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124 .\" ========================================================================
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125 .\"
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126 .IX Title "PATHLENGTHFINGERPRINTS 1"
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127 .TH PATHLENGTHFINGERPRINTS 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 PathLengthFingerprints.pl \- Generate atom path length based fingerprints for SD files
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 PathLengthFingerprints.pl SDFile(s)...
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137 .PP
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138 PathLengthFingerprints.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"AtomicInvariant1,AtomicInvariant2...\*(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 \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR]
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145 [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,... \*(R"\fR] [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR]
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146 [\fB\-\-DetectAromaticity\fR \fIYes | No\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR]
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147 [\fB\-\-fold\fR \fIYes | No\fR] [\fB\-\-FoldedSize\fR \fInumber\fR] [\fB\-h, \-\-help\fR]
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148 [\fB\-i, \-\-IgnoreHydrogens\fR \fIYes | No\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR]
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149 [\fB\-m, \-\-mode\fR \fIPathLengthBits | PathLengthCount\fR]
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150 [\fB\-\-MinPathLength\fR \fInumber\fR] [\fB\-\-MaxPathLength\fR \fInumber\fR] [\fB\-n, \-\-NumOfBitsToSetPerPath\fR \fInumber\fR]
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151 [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR]
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152 [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR]
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153 [\fB\-p, \-\-PathMode\fR \fIAtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings\fR]
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154 [\fB\-s, \-\-size\fR \fInumber\fR] [\fB\-u, \-\-UseBondSymbols\fR \fIYes | No\fR] [\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR]
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155 [\fB\-\-UseUniquePaths\fR \fIYes | No\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR]
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156 [\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
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157 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
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158 .SH "DESCRIPTION"
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159 .IX Header "DESCRIPTION"
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160 Generate atom path length fingerprints for \fISDFile(s)\fR and create appropriate \s-1SD\s0, \s-1FP\s0 or
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161 \&\s-1CSV/TSV\s0 text file(s) containing fingerprints bit-vector or vector strings corresponding to
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162 molecular fingerprints.
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163 .PP
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164 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
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165 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
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166 can be specified either by \fI*.sdf\fR or the current directory name.
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167 .PP
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168 The current release of MayaChemTools supports generation of path length fingerprints
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169 corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
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170 .PP
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171 .Vb 3
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172 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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173 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
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174 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
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175 .Ve
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176 .PP
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177 Based on the values specified for \fB\-p, \-\-PathMode\fR, \fB\-\-MinPathLength\fR and \fB\-\-MaxPathLength\fR,
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178 all appropriate atom paths are generated for each atom in the molecule and collected in a list and
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179 the list is filtered to remove any structurally duplicate paths as indicated by the value of
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180 \&\fB\-\-UseUniquePaths\fR option.
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181 .PP
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182 For each atom path in the filtered atom paths list, an atom path string is created using value of
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183 \&\fB\-a, \-\-AtomIdentifierType\fR and specified values to use for a particular atom identifier type.
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184 Value of \fB\-u, \-\-UseBondSymbols\fR controls whether bond order symbols are used during generation
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185 of atom path string. For each atom path, only lexicographically smaller atom path strings are kept.
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186 .PP
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187 For \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option, each atom path is hashed to a 32 bit unsigned
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188 integer key using \fBTextUtil::HashCode\fR function. Using the hash key as a seed for a random number
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189 generator, a random integer value between 0 and \fB\-\-Size\fR is used to set corresponding bits
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190 in the fingerprint bit-vector string. Value of \fB\-\-NumOfBitsToSetPerPath\fR option controls the number
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191 of time a random number is generated to set corresponding bits.
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192 .PP
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193 For \fI PathLengthCount\fR value of \fB\-m, \-\-mode\fR option, the number of times an atom path appears
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194 is tracked and a fingerprints count-string corresponding to count of atom paths is generated.
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195 .PP
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196 Example of \fI\s-1SD\s0\fR file containing path length 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 \& $$$$
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202 \& ... ...
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203 \& ... ...
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204 \& ... ...
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205 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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206 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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207 \& ... ...
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208 \& 2 3 1 0 0 0 0
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209 \& ... ...
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210 \& M END
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211 \& > <CmpdID>
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212 \& Cmpd1
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213 \&
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214 \& > <PathLengthFingerprints>
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215 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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216 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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217 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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218 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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219 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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220 \& aa0660a11014a011d46
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221 \&
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222 \& $$$$
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223 \& ... ...
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224 \& ... ...
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225 .Ve
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226 .PP
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227 Example of \fI\s-1FP\s0\fR file containing path length fingerprints string data:
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228 .PP
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229 .Vb 10
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230 \& #
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231 \& # Package = MayaChemTools 7.4
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232 \& # ReleaseDate = Oct 21, 2010
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233 \& #
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234 \& # TimeStamp = Mon Mar 7 15:14:01 2011
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235 \& #
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236 \& # FingerprintsStringType = FingerprintsBitVector
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237 \& #
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238 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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239 \& # Size = 1024
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240 \& # BitStringFormat = HexadecimalString
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241 \& # BitsOrder = Ascending
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242 \& #
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243 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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244 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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245 \& ... ...
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246 \& ... ..
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247 .Ve
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248 .PP
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249 Example of \s-1CSV\s0 \fIText\fR file containing pathlength fingerprints string data:
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250 .PP
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251 .Vb 7
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252 \& "CompoundID","PathLengthFingerprints"
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253 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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254 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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255 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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256 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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257 \& ... ...
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258 \& ... ...
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259 .Ve
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260 .PP
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261 The current release of MayaChemTools generates the following types of path length
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262 fingerprints bit-vector and vector strings:
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263 .PP
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264 .Vb 6
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265 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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266 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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267 \& 0100010101011000101001011100110001000010001001101000001001001001001000
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268 \& 0010110100000111001001000001001010100100100000000011000000101001011100
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269 \& 0010000001000101010100000100111100110111011011011000000010110111001101
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270 \& 0101100011000000010001000011000010100011101100001000001000100000000...
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271 \&
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272 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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273 \& th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
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274 \& 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
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275 \& 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
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276 \& 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
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277 \& 6ea05280140069c780290c43
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278 \&
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279 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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280 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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281 \& C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
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282 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
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283 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
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284 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
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285 \&
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286 \& FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen
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287 \& gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_
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288 \& 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3
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289 \& 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C
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290 \& _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C
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291 \& _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ...
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292 \&
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293 \& FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
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294 \& h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
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295 \& O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
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296 \& aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
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297 \& 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
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298 \& sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
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299 \&
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300 \& FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1
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301 \& :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1
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302 \& HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar:
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303 \& Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI
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304 \& 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr
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305 \& 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...
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306 \&
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307 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
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308 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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309 \& 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
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310 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
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311 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
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312 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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313 \&
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314 \& FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength
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315 \& 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C
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316 \& 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1
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317 \& 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18
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318 \& :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1
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319 \& C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...
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320 \&
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321 \& FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength
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322 \& 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1
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323 \& N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C.
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324 \& ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C
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325 \& .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C
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326 \& .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3...
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327 \&
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328 \& FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8
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329 \& ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O
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330 \& 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N
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331 \& oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N
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332 \& one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20
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333 \& None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...
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334 \&
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335 \& FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8;
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336 \& 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_
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337 \& 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_
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338 \& 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_
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339 \& 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3
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340 \& 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3...
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341 .Ve
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342 .SH "OPTIONS"
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343 .IX Header "OPTIONS"
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344 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
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345 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
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346 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
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347 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
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348 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
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349 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
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350 .Sp
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351 The supported aromaticity model names along with model specific control parameters
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|
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352 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
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353 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
|
|
|
354 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
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355 for detecting aromaticity corresponding to a specific model.
|
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356 .Sp
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357 This option is ignored during \fINo\fR value of \fB\-\-DetectAromaticity\fR option.
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358 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
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359 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
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360 Specify atom identifier type to use for assignment of atom types to hydrogen and/or
|
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|
361 non-hydrogen atoms during calculation of atom types fingerprints. Possible values in the
|
|
|
362 current release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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|
|
363 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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|
|
364 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
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|
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365 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
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366 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
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367 Specify atom identifier type to use during generation of atom path strings
|
|
|
368 corresponding to path length fingerprints. Possible values in the current release are:
|
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|
369 \&\fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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|
370 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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|
371 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
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372 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant1,AtomicInvariant2...""\fR" 4
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373 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant1,AtomicInvariant2...''\fR" 4
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374 .IX Item "--AtomicInvariantsToUse AtomicInvariant1,AtomicInvariant2..."
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375 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
|
376 option. It's a list of comma separated valid atomic invariant atom types.
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|
|
377 .Sp
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378 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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379 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0\fR.
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380 .Sp
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381 The atomic invariants abbreviations correspond to:
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382 .Sp
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383 .Vb 1
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384 \& AS = Atom symbol corresponding to element symbol
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385 \&
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386 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
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387 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
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388 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
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|
|
389 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
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|
390 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
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391 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
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|
392 \& H<n> = Number of implicit and explicit hydrogens for atom
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|
|
393 \& Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
394 \& RA = Ring atom annotation indicating whether atom is a ring
|
|
|
395 \& FC<+n/\-n> = Formal charge assigned to atom
|
|
|
396 \& MN<n> = Mass number indicating isotope other than most abundant isotope
|
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|
397 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
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398 \& 3 (triplet)
|
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399 .Ve
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400 .Sp
|
|
|
401 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
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402 .Sp
|
|
|
403 .Vb 1
|
|
|
404 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
|
|
|
405 .Ve
|
|
|
406 .Sp
|
|
|
407 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
408 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
409 .Sp
|
|
|
410 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
411 are also allowed:
|
|
|
412 .Sp
|
|
|
413 .Vb 12
|
|
|
414 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
415 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
416 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
417 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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|
|
418 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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419 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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420 \& H : NumOfImplicitAndExplicitHydrogens
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|
421 \& Ar : Aromatic
|
|
|
422 \& RA : RingAtom
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|
423 \& FC : FormalCharge
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424 \& MN : MassNumber
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|
425 \& SM : SpinMultiplicity
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426 .Ve
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427 .Sp
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|
|
428 Examples:
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|
|
429 .Sp
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|
430 \&\fBBenzene\fR: Using value of \fI\s-1AS\s0\fR for \fB\-\-AtomicInvariantsToUse\fR, \fIYes\fR for \fBUseBondSymbols\fR,
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|
|
431 and \fI AllAtomPathsWithRings\fR for \fB\-p, \-\-PathMode\fR, atom path strings generated are:
|
|
|
432 .Sp
|
|
|
433 .Vb 1
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|
|
434 \& C C:C C:C:C C:C:C:C C:C:C:C:C C:C:C:C:C:C C:C:C:C:C:C:C
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|
|
435 .Ve
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|
|
436 .Sp
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|
|
437 And using \fI\s-1AS\s0,X,BO\fR for \fB\-\-AtomicInvariantsToUse\fR generates following atom path
|
|
|
438 strings:
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|
439 .Sp
|
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|
440 .Vb 5
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|
441 \& C.X2.BO3 C.X2.BO3:C.X2.BO3 C.X2.BO3:C.X2.BO3:C.X2.BO3
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|
|
442 \& C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
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443 \& C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
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|
444 \& C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
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445 \& C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
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|
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446 .Ve
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|
447 .Sp
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|
448 \&\fBUrea\fR: Using value of \fI\s-1AS\s0\fR for \fB\-\-AtomicInvariantsToUse\fR, \fIYes\fR for \fBUseBondSymbols\fR,
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|
|
449 and \fI AllAtomPathsWithRings\fR for \fB\-p, \-\-PathMode\fR, atom path strings are:
|
|
|
450 .Sp
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|
|
451 .Vb 1
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452 \& C N O C=O CN NC=O NCN
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453 .Ve
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454 .Sp
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|
|
455 And using \fI\s-1AS\s0,X,BO\fR for \fB\-\-AtomicInvariantsToUse\fR generates following atom path
|
|
|
456 strings:
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|
457 .Sp
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|
458 .Vb 3
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|
459 \& C.X3.BO4 N.X1.BO1 O.X1.BO2 C.X3.BO4=O.X1.BO2
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|
|
460 \& C.X3.BO4N.X1.BO1 N.X1.BO1C.X3.BO4=O.X1.BO2
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461 \& N.X1.BO1C.X3.BO4N.X1.BO1
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462 .Ve
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463 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
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|
464 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
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|
|
465 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
|
|
|
466 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
|
|
|
467 option. It's a list of comma separated valid functional classes.
|
|
|
468 .Sp
|
|
|
469 Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
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|
470 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
|
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|
471 .Sp
|
|
|
472 The functional class abbreviations correspond to:
|
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|
473 .Sp
|
|
|
474 .Vb 9
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|
|
475 \& HBD: HydrogenBondDonor
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|
|
476 \& HBA: HydrogenBondAcceptor
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|
|
477 \& PI : PositivelyIonizable
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|
|
478 \& NI : NegativelyIonizable
|
|
|
479 \& Ar : Aromatic
|
|
|
480 \& Hal : Halogen
|
|
|
481 \& H : Hydrophobic
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|
|
482 \& RA : RingAtom
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|
|
483 \& CA : ChainAtom
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|
|
484 \&
|
|
|
485 \& Functional class atom type specification for an atom corresponds to:
|
|
|
486 \&
|
|
|
487 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
488 .Ve
|
|
|
489 .Sp
|
|
|
490 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
|
|
|
491 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
|
|
|
492 .Sp
|
|
|
493 .Vb 4
|
|
|
494 \& HydrogenBondDonor: NH, NH2, OH
|
|
|
495 \& HydrogenBondAcceptor: N[!H], O
|
|
|
496 \& PositivelyIonizable: +, NH2
|
|
|
497 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
498 .Ve
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|
|
499 .IP "\fB\-\-BitsOrder\fR \fIAscending | Descending\fR" 4
|
|
|
500 .IX Item "--BitsOrder Ascending | Descending"
|
|
|
501 Bits order to use during generation of fingerprints bit-vector string for \fIPathLengthBits\fR value of
|
|
|
502 \&\fB\-m, \-\-mode\fR option. Possible values: \fIAscending, Descending\fR. Default: \fIAscending\fR.
|
|
|
503 .Sp
|
|
|
504 \&\fIAscending\fR bit order which corresponds to first bit in each byte as the lowest bit as
|
|
|
505 opposed to the highest bit.
|
|
|
506 .Sp
|
|
|
507 Internally, bits are stored in \fIAscending\fR order using Perl vec function. Regardless
|
|
|
508 of machine order, big-endian or little-endian, vec function always considers first
|
|
|
509 string byte as the lowest byte and first bit within each byte as the lowest bit.
|
|
|
510 .IP "\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR" 4
|
|
|
511 .IX Item "-b, --BitStringFormat BinaryString | HexadecimalString"
|
|
|
512 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
|
|
|
513 \&\fB\-\-output\fR used during \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option. Possible
|
|
|
514 values: \fIBinaryString, HexadecimalString\fR. Default value: \fIHexadecimalString\fR.
|
|
|
515 .Sp
|
|
|
516 \&\fIBinaryString\fR corresponds to an \s-1ASCII\s0 string containing 1s and 0s. \fIHexadecimalString\fR
|
|
|
517 contains bit values in \s-1ASCII\s0 hexadecimal format.
|
|
|
518 .Sp
|
|
|
519 Examples:
|
|
|
520 .Sp
|
|
|
521 .Vb 6
|
|
|
522 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
523 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
524 \& 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
525 \& 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
526 \& 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
527 \& 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
528 \&
|
|
|
529 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
530 \& th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
|
|
|
531 \& 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
|
|
|
532 \& 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
|
|
|
533 \& 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
|
|
|
534 \& 6ea05280140069c780290c43
|
|
|
535 .Ve
|
|
|
536 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
|
|
|
537 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
|
|
|
538 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
|
|
|
539 .Sp
|
|
|
540 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
|
|
|
541 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
|
|
|
542 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
|
|
|
543 look like Cmpd<Number>.
|
|
|
544 .Sp
|
|
|
545 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
546 .Sp
|
|
|
547 .Vb 2
|
|
|
548 \& MolID
|
|
|
549 \& ExtReg
|
|
|
550 .Ve
|
|
|
551 .Sp
|
|
|
552 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
|
|
|
553 .Sp
|
|
|
554 .Vb 1
|
|
|
555 \& Compound
|
|
|
556 .Ve
|
|
|
557 .Sp
|
|
|
558 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
559 instead of default value of Cmpd<Number>.
|
|
|
560 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
|
|
|
561 .IX Item "--CompoundIDLabel text"
|
|
|
562 Specify compound \s-1ID\s0 column label for \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
|
|
|
563 of \fB\-\-DataFieldsMode\fR option. Default: \fICompoundID\fR.
|
|
|
564 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
|
|
|
565 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
|
|
|
566 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
|
|
|
567 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
|
|
|
568 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
|
|
|
569 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
570 .Sp
|
|
|
571 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
|
|
|
572 Default: \fILabelPrefix\fR.
|
|
|
573 .Sp
|
|
|
574 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
|
|
|
575 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
|
|
|
576 values are replaced with sequential compound IDs.
|
|
|
577 .Sp
|
|
|
578 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
579 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,... ""\fR" 4
|
|
|
580 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,... ''\fR" 4
|
|
|
581 .IX Item "--DataFields FieldLabel1,FieldLabel2,... "
|
|
|
582 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
|
|
|
583 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
|
|
|
584 .Sp
|
|
|
585 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
|
|
|
586 .Sp
|
|
|
587 Examples:
|
|
|
588 .Sp
|
|
|
589 .Vb 2
|
|
|
590 \& Extreg
|
|
|
591 \& MolID,CompoundName
|
|
|
592 .Ve
|
|
|
593 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
|
|
|
594 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
|
|
|
595 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
|
|
|
596 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
|
|
|
597 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
|
|
|
598 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
|
|
|
599 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
|
|
|
600 .IP "\fB\-\-DetectAromaticity\fR \fIYes | No\fR" 4
|
|
|
601 .IX Item "--DetectAromaticity Yes | No"
|
|
|
602 Detect aromaticity before generating fingerprints. Possible values: \fIYes or No\fR.
|
|
|
603 Default value: \fIYes\fR.
|
|
|
604 .Sp
|
|
|
605 \&\fINo\fR \fB\-\-DetectAromaticity\fR forces usage of atom and bond aromaticity values
|
|
|
606 from \fISDFile(s)\fR and skips the step which detects and assigns aromaticity.
|
|
|
607 .Sp
|
|
|
608 \&\fINo\fR \fB\-\-DetectAromaticity\fR value is only allowed uring \fIAtomicInvariantsAtomTypes\fR
|
|
|
609 value of \fB\-a, \-\-AtomIdentifierType\fR options; for all possible values \fB\-a, \-\-AtomIdentifierType\fR
|
|
|
610 values, it must be \fIYes\fR.
|
|
|
611 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
|
|
|
612 .IX Item "-f, --Filter Yes | No"
|
|
|
613 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
|
|
|
614 Default value: \fIYes\fR.
|
|
|
615 .Sp
|
|
|
616 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
617 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
618 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
|
|
|
619 .IX Item "--FingerprintsLabel text"
|
|
|
620 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
|
|
|
621 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIPathLenghFingerprints\fR.
|
|
|
622 .IP "\fB\-\-fold\fR \fIYes | No\fR" 4
|
|
|
623 .IX Item "--fold Yes | No"
|
|
|
624 Fold fingerprints to increase bit density during \fIPathLengthBits\fR value of
|
|
|
625 \&\fB\-m, \-\-mode\fR option. Possible values: \fIYes or No\fR. Default value: \fINo\fR.
|
|
|
626 .IP "\fB\-\-FoldedSize\fR \fInumber\fR" 4
|
|
|
627 .IX Item "--FoldedSize number"
|
|
|
628 Size of folded fingerprint during \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option. Default
|
|
|
629 value: \fI256\fR. Valid values correspond to any positive integer which is less than
|
|
|
630 \&\fB\-s, \-\-size\fR and meets the criteria for its value.
|
|
|
631 .Sp
|
|
|
632 Examples:
|
|
|
633 .Sp
|
|
|
634 .Vb 2
|
|
|
635 \& 128
|
|
|
636 \& 512
|
|
|
637 .Ve
|
|
|
638 .IP "\fB\-h, \-\-help\fR" 4
|
|
|
639 .IX Item "-h, --help"
|
|
|
640 Print this help message
|
|
|
641 .IP "\fB\-i, \-\-IgnoreHydrogens\fR \fIYes | No\fR" 4
|
|
|
642 .IX Item "-i, --IgnoreHydrogens Yes | No"
|
|
|
643 Ignore hydrogens during fingerprints generation. Possible values: \fIYes or No\fR.
|
|
|
644 Default value: \fIYes\fR.
|
|
|
645 .Sp
|
|
|
646 For \fIyes\fR value of \fB\-i, \-\-IgnoreHydrogens\fR, any explicit hydrogens are also used for
|
|
|
647 generation of atoms path lengths and fingerprints; implicit hydrogens are still ignored.
|
|
|
648 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
|
|
|
649 .IX Item "-k, --KeepLargestComponent Yes | No"
|
|
|
650 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
651 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
652 .Sp
|
|
|
653 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
654 in two different ways: use all connected components or just the largest connected
|
|
|
655 component. By default, all atoms except for the largest connected component are
|
|
|
656 deleted before generation of fingerprints.
|
|
|
657 .IP "\fB\-m, \-\-mode\fR \fIPathLengthBits | PathLengthCount\fR" 4
|
|
|
658 .IX Item "-m, --mode PathLengthBits | PathLengthCount"
|
|
|
659 Specify type of path length fingerprints to generate for molecules in \fISDFile(s)\fR. Possible
|
|
|
660 values: \fIPathLengthBits, PathLengthCount\fR. Default value: \fIPathLengthBits\fR.
|
|
|
661 .Sp
|
|
|
662 For \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option, a fingerprint bit-vector string containing
|
|
|
663 zeros and ones is generated and for \fIPathLengthCount\fR value, a fingerprint vector string
|
|
|
664 corresponding to number of atom paths is generated.
|
|
|
665 .IP "\fB\-\-MinPathLength\fR \fInumber\fR" 4
|
|
|
666 .IX Item "--MinPathLength number"
|
|
|
667 Minimum atom path length to include in fingerprints. Default value: \fI1\fR. Valid values:
|
|
|
668 positive integers and less than \fB\-\-MaxPathLength\fR. Path length of 1 correspond to
|
|
|
669 a path containing only one atom.
|
|
|
670 .IP "\fB\-\-MaxPathLength\fR \fInumber\fR" 4
|
|
|
671 .IX Item "--MaxPathLength number"
|
|
|
672 Maximum atom path length to include in fingerprints. Default value: \fI8\fR. Valid values:
|
|
|
673 positive integers and greater than \fB\-\-MinPathLength\fR.
|
|
|
674 .IP "\fB\-n, \-\-NumOfBitsToSetPerPath\fR \fInumber\fR" 4
|
|
|
675 .IX Item "-n, --NumOfBitsToSetPerPath number"
|
|
|
676 Number of bits to set per path during generation of fingerprints bit-vector string for \fIPathLengthBits\fR
|
|
|
677 value of \fB\-m, \-\-mode\fR option. Default value: \fI1\fR. Valid values: positive integers.
|
|
|
678 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
|
|
|
679 .IX Item "--OutDelim comma | tab | semicolon"
|
|
|
680 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
|
|
|
681 Default value: \fIcomma\fR.
|
|
|
682 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
|
|
|
683 .IX Item "--output SD | FP | text | all"
|
|
|
684 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
|
|
|
685 .IP "\fB\-o, \-\-overwrite\fR" 4
|
|
|
686 .IX Item "-o, --overwrite"
|
|
|
687 Overwrite existing files.
|
|
|
688 .IP "\fB\-p, \-\-PathMode\fR \fIAtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings\fR" 4
|
|
|
689 .IX Item "-p, --PathMode AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings"
|
|
|
690 Specify type of atom paths to use for generating pathlength fingerprints for molecules in
|
|
|
691 \&\fISDFile(s)\fR. Possible values:\fIAtomPathsWithoutRings, AtomPathsWithRings,
|
|
|
692 AllAtomPathsWithoutRings, AllAtomPathsWithRings\fR. Default value: \fIAllAtomPathsWithRings\fR.
|
|
|
693 .Sp
|
|
|
694 For molecules with no rings, first two and last two options are equivalent and generate
|
|
|
695 same set of atom paths starting from each atom with length between \fB\-\-MinPathLength\fR
|
|
|
696 and \fB\-\-MaxPathLength\fR. However, all these four options can result in the same set of
|
|
|
697 final atom paths for molecules containing fused, bridged or spiro rings.
|
|
|
698 .Sp
|
|
|
699 For molecules containing rings, atom paths starting from each atom can be traversed in
|
|
|
700 four different ways:
|
|
|
701 .Sp
|
|
|
702 \&\fIAtomPathsWithoutRings\fR \- Atom paths containing no rings and without sharing of bonds
|
|
|
703 in traversed paths.
|
|
|
704 .Sp
|
|
|
705 \&\fIAtomPathsWithRings\fR \- Atom paths containing rings and without any sharing of bonds in
|
|
|
706 traversed paths.
|
|
|
707 .Sp
|
|
|
708 \&\fIAllAtomPathsWithoutRings\fR \- All possible atom paths containing no rings and without any
|
|
|
709 sharing of bonds in traversed paths.
|
|
|
710 .Sp
|
|
|
711 \&\fIAllAtomPathsWithRings\fR \- All possible atom paths containing rings and with sharing of
|
|
|
712 bonds in traversed paths.
|
|
|
713 .Sp
|
|
|
714 Atom path traversal is terminated at the ring atom.
|
|
|
715 .Sp
|
|
|
716 Based on values specified for for \fB\-p, \-\-PathMode\fR, \fB\-\-MinPathLength\fR and
|
|
|
717 \&\fB\-\-MaxPathLength\fR, all appropriate atom paths are generated for each atom in the molecule
|
|
|
718 and collected in a list.
|
|
|
719 .Sp
|
|
|
720 For each atom path in the filtered atom paths list, an atom path string is created using value of
|
|
|
721 \&\fB\-a, \-\-AtomIdentifierType\fR and specified values to use for a particular atom identifier type.
|
|
|
722 Value of \fB\-u, \-\-UseBondSymbols\fR controls whether bond order symbols are used during generation
|
|
|
723 of atom path string. Atom symbol corresponds to element symbol and characters used to represent
|
|
|
724 bond order are: \fI1 \- None; 2 \- '='; 3 \- '#'; 1.5 or aromatic \- ':'; others: bond order value\fR. By default,
|
|
|
725 bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings
|
|
|
726 results in fingerprints which correspond purely to atom paths without considering bonds.
|
|
|
727 .Sp
|
|
|
728 \&\fBUseUniquePaths\fR controls the removal of structurally duplicate atom path strings are removed
|
|
|
729 from the list.
|
|
|
730 .Sp
|
|
|
731 For \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option, each atom path is hashed to a 32 bit unsigned
|
|
|
732 integer key using \fBTextUtil::HashCode\fR function. Using the hash key as a seed for a random number
|
|
|
733 generator, a random integer value between 0 and \fB\-\-Size\fR is used to set corresponding bits
|
|
|
734 in the fingerprint bit-vector string. Value of \fB\-\-NumOfBitsToSetPerPaths\fR option controls the number
|
|
|
735 of time a random number is generated to set corresponding bits.
|
|
|
736 .Sp
|
|
|
737 For \fI PathLengthCount\fR value of \fB\-m, \-\-mode\fR option, the number of times an atom path appears
|
|
|
738 is tracked and a fingerprints count-string corresponding to count of atom paths is generated.
|
|
|
739 .Sp
|
|
|
740 For molecule containing rings, combination of \fB\-p, \-\-PathMode\fR and \fB\-\-UseBondSymbols\fR allows
|
|
|
741 generation of up to 8 different types of atom path length strings:
|
|
|
742 .Sp
|
|
|
743 .Vb 1
|
|
|
744 \& AllowSharedBonds AllowRings UseBondSymbols
|
|
|
745 \&
|
|
|
746 \& 0 0 1 \- AtomPathsNoCyclesWithBondSymbols
|
|
|
747 \& 0 1 1 \- AtomPathsWithCyclesWithBondSymbols
|
|
|
748 \&
|
|
|
749 \& 1 0 1 \- AllAtomPathsNoCyclesWithBondSymbols
|
|
|
750 \& 1 1 1 \- AllAtomPathsWithCyclesWithBondSymbols
|
|
|
751 \& [ DEFAULT ]
|
|
|
752 \&
|
|
|
753 \& 0 0 0 \- AtomPathsNoCyclesNoBondSymbols
|
|
|
754 \& 0 1 0 \- AtomPathsWithCyclesNoBondSymbols
|
|
|
755 \&
|
|
|
756 \& 1 0 0 \- AllAtomPathsNoCyclesNoBondSymbols
|
|
|
757 \& 1 1 0 \- AllAtomPathsWithCyclesNoWithBondSymbols
|
|
|
758 .Ve
|
|
|
759 .Sp
|
|
|
760 Default atom path length fingerprints generation for molecules containing rings with
|
|
|
761 \&\fIAllAtomPathsWithRings\fR value for \fB\-p, \-\-PathMode\fR, \fIYes\fR value for \fB\-\-UseBondSymbols\fR,
|
|
|
762 \&\fI2\fR value for \fB\-\-MinPathLength\fR and \fI8\fR value for \fB\-\-MaxPathLength\fR is the most time
|
|
|
763 consuming. Combinations of other options can substantially speed up fingerprint generation
|
|
|
764 for molecules containing complex ring systems.
|
|
|
765 .Sp
|
|
|
766 Additionally, value for option \fB\-a, \-\-AtomIdentifierType\fR in conjunction with corresponding specified
|
|
|
767 values for atom types changes the nature of atom path length strings and the fingerprints.
|
|
|
768 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
|
|
|
769 .IX Item "-q, --quote Yes | No"
|
|
|
770 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
|
|
|
771 \&\fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
772 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
|
|
|
773 .IX Item "-r, --root RootName"
|
|
|
774 New file name is generated using the root: <Root>.<Ext>. Default for new file
|
|
|
775 names: <SDFileName><PathLengthFP>.<Ext>. The file type determines <Ext> value.
|
|
|
776 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
|
|
|
777 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
778 .IP "\fB\-s, \-\-size\fR \fInumber\fR" 4
|
|
|
779 .IX Item "-s, --size number"
|
|
|
780 Size of fingerprints. Default value: \fI1024\fR. Valid values correspond to any positive
|
|
|
781 integer which satisfies the following criteria: power of 2, >= 32 and <= 2 ** 32.
|
|
|
782 .Sp
|
|
|
783 Examples:
|
|
|
784 .Sp
|
|
|
785 .Vb 3
|
|
|
786 \& 256
|
|
|
787 \& 512
|
|
|
788 \& 2048
|
|
|
789 .Ve
|
|
|
790 .IP "\fB\-u, \-\-UseBondSymbols\fR \fIYes | No\fR" 4
|
|
|
791 .IX Item "-u, --UseBondSymbols Yes | No"
|
|
|
792 Specify whether to use bond symbols for atom paths during generation of atom path strings.
|
|
|
793 Possible values: \fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
794 .Sp
|
|
|
795 \&\fINo\fR value option for \fB\-u, \-\-UseBondSymbols\fR allows the generation of fingerprints corresponding
|
|
|
796 purely to atoms disregarding all bonds.
|
|
|
797 .IP "\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR" 4
|
|
|
798 .IX Item "--UsePerlCoreRandom Yes | No"
|
|
|
799 Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function
|
|
|
800 during random number generation for setting bits in fingerprints bit-vector strings. Possible
|
|
|
801 values: \fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
802 .Sp
|
|
|
803 \&\fINo\fR value option for \fB\-\-UsePerlCoreRandom\fR allows the generation of fingerprints
|
|
|
804 bit-vector strings which are same across different platforms.
|
|
|
805 .Sp
|
|
|
806 The random number generator implemented in MayaChemTools is a variant of
|
|
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807 linear congruential generator (\s-1LCG\s0) as described by Miller et al. [ Ref 120 ].
|
|
|
808 It is also referred to as Lehmer random number generator or Park-Miller
|
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|
809 random number generator.
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810 .Sp
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|
|
811 Unlike Perl's core random number generator function rand, the random number
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812 generator implemented in MayaChemTools, MathUtil::random, generates consistent
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813 random values across different platforms for a specific random seed and leads
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814 to generation of portable fingerprints bit-vector strings.
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815 .IP "\fB\-\-UseUniquePaths\fR \fIYes | No\fR" 4
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|
|
816 .IX Item "--UseUniquePaths Yes | No"
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|
|
817 Specify whether to use structurally unique atom paths during generation of atom path strings.
|
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818 Possible values: \fIYes or No\fR. Default value: \fIYes\fR.
|
|
|
819 .Sp
|
|
|
820 \&\fINo\fR value option for \fB\-\-UseUniquePaths\fR allows usage of all atom paths generated by
|
|
|
821 \&\fB\-p, \-\-PathMode\fR option value for generation of atom path strings leading to duplicate
|
|
|
822 path count during \fIPathLengthCount\fR value of \fB\-m, \-\-mode\fR option. It doesn't change fingerprint
|
|
|
823 string generated during \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR.
|
|
|
824 .Sp
|
|
|
825 For example, during \fIAllAtomPathsWithRings\fR value of \fB\-p, \-\-PathMode\fR option, benzene has
|
|
|
826 12 linear paths of length 2 and 12 cyclic paths length of 7, but only 6 linear paths of length 2 and
|
|
|
827 1 cyclic path of length 7 are structurally unique.
|
|
|
828 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
|
|
|
829 .IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
|
|
|
830 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
|
|
|
831 \&\fB\-\-output\fR used during \fIPathLengthCount\fR value of \fB\-m, \-\-mode\fR option. Possible
|
|
|
832 values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
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|
833 ValuesAndIDsPairsString\fR. Defaultvalue: \fIIDsAndValuesString\fR.
|
|
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834 .Sp
|
|
|
835 Examples:
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|
836 .Sp
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|
837 .Vb 6
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|
838 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
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839 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
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|
|
840 \& C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
|
|
|
841 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
842 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
843 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
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|
|
844 \&
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|
845 \& FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
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|
846 \& h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
|
|
|
847 \& O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
|
|
|
848 \& aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
|
|
|
849 \& 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
|
|
|
850 \& sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
|
|
|
851 .Ve
|
|
|
852 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
|
|
|
853 .IX Item "-w, --WorkingDir DirName"
|
|
|
854 Location of working directory. Default: current directory.
|
|
|
855 .SH "EXAMPLES"
|
|
|
856 .IX Header "EXAMPLES"
|
|
|
857 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
858 through 8 in hexadecimal bit-vector string format of size 1024 and create a
|
|
|
859 SamplePLFPHex.csv file containing sequential compound IDs along with fingerprints
|
|
|
860 bit-vector strings data, type:
|
|
|
861 .PP
|
|
|
862 .Vb 1
|
|
|
863 \& % PathLengthFingerprints.pl \-o \-r SamplePLFPHex Sample.sdf
|
|
|
864 .Ve
|
|
|
865 .PP
|
|
|
866 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
867 through 8 in hexadecimal bit-vector string format of size 1024 and create SamplePLFPHex.sdf,
|
|
|
868 SamplePLFPHex.fpf, and SamplePLFPHex.csv files containing sequential compound IDs
|
|
|
869 in \s-1CSV\s0 file along with fingerprints bit-vector strings data, type:
|
|
|
870 .PP
|
|
|
871 .Vb 1
|
|
|
872 \& % PathLengthFingerprints.pl \-\-output all \-o \-r SamplePLFPHex Sample.sdf
|
|
|
873 .Ve
|
|
|
874 .PP
|
|
|
875 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
876 through 8 in binary bit-vector string format of size 1024 and create a
|
|
|
877 SamplePLFPBin.csv file containing sequential compound IDs along with fingerprints
|
|
|
878 bit-vector strings data, type:
|
|
|
879 .PP
|
|
|
880 .Vb 2
|
|
|
881 \& % PathLengthFingerprints.pl \-\-BitStringFormat BinaryString \-\-size 2048
|
|
|
882 \& \-o \-r SamplePLFPBin Sample.sdf
|
|
|
883 .Ve
|
|
|
884 .PP
|
|
|
885 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
886 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
887 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
888 .PP
|
|
|
889 .Vb 2
|
|
|
890 \& % PathLengthFingerprints.pl \-m PathLengthCount \-o \-r SamplePLFPCount
|
|
|
891 \& Sample.sdf
|
|
|
892 .Ve
|
|
|
893 .PP
|
|
|
894 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
895 length 1 through 8 in IDsAndValuesString format using E\-state atom types and
|
|
|
896 create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
|
|
|
897 vector strings data, type:
|
|
|
898 .PP
|
|
|
899 .Vb 2
|
|
|
900 \& % PathLengthFingerprints.pl \-m PathLengthCount \-\-AtomIdentifierType
|
|
|
901 \& EStateAtomTypes \-o \-r SamplePLFPCount Sample.sdf
|
|
|
902 .Ve
|
|
|
903 .PP
|
|
|
904 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
905 length 1 through 8 in IDsAndValuesString format using SLogP atom types and
|
|
|
906 create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
|
|
|
907 vector strings data, type:
|
|
|
908 .PP
|
|
|
909 .Vb 2
|
|
|
910 \& % PathLengthFingerprints.pl \-m PathLengthCount \-\-AtomIdentifierType
|
|
|
911 \& SLogPAtomTypes \-o \-r SamplePLFPCount Sample.sdf
|
|
|
912 .Ve
|
|
|
913 .PP
|
|
|
914 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
915 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
916 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
917 .PP
|
|
|
918 .Vb 2
|
|
|
919 \& % PathLengthFingerprints.pl \-m PathLengthCount \-\-VectorStringFormat
|
|
|
920 \& ValuesAndIDsPairsString \-o \-r SamplePLFPCount Sample.sdf
|
|
|
921 .Ve
|
|
|
922 .PP
|
|
|
923 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
924 length 1 through 8 in IDsAndValuesString format using \s-1AS\s0,X,BO as atomic invariants and
|
|
|
925 create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
|
|
|
926 vector strings data, type:
|
|
|
927 .PP
|
|
|
928 .Vb 3
|
|
|
929 \& % PathLengthFingerprints.pl \-m PathLengthCount \-\-AtomIdentifierType
|
|
|
930 \& AtomicInvariantsAtomTypes \-\-AtomicInvariantsToUse "AS,X,BO" \-o
|
|
|
931 \& \-r SamplePLFPCount Sample.sdf
|
|
|
932 .Ve
|
|
|
933 .PP
|
|
|
934 To generate path length fingerprints corresponding to count of all paths from
|
|
|
935 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
936 containing compound IDs from MolName line along with fingerprints vector strings data, type:
|
|
|
937 .PP
|
|
|
938 .Vb 3
|
|
|
939 \& % PathLengthFingerprints.pl \-m PathLengthCount \-\-UseUniquePaths No
|
|
|
940 \& \-o \-\-CompoundIDMode MolName \-r SamplePLFPCount \-\-UseUniquePaths No
|
|
|
941 \& Sample.sdf
|
|
|
942 .Ve
|
|
|
943 .PP
|
|
|
944 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
945 through 8 in hexadecimal bit-vector string format of size 512 after folding and create
|
|
|
946 SamplePLFPHex.sdf, SamplePLFPHex.fpf, and SamplePLFPHex.sdf files containing sequential
|
|
|
947 compound IDs along with fingerprints bit-vector strings data, type:
|
|
|
948 .PP
|
|
|
949 .Vb 2
|
|
|
950 \& % PathLengthFingerprints.pl \-\-output all \-\-Fold Yes \-\-FoldedSize 512
|
|
|
951 \& \-o \-r SamplePLFPHex Sample.sdf
|
|
|
952 .Ve
|
|
|
953 .PP
|
|
|
954 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
955 through 8 containing no rings and without sharing of bonds in hexadecimal bit-vector
|
|
|
956 string format of size 1024 and create a SamplePLFPHex.csv file containing sequential
|
|
|
957 compound IDs along with fingerprints bit-vector strings data and all data fields, type:
|
|
|
958 .PP
|
|
|
959 .Vb 2
|
|
|
960 \& % PathLengthFingerprints.pl \-p AtomPathsWithoutRings \-\-DataFieldsMode All
|
|
|
961 \& \-o \-r SamplePLFPHex Sample.sdf
|
|
|
962 .Ve
|
|
|
963 .PP
|
|
|
964 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
965 through 8 containing rings and without sharing of bonds in hexadecimal bit-vector
|
|
|
966 string format of size 1024 and create a SamplePLFPHex.tsv file containing compound IDs
|
|
|
967 derived from combination of molecule name line and an explicit compound prefix
|
|
|
968 along with fingerprints bit-vector strings data and all data fields, type:
|
|
|
969 .PP
|
|
|
970 .Vb 4
|
|
|
971 \& % PathLengthFingerprints.pl \-p AtomPathsWithRings \-\-DataFieldsMode
|
|
|
972 \& CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix \-\-CompoundID Cmpd
|
|
|
973 \& \-\-CompoundIDLabel MolID \-\-FingerprintsLabel PathLengthFP \-\-OutDelim Tab
|
|
|
974 \& \-r SamplePLFPHex \-o Sample.sdf
|
|
|
975 .Ve
|
|
|
976 .PP
|
|
|
977 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
978 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
979 containing sequential compound IDs along with fingerprints vector strings data using
|
|
|
980 aromaticity specified in \s-1SD\s0 file, type:
|
|
|
981 .PP
|
|
|
982 .Vb 2
|
|
|
983 \& % PathLengthFingerprints.pl \-m PathLengthCount \-\-DetectAromaticity No
|
|
|
984 \& \-o \-r SamplePLFPCount Sample.sdf
|
|
|
985 .Ve
|
|
|
986 .PP
|
|
|
987 To generate path length fingerprints corresponding to all unique paths from length 2
|
|
|
988 through 6 in hexadecimal bit-vector string format of size 1024 and create a
|
|
|
989 SamplePLFPHex.csv file containing sequential compound IDs along with fingerprints
|
|
|
990 bit-vector strings data, type:
|
|
|
991 .PP
|
|
|
992 .Vb 2
|
|
|
993 \& % PathLengthFingerprints.pl \-\-MinPathLength 2 \-\-MaxPathLength 6
|
|
|
994 \& \-o \-r SamplePLFPHex Sample.sdf
|
|
|
995 .Ve
|
|
|
996 .SH "AUTHOR"
|
|
|
997 .IX Header "AUTHOR"
|
|
|
998 Manish Sud <msud@san.rr.com>
|
|
|
999 .SH "SEE ALSO"
|
|
|
1000 .IX Header "SEE ALSO"
|
|
|
1001 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
1002 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
|
|
|
1003 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
1004 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
1005 .SH "COPYRIGHT"
|
|
|
1006 .IX Header "COPYRIGHT"
|
|
|
1007 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1008 .PP
|
|
|
1009 This file is part of MayaChemTools.
|
|
|
1010 .PP
|
|
|
1011 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1012 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
1013 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1014 any later version.
|
