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124 .\" ========================================================================
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125 .\"
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126 .IX Title "EXTENDEDCONNECTIVITYFINGERPRINTS 1"
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127 .TH EXTENDEDCONNECTIVITYFINGERPRINTS 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 ExtendedConnectivityFingerprints.pl \- Generate extended connectivity fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 ExtendedConnectivityFingerprints.pl SDFile(s)...
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137 .PP
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138 ExtendedConnectivityFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
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139 [\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes\fR]
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140 [\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR]
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141 [\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\fR]
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142 [\fB\-\-BitsOrder\fR \fIAscending | Descending\fR] [\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\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\-m, \-\-mode\fR \fIExtendedConnectivity | ExtendedConnecticityCount | ExtendedConnecticityBits\fR]
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148 [\fB\-n, \-\-NeighborhoodRadius\fR \fInumber\fR] [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR]
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149 [\fB\-o, \-\-overwrite\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-s, \-\-size\fR \fInumber\fR]
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150 [\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR]
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151 [\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
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152 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
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153 .SH "DESCRIPTION"
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154 .IX Header "DESCRIPTION"
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155 Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for \fISDFile(s)\fR and create appropriate
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156 \&\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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157 .PP
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158 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
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159 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
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160 can be specified either by \fI*.sdf\fR or the current directory name.
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161 .PP
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162 The current release of MayaChemTools supports generation of extended connectivity fingerprints
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163 corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
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164 .PP
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165 .Vb 3
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166 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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167 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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168 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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169 .Ve
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170 .PP
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171 Based on values specified for \fB\-a, \-\-AtomIdentifierType\fR, \fB\-\-AtomicInvariantsToUse\fR
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172 and \fB\-\-FunctionalClassesToUse\fR, initial atom types are assigned to all non-hydrogen atoms in
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173 a molecule and these atom types strings are converted into initial atom identifier integers using
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174 \&\fBTextUtil::HashCode\fR function. The duplicate atom identifiers are removed.
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175 .PP
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176 For \fB\-n, \-\-NeighborhoodRadius\fR value of \fI0\fR, the initial set of unique atom identifiers comprises
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177 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
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178 atom up to specified \fB\-n, \-\-NeighborhoodRadius\fR value. For each non-hydrogen central atom
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179 at a specific radius, its neighbors at next radius level along with their bond orders and previously
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180 calculated atom identifiers are collected which in turn are used to generate a new integer
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181 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
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182 followed by atom identifiers to make these values graph invariant.
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183 .PP
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184 After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
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185 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
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186 value generated using \fBTextUtil::HashCode\fR are tracked by keeping the atom identifiers at
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187 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
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188 radius are also tracked by identifying equivalent atoms and bonds corresponding to substructures
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189 used for generating atom identifier and keeping integer atom identifier with lowest value.
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190 .PP
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191 For \fIExtendedConnnectivity\fR value of fingerprints \fB\-m, \-\-mode\fR, the duplicate identifiers are
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192 removed from the list and the unique atom identifiers constitute the extended connectivity
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193 fingerprints of a molecule.
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194 .PP
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195 For \fIExtendedConnnectivityCount\fR value of fingerprints \fB\-m, \-\-mode\fR, the occurrence of each
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196 unique atom identifiers appears is counted and the unique atom identifiers along with their
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197 count constitute the extended connectivity fingerprints of a molecule.
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198 .PP
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199 For \fIExtendedConnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, the unique atom identifiers
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200 are used as a random number seed to generate a random integer value between 0 and \fB\-\-Size\fR which
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201 in turn is used to set corresponding bits in the fingerprint bit-vector string.
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202 .PP
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203 Example of \fI\s-1SD\s0\fR file containing extended connectivity fingerprints string data:
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204 .PP
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205 .Vb 10
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206 \& ... ...
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207 \& ... ...
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208 \& $$$$
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209 \& ... ...
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210 \& ... ...
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211 \& ... ...
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212 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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213 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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214 \& ... ...
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215 \& 2 3 1 0 0 0 0
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216 \& ... ...
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217 \& M END
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218 \& > <CmpdID>
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219 \& Cmpd1
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220 \&
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221 \& > <ExtendedConnectivityFingerprints>
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222 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu
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223 \& s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66
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224 \& 6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087
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225 \& 99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90
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226 \& 6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853...
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227 \&
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228 \& $$$$
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229 \& ... ...
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230 \& ... ...
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231 .Ve
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232 .PP
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233 Example of \fI\s-1FP\s0\fR file containing extended connectivity fingerprints string data:
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234 .PP
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235 .Vb 10
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236 \& #
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237 \& # Package = MayaChemTools 7.4
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238 \& # Release Date = Oct 21, 2010
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239 \& #
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240 \& # TimeStamp = Fri Mar 11 14:43:57 2011
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241 \& #
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242 \& # FingerprintsStringType = FingerprintsVector
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243 \& #
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244 \& # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2
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245 \& # VectorStringFormat = ValuesString
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246 \& # VectorValuesType = AlphaNumericalValues
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247 \& #
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248 \& Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432...
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249 \& Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699...
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250 \& ... ...
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251 \& ... ..
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252 .Ve
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253 .PP
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254 Example of \s-1CSV\s0 \fIText\fR file containing extended connectivity fingerprints string data:
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255 .PP
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256 .Vb 8
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257 \& "CompoundID","ExtendedConnectivityFingerprints"
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258 \& "Cmpd1","FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy
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259 \& pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352
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260 \& 413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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261 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551
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262 \& 41035 906706094 988546669 1018231313 1032696425 1197507444 13312500..."
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263 \& ... ...
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264 \& ... ...
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265 .Ve
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266 .PP
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267 The current release of MayaChemTools generates the following types of extended connectivity
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268 fingerprints vector strings:
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269 .PP
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270 .Vb 6
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271 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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272 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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273 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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274 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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275 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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276 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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277 \&
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278 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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279 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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280 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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281 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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282 \& 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
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283 \& 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
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284 \&
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285 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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286 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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287 \& 0000000001010000000110000011000000000000100000000000000000000000100001
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288 \& 1000000110000000000000000000000000010011000000000000000000000000010000
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289 \& 0000000000000000000000000010000000000000000001000000000000000000000000
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290 \& 0000000000010000100001000000000000101000000000000000100000000000000...
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291 \&
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292 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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293 \& es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
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294 \& 0300000091000004000000020000100000000124008200020000000040020000000000
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295 \& 2080000000820040010020000000008040000000000080001000000000400000000000
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296 \& 4040000090000061010000000800200000000000001400000000020080000000000020
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297 \& 00008020200000408000
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298 \&
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299 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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300 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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301 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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302 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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303 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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|
|
304 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
|
|
305 \&
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|
|
306 \& FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
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|
|
307 \& Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
|
|
|
308 \& 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
|
|
|
309 \& 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
|
|
|
310 \& 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
|
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|
311 \& 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1
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|
312 \&
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313 \& FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
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|
|
314 \& s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
|
|
|
315 \& 0000000001000100000000001000000000000000000000000000000000101000000010
|
|
|
316 \& 0000001000000000010000000000000000000000000000000000000000000000000100
|
|
|
317 \& 0000000000001000000000000001000000000001001000000000000000000000000000
|
|
|
318 \& 0000000000000000100000000000001000000000000000000000000000000000000...
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|
|
319 \&
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|
|
320 \& FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
|
|
|
321 \& lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
|
|
|
322 \& 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
|
|
|
323 \& 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
|
|
|
324 \& 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
|
|
|
325 \& 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...
|
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|
326 \&
|
|
|
327 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
328 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
329 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
330 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
331 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
332 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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333 \&
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|
|
334 \& FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
|
|
|
335 \& haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
|
|
|
336 \& 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
|
|
|
337 \& 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
|
|
|
338 \& 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
|
|
|
339 \& 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...
|
|
|
340 \&
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|
|
341 \& FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
|
|
|
342 \& aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
|
|
|
343 \& 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
|
|
|
344 \& 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
|
|
|
345 \& 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
|
|
|
346 \& 41915747 679881756 721736571 794256218 908276640 992898760 10987549...
|
|
|
347 \&
|
|
|
348 \& FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
|
|
|
349 \& aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
|
|
|
350 \& 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
|
|
|
351 \& 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
|
|
|
352 \& 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
|
|
|
353 \& 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...
|
|
|
354 \&
|
|
|
355 \& FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
|
|
|
356 \& NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
|
|
|
357 \& 700688206 265614156 363161397 681332588 810600886 885767127 950172500
|
|
|
358 \& 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
|
|
|
359 \& 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
|
|
|
360 \& 654 256360355 279492740 291251259 317592700 333763396 972105960 101...
|
|
|
361 \&
|
|
|
362 \& FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
|
|
|
363 \& umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
|
|
|
364 \& 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
|
|
|
365 \& 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
|
|
|
366 \& 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
|
|
|
367 \& 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...
|
|
|
368 .Ve
|
|
|
369 .SH "OPTIONS"
|
|
|
370 .IX Header "OPTIONS"
|
|
|
371 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
|
|
|
372 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
|
|
|
373 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
374 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
375 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
376 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
|
|
|
377 .Sp
|
|
|
378 The supported aromaticity model names along with model specific control parameters
|
|
|
379 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
|
|
|
380 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
|
|
|
381 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
|
|
|
382 for detecting aromaticity corresponding to a specific model.
|
|
|
383 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
|
|
|
384 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
|
|
|
385 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
|
|
|
386 atoms during calculation of extended connectivity fingerprints [ Ref 48, Ref 52]. Possible values
|
|
|
387 in the current release are: \fIAtomicInvariantsAtomTypes, FunctionalClassAtomTypes,
|
|
|
388 DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
389 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
|
|
|
390 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
|
|
|
391 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
|
|
|
392 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
|
|
|
393 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
|
394 option. It's a list of comma separated valid atomic invariant atom types.
|
|
|
395 .Sp
|
|
|
396 Possible values for atomic invarians are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0,
|
|
|
397 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value [ Ref 24 ]: \fI\s-1AS\s0,X,BO,H,FC,MN\fR.
|
|
|
398 .Sp
|
|
|
399 The atomic invariants abbreviations correspond to:
|
|
|
400 .Sp
|
|
|
401 .Vb 1
|
|
|
402 \& AS = Atom symbol corresponding to element symbol
|
|
|
403 \&
|
|
|
404 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
|
|
|
405 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
|
|
|
406 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
|
|
|
407 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
|
408 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
|
409 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
|
|
|
410 \& H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
411 \& Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
412 \& RA = Ring atom annotation indicating whether atom is a ring
|
|
|
413 \& FC<+n/\-n> = Formal charge assigned to atom
|
|
|
414 \& MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
415 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
416 \& 3 (triplet)
|
|
|
417 .Ve
|
|
|
418 .Sp
|
|
|
419 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
420 .Sp
|
|
|
421 .Vb 1
|
|
|
422 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
|
|
|
423 .Ve
|
|
|
424 .Sp
|
|
|
425 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
426 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
427 .Sp
|
|
|
428 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
429 are also allowed:
|
|
|
430 .Sp
|
|
|
431 .Vb 12
|
|
|
432 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
433 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
434 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
435 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
436 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
437 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
438 \& H : NumOfImplicitAndExplicitHydrogens
|
|
|
439 \& Ar : Aromatic
|
|
|
440 \& RA : RingAtom
|
|
|
441 \& FC : FormalCharge
|
|
|
442 \& MN : MassNumber
|
|
|
443 \& SM : SpinMultiplicity
|
|
|
444 .Ve
|
|
|
445 .Sp
|
|
|
446 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
|
|
|
447 atom types.
|
|
|
448 .IP "\fB\-\-BitsOrder\fR \fIAscending | Descending\fR" 4
|
|
|
449 .IX Item "--BitsOrder Ascending | Descending"
|
|
|
450 Bits order to use during generation of fingerprints bit-vector string for \fIExtendedConnectivityBits\fR
|
|
|
451 value of \fB\-m, \-\-mode\fR option. Possible values: \fIAscending, Descending\fR. Default: \fIAscending\fR.
|
|
|
452 .Sp
|
|
|
453 \&\fIAscending\fR bit order which corresponds to first bit in each byte as the lowest bit as
|
|
|
454 opposed to the highest bit.
|
|
|
455 .Sp
|
|
|
456 Internally, bits are stored in \fIAscending\fR order using Perl vec function. Regardless
|
|
|
457 of machine order, big-endian or little-endian, vec function always considers first
|
|
|
458 string byte as the lowest byte and first bit within each byte as the lowest bit.
|
|
|
459 .IP "\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR" 4
|
|
|
460 .IX Item "-b, --BitStringFormat BinaryString | HexadecimalString"
|
|
|
461 Format of fingerprints bit-vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
|
|
|
462 \&\fB\-\-output\fR used during \fIExtendedConnectivityBits\fR value of \fB\-m, \-\-mode\fR option. Possible
|
|
|
463 values: \fIBinaryString, HexadecimalString\fR. Default value: \fIBinaryString\fR.
|
|
|
464 .Sp
|
|
|
465 \&\fIBinaryString\fR corresponds to an \s-1ASCII\s0 string containing 1s and 0s. \fIHexadecimalString\fR
|
|
|
466 contains bit values in \s-1ASCII\s0 hexadecimal format.
|
|
|
467 .Sp
|
|
|
468 Examples:
|
|
|
469 .Sp
|
|
|
470 .Vb 6
|
|
|
471 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
472 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
473 \& 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
474 \& 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
475 \& 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
476 \& 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
477 \&
|
|
|
478 \& FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
|
|
|
479 \& s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
|
|
|
480 \& 0000000001000100000000001000000000000000000000000000000000101000000010
|
|
|
481 \& 0000001000000000010000000000000000000000000000000000000000000000000100
|
|
|
482 \& 0000000000001000000000000001000000000001001000000000000000000000000000
|
|
|
483 \& 0000000000000000100000000000001000000000000000000000000000000000000...
|
|
|
484 .Ve
|
|
|
485 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
|
|
|
486 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
|
|
|
487 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
|
|
|
488 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
|
489 option. It's a list of comma separated valid functional classes.
|
|
|
490 .Sp
|
|
|
491 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.
|
|
|
492 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
|
|
|
493 .Sp
|
|
|
494 The functional class abbreviations correspond to:
|
|
|
495 .Sp
|
|
|
496 .Vb 9
|
|
|
497 \& HBD: HydrogenBondDonor
|
|
|
498 \& HBA: HydrogenBondAcceptor
|
|
|
499 \& PI : PositivelyIonizable
|
|
|
500 \& NI : NegativelyIonizable
|
|
|
501 \& Ar : Aromatic
|
|
|
502 \& Hal : Halogen
|
|
|
503 \& H : Hydrophobic
|
|
|
504 \& RA : RingAtom
|
|
|
505 \& CA : ChainAtom
|
|
|
506 \&
|
|
|
507 \& Functional class atom type specification for an atom corresponds to:
|
|
|
508 \&
|
|
|
509 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
510 .Ve
|
|
|
511 .Sp
|
|
|
512 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
|
513 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
|
514 .Sp
|
|
|
515 .Vb 4
|
|
|
516 \& HydrogenBondDonor: NH, NH2, OH
|
|
|
517 \& HydrogenBondAcceptor: N[!H], O
|
|
|
518 \& PositivelyIonizable: +, NH2
|
|
|
519 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
520 .Ve
|
|
|
521 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
|
|
|
522 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
|
|
|
523 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
|
|
|
524 .Sp
|
|
|
525 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
|
|
|
526 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
|
|
|
527 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
|
|
|
528 look like Cmpd<Number>.
|
|
|
529 .Sp
|
|
|
530 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
531 .Sp
|
|
|
532 .Vb 2
|
|
|
533 \& MolID
|
|
|
534 \& ExtReg
|
|
|
535 .Ve
|
|
|
536 .Sp
|
|
|
537 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
538 .Sp
|
|
|
539 .Vb 1
|
|
|
540 \& Compound
|
|
|
541 .Ve
|
|
|
542 .Sp
|
|
|
543 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
544 instead of default value of Cmpd<Number>.
|
|
|
545 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
|
|
|
546 .IX Item "--CompoundIDLabel text"
|
|
|
547 Specify compound \s-1ID\s0 column label for \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
|
|
|
548 of \fB\-\-DataFieldsMode\fR option. Default: \fICompoundID\fR.
|
|
|
549 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
|
|
|
550 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
|
|
|
551 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
|
|
|
552 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
|
|
|
553 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
|
|
|
554 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
555 .Sp
|
|
|
556 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
|
|
|
557 Default: \fILabelPrefix\fR.
|
|
|
558 .Sp
|
|
|
559 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
|
|
|
560 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
|
|
|
561 values are replaced with sequential compound IDs.
|
|
|
562 .Sp
|
|
|
563 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
564 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
|
|
|
565 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
|
|
|
566 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
|
|
|
567 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
|
|
|
568 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
|
|
|
569 .Sp
|
|
|
570 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
571 .Sp
|
|
|
572 Examples:
|
|
|
573 .Sp
|
|
|
574 .Vb 2
|
|
|
575 \& Extreg
|
|
|
576 \& MolID,CompoundName
|
|
|
577 .Ve
|
|
|
578 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
|
|
|
579 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
|
|
|
580 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
|
|
|
581 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
|
|
|
582 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
|
|
|
583 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
|
|
|
584 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
|
|
|
585 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
|
|
|
586 .IX Item "-f, --Filter Yes | No"
|
|
|
587 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
|
|
|
588 Default value: \fIYes\fR.
|
|
|
589 .Sp
|
|
|
590 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
591 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
592 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
593 .IX Item "--FingerprintsLabel text"
|
|
|
594 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
595 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIExtendedConnectivityFingerprints\fR.
|
|
|
596 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
597 .IX Item "-h, --help"
|
|
|
598 Print this help message.
|
|
|
599 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
|
|
600 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
601 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
602 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
603 .Sp
|
|
|
604 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
605 in two different ways: use all connected components or just the largest connected
|
|
|
606 component. By default, all atoms except for the largest connected component are
|
|
|
607 deleted before generation of fingerprints.
|
|
|
608 .IP "\fB\-m, \-\-mode\fR \fIExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits\fR" 4
|
|
|
609 .IX Item "-m, --mode ExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits"
|
|
|
610 Specify type of extended connectivity fingerprints to generate for molecules in \fISDFile(s)\fR.
|
|
|
611 Possible values: \fIExtendedConnectivity, ExtendedConnecticityCount or
|
|
|
612 ExtendedConnectivityBits\fR. Default value: \fIExtendedConnectivity\fR.
|
|
|
613 .Sp
|
|
|
614 For \fIExtendedConnnectivity\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint vector
|
|
|
615 containing unique atom identifiers constitute the extended connectivity fingerprints
|
|
|
616 of a molecule.
|
|
|
617 .Sp
|
|
|
618 For \fIExtendedConnnectivityCount\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint vector
|
|
|
619 containing unique atom identifiers along with their count constitute the extended connectivity
|
|
|
620 fingerprints of a molecule.
|
|
|
621 .Sp
|
|
|
622 For \fIExtendedConnnectivityBits\fR value of fingerprints \fB\-m, \-\-mode\fR, a fingerprint bit vector
|
|
|
623 indicating presence/absence of structurally unique atom identifiers constitute the extended
|
|
|
624 connectivity fingerprints of a molecule.
|
|
|
625 .IP "\fB\-n, \-\-NeighborhoodRadius\fR \fInumber\fR" 4
|
|
|
626 .IX Item "-n, --NeighborhoodRadius number"
|
|
|
627 Atomic neighborhood radius for generating extended connectivity neighborhoods. Default
|
|
|
628 value: \fI2\fR. Valid values: >= 0. Neighborhood radius of zero correspond to just the list
|
|
|
629 of non-hydrogen atoms.
|
|
|
630 .Sp
|
|
|
631 Default value of \fI2\fR for atomic neighborhood radius generates extended connectivity
|
|
|
632 fingerprints corresponding to path length or diameter value of \fI4\fR [ Ref 52b ].
|
|
|
633 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
634 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
635 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
|
|
636 Default value: \fIcomma\fR.
|
|
|
637 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
|
|
|
638 .IX Item "--output SD | FP | text | all"
|
|
|
639 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
|
|
|
640 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
641 .IX Item "-o, --overwrite"
|
|
|
642 Overwrite existing files.
|
|
|
643 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
|
|
|
644 .IX Item "-q, --quote Yes | No"
|
|
|
645 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
|
|
|
646 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
647 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
|
|
|
648 .IX Item "-r, --root RootName"
|
|
|
649 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
650 <SDFileName><ExtendedConnectivityFP>.<Ext>. The file type determines <Ext>
|
|
|
651 value. The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
|
|
|
652 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
653 .IP "\fB\-s, \-\-size\fR \fInumber\fR" 4
|
|
|
654 .IX Item "-s, --size number"
|
|
|
655 Size of bit-vector to use during generation of fingerprints bit-vector string for
|
|
|
656 \&\fIExtendedConnectivityBits\fR value of \fB\-m, \-\-mode\fR. Default value: \fI1024\fR.
|
|
|
657 Valid values correspond to any positive integer which satisfies the following criteria:
|
|
|
658 power of 2, >= 32 and <= 2 ** 32.
|
|
|
659 .Sp
|
|
|
660 Examples:
|
|
|
661 .Sp
|
|
|
662 .Vb 3
|
|
|
663 \& 512
|
|
|
664 \& 1024
|
|
|
665 \& 2048
|
|
|
666 .Ve
|
|
|
667 .IP "\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR" 4
|
|
|
668 .IX Item "--UsePerlCoreRandom Yes | No"
|
|
|
669 Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function
|
|
|
670 during random number generation for setting bits in fingerprints bit-vector strings. Possible
|
|
|
671 values: \fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
672 .Sp
|
|
|
673 \&\fINo\fR value option for \fB\-\-UsePerlCoreRandom\fR allows the generation of fingerprints
|
|
|
674 bit-vector strings which are same across different platforms.
|
|
|
675 .Sp
|
|
|
676 The random number generator implemented in MayaChemTools is a variant of
|
|
|
677 linear congruential generator (\s-1LCG\s0) as described by Miller et al. [ Ref 120 ].
|
|
|
678 It is also referred to as Lehmer random number generator or Park-Miller
|
|
|
679 random number generator.
|
|
|
680 .Sp
|
|
|
681 Unlike Perl's core random number generator function rand, the random number
|
|
|
682 generator implemented in MayaChemTools, MathUtil::random, generates consistent
|
|
|
683 random values across different platforms for a specific random seed and leads
|
|
|
684 to generation of portable fingerprints bit-vector strings.
|
|
|
685 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
|
|
|
686 .IX Item "-v, --VectorStringFormat ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
|
|
|
687 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
|
|
|
688 \&\fB\-\-output\fR used during <ExtendedConnectivityCount> value of \fB\-m, \-\-mode\fR option. Possible
|
|
|
689 values: \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
690 ValuesAndIDsPairsString\fR.
|
|
|
691 .Sp
|
|
|
692 Default value during <ExtendedConnectivityCount> value of \fB\-m, \-\-mode\fR option:
|
|
|
693 \&\fIIDsAndValuesString\fR.
|
|
|
694 .Sp
|
|
|
695 Default value during <ExtendedConnectivity> value of \fB\-m, \-\-mode\fR option: \fIValuesString\fR.
|
|
|
696 .Sp
|
|
|
697 Examples:
|
|
|
698 .Sp
|
|
|
699 .Vb 6
|
|
|
700 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
701 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
702 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
703 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
704 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
705 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
706 \&
|
|
|
707 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
708 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
709 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
710 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
711 \& 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
|
|
|
712 \& 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
|
|
|
713 .Ve
|
|
|
714 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
|
|
|
715 .IX Item "-w, --WorkingDir DirName"
|
|
|
716 Location of working directory. Default: current directory.
|
|
|
717 .SH "EXAMPLES"
|
|
|
718 .IX Header "EXAMPLES"
|
|
|
719 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
720 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
721 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
722 .PP
|
|
|
723 .Vb 1
|
|
|
724 \& % ExtendedConnectivityFingerprints.pl \-r SampleECAIFP \-o Sample.sdf
|
|
|
725 .Ve
|
|
|
726 .PP
|
|
|
727 To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
|
|
|
728 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
729 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
730 .PP
|
|
|
731 .Vb 2
|
|
|
732 \& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityCount
|
|
|
733 \& \-r SampleECAIFP \-o Sample.sdf
|
|
|
734 .Ve
|
|
|
735 .PP
|
|
|
736 To generate extended connectivity bits fingerprints as hexadecimal bit-string corresponding to
|
|
|
737 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
|
|
|
738 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
|
|
|
739 vector strings data, type:
|
|
|
740 .PP
|
|
|
741 .Vb 2
|
|
|
742 \& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityBits
|
|
|
743 \& \-r SampleECAIFP \-o Sample.sdf
|
|
|
744 .Ve
|
|
|
745 .PP
|
|
|
746 To generate extended connectivity bits fingerprints as binary bit-string corresponding to
|
|
|
747 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
|
|
|
748 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
|
|
|
749 vector strings data, type:
|
|
|
750 .PP
|
|
|
751 .Vb 2
|
|
|
752 \& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityBits
|
|
|
753 \& \-\-BitStringFormat BinaryString \-r SampleECAIFP \-o Sample.sdf
|
|
|
754 .Ve
|
|
|
755 .PP
|
|
|
756 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
757 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
|
|
|
758 and SampleECAIFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along with fingerprints
|
|
|
759 vector strings data, type:
|
|
|
760 .PP
|
|
|
761 .Vb 2
|
|
|
762 \& % ExtendedConnectivityFingerprints.pl \-\-output all \-r SampleECAIFP
|
|
|
763 \& \-o Sample.sdf
|
|
|
764 .Ve
|
|
|
765 .PP
|
|
|
766 To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
|
|
|
767 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
|
|
|
768 and SampleECAIFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along with fingerprints
|
|
|
769 vector strings data, type:
|
|
|
770 .PP
|
|
|
771 .Vb 2
|
|
|
772 \& % ExtendedConnectivityFingerprints.pl \-m ExtendedConnectivityCount
|
|
|
773 \& \-\-output all \-r SampleECAIFP \-o Sample.sdf
|
|
|
774 .Ve
|
|
|
775 .PP
|
|
|
776 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
777 2 using functional class atom types in vector string format and create a SampleECFCFP.csv file
|
|
|
778 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
779 .PP
|
|
|
780 .Vb 2
|
|
|
781 \& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
|
|
|
782 \& \-r SampleECFCFP \-o Sample.sdf
|
|
|
783 .Ve
|
|
|
784 .PP
|
|
|
785 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
786 2 using \s-1DREIDING\s0 atom types in vector string format and create a SampleECFP.csv file
|
|
|
787 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
788 .PP
|
|
|
789 .Vb 2
|
|
|
790 \& % ExtendedConnectivityFingerprints.pl \-a DREIDINGAtomTypes
|
|
|
791 \& \-r SampleECFP \-o Sample.sdf
|
|
|
792 .Ve
|
|
|
793 .PP
|
|
|
794 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
795 2 using E\-state atom types in vector string format and create a SampleECFP.csv file
|
|
|
796 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
797 .PP
|
|
|
798 .Vb 2
|
|
|
799 \& % ExtendedConnectivityFingerprints.pl \-a EStateAtomTypes
|
|
|
800 \& \-r SampleECFP \-o Sample.sdf
|
|
|
801 .Ve
|
|
|
802 .PP
|
|
|
803 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
804 2 using \s-1MMFF94\s0 atom types in vector string format and create a SampleECFP.csv file
|
|
|
805 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
806 .PP
|
|
|
807 .Vb 2
|
|
|
808 \& % ExtendedConnectivityFingerprints.pl \-a MMFF94AtomTypes
|
|
|
809 \& \-r SampleECFP \-o Sample.sdf
|
|
|
810 .Ve
|
|
|
811 .PP
|
|
|
812 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
813 2 using SLogP atom types in vector string format and create a SampleECFP.csv file
|
|
|
814 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
815 .PP
|
|
|
816 .Vb 2
|
|
|
817 \& % ExtendedConnectivityFingerprints.pl \-a SLogPAtomTypes
|
|
|
818 \& \-r SampleECFP \-o Sample.sdf
|
|
|
819 .Ve
|
|
|
820 .PP
|
|
|
821 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
822 2 using \s-1SYBYL\s0 atom types in vector string format and create a SampleECFP.csv file
|
|
|
823 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
824 .PP
|
|
|
825 .Vb 2
|
|
|
826 \& % ExtendedConnectivityFingerprints.pl \-a SYBYLAtomTypes
|
|
|
827 \& \-r SampleECFP \-o Sample.sdf
|
|
|
828 .Ve
|
|
|
829 .PP
|
|
|
830 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
831 2 using \s-1TPSA\s0 atom types in vector string format and create a SampleECFP.csv file
|
|
|
832 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
833 .PP
|
|
|
834 .Vb 2
|
|
|
835 \& % ExtendedConnectivityFingerprints.pl \-a TPSAAtomTypes
|
|
|
836 \& \-r SampleECFP \-o Sample.sdf
|
|
|
837 .Ve
|
|
|
838 .PP
|
|
|
839 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
840 2 using \s-1UFF\s0 atom types in vector string format and create a SampleECFP.csv file
|
|
|
841 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
842 .PP
|
|
|
843 .Vb 2
|
|
|
844 \& % ExtendedConnectivityFingerprints.pl \-a UFFAtomTypes
|
|
|
845 \& \-r SampleECFP \-o Sample.sdf
|
|
|
846 .Ve
|
|
|
847 .PP
|
|
|
848 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
849 3 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
850 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
851 .PP
|
|
|
852 .Vb 2
|
|
|
853 \& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes \-n 3
|
|
|
854 \& \-r SampleECAIFP \-o Sample.sdf
|
|
|
855 .Ve
|
|
|
856 .PP
|
|
|
857 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
858 3 using functional class atom types in vector string format and create a SampleECFCFP.csv file
|
|
|
859 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
860 .PP
|
|
|
861 .Vb 2
|
|
|
862 \& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes \-n 3
|
|
|
863 \& \-r SampleECFCFP \-o Sample.sdf
|
|
|
864 .Ve
|
|
|
865 .PP
|
|
|
866 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
867 2 using only \s-1AS\s0,X atomic invariants atom types in vector string format and create a
|
|
|
868 SampleECAIFP.csv file containing sequential compound IDs along with fingerprints vector
|
|
|
869 strings data, type:
|
|
|
870 .PP
|
|
|
871 .Vb 2
|
|
|
872 \& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
|
|
|
873 \& \-\-AtomicInvariantsToUse "AS,X" \-r SampleECAIFP \-o Sample.sdf
|
|
|
874 .Ve
|
|
|
875 .PP
|
|
|
876 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
877 2 using only \s-1HBD\s0,HBA functional class atom types in vector string format and create a
|
|
|
878 SampleECFCFP.csv file containing sequential compound IDs along with fingerprints vector
|
|
|
879 strings data, type:
|
|
|
880 .PP
|
|
|
881 .Vb 2
|
|
|
882 \& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
|
|
|
883 \& \-\-FunctionalClassesToUse "HBD,HBA" \-r SampleECFCFP \-o Sample.sdf
|
|
|
884 .Ve
|
|
|
885 .PP
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886 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
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887 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
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888 file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings
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889 data, type:
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890 .PP
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891 .Vb 3
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892 \& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
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893 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
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894 \& \-r SampleECAIFP \-o Sample.sdf
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895 .Ve
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896 .PP
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897 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
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898 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
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899 file containing compound IDs using specified data field along with fingerprints vector strings
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900 data, type:
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901 .PP
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902 .Vb 3
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903 \& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
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904 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID Mol_ID
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905 \& \-r SampleECFCFP \-o Sample.sdf
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906 .Ve
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907 .PP
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908 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
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909 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
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910 file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
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911 prefix along with fingerprints vector strings data, type:
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912 .PP
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913 .Vb 3
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914 \& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
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915 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
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916 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleECAIFP \-o Sample.sdf
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917 .Ve
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918 .PP
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919 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
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920 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
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921 file containing specific data fields columns along with fingerprints vector strings
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922 data, type:
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923 .PP
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924 .Vb 3
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925 \& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
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926 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleECFCFP
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927 \& \-o Sample.sdf
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928 .Ve
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929 .PP
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930 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
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931 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
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932 file containing common data fields columns along with fingerprints vector strings data, type:
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933 .PP
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934 .Vb 2
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935 \& % ExtendedConnectivityFingerprints.pl \-a AtomicInvariantsAtomTypes
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936 \& \-\-DataFieldsMode Common \-r SampleECAIFP \-o Sample.sdf
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937 .Ve
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938 .PP
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939 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
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940 2 using functional class atom types in vector string format and create SampleECFCFP.sdf, SampleECFCFP.fpf
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941 and SampleECFCFP.csv files containing all data fields columns in \s-1CSV\s0 file along with fingerprints
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942 vector strings data, type:
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943 .PP
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944 .Vb 3
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945 \& % ExtendedConnectivityFingerprints.pl \-a FunctionalClassAtomTypes
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946 \& \-\-DataFieldsMode All \-\-output all \-r SampleECFCFP
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947 \& \-o Sample.sdf
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948 .Ve
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949 .SH "AUTHOR"
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950 .IX Header "AUTHOR"
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951 Manish Sud <msud@san.rr.com>
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952 .SH "SEE ALSO"
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953 .IX Header "SEE ALSO"
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954 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
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955 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
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956 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
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957 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
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958 .SH "COPYRIGHT"
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959 .IX Header "COPYRIGHT"
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960 Copyright (C) 2015 Manish Sud. All rights reserved.
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961 .PP
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962 This file is part of MayaChemTools.
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963 .PP
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964 MayaChemTools is free software; you can redistribute it and/or modify it under
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965 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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966 Software Foundation; either version 3 of the License, or (at your option)
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967 any later version.
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