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124 .\" ========================================================================
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125 .\"
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126 .IX Title "FINGERPRINTSFILEUTIL 1"
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127 .TH FINGERPRINTSFILEUTIL 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 FingerprintsFileUtil
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use Fingerprints::FingerprintsFileUtil;
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137 .PP
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138 use Fingerprints::FingerprintsFileUtil qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBFingerprintsFileUtil\fR module provides the following functions:
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142 .PP
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143 GetFingerprintsFileType, NewFingerprintsFileIO, ReadAndProcessFingerpritsData
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144 .PP
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145 \&\fBFingerprintsFileUtil\fR module provides function to handle fingerprints data strings
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146 in \s-1FP\s0, \s-1SD\s0 and \s-1CSV/TSV\s0 text files present in one of the following two types: fingerprints
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147 bit-vectors and fingerprints vector strings
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148 .PP
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149 Example of \fB\s-1FP\s0\fR file format containing fingerprints bit-vector string data:
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150 .PP
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151 .Vb 10
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152 \& #
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153 \& # Package = MayaChemTools 7.4
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154 \& # ReleaseDate = Oct 21, 2010
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155 \& #
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156 \& # TimeStamp = Mon Mar 7 15:14:01 2011
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157 \& #
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158 \& # FingerprintsStringType = FingerprintsBitVector
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159 \& #
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160 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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161 \& # Size = 1024
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162 \& # BitStringFormat = HexadecimalString
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163 \& # BitsOrder = Ascending
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164 \& #
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165 \& Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
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166 \& Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
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167 \& ... ...
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168 \& ... ..
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169 .Ve
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170 .PP
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171 Example of \fB\s-1FP\s0\fR file format containing fingerprints vector string data:
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172 .PP
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173 .Vb 10
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174 \& #
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175 \& # Package = MayaChemTools 7.4
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176 \& # ReleaseDate = Oct 21, 2010
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177 \& #
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178 \& # TimeStamp = Mon Mar 7 15:14:01 2011
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179 \& #
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180 \& # FingerprintsStringType = FingerprintsVector
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181 \& #
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182 \& # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
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183 \& # VectorStringFormat = IDsAndValuesString
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184 \& # VectorValuesType = NumericalValues
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185 \& #
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186 \& Cmpd1 338;C F N O C:C C:N C=O CC CF CN CO C:C:C C:C:N C:CC C:CF C:CN C:
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187 \& N:C C:NC CC:N CC=O CCC CCN CCO CNC NC=O O=CO C:C:C:C C:C:C:N C:C:CC...;
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188 \& 33 1 2 5 21 2 2 12 1 3 3 20 2 10 2 2 1 2 2 2 8 2 5 1 1 1 19 2 8 2 2 2 2
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189 \& 6 2 2 2 2 2 2 2 2 3 2 2 1 4 1 5 1 1 18 6 2 2 1 2 10 2 1 2 1 2 2 2 2 ...
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190 \& Cmpd2 103;C N O C=N C=O CC CN CO CC=O CCC CCN CCO CNC N=CN NC=O NCN O=C
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191 \& O C CC=O CCCC CCCN CCCO CCNC CNC=N CNC=O CNCN CCCC=O CCCCC CCCCN CC...;
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192 \& 15 4 4 1 2 13 5 2 2 15 5 3 2 2 1 1 1 2 17 7 6 5 1 1 1 2 15 8 5 7 2 2 2 2
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193 \& 1 2 1 1 3 15 7 6 8 3 4 4 3 2 2 1 2 3 14 2 4 7 4 4 4 4 1 1 1 2 1 1 1 ...
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194 \& ... ...
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195 \& ... ...
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196 .Ve
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197 .PP
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198 Example of \fB\s-1SD\s0\fR file format containing fingerprints vector string data:
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199 .PP
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200 .Vb 10
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201 \& ... ...
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202 \& ... ...
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203 \& $$$$
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204 \& ... ...
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205 \& ... ...
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206 \& ... ...
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207 \& 41 44 0 0 0 0 0 0 0 0999 V2000
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208 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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209 \& ... ...
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210 \& 2 3 1 0 0 0 0
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211 \& ... ...
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212 \& M END
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213 \& > <CmpdID>
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214 \& Test
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215 \&
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216 \& > <PathLengthFingerprints>
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217 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
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218 \& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
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219 \& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
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220 \& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
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221 \& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
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222 \& aa0660a11014a011d46
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223 \&
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224 \& $$$$
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225 \& ... ...
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226 \& ... ...
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227 .Ve
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228 .PP
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229 Example of \s-1CSV\s0 \fBtext\fR file format containing fingerprints bit-vector string data:
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230 .PP
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231 .Vb 7
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232 \& "CompoundID","PathLengthFingerprints"
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233 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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234 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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235 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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236 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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237 \& ... ...
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238 \& ... ...
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239 .Ve
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240 .PP
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241 The current release of MayaChemTools supports the following types of fingerprint
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242 bit-vector and vector strings:
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243 .PP
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244 .Vb 6
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245 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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246 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
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247 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
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248 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
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249 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
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250 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
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251 \&
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252 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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253 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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254 \& .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
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255 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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256 \&
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257 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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258 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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259 \& N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
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260 \&
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261 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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262 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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263 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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264 \& 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
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265 \& O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
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266 \& 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...
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267 \&
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268 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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269 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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270 \& H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
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271 \& .024 \-2.270
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272 \&
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273 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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274 \& ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
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275 \& 4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
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276 \& 4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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277 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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278 \&
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279 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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280 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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281 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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282 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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283 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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284 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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285 \&
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286 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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287 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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288 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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289 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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290 \& 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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291 \& 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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292 \&
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293 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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294 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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295 \& 0000000001010000000110000011000000000000100000000000000000000000100001
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296 \& 1000000110000000000000000000000000010011000000000000000000000000010000
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297 \& 0000000000000000000000000010000000000000000001000000000000000000000000
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298 \& 0000000000010000100001000000000000101000000000000000100000000000000...
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299 \&
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300 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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301 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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302 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
|
|
303 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
|
|
304 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
|
|
|
305 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
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306 \&
|
|
|
307 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
308 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
309 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
310 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
311 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
312 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
|
|
|
313 \&
|
|
|
314 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
|
|
|
315 \& 0000000000000000000000000000000001001000010010000000010010000000011100
|
|
|
316 \& 0100101010111100011011000100110110000011011110100110111111111111011111
|
|
|
317 \& 11111111111110111000
|
|
|
318 \&
|
|
|
319 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
|
|
|
320 \& 1110011111100101111111000111101100110000000000000011100010000000000000
|
|
|
321 \& 0000000000000000000000000000000000000000000000101000000000000000000000
|
|
|
322 \& 0000000000000000000000000000000000000000000000000000000000000000000000
|
|
|
323 \& 0000000000000000000000000000000000000011000000000000000000000000000000
|
|
|
324 \& 0000000000000000000000000000000000000000
|
|
|
325 \&
|
|
|
326 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
|
|
|
327 \& ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
328 \& 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0
|
|
|
329 \& 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0
|
|
|
330 \& 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1
|
|
|
331 \& 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1
|
|
|
332 \&
|
|
|
333 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
|
|
|
334 \& ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0
|
|
|
335 \& 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0
|
|
|
336 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
337 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0
|
|
|
338 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
|
|
|
339 \&
|
|
|
340 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
341 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
342 \& 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
343 \& 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
344 \& 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
345 \& 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
346 \&
|
|
|
347 \& FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
348 \& 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
349 \& 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
|
|
|
350 \& 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
351 \& 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
352 \& 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
|
|
|
353 \&
|
|
|
354 \& FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
|
|
|
355 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
|
|
|
356 \& 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
|
|
|
357 \& 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
|
|
|
358 \& CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
|
|
|
359 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
|
|
|
360 \&
|
|
|
361 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
362 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
363 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
|
|
|
364 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
|
|
|
365 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
366 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
|
|
|
367 \&
|
|
|
368 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
369 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
|
|
|
370 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
|
|
|
371 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
|
|
|
372 \& 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
|
|
|
373 \& 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
|
|
|
374 \&
|
|
|
375 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
|
|
|
376 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
|
|
|
377 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
|
|
|
378 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
|
|
|
379 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
|
|
|
380 \&
|
|
|
381 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
|
|
|
382 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
|
|
|
383 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
|
|
|
384 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
|
|
|
385 \& 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
|
|
|
386 \&
|
|
|
387 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
|
|
|
388 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
|
|
|
389 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
|
|
|
390 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
|
|
|
391 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
|
|
|
392 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
|
|
|
393 \& 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
|
|
|
394 \&
|
|
|
395 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
|
|
|
396 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
|
|
|
397 \& .3\-D10 C.2\-D1\-C.2\-D9\-C.ar\-D10 C.2\-D1\-C.3\-D1\-C.3\-D2 C.2\-D1\-C.3\-D10\-C.3\-
|
|
|
398 \& D9 C.2\-D1\-C.3\-D2\-C.3\-D3 C.2\-D1\-C.3\-D2\-C.ar\-D3 C.2\-D1\-C.3\-D3\-C.3\-D4 C.2
|
|
|
399 \& \-D1\-C.3\-D3\-N.ar\-D4 C.2\-D1\-C.3\-D3\-O.3\-D2 C.2\-D1\-C.3\-D4\-C.3\-D5 C.2\-D1\-C.
|
|
|
400 \& 3\-D5\-C.3\-D6 C.2\-D1\-C.3\-D5\-O.3\-D4 C.2\-D1\-C.3\-D6\-C.3\-D7 C.2\-D1\-C.3\-D7...
|
|
|
401 \&
|
|
|
402 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
|
|
|
403 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
|
|
|
404 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
|
|
|
405 \& HBD H\-D3\-H H\-D3\-HBA H\-D3\-HBD H\-D3\-NI HBA\-D3\-NI HBD\-D3\-NI H\-D4\-H H\-D4\-H
|
|
|
406 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
|
|
|
407 \& 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10
|
|
|
408 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
|
|
|
409 \&
|
|
|
410 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
|
|
|
411 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
|
|
|
412 \& 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1
|
|
|
413 \& 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0
|
|
|
414 \& 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0
|
|
|
415 \& 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...
|
|
|
416 \&
|
|
|
417 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
|
|
|
418 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
|
|
|
419 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
|
|
|
420 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
|
|
|
421 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
|
|
|
422 \& 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23
|
|
|
423 \& 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1
|
|
|
424 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
|
|
|
425 \&
|
|
|
426 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
|
|
|
427 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
|
|
|
428 \& 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0
|
|
|
429 \& 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26
|
|
|
430 \& 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0
|
|
|
431 \& 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ...
|
|
|
432 .Ve
|
|
|
433 .SH "FUNCTIONS"
|
|
|
434 .IX Header "FUNCTIONS"
|
|
|
435 .IP "\fBGetFingerprintsFileType\fR" 4
|
|
|
436 .IX Item "GetFingerprintsFileType"
|
|
|
437 .Vb 1
|
|
|
438 \& $FileType = GetFingerprintsFileType($FileName);
|
|
|
439 .Ve
|
|
|
440 .Sp
|
|
|
441 Returns fingerprints \fBFileType\fR of \fIFileName\fR determined using extension of file name.
|
|
|
442 Possible \fBFileType\fR values: \fI\s-1FP\s0, \s-1SD\s0, Text\fR. Supported file name extensions for various
|
|
|
443 file types are: \fB\s-1FP\s0\fR \- \fIfpf, fp\fR; \fB\s-1SD\s0\fR \- \fIsdf, sd\fR; \fBText\fR \- \fIcsv, tsv\fR.
|
|
|
444 .IP "\fBNewFingerprintsFileIO\fR" 4
|
|
|
445 .IX Item "NewFingerprintsFileIO"
|
|
|
446 .Vb 1
|
|
|
447 \& $FingerprintsFileIO = NewFingerprintsFileIO(%IOParameters);
|
|
|
448 .Ve
|
|
|
449 .Sp
|
|
|
450 Using specified \fIIOParameters\fR property names and values hash, \fBNewFingerprintsFileIO\fR
|
|
|
451 method creates a new object using appropriate fingerprints file \s-1IO\s0 class \- \fBFingerprintsFPFileIO,
|
|
|
452 FingerprintsSDFileIO, or FingerprintsTextFileIO\fR \- and returns a reference to a newly created
|
|
|
453 \&\fBFingerprintsFileIO\fR object.
|
|
|
454 .Sp
|
|
|
455 The \fIIOParameters\fR hash must contain \fIName\fR and \fIMode\fR as key/value pairs to create
|
|
|
456 a new \fBFingerprintsFileIO\fR object.
|
|
|
457 .Sp
|
|
|
458 Based on type of file \- \fB\s-1FP\s0, \s-1SD\s0 or Text\fR \- \fBNewFingerprintsFileIO\fR use \fBnew\fR method
|
|
|
459 from appropriate class \- \fBFingerprintsFPFileIO\fR \- along with \fIIOParameters\fR to create
|
|
|
460 \&\fBFingerprintsFileIO\fR object.
|
|
|
461 .IP "\fBReadAndProcessFingerpritsData\fR" 4
|
|
|
462 .IX Item "ReadAndProcessFingerpritsData"
|
|
|
463 .Vb 2
|
|
|
464 \& ($CompoundIDsRef, $FingerprintsObjectRef) =
|
|
|
465 \& ReadAndProcessFingerpritsData($FingerprintsFileIO);
|
|
|
466 .Ve
|
|
|
467 .Sp
|
|
|
468 Processes fingerprints bit-vector and vector string data in a file using \fIFingerprintsFileIO\fR
|
|
|
469 object and returns a references to arrays of \fBCompoundIDs\fR and \fIFingerprintsObjects\fR.
|
|
|
470 .Sp
|
|
|
471 The file open and close is automatically performed during processing.
|
|
|
472 .SH "AUTHOR"
|
|
|
473 .IX Header "AUTHOR"
|
|
|
474 Manish Sud <msud@san.rr.com>
|
|
|
475 .SH "SEE ALSO"
|
|
|
476 .IX Header "SEE ALSO"
|
|
|
477 FingerprintsFPFileIO.pm, FingerprintsSDFileIO.pm, FingerprintsTextFileIO.pm
|
|
|
478 .SH "COPYRIGHT"
|
|
|
479 .IX Header "COPYRIGHT"
|
|
|
480 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
481 .PP
|
|
|
482 This file is part of MayaChemTools.
|
|
|
483 .PP
|
|
|
484 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
485 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
|
|
|
486 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
487 any later version.
|
