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124 .\" ========================================================================
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125 .\"
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126 .IX Title "ATOMNEIGHBORHOODSFINGERPRINTS 1"
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127 .TH ATOMNEIGHBORHOODSFINGERPRINTS 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 AtomNeighborhoodsFingerprints.pl \- Generate atom neighborhoods fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 AtomNeighborhoodsFingerprints.pl SDFile(s)...
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137 .PP
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138 AtomNeighborhoodsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
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139 [\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes |
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140 DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR]
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141 [\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR]
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142 [\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\fR]
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143 [\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR]
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144 [\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,...\*(R"\fR]
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145 [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR]
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146 [\fB\-\-FingerprintsLabel\fR \fItext\fR] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR]
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147 [\fB\-\-MinNeighborhoodRadius\fR \fInumber\fR] [\fB\-\-MaxNeighborhoodRadius\fR \fInumber\fR]
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148 [\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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149 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\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 atom neighborhoods fingerprints [ Ref 53\-56, Ref 73 ] for \fISDFile(s)\fR and create appropriate
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154 \&\s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector strings corresponding to molecular fingerprints.
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155 .PP
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156 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
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157 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
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158 can be specified either by \fI*.sdf\fR or the current directory name.
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159 .PP
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160 The current release of MayaChemTools supports generation of atom neighborhoods fingerprints
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161 corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
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162 .PP
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163 .Vb 3
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164 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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165 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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166 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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167 .Ve
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168 .PP
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169 Based on the values specified for \fB\-a, \-\-AtomIdentifierType\fR and \fB\-\-AtomicInvariantsToUse\fR,
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170 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
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171 around each non-hydrogen central atom corresponding to radii between specified values
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172 \&\fB\-\-MinNeighborhoodRadius\fR and \fB\-\-MaxNeighborhoodRadius\fR, unique atom types at
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173 each radii level are counted and an atom neighborhood identifier is generated.
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174 .PP
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175 The format of an atom neighborhood identifier around a central non-hydrogen atom at a
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176 specific radius is:
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177 .PP
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178 .Vb 1
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179 \& NR<n>\-<AtomType>\-ATC<n>
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180 \&
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181 \& NR: Neighborhood radius
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182 \& AtomType: Assigned atom type
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183 \& ATC: Atom type count
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184 .Ve
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185 .PP
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186 The atom neighborhood identifier for a non-hydrogen central atom corresponding to all specified radii
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187 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:
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188 .PP
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189 .Vb 1
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190 \& NR<n>\-<AtomType>\-ATC<n>:NR<n>\-<AtomType>\-ATC<n>:...
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191 .Ve
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192 .PP
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193 The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
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194 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.
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195 .PP
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196 Example of \fI\s-1SD\s0\fR file containing atom neighborhood fingerprints string data:
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197 .PP
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198 .Vb 10
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199 \& ... ...
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200 \& ... ...
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201 \& $$$$
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202 \& ... ...
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203 \& ... ...
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204 \& ... ...
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205 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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206 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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207 \& ... ...
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208 \& 2 3 1 0 0 0 0
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209 \& ... ...
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210 \& M END
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211 \& > <CmpdID>
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212 \& Cmpd1
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213 \&
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214 \& > <AtomNeighborhoodsFingerprints>
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215 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu
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216 \& s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-ATC1
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217 \& :NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X1.B
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218 \& O1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1
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219 \& NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C...
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220 \&
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221 \& $$$$
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222 \& ... ...
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223 \& ... ...
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224 .Ve
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225 .PP
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226 Example of \fI\s-1FP\s0\fR file containing atom neighborhood fingerprints string data:
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227 .PP
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228 .Vb 10
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229 \& #
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230 \& # Package = MayaChemTools 7.4
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231 \& # Release Date = Oct 21, 2010
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232 \& #
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233 \& # TimeStamp = Fri Mar 11 14:15:27 2011
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234 \& #
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235 \& # FingerprintsStringType = FingerprintsVector
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236 \& #
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237 \& # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu...
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238 \& # VectorStringFormat = ValuesString
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239 \& # VectorValuesType = AlphaNumericalValues
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240 \& #
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241 \& Cmpd1 41;NR0\-C.X1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-A...
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242 \& Cmpd2 23;NR0\-C.X1.BO1.H3\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR2\-C.X3.BO3.H1\-A...
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243 \& ... ...
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244 \& ... ..
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245 .Ve
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246 .PP
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247 Example of \s-1CSV\s0 \fIText\fR file containing atom neighborhood fingerprints string data:
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248 .PP
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249 .Vb 8
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250 \& "CompoundID","AtomNeighborhoodsFingerprints"
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251 \& "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes
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252 \& :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.B
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253 \& O1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1
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254 \& NR0\-C.X1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3
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255 \& .BO4\-ATC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1..."
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256 \& ... ...
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257 \& ... ...
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258 .Ve
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259 .PP
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260 The current release of MayaChemTools generates the following types of atom neighborhoods
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261 fingerprints vector strings:
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262 .PP
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263 .Vb 6
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264 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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265 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
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266 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
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267 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
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268 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
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269 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
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270 \&
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271 \& FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
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272 \& adius2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:
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273 \& NR1\-O_2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N
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274 \& _3\-ATC1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-AT
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275 \& C1:NR2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR
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276 \& 1\-N_R\-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-...
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277 \&
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278 \& FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
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279 \& ius2;41;AlphaNumericalValues;ValuesString;NR0\-aaCH\-ATC1:NR1\-aaCH\-ATC1:
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280 \& NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-aaCH\-ATC1:NR
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281 \& 1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-
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282 \& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 NR0\-
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283 \& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 N...
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284 \&
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285 \& FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
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286 \& s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-Ar\-ATC1:NR1\-Ar\-
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287 \& ATC1:NR1\-Ar.HBA\-ATC1:NR1\-None\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC4 NR0\-Ar\-AT
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288 \& C1:NR1\-Ar\-ATC2:NR1\-Ar.HBA\-ATC1:NR2\-Ar\-ATC5:NR2\-None\-ATC1 NR0\-Ar\-ATC1:N
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289 \& R1\-Ar\-ATC2:NR1\-HBD\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC1 NR0\-Ar\-ATC1:NR1\-Ar\-A
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290 \& TC2:NR1\-Hal\-ATC1:NR2\-Ar\-ATC2 NR0\-Ar\-ATC1:NR1\-Ar\-ATC2:NR1\-None\-ATC1:...
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291 \&
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292 \& FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
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|
293 \& ius2;41;AlphaNumericalValues;ValuesString;NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR
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294 \& 1\-CB\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C5B\-ATC1:NR2\-CB\-ATC3:NR2\-CR\-ATC
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295 \& 1 NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR1\-CR\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C
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296 \& 5B\-ATC1:NR2\-C=ON\-ATC1:NR2\-CR\-ATC3 NR0\-C5B\-ATC1:NR1\-C5A\-ATC1:NR1\-C5B\-AT
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297 \& C1:NR1\-C=ON\-ATC1:NR2\-C5A\-ATC1:NR2\-CB\-ATC1:NR2\-CR\-ATC1:NR2\-N5\-ATC1:N...
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298 \&
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299 \& FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
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300 \& us2;41;AlphaNumericalValues;ValuesString;NR0\-C1\-ATC1:NR1\-C10\-ATC1:NR1\-
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301 \& CS\-ATC1:NR2\-C1\-ATC1:NR2\-N11\-ATC1:NR2\-O2\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:
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302 \& NR2\-C1\-ATC1:NR2\-C21\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:NR2\-C1\-ATC1:NR2\-C21\-
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303 \& ATC1 NR0\-C1\-ATC1:NR1\-C5\-ATC1:NR1\-CS\-ATC1:NR2\-C1\-ATC1:NR2\-O2\-ATC2:NR2\-O
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304 \& 9\-ATC1 NR0\-C1\-ATC1:NR1\-CS\-ATC2:NR2\-C1\-ATC2:NR2\-O2\-ATC2 NR0\-C10\-ATC1...
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305 \&
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306 \& FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
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307 \& us2;41;AlphaNumericalValues;ValuesString;NR0\-C.2\-ATC1:NR1\-C.3\-ATC1:NR1
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|
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308 \& \-O.co2\-ATC2:NR2\-C.3\-ATC1 NR0\-C.2\-ATC1:NR1\-C.ar\-ATC1:NR1\-N.am\-ATC1:NR1\-
|
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|
309 \& O.2\-ATC1:NR2\-C.ar\-ATC3 NR0\-C.3\-ATC1:NR1\-C.2\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-
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310 \& ATC1:NR2\-O.3\-ATC1:NR2\-O.co2\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR1\-N.ar\-AT
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311 \& C1:NR2\-C.3\-ATC1:NR2\-C.ar\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-ATC...
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312 \&
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313 \& FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
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314 \& s2;41;AlphaNumericalValues;ValuesString;NR0\-N21\-ATC1:NR1\-None\-ATC3:NR2
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315 \& \-None\-ATC5 NR0\-N7\-ATC1:NR1\-None\-ATC2:NR2\-None\-ATC3:NR2\-O3\-ATC1 NR0\-Non
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316 \& e\-ATC1:NR1\-N21\-ATC1:NR1\-None\-ATC1:NR2\-None\-ATC3 NR0\-None\-ATC1:NR1\-N21\-
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317 \& ATC1:NR1\-None\-ATC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N21\-ATC1:NR1\-None\-A
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318 \& TC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N7\-ATC1:NR1\-None\-ATC1:NR1\-O3\-AT...
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319 \&
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320 \& FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
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321 \& 2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:NR1\-O
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322 \& _2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N_3\-AT
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323 \& C1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-ATC1:NR
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324 \& 2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR1\-N_R
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325 \& \-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-C_3\-A...
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326 .Ve
|
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327 .SH "OPTIONS"
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328 .IX Header "OPTIONS"
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329 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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330 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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331 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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332 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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333 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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334 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
|
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335 .Sp
|
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336 The supported aromaticity model names along with model specific control parameters
|
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|
337 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
|
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|
338 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
|
|
|
339 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
|
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340 for detecting aromaticity corresponding to a specific model.
|
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|
341 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
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342 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
|
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|
343 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
|
|
|
344 atoms during calculation of atom neighborhoods fingerprints. Possible values in the current
|
|
|
345 release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
346 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
347 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
|
|
|
348 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
|
|
|
349 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
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|
350 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
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|
|
351 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
|
352 option. It's a list of comma separated valid atomic invariant atom types.
|
|
|
353 .Sp
|
|
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354 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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355 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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356 .Sp
|
|
|
357 The atomic invariants abbreviations correspond to:
|
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358 .Sp
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359 .Vb 1
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360 \& AS = Atom symbol corresponding to element symbol
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361 \&
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362 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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363 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
|
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364 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
|
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365 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
|
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366 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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|
367 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
|
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368 \& H<n> = Number of implicit and explicit hydrogens for atom
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369 \& Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
370 \& RA = Ring atom annotation indicating whether atom is a ring
|
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371 \& FC<+n/\-n> = Formal charge assigned to atom
|
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|
372 \& MN<n> = Mass number indicating isotope other than most abundant isotope
|
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373 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
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374 \& 3 (triplet)
|
|
|
375 .Ve
|
|
|
376 .Sp
|
|
|
377 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
378 .Sp
|
|
|
379 .Vb 1
|
|
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380 \& 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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|
381 .Ve
|
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|
382 .Sp
|
|
|
383 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
|
|
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384 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
385 .Sp
|
|
|
386 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
387 are also allowed:
|
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|
388 .Sp
|
|
|
389 .Vb 12
|
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|
390 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
391 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
392 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
393 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
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|
394 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
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|
395 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
396 \& H : NumOfImplicitAndExplicitHydrogens
|
|
|
397 \& Ar : Aromatic
|
|
|
398 \& RA : RingAtom
|
|
|
399 \& FC : FormalCharge
|
|
|
400 \& MN : MassNumber
|
|
|
401 \& SM : SpinMultiplicity
|
|
|
402 .Ve
|
|
|
403 .Sp
|
|
|
404 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
|
|
|
405 atom types.
|
|
|
406 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
|
|
|
407 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
|
|
|
408 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
|
|
|
409 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
|
410 option. It's a list of comma separated valid functional classes.
|
|
|
411 .Sp
|
|
|
412 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.
|
|
|
413 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
|
|
|
414 .Sp
|
|
|
415 The functional class abbreviations correspond to:
|
|
|
416 .Sp
|
|
|
417 .Vb 9
|
|
|
418 \& HBD: HydrogenBondDonor
|
|
|
419 \& HBA: HydrogenBondAcceptor
|
|
|
420 \& PI : PositivelyIonizable
|
|
|
421 \& NI : NegativelyIonizable
|
|
|
422 \& Ar : Aromatic
|
|
|
423 \& Hal : Halogen
|
|
|
424 \& H : Hydrophobic
|
|
|
425 \& RA : RingAtom
|
|
|
426 \& CA : ChainAtom
|
|
|
427 \&
|
|
|
428 \& Functional class atom type specification for an atom corresponds to:
|
|
|
429 \&
|
|
|
430 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
431 .Ve
|
|
|
432 .Sp
|
|
|
433 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
|
434 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
|
435 .Sp
|
|
|
436 .Vb 4
|
|
|
437 \& HydrogenBondDonor: NH, NH2, OH
|
|
|
438 \& HydrogenBondAcceptor: N[!H], O
|
|
|
439 \& PositivelyIonizable: +, NH2
|
|
|
440 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
441 .Ve
|
|
|
442 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
|
|
|
443 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
|
|
|
444 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
|
|
|
445 .Sp
|
|
|
446 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
|
|
|
447 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
|
|
|
448 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
|
|
|
449 look like Cmpd<Number>.
|
|
|
450 .Sp
|
|
|
451 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
452 .Sp
|
|
|
453 .Vb 2
|
|
|
454 \& MolID
|
|
|
455 \& ExtReg
|
|
|
456 .Ve
|
|
|
457 .Sp
|
|
|
458 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
459 .Sp
|
|
|
460 .Vb 1
|
|
|
461 \& Compound
|
|
|
462 .Ve
|
|
|
463 .Sp
|
|
|
464 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
465 instead of default value of Cmpd<Number>.
|
|
|
466 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
|
|
|
467 .IX Item "--CompoundIDLabel text"
|
|
|
468 Specify compound \s-1ID\s0 column label for \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
|
|
|
469 of \fB\-\-DataFieldsMode\fR option. Default: \fICompoundID\fR.
|
|
|
470 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
|
|
|
471 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
|
|
|
472 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
|
|
|
473 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
|
|
|
474 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
|
|
|
475 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
476 .Sp
|
|
|
477 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
|
|
|
478 Default: \fILabelPrefix\fR.
|
|
|
479 .Sp
|
|
|
480 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
|
|
|
481 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
|
|
|
482 values are replaced with sequential compound IDs.
|
|
|
483 .Sp
|
|
|
484 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
485 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
|
|
|
486 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
|
|
|
487 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
|
|
|
488 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
|
|
|
489 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
|
|
|
490 .Sp
|
|
|
491 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
492 .Sp
|
|
|
493 Examples:
|
|
|
494 .Sp
|
|
|
495 .Vb 2
|
|
|
496 \& Extreg
|
|
|
497 \& MolID,CompoundName
|
|
|
498 .Ve
|
|
|
499 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
|
|
|
500 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
|
|
|
501 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
|
|
|
502 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
|
|
|
503 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
|
|
|
504 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
|
|
|
505 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
|
|
|
506 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
|
|
|
507 .IX Item "-f, --Filter Yes | No"
|
|
|
508 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
|
|
|
509 Default value: \fIYes\fR.
|
|
|
510 .Sp
|
|
|
511 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
512 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
513 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
514 .IX Item "--FingerprintsLabel text"
|
|
|
515 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
516 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIAtomNeighborhoodsFingerprints\fR.
|
|
|
517 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
518 .IX Item "-h, --help"
|
|
|
519 Print this help message.
|
|
|
520 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
|
|
521 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
522 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
523 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
524 .Sp
|
|
|
525 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
526 in two different ways: use all connected components or just the largest connected
|
|
|
527 component. By default, all atoms except for the largest connected component are
|
|
|
528 deleted before generation of fingerprints.
|
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529 .IP "\fB\-\-MinNeighborhoodRadius\fR \fInumber\fR" 4
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530 .IX Item "--MinNeighborhoodRadius number"
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531 Minimum atom neighborhood radius for generating atom neighborhoods. Default value: \fI0\fR.
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532 Valid values: positive integers and less than \fB\-\-MaxNeighborhoodRadius\fR. Neighborhood
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533 radius of zero corresponds to list of non-hydrogen atoms.
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534 .IP "\fB\-\-MaxNeighborhoodRadius\fR \fInumber\fR" 4
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535 .IX Item "--MaxNeighborhoodRadius number"
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536 Maximum atom neighborhood radius for generating atom neighborhoods. Default value: \fI2\fR.
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537 Valid values: positive integers and greater than \fB\-\-MineighborhoodRadius\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><AtomNeighborhoodsFP>.<Ext>. The file type determines <Ext>
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|
556 value. The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\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\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
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|
559 .IX Item "-w, --WorkingDir DirName"
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|
560 Location of working directory. Default: current directory.
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|
561 .SH "EXAMPLES"
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|
562 .IX Header "EXAMPLES"
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|
563 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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|
564 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
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|
565 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
566 .PP
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|
567 .Vb 1
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|
568 \& % AtomNeighborhoodsFingerprints.pl \-r SampleANFP \-o Sample.sdf
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|
569 .Ve
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|
570 .PP
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|
571 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
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|
572 2 using \s-1DREIDING\s0 atom types in vector string format and create a SampleANFP.csv
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|
573 file containing sequential compound IDs along with fingerprints vector strings data, type:
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|
574 .PP
|
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|
575 .Vb 2
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|
|
576 \& % AtomNeighborhoodsFingerprints.pl \-a DREIDINGAtomTypes \-r SampleANFP
|
|
|
577 \& \-o Sample.sdf
|
|
|
578 .Ve
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|
579 .PP
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|
580 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
581 2 using EStateAtomTypes types in vector string format and create a SampleANFP.csv
|
|
|
582 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
583 .PP
|
|
|
584 .Vb 2
|
|
|
585 \& % AtomNeighborhoodsFingerprints.pl \-a EStateAtomTypes \-r SampleANFP
|
|
|
586 \& \-o Sample.sdf
|
|
|
587 .Ve
|
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|
588 .PP
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|
|
589 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
590 2 using \s-1SYBYL\s0 atom types in vector string format and create a SampleANFP.csv
|
|
|
591 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
592 .PP
|
|
|
593 .Vb 2
|
|
|
594 \& % AtomNeighborhoodsFingerprints.pl \-a SYBYLAtomTypes \-r SampleANFP
|
|
|
595 \& \-o Sample.sdf
|
|
|
596 .Ve
|
|
|
597 .PP
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|
|
598 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
599 2 using FunctionalClass atom types in vector string format and create a SampleANFP.csv
|
|
|
600 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
601 .PP
|
|
|
602 .Vb 2
|
|
|
603 \& % AtomNeighborhoodsFingerprints.pl \-a FunctionalClassAtomTypes
|
|
|
604 \& \-r SampleANFP \-o Sample.sdf
|
|
|
605 .Ve
|
|
|
606 .PP
|
|
|
607 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
608 2 using \s-1MMFF94\s0 atom types in vector string format and create a SampleANFP.csv
|
|
|
609 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
610 .PP
|
|
|
611 .Vb 2
|
|
|
612 \& % AtomNeighborhoodsFingerprints.pl \-a MMFF94AtomTypes \-r SampleANFP
|
|
|
613 \& \-o Sample.sdf
|
|
|
614 .Ve
|
|
|
615 .PP
|
|
|
616 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
617 2 using SLogP atom types in vector string format and create a SampleANFP.csv
|
|
|
618 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
619 .PP
|
|
|
620 .Vb 2
|
|
|
621 \& % AtomNeighborhoodsFingerprints.pl \-a SLogPAtomTypes \-r SampleANFP
|
|
|
622 \& \-o Sample.sdf
|
|
|
623 .Ve
|
|
|
624 .PP
|
|
|
625 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
626 2 using \s-1SYBYL\s0 atom types in vector string format and create a SampleANFP.csv
|
|
|
627 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
628 .PP
|
|
|
629 .Vb 2
|
|
|
630 \& % AtomNeighborhoodsFingerprints.pl \-a SYBYLAtomTypes \-r SampleANFP
|
|
|
631 \& \-o Sample.sdf
|
|
|
632 .Ve
|
|
|
633 .PP
|
|
|
634 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
635 2 using \s-1TPSA\s0 atom types in vector string format and create a SampleANFP.csv
|
|
|
636 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
637 .PP
|
|
|
638 .Vb 2
|
|
|
639 \& % AtomNeighborhoodsFingerprints.pl \-a TPSAAtomTypes \-r SampleANFP
|
|
|
640 \& \-o Sample.sdf
|
|
|
641 .Ve
|
|
|
642 .PP
|
|
|
643 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
644 2 using \s-1UFF\s0 atom types in vector string format and create a SampleANFP.csv
|
|
|
645 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
646 .PP
|
|
|
647 .Vb 2
|
|
|
648 \& % AtomNeighborhoodsFingerprints.pl \-a UFFAtomTypes \-r SampleANFP
|
|
|
649 \& \-o Sample.sdf
|
|
|
650 .Ve
|
|
|
651 .PP
|
|
|
652 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
653 2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
|
|
|
654 SampleANFP.fpf and SampleANFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along
|
|
|
655 with fingerprints vector strings data, type:
|
|
|
656 .PP
|
|
|
657 .Vb 2
|
|
|
658 \& % AtomNeighborhoodsFingerprints.pl \-\-output all \-r SampleANFP
|
|
|
659 \& \-o Sample.sdf
|
|
|
660 .Ve
|
|
|
661 .PP
|
|
|
662 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 1 to
|
|
|
663 3 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
664 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
665 .PP
|
|
|
666 .Vb 3
|
|
|
667 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
668 \& \-\-MinNeighborhoodRadius 1 \-\-MaxNeighborhoodRadius 3 \-r SampleANFP
|
|
|
669 \& \-o Sample.sdf
|
|
|
670 .Ve
|
|
|
671 .PP
|
|
|
672 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
673 2 using only \s-1AS\s0,X atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
674 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
675 .PP
|
|
|
676 .Vb 3
|
|
|
677 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
678 \& \-\-AtomicInvariantsToUse "AS,X" \-\-MinNeighborhoodRadius 0
|
|
|
679 \& \-\-MaxNeighborhoodRadius 3 \-r SampleANFP \-o Sample.sdf
|
|
|
680 .Ve
|
|
|
681 .PP
|
|
|
682 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
683 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
684 file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings data, type:
|
|
|
685 .PP
|
|
|
686 .Vb 3
|
|
|
687 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
688 \& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolName
|
|
|
689 \& \-r SampleANFP \-o Sample.sdf
|
|
|
690 .Ve
|
|
|
691 .PP
|
|
|
692 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
693 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
694 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
695 data, type:
|
|
|
696 .PP
|
|
|
697 .Vb 3
|
|
|
698 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
699 \& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode DataField \-\-CompoundID
|
|
|
700 \& Mol_ID \-r SampleANFP \-o Sample.sdf
|
|
|
701 .Ve
|
|
|
702 .PP
|
|
|
703 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
704 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
705 file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
|
|
|
706 prefix along with fingerprints vector strings data, type:
|
|
|
707 .PP
|
|
|
708 .Vb 3
|
|
|
709 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
710 \& \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix
|
|
|
711 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleANFP \-o Sample.sdf
|
|
|
712 .Ve
|
|
|
713 .PP
|
|
|
714 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
715 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
716 file containing specific data fields columns along with fingerprints vector strings
|
|
|
717 data, type:
|
|
|
718 .PP
|
|
|
719 .Vb 3
|
|
|
720 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
721 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleANFP
|
|
|
722 \& \-o Sample.sdf
|
|
|
723 .Ve
|
|
|
724 .PP
|
|
|
725 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
726 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
727 file containing common data fields columns along with fingerprints vector strings
|
|
|
728 data, type:
|
|
|
729 .PP
|
|
|
730 .Vb 2
|
|
|
731 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
732 \& \-\-DataFieldsMode Common \-r SampleANFP \-o Sample.sdf
|
|
|
733 .Ve
|
|
|
734 .PP
|
|
|
735 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
736 2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
|
|
|
737 SampleANFP.fpf and SampleANFP.csv files containing all data fields columns in \s-1CSV\s0 file along with
|
|
|
738 fingerprints data, type:
|
|
|
739 .PP
|
|
|
740 .Vb 3
|
|
|
741 \& % AtomNeighborhoodsFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
742 \& \-\-DataFieldsMode All \-\-output all \-r SampleANFP
|
|
|
743 \& \-o Sample.sdf
|
|
|
744 .Ve
|
|
|
745 .SH "AUTHOR"
|
|
|
746 .IX Header "AUTHOR"
|
|
|
747 Manish Sud <msud@san.rr.com>
|
|
|
748 .SH "SEE ALSO"
|
|
|
749 .IX Header "SEE ALSO"
|
|
|
750 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, SimilaritySearchingFingerprints.pl,
|
|
|
751 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
752 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
753 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
754 .SH "COPYRIGHT"
|
|
|
755 .IX Header "COPYRIGHT"
|
|
|
756 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
757 .PP
|
|
|
758 This file is part of MayaChemTools.
|
|
|
759 .PP
|
|
|
760 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
761 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
762 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
763 any later version.
|
