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124 .\" ========================================================================
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125 .\"
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126 .IX Title "TOPOLOGICALATOMPAIRSFINGERPRINTS 1"
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127 .TH TOPOLOGICALATOMPAIRSFINGERPRINTS 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 TopologicalAtomPairsFingerprints.pl \- Generate topological atom pairs fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 TopologicalAtomPairsFingerprints.pl SDFile(s)...
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137 .PP
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138 TopologicalAtomPairsFingerprints.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]
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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 pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] 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 pairs
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162 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 pair
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174 identifier is generated for each unique atom pair; the format of the atom pair identifier is:
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175 .PP
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176 .Vb 1
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177 \& <AtomType1>\-D<n>\-<AtomType2>
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178 \&
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179 \& AtomType1, AtomType2: Atom types assigned to atom1 and atom2
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180 \& D: Distance between atom1 and atom2
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181 \&
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182 \& where AtomType1 <= AtomType2
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183 .Ve
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184 .PP
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185 The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
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186 topological atom pairs fingerprints of the molecule.
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187 .PP
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188 Example of \fI\s-1SD\s0\fR file containing topological atom pairs fingerprints string data:
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189 .PP
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190 .Vb 10
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191 \& ... ...
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192 \& ... ...
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193 \& $$$$
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194 \& ... ...
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195 \& ... ...
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196 \& ... ...
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197 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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198 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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199 \& ... ...
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200 \& 2 3 1 0 0 0 0
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201 \& ... ...
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202 \& M END
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203 \& > <CmpdID>
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204 \& Cmpd1
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205 \&
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206 \& > <TopologicalAtomPairsFingerprints>
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207 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi
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208 \& stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H
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209 \& 3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.H1
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210 \& C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-C.X2...;
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211 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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212 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
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213 \&
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214 \& $$$$
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215 \& ... ...
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216 \& ... ...
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217 .Ve
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218 .PP
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219 Example of \fI\s-1FP\s0\fR file containing topological atom pairs fingerprints string data:
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220 .PP
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221 .Vb 10
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222 \& #
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223 \& # Package = MayaChemTools 7.4
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224 \& # Release Date = Oct 21, 2010
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225 \& #
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226 \& # TimeStamp = Fri Mar 11 15:04:36 2011
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227 \& #
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228 \& # FingerprintsStringType = FingerprintsVector
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229 \& #
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230 \& # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi...
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231 \& # VectorStringFormat = IDsAndValuesString
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232 \& # VectorValuesType = NumericalValues
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233 \& #
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234 \& Cmpd1 223;C.X1.BO1.H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2...;1 1...
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235 \& Cmpd2 128;C.X1.BO1.H3\-D1\-C.X2.BO2.H2 C.X1.BO1.H3\-D1\-C.X3.BO4...;1 1...
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236 \& ... ...
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237 \& ... ..
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238 .Ve
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239 .PP
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240 Example of \s-1CSV\s0 \fIText\fR file containing topological atom pairs fingerprints string data:
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241 .PP
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242 .Vb 9
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243 \& "CompoundID","TopologicalAtomPairsFingerprints"
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244 \& "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy
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245 \& pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C
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246 \& .X1.BO1.H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X
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247 \& 3.BO3.H1C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1...;
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248 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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249 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
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250 \& ... ...
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251 \& ... ...
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252 .Ve
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253 .PP
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254 The current release of MayaChemTools generates the following types of topological atom pairs
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255 fingerprints vector strings:
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256 .PP
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257 .Vb 6
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258 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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259 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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260 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
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261 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
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262 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
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263 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
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264 \&
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265 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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266 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
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267 \& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\-
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268 \& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2
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269 \& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X
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270 \& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO...
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271 \&
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272 \& FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
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273 \& :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2\-D1\-C_3 C_2\-D
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274 \& 1\-C_R C_2\-D1\-N_3 C_2\-D1\-O_2 C_2\-D1\-O_3 C_3\-D1\-C_3 C_3\-D1\-C_R C_3\-D1\-N_
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275 \& R C_3\-D1\-O_3 C_R\-D1\-C_R C_R\-D1\-F_ C_R\-D1\-N_3 C_R\-D1\-N_R C_2\-D2\-C_3 C_2
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276 \& 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
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277 \& 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...
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278 \&
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279 \& FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
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280 \& axDistance10;251;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH aaCH\-
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281 \& D1\-aasC aasC\-D1\-aasC aasC\-D1\-aasN aasC\-D1\-dssC aasC\-D1\-sF aasC\-D1\-ssNH
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282 \& aasC\-D1\-sssCH aasN\-D1\-ssCH2 dO\-D1\-dssC dssC\-D1\-sOH dssC\-D1\-ssCH2 d...;
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283 \& 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
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284 \& 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...
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285 \&
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286 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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287 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
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288 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
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289 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
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290 \& 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
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291 \& 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
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292 \&
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293 \& FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
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294 \& axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A\-D1\-C5B 2
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295 \& C5A\-D1\-CB 1 C5A\-D1\-CR 1 C5A\-D1\-N5 2 C5B\-D1\-C5B 1 C5B\-D1\-C=ON 1 C5B\-D1\-
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296 \& CB 1 C=ON\-D1\-NC=O 1 C=ON\-D1\-O=CN 1 CB\-D1\-CB 18 CB\-D1\-F 1 CB\-D1\-NC=O 1
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297 \& COO\-D1\-CR 1 COO\-D1\-O=CO 1 COO\-D1\-OC=O 1 CR\-D1\-CR 7 CR\-D1\-N5 1 CR\-D1\-OR
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298 \& 2 C5A\-D2\-C5A 1 C5A\-D2\-C5B 2 C5A\-D2\-C=ON 1 C5A\-D2\-CB 3 C5A\-D2\-CR 4 ...
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299 \&
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300 \& FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
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301 \& xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1\-D1\-C10 1 C1
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302 \& \-D1\-C11 2 C1\-D1\-C5 1 C1\-D1\-CS 4 C10\-D1\-N11 1 C11\-D1\-C21 1 C14\-D1\-C18 2
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303 \& C14\-D1\-F 1 C18\-D1\-C18 10 C18\-D1\-C20 4 C18\-D1\-C22 2 C20\-D1\-C20 3 C20\-D
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304 \& 1\-C21 1 C20\-D1\-N11 1 C21\-D1\-C21 1 C21\-D1\-C5 1 C21\-D1\-N11 1 C22\-D1\-N4 1
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305 \& C5\-D1\-N4 1 C5\-D1\-O10 1 C5\-D1\-O2 1 C5\-D1\-O9 1 CS\-D1\-O2 2 C1\-D2\-C1 3...
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306 \&
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307 \& FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
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308 \& xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2\-D1\-C.3 1 C
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309 \& .2\-D1\-C.ar 1 C.2\-D1\-N.am 1 C.2\-D1\-O.2 1 C.2\-D1\-O.co2 2 C.3\-D1\-C.3 7 C.
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310 \& 3\-D1\-C.ar 1 C.3\-D1\-N.ar 1 C.3\-D1\-O.3 2 C.ar\-D1\-C.ar 23 C.ar\-D1\-F 1 C.a
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311 \& r\-D1\-N.am 1 C.ar\-D1\-N.ar 2 C.2\-D2\-C.3 1 C.2\-D2\-C.ar 3 C.3\-D2\-C.3 5 C.3
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312 \& \-D2\-C.ar 5 C.3\-D2\-N.ar 2 C.3\-D2\-O.3 4 C.3\-D2\-O.co2 2 C.ar\-D2\-C.ar 2...
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313 \&
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314 \& FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
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315 \& Distance10;64;NumericalValues;IDsAndValuesPairsString;N21\-D1\-None 3 N7
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316 \& \-D1\-None 2 None\-D1\-None 34 None\-D1\-O3 2 None\-D1\-O4 3 N21\-D2\-None 5 N7\-
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317 \& D2\-None 3 N7\-D2\-O3 1 None\-D2\-None 44 None\-D2\-O3 2 None\-D2\-O4 5 O3\-D2\-O
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318 \& 4 1 N21\-D3\-None 7 N7\-D3\-None 4 None\-D3\-None 45 None\-D3\-O3 4 None\-D3\-O4
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319 \& 5 N21\-D4\-N7 1 N21\-D4\-None 5 N21\-D4\-O3 1 N21\-D4\-O4 1 N7\-D4\-None 4 N...
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320 \&
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321 \& FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
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322 \& istance10;157;NumericalValues;IDsAndValuesPairsString;C_2\-D1\-C_3 1 C_2
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323 \& \-D1\-C_R 1 C_2\-D1\-N_3 1 C_2\-D1\-O_2 2 C_2\-D1\-O_3 1 C_3\-D1\-C_3 7 C_3\-D1\-C
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324 \& _R 1 C_3\-D1\-N_R 1 C_3\-D1\-O_3 2 C_R\-D1\-C_R 23 C_R\-D1\-F_ 1 C_R\-D1\-N_3 1
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325 \& C_R\-D1\-N_R 2 C_2\-D2\-C_3 1 C_2\-D2\-C_R 3 C_3\-D2\-C_3 5 C_3\-D2\-C_R 5 C_3\-D
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326 \& 2\-N_R 2 C_3\-D2\-O_2 1 C_3\-D2\-O_3 5 C_R\-D2\-C_R 28 C_R\-D2\-F_ 2 C_R\-D2\-...
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327 .Ve
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328 .SH "OPTIONS"
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329 .IX Header "OPTIONS"
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330 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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331 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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332 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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333 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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334 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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335 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
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336 .Sp
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337 The supported aromaticity model names along with model specific control parameters
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338 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
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339 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
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340 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
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341 for detecting aromaticity corresponding to a specific model.
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342 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
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343 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
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344 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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345 atoms during calculation of topological atom pairs fingerprints. Possible values in the current
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346 release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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347 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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348 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
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349 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
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350 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
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351 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
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352 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
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353 option. It's a list of comma separated valid atomic invariant atom types.
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354 .Sp
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355 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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356 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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357 .Sp
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358 The atomic invariants abbreviations correspond to:
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359 .Sp
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360 .Vb 1
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361 \& AS = Atom symbol corresponding to element symbol
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362 \&
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363 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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364 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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365 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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366 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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367 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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368 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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369 \& H<n> = Number of implicit and explicit hydrogens for atom
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370 \& Ar = Aromatic annotation indicating whether atom is aromatic
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371 \& RA = Ring atom annotation indicating whether atom is a ring
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372 \& FC<+n/\-n> = Formal charge assigned to atom
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373 \& MN<n> = Mass number indicating isotope other than most abundant isotope
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374 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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375 \& 3 (triplet)
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376 .Ve
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377 .Sp
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378 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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379 .Sp
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380 .Vb 1
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381 \& 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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382 .Ve
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383 .Sp
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384 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
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385 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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386 .Sp
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387 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
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388 are also allowed:
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389 .Sp
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390 .Vb 12
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391 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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392 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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393 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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394 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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395 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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396 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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397 \& H : NumOfImplicitAndExplicitHydrogens
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398 \& Ar : Aromatic
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399 \& RA : RingAtom
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400 \& FC : FormalCharge
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401 \& MN : MassNumber
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402 \& SM : SpinMultiplicity
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403 .Ve
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404 .Sp
|
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405 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
|
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406 atom types.
|
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407 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
|
|
|
408 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
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409 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
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410 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
|
411 option. It's a list of comma separated valid functional classes.
|
|
|
412 .Sp
|
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|
413 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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414 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
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415 .Sp
|
|
|
416 The functional class abbreviations correspond to:
|
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417 .Sp
|
|
|
418 .Vb 9
|
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|
419 \& HBD: HydrogenBondDonor
|
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420 \& HBA: HydrogenBondAcceptor
|
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421 \& PI : PositivelyIonizable
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422 \& NI : NegativelyIonizable
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423 \& Ar : Aromatic
|
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424 \& Hal : Halogen
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425 \& H : Hydrophobic
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426 \& RA : RingAtom
|
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|
427 \& CA : ChainAtom
|
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|
428 \&
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|
|
429 \& Functional class atom type specification for an atom corresponds to:
|
|
|
430 \&
|
|
|
431 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
432 .Ve
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433 .Sp
|
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|
434 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
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435 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
|
436 .Sp
|
|
|
437 .Vb 4
|
|
|
438 \& HydrogenBondDonor: NH, NH2, OH
|
|
|
439 \& HydrogenBondAcceptor: N[!H], O
|
|
|
440 \& PositivelyIonizable: +, NH2
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441 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
442 .Ve
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443 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
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|
444 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
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445 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
|
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|
446 .Sp
|
|
|
447 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
|
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448 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
|
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|
449 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
|
|
|
450 look like Cmpd<Number>.
|
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451 .Sp
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|
452 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
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453 .Sp
|
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|
454 .Vb 2
|
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455 \& MolID
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456 \& ExtReg
|
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457 .Ve
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458 .Sp
|
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|
459 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
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460 .Sp
|
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|
461 .Vb 1
|
|
|
462 \& Compound
|
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463 .Ve
|
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|
464 .Sp
|
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|
465 The value specified above generates compound IDs which correspond to Compound<Number>
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|
466 instead of default value of Cmpd<Number>.
|
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|
467 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
|
|
|
468 .IX Item "--CompoundIDLabel text"
|
|
|
469 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
|
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|
470 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
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|
|
471 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
|
|
|
472 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
|
|
|
473 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
|
|
|
474 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
|
|
|
475 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
|
|
|
476 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
477 .Sp
|
|
|
478 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
|
|
|
479 Default value: \fILabelPrefix\fR.
|
|
|
480 .Sp
|
|
|
481 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
|
|
|
482 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
|
|
|
483 values are replaced with sequential compound IDs.
|
|
|
484 .Sp
|
|
|
485 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
486 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
|
|
|
487 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
|
|
|
488 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
|
|
|
489 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
|
|
|
490 with generated fingerprints for \fItext | both\fR values of \fB\-\-output\fR option.
|
|
|
491 .Sp
|
|
|
492 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
493 .Sp
|
|
|
494 Examples:
|
|
|
495 .Sp
|
|
|
496 .Vb 2
|
|
|
497 \& Extreg
|
|
|
498 \& MolID,CompoundName
|
|
|
499 .Ve
|
|
|
500 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
|
|
|
501 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
|
|
|
502 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
|
|
|
503 with generated fingerprints for \fItext | both\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
|
|
|
504 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
|
|
|
505 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
|
|
|
506 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
|
|
|
507 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
|
|
|
508 .IX Item "-f, --Filter Yes | No"
|
|
|
509 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
|
|
|
510 Default value: \fIYes\fR.
|
|
|
511 .Sp
|
|
|
512 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
513 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
514 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
515 .IX Item "--FingerprintsLabel text"
|
|
|
516 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
517 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalAtomPairsFingerprints\fR.
|
|
|
518 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
519 .IX Item "-h, --help"
|
|
|
520 Print this help message.
|
|
|
521 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
|
|
522 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
523 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
524 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
525 .Sp
|
|
|
526 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
527 in two different ways: use all connected components or just the largest connected
|
|
|
528 component. By default, all atoms except for the largest connected component are
|
|
|
529 deleted before generation of fingerprints.
|
|
|
530 .IP "\fB\-\-MinDistance\fR \fInumber\fR" 4
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|
531 .IX Item "--MinDistance number"
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|
532 Minimum bond distance between atom pairs for generating topological atom pairs. Default value:
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533 \&\fI1\fR. Valid values: positive integers and less than \fB\-\-MaxDistance\fR.
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|
534 .IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4
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|
535 .IX Item "--MaxDistance number"
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|
536 Maximum bond distance between atom pairs for generating topological atom pairs. Default value:
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|
537 \&\fI10\fR. Valid values: positive integers and greater than \fB\-\-MinDistance\fR.
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538 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
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|
539 .IX Item "--OutDelim comma | tab | semicolon"
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|
540 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
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|
541 Default value: \fIcomma\fR
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|
542 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
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|
543 .IX Item "--output SD | FP | text | all"
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|
544 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
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545 .IP "\fB\-o, \-\-overwrite\fR" 4
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|
546 .IX Item "-o, --overwrite"
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|
547 Overwrite existing files.
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548 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
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549 .IX Item "-q, --quote Yes | No"
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|
550 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
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|
551 \&\fIYes or No\fR. Default value: \fIYes\fR.
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|
552 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
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553 .IX Item "-r, --root RootName"
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554 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
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555 <SDFileName><TopologicalAtomPairsFP>.<Ext>. The file type determines <Ext> value.
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|
556 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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|
557 delimited text files, respectively.This option is ignored for multiple input files.
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|
558 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
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|
559 .IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
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|
|
560 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
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|
561 \&\fB\-\-output\fR option. Possible values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
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|
562 ValuesAndIDsPairsString\fR. Default value: \fIIDsAndValuesString\fR.
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563 .Sp
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|
564 Examples:
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565 .Sp
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566 .Vb 6
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|
567 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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|
568 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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|
|
569 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
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|
|
570 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
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|
|
571 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
572 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
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|
573 \&
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|
574 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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|
|
575 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
|
|
|
576 \& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\-
|
|
|
577 \& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2
|
|
|
578 \& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X
|
|
|
579 \& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO...
|
|
|
580 .Ve
|
|
|
581 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
|
|
|
582 .IX Item "-w, --WorkingDir DirName"
|
|
|
583 Location of working directory. Default value: current directory.
|
|
|
584 .SH "EXAMPLES"
|
|
|
585 .IX Header "EXAMPLES"
|
|
|
586 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
587 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
588 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
589 .PP
|
|
|
590 .Vb 1
|
|
|
591 \& % TopologicalAtomPairsFingerprints.pl \-r SampleTAPFP \-o Sample.sdf
|
|
|
592 .Ve
|
|
|
593 .PP
|
|
|
594 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
595 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
|
|
|
596 SampleTAPFP.fpf and SampleTAPFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along
|
|
|
597 with fingerprints vector strings data, type:
|
|
|
598 .PP
|
|
|
599 .Vb 2
|
|
|
600 \& % TopologicalAtomPairsFingerprints.pl \-\-output all \-r SampleTAPFP
|
|
|
601 \& \-o Sample.sdf
|
|
|
602 .Ve
|
|
|
603 .PP
|
|
|
604 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
605 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
606 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
607 .PP
|
|
|
608 .Vb 2
|
|
|
609 \& % TopologicalAtomPairsFingerprints.pl \-a DREIDINGAtomTypes
|
|
|
610 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
611 .Ve
|
|
|
612 .PP
|
|
|
613 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
614 10 using E\-state types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
615 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
616 .PP
|
|
|
617 .Vb 2
|
|
|
618 \& % TopologicalAtomPairsFingerprints.pl \-a EStateAtomTypes
|
|
|
619 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
620 .Ve
|
|
|
621 .PP
|
|
|
622 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
623 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
624 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
625 .PP
|
|
|
626 .Vb 2
|
|
|
627 \& % TopologicalAtomPairsFingerprints.pl \-a DREIDINGAtomTypes
|
|
|
628 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
629 .Ve
|
|
|
630 .PP
|
|
|
631 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
632 10 using functional class atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
633 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
634 .PP
|
|
|
635 .Vb 2
|
|
|
636 \& % TopologicalAtomPairsFingerprints.pl \-a FunctionalClassAtomTypes
|
|
|
637 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
638 .Ve
|
|
|
639 .PP
|
|
|
640 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
641 10 using \s-1MMFF94\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
642 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
643 .PP
|
|
|
644 .Vb 2
|
|
|
645 \& % TopologicalAtomPairsFingerprints.pl \-a MMFF94AtomTypes
|
|
|
646 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
647 .Ve
|
|
|
648 .PP
|
|
|
649 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
650 10 using SLogP atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
651 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
652 .PP
|
|
|
653 .Vb 2
|
|
|
654 \& % TopologicalAtomPairsFingerprints.pl \-a SLogPAtomTypes
|
|
|
655 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
656 .Ve
|
|
|
657 .PP
|
|
|
658 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
659 10 using \s-1SYBYL\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
660 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
661 .PP
|
|
|
662 .Vb 2
|
|
|
663 \& % TopologicalAtomPairsFingerprints.pl \-a SYBYLAtomTypes
|
|
|
664 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
665 .Ve
|
|
|
666 .PP
|
|
|
667 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
668 10 using \s-1TPSA\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
669 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
670 .PP
|
|
|
671 .Vb 2
|
|
|
672 \& % TopologicalAtomPairsFingerprints.pl \-a TPSAAtomTypes
|
|
|
673 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
674 .Ve
|
|
|
675 .PP
|
|
|
676 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
677 10 using \s-1UFF\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
678 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
679 .PP
|
|
|
680 .Vb 2
|
|
|
681 \& % TopologicalAtomPairsFingerprints.pl \-a UFFAtomTypes
|
|
|
682 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
683 .Ve
|
|
|
684 .PP
|
|
|
685 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
686 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTAPFP.csv
|
|
|
687 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
688 .PP
|
|
|
689 .Vb 2
|
|
|
690 \& % TopologicalAtomPairsFingerprints.pl \-\-VectorStringFormat
|
|
|
691 \& IDsAndValuesPairsString \-r SampleTAPFP \-o Sample.sdf
|
|
|
692 .Ve
|
|
|
693 .PP
|
|
|
694 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
695 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
696 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
697 .PP
|
|
|
698 .Vb 2
|
|
|
699 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
700 \& \-\-MinDistance 1 \-\-MaxDistance 6 \-r SampleTAPFP \-o Sample.sdf
|
|
|
701 .Ve
|
|
|
702 .PP
|
|
|
703 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
704 10 using only \s-1AS\s0,X atomic invariants atom types in IDsAndValuesString format and create a
|
|
|
705 SampleTAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
|
|
|
706 data, type:
|
|
|
707 .PP
|
|
|
708 .Vb 3
|
|
|
709 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
710 \& \-\-AtomicInvariantsToUse "AS,X" \-\-MinDistance 1 \-\-MaxDistance 6
|
|
|
711 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
712 .Ve
|
|
|
713 .PP
|
|
|
714 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
715 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
716 file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings
|
|
|
717 data, type:
|
|
|
718 .PP
|
|
|
719 .Vb 3
|
|
|
720 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
721 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
|
|
|
722 \& \-r SampleTAPFP \-o Sample.sdf
|
|
|
723 .Ve
|
|
|
724 .PP
|
|
|
725 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
726 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
727 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
728 data, type:
|
|
|
729 .PP
|
|
|
730 .Vb 3
|
|
|
731 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
732 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID
|
|
|
733 \& Mol_ID \-r SampleTAPFP \-o Sample.sdf
|
|
|
734 .Ve
|
|
|
735 .PP
|
|
|
736 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
737 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
738 file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
|
|
|
739 prefix along with fingerprints vector strings data, type:
|
|
|
740 .PP
|
|
|
741 .Vb 3
|
|
|
742 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
743 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
|
|
|
744 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTAPFP \-o Sample.sdf
|
|
|
745 .Ve
|
|
|
746 .PP
|
|
|
747 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
748 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
749 file containing specific data fields columns along with fingerprints vector strings
|
|
|
750 data, type:
|
|
|
751 .PP
|
|
|
752 .Vb 3
|
|
|
753 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
754 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTAPFP
|
|
|
755 \& \-o Sample.sdf
|
|
|
756 .Ve
|
|
|
757 .PP
|
|
|
758 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
759 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
760 file containing common data fields columns along with fingerprints vector strings
|
|
|
761 data, type:
|
|
|
762 .PP
|
|
|
763 .Vb 2
|
|
|
764 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
765 \& \-\-DataFieldsMode Common \-r SampleTAPFP \-o Sample.sdf
|
|
|
766 .Ve
|
|
|
767 .PP
|
|
|
768 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
769 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
|
|
|
770 SampleTAPFP.fpf and SampleTAPFP.csv files containing all data fields columns in \s-1CSV\s0 file along
|
|
|
771 with fingerprints data, type:
|
|
|
772 .PP
|
|
|
773 .Vb 3
|
|
|
774 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
775 \& \-\-DataFieldsMode All \-\-output all \-r SampleTAPFP
|
|
|
776 \& \-o Sample.sdf
|
|
|
777 .Ve
|
|
|
778 .SH "AUTHOR"
|
|
|
779 .IX Header "AUTHOR"
|
|
|
780 Manish Sud <msud@san.rr.com>
|
|
|
781 .SH "SEE ALSO"
|
|
|
782 .IX Header "SEE ALSO"
|
|
|
783 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
784 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
|
|
|
785 PathLengthFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
786 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
787 .SH "COPYRIGHT"
|
|
|
788 .IX Header "COPYRIGHT"
|
|
|
789 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
790 .PP
|
|
|
791 This file is part of MayaChemTools.
|
|
|
792 .PP
|
|
|
793 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
794 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
795 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
796 any later version.
|
