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123 .rm #[ #] #H #V #F C
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124 .\" ========================================================================
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125 .\"
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126 .IX Title "FINGERPRINTSTEXTFILEIO 1"
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127 .TH FINGERPRINTSTEXTFILEIO 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 FingerprintsTextFileIO
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use FileIO::FingerprintsTextFileIO;
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137 .PP
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138 use FileIO::FingerprintsTextFileIO qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBFingerprintsTextFileIO\fR class provides the following methods:
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142 .PP
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143 new, GetDataColLabels, GetDataLineWords, GetFingerprints, GetFingerprintsString,
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144 IsFingerprintsDataValid, IsFingerprintsFileDataValid, IsFingerprintsTextFile,
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145 Next, Read, SetBitStringFormat, SetBitsOrder, SetColMode, SetDataColLabels,
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146 SetDataLineWords, SetDetailLevel, SetFingerprints, SetFingerprintsString,
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147 SetFingerprintsStringMode, SetInDelim, SetOutDelim, SetVectorStringFormat,
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148 WriteFingerprints, WriteFingerprintsString
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149 .PP
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150 The following methods can also be used as functions:
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151 .PP
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152 IsFingerprintsTextFile
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153 .PP
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154 \&\fBFingerprintsTextFileIO\fR class is derived from \fIFileIO\fR class and uses its methods to support
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155 generic file related functionality.
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156 .PP
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157 The fingerprints \s-1CSV/TSV\s0 text file format with \fB.csv\fR or \fB.tsv\fR file extensions supports two
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158 types of fingerprints string data: fingerprints bit-vectors and fingerprints vector strings. The
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159 fingerprints string data is treated as column value in a text file.
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160 .PP
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161 Example of text file format containing fingerprints string data:
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162 .PP
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163 .Vb 7
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164 \& "CompoundID","PathLengthFingerprints"
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165 \& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
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166 \& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
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167 \& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
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168 \& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
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169 \& ... ...
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170 \& ... ...
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171 .Ve
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172 .PP
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173 The current release of MayaChemTools supports the following types of fingerprint
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174 bit-vector and vector strings:
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175 .PP
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176 .Vb 6
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177 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
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178 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
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179 \& 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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180 \& 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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181 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
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182 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
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183 \&
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184 \& FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
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185 \& ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
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186 \& .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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187 \& O.X1.BO2;2 4 14 3 10 1 1 1 3 2
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188 \&
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189 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
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190 \& ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
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191 \& 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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192 \&
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193 \& FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
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194 \& umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
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195 \& 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
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196 \& 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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197 \& 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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198 \& 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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199 \&
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200 \& FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
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201 \& AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
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202 \& 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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203 \& .024 \-2.270
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204 \&
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205 \& FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
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206 \& 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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207 \& 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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208 \& 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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209 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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210 \&
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211 \& FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
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212 \& us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
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213 \& 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
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214 \& 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
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215 \& 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
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216 \& 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
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217 \&
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218 \& FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
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219 \& :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
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220 \& 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
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221 \& 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
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222 \& 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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223 \& 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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224 \&
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225 \& FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
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226 \& es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
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227 \& 0000000001010000000110000011000000000000100000000000000000000000100001
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228 \& 1000000110000000000000000000000000010011000000000000000000000000010000
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229 \& 0000000000000000000000000010000000000000000001000000000000000000000000
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230 \& 0000000000010000100001000000000000101000000000000000100000000000000...
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231 \&
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232 \& FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
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233 \& s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
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234 \& 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
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235 \& 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
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236 \& 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
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237 \& 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
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238 \&
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239 \& FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
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240 \& haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
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241 \& 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
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242 \& 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
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243 \& 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
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244 \& 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
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245 \&
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246 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000
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247 \& 0000000000000000000000000000000001001000010010000000010010000000011100
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248 \& 0100101010111100011011000100110110000011011110100110111111111111011111
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249 \& 11111111111110111000
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250 \&
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251 \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011
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252 \& 1110011111100101111111000111101100110000000000000011100010000000000000
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253 \& 0000000000000000000000000000000000000000000000101000000000000000000000
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254 \& 0000000000000000000000000000000000000000000000000000000000000000000000
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255 \& 0000000000000000000000000000000000000011000000000000000000000000000000
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256 \& 0000000000000000000000000000000000000000
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257 \&
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258 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri
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259 \& 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
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260 \& 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
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261 \& 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
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262 \& 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
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263 \& 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
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264 \&
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265 \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri
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266 \& 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
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267 \& 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
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268 \& 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
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269 \& 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
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270 \& 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
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271 \&
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272 \& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
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273 \& th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
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274 \& 0100010101011000101001011100110001000010001001101000001001001001001000
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275 \& 0010110100000111001001000001001010100100100000000011000000101001011100
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276 \& 0010000001000101010100000100111100110111011011011000000010110111001101
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277 \& 0101100011000000010001000011000010100011101100001000001000100000000...
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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:MMFF94AtomTypes:MinLength1:MaxLengt
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287 \& h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
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288 \& 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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289 \& 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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290 \& 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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291 \& OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
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292 \&
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293 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
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294 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
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295 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
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296 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
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297 \& 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
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298 \& 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...
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299 \&
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300 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
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301 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
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302 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
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303 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
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304 \& 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
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305 \& 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 ...
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306 \&
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307 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
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308 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
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309 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
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310 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
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311 \& 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
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312 \&
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313 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
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314 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
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315 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
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316 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
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317 \& 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
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318 \&
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319 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
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320 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
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321 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
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322 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
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323 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
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324 \& 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
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325 \& 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...
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326 \&
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327 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
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328 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
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329 \& .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\-
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330 \& 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
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331 \& \-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.
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332 \& 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...
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333 \&
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334 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min
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335 \& Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H\-D1\-H H
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336 \& \-D1\-NI HBA\-D1\-NI HBD\-D1\-NI H\-D2\-H H\-D2\-HBA H\-D2\-HBD HBA\-D2\-HBA HBA\-D2\-
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337 \& 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
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338 \& BA H\-D4\-HBD HBA\-D4\-HBA HBA\-D4\-HBD HBD\-D4\-HBD H\-D5\-H H\-D5\-HBA H\-D5\-...;
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339 \& 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
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340 \& 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1
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341 \&
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342 \& FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist
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343 \& ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0
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344 \& 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
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345 \& 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
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346 \& 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
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347 \& 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...
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348 \&
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349 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize:
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350 \& MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1\-
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351 \& Ar1\-Ar1 Ar1\-Ar1\-H1 Ar1\-Ar1\-HBA1 Ar1\-Ar1\-HBD1 Ar1\-H1\-H1 Ar1\-H1\-HBA1 Ar1
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352 \& \-H1\-HBD1 Ar1\-HBA1\-HBD1 H1\-H1\-H1 H1\-H1\-HBA1 H1\-H1\-HBD1 H1\-HBA1\-HBA1 H1\-
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353 \& HBA1\-HBD1 H1\-HBA1\-NI1 H1\-HBD1\-NI1 HBA1\-HBA1\-NI1 HBA1\-HBD1\-NI1 Ar1\-...;
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354 \& 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
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355 \& 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
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356 \& 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ...
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357 \&
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358 \& FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD
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359 \& istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106
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360 \& 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
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|
361 \& 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
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362 \& 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
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|
363 \& 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 ...
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364 .Ve
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365 .SS "\s-1METHODS\s0"
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366 .IX Subsection "METHODS"
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367 .IP "\fBnew\fR" 4
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368 .IX Item "new"
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369 .Vb 1
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370 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(%IOParameters);
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371 .Ve
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372 .Sp
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373 Using specified \fIIOParameters\fR names and values hash, \fBnew\fR method creates a new
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374 object and returns a reference to a newly created \fBFingerprintsTextFileIO\fR object. By default,
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375 the following properties are initialized during \fIRead\fR mode:
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376 .Sp
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377 .Vb 11
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378 \& Name = \*(Aq\*(Aq;
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379 \& Mode = \*(AqRead\*(Aq;
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380 \& Status = 0;
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381 \& FingerprintsStringMode = \*(AqAutoDetect\*(Aq;
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382 \& FingerprintsCol = \*(AqAutoDetect\*(Aq;
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383 \& ColMode = \*(AqColNum\*(Aq;
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384 \& CompoundIDCol = \*(AqAutoDetect\*(Aq;
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385 \& CompoundIDPrefix = \*(AqCmpd\*(Aq;
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386 \& InDelim = \*(AqComma\*(Aq;
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387 \& ValidateData = 1;
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388 \& DetailLevel = 1;
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389 .Ve
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390 .Sp
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391 During \fIWrite\fR mode, the following properties get initialize by default:
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392 .Sp
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393 .Vb 1
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394 \& FingerprintsStringMode = undef;
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395 \&
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396 \& BitStringFormat = HexadecimalString;
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397 \& BitsOrder = Ascending;
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398 \&
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399 \& VectorStringFormat = NumericalValuesString or ValuesString;
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400 \& OutDelim = \*(AqComma\*(Aq;
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401 \& OutQuote = 1;
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402 .Ve
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403 .Sp
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404 Examples:
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405 .Sp
|
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406 .Vb 3
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407 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
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408 \& \*(AqName\*(Aq => \*(AqSample.csv\*(Aq,
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409 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq);
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410 \&
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411 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
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412 \& \*(AqName\*(Aq => \*(AqSample.csv\*(Aq,
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413 \& \*(AqMode\*(Aq => \*(AqRead\*(Aq,;
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414 \& \*(AqFingerprintsStringMode\*(Aq =>
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415 \& \*(AqAutoDetect\*(Aq,
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416 \& \*(AqColMode\*(Aq => \*(AqColLabel\*(Aq,
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417 \& \*(AqFingerprintsCol\*(Aq => \*(AqFingerprints\*(Aq,
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418 \& \*(AqCompoundIDCol\*(Aq => \*(AqCompoundID\*(Aq,
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419 \& \*(AqInDelim\*(Aq => \*(AqComma\*(Aq);
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420 \&
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421 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
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422 \& \*(AqName\*(Aq => \*(AqSample.csv\*(Aq,
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423 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
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424 \& \*(AqFingerprintsStringMode\*(Aq =>
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425 \& \*(AqFingerprintsBitVectorString\*(Aq,
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426 \& \*(AqOverwrite\*(Aq => 1,
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427 \& \*(AqBitStringFormat\*(Aq => \*(AqHexadecimalString\*(Aq,
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428 \& \*(AqBitsOrder\*(Aq => \*(AqAscending\*(Aq);
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429 \&
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430 \& $NewFingerprintsTextFileIO = new FileIO::FingerprintsTextFileIO(
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431 \& \*(AqName\*(Aq => \*(AqSample.tsv\*(Aq,
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432 \& \*(AqMode\*(Aq => \*(AqWrite\*(Aq,
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433 \& \*(AqFingerprintsStringMode\*(Aq =>
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434 \& \*(AqFingerprintsVectorString\*(Aq,
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435 \& \*(AqOverwrite\*(Aq => 1,
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436 \& \*(AqVectorStringFormat\*(Aq => \*(AqIDsAndValuesString\*(Aq,
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437 \& \*(AqOutDelim\*(Aq => \*(AqTab\*(Aq,
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438 \& \*(AqOutQuote\*(Aq => 0);
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439 .Ve
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|
440 .IP "\fBGetDataColLabels\fR" 4
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|
441 .IX Item "GetDataColLabels"
|
|
|
442 .Vb 2
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|
|
443 \& @ColLabels = $FingerprintsTextFileIO\->GetDataColLabels();
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|
444 \& $NumOfColLabels = $FingerprintsTextFileIO\->GetDataColLabels();
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445 .Ve
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446 .Sp
|
|
|
447 Returns an array of \fBColLabels\fR from first line in text file. In scalar context, it returns
|
|
|
448 number of column labels.
|
|
|
449 .IP "\fBGetDataLineWords\fR" 4
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|
|
450 .IX Item "GetDataLineWords"
|
|
|
451 .Vb 2
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|
452 \& @DataWords = $FingerprintsTextFileIO\->GetDataLineWords();
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|
453 \& $NumOfDataWords = $FingerprintsTextFileIO\->GetDataLineWords();
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454 .Ve
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455 .Sp
|
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|
456 Returns an array of \fBDataWords\fR in current data line. In scalar context, it returns
|
|
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457 number of data words.
|
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|
458 .IP "\fBGetFingerprints\fR" 4
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459 .IX Item "GetFingerprints"
|
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460 .Vb 1
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|
461 \& $FingerprintsObject = $FingerprintsTextFileIO\->GetFingerprints();
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462 .Ve
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463 .Sp
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|
464 Returns \fBFingerprintsObject\fR generated for current data line using fingerprints bit-vector
|
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|
465 or vector string data. The fingerprints object corresponds to any of the supported fingerprints
|
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466 such as PathLengthFingerprints, ExtendedConnectivity, and so on.
|
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467 .IP "\fBGetFingerprintsString\fR" 4
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468 .IX Item "GetFingerprintsString"
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469 .Vb 1
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|
470 \& $FingerprintsString = $FingerprintsTextFileIO\->GetFingerprintsString();
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471 .Ve
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472 .Sp
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|
473 Returns \fBFingerprintsString\fR for current data line.
|
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|
474 .IP "\fBIsFingerprintsDataValid\fR" 4
|
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|
475 .IX Item "IsFingerprintsDataValid"
|
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476 .Vb 1
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|
477 \& $Status = $FingerprintsTextFileIO\->IsFingerprintsDataValid();
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478 .Ve
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479 .Sp
|
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|
480 Returns 1 or 0 based on whether \fBFingerprintsObject\fR is valid.
|
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|
481 .IP "\fBIsFingerprintsFileDataValid\fR" 4
|
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482 .IX Item "IsFingerprintsFileDataValid"
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483 .Vb 1
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|
484 \& $Status = $FingerprintsTextFileIO\->IsFingerprintsFileDataValid();
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485 .Ve
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486 .Sp
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|
487 Returns 1 or 0 based on whether text file contains valid fingerprints data.
|
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|
488 .IP "\fBIsFingerprintsTextFile\fR" 4
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|
489 .IX Item "IsFingerprintsTextFile"
|
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|
490 .Vb 2
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|
491 \& $Status = $FingerprintsTextFileIO\->IsFingerprintsTextFile($FileName);
|
|
|
492 \& $Status = FileIO::FingerprintsTextFileIO::IsFingerprintsTextFile($FileName);
|
|
|
493 .Ve
|
|
|
494 .Sp
|
|
|
495 Returns 1 or 0 based on whether \fIFileName\fR is a fingerprints text file.
|
|
|
496 .IP "\fBNext or Read\fR" 4
|
|
|
497 .IX Item "Next or Read"
|
|
|
498 .Vb 2
|
|
|
499 \& $FingerprintsTextFileIO = $FingerprintsTextFileIO\->Next();
|
|
|
500 \& $FingerprintsTextFileIO = $FingerprintsTextFileIO\->Read();
|
|
|
501 .Ve
|
|
|
502 .Sp
|
|
|
503 Reads next available fingerprints line in text file, processes the data, generates appropriate
|
|
|
504 fingerprints object, and returns \fBFingerprintsTextFileIO\fR. The generated fingerprints object
|
|
|
505 is available using method \fBGetFingerprints\fR.
|
|
|
506 .IP "\fBSetBitStringFormat\fR" 4
|
|
|
507 .IX Item "SetBitStringFormat"
|
|
|
508 .Vb 1
|
|
|
509 \& $FingerprintsTextFileIO\->SetBitStringFormat($Format);
|
|
|
510 .Ve
|
|
|
511 .Sp
|
|
|
512 Sets bit string \fIFormat\fR for fingerprints bit-vector string data in a text file and returns
|
|
|
513 \&\fBFingerprintsTextFileIO\fR. Possible values for \fBBitStringFormat\fR: \fIBinaryString or HexadecimalString\fR.
|
|
|
514 .IP "\fBSetBitsOrder\fR" 4
|
|
|
515 .IX Item "SetBitsOrder"
|
|
|
516 .Vb 1
|
|
|
517 \& $FingerprintsTextFileIO\->SetBitsOrder($BitsOrder);
|
|
|
518 .Ve
|
|
|
519 .Sp
|
|
|
520 Sets \fIBitsOrder\fR for fingerprints bit-vector string data in a text file and returns \fBFingerprintsTextFileIO\fR.
|
|
|
521 Possible values for \fBBitsOrder\fR: \fIAscending or Descending\fR.
|
|
|
522 .IP "\fBSetColMode\fR" 4
|
|
|
523 .IX Item "SetColMode"
|
|
|
524 .Vb 1
|
|
|
525 \& $FingerprintsTextFileIO\->SetColMode($ColMode);
|
|
|
526 .Ve
|
|
|
527 .Sp
|
|
|
528 Sets \fIColMode\fR for a text file and returns \fBFingerprintsTextFileIO\fR. Possible values for \fBColMode\fR:
|
|
|
529 \&\fIColNum or ColLabel\fR.
|
|
|
530 .IP "\fBSetDataColLabels\fR" 4
|
|
|
531 .IX Item "SetDataColLabels"
|
|
|
532 .Vb 2
|
|
|
533 \& $FingerprintsTextFileIO\->SetDataColLabels(@ColLabels);
|
|
|
534 \& $FingerprintsTextFileIO\->SetDataColLabels(\e@ColLabels);
|
|
|
535 .Ve
|
|
|
536 .Sp
|
|
|
537 Sets \fIColLabels\fR for a text file using an array or a reference to an array containing column labels
|
|
|
538 and returns \fBFingerprintsTextFileIO\fR.
|
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539 .IP "\fBSetDataLineWords\fR" 4
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540 .IX Item "SetDataLineWords"
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541 .Vb 2
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542 \& $FingerprintsTextFileIO\->SetDataLineWords(@LineWords);
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543 \& $FingerprintsTextFileIO\->SetDataLineWords(\e@LineWords);
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544 .Ve
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545 .Sp
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546 Sets \fIDataLineWords\fR for a text file using an array or a reference to an array containing data words
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547 and returns \fBFingerprintsTextFileIO\fR.
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548 .IP "\fBSetDetailLevel\fR" 4
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549 .IX Item "SetDetailLevel"
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550 .Vb 1
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551 \& $FingerprintsTextFileIO\->SetDetailLevel($Level);
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552 .Ve
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553 .Sp
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554 Sets details \fILevel\fR for generating diagnostics messages during text file processing and returns
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555 \&\fBFingerprintsTextFileIO\fR. Possible values: \fIPositive integers\fR.
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556 .IP "\fBSetFingerprints\fR" 4
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557 .IX Item "SetFingerprints"
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558 .Vb 1
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559 \& $FingerprintsTextFileIO\->SetFingerprints($FingerprintsObject);
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560 .Ve
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561 .Sp
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562 Sets \fIFingerprintsObject\fR for current data line and returns \fBFingerprintsTextFileIO\fR.
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563 .IP "\fBSetFingerprintsString\fR" 4
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564 .IX Item "SetFingerprintsString"
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565 .Vb 1
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566 \& $FingerprintsTextFileIO\->SetFingerprintsString($FingerprintsString);
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567 .Ve
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568 .Sp
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569 Sets \fIFingerprintsString\fR for current data line and returns \fBFingerprintsTextFileIO\fR.
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570 .IP "\fBSetFingerprintsStringMode\fR" 4
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571 .IX Item "SetFingerprintsStringMode"
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572 .Vb 1
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573 \& $FingerprintsTextFileIO\->SetFingerprintsStringMode($Mode);
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574 .Ve
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575 .Sp
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576 Sets \fIFingerprintsStringMode\fR for text file and returns \fBFingerprintsTextFileIO\fR.
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577 Possible values: \fIAutoDetect, FingerprintsBitVectorString, or FingerprintsVectorString\fR
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578 .IP "\fBSetInDelim\fR" 4
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579 .IX Item "SetInDelim"
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580 .Vb 1
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581 \& $FingerprintsTextFileIO\->SetInDelim($InDelim);
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582 .Ve
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583 .Sp
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584 Sets \fIInDelim\fR for text file and returns \fBFingerprintsTextFileIO\fR. Possible values: \fIcomma,
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585 semicolon, tab\fR.
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586 .IP "\fBSetOutDelim\fR" 4
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587 .IX Item "SetOutDelim"
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588 .Vb 1
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589 \& $FingerprintsTextFileIO\->SetOutDelim($OutDelim);
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590 .Ve
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591 .Sp
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592 Sets \fIOutDelim\fR for text file and returns \fBFingerprintsTextFileIO\fR. Possible values: \fIcomma,
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593 semicolon, tab\fR.
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594 .IP "\fBSetVectorStringFormat\fR" 4
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595 .IX Item "SetVectorStringFormat"
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596 .Vb 1
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597 \& $FingerprintsTextFileIO\->SetVectorStringFormat($Format);
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598 .Ve
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599 .Sp
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600 Sets \fIVectorStringFormat\fR for text file and returns \fBFingerprintsTextFileIO\fR. Possible values:
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601 \&\fIIDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString\fR.
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602 .IP "\fBWriteFingerprints\fR" 4
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603 .IX Item "WriteFingerprints"
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604 .Vb 2
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605 \& $FingerprintsTextFileIO\->WriteFingerprints($FingerprintsObject,
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606 \& @DataColValues);
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607 .Ve
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608 .Sp
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609 Writes fingerprints string generated from \fIFingerprintsObject\fR object and other data including
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610 \&\fIDataColValues\fR to text file and returns \fBFingerprintsTextFileIO\fR.
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611 .IP "\fBWriteFingerprintsString\fR" 4
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612 .IX Item "WriteFingerprintsString"
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613 .Vb 2
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614 \& $FingerprintsSDFileIO\->WriteFingerprints($FingerprintsString,
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615 \& @DataColValues);
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616 .Ve
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617 .Sp
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618 Writes \fIFingerprintsString\fR and other data including \fIDataColValues\fR to text file and returns
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619 \&\fBFingerprintsTextFileIO\fR.
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620 .Sp
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621 Caveats:
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622 .Sp
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623 .Vb 3
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624 \& o FingerprintsStringMode, BitStringFormat, BitsOrder, VectorStringFormat
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625 \& values are ignored during writing of fingerprints and it\*(Aqs written to the file
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626 \& as it is.
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627 .Ve
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628 .SH "AUTHOR"
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|
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629 .IX Header "AUTHOR"
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630 Manish Sud <msud@san.rr.com>
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631 .SH "SEE ALSO"
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632 .IX Header "SEE ALSO"
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633 FingerprintsSDFileIO.pm, FingerprintsFPFileIO.pm
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634 .SH "COPYRIGHT"
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635 .IX Header "COPYRIGHT"
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636 Copyright (C) 2015 Manish Sud. All rights reserved.
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637 .PP
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638 This file is part of MayaChemTools.
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639 .PP
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640 MayaChemTools is free software; you can redistribute it and/or modify it under
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641 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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642 Software Foundation; either version 3 of the License, or (at your option)
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643 any later version.
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