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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ESTATEINDICIESFINGERPRINTS 1"
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127 .TH ESTATEINDICIESFINGERPRINTS 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 EStateIndiciesFingerprints.pl \- Generate E\-state indicies fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 EStateIndiciesFingerprints.pl SDFile(s)...
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137 .PP
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138 EStateIndiciesFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
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139 [\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR]
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140 [\fB\-\-CompoundIDLabel\fR \fItext\fR] [\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR]
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141 [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,...\*(R"\fR] [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR]
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142 [\fB\-e, \-\-EStateAtomTypesSetToUse\fR \fIArbitrarySize or FixedSize\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR]
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143 [\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR]
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144 [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR]
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145 [\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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146 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-s, \-\-size\fR \fInumber\fR] [\fB\-\-ValuesPrecision\fR \fInumber\fR]
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147 [\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
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148 [\fB\-w, \-\-WorkingDir\fR \fIDirName\fR]
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149 .SH "DESCRIPTION"
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150 .IX Header "DESCRIPTION"
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151 Generate E\-state indicies fingerprints [ Ref 75\-78 ] for \fISDFile(s)\fR and create appropriate \s-1SD\s0,
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152 \&\s-1FP\s0, or \s-1CSV/TSV\s0 text file(s) containing fingerprints bit-vector or 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 E\-state atom types are assigned to all non-hydrogen atoms in a molecule using module
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160 AtomTypes::EStateAtomTypes.pm and E\-state values are calculated using module
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161 AtomicDescriptors::EStateValues.pm. Using E\-state atom types and E\-state values,
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162 \&\fBEStateIndiciesFingerprints\fR constituting sum of E\-state values for E\-sate atom types
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163 is generated.
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164 .PP
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165 Two types of E\-state atom types set size are allowed:
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166 .PP
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167 .Vb 4
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168 \& ArbitrarySize \- Corresponds to only E\-state atom types detected
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169 \& in molecule
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170 \& FixedSize \- Corresponds to fixed number of E\-state atom types previously
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171 \& defined
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172 .Ve
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173 .PP
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174 Module AtomTypes::EStateAtomTypes.pm, used to assign E\-state atom types to
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175 non-hydrogen atoms in the molecule, is able to assign atom types to any valid
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176 atom group. However, for \fIFixedSize\fR value of \fBEStateAtomTypesSetToUse\fR, only a
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177 fixed set of E\-state atom types corresponding to specific atom groups [ Appendix \s-1III\s0 in
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178 Ref 77 ] are used for fingerprints.
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179 .PP
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180 The fixed size E\-state atom type set size used during generation of fingerprints contains
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181 87 E\-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
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182 MayaChemTools.
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183 .PP
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184 Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
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185 E\-state indicies fingerprints:
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186 .PP
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187 .Vb 1
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188 \& Type EStateAtomTypesSetToUse
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189 \&
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190 \& EStateIndicies ArbitrarySize [ default fingerprints ]
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191 \& EStateIndicies FixedSize
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192 .Ve
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193 .PP
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194 Example of \fI\s-1SD\s0\fR file containing E\-state indicies fingerprints string data:
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195 .PP
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196 .Vb 10
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197 \& ... ...
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198 \& ... ...
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199 \& $$$$
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200 \& ... ...
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201 \& ... ...
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202 \& ... ...
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203 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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204 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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205 \& ... ...
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206 \& 2 3 1 0 0 0 0
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207 \& ... ...
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208 \& M END
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209 \& > <CmpdID>
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210 \& Cmpd1
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211 \&
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212 \& > <EStateIndiciesFingerprints>
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213 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDsA
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214 \& ndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssNH
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215 \& SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3.02
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216 \& 4 \-2.270
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217 \&
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218 \& $$$$
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219 \& ... ...
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220 \& ... ...
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221 .Ve
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222 .PP
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223 Example of \fI\s-1FP\s0\fR file containing E\-state indicies fingerprints string data:
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224 .PP
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225 .Vb 10
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226 \& #
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227 \& # Package = MayaChemTools 7.4
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228 \& # Release Date = Oct 21, 2010
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229 \& #
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230 \& # TimeStamp = Fri Mar 11 14:35:11 2011
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231 \& #
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232 \& # FingerprintsStringType = FingerprintsVector
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233 \& #
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234 \& # Description = EStateIndicies:ArbitrarySize
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235 \& # VectorStringFormat = IDsAndValuesString
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236 \& # VectorValuesType = NumericalValues
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237 \& #
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238 \& Cmpd1 11;SaaCH SaasC SaasN SdO SdssC...;24.778 4.387 1.993 25.023 \-1...
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239 \& Cmpd2 9;SdNH SdO SdssC SsCH3 SsNH...;7.418 22.984 \-1.583 5.387 5.400...
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240 \& ... ...
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241 \& ... ..
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242 .Ve
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243 .PP
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244 Example of \s-1CSV\s0 \fIText\fR file containing E\-state indicies fingerprints string data:
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245 .PP
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246 .Vb 10
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247 \& "CompoundID","EStateIndiciesFingerprints"
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248 \& "Cmpd1","FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalVa
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249 \& lues;IDsAndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssC
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250 \& H2 SssNH SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0
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251 \& .073 3.024 \-2.270"
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252 \& "Cmpd2","FingerprintsVector;EStateIndicies:ArbitrarySize;9;NumericalVal
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253 \& ues;IDsAndValuesString;SdNH SdO SdssC SsCH3 SsNH2 SsOH SssCH2 SssNH Sss
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254 \& sCH;7.418 22.984 \-1.583 5.387 5.400 19.852 1.737 5.624 \-3.319"
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255 \& ... ...
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256 \& ... ...
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257 .Ve
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258 .PP
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259 The current release of MayaChemTools generates the following types of E\-state
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260 fingerprints vector strings:
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261 .PP
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262 .Vb 4
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263 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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264 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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265 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
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266 \& .024 \-2.270
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267 \&
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268 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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269 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
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270 \& 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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271 \& 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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272 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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273 \&
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274 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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275 \& IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
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276 \& SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
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277 \& C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
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278 \& 0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435 4.387 0 0 0
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279 \& 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
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280 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
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281 .Ve
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282 .SH "OPTIONS"
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283 .IX Header "OPTIONS"
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284 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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285 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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286 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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287 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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288 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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289 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
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290 .Sp
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291 The supported aromaticity model names along with model specific control parameters
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292 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
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293 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
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294 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
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295 for detecting aromaticity corresponding to a specific model.
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296 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
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297 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
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298 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
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299 .Sp
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300 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
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301 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
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302 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
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303 look like Cmpd<Number>.
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304 .Sp
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305 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
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306 .Sp
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307 .Vb 2
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308 \& MolID
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309 \& ExtReg
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310 .Ve
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311 .Sp
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312 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
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313 .Sp
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314 .Vb 1
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315 \& Compound
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316 .Ve
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317 .Sp
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318 The value specified above generates compound IDs which correspond to Compound<Number>
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319 instead of default value of Cmpd<Number>.
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320 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
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321 .IX Item "--CompoundIDLabel text"
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322 Specify compound \s-1ID\s0 column label for \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
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323 of \fB\-\-DataFieldsMode\fR option. Default: \fICompoundID\fR.
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324 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
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325 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
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326 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
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327 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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328 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
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329 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
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330 .Sp
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331 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
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332 Default: \fILabelPrefix\fR.
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333 .Sp
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334 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
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335 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
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336 values are replaced with sequential compound IDs.
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337 .Sp
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338 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
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339 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
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340 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
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341 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
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342 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
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343 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
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344 .Sp
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345 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
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346 .Sp
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347 Examples:
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348 .Sp
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349 .Vb 2
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350 \& Extreg
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351 \& MolID,CompoundName
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352 .Ve
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353 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
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354 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
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355 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
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356 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
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357 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
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358 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
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359 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
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360 .IP "\fB\-e, \-\-EStateAtomTypesSetToUse\fR \fIArbitrarySize | FixedSize\fR" 4
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361 .IX Item "-e, --EStateAtomTypesSetToUse ArbitrarySize | FixedSize"
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362 E\-state atom types set size to use during generation of E\-state indicies fingerprints.
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363 Possible values: \fIArbitrarySize | FixedSize\fR; Default value: \fIArbitrarySize\fR.
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364 .Sp
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365 \&\fIArbitrarySize\fR corrresponds to only E\-state atom types detected in molecule; \fIFixedSize\fR
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366 corresponds to fixed number of previously defined E\-state atom types.
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367 .Sp
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368 For \fIEStateIndicies\fR, a fingerprint vector string is generated. The vector string corresponding to
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369 \&\fIEStateIndicies\fR contains sum of E\-state values for E\-state atom types.
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370 .Sp
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371 Module \fBAtomTypes::EStateAtomTypes.pm\fR is used to assign E\-state atom types to
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372 non-hydrogen atoms in the molecule which is able to assign atom types to any valid
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373 atom group. However, for \fIFixedSize\fR value of \fBEStateAtomTypesSetToUse\fR,
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374 only a fixed set of E\-state atom types corresponding to specific atom groups [ Appendix
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375 \&\s-1III\s0 in Ref 77 ] are used for fingerprints.
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376 .Sp
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377 The fixed size E\-state atom type set size used during generation of fingerprints contains
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378 87 E\-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
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379 MayaChemTools.
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380 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
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381 .IX Item "-f, --Filter Yes | No"
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382 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
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383 Default value: \fIYes\fR.
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384 .Sp
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385 By default, compound data is checked before calculating fingerprints and compounds containing
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386 atom data corresponding to non-element symbols or no atom data are ignored.
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387 .IP "\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR" 4
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388 .IX Item "--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs"
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389 Specify how fingerprints label is generated in conjunction with \fB\-\-FingerprintsLabel\fR option value:
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390 use fingerprints label generated only by \fB\-\-FingerprintsLabel\fR option value or append E\-state
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391 atom type value IDs to \fB\-\-FingerprintsLabel\fR option value.
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392 .Sp
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393 Possible values: \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR. Default value:
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394 \&\fIFingerprintsLabelOnly\fR.
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395 .Sp
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396 This option is only used for \fIFixedSize\fR value of \fB\-e, \-\-EStateAtomTypesSetToUse\fR option during
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397 generation of \fIEStateIndicies\fR E\-state fingerprints.
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398 .Sp
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399 E\-state atom type IDs appended to \fB\-\-FingerprintsLabel\fR value during \fIFingerprintsLabelWithIDs\fR
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400 values of \fB\-\-FingerprintsLabelMode\fR correspond to fixed number of previously defined E\-state
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401 atom types.
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402 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
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403 .IX Item "--FingerprintsLabel text"
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404 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
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405 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIEStateIndiciesFingerprints\fR.
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406 .IP "\fB\-h, \-\-help\fR" 4
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407 .IX Item "-h, --help"
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408 Print this help message.
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409 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
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410 .IX Item "-k, --KeepLargestComponent Yes | No"
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|
411 Generate fingerprints for only the largest component in molecule. Possible values:
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412 \&\fIYes or No\fR. Default value: \fIYes\fR.
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413 .Sp
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414 For molecules containing multiple connected components, fingerprints can be generated
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415 in two different ways: use all connected components or just the largest connected
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416 component. By default, all atoms except for the largest connected component are
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417 deleted before generation of fingerprints.
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418 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
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419 .IX Item "--OutDelim comma | tab | semicolon"
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420 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
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421 Default value: \fIcomma\fR.
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422 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
|
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423 .IX Item "--output SD | FP | text | all"
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424 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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|
425 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
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426 .IX Item "-o, --overwrite"
|
|
|
427 Overwrite existing files.
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|
428 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
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429 .IX Item "-q, --quote Yes | No"
|
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|
430 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
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|
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431 \&\fIYes or No\fR. Default value: \fIYes\fR.
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432 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
|
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433 .IX Item "-r, --root RootName"
|
|
|
434 New file name is generated using the root: <Root>.<Ext>. Default for new file
|
|
|
435 names: <SDFileName><EStateIndiciesFP>.<Ext>. The file type determines <Ext> value.
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|
436 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
|
|
|
437 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
438 .IP "\fB\-\-ValuesPrecision\fR \fInumber\fR" 4
|
|
|
439 .IX Item "--ValuesPrecision number"
|
|
|
440 Precision of values for E\-state indicies option. Default value: up to \fI3\fR decimal places.
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|
|
441 Valid values: positive integers.
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|
|
442 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
|
|
|
443 .IX Item "-v, --VectorStringFormat ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
|
|
|
444 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
|
|
|
445 \&\fB\-\-output\fR used for \fIEStateIndicies\fR. Possible values: \fIValuesString, IDsAndValuesString,
|
|
|
446 IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString\fR.
|
|
|
447 .Sp
|
|
|
448 Default value during \fIArbitrarySize\fR value of \fB\-e, \-\-EStateAtomTypesSetToUse\fR
|
|
|
449 option: \fIIDsAndValuesString\fR. Default value during \fIFixedSize\fR value of
|
|
|
450 \&\fB\-e, \-\-EStateAtomTypesSetToUse\fR option: \fIValuesString\fR.
|
|
|
451 .Sp
|
|
|
452 Examples:
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|
|
453 .Sp
|
|
|
454 .Vb 4
|
|
|
455 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
|
|
|
456 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
|
|
|
457 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
|
|
|
458 \& .024 \-2.270
|
|
|
459 .Ve
|
|
|
460 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
|
|
|
461 .IX Item "-w, --WorkingDir DirName"
|
|
|
462 Location of working directory. Default: current directory.
|
|
|
463 .SH "EXAMPLES"
|
|
|
464 .IX Header "EXAMPLES"
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|
|
465 To generate E\-state fingerprints of arbitrary size in vector string format and create a
|
|
|
466 SampleESFP.csv file containing sequential compound IDs along with fingerprints
|
|
|
467 vector strings data, type:
|
|
|
468 .PP
|
|
|
469 .Vb 1
|
|
|
470 \& % EStateIndiciesFingerprints.pl \-r SampleESFP \-o Sample.sdf
|
|
|
471 .Ve
|
|
|
472 .PP
|
|
|
473 To generate E\-state fingerprints of fixed size in vector string format and create a
|
|
|
474 SampleESFP.csv file containing sequential compound IDs along with fingerprints
|
|
|
475 vector strings data, type:
|
|
|
476 .PP
|
|
|
477 .Vb 2
|
|
|
478 \& % EStateIndiciesFingerprints.pl \-e FixedSize \-r SampleESFP
|
|
|
479 \& \-o Sample.sdf
|
|
|
480 .Ve
|
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|
481 .PP
|
|
|
482 To generate E\-state fingerprints of fixed size in vector string with IDsAndValues
|
|
|
483 format and create a SampleESFP.csv file containing sequential compound IDs
|
|
|
484 along with fingerprints vector strings data, type:
|
|
|
485 .PP
|
|
|
486 .Vb 2
|
|
|
487 \& % EStateIndiciesFingerprints.pl \-e FixedSize \-v IDsAndValuesString
|
|
|
488 \& \-r SampleESFP \-o Sample.sdf
|
|
|
489 .Ve
|
|
|
490 .PP
|
|
|
491 To generate E\-state fingerprints of fixed size in vector string format
|
|
|
492 and create a SampleESFP.csv file containing compound \s-1ID\s0 from molecule
|
|
|
493 name line along with fingerprints vector strings data, type
|
|
|
494 .PP
|
|
|
495 .Vb 3
|
|
|
496 \& % EStateIndiciesFingerprints.pl \-e FixedSize
|
|
|
497 \& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolName
|
|
|
498 \& \-r SampleESFP \-o Sample.sdf
|
|
|
499 .Ve
|
|
|
500 .PP
|
|
|
501 To generate E\-state fingerprints of fixed size in vector string format
|
|
|
502 and create a SampleESFP.csv file containing compound IDs using specified
|
|
|
503 data field along with fingerprints vector strings data, type:
|
|
|
504 .PP
|
|
|
505 .Vb 3
|
|
|
506 \& % EStateIndiciesFingerprints.pl \-e FixedSize
|
|
|
507 \& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode DataField \-\-CompoundID
|
|
|
508 \& Mol_ID \-r SampleESFP \-o Sample.sdf
|
|
|
509 .Ve
|
|
|
510 .PP
|
|
|
511 To generate E\-state fingerprints of fixed size in vector string format
|
|
|
512 and create a SampleESFP.csv file containing compound \s-1ID\s0 using combination
|
|
|
513 of molecule name line and an explicit compound prefix along with fingerprints vector
|
|
|
514 strings data, type:
|
|
|
515 .PP
|
|
|
516 .Vb 3
|
|
|
517 \& % EStateIndiciesFingerprints.pl \-e FixedSize
|
|
|
518 \& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix
|
|
|
519 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleESFP \-o Sample.sdf
|
|
|
520 .Ve
|
|
|
521 .PP
|
|
|
522 To generate E\-state fingerprints of fixed size in vector string format
|
|
|
523 and create a SampleESFP.csv file containing specific data fields columns along
|
|
|
524 with fingerprints vector strings data, type:
|
|
|
525 .PP
|
|
|
526 .Vb 3
|
|
|
527 \& % EStateIndiciesFingerprints.pl \-e FixedSize
|
|
|
528 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleESFP
|
|
|
529 \& \-o Sample.sdf
|
|
|
530 .Ve
|
|
|
531 .PP
|
|
|
532 To generate E\-state fingerprints of fixed size in vector string format
|
|
|
533 and create a SampleESFP.csv file containing common data fields columns along
|
|
|
534 with fingerprints vector strings data, type:
|
|
|
535 .PP
|
|
|
536 .Vb 2
|
|
|
537 \& % EStateIndiciesFingerprints.pl \-e FixedSize
|
|
|
538 \& \-\-DataFieldsMode Common \-r SampleESFP \-o Sample.sdf
|
|
|
539 .Ve
|
|
|
540 .PP
|
|
|
541 To generate E\-state fingerprints of fixed size in vector string format and create
|
|
|
542 SampleESFP.sdf, SampleESFP.fpf, and SampleESFP.csv files containing all data
|
|
|
543 fields columns in \s-1CSV\s0 file along with fingerprints vector strings data, type:
|
|
|
544 .PP
|
|
|
545 .Vb 2
|
|
|
546 \& % EStateIndiciesFingerprints.pl \-e FixedSize
|
|
|
547 \& \-\-DataFieldsMode All \-\-output all \-r SampleESFP \-o Sample.sdf
|
|
|
548 .Ve
|
|
|
549 .SH "AUTHOR"
|
|
|
550 .IX Header "AUTHOR"
|
|
|
551 Manish Sud <msud@san.rr.com>
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|
|
552 .SH "SEE ALSO"
|
|
|
553 .IX Header "SEE ALSO"
|
|
|
554 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
555 ExtendedConnectivityFingerprints.pl, MACCSKeysFingeprints.pl, PathLengthFingerprints.pl,
|
|
|
556 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
557 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
558 .SH "COPYRIGHT"
|
|
|
559 .IX Header "COPYRIGHT"
|
|
|
560 Copyright (C) 2015 Manish Sud. All rights reserved.
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|
|
561 .PP
|
|
|
562 This file is part of MayaChemTools.
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|
|
563 .PP
|
|
|
564 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
565 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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|
|
566 Software Foundation; either version 3 of the License, or (at your option)
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|
|
567 any later version.
|
