@@ -1,100 +1,23 @@ -CC1C2CC(C2(C)C)CC1NC(=O)C3C(C(ON3Cc4cccc(c4)CN(Cc5ccccc5C(=O)O)C(CC(C)C)CN(C)C)CO)C(C)O 25007168 -CC1C(OC(=O)N1C(=O)CC(C)C)c2ccccc2 11436915 -CC=CCC(CCCO[Si](c1ccccc1)(c2ccccc2)C(C)(C)C)O 11440475 -CC(C)(C)OC(=O)C(CC=C)NC(=O)C(C)(CCC=C)N(Cc1ccccc1)C(=O)CNC(=O)c2ccccc2 11444185 -CCC1C(N(N=C1c2ccc(cc2)OC)c3ccccc3)c4ccccc4 11439705 -CC(c1ccccc1)NC(=O)C=C 11480756 -CC(=O)N(CCCCCOCc1ccccc1)c2cc3c(cn2)CC(C(=O)N3)c4cc(cc(c4)OC)OC 11443759 -CC(C)CC(=NOC1CC2C(=O)NC3(CC3C=CCCCCCC(C(=O)N2C1)NC(=O)OC4CCC4)C(=O)NS(=O)(=O)C5CC5)c6ccccc6 25010500 -COCC1C(C(C(C(O1)CCNC(=O)C(CNC(=O)OCc2ccccc2)NC(=O)OCc3ccccc3)OC)OS(=O)(=O)O)OC4C(C(C(C(O4)C(=O)O)OC5C(C(C(C(O5)COS(=O)(=O)O)OC6C(C(C(C(O6)C(=O)O)OC7C(C(C(C(O7)COS(=O)(=O)O)O)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O)NS(=O)(=O)O)O)OS(=O)(=O)O 11768481 -C=CC1CCCN1Cc2ccccc2 11480905 -CCCC(C(=O)NC(C(C)CC)C(=O)NC(CCCN=C(N)N)C(=O)N1CCCC1C(=O)CC(=O)N)NC(=O)C(C(C)O)NC(=O)C(C(C)CC)NC(=O)C(C(C)C)NC(=O)CNC(=O)CN(C)C(=O)C 24821384 -CC(c1ccco1)NC(=O)C 11469175 -c1ccc(cc1)CN2CCCCC2C3CCCCOC3=O 11437678 -CN1CC23c4c5c6c7c8c9c%10c%11c%12c%13c%14c%10c%10c8c6c6c4c4c8c6c%10c%14c6c8c8c%10c6c%13c6c%12c%12c%13c%11c9c9c7c7c5c2c2c5c7c9c%13c7c%12c9c6c%10c6c9c(c75)c2c2c6c8c4C32C1c1ccc(cc1)I 24895527 -CCCCCCCC(CC(=O)NC1C(C(C(OC1OCC=C)COC2C(C(C(C(O2)COCc3ccccc3)OP4(=O)OCc5ccccc5CO4)OC(=O)CC(CCCCCCC)OCc6ccccc6)NC(=O)OCC(Cl)(Cl)Cl)O)OC(=O)CC(CCCCCCC)OCc7ccccc7)OCc8ccccc8 11457628 -CCOc1ccccc1CN(Cc2cccc(c2)CN3C(C(C(O3)CO)C(C)O)C(=O)NC4CC5CC(C4C)C5(C)C)C(CC(C)C)CN(C)C 25004628 -CC1CCC2C(C(CC3(O2)CCC(C4(O3)CC(C(O4)CC=CCC=CCC(C(=O)OC)O)OC(=O)CC5CCCC(O5)CC(CC(CC6C(C=CC7(O6)CCC(C(O7)C(C1O)O)OC)C)O)O)C)OC)Cl 24866564 -CC(C)(C)C(=O)N1C(OC(=N1)c2ccccc2F)(CN)c3ccccc3 11439676 -CC(C)N(C(C)C)P(OCCC#N)OC1C2C(CO[Si](O[Si](O2)(C(C)C)C(C)C)(C(C)C)C(C)C)OC1n3cnc4c3c(ncn4)NCCOCCOCCNC(=O)CCCCC5C6C(CS5)NC(=O)N6 24808836 -CC(=O)OCC1C(C(C(C(O1)OC2C(OC(C(C2OC3C(C(C(C(O3)C(COC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C)OC)CO[Si](c4ccccc4)(c5ccccc5)C(C)(C)C)OC(=O)C)OC(=O)C)OC6C(C(C(C(O6)COC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C 11480372 -CC(=O)C=CC(=O)OC1C(C(C(O1)COCc2ccccc2)OCc3ccccc3)OCc4ccccc4 11443736 -CC1C(C2C(C(O1)OC3C4C(C(OC(O4)c5ccccc5)COCc6ccccc6)OC(C3OCc7ccccc7)OC8C(C(OC(C8OCc9ccccc9)OC1C(OC(C3C1OC(O3)(C)C)OC)C)CCOCc1ccccc1)OC(=O)Cc1ccccc1C#N)OC(O2)(C)C)OCc1ccccc1 11622301 -c1ccc(cc1)Sc2c(nccn2)Br 11482531 -[B].CC(C(=O)O)P(c1ccccc1)c2ccccc2 11437198 -CC(C(=O)NC(c1ccccc1)C(=O)O)NC(=O)Cc2cc(cc(c2)F)F 11440276 -C=CCC(CO)C=Cc1ccccc1 11469532 -CC(C)C(CC(=O)c1ccco1)O 11480835 -COCOCC(CO)NC(=O)OCc1ccccc1 11437122 -COC(c1ccccc1)C(=O)N2Cc3c([nH]nc3NC(=O)c4ccc(cc4)N5CCN(CC5)C6CC6)C2 11443428 -COc1cc2c(cc1OC)C(N(CC2)C(c3ccccc3)C(=O)N)CCc4ccc(c(c4)C(F)(F)F)F 11443734 -CC(=O)OCC1C(C(C(C(O1)OC)OC(=O)OCc2ccccc2)OCc3ccccc3)OC(=O)C 11443451 -CC(C)c1cc(c(c(c1)C(C)C)c2cc3ccccc3c-4c2OP(=O)(Oc5c4c6ccccc6cc5c7c(cc(cc7C(C)C)C(C)C)C(C)C)O)C(C)C.c1ccc(cc1)C(C(c2ccccc2)N)N 24878763 -C1CCC(CC1)(CS(=O)(=O)O)N 16724650 -COc1cc2c(c(c1)OC)C(N(CC2)C(=O)c3ccc(cc3)C(F)(F)F)c4ccc(cc4)c5ccccc5 11443754 -CC(C(=O)N1CCN(CC1)c2nc(nc(n2)N3CCN(CC3)C(=O)Cn4cc(nn4)CCCCN)Nc5ccc(c(c5)C(=O)O)c6c7ccc(cc7oc-8cc(=O)ccc68)O)n9cc(nn9)CCC(=O)O 24796268 -CCOC(=O)c1cc(n(c1C)CC(=O)NC2C3N(C2=O)C(=C(CS3)COC(=O)C)C(=O)O)c4ccccc4 11444099 -CC(=O)OCC1=C(N2C(C(C2=O)N3C(=O)CCCC3=O)SC1)C(=O)OC(c4ccccc4)c5ccccc5 11444012 -CC(C(=O)O)P(c1ccccc1)c2ccccc2 11437199 -Cc1cn(c(=O)[nH]c1=O)C2C(C(C(O2)COP(N(C(C)C)C(C)C)OCCC#N)OP(=O)(O)OCC3C(CC(O3)n4ccc(nc4=O)NCc5ccccc5)OP(=O)(O)OCC6C(CC(O6)n7ccc(nc7=O)NCc8ccccc8)OP(=O)(O)OCC9C(CC(O9)n1ccc(nc1=O)NCc1ccccc1)OC(=O)CCC(=O)C)O 11615145 -CC(Cn1cccc1)C=O 11469113 -CCC=CC1C(O1)C2=C(C(=O)C3(O2)C(C(NC3=O)(C(c4ccccc4)O)O)O[Si](CC)(CC)CC)C 11443723 -CC(C)C(c1ccccc1)NC(=O)c2ccc3c(c2)c(=C(C#N)C#N)c4ccccc4c3=C(C#N)C#N 11442997 -CC(C)(C)OC(=O)NC(CCC(=O)OCc1ccccc1)C(=O)Nc2cc3c(cc2CC=C)OCO3 11443346 c1ccc(cc1)S(=O)(=O)CCS 447093 -CC(c1ccccc1)N2C(C(C2=O)C=Cc3ccccc3)c4ccccc4 11439611 -[Si][As]([Si])[Si] 6327292 -CC(C)Cc1ccc(cc1)C(C)C(=O)OCCCNC(=O)c2cccnc2 11440058 -Cc1c2c(cccc2n(c1c3ccccc3)Cc4ccccc4)c5ccc(cc5)OCc6n[nH]nn6 11442814 -CCOC(=O)C(C(C1C(O1)c2ccccc2)O)O 11436671 -CCC(C)C(C(=O)NC(CC(=O)O)C(=O)NC(CC(C)C)C(=O)NC(C(C)C)C(=O)O)NC(=O)C1CCCN1C(=O)C(Cc2ccc(cc2)O)N 25002969 -CC(C)C(C(=O)NC(CCCCN)C(=O)NC(CCCCN)C(=O)NCC(=O)NCC(=O)NC(Cc1ccccc1)C(=O)NC(Cc2c[nH]c3c2cccc3)C(=O)NC(CS)C(=O)O)NC(=O)C(CS)N 24900670 -CC1CC(OC1=O)(C)c2ccccc2 11458174 -CCC(C)C(C(=O)NC(CC(C)C)C(=O)NCC(=O)NC(CCCCN)C(=O)NC(C(C)CC)C(=O)NC(Cc1c[nH]c2c1cccc2)C(=O)NC(CCCCN)C(=O)NC(C(C)CC)C(=O)NC(CCCCN)C(=O)NC(CCCCN)C(=O)NC(CC(C)C)C(=O)NC(Cc3ccccc3)C(=O)N)N 11446251 -CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)CO)O)N=C(C)N6CCc7c6cccc7)O.Cl 25004098 -CC(C(=O)NC(CCC(=O)NC(CCCCNC(=O)OCC[Si](C)(C)C)C(=O)NC(C)C(=O)NC(C)C(=O)OCC[Si](C)(C)C)C(=O)OCC[Si](C)(C)C)NC(=O)C(C)OC1C(C(OC(C1OC2C(C(C(C(O2)COC(=O)C)OC(=O)C)OC(=O)C)NC(=O)C)COC(=O)C)OP(=O)(OCc3ccccc3)OCc4ccccc4)NC(=O)C 11491891 -CCC=CC1C(O1)C2=C(C(=O)C3(O2)C(C(NC3=O)(C(c4ccccc4)O)O)O[Si](CC)(CC)CC)C 11443723 -c1ccc(cc1)COC(=O)C(C#N)c2cccs2 11436798 -CS(=O)(=O)N1CCc2c(c(nn2CC(CN3CCC(CC3)N4CCCC4=O)O)c5ccc(c(c5)CNC(=O)C=Cc6ccccc6)C(F)(F)F)C1 25003062 -Cc1ccnc(c1)NCCCC(=O)NCC(=O)NC(CC(=O)O)c2ccc(cc2)c3cccc(c3)CCCOCCOCCOCCCNC(=O)CCCC(=O)Nc4ccc(cc4)CCC(=O)CC(=O)C 24803779 -CS(=O)(=O)NC(CCc1ccccc1)C(=O)N2CC(CC2C(=O)NC(CCCCN)C(=O)C(=O)NCc3ccccc3)OCc4ccc(cc4)Cl 25006265 -CCCC(CC=C)N(CC=C)C(C)c1ccccc1 11436807 -c1ccc(cc1)n2cccc2C#N 11506526 -CCC(C(=O)NC(CC=Cc1ccccc1)C#N)N 11436803 -CN1CCN(CC1)Cc2ccc(cc2)C(=O)N(C3CCCCC3)Nc4c5c(nc(n4)C#N)n(cn5)C(=O)N6CCN(CC6)C.C(=O)(C(F)(F)F)O 25007644 -CCC1C(C=C(C=CC(=O)C(CC2CCOCC(=NOCc3ccc(nc3)c4cnccn4)COC(CC(=O)O1)C(C2OC5C(C(C(C(O5)C)O)N(C)C)O)C)C)C)COC6CCC(C(C6OC)OC)O 25003997 -CC(C)(C)C(C(=O)N1CC(CC1C(=O)NC2(CC2C=C)C(=O)NS(=O)(=O)C3CC3)(c4ccc(cc4)c5ccccc5)OC)NC(=O)OCCCF 25003040 -CC(C(=O)N(C)c1ccccc1)I 11471779 -COC(=O)C(CC=C)NS(=O)(=O)c1ccccc1 11437131 -CC1(OC(C(O1)C(CO)OCc2ccccc2)C=C)C 11437398 -CCC1C(C=C(C=CC(=O)C(CC2CCOCC(=NOCc3ccc(nc3)c4nnc(s4)N)COC(CC(=O)O1)C(C2OC5C(C(C(C(O5)C)O)N(C)C)O)C)C)C)COC6CCC(C(C6OC)OC)O 25005356 -CCC1C(C(C(C(=NNC(c2ccccc2)(c3ccccc3)c4ccccc4)C(CC(C(C(C(C(C(=O)O1)C)OC5CC(C(C(O5)C)O)(C)OC)C)OC6C(C(CC(O6)C)N(C)C)O)(C)O)C)C)O)(C)O 24879714 -c1ccc(cc1)CCC(C2CCC2)N=C(N)N=C(N)N 11437260 -CCCCCCCCCCCCCCCCC(C)C=C(C)C(=O)OC1C(C(OC(C1OC(=O)CCCCCCCCCCCCCCC)OC2C(C(C(C(O2)CO)O)OS(=O)(=O)O)OS(=O)(=O)O)CO)O 24996172 -Cc1cc(on1)CC(n2cccc2)O 11492083 +C=CC(CO)c1ccccc1 11446423 +C=CCCCC(c1ccco1)O 11446541 +CC1C(OC(=O)C1=C)c2ccccc2 11446798 +c1ccc(cc1)C23CCCC2CCO3 11446800 +CC(=O)NCCC=Cc1ccccc1 11446815 +C=CCC(=O)C(=Cc1ccccc1)F 11446820 +CC(C)(Cc1ccccc1)C(=O)C=O 11446821 +CC(=CCC(=O)Sc1ccccc1)C 11447122 +c1ccc(cc1)C2C(C2(Cl)Cl)C(=O)O 11447577 +COC(=O)CCC=CCOCc1ccccc1 11436250 CCOC1(CC1Cc2ccccc2)OC(=O)C 11436251 -CC1C(C(C(C(O1)OC2C(C(C(OC2OC(=O)C34CCC5(C(=CCC6C5(CCC7C6(CCC(C7(C)C)OC8C(C(C(C(O8)COC9C(C(C(CO9)O)O)OC1C(C(C(CO1)O)O)O)O)O)OC1C(C(C(C(O1)CO)O)O)O)C)C)C3CC(C(C4)OC(=O)C=Cc1ccccc1)(C)C)C)CO)O)O)O)OC1C(C(C(C(O1)CO)O)O)O)O 11457633 -CC(C(c1ccccc1)O)NCCCC2=CCC=CC2 11437193 -C[Si](C)(C)OC(CCOCc1ccccc1)CC=O 11437464 -COCC(=NOC1CC2C(=O)NC3(CC3C=CCCCCCC(C(=O)N2C1)NC(=O)OC4CCCC4)C(=O)NS(=O)(=O)C5CC5)c6ccccc6 25009415 -CC(c1ccccc1)C(=O)N2Cc3c([nH]nc3NC(=O)c4ccc(cc4)N5CCN(CC5)C(C)(C)C)C2 11443429 -CC(C)(C)c1c(c2cc(ccc2c(n1)OCCOC)OC)c3ccccc3 11439967 -CC(C)[Si](C(C)C)(C(C)C)OC1CC(N(C1CO[Si](C)(C)C(C)(C)C)C(=O)OCc2ccccc2)O 11444054 -CS(=O)(=O)N1CCc2c(c(nn2CC(CN3CCC(CC3)N4CCCC4=O)O)c5ccc(c(c5)CNC(=O)c6ccc(cc6O)F)C(F)(F)F)C1 25003061 -c1ccc(cc1)Cn2cnc3ccc(cc3c2=O)c4cn(nn4)c5ccccc5 11440363 -c1ccc(cc1)C2=C3CCOC(C3OC2=O)C4CC4 11436780 -CC(C)(C)OC(=O)NC(CC(=O)NC(c1ccccc1)(c2ccccc2)c3ccccc3)C(=O)N4CCCC4 11443912 -CC(=O)C(C(c1ccccc1)Nc2ccc(cc2)OC)O 11437611 -CC1COC(CS1=O)c2ccccc2 11481241 -Cc1c2c([n+]3n1C(=O)C(=C3O)c4ccccc4)CCCC2 11437445 -CC(C)CC(C(=O)NC(CC(C)C)C(=O)NC(C)C(=O)NC(CCSC)C(=O)NC(CCC(=O)N)C(=O)NC(C)C(=O)NC(Cc1cnc[nH]1)C(=O)NC(CC(C)C)C(=O)O)NC(=O)C(CCCCN)N 24986617 -CC1=C2C(C(=O)C3(C(CC4C(C3C(C(C2(C)C)(CC1OC(=O)C(C(c5ccccc5)NC(=O)c6ccccc6)O)O)OC(=O)c7ccccc7)(CO4)OC(=O)C)O)C)OC(=O)Nc8ccc(cc8)[N+](=O)[O-] 24866901 -CC1=CC(C2=C(N1)c3ccccc3C2=O)c4ccccc4 11437249 -CC(C)(C)OC(=O)NC(CCC(=O)OCc1ccccc1)C(=O)Nc2cc3c(cc2CC=C)OCO3 11443346 -CC1C2CC(C2(C)C)CC1NC(=O)C3C(C(ON3Cc4cccc(c4)CN(Cc5c(cccc5Cl)F)C(CC(C)(C)C)CN(C)C)CO)C(C)O 25003952 -CCC(C1C=CC2C(N1N(Cc3ccccc3)C[Si](C)(C)C)C(=O)N(S2=O)C(C)c4ccccc4)O 11443882 -CCC=C(c1ccccc1)C2C(CN2C(C)(C)C3CCC(CC3=O)C)(c4ccccc4)OCc5ccccc5 11443822 -C=CCC(=C1c2ccccc2N(C1=O)Cc3ccccc3)c4ccccc4 11439545 -c1ccc(cc1)CSC2C(C(C(CO2)OC3C(C(C(CO3)OC4C(C(C(CO4)OC5C(C(C(CO5)OC6C(C(C(CO6)OC7C(C(C(CO7)OC8C(C(C(CO8)OC9C(C(C(CO9)OC1C(C(C(CO1)OC1C(C(C(CO1)OC1C(C(C(CO1)OC1C(C(C(CO1)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O 11629577 -Cc1cccc(c1)NC(=O)N2CCC3(CC2)C(N(C3=O)c4ccc(cc4)C(F)(F)F)c5ccc(cc5)OCC(=O)NC(C)C(=O)NC(C)C(=O)O 25003637 -CC(C)[Si](C(C)C)(C(C)C)OC1C=COC2C1OC(OC2)c3ccccc3 11440706 +CC(CC(CC=C)O)COCc1ccccc1 11436255 +c1ccc(cc1)CC(=O)NCCCCCCN 11436256 +CC(C)(C=C)NC(=S)NCc1ccccc1 11436257 +c1cc(c-2c(c1)C(=O)c3n2ccc3)c4ccco4 11436269 +CC1=C(C(=O)N(C1Cl)Cc2ccccc2)C 11436281 +C=CC(CCCC=NCc1ccccc1)Cl 11436282 +Cn1c2c(cc(n(c2=O)O)c3ccccc3)cn1 11436428 +Cc1c2nc(nn2c(=S)[nH]n1)c3ccccc3 11436468 +C=C(CNc1ccccc1)c2ccc(cc2)Cl 11436473 +CC(=O)NNC=C1C(=O)OC(=N1)c2ccccc2 11436502 +C=C1CCCN(C1=O)C(=O)OCc2ccccc2 11436506 \ No newline at end of file data/fingerprint.txt @@ -4,8 +4,8 @@ <param name="japex.classPath" value="build/classes"/> <param name="japex.resultUnit" value="ms"/> - <param name="japex.warmupIterations" value="10"/> - <param name="japex.runIterations" value="50"/> + <param name="japex.warmupIterations" value="5"/> + <param name="japex.runIterations" value="25"/> <param name="japex.reportsDirectory" value="build/reports"/> @@ -13,16 +13,52 @@ <driver name="CDK-1.2.x"> <param name="japex.driverClass" value="net.openmolecules.benchmark.driver.FingerprintCDKBench"/> <param name="japex.classPath" value="${basedir}/lib/cdk-1.2.x-20090116.jar"/> - <param name="description" value="Benchmark of path based hashed fingperints"/> + <param name="description" value="Benchmark of path based hashed fingperints based on 22 molecules. + Before fingerprints, atom typing and aromatcity perception is performed."/> </driver> <driver name="CDK-trunk-13858"> <param name="japex.driverClass" value="net.openmolecules.benchmark.driver.FingerprintCDKBench"/> <param name="japex.classPath" value="${basedir}/lib/cdk-trunk-13858.jar"/> - <param name="description" value="Benchmark of path based hashed fingperints"/> + <param name="description" value="Benchmark of path based hashed fingperints based on 22 molecules + Before fingerprints, atom typing and aromaticity perception is performed"/> </driver> </driverGroup> <testCase name="test1"> <param name="japex.inputFile" value="data/fingerprint.txt" /> - </testCase> -</testSuite> \ No newline at end of file + <param name="fplength" value="1024" /> + <param name="fpdepth" value="4" /> + <param name="type" value="standard" /> + </testCase> + <testCase name="test2"> + <param name="japex.inputFile" value="data/fingerprint.txt" /> + <param name="fplength" value="1024" /> + <param name="fpdepth" value="6" /> + <param name="type" value="standard" /> + </testCase> + <testCase name="test3"> + <param name="japex.inputFile" value="data/fingerprint.txt" /> + <param name="fplength" value="1024" /> + <param name="fpdepth" value="8" /> + <param name="type" value="standard" /> + </testCase> + + <testCase name="test4"> + <param name="japex.inputFile" value="data/fingerprint.txt" /> + <param name="fplength" value="1024" /> + <param name="fpdepth" value="4" /> + <param name="type" value="extended" /> + </testCase> + <testCase name="test5"> + <param name="japex.inputFile" value="data/fingerprint.txt" /> + <param name="fplength" value="1024" /> + <param name="fpdepth" value="6" /> + <param name="type" value="extended" /> + </testCase> + <testCase name="test6"> + <param name="japex.inputFile" value="data/fingerprint.txt" /> + <param name="fplength" value="1024" /> + <param name="fpdepth" value="8" /> + <param name="type" value="extended" /> + </testCase> +</testSuite> fingerprint-config.xml @@ -26,12 +26,14 @@ package net.openmolecules.benchmark.driver; import com.sun.japex.JapexDriverBase; import com.sun.japex.TestCase; -import org.openscience.cdk.DefaultChemObjectBuilder; +import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.fingerprint.ExtendedFingerprinter; import org.openscience.cdk.fingerprint.Fingerprinter; +import org.openscience.cdk.fingerprint.IFingerprinter; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.io.iterator.IteratingSMILESReader; -import org.openscience.cdk.smiles.SmilesParser; +import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import java.io.FileInputStream; import java.io.FileNotFoundException; @@ -49,31 +51,37 @@ import java.util.List; */ public class FingerprintCDKBench extends JapexDriverBase { private List<IAtomContainer> mols; - private SmilesParser smilesParser; - private Fingerprinter fingerprinter; - - private int length = 6; - private int depth = 1024; + private IFingerprinter fingerprinter; public void initializeDriver() { } public void prepare(TestCase testCase) { - fingerprinter = new Fingerprinter(length, depth); - smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance()); String fileName = testCase.getParam("japex.inputFile"); + int length = Integer.parseInt(testCase.getParam("fplength")); + int depth = Integer.parseInt(testCase.getParam("fpdepth")); + String type = testCase.getParam("type"); + if (type.equals("standard")) fingerprinter = new Fingerprinter(length, depth); + else if (type.equals("extended")) fingerprinter = new ExtendedFingerprinter(length, depth); + mols = new ArrayList<IAtomContainer>(); try { IteratingSMILESReader reader = new IteratingSMILESReader(new FileInputStream(fileName)); - while (reader.hasNext()) mols.add((IAtomContainer) reader.next()); + while (reader.hasNext()) { + IAtomContainer tmp = (IAtomContainer) reader.next(); + AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(tmp); + CDKHueckelAromaticityDetector.detectAromaticity(tmp); + mols.add(tmp); + } } catch (FileNotFoundException e) { + } catch (CDKException e) { } } public void run(TestCase testCase) { for (IAtomContainer atomContainer : mols) { try { - fingerprinter.getFingerprint(atomContainer); + fingerprinter.getFingerprint(atomContainer); } catch (CDKException e) { } } src/net/openmolecules/benchmark/driver/FingerprintCDKBench.java 31e4ef035e651e1d62605df327c2461b7c583ce1 Rajarshi Guha rajarshi.guha@gmail.com http://github.com/rapodaca/cheminfbenchmark/commit/599050723be31a4267fef216c96668234058a123 599050723be31a4267fef216c96668234058a123 2009-01-17T18:58:03-08:00 2009-01-17T18:58:03-08:00 version of fp benchmark that runs in reasonable time. Also updated to take fp params via the config file, so we can test multiple fingerprints and parameters ffcae5b7cdd4ad6c1f30cbf88663a675b3a0798d Rajarshi Guha rajarshi.guha@gmail.com