP
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579 \& \-o Sample.sdf
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580 .Ve
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581 .PP
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582 To generate topological atom torsions fingerprints using atomic invariants atom types in
|
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583 IDsAndValuesPairsString format and create a SampleTATFP.csv file containing sequential
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584 compound IDs along with fingerprints vector strings data, type:
|
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585 .PP
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586 .Vb 2
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587 \& % TopologicalAtomTorsionsFingerprints.pl \-\-VectorStringFormat
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588 \& IDsAndValuesPairsString \-r SampleTATFP \-o Sample.sdf
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589 .Ve
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590 .PP
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591 To generate topological atom torsions fingerprints using \s-1DREIDING\s0 atom types in
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592 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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593 compound IDs along with fingerprints vector strings data, type:
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594 .PP
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595 .Vb 2
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596 \& % TopologicalAtomTorsionsFingerprints.pl \-a DREIDINGAtomTypes
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597 \& \-r SampleTATFP \-o Sample.sdf
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598 .Ve
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599 .PP
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600 To generate topological atom torsions fingerprints using E\-state atom types in
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601 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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602 compound IDs along with fingerprints vector strings data, type:
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603 .PP
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604 .Vb 2
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605 \& % TopologicalAtomTorsionsFingerprints.pl \-a EStateAtomTypes
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606 \& \-r SampleTATFP \-o Sample.sdf
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607 .Ve
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608 .PP
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609 To generate topological atom torsions fingerprints using functional class atom types in
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|
|
610 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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611 compound IDs along with fingerprints vector strings data, type:
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612 .PP
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613 .Vb 2
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614 \& % TopologicalAtomTorsionsFingerprints.pl \-a FunctionalClassAtomTypes
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615 \& \-r SampleTATFP \-o Sample.sdf
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616 .Ve
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617 .PP
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618 To generate topological atom torsions fingerprints using \s-1MMFF94\s0 atom types in
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619 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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|
620 compound IDs along with fingerprints vector strings data, type:
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621 .PP
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622 .Vb 2
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623 \& % TopologicalAtomTorsionsFingerprints.pl \-a MMFF94AtomTypes
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624 \& \-r SampleTATFP \-o Sample.sdf
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625 .Ve
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626 .PP
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627 To generate topological atom torsions fingerprints using SLogP atom types in
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|
|
628 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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|
|
629 compound IDs along with fingerprints vector strings data, type:
|
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630 .PP
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631 .Vb 2
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632 \& % TopologicalAtomTorsionsFingerprints.pl \-a SLogPAtomTypes
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633 \& \-r SampleTATFP \-o Sample.sdf
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|
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634 .Ve
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635 .PP
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636 To generate topological atom torsions fingerprints using \s-1SYBYL\s0 atom types in
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|
|
637 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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|
638 compound IDs along with fingerprints vector strings data, type:
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|
|
639 .PP
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|
|
640 .Vb 2
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641 \& % TopologicalAtomTorsionsFingerprints.pl \-a SYBYLAtomTypes
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642 \& \-r SampleTATFP \-o Sample.sdf
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643 .Ve
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|
|
644 .PP
|
|
|
645 To generate topological atom torsions fingerprints using \s-1TPSA\s0 atom types in
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|
|
646 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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|
|
647 compound IDs along with fingerprints vector strings data, type:
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|
|
648 .PP
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|
649 .Vb 2
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|
650 \& % TopologicalAtomTorsionsFingerprints.pl \-a TPSAAtomTypes
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651 \& \-r SampleTATFP \-o Sample.sdf
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|
|
652 .Ve
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653 .PP
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|
654 To generate topological atom torsions fingerprints using \s-1UFF\s0 atom types in
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|
|
655 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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|
|
656 compound IDs along with fingerprints vector strings data, type:
|
|
|
657 .PP
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|
|
658 .Vb 2
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|
|
659 \& % TopologicalAtomTorsionsFingerprints.pl \-a UFFAtomTypes
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|
660 \& \-r SampleTATFP \-o Sample.sdf
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|
|
661 .Ve
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|
662 .PP
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|
663 To generate topological atom torsions fingerprints using only \s-1AS\s0,X atomic invariants atom
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|
|
664 types in IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
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|
|
665 compound IDs along with fingerprints vector strings data, type:
|
|
|
666 .PP
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|
667 .Vb 2
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|
668 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
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|
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669 \& \-\-AtomicInvariantsToUse "AS,X" \-r SampleTATFP \-o Sample.sdf
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|
|
670 .Ve
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671 .PP
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|
|
672 To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
673 IDsAndValuesString format and create a SampleTATFP.csv file containing compoundID
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|
|
674 from molecule name line along with fingerprints vector strings, type:
|
|
|
675 .PP
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|
676 .Vb 3
|
|
|
677 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
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|
|
678 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
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|
|
679 \& \-r SampleTATFP \-o Sample.sdf
|
|
|
680 .Ve
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|
681 .PP
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|
682 To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
683 IDsAndValuesString format and create a SampleTATFP.csv file containing compound IDs
|
|
|
684 using specified data field along with fingerprints vector strings, type:
|
|
|
685 .PP
|
|
|
686 .Vb 3
|
|
|
687 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
688 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID
|
|
|
689 \& Mol_ID \-r SampleTATFP \-o Sample.sdf
|
|
|
690 .Ve
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|
691 .PP
|
|
|
692 To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
693 IDsAndValuesString format and create a SampleTATFP.csv file containing compound \s-1ID\s0
|
|
|
694 using combination of molecule name line and an explicit compound prefix along with
|
|
|
695 fingerprints vector strings data, type:
|
|
|
696 .PP
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|
|
697 .Vb 3
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|
|
698 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
699 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
|
|
|
700 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTATFP \-o Sample.sdf
|
|
|
701 .Ve
|
|
|
702 .PP
|
|
|
703 To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
704 IDsAndValuesString format and create a SampleTATFP.csv file containing specific data
|
|
|
705 fields columns along with fingerprints vector strings, type:
|
|
|
706 .PP
|
|
|
707 .Vb 3
|
|
|
708 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
709 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTATFP
|
|
|
710 \& \-o Sample.sdf
|
|
|
711 .Ve
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|
|
712 .PP
|
|
|
713 To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
714 IDsAndValuesString format and create a SampleTATFP.csv file containing common
|
|
|
715 data fields columns along with fingerprints vector strings, type:
|
|
|
716 .PP
|
|
|
717 .Vb 2
|
|
|
718 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
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|
|
719 \& \-\-DataFieldsMode Common \-r SampleTATFP \-o Sample.sdf
|
|
|
720 .Ve
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|
721 .PP
|
|
|
722 To generate topological atom torsions fingerprints using atomic invariants atom types in
|
|
|
723 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
|
|
|
724 files containing all data fields columns in \s-1CSV\s0 file along with fingerprints data, type:
|
|
|
725 .PP
|
|
|
726 .Vb 3
|
|
|
727 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
728 \& \-\-DataFieldsMode All \-\-output all \-r SampleTATFP
|
|
|
729 \& \-o Sample.sdf
|
|
|
730 .Ve
|
|
|
731 .SH "AUTHOR"
|
|
|
732 .IX Header "AUTHOR"
|
|
|
733 Manish Sud <msud@san.rr.com>
|
|
|
734 .SH "SEE ALSO"
|
|
|
735 .IX Header "SEE ALSO"
|
|
|
736 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
737 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
|
|
|
738 PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl,
|
|
|
739 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
740 .SH "COPYRIGHT"
|
|
|
741 .IX Header "COPYRIGHT"
|
|
|
742 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
743 .PP
|
|
|
744 This file is part of MayaChemTools.
|
|
|
745 .PP
|
|
|
746 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
747 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
748 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
749 any later version.
|
