diff --git a/images/figures/figure_5.jpeg b/images/figures/figure_5.jpeg deleted file mode 100644 index 4a54cf53..00000000 Binary files a/images/figures/figure_5.jpeg and /dev/null differ diff --git a/images/figures/figure_5.png b/images/figures/figure_5.png new file mode 100644 index 00000000..cbe4d0dd Binary files /dev/null and b/images/figures/figure_5.png differ diff --git a/paper.md b/paper.md index 2fdf453f..0ba7022e 100644 --- a/paper.md +++ b/paper.md @@ -218,7 +218,7 @@ An interesting observation from the present data is the ability of tools to hand documentation as a `C&1&1&1&1`. As shown in Table 2, this fails in both `RDKit` and `Indigo` indicating that improve handling of the `&` operator is required.

- + Figure 6: Penalty Score distributions

diff --git a/tests/cgenff/global_chem_test/18/log/trial.log b/tests/cgenff/global_chem_test/18/log/trial.log new file mode 100644 index 00000000..2c52692c --- /dev/null +++ b/tests/cgenff/global_chem_test/18/log/trial.log @@ -0,0 +1,115 @@ +Compound Success: O(c1ccc(OC)cc1CCN)C , IUPAC Name: 2c-h +Compound Success: CCC(=O)N(CC(C)N(C)CCC1=CC=CC=C1)C2=CC=CC=C2 , IUPAC Name: diampromideCompound Success: CCC(=O)N(C1CCN(CC1C)CCC2=CC=CS2)C3=CC=CC=C3 , IUPAC Name: 3-methylthiofentanyl +Compound Success: CC1=NC2=CC=CC=C2C(=O)N1C3=CC=CC=C3Cl , IUPAC Name: mecloqualone + +Compound Success: CC(CC1=CC2=C(C=C1)OCO2)N , IUPAC Name: 3,4-methylenedioxyamphetamine +Compound Success: C1CCC23CCN(C(C2C1)CC4=C3C=C(C=C4)O)CC(=O)C5=CC=CC=C5 , IUPAC Name: levophenacylmorphan +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3CCC4 , IUPAC Name: desomorphine +Compound Success: COC1=CC=CC=C1CNCCC2=CC(=C(C=C2OC)I)OC , IUPAC Name: 2c-i-nbome +Compound Success: CC(=O)OC1C=CC2C3CC4=C5C2(C1OC5=C(C=C4)OC(=O)C)CCN3C , IUPAC Name: heroin +Compound Success: CC(=O)OC1CCC2C3CC4=C5C2(C1OC5=C(C=C4)OC)CCN3C , IUPAC Name: acetyldihydrocodeine +Compound Success: CN(C)CCC1=CNC2=C1C(=CC=C2)O , IUPAC Name: psilocyn +Compound Success: COc2ccccc2CNCCc(cc1OC)c(OC)cc1Cl , IUPAC Name: 2c-c-nbome +Compound Success: CCC(=O)N(C1CCN(CC1)CC(C2=CC=CS2)O)C3=CC=CC=C3 , IUPAC Name: beta-hydroxythiofentanyl +Compound Success: CCC(=O)OC1(CCN(CC1CC=C)C)C2=CC=CC=C2 , IUPAC Name: allylprodine +Compound Success: CC1=CC=CC=C1N2C(=NC3=CC=CC=C3C2=O)C , IUPAC Name: methaqualone +Compound Success: CCN(CC)C(=O)C1CN(C2CC3=CNC4=CC=CC(=C34)C2=C1)C , IUPAC Name: lysergicaciddiethylamide +Compound Success: C[N+]1(CCC23C4C1CC5=C2C(=C(C=C5)OC)OC3C(C=C4)O)[O-] , IUPAC Name: codeine-n-oxide +Compound Success: CCC(=O)C(CC(C)N1CCOCC1)(C2=CC=CC=C2)C3=CC=CC=C3 , IUPAC Name: phenadoxone +Compound Success: CC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3 , IUPAC Name: acetylfentanyl +Compound Success: C(CC(=O)O)CO , IUPAC Name: gamma-hydroxybutyricacid +Compound Success: COc1cc(CC)c(cc1CCN)OC , IUPAC Name: 2c-e +Compound Success: CC(CC1=CC2=C(C(=C1)OC)OCO2)N , IUPAC Name: 5-methoxy-3,4-methylenedioxy-amphetamine +Compound Success: CN1CCCC(C1)OC(=O)C(C2=CC=CC=C2)(C3=CC=CC=C3)O , IUPAC Name: n-methyl-3-piperidylbenzilate +Compound Success: CC(CC1=CC2=C(C=C1)OCO2)NO , IUPAC Name: n-hydroxy-3,4-methylenedioxyamphetamine +Compound Success: CCCCCN1C2=CC=CC=C2C(=N1)C(=O)NC(C(C)C)C(=O)N , IUPAC Name: ab-pinaca +Compound Success: FCCCCCN1C=C(C(OC2=C(C=CC=C3)C3=CC=C2)=O)C4=CC=CC=C41 , IUPAC Name: nm2201 +Compound Success: CC1=CCC2C3CC4=C5C2(C1OC5=C(C=C4)O)CCN3C , IUPAC Name: methyldesorphine +Compound Success: CN(C)CCC1=CNC2=C1C(=CC=C2)OP(=O)(O)O , IUPAC Name: psilocybin +Compound Success: CCOC(=O)C1(CCN(CC1)CCC(C2=CC=CC=C2)O)C3=CC=CC=C3 , IUPAC Name: phenoperidine +Compound Success: O=C(N(C1=CC=CC=C1)C2CCN(CCC3=CC=CC=C3)CC2)OCC , IUPAC Name: fentanylcarbamate +Compound Success: CCCCCn3c1ccccc1c(c3)C(=O)c4c2ccccc2c(OC)cc4 , IUPAC Name: jwh-081 +Compound Success: CC(C)C(C(=O)OC)NC(=O)C1=NN(C2=CC=CC=C21)CCCCCF , IUPAC Name: 5f-amb +Compound Success: CC(C)(C)C(C(=O)OC)NC(=O)C1=NN(C2=CC=CC=C21)CC3=CC=C(C=C3)F , IUPAC Name: mdmb-fubinaca +Compound Success: CCCCCCCCCCCCCC(=O)OC1C=CC2C3CC4=C5C2(C1OC5=C(C=C4)OCC6=CC=CC=C6)CCN3C , IUPAC Name: myrophine +Compound Success: CC(C)(C1CC23C=CC1(C4C25CCN(C3CC6=C5C(=C(C=C6)O)O4)CC7CC7)OC)O , IUPAC Name: cyprenorphine +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)OS(=O)(=O)C)OC3C(C=C4)O , IUPAC Name: morphinemethylsulfonate +Compound Success: O=C(CC)N(C1CCN(CCC2=CC=CC=C2)CC1)C3=CC=C(C)C=C3 , IUPAC Name: para-methylfentanylCompound Success: CC(CC1=CC(=C(C(=C1)OC)OC)OC)N , IUPAC Name: 3,4,5-trimethoxyamphetamine + +Compound Success: CCC1CN(CCC1(C2=CC=CC=C2)OC(=O)CC)C , IUPAC Name: alphameprodine +Compound Success: C1CN(CCC1N(C2=CC=CC=C2)C(=O)C3=CC=CO3)CCC4=CC=CC=C4 , IUPAC Name: furanylfentanyl +Compound Success: CC(CC1=CC=CC=C1)N2CCC(CC2)N(C3=CC=CC=C3)C(=O)C , IUPAC Name: acetyl-alpha-methylfentanyl +Compound Success: C1CCC(CC1)(C2=CC=CS2)N3CCCCC3 , IUPAC Name: thiophene-phencyclidine +Compound Success: C1CC1C(=O)N(C2CCN(CC2)CCC3=CC=CC=C3)C4=CC=CC=C4 , IUPAC Name: cyclopropylfentanyl +Compound Success: c1ccccc1C3(N2CCCC2)CCCCC3 , IUPAC Name: pyrrolidine-phencyclidine +Compound Success: FC1=CC=CC(=C1)C(C(C)NC)=O , IUPAC Name: 3-fmc +Compound Success: CCCC(C(=O)C1=CC=CC=C1)NC , IUPAC Name: pentedrone +Compound Failed: C[N+]1(CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O)C.[Br-] , IUPAC Name: morphinemethylbromide +Compound Success: CCOC(=O)C1(CCN(CC1)CCN2CCOCC2)C3=CC=CC=C3 , IUPAC Name: morpheridine +Compound Success: CCC(=O)OC1(CCCN(CC1C)C)C2=CC=CC=C2 , IUPAC Name: proheptazine +Compound Success: CCC(CC1=CNC2=CC=CC=C21)N , IUPAC Name: alpha-ethyltryptamine +Compound Success: CCC(=O)OC1(CC(N(CC1C)C)C)C2=CC=CC=C2 , IUPAC Name: trimeperidineCompound Success: Clc2ccccc2CC(=O)c1cn(CCCCC)c3ccccc13 , IUPAC Name: jwh-203 + +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)OCCN6CCOCC6)OC3C(C=C4)O , IUPAC Name: pholcodine +Compound Success: O=C(CCC1=CC=CC=C1)N(C2CCN(CCC3=CC=CC=C3)CC2)C4=CC=CC=C4 , IUPAC Name: beta′-phenylfentanyl +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)OC)OC3C(C=C4)OC(=O)C6=CN=CC=C6 , IUPAC Name: nicocodeine +Compound Success: FCCCCCN1C=C(C(C2C(C)(C)C2(C)C)=O)C3=C1C=CC=C3 , IUPAC Name: 5-fluoro-ur-144 +Compound Success: CC(CC1=CNC2=CC=CC=C21)N , IUPAC Name: alpha-methyltryptamine +Compound Success: CCC(C(=O)C1=CC2=C(C=C1)OCO2)NC , IUPAC Name: butyloneCompound Success: C1CC(OC1)C(=O)N(C2CCN(CC2)CCC3=CC=CC=C3)C4=CC=CC=C4 , IUPAC Name: tetrahydrofuranylfentanylCompound Success: CCC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3F , IUPAC Name: ortho-fluorofentanyl + + +Compound Success: C[C@@H](CN1CCOCC1)C(c1ccccc1)(c1ccccc1)C(=O)N1CCCC1 , IUPAC Name: levomoramideCompound Success: CCC(=O)C(CC(C)N1CCCCC1)(C2=CC=CC=C2)C3=CC=CC=C3 , IUPAC Name: dipipanone + +Compound Success: CCOC(=O)C1(CCN(CC1)CCOCC2CCCO2)C3=CC=CC=C3 , IUPAC Name: furethidine +Compound Success: C1=CC=C2C(=C1)C(=CN2CCCCCF)C(=O)OC3=CC=CC4=C3N=CC=C4 , IUPAC Name: quinolin-8-yl1-(5-fluoropentyl)-1h-indole-3-carboxylate +Compound Success: CCCC(C(=O)C1=CC=C(C=C1)Cl)N2CCCC2 , IUPAC Name: 4′-chloro-alpha-pvp +Compound Success: CC(CC1=CC=C(C=C1)OC)NC , IUPAC Name: para-methoxymethamphetamine +Compound Success: Ic1cc(OC)c(cc1OC)CCN , IUPAC Name: 2c-i +Compound Success: CCOC(=O)C(CCN1CCOCC1)(c1ccccc1)c1ccccc1 , IUPAC Name: dioxaphetylbutyrateCompound Success: COc2ccccc2CC(=O)c(c3ccccc13)cn1CCCCC , IUPAC Name: jwh-250 + +Compound Success: CCOC(=O)C1(CCC=CC1N(C)C)C2=CC=CC=C2 , IUPAC Name: tilidine +Compound Success: CCC(=O)N(C1=CC=CC=C1)C(C)CN2CCCCC2 , IUPAC Name: phenampromide +Compound Success: CCSc1cc(OC)c(cc1OC)CCN , IUPAC Name: 2c-t-2 +Compound Success: O=C(N[C@H](C(OC)=O)C(C)(C)C)C1=CN(CCCCCF)C2=C1C=CC=C2 , IUPAC Name: 5f-mdmb-pica +Compound Success: CC(CN1CCOCC1)C(C2=CC=CC=C2)(C3=CC=CC=C3)C(=O)N4CCCC4 , IUPAC Name: racemoramide +Compound Success: O=C(N(C1CCN(CCC2=CC=CC=C2)CC1)C3=CC=CC=C3)C4=CC=CS4 , IUPAC Name: thiofuranylfentanyl +Compound Success: CCC(=O)N(C1CCN(CC1C)CC(C2=CC=CC=C2)O)C3=CC=CC=C3 , IUPAC Name: beta-hydroxy-3-methylfentanyl +Compound Success: CCCSC1=C(C=C(C(=C1)OC)CCN)OC , IUPAC Name: 2,5-dimethoxy-4-(n)-propylthiophenethylamine +Compound Success: COC1=CC(=CC(=C1OC)OC)CCN , IUPAC Name: peyoteCompound Success: CCC1CC2CC3C1N(C2)CCC4=C3NC5=C4C=C(C=C5)OC , IUPAC Name: ibogaine + +Compound Success: O=C(NC(C)(C)C1=CC=CC=C1)C2=NN(CCCCC#N)C3=C2C=CC=C3 , IUPAC Name: 4-cn-cumyl-butinaca +Compound Success: CCCCCCCC(C)(C)C1=CC(=C(C=C1)C2CCCC(C2)O)O , IUPAC Name: cannabicyclohexanol +Compound Success: CC1=CC=C(C(C(CCCC)N2CCCC2)=O)C=C1 , IUPAC Name: 4′-methyl-alpha-pyrrolidinohexanophenone +Compound Success: C1CCN(CC1)C2(CCN(CC2)CCC(C#N)(C3=CC=CC=C3)C4=CC=CC=C4)C(=O)N , IUPAC Name: piritramide +Compound Success: C1C2CC3CC1CC(C2)(C3)NC(=O)C4=NN(C5=CC=CC=C54)CC6=CC=C(C=C6)F , IUPAC Name: fub-apinaca +Compound Success: CC(N=C(N)O1)C1C2=CC=C(C)C=C2 , IUPAC Name: 4,4′-dimethylaminorex +Compound Success: C1C(CCN(C1)CCc1ccccc1)N(c1ccc(cc1)F)C(=O)CCC , IUPAC Name: para-fluorobutyrylfentanyl +Compound Success: CCNC(C)C(=O)C1=CC=C(C=C1)C , IUPAC Name: 4-mec +Compound Success: CC(CC1=CC=CC=C1)N(C)C , IUPAC Name: n,n-dimethylamphetamine +Compound Success: O=C(CCC)N(C1CCN(CCC2=CC=CC=C2)CC1)C3=CC=C(OC)C=C3 , IUPAC Name: para-methoxybutyrylfentanyl +Compound Success: CN(C)C1CCCCC1N(C)C(=O)C2=CC(=C(C=C2)Cl)Cl , IUPAC Name: pinky +Compound Success: CC(C)N(CCC1=CNC2=C1C=C(C=C2)OC)C(C)C , IUPAC Name: 5-methoxy-n,n-diisopropyltryptamine +Compound Success: O=C(C1=NN(C2=C1C=CC=C2)CCCCCF)NC34CC5CC(C4)CC(C5)C3 , IUPAC Name: 5f-apinaca +Compound Success: CCCCN1C=C(C2=CC=CC=C21)C(=O)C3=CC=CC4=CC=CC=C43 , IUPAC Name: jwh-073 +Compound Success: CC(C)C(C(=O)OC)NC(=O)C1=CN(C2=CC=CC=C21)CC3CCCCC3 , IUPAC Name: mmb-chmica +Compound Success: CCCCCN1C=C(C(C2=CC=CC3=CC=CC=C32)=O)C4=CC=CC=C41 , IUPAC Name: jwh-018 +Compound Success: CC(CC1=C(C=CC(=C1)OC)OC)N , IUPAC Name: 2,5-dimethoxyamphetamineCompound Success: CCNC(C)C(=O)C1=CC2=C(C=C1)OCO2 , IUPAC Name: ethylone + +Compound Success: CC(NCC)CC1=CC=CC=C1 , IUPAC Name: n-ethylamphetamineCompound Success: CCCCCn1cc(c2c1cccc2)C(=O)c3ccc(cc3)OC , IUPAC Name: rcs-4 +Compound Success: O=C(C1=CC=CO1)N(C2CCN(CCC3=CC=CC=C3)CC2)C4=CC=C(F)C=C4 , IUPAC Name: para-fluorofuranylfentanyl + +Compound Success: C1(=CC=CC=C1)C(C(CCCC)N2CCCC2)=O , IUPAC Name: alpha-pyrrolidinohexiophenone +Compound Success: CCN(CC)C(C)C=C(C1=CC=CS1)C2=CC=CS2 , IUPAC Name: diethylthiambutene +Compound Success: CN1CCC23C4C(CCC2(C1CC5=C3C(=C(C=C5)O)O4)O)O , IUPAC Name: hydromorphinol +Compound Success: O=C(OC1CCCN(CC)C1)C(O)(c2ccccc2)c3ccccc3 , IUPAC Name: n-ethyl-3-piperidylbenzilate +Compound Success: COc1ccccc1CC(=O)c2cn(c3c2cccc3)CCC4CCCCC4 , IUPAC Name: rcs-8 +Compound Success: CC(C)C(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3 , IUPAC Name: isobutyrylfentanylCompound Success: COC1=CC(=CC(=C1OC)OC)CCN , IUPAC Name: mescaline + +Compound Success: CC1=CC=C(C=C1)C(=O)C(C)N2CCCC2 , IUPAC Name: 4-mepppCompound Success: C1CCC23CCN(C(C2C1)CC4=C3C=C(C=C4)O)CCC5=CC=CC=C5 , IUPAC Name: phenomorphan + +Compound Success: CCC(C(CC(C)N(C)C)(C1=CC=CC=C1)C2=CC=CC=C2)O , IUPAC Name: alphamethadol +Compound Success: CC=CC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3 , IUPAC Name: crotonylfentanyl +Compound Success: CCCC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=C(C=C3)F , IUPAC Name: ortho-fluorobutyrylfentanyl +Compound Success: CCC(C(CC(C)N(C)C)(C1=CC=CC=C1)C2=CC=CC=C2)O , IUPAC Name: dimepheptanol +Compound Success: CN(C)CCC1=CNC2=C1C=C(C=C2)O , IUPAC Name: bufotenine +Compound Success: O=C(C1=NN(CCCCC)C2=C1C=CC=C2)NC(C(C)(C)C)C(N)=O , IUPAC Name: n-(1-amino-3,3-dimethyl-1-oxobutan-2-yl)-1-pentyl-1h-indazole-3-carboxamideCompound Success: CCN(CC)CCN1C2=C(C=C(C=C2)[N+](=O)[O-])N=C1CC3=CC=C(C=C3)OCC , IUPAC Name: etonitazene diff --git a/tests/cgenff/global_chem_test/19/log/trial.log b/tests/cgenff/global_chem_test/19/log/trial.log new file mode 100644 index 00000000..38840fa7 --- /dev/null +++ b/tests/cgenff/global_chem_test/19/log/trial.log @@ -0,0 +1,61 @@ + 1,1 Top +Compound Success: CN1CCC23CCCCC2C1CC4=C3C=C(C=C4)OC , IUPAC Name: racemethorphan +Compound Success: CC(CC1=CC=CC=C1)NC(=O)C(CCCCN)N , IUPAC Name: lisdexamfetamine +Compound Success: CCC(=O)OC1(CCN(CC1C)C)C2=CC=CC=C2 , IUPAC Name: alphaprodineCompound Success: C1CCC(CC1)(C2=CC=CC=C2)N3CCCCC3 , IUPAC Name: phencyclidine + +Compound Success: CC1C2CC3=C(C1(CCN2C)C)C=C(C=C3)O , IUPAC Name: metazocine +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)OC)OC3C(C=C4)O , IUPAC Name: codeine +Compound Success: CCOC1=C2C3=C(CC4C5C3(CCN4C)C(O2)C(C=C5)O)C=C1 , IUPAC Name: ethylmorphine +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)OC)OC3C(=O)CC4 , IUPAC Name: hydrocodone +Compound Success: CN1CCC23CCCCC2C1CC4=C3C=C(C=C4)OC , IUPAC Name: levomethorphan +Compound Success: O=C(OCC)C2(c1ccccc1)CCNCC2 , IUPAC Name: pethidine-intermediate-b +Compound Success: CCC(=O)N(C1=CC=CC=C1)C2(CCN(CC2)CCC3=CC=CC=C3)C(=O)OC , IUPAC Name: carfentanil +Compound Success: CCC(=O)N(C1=CC=CC=C1)C2(CCN(CC2)CCC3=CC=CS3)COC , IUPAC Name: sufentanil +Compound Success: CCC(C1=CC(=CC=C1)O)C(C)CN(C)C , IUPAC Name: tapentadol +Compound Success: COC(=O)C(C1CCCCN1)C2=CC=CC=C2 , IUPAC Name: methylphenidate +Compound Success: CCCC(C)C1(C(=O)NC(=O)NC1=O)CC=C , IUPAC Name: secobarbital +Compound Success: CC12C(=O)CCC3C14CCN(C3CC5=C4C(=C(C=C5)O)O2)C , IUPAC Name: metopon +Compound Success: CN1CCC(CC1)(C#N)c2ccccc2 , IUPAC Name: pethidine-intermediate-a +Compound Success: CC(CC1=CC=CC=C1)N , IUPAC Name: amphetamine +Compound Success: CC1C2CC3=C(C1(CCN2CCC4=CC=CC=C4)C)C=C(C=C3)O , IUPAC Name: phenazocine +Compound Success: CCC(=O)C(CC(C)N(C)C)(C1=CC=CC=C1)C2=CC=CC=C2 , IUPAC Name: methadone +Compound Success: CCC(=O)C(C1=CC=CC=C1)(C2=CC=CC=C2)C(C)CN(C)C , IUPAC Name: isomethadone +Compound Success: COC1=C(SC=C1)CNCCC2(CCOC3(C2)CCCC3)C4=CC=CC=N4 , IUPAC Name: oliceridine +Compound Success: CCC(=O)N(C1=CC=CC=C1)C2(CCN(CC2)CCN3C(=O)N(N=N3)CC)COC , IUPAC Name: alfentanil +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O , IUPAC Name: morphine +Compound Success: CN1CCC23CCCCC2C1CC4=C3C=C(C=C4)O , IUPAC Name: levorphanol +Compound Success: CCCCCCC(C)(C)C1=CC(=C2C3CC(=O)CCC3C(OC2=C1)(C)C)O , IUPAC Name: nabilone +Compound Success: C1CN(CCC1NC2=CC=CC=C2)CCC3=CC=CC=C3 , IUPAC Name: 4-anilino-n-phenethylpiperidine +Compound Success: CN1CCC23CCCCC2C1CC4=C3C=C(C=C4)O , IUPAC Name: racemorphan +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O , IUPAC Name: granulated-opium +Compound Success: CN1CCC23C4C(=CC=C2C1CC5=C3C(=C(C=C5)O)O4)OC , IUPAC Name: oripavine +Compound Success: CCCC(C)(C1CC23CCC1(C4C25CCN(C3CC6=C5C(=C(C=C6)O)O4)C)OC)O , IUPAC Name: dihydroetorphine +Compound Success: CN1CCC23C4C(=CC=C2C1CC5=C3C(=C(C=C5)OC)O4)OC , IUPAC Name: thebaine +Compound Success: CCC(=O)OC(CC1=CC=CC=C1)(C2=CC=CC=C2)C(C)CN(C)C , IUPAC Name: dextropropoxyphene +Compound Success: CCC1(CCC(=O)NC1=O)C2=CC=CC=C2 , IUPAC Name: glutethimide +Compound Success: CC(CC(C#N)(C1=CC=CC=C1)C2=CC=CC=C2)N(C)C , IUPAC Name: methadone-intermediate +Compound Success: CN1CCC(CC1)(C2=CC=CC=C2)C(=O)O , IUPAC Name: pethidine-intermediate-c +Compound Success: CCOC(=O)C1(CCN(CC1)CCCNC2=CC=CC=C2)C3=CC=CC=C3 , IUPAC Name: piminodine +Compound Success: C1CCC(CC1)(C2=CC=CC=C2)N , IUPAC Name: 1-phenylcyclohexylamine +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)OC)OC3C(CC4)O , IUPAC Name: dihydrocodeine +Compound Success: CN1CC[C@]23[C@H]4OC5=C(O)C=CC(C[C@@H]1[C@]2(O)CCC4=O)=C35 , IUPAC Name: oxymorphone +Compound Success: C1CC2(C3CC4=C5C2(CCN3)C(C1=O)OC5=C(C=C4)O)O , IUPAC Name: noroxymorphone +Compound Success: CC(CC1=CC=CC=C1)NC , IUPAC Name: methamphetamine +Compound Success: CC1C(OCCN1)C2=CC=CC=C2 , IUPAC Name: phenmetrazine +Compound Success: COCC(=O)N(C1=CC=CC=C1)C2(CCN(CC2)CCC3=CC=CS3)C(=O)OC , IUPAC Name: thiafentanil +Compound Success: CCC(=O)N(C1CCN(CC1)CCC2=CC=CC=C2)C3=CC=CC=C3 , IUPAC Name: fentanyl +Compound Failed: CCCC(C)(C1CC23C=CC1(C4C25CCN(C3CC6=C5C(=C(C=C6)O)O4)C)OC)O.Cl ,IUPAC Name: etorphinehydrochloride + Compound Success: CCOC(=O)C1(CCN(CC1)CCC(C#N)(C2=CC=CC=C2)C3=CC=CC=C3)C4=CC=CC=C4 ,IUPAC Name: diphenoxylate +Compound Success: CCC1(C(=O)NC(=O)NC1=O)CCC(C)C , IUPAC Name: amobarbital +Compound Success: CCOC(=O)C1(CCN(CC1)CCC2=CC=C(C=C2)N)C3=CC=CC=C3 , IUPAC Name: anileridine +Compound Success: CC(=O)CC1=CC=CC=C1 , IUPAC Name: phenylacetone +Compound Success: CCC(=O)N1C2=CC=CC=C2N(C1=O)C3CCN(CC3)CCC(C#N)(C4=CC=CC=C4)C5=CC=CC=C5 , IUPAC Name: bezitramide +Compound Success: CCCCCC1=CC(=C2C3C=C(CCC3C(OC2=C1)(C)C)C)O , IUPAC Name: dronabinol +Compound Success: C1CCC(CC1)(C#N)N2CCCCC2 , IUPAC Name: 1-piperidinocyclohexanecarbonitrile +Compound Success: O=C(C1(CCN(CC1)C)C2=CC=CC=C2)OCC , IUPAC Name: pethidine +Compound Success: O=C(O)C(c1ccccc1)(c2ccccc2)C(C)CN3CCOCC3 , IUPAC Name: moramide-intermediate +Compound Success: CC[C@]([H])(C(C[C@@]([H])(C)N(C)C)(c1ccccc1)c2ccccc2)OC(=O)C , IUPAC Name: levo-alphacetylmethadol +Compound Success: CCC(=O)N(C1=CC=CC=C1)C2(CCN(CC2)CCC(=O)OC)C(=O)OC , IUPAC Name: remifentanil +Compound Success: CN1CCC23C4C(=O)CCC2(C1CC5=C3C(=C(C=C5)OC)O4)O , IUPAC Name: oxycodone +Compound Success: CN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(=O)CC4 , IUPAC Name: hydromorphone +Compound Success: CCCC(C)C1(C(=O)NC(=O)NC1=O)CC , IUPAC Name: pentobarbital diff --git a/tests/cgenff/global_chem_test/20/log/trial.log b/tests/cgenff/global_chem_test/20/log/trial.log new file mode 100644 index 00000000..af00e547 --- /dev/null +++ b/tests/cgenff/global_chem_test/20/log/trial.log @@ -0,0 +1,22 @@ +Compound Success: CCC1(C(=O)NC(=O)NC1=O)CCC(C)C , IUPAC Name: amobarbital +Compound Success: CC(CC(C)(C)O)OC(C(Cl)(Cl)Cl)O , IUPAC Name: chlorhexadol +Compound Success: C1=CC=C(C=C1)N2C=C(C=C(C2=O)C3=CC=CC=C3C#N)C4=CC=CC=N4 , IUPAC Name: perampanel +Compound Success: CCCC(C)C1(C(=O)NC(=O)NC1=O)CC , IUPAC Name: pentobarbital +Compound Success: CCC(=O)N(C1CCNCC1)C2=CC=CC=C2 , IUPAC Name: norfentanyl +Compound Success: CN(C)CCC(C1=CC=C(C=C1)Cl)C2=CC=CC=N2 , IUPAC Name: chlorphentermine +Compound Success: CCC(CC)(S(=O)(=O)CC)S(=O)(=O)CC , IUPAC Name: sulfondiethylmethane +Compound Success: C=CCN1CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O , IUPAC Name: nalorphine_9400 +Compound Success: CCC1(C(=O)C(CNC1=O)C)CC , IUPAC Name: methyprylon +Compound Success: CNC1(CCCCC1=O)C2=CC=CC=C2Cl , IUPAC Name: ketamine +Compound Success: CC1C(OCCN1C)C2=CC=CC=C2 , IUPAC Name: phendimetrazine +Compound Success: CC(C)(CC1=CC=CC=C1Cl)N , IUPAC Name: clortermine +Compound Success: CC(CC1=CC=CC=C1)N(C)CC2=CC=CC=C2 , IUPAC Name: benzphetamineCompound Success: CCC(CC)(CNC(=O)CCCO)C1=CC(=CC=C1)OC , IUPAC Name: embutramide + +Compound Success: CC1=NN(C2=C1C(=NCC(=O)N2C)C3=CC=CC=C3F)C , IUPAC Name: flupyrazaponCompound Success: CN1CC(C=C2C1CC3=CNC4=CC=CC2=C34)C(=O)N , IUPAC Name: lysergicacidamide + +Compound Success: CCC(C)(S(=O)(=O)CC)S(=O)(=O)CC , IUPAC Name: sulfonethylmethane +Compound Success: CCNC1(CCCCC1=O)C2=CC=CS2 , IUPAC Name: tiletamine +Compound Success: CC(C)(C)C(C)(C1CC23CCC1(C4C25CCN(C3CC6=C5C(=C(C=C6)O)O4)CC7CC7)OC)O , IUPAC Name: buprenorphine +Compound Success: O=S(=O)(C(C)(C)S(=O)(=O)CC)CC , IUPAC Name: sulfonmethane +Compound Success: CCCC(C)C1(C(=O)NC(=O)NC1=O)CC=C , IUPAC Name: secobarbital +Compound Success: CN1CC(C=C2C1CC3=CNC4=CC=CC2=C34)C(=O)O , IUPAC Name: lysergicacid \ No newline at end of file diff --git a/tests/cgenff/global_chem_test/21/log/trial.log b/tests/cgenff/global_chem_test/21/log/trial.log new file mode 100644 index 00000000..8342ee50 --- /dev/null +++ b/tests/cgenff/global_chem_test/21/log/trial.log @@ -0,0 +1,75 @@ +Compound Success: CN(C)C(CC1=CC=CC=C1)C2=CC=CC=C2 , IUPAC Name: spa((-)-1-dimethylamino-1,2-diphenylethane) +Compound Success: CCC1(C(=O)NC(=O)NC1=O)C2=CC=CC=C2 , IUPAC Name: phenobarbital +Compound Success: CCC#CC(C)C1(C(=O)NC(=O)N(C1=O)C)CC=C , IUPAC Name: methohexital +Compound Success: CC(C)C1=C(C(=CC=C1)C(C)C)OCOP(=O)(O)O , IUPAC Name: fospropofolCompound Success: CCC1=CC2=C(S1)N(C(=O)CN=C2C3=CC=CC=C3Cl)C , IUPAC Name: clotiazepam +Compound Success: CC(=O)C1CCC2C1(CC(=O)C3C2CCC4C3(CCC(C4)O)C)C , IUPAC Name: alfaxalone +Compound Success: CC1=CN=C2N1C3=C(C=C(C=C3)Br)C(=NC2CCC(=O)OC)C4=CC=CC=N4 , IUPAC Name: remimazolamCompound Success: CC(=O)C1CCC2C1(CCC3C2CCC4C3(CCC(C4)O)C)C , IUPAC Name: brexanolone +Compound Success: CC(C)CC(C1(CCC1)C2=CC=C(C=C2)Cl)N(C)C , IUPAC Name: sibutramine +Compound Success: CCC(=O)OC(CC1=CC=CC=C1)(C2=CC=CC=C2)C(C)CN(C)C , IUPAC Name: dextropropoxyphene +Compound Success: CN1C(=O)CN=C(C2=C1C=CC(=C2)[N+](=O)[O-])C3=CC=CC=C3F , IUPAC Name: flunitrazepam +Compound Success: C1C(=O)NC2=C(C=C(C=C2)[N+](=O)[O-])C(=N1)C3=CC=CC=C3 , IUPAC Name: nitrazepam +Compound Success: CN1C(=O)CN=C(C2=C1C=CC(=C2)[N+](=O)[O-])C3=CC=CC=C3 , IUPAC Name: nimetazepam +Compound Success: CC1CCN(CCN1C(=O)C2=C(C=CC(=C2)C)N3N=CC=N3)C4=NC5=C(O4)C=CC(=C5)Cl , IUPAC Name: suvorexant +Compound Success: CN1C2=C(C=C(C=C2)Cl)C(=NC(C1=O)OC(=O)N(C)C)C3=CC=CC=C3 , IUPAC Name: camazepam +Compound Success: CC1=CC(=O)N(N1C)C2=CC=CC=C2.C(C(Cl)(Cl)Cl)(O)O.C(C(Cl)(Cl)Cl)(O)O , IUPAC Name: dichloralphenazone +Compound Success: CCN(CC)C(C)C(=O)C1=CC=CC=C1 , IUPAC Name: diethylpropion +Compound Success: C(C(COC(C(Cl)(Cl)Cl)O)(COC(C(Cl)(Cl)Cl)O)COC(C(Cl)(Cl)Cl)O)OC(C(Cl)(Cl)Cl)O , IUPAC Name: petrichloral +Compound Success: CN1C2=C(C=C(C=C2)Cl)C(=NC(C1=O)O)C3=CC=CC=C3Cl , IUPAC Name: lormetazepam +Compound Success: C1=CC=C(C(=C1)C2=NC(C(=O)NC3=C2C=C(C=C3)Cl)O)Cl , IUPAC Name: lorazepam +Compound Success: CC1C2CC3=C(C1(CCN2CC=C(C)C)C)C=C(C=C3)O , IUPAC Name: pentazocine +Compound Success: C1=CC=C(C=C1)C2=NC(C(=O)NC3=C2C=C(C=C3)Cl)C(=O)O , IUPAC Name: clorazepate +Compound Success: C1=CC=C(C=C1)C2C(=O)N=C(O2)N , IUPAC Name: pemoline +Compound Success: COC(=O)C(C1CCCCN1C(=O)OC[N+]2=CC=CC(=C2)C(=O)NC(CO)C(=O)[O-])C3=CC=CC=C3 , IUPAC Name: serdexmethylphenidate +Compound Success: C1CCNC(C1)C(C2=CC=CC=C2)(C3=CC=CC=C3)O , IUPAC Name: pipradrol +Compound Success: C1C(=O)N(C2=C(C=C(C=C2)Cl)C(=N1)C3=CC=CC=C3)CC(F)(F)F , IUPAC Name: halazepam +Compound Success: C1=CC=C(C=C1)C2=NC(C(=O)NC3=C2C=C(C=C3)Cl)O , IUPAC Name: oxazepam +Compound Success: CCCC(C)(COC(=O)N)COC(=O)NC(C)C , IUPAC Name: carisoprodol +Compound Success: CC(C(C1=CC=CC=C1)O)N , IUPAC Name: (+)-norpseudoephedrine +Compound Success: C1CCC2(C3CC4=C(C2(C1)CCN3CC5CCC5)C=C(C=C4)O)O , IUPAC Name: butorphanol +Compound Success: CCOC(=O)C1C(=O)NC2=C(C=C(C=C2)Cl)C(=N1)C3=CC=CC=C3F , IUPAC Name: ethyl +Compound Success: CC1=NC(=NC=C1OCC2(CC2C(=O)NC3=NC=C(C=C3)F)C4=CC(=CC=C4)F)C , IUPAC Name: lemborexant +Compound Success: CN1CCN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3 , IUPAC Name: medazepam +Compound Success: C(C(Cl)(Cl)Cl)(O)O , IUPAC Name: chloralhydrateCompound Success: C1C(=O)NC2=C(C=C(C=C2)[N+](=O)[O-])C(=N1)C3=CC=CC=C3Cl , IUPAC Name: clonazepam + +Compound Success: CCN(CC)CCN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3F , IUPAC Name: flurazepamCompound Success: CCC1(C(=O)NC(=O)N(C1=O)C)C2=CC=CC=C2 , IUPAC Name: methylphenobarbital + +Compound Success: CC1CNCCC2=C1C=C(C=C2)Cl , IUPAC Name: lorcaserin +Compound Success: CCC1(C(=O)NC(=O)NC1=O)CC , IUPAC Name: barbital +Compound Success: CN1C2=C(C=C(C=C2)Cl)C(=NC(C1=O)O)C3=CC=CC=C3 , IUPAC Name: temazepam +Compound Success: CC(CC1=CC=CC=C1)NCCCCl , IUPAC Name: mefenorex +Compound Success: CN(C)CC1CCCCC1(C2=CC(=CC=C2)OC)O , IUPAC Name: 2-[(dimethylamino)methyl]-1-(3-methoxyphenyl)cyclohexanol +Compound Success: CN1CCN(CC1)C(=O)OC2C3=NC=CN=C3C(=O)N2C4=NC=C(C=C4)Cl , IUPAC Name: zopiclone +Compound Success: C1CN2C(=N1)C3=CC=CC=C3C2(C4=CC=C(C=C4)Cl)O , IUPAC Name: mazindol +Compound Success: CCC(C)C(C)(COC(=O)N)COC(=O)N , IUPAC Name: mebutamate +Compound Success: CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3 , IUPAC Name: diazepam +Compound Success: C1C2=NN=CN2C3=C(C=C(C=C3)Cl)C(=N1)C4=CC=CC=C4 , IUPAC Name: estazolam +Compound Success: CCNC1C2CCC(C2)C1C3=CC=CC=C3 , IUPAC Name: fencamfamin +Compound Success: CCNC(C)CC1=CC(=CC=C1)C(F)(F)F , IUPAC Name: fenfluramine +Compound Success: C[N+](C)(C)CC(=O)[O-].C(C(Cl)(Cl)Cl)(O)O , IUPAC Name: chloralbetaine +Compound Success: C1COC2(N1CC(=O)NC3=C2C=C(C=C3)Br)C4=CC=CC=C4F , IUPAC Name: haloxazolam +Compound Success: C1CC1CN2C(=O)CN=C(C3=C2C=CC(=C3)Cl)C4=CC=CC=C4 , IUPAC Name: prazepam +Compound Success: CCCC(C)(COC(=O)N)COC(=O)N , IUPAC Name: meprobamate +Compound Success: C1=CC=C(C=C1)CC(COC(=O)N)N , IUPAC Name: solriamfetol +Compound Success: CN1C(=O)CC(=O)N(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3 , IUPAC Name: clobazam +Compound Success: CC(C)(CC1=CC=CC=C1)N , IUPAC Name: phentermine +Compound Success: CCN(C1=CC=CC(=C1)C2=CC=NC3=C(C=NN23)C#N)C(=O)C , IUPAC Name: zaleplon +Compound Success: C1COC2(N1CC(=O)NC3=C2C=C(C=C3)Cl)C4=CC=CC=C4Cl , IUPAC Name: cloxazolam +Compound Success: CC1CN2CC(=O)NC3=C(C2(O1)C4=CC=CC=C4)C=C(C=C3)Cl , IUPAC Name: oxazolam +Compound Success: CC1OC(OC(O1)C)C , IUPAC Name: paraldehyde +Compound Success: O=C(OC1(C#C)CCCCC1)N , IUPAC Name: ethinamate +Compound Success: C1C(=O)NC2=C(C=C(C=C2)Cl)C(=N1)C3=CC=CC=C3 , IUPAC Name: nordiazepam +Compound Success: CCC(C=CCl)(C#C)O , IUPAC Name: ethchlorvynol +Compound Success: CC1=NN=C2N1C3=C(C=C(C=C3)Cl)C(=NC2)C4=CC=CC=C4 , IUPAC Name: alprazolam +Compound Success: C#CCN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3 , IUPAC Name: pinazepam +Compound Success: C1C(=O)NC2=C(C=C(C=C2)Cl)C(=N1)C3=CC=CC=C3Cl , IUPAC Name: delorazepam +Compound Success: CC1=NN=C2N1C3=C(C=C(C=C3)Cl)C(=NC2)C4=CC=CC=C4Cl , IUPAC Name: triazolam +Compound Success: CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CCCCC3 , IUPAC Name: tetrazepam +Compound Success: CN1CCN(CC1)C=C2C(=O)N3C(=N2)CN=C(C4=C3C=CC(=C4)[N+](=O)[O-])C5=CC=CC=C5Cl , IUPAC Name: loprazolam +Compound Success: CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3F , IUPAC Name: fludiazepam +Compound Success: CC1=CC(=O)N2CC(=O)N(C3=C(C2(O1)C4=CC=CC=C4)C=C(C=C3)Cl)C , IUPAC Name: ketazolam +Compound Success: C1C(=O)NC2=C(C=C(C=C2)Br)C(=N1)C3=CC=CC=N3 , IUPAC Name: bromazepam +Compound Success: CC(CC1=CC=CC=C1)NCCC#N , IUPAC Name: fenproporex +Compound Success: CC1=CC=C(C=C1)C2=C(N3C=C(C=CC3=N2)C)CC(=O)N(C)C , IUPAC Name: zolpidem +Compound Success: CN=C1CN(C(=C2C=C(C=CC2=N1)Cl)C3=CC=CC=C3)O , IUPAC Name: chlordiazepoxide +Compound Success: CC1=NC=C2N1C3=C(C=C(C=C3)Cl)C(=NC2)C4=CC=CC=C4F , IUPAC Name: midazolam +Compound Success: C1C(=S)N(C2=C(C=C(C=C2)Cl)C(=N1)C3=CC=CC=C3F)CC(F)(F)F , IUPAC Name: quazepam \ No newline at end of file diff --git a/tests/cgenff/global_chem_test/22/log/trial.log b/tests/cgenff/global_chem_test/22/log/trial.log new file mode 100644 index 00000000..125b5bef --- /dev/null +++ b/tests/cgenff/global_chem_test/22/log/trial.log @@ -0,0 +1,7 @@ +Compound Success: CC(=O)NC(COC)C(=O)NCC1=CC=CC=C1 , IUPAC Name: lacosamide +Compound Success: C1=CC=C(C(=C1)C(CN2N=CN=N2)OC(=O)N)Cl , IUPAC Name: cenobamate +Compound Success: CCCC(C(=O)C1=CC=C(C=C1)C)N2CCCC2 , IUPAC Name: pyrovalerone +Compound Success: CC(C)CC(CC(=O)O)CN , IUPAC Name: pregabalin +Compound Success: CCCC1CC(=O)N(C1)C(CC)C(=O)N , IUPAC Name: brivaracetamCompound Success: CCOC(=O)NC1=C(C=C(C=C1)NCC2=CC=C(C=C2)F)N , IUPAC Name: ezogabine + +Compound Success: CC1=CC(=CC(=C1CC(C(=O)N(CC2=CC(=C(C=C2)OC)C(=O)O)C(C)C3=NC=C(N3)C4=CC=CC=C4)N)C)C(=O)N , IUPAC Name: eluxadoline \ No newline at end of file diff --git a/tests/cgenff/global_chem_test/total_failed.log b/tests/cgenff/global_chem_test/total_failed.log index 7c6b2d3f..87caa2f9 100644 --- a/tests/cgenff/global_chem_test/total_failed.log +++ b/tests/cgenff/global_chem_test/total_failed.log @@ -78,4 +78,6 @@ Compound Failed: C[Si](C(C)(C)C)C , IUPAC Name: tbdms Compound Failed: O=I=O , IUPAC Name: iodyl Compound Failed: C/C=C/[C]=O , IUPAC Name: crotonoyl Compound Failed: O=[C]CCCC[C]=O , IUPAC Name: hexanedioyl -Compound Failed: CC(C)(C)[C]=O , IUPAC Name: pivaloyl \ No newline at end of file +Compound Failed: CC(C)(C)[C]=O , IUPAC Name: pivaloyl +Compound Failed: CCCC(C)(C1CC23C=CC1(C4C25CCN(C3CC6=C5C(=C(C=C6)O)O4)C)OC)O.Cl ,IUPAC Name: etorphinehydrochloride +Compound Failed: C[N+]1(CCC23C4C1CC5=C2C(=C(C=C5)O)OC3C(C=C4)O)C.[Br-] , IUPAC Name: morphinemethylbromide