├── 1-benchmarks └── chembl.smi.gz ├── 2-aromaticsmiles ├── chembl │ ├── BIOVIADraw_2017.smi.gz │ ├── Cactvs_3.4.6.19.smi.gz │ ├── ChemDoodleAPI_2.3.0.smi.gz │ ├── KnowItAll_2018.smi.gz │ ├── avalon_1.2.0.smi.gz │ ├── cdk_2.0.smi.gz │ ├── indigo_1.2.3.r0.smi.gz │ ├── iwtoolkit_1.0.smi.gz │ ├── jchem_17.23.smi.gz │ ├── oechem_June2017.smi.gz │ ├── openbabel_dev4Aug17.smi.gz │ ├── openchemlib_2018.5.0.smi.gz │ └── rdkit_2017.03.3.smi.gz ├── cornercases │ └── cornercases.smi └── valencemodel │ ├── explicitvalence.smi │ └── smilesvalence.smi ├── 3-results ├── chembl │ ├── BIOVIADraw_2018_reading_BIOVIADraw_2017.txt.gz │ ├── BIOVIADraw_2018_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── BIOVIADraw_2018_reading_avalon_1.2.0.txt.gz │ ├── BIOVIADraw_2018_reading_cdk_2.0.txt.gz │ ├── BIOVIADraw_2018_reading_indigo_1.2.3.r0.txt.gz │ ├── BIOVIADraw_2018_reading_iwtoolkit_1.0.txt.gz │ ├── BIOVIADraw_2018_reading_jchem_17.23.txt.gz │ ├── BIOVIADraw_2018_reading_oechem_June2017.txt.gz │ ├── BIOVIADraw_2018_reading_openbabel_dev4Aug17.txt.gz │ ├── BIOVIADraw_2018_reading_openchemlib_2018.5.0.txt.gz │ ├── BIOVIADraw_2018_reading_rdkit_2017.03.3.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_BIOVIADraw_2017.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_avalon_1.2.0.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_cdk_2.0.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_indigo_1.2.3.r0.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_iwtoolkit_1.0.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_jchem_17.23.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_oechem_June2017.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_openbabel_dev4Aug17.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_openchemlib_2018.5.0.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_rdkit_2017.03.3.txt.gz │ ├── ChemDraw_17.1_reading_BIOVIADraw_2017.txt.gz │ ├── ChemDraw_17.1_reading_Cactvs_3.4.6.19.txt.gz │ ├── ChemDraw_17.1_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── ChemDraw_17.1_reading_KnowItAll_2018.txt.gz │ ├── ChemDraw_17.1_reading_avalon_1.2.0.txt.gz │ ├── ChemDraw_17.1_reading_cdk_2.0.txt.gz │ ├── ChemDraw_17.1_reading_indigo_1.2.3.r0.txt.gz │ ├── ChemDraw_17.1_reading_iwtoolkit_1.0.txt.gz │ ├── ChemDraw_17.1_reading_jchem_17.23.txt.gz │ ├── ChemDraw_17.1_reading_oechem_June2017.txt.gz │ ├── ChemDraw_17.1_reading_openbabel_dev4Aug17.txt.gz │ ├── ChemDraw_17.1_reading_openchemlib_2018.5.0.txt.gz │ ├── ChemDraw_17.1_reading_rdkit_2017.03.3.txt.gz │ ├── KnowItAll_2018_reading_BIOVIADraw_2017.txt.gz │ ├── KnowItAll_2018_reading_Cactvs_3.4.6.19.txt.gz │ ├── KnowItAll_2018_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── KnowItAll_2018_reading_KnowItAll_2018.txt.gz │ ├── KnowItAll_2018_reading_avalon_1.2.0.txt.gz │ ├── KnowItAll_2018_reading_cdk_2.0.txt.gz │ ├── KnowItAll_2018_reading_indigo_1.2.3.r0.txt.gz │ ├── KnowItAll_2018_reading_iwtoolkit_1.0.txt.gz │ ├── KnowItAll_2018_reading_jchem_17.23.txt.gz │ ├── KnowItAll_2018_reading_oechem_June2017.txt.gz │ ├── KnowItAll_2018_reading_openbabel_dev4Aug17.txt.gz │ ├── KnowItAll_2018_reading_openchemlib_2018.5.0.txt.gz │ ├── KnowItAll_2018_reading_rdkit_2017.03.3.txt.gz │ ├── avalon_1.2.0_reading_BIOVIADraw_2017.txt.gz │ ├── avalon_1.2.0_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── avalon_1.2.0_reading_avalon_1.2.0.txt.gz │ ├── avalon_1.2.0_reading_cdk_2.0.txt.gz │ ├── avalon_1.2.0_reading_indigo_1.2.3.r0.txt.gz │ ├── avalon_1.2.0_reading_iwtoolkit_1.0.txt.gz │ ├── avalon_1.2.0_reading_jchem_17.23.txt.gz │ ├── avalon_1.2.0_reading_oechem_June2017.txt.gz │ ├── avalon_1.2.0_reading_openbabel_dev4Aug17.txt.gz │ ├── avalon_1.2.0_reading_openchemlib_2018.5.0.txt.gz │ ├── avalon_1.2.0_reading_rdkit_2017.03.3.txt.gz │ ├── cdk_2.1_reading_BIOVIADraw_2017.txt.gz │ ├── cdk_2.1_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── cdk_2.1_reading_avalon_1.2.0.txt.gz │ ├── cdk_2.1_reading_cdk_2.0.txt.gz │ ├── cdk_2.1_reading_indigo_1.2.3.r0.txt.gz │ ├── cdk_2.1_reading_iwtoolkit_1.0.txt.gz │ ├── cdk_2.1_reading_jchem_17.23.txt.gz │ ├── cdk_2.1_reading_oechem_June2017.txt.gz │ ├── cdk_2.1_reading_openbabel_dev4Aug17.txt.gz │ ├── cdk_2.1_reading_openchemlib_2018.5.0.txt.gz │ ├── cdk_2.1_reading_rdkit_2017.03.3.txt.gz │ ├── indigo_1.3.0b.r16_reading_BIOVIADraw_2017.txt.gz │ ├── indigo_1.3.0b.r16_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── indigo_1.3.0b.r16_reading_avalon_1.2.0.txt.gz │ ├── indigo_1.3.0b.r16_reading_cdk_2.0.txt.gz │ ├── indigo_1.3.0b.r16_reading_indigo_1.2.3.r0.txt.gz │ ├── indigo_1.3.0b.r16_reading_iwtoolkit_1.0.txt.gz │ ├── indigo_1.3.0b.r16_reading_jchem_17.23.txt.gz │ ├── indigo_1.3.0b.r16_reading_oechem_June2017.txt.gz │ ├── indigo_1.3.0b.r16_reading_openbabel_dev4Aug17.txt.gz │ ├── indigo_1.3.0b.r16_reading_openchemlib_2018.5.0.txt.gz │ ├── indigo_1.3.0b.r16_reading_rdkit_2017.03.3.txt.gz │ ├── iwtoolkit_1.0_reading_BIOVIADraw_2017.txt.gz │ ├── iwtoolkit_1.0_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── iwtoolkit_1.0_reading_avalon_1.2.0.txt.gz │ ├── iwtoolkit_1.0_reading_cdk_2.0.txt.gz │ ├── iwtoolkit_1.0_reading_indigo_1.2.3.r0.txt.gz │ ├── iwtoolkit_1.0_reading_iwtoolkit_1.0.txt.gz │ ├── iwtoolkit_1.0_reading_jchem_17.23.txt.gz │ ├── iwtoolkit_1.0_reading_oechem_June2017.txt.gz │ ├── iwtoolkit_1.0_reading_openbabel_dev4Aug17.txt.gz │ ├── iwtoolkit_1.0_reading_openchemlib_2018.5.0.txt.gz │ ├── iwtoolkit_1.0_reading_rdkit_2017.03.3.txt.gz │ ├── jchem_18.18_reading_BIOVIADraw_2017.txt.gz │ ├── jchem_18.18_reading_Cactvs_3.4.6.19.txt.gz │ ├── jchem_18.18_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── jchem_18.18_reading_KnowItAll_2018.txt.gz │ ├── jchem_18.18_reading_avalon_1.2.0.txt.gz │ ├── jchem_18.18_reading_cdk_2.0.txt.gz │ ├── jchem_18.18_reading_indigo_1.2.3.r0.txt.gz │ ├── jchem_18.18_reading_iwtoolkit_1.0.txt.gz │ ├── jchem_18.18_reading_jchem_17.23.txt.gz │ ├── jchem_18.18_reading_oechem_June2017.txt.gz │ ├── jchem_18.18_reading_openbabel_dev4Aug17.txt.gz │ ├── jchem_18.18_reading_openchemlib_2018.5.0.txt.gz │ ├── jchem_18.18_reading_rdkit_2017.03.3.txt.gz │ ├── oechem_Feb2018_reading_BIOVIADraw_2017.txt.gz │ ├── oechem_Feb2018_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── oechem_Feb2018_reading_avalon_1.2.0.txt.gz │ ├── oechem_Feb2018_reading_cdk_2.0.txt.gz │ ├── oechem_Feb2018_reading_indigo_1.2.3.r0.txt.gz │ ├── oechem_Feb2018_reading_iwtoolkit_1.0.txt.gz │ ├── oechem_Feb2018_reading_jchem_17.23.txt.gz │ ├── oechem_Feb2018_reading_oechem_June2017.txt.gz │ ├── oechem_Feb2018_reading_openbabel_dev4Aug17.txt.gz │ ├── oechem_Feb2018_reading_openchemlib_2018.5.0.txt.gz │ ├── oechem_Feb2018_reading_rdkit_2017.03.3.txt.gz │ ├── openbabel_dev9May18_reading_BIOVIADraw_2017.txt.gz │ ├── openbabel_dev9May18_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── openbabel_dev9May18_reading_avalon_1.2.0.txt.gz │ ├── openbabel_dev9May18_reading_cdk_2.0.txt.gz │ ├── openbabel_dev9May18_reading_indigo_1.2.3.r0.txt.gz │ ├── openbabel_dev9May18_reading_iwtoolkit_1.0.txt.gz │ ├── openbabel_dev9May18_reading_jchem_17.23.txt.gz │ ├── openbabel_dev9May18_reading_oechem_June2017.txt.gz │ ├── openbabel_dev9May18_reading_openbabel_dev4Aug17.txt.gz │ ├── openbabel_dev9May18_reading_openchemlib_2018.5.0.txt.gz │ ├── openbabel_dev9May18_reading_rdkit_2017.03.3.txt.gz │ ├── openchemlib_2018.5.0_reading_BIOVIADraw_2017.txt.gz │ ├── openchemlib_2018.5.0_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── openchemlib_2018.5.0_reading_avalon_1.2.0.txt.gz │ ├── openchemlib_2018.5.0_reading_cdk_2.0.txt.gz │ ├── openchemlib_2018.5.0_reading_indigo_1.2.3.r0.txt.gz │ ├── openchemlib_2018.5.0_reading_iwtoolkit_1.0.txt.gz │ ├── openchemlib_2018.5.0_reading_jchem_17.23.txt.gz │ ├── openchemlib_2018.5.0_reading_oechem_June2017.txt.gz │ ├── openchemlib_2018.5.0_reading_openbabel_dev4Aug17.txt.gz │ ├── openchemlib_2018.5.0_reading_openchemlib_2018.5.0.txt.gz │ ├── openchemlib_2018.5.0_reading_rdkit_2017.03.3.txt.gz │ ├── rdkit_2018.03.1_reading_BIOVIADraw_2017.txt.gz │ ├── rdkit_2018.03.1_reading_ChemDoodleAPI_2.3.0.txt.gz │ ├── rdkit_2018.03.1_reading_avalon_1.2.0.txt.gz │ ├── rdkit_2018.03.1_reading_cdk_2.0.txt.gz │ ├── rdkit_2018.03.1_reading_indigo_1.2.3.r0.txt.gz │ ├── rdkit_2018.03.1_reading_iwtoolkit_1.0.txt.gz │ ├── rdkit_2018.03.1_reading_jchem_17.23.txt.gz │ ├── rdkit_2018.03.1_reading_oechem_June2017.txt.gz │ ├── rdkit_2018.03.1_reading_openbabel_dev4Aug17.txt.gz │ ├── rdkit_2018.03.1_reading_openchemlib_2018.5.0.txt.gz │ └── rdkit_2018.03.1_reading_rdkit_2017.03.3.txt.gz └── valencemodel │ ├── BIOVIADraw_2018_reading_explicitvalence.txt.gz │ ├── BIOVIADraw_2018_reading_smilesvalence.txt.gz │ ├── Cactvs_3.4.6.25_OPTION_reading_smilesvalence.txt.gz │ ├── Cactvs_3.4.6.25_reading_explicitvalence.txt.gz │ ├── Cactvs_3.4.6.25_reading_smilesvalence.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_explicitvalence.txt.gz │ ├── ChemDoodleAPI_2.3.0_reading_smilesvalence.txt.gz │ ├── ChemDraw_17.1_reading_explicitvalence.txt.gz │ ├── ChemDraw_17.1_reading_smilesvalence.txt.gz │ ├── KnowItAll_2018_reading_explicitvalence.txt.gz │ ├── KnowItAll_2018_reading_smilesvalence.txt.gz │ ├── WeiningerCEX_132_reading_smilesvalence.txt.gz │ ├── avalon_1.2.0_reading_explicitvalence.txt.gz │ ├── avalon_1.2.0_reading_smilesvalence.txt.gz │ ├── cdk_2.1_reading_explicitvalence.txt.gz │ ├── cdk_2.1_reading_smilesvalence.txt.gz │ ├── indigo_1.3.0b.r16_reading_explicitvalence.txt.gz │ ├── indigo_1.3.0b.r16_reading_smilesvalence.txt.gz │ ├── iwtoolkit_1.0_reading_explicitvalence.txt.gz │ ├── iwtoolkit_1.0_reading_smilesvalence.txt.gz │ ├── iwtoolkit_Oct2017_OPTION_reading_smilesvalence.txt.gz │ ├── jchem_18.18_reading_explicitvalence.txt.gz │ ├── jchem_18.18_reading_smilesvalence.txt.gz │ ├── oechem_Feb2018_reading_explicitvalence.txt.gz │ ├── oechem_Feb2018_reading_smilesvalence.txt.gz │ ├── openbabel_dev9May18.smi_reading_explicitvalence.txt.gz │ ├── openbabel_dev9May18.smi_reading_smilesvalence.txt.gz │ ├── openchemlib_2018.5.0_reading_explicitvalence.txt.gz │ ├── openchemlib_2018.5.0_reading_smilesvalence.txt.gz │ ├── rdkit_2018.03.1_reading_explicitvalence.txt.gz │ └── rdkit_2018.03.1_reading_smilesvalence.txt.gz ├── 4-stereosmiles ├── cistrans.smi ├── cistrans_nitrogen.smi ├── tetrahedral.smi └── tetrahedral_distantbcdigit.smi ├── 5-results ├── cistrans │ ├── BIOVIADraw_2018.smi │ ├── ChemDraw_17.1.smi │ ├── KnowItAll_2018.smi │ ├── avalon_1.2.0.smi │ ├── cdk_2.1.smi │ ├── indigo_1.3.0b.r16.smi │ ├── iwtoolkit_1.0.smi │ ├── oechem_Feb2018.smi │ ├── openbabel.smi │ ├── openchemlib_2018.7.0.smi │ └── rdkit_2018.03.1.smi ├── cistrans_nitrogen │ ├── BIOVIADraw_2018.smi │ ├── ChemDraw_17.1.smi │ ├── KnowItAll_2018.smi │ ├── avalon_1.2.0.smi │ ├── cdk_2.1.smi │ ├── indigo_1.3.0b.r16.smi │ ├── iwtoolkit_1.0.smi │ ├── oechem_Feb2018.smi │ ├── openbabel.smi │ ├── openchemlib_2018.7.0.smi │ └── rdkit_2018.03.1.smi ├── tetrahedral │ ├── BIOVIADraw_2018.smi │ ├── ChemDraw_17.1.smi │ ├── KnowItAll_2018.smi │ ├── avalon_1.2.0.smi │ ├── cactvs_3_426.smi │ ├── cdk_2.1.smi │ ├── indigo_1.3.0b.r16.smi │ ├── iwtoolkit_1.0.smi │ ├── oechem_Feb2018.smi │ ├── openbabel.smi │ ├── openchemlib_2018.7.0.smi │ └── rdkit_2018.03.1.smi └── tetrahedral_distantbcdigit │ ├── BIOVIADraw_2018.smi │ ├── ChemDraw_17.1.smi │ ├── KnowItAll_2018.smi │ ├── avalon_1.2.0.smi │ ├── cactvs_3_426.smi │ ├── cdk_2.1.smi │ ├── indigo_1.3.0b.r16.smi │ ├── iwtoolkit_1.0.smi │ ├── oechem_Feb2018.smi │ ├── openbabel.smi │ ├── openchemlib_2018.7.0.smi │ └── rdkit_2018.03.1.smi ├── LICENSE ├── README.md └── scripts ├── BIOVIADirect.py ├── BIOVIADraw.py ├── CDK.py ├── Cactvs.py ├── ChemDoodle.py ├── ChemDraw.py ├── ChemDraw_FindKekuleFailures.py ├── ConvertMolfiles.py ├── Indigo.py ├── JChem.py ├── OEChem.py ├── OpenBabel.py ├── OpenChemLib.py ├── RDKit.py ├── WeiningerCEX.py ├── avalon.c ├── avalon.py ├── common.py ├── common_molfile.py ├── iwtoolkit.cpp └── iwtoolkit.py /1-benchmarks/chembl.smi.gz: 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[N](C)(C)(C)(C)C N5 18 | [N](C)(C)(C)(C)(C)C N6 19 | [OH2] O0 20 | [OH]C O1 21 | [O](C)C O2 22 | [O](C)(C)C O3 23 | [PH3] P0 24 | [PH2]C P1 25 | [PH](C)C P2 26 | [P](C)(C)C P3 27 | [PH](C)(C)(C)C P4 28 | [P](C)(C)(C)(C)C P5 29 | [P](C)(C)(C)(C)(C)C P6 30 | [SH2] S0 31 | [SH]C S1 32 | [S](C)C S2 33 | [SH](C)(C)C S3 34 | [S](C)(C)(C)C S4 35 | [SH](C)(C)(C)(C)C S5 36 | [S](C)(C)(C)(C)(C)C S6 37 | [S](C)(C)(C)(C)(C)(C)C S7 38 | [FH] F0 39 | [F]C F1 40 | [F](C)C F2 41 | [F](C)(C)C F3 42 | [F](C)(C)(C)C F4 43 | [F](C)(C)(C)(C)C F5 44 | [ClH] Cl0 45 | [Cl]C Cl1 46 | [Cl](C)C Cl2 47 | [Cl](C)(C)C Cl3 48 | [Cl](C)(C)(C)C Cl4 49 | [Cl](C)(C)(C)(C)C Cl5 50 | [BrH] Br0 51 | [Br]C Br1 52 | [Br](C)C Br2 53 | [Br](C)(C)C Br3 54 | [Br](C)(C)(C)C Br4 55 | [Br](C)(C)(C)(C)C Br5 56 | [IH] I0 57 | [I]C I1 58 | [I](C)C I2 59 | [I](C)(C)C I3 60 | [I](C)(C)(C)C I4 61 | [I](C)(C)(C)(C)C I5 62 | -------------------------------------------------------------------------------- /2-aromaticsmiles/valencemodel/smilesvalence.smi: -------------------------------------------------------------------------------- 1 | B B0 2 | BC B1 3 | B(C)C B2 4 | B(C)(C)C B3 5 | B(C)(C)(C)C B4 6 | C C0 7 | CC C1 8 | C(C)C C2 9 | C(C)(C)C C3 10 | C(C)(C)(C)C C4 11 | C(C)(C)(C)(C)C C5 12 | N N0 13 | NC N1 14 | N(C)C N2 15 | N(C)(C)C N3 16 | N(C)(C)(C)C N4 17 | N(C)(C)(C)(C)C N5 18 | N(C)(C)(C)(C)(C)C N6 19 | O O0 20 | OC O1 21 | O(C)C O2 22 | O(C)(C)C O3 23 | P P0 24 | PC P1 25 | P(C)C P2 26 | P(C)(C)C P3 27 | P(C)(C)(C)C P4 28 | P(C)(C)(C)(C)C P5 29 | P(C)(C)(C)(C)(C)C P6 30 | S S0 31 | SC S1 32 | S(C)C S2 33 | S(C)(C)C S3 34 | S(C)(C)(C)C S4 35 | S(C)(C)(C)(C)C S5 36 | S(C)(C)(C)(C)(C)C S6 37 | S(C)(C)(C)(C)(C)(C)C S7 38 | F F0 39 | FC F1 40 | F(C)C F2 41 | F(C)(C)C F3 42 | F(C)(C)(C)C F4 43 | F(C)(C)(C)(C)C F5 44 | Cl Cl0 45 | ClC Cl1 46 | Cl(C)C Cl2 47 | Cl(C)(C)C Cl3 48 | Cl(C)(C)(C)C Cl4 49 | Cl(C)(C)(C)(C)C Cl5 50 | Br Br0 51 | BrC Br1 52 | Br(C)C Br2 53 | Br(C)(C)C Br3 54 | 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-------------------------------------------------------------------------------- /4-stereosmiles/cistrans.smi: -------------------------------------------------------------------------------- 1 | C(=C\F)/I 1 2 | C(=C/F)\I 1 3 | C(=C\I)/F 1 4 | C(=C/I)\F 1 5 | C(\F)=C/I 1 6 | C(/F)=C\I 1 7 | C(\I)=C/F 1 8 | C(/I)=C\F 1 9 | F/C=C/I 1 10 | F\C=C\I 1 11 | I/C=C/F 1 12 | I\C=C\F 1 13 | C(=C\1)/I.F1 1 14 | C(=C1)/I.F/1 1 15 | C/1(=C\F).I1 1 16 | C1(=C\F).I\1 1 17 | C\1=C/I.F1 1 18 | C1=C/I.F/1 1 19 | C/2(=C\1).F1.I2 1 20 | C2(=C1).F/1.I\2 1 21 | C2=C1.F/1.I\2 1 22 | C/2=C\1.F1.I2 1 23 | C(=C\C=C/I)/F 2 24 | C(=C/C=C\I)\F 2 25 | C(=C\C=C\F)\I 2 26 | C(=C/C=C/F)/I 2 27 | C(=C\F)/C=C\I 2 28 | C(=C/F)\C=C/I 2 29 | C(=C\I)\C=C\F 2 30 | C(=C/I)/C=C/F 2 31 | C(\C=C/I)=C/F 2 32 | C(/C=C\I)=C\F 2 33 | C(\C=C\F)=C\I 2 34 | C(/C=C/F)=C/I 2 35 | C(\F)=C/C=C\I 2 36 | C(/F)=C\C=C/I 2 37 | C(\I)=C\C=C\F 2 38 | C(/I)=C/C=C/F 2 39 | F/C=C/C=C\I 2 40 | F\C=C\C=C/I 2 41 | I/C=C\C=C\F 2 42 | I\C=C/C=C/F 2 43 | C/1=C/C=C/F.I1 2 44 | C1=C/C=C/F.I\1 2 45 | C(/I)=C/C=C/1.F1 2 46 | C(/I)=C/C=C1.F\1 2 47 | Br/C(/I)=C(/Cl)\F 3 48 | Br\C(\I)=C(\Cl)/F 3 49 | Br/C(/I)=C(\F)/Cl 3 50 | Br\C(\I)=C(/F)\Cl 3 51 | Br/C(=C(/Cl)\F)/I 3 52 | Br\C(=C(\Cl)/F)\I 3 53 | Br/C(=C(\F)/Cl)/I 3 54 | Br\C(=C(/F)\Cl)\I 3 55 | C(=C(\Br)/I)(/Cl)\F 3 56 | C(=C(/Br)\I)(\Cl)/F 3 57 | C(=C(\Br)/I)(\F)/Cl 3 58 | C(=C(/Br)\I)(/F)\Cl 3 59 | C(=C(\Cl)/F)(/Br)\I 3 60 | C(=C(/Cl)\F)(\Br)/I 3 61 | C(=C(\Cl)/F)(\I)/Br 3 62 | C(=C(/Cl)\F)(/I)\Br 3 63 | C(=C(\F)/Cl)(/I)\Br 3 64 | C(=C(/F)\Cl)(\I)/Br 3 65 | C(=C(\F)/Cl)(\Br)/I 3 66 | C(=C(/F)\Cl)(/Br)\I 3 67 | C(=C(\I)/Br)(/F)\Cl 3 68 | C(=C(/I)\Br)(\F)/Cl 3 69 | C(=C(\I)/Br)(\Cl)/F 3 70 | C(=C(/I)\Br)(/Cl)\F 3 71 | C(\Br)(/I)=C(/Cl)\F 3 72 | C(/Br)(\I)=C(\Cl)/F 3 73 | C(\Br)(/I)=C(\F)/Cl 3 74 | C(/Br)(\I)=C(/F)\Cl 3 75 | C(\Br)(=C(/Cl)\F)/I 3 76 | C(/Br)(=C(\Cl)/F)\I 3 77 | C(\Br)(=C(\F)/Cl)/I 3 78 | C(/Br)(=C(/F)\Cl)\I 3 79 | C(\Cl)(/F)=C(/Br)\I 3 80 | C(/Cl)(\F)=C(\Br)/I 3 81 | C(\Cl)(/F)=C(\I)/Br 3 82 | C(/Cl)(\F)=C(/I)\Br 3 83 | C(\Cl)(=C(/Br)\I)/F 3 84 | C(/Cl)(=C(\Br)/I)\F 3 85 | C(\Cl)(=C(\I)/Br)/F 3 86 | C(/Cl)(=C(/I)\Br)\F 3 87 | C(\F)(/Cl)=C(/I)\Br 3 88 | C(/F)(\Cl)=C(\I)/Br 3 89 | C(\F)(/Cl)=C(\Br)/I 3 90 | C(/F)(\Cl)=C(/Br)\I 3 91 | C(\F)(=C(/I)\Br)/Cl 3 92 | C(/F)(=C(\I)/Br)\Cl 3 93 | C(\F)(=C(\Br)/I)/Cl 3 94 | C(/F)(=C(/Br)\I)\Cl 3 95 | C(\I)(/Br)=C(/F)\Cl 3 96 | C(/I)(\Br)=C(\F)/Cl 3 97 | C(\I)(/Br)=C(\Cl)/F 3 98 | C(/I)(\Br)=C(/Cl)\F 3 99 | C(\I)(=C(/F)\Cl)/Br 3 100 | C(/I)(=C(\F)/Cl)\Br 3 101 | C(\I)(=C(\Cl)/F)/Br 3 102 | C(/I)(=C(/Cl)\F)\Br 3 103 | Cl/C(/F)=C(/Br)\I 3 104 | Cl\C(\F)=C(\Br)/I 3 105 | Cl/C(/F)=C(\I)/Br 3 106 | Cl\C(\F)=C(/I)\Br 3 107 | Cl/C(=C(/Br)\I)/F 3 108 | Cl\C(=C(\Br)/I)\F 3 109 | Cl/C(=C(\I)/Br)/F 3 110 | Cl\C(=C(/I)\Br)\F 3 111 | F/C(/Cl)=C(/I)\Br 3 112 | F\C(\Cl)=C(\I)/Br 3 113 | F/C(/Cl)=C(\Br)/I 3 114 | F\C(\Cl)=C(/Br)\I 3 115 | F/C(=C(/I)\Br)/Cl 3 116 | F\C(=C(\I)/Br)\Cl 3 117 | F/C(=C(\Br)/I)/Cl 3 118 | F\C(=C(/Br)\I)\Cl 3 119 | I/C(/Br)=C(/F)\Cl 3 120 | I\C(\Br)=C(\F)/Cl 3 121 | I/C(/Br)=C(\Cl)/F 3 122 | I\C(\Br)=C(/Cl)\F 3 123 | I/C(=C(/F)\Cl)/Br 3 124 | I\C(=C(\F)/Cl)\Br 3 125 | I/C(=C(\Cl)/F)/Br 3 126 | I\C(=C(/Cl)\F)\Br 3 127 | -------------------------------------------------------------------------------- /4-stereosmiles/cistrans_nitrogen.smi: -------------------------------------------------------------------------------- 1 | C(=N\I)/F 1 2 | C(=N/I)\F 1 3 | C(\F)=N/I 1 4 | C(/F)=N\I 1 5 | F/C=N/I 1 6 | F\C=N\I 1 7 | I/N=C/F 1 8 | I\N=C\F 1 9 | N(=C\F)/I 1 10 | N(=C/F)\I 1 11 | N(\I)=C/F 1 12 | N(/I)=C\F 1 13 | -------------------------------------------------------------------------------- /4-stereosmiles/tetrahedral.smi: -------------------------------------------------------------------------------- 1 | Br[C@@](Cl)(F)I 1 2 | Br[C@@](F)(I)Cl 1 3 | Br[C@@](I)(Cl)F 1 4 | Br[C@](Cl)(I)F 1 5 | Br[C@](F)(Cl)I 1 6 | Br[C@](I)(F)Cl 1 7 | [C@@](Br)(Cl)(F)I 1 8 | [C@](Br)(Cl)(I)F 1 9 | [C@](Br)(F)(Cl)I 1 10 | [C@@](Br)(F)(I)Cl 1 11 | [C@@](Br)(I)(Cl)F 1 12 | [C@](Br)(I)(F)Cl 1 13 | [C@](Cl)(Br)(F)I 1 14 | [C@@](Cl)(Br)(I)F 1 15 | [C@@](Cl)(F)(Br)I 1 16 | [C@](Cl)(F)(I)Br 1 17 | [C@](Cl)(I)(Br)F 1 18 | [C@@](Cl)(I)(F)Br 1 19 | [C@@](F)(Br)(Cl)I 1 20 | [C@](F)(Br)(I)Cl 1 21 | [C@](F)(Cl)(Br)I 1 22 | [C@@](F)(Cl)(I)Br 1 23 | [C@@](F)(I)(Br)Cl 1 24 | [C@](F)(I)(Cl)Br 1 25 | [C@](I)(Br)(Cl)F 1 26 | [C@@](I)(Br)(F)Cl 1 27 | [C@@](I)(Cl)(Br)F 1 28 | [C@](I)(Cl)(F)Br 1 29 | [C@](I)(F)(Br)Cl 1 30 | [C@@](I)(F)(Cl)Br 1 31 | Cl[C@@](Br)(I)F 1 32 | Cl[C@@](F)(Br)I 1 33 | Cl[C@@](I)(F)Br 1 34 | Cl[C@](Br)(F)I 1 35 | Cl[C@](F)(I)Br 1 36 | Cl[C@](I)(Br)F 1 37 | F[C@@](Br)(Cl)I 1 38 | F[C@@](Cl)(I)Br 1 39 | F[C@@](I)(Br)Cl 1 40 | F[C@](Br)(I)Cl 1 41 | F[C@](Cl)(Br)I 1 42 | F[C@](I)(Cl)Br 1 43 | I[C@@](Br)(F)Cl 1 44 | I[C@@](Cl)(Br)F 1 45 | I[C@@](F)(Cl)Br 1 46 | I[C@](Br)(Cl)F 1 47 | I[C@](Cl)(F)Br 1 48 | I[C@](F)(Br)Cl 1 49 | [C@@]1(Cl)(F)I.Br1 1 50 | Br[C@@]1(F)I.Cl1 1 51 | Br[C@]1(Cl)I.F1 1 52 | Br[C@@H](F)I 2 53 | Br[C@H](I)F 2 54 | [C@H](Br)(F)I 2 55 | [C@@H](Br)(I)F 2 56 | [C@@H](F)(Br)I 2 57 | [C@H](F)(I)Br 2 58 | [C@H](I)(Br)F 2 59 | [C@@H](I)(F)Br 2 60 | F[C@@H](I)Br 2 61 | F[C@H](Br)I 2 62 | I[C@@H](Br)F 2 63 | I[C@H](F)Br 2 64 | [C@H]1(F)I.Br1 2 65 | Br[C@@H]1I.F1 2 66 | Br[C@H]1F.I1 2 67 | -------------------------------------------------------------------------------- /4-stereosmiles/tetrahedral_distantbcdigit.smi: -------------------------------------------------------------------------------- 1 | [C@@]1(Cl)(F)I.Br1 1 2 | [C@](Cl)1(F)I.Br1 1 3 | [C@@](Cl)(F)1I.Br1 1 4 | [C@](Cl)(F)(I)1.Br1 1 5 | Br[C@]1(Cl)I.F1 1 6 | Br[C@@](Cl)1I.F1 1 7 | Br[C@](Cl)(I)1.F1 1 8 | [C@H]1(F)I.Br1 2 9 | [C@@H](F)1I.Br1 2 10 | [C@H](F)(I)1.Br1 2 11 | Br[C@H]1F.I1 2 12 | Br[C@@H](F)1.I1 2 13 | -------------------------------------------------------------------------------- /5-results/cistrans/BIOVIADraw_2018.smi: -------------------------------------------------------------------------------- 1 | F\C=C\I 1 2 | F\C=C\I 1 3 | F\C=C\I 1 4 | F\C=C\I 1 5 | F\C=C\I 1 6 | F\C=C\I 1 7 | F\C=C\I 1 8 | F\C=C\I 1 9 | F\C=C\I 1 10 | F\C=C\I 1 11 | F\C=C\I 1 12 | F\C=C\I 1 13 | F\C=C\I 1 14 | F\C=C\I 1 15 | F\C=C\I 1 16 | F\C=C\I 1 17 | F\C=C\I 1 18 | F\C=C\I 1 19 | F\C=C\I 1 20 | F\C=C\I 1 21 | F\C=C\I 1 22 | F\C=C\I 1 23 | F\C=C\C=C/I 2 24 | F\C=C\C=C/I 2 25 | F\C=C\C=C/I 2 26 | F\C=C\C=C/I 2 27 | F\C=C\C=C/I 2 28 | F\C=C\C=C/I 2 29 | F\C=C\C=C/I 2 30 | F\C=C\C=C/I 2 31 | F\C=C\C=C/I 2 32 | F\C=C\C=C/I 2 33 | F\C=C\C=C/I 2 34 | F\C=C\C=C/I 2 35 | F\C=C\C=C/I 2 36 | F\C=C\C=C/I 2 37 | F\C=C\C=C/I 2 38 | F\C=C\C=C/I 2 39 | F\C=C\C=C/I 2 40 | F\C=C\C=C/I 2 41 | F\C=C\C=C/I 2 42 | F\C=C\C=C/I 2 43 | F\C=C\C=C/I 2 44 | F\C=C\C=C/I 2 45 | F\C=C\C=C/I 2 46 | F\C=C\C=C/I 2 47 | F\C(=C(/Br)\I)\Cl 3 48 | F\C(=C(/Br)\I)\Cl 3 49 | F\C(=C(/Br)\I)\Cl 3 50 | F\C(=C(/Br)\I)\Cl 3 51 | F\C(=C(/Br)\I)\Cl 3 52 | F\C(=C(/Br)\I)\Cl 3 53 | F\C(=C(/Br)\I)\Cl 3 54 | F\C(=C(/Br)\I)\Cl 3 55 | F\C(=C(/Br)\I)\Cl 3 56 | F\C(=C(/Br)\I)\Cl 3 57 | F\C(=C(/Br)\I)\Cl 3 58 | F\C(=C(/Br)\I)\Cl 3 59 | F\C(=C(/Br)\I)\Cl 3 60 | F\C(=C(/Br)\I)\Cl 3 61 | F\C(=C(/Br)\I)\Cl 3 62 | F\C(=C(/Br)\I)\Cl 3 63 | F\C(=C(/Br)\I)\Cl 3 64 | F\C(=C(/Br)\I)\Cl 3 65 | F\C(=C(/Br)\I)\Cl 3 66 | F\C(=C(/Br)\I)\Cl 3 67 | F\C(=C(/Br)\I)\Cl 3 68 | F\C(=C(/Br)\I)\Cl 3 69 | F\C(=C(/Br)\I)\Cl 3 70 | F\C(=C(/Br)\I)\Cl 3 71 | F\C(=C(/Br)\I)\Cl 3 72 | F\C(=C(/Br)\I)\Cl 3 73 | F\C(=C(/Br)\I)\Cl 3 74 | F\C(=C(/Br)\I)\Cl 3 75 | F\C(=C(/Br)\I)\Cl 3 76 | F\C(=C(/Br)\I)\Cl 3 77 | F\C(=C(/Br)\I)\Cl 3 78 | F\C(=C(/Br)\I)\Cl 3 79 | F\C(=C(/Br)\I)\Cl 3 80 | F\C(=C(/Br)\I)\Cl 3 81 | F\C(=C(/Br)\I)\Cl 3 82 | F\C(=C(/Br)\I)\Cl 3 83 | F\C(=C(/Br)\I)\Cl 3 84 | F\C(=C(/Br)\I)\Cl 3 85 | F\C(=C(/Br)\I)\Cl 3 86 | F\C(=C(/Br)\I)\Cl 3 87 | F\C(=C(/Br)\I)\Cl 3 88 | F\C(=C(/Br)\I)\Cl 3 89 | F\C(=C(/Br)\I)\Cl 3 90 | F\C(=C(/Br)\I)\Cl 3 91 | F\C(=C(/Br)\I)\Cl 3 92 | F\C(=C(/Br)\I)\Cl 3 93 | F\C(=C(/Br)\I)\Cl 3 94 | F\C(=C(/Br)\I)\Cl 3 95 | F\C(=C(/Br)\I)\Cl 3 96 | F\C(=C(/Br)\I)\Cl 3 97 | F\C(=C(/Br)\I)\Cl 3 98 | F\C(=C(/Br)\I)\Cl 3 99 | F\C(=C(/Br)\I)\Cl 3 100 | F\C(=C(/Br)\I)\Cl 3 101 | F\C(=C(/Br)\I)\Cl 3 102 | F\C(=C(/Br)\I)\Cl 3 103 | F\C(=C(/Br)\I)\Cl 3 104 | F\C(=C(/Br)\I)\Cl 3 105 | F\C(=C(/Br)\I)\Cl 3 106 | F\C(=C(/Br)\I)\Cl 3 107 | F\C(=C(/Br)\I)\Cl 3 108 | F\C(=C(/Br)\I)\Cl 3 109 | F\C(=C(/Br)\I)\Cl 3 110 | F\C(=C(/Br)\I)\Cl 3 111 | F\C(=C(/Br)\I)\Cl 3 112 | F\C(=C(/Br)\I)\Cl 3 113 | F\C(=C(/Br)\I)\Cl 3 114 | F\C(=C(/Br)\I)\Cl 3 115 | F\C(=C(/Br)\I)\Cl 3 116 | F\C(=C(/Br)\I)\Cl 3 117 | F\C(=C(/Br)\I)\Cl 3 118 | F\C(=C(/Br)\I)\Cl 3 119 | F\C(=C(/Br)\I)\Cl 3 120 | F\C(=C(/Br)\I)\Cl 3 121 | F\C(=C(/Br)\I)\Cl 3 122 | F\C(=C(/Br)\I)\Cl 3 123 | F\C(=C(/Br)\I)\Cl 3 124 | F\C(=C(/Br)\I)\Cl 3 125 | F\C(=C(/Br)\I)\Cl 3 126 | F\C(=C(/Br)\I)\Cl 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/ChemDraw_17.1.smi: -------------------------------------------------------------------------------- 1 | F\C=C\I 1 2 | F\C=C\I 1 3 | F\C=C\I 1 4 | F\C=C\I 1 5 | F\C=C\I 1 6 | F\C=C\I 1 7 | F\C=C\I 1 8 | F\C=C\I 1 9 | F\C=C\I 1 10 | F\C=C\I 1 11 | F\C=C\I 1 12 | F\C=C\I 1 13 | F\C=C\I 1 14 | F\C=C\I 1 15 | F\C=C\I 1 16 | F\C=C\I 1 17 | F\C=C\I 1 18 | F\C=C\I 1 19 | F\C=C\I 1 20 | F\C=C\I 1 21 | F\C=C\I 1 22 | F\C=C\I 1 23 | F\C=C\C=C/I 2 24 | F\C=C\C=C/I 2 25 | F\C=C\C=C/I 2 26 | F\C=C\C=C/I 2 27 | F\C=C\C=C/I 2 28 | F\C=C\C=C/I 2 29 | F\C=C\C=C/I 2 30 | F\C=C\C=C/I 2 31 | F\C=C\C=C/I 2 32 | F\C=C\C=C/I 2 33 | F\C=C\C=C/I 2 34 | F\C=C\C=C/I 2 35 | F\C=C\C=C/I 2 36 | F\C=C\C=C/I 2 37 | F\C=C\C=C/I 2 38 | F\C=C\C=C/I 2 39 | F\C=C\C=C/I 2 40 | F\C=C\C=C/I 2 41 | F\C=C\C=C/I 2 42 | F\C=C\C=C/I 2 43 | F\C=C\C=C/I 2 44 | F\C=C\C=C/I 2 45 | F\C=C\C=C/I 2 46 | F\C=C\C=C/I 2 47 | Br/C(=C(\F)/Cl)/I 3 48 | Br/C(=C(\F)/Cl)/I 3 49 | Br/C(=C(\F)/Cl)/I 3 50 | Br/C(=C(\F)/Cl)/I 3 51 | Br/C(=C(\F)/Cl)/I 3 52 | Br/C(=C(\F)/Cl)/I 3 53 | Br/C(=C(\F)/Cl)/I 3 54 | Br/C(=C(\F)/Cl)/I 3 55 | Br/C(=C(\F)/Cl)/I 3 56 | Br/C(=C(\F)/Cl)/I 3 57 | Br/C(=C(\F)/Cl)/I 3 58 | Br/C(=C(\F)/Cl)/I 3 59 | Br/C(=C(\F)/Cl)/I 3 60 | Br/C(=C(\F)/Cl)/I 3 61 | Br/C(=C(\F)/Cl)/I 3 62 | Br/C(=C(\F)/Cl)/I 3 63 | Br/C(=C(\F)/Cl)/I 3 64 | Br/C(=C(\F)/Cl)/I 3 65 | Br/C(=C(\F)/Cl)/I 3 66 | Br/C(=C(\F)/Cl)/I 3 67 | Br/C(=C(\F)/Cl)/I 3 68 | Br/C(=C(\F)/Cl)/I 3 69 | Br/C(=C(\F)/Cl)/I 3 70 | Br/C(=C(\F)/Cl)/I 3 71 | Br/C(=C(\F)/Cl)/I 3 72 | Br/C(=C(\F)/Cl)/I 3 73 | Br/C(=C(\F)/Cl)/I 3 74 | Br/C(=C(\F)/Cl)/I 3 75 | Br/C(=C(\F)/Cl)/I 3 76 | Br/C(=C(\F)/Cl)/I 3 77 | Br/C(=C(\F)/Cl)/I 3 78 | Br/C(=C(\F)/Cl)/I 3 79 | Br/C(=C(\F)/Cl)/I 3 80 | Br/C(=C(\F)/Cl)/I 3 81 | Br/C(=C(\F)/Cl)/I 3 82 | Br/C(=C(\F)/Cl)/I 3 83 | Br/C(=C(\F)/Cl)/I 3 84 | Br/C(=C(\F)/Cl)/I 3 85 | Br/C(=C(\F)/Cl)/I 3 86 | Br/C(=C(\F)/Cl)/I 3 87 | Br/C(=C(\F)/Cl)/I 3 88 | Br/C(=C(\F)/Cl)/I 3 89 | Br/C(=C(\F)/Cl)/I 3 90 | Br/C(=C(\F)/Cl)/I 3 91 | Br/C(=C(\F)/Cl)/I 3 92 | Br/C(=C(\F)/Cl)/I 3 93 | Br/C(=C(\F)/Cl)/I 3 94 | Br/C(=C(\F)/Cl)/I 3 95 | Br/C(=C(\F)/Cl)/I 3 96 | Br/C(=C(\F)/Cl)/I 3 97 | Br/C(=C(\F)/Cl)/I 3 98 | Br/C(=C(\F)/Cl)/I 3 99 | Br/C(=C(\F)/Cl)/I 3 100 | Br/C(=C(\F)/Cl)/I 3 101 | Br/C(=C(\F)/Cl)/I 3 102 | Br/C(=C(\F)/Cl)/I 3 103 | Br/C(=C(\F)/Cl)/I 3 104 | Br/C(=C(\F)/Cl)/I 3 105 | Br/C(=C(\F)/Cl)/I 3 106 | Br/C(=C(\F)/Cl)/I 3 107 | Br/C(=C(\F)/Cl)/I 3 108 | Br/C(=C(\F)/Cl)/I 3 109 | Br/C(=C(\F)/Cl)/I 3 110 | Br/C(=C(\F)/Cl)/I 3 111 | Br/C(=C(\F)/Cl)/I 3 112 | Br/C(=C(\F)/Cl)/I 3 113 | Br/C(=C(\F)/Cl)/I 3 114 | Br/C(=C(\F)/Cl)/I 3 115 | Br/C(=C(\F)/Cl)/I 3 116 | Br/C(=C(\F)/Cl)/I 3 117 | Br/C(=C(\F)/Cl)/I 3 118 | Br/C(=C(\F)/Cl)/I 3 119 | Br/C(=C(\F)/Cl)/I 3 120 | Br/C(=C(\F)/Cl)/I 3 121 | Br/C(=C(\F)/Cl)/I 3 122 | Br/C(=C(\F)/Cl)/I 3 123 | Br/C(=C(\F)/Cl)/I 3 124 | Br/C(=C(\F)/Cl)/I 3 125 | Br/C(=C(\F)/Cl)/I 3 126 | Br/C(=C(\F)/Cl)/I 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/KnowItAll_2018.smi: -------------------------------------------------------------------------------- 1 | F\C=C\I 1 2 | F\C=C\I 1 3 | F\C=C\I 1 4 | F\C=C\I 1 5 | F\C=C\I 1 6 | F\C=C\I 1 7 | F\C=C\I 1 8 | F\C=C\I 1 9 | F\C=C\I 1 10 | F\C=C\I 1 11 | F\C=C\I 1 12 | F\C=C\I 1 13 | F\C=C\I 1 14 | F\C=C\I 1 15 | F\C=C\I 1 16 | F\C=C\I 1 17 | F\C=C\I 1 18 | F\C=C\I 1 19 | F\C=C\I 1 20 | F\C=C\I 1 21 | F\C=C\I 1 22 | F\C=C\I 1 23 | F\C=C\C=C/I 2 24 | F\C=C\C=C/I 2 25 | F\C=C\C=C/I 2 26 | F\C=C\C=C/I 2 27 | F\C=C\C=C/I 2 28 | F\C=C\C=C/I 2 29 | F\C=C\C=C/I 2 30 | F\C=C\C=C/I 2 31 | F\C=C\C=C/I 2 32 | F\C=C\C=C/I 2 33 | F\C=C\C=C/I 2 34 | F\C=C\C=C/I 2 35 | F\C=C\C=C/I 2 36 | F\C=C\C=C/I 2 37 | F\C=C\C=C/I 2 38 | F\C=C\C=C/I 2 39 | F\C=C\C=C/I 2 40 | F\C=C\C=C/I 2 41 | F\C=C\C=C/I 2 42 | F\C=C\C=C/I 2 43 | F\C=C\C=C/I 2 44 | F\C=C\C=C/I 2 45 | F\C=C\C=C/I 2 46 | F\C=C\C=C/I 2 47 | F\C(Cl)=C/(Br)I 3 48 | F\C(Cl)=C/(Br)I 3 49 | F\C(Cl)=C/(Br)I 3 50 | F\C(Cl)=C/(Br)I 3 51 | F\C(Cl)=C/(Br)I 3 52 | F\C(Cl)=C/(Br)I 3 53 | F\C(Cl)=C/(Br)I 3 54 | F\C(Cl)=C/(Br)I 3 55 | F\C(Cl)=C/(Br)I 3 56 | F\C(Cl)=C/(Br)I 3 57 | F\C(Cl)=C/(Br)I 3 58 | F\C(Cl)=C/(Br)I 3 59 | F\C(Cl)=C/(Br)I 3 60 | F\C(Cl)=C/(Br)I 3 61 | F\C(Cl)=C/(Br)I 3 62 | F\C(Cl)=C/(Br)I 3 63 | F\C(Cl)=C/(Br)I 3 64 | F\C(Cl)=C/(Br)I 3 65 | F\C(Cl)=C/(Br)I 3 66 | F\C(Cl)=C/(Br)I 3 67 | F\C(Cl)=C/(Br)I 3 68 | F\C(Cl)=C/(Br)I 3 69 | F\C(Cl)=C/(Br)I 3 70 | F\C(Cl)=C/(Br)I 3 71 | F\C(Cl)=C/(Br)I 3 72 | F\C(Cl)=C/(Br)I 3 73 | F\C(Cl)=C/(Br)I 3 74 | F\C(Cl)=C/(Br)I 3 75 | F\C(Cl)=C/(Br)I 3 76 | F\C(Cl)=C/(Br)I 3 77 | F\C(Cl)=C/(Br)I 3 78 | F\C(Cl)=C/(Br)I 3 79 | F\C(Cl)=C/(Br)I 3 80 | F\C(Cl)=C/(Br)I 3 81 | F\C(Cl)=C/(Br)I 3 82 | F\C(Cl)=C/(Br)I 3 83 | F\C(Cl)=C/(Br)I 3 84 | F\C(Cl)=C/(Br)I 3 85 | F\C(Cl)=C/(Br)I 3 86 | F\C(Cl)=C/(Br)I 3 87 | F\C(Cl)=C/(Br)I 3 88 | F\C(Cl)=C/(Br)I 3 89 | F\C(Cl)=C/(Br)I 3 90 | F\C(Cl)=C/(Br)I 3 91 | F\C(Cl)=C/(Br)I 3 92 | F\C(Cl)=C/(Br)I 3 93 | F\C(Cl)=C/(Br)I 3 94 | F\C(Cl)=C/(Br)I 3 95 | F\C(Cl)=C/(Br)I 3 96 | F\C(Cl)=C/(Br)I 3 97 | F\C(Cl)=C/(Br)I 3 98 | F\C(Cl)=C/(Br)I 3 99 | F\C(Cl)=C/(Br)I 3 100 | F\C(Cl)=C/(Br)I 3 101 | F\C(Cl)=C/(Br)I 3 102 | F\C(Cl)=C/(Br)I 3 103 | F\C(Cl)=C/(Br)I 3 104 | F\C(Cl)=C/(Br)I 3 105 | F\C(Cl)=C/(Br)I 3 106 | F\C(Cl)=C/(Br)I 3 107 | F\C(Cl)=C/(Br)I 3 108 | F\C(Cl)=C/(Br)I 3 109 | F\C(Cl)=C/(Br)I 3 110 | F\C(Cl)=C/(Br)I 3 111 | F\C(Cl)=C/(Br)I 3 112 | F\C(Cl)=C/(Br)I 3 113 | F\C(Cl)=C/(Br)I 3 114 | F\C(Cl)=C/(Br)I 3 115 | F\C(Cl)=C/(Br)I 3 116 | F\C(Cl)=C/(Br)I 3 117 | F\C(Cl)=C/(Br)I 3 118 | F\C(Cl)=C/(Br)I 3 119 | F\C(Cl)=C/(Br)I 3 120 | F\C(Cl)=C/(Br)I 3 121 | F\C(Cl)=C/(Br)I 3 122 | F\C(Cl)=C/(Br)I 3 123 | F\C(Cl)=C/(Br)I 3 124 | F\C(Cl)=C/(Br)I 3 125 | F\C(Cl)=C/(Br)I 3 126 | F\C(Cl)=C/(Br)I 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/avalon_1.2.0.smi: -------------------------------------------------------------------------------- 1 | F/C=C/I 1 2 | F/C=C/I 1 3 | I/C=C/F 1 4 | I/C=C/F 1 5 | F\C=C\I 1 6 | F\C=C\I 1 7 | I\C=C\F 1 8 | I\C=C\F 1 9 | F\C=C\I 1 10 | F\C=C\I 1 11 | I\C=C\F 1 12 | I\C=C\F 1 13 | I\C=C\F 1 14 | I\C=C\F 1 15 | F/C=C/I 1 16 | F/C=C/I 1 17 | I/C=C/F 1 18 | I/C=C/F 1 19 | F/C=C/I 1 20 | F/C=C/I 1 21 | F/C=C/I 1 22 | F/C=C/I 1 23 | I/C=C\C=C\F 2 24 | I/C=C\C=C\F 2 25 | F\C=C\C=C/I 2 26 | F\C=C\C=C/I 2 27 | F/C=C/C=C\I 2 28 | F/C=C/C=C\I 2 29 | I\C=C/C=C/F 2 30 | I\C=C/C=C/F 2 31 | I\C=C/C=C/F 2 32 | I\C=C/C=C/F 2 33 | F/C=C/C=C\I 2 34 | F/C=C/C=C\I 2 35 | F/C=C/C=C\I 2 36 | F/C=C/C=C\I 2 37 | I\C=C/C=C/F 2 38 | I\C=C/C=C/F 2 39 | F/C=C/C=C\I 2 40 | F/C=C/C=C\I 2 41 | I\C=C/C=C/F 2 42 | I\C=C/C=C/F 2 43 | F\C=C\C=C/I 2 44 | F\C=C\C=C/I 2 45 | I\C=C/C=C/F 2 46 | I\C=C/C=C/F 2 47 | Br\C(\I)=C(\Cl)/F 3 48 | Br\C(\I)=C(\Cl)/F 3 49 | Br\C(\I)=C(/F)\Cl 3 50 | Br\C(\I)=C(/F)\Cl 3 51 | Br/C(=C(/Cl)\F)/I 3 52 | Br/C(=C(/Cl)\F)/I 3 53 | Br/C(=C(\F)/Cl)/I 3 54 | Br/C(=C(\F)/Cl)/I 3 55 | Br/C(=C(/Cl)\F)/I 3 56 | Br/C(=C(/Cl)\F)/I 3 57 | Br\C(=C(/F)\Cl)\I 3 58 | Br\C(=C(/F)\Cl)\I 3 59 | Cl/C(=C(/Br)\I)/F 3 60 | Cl/C(=C(/Br)\I)/F 3 61 | Cl\C(=C(/I)\Br)\F 3 62 | Cl\C(=C(/I)\Br)\F 3 63 | F/C(=C(/I)\Br)/Cl 3 64 | F/C(=C(/I)\Br)/Cl 3 65 | F\C(=C(/Br)\I)\Cl 3 66 | F\C(=C(/Br)\I)\Cl 3 67 | I/C(=C(/F)\Cl)/Br 3 68 | I/C(=C(/F)\Cl)/Br 3 69 | I\C(=C(/Cl)\F)\Br 3 70 | I\C(=C(/Cl)\F)\Br 3 71 | Br\C(\I)=C(\Cl)/F 3 72 | Br\C(\I)=C(\Cl)/F 3 73 | Br\C(\I)=C(/F)\Cl 3 74 | Br\C(\I)=C(/F)\Cl 3 75 | Br/C(=C(/Cl)\F)/I 3 76 | Br/C(=C(/Cl)\F)/I 3 77 | Br/C(=C(\F)/Cl)/I 3 78 | Br/C(=C(\F)/Cl)/I 3 79 | Cl\C(\F)=C(\Br)/I 3 80 | Cl\C(\F)=C(\Br)/I 3 81 | Cl\C(\F)=C(/I)\Br 3 82 | Cl\C(\F)=C(/I)\Br 3 83 | Cl/C(=C(/Br)\I)/F 3 84 | Cl/C(=C(/Br)\I)/F 3 85 | Cl/C(=C(\I)/Br)/F 3 86 | Cl/C(=C(\I)/Br)/F 3 87 | F\C(\Cl)=C(\I)/Br 3 88 | F\C(\Cl)=C(\I)/Br 3 89 | F\C(\Cl)=C(/Br)\I 3 90 | F\C(\Cl)=C(/Br)\I 3 91 | F/C(=C(/I)\Br)/Cl 3 92 | F/C(=C(/I)\Br)/Cl 3 93 | F/C(=C(\Br)/I)/Cl 3 94 | F/C(=C(\Br)/I)/Cl 3 95 | I\C(\Br)=C(\F)/Cl 3 96 | I\C(\Br)=C(\F)/Cl 3 97 | I\C(\Br)=C(/Cl)\F 3 98 | I\C(\Br)=C(/Cl)\F 3 99 | I/C(=C(/F)\Cl)/Br 3 100 | I/C(=C(/F)\Cl)/Br 3 101 | I/C(=C(\Cl)/F)/Br 3 102 | I/C(=C(\Cl)/F)/Br 3 103 | Cl\C(\F)=C(\Br)/I 3 104 | Cl\C(\F)=C(\Br)/I 3 105 | Cl\C(\F)=C(/I)\Br 3 106 | Cl\C(\F)=C(/I)\Br 3 107 | Cl/C(=C(/Br)\I)/F 3 108 | Cl/C(=C(/Br)\I)/F 3 109 | Cl/C(=C(\I)/Br)/F 3 110 | Cl/C(=C(\I)/Br)/F 3 111 | F\C(\Cl)=C(\I)/Br 3 112 | F\C(\Cl)=C(\I)/Br 3 113 | F\C(\Cl)=C(/Br)\I 3 114 | F\C(\Cl)=C(/Br)\I 3 115 | F/C(=C(/I)\Br)/Cl 3 116 | F/C(=C(/I)\Br)/Cl 3 117 | F/C(=C(\Br)/I)/Cl 3 118 | F/C(=C(\Br)/I)/Cl 3 119 | I\C(\Br)=C(\F)/Cl 3 120 | I\C(\Br)=C(\F)/Cl 3 121 | I\C(\Br)=C(/Cl)\F 3 122 | I\C(\Br)=C(/Cl)\F 3 123 | I/C(=C(/F)\Cl)/Br 3 124 | I/C(=C(/F)\Cl)/Br 3 125 | I/C(=C(\Cl)/F)/Br 3 126 | I/C(=C(\Cl)/F)/Br 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/cdk_2.1.smi: -------------------------------------------------------------------------------- 1 | C(=C\I)/F 1 2 | C(=C\I)/F 1 3 | C(=C\I)/F 1 4 | C(=C\I)/F 1 5 | C(=C\I)/F 1 6 | C(=C\I)/F 1 7 | C(=C\I)/F 1 8 | C(=C\I)/F 1 9 | C(=C\I)/F 1 10 | C(=C\I)/F 1 11 | C(=C\I)/F 1 12 | C(=C\I)/F 1 13 | C(=C\I)/F 1 14 | C(=C\I)/F 1 15 | C(=C\I)/F 1 16 | C(=C\I)/F 1 17 | C(=C\I)/F 1 18 | C(=C\I)/F 1 19 | C(=C\I)/F 1 20 | C(=C\I)/F 1 21 | C(=C\I)/F 1 22 | C(=C\I)/F 1 23 | C(=C\F)/C=C\I 2 24 | C(=C\F)/C=C\I 2 25 | C(=C\F)/C=C\I 2 26 | C(=C\F)/C=C\I 2 27 | C(=C\F)/C=C\I 2 28 | C(=C\F)/C=C\I 2 29 | C(=C\F)/C=C\I 2 30 | C(=C\F)/C=C\I 2 31 | C(=C\F)/C=C\I 2 32 | C(=C\F)/C=C\I 2 33 | C(=C\F)/C=C\I 2 34 | C(=C\F)/C=C\I 2 35 | C(=C\F)/C=C\I 2 36 | C(=C\F)/C=C\I 2 37 | C(=C\F)/C=C\I 2 38 | C(=C\F)/C=C\I 2 39 | C(=C\F)/C=C\I 2 40 | C(=C\F)/C=C\I 2 41 | C(=C\F)/C=C\I 2 42 | C(=C\F)/C=C\I 2 43 | C(=C\F)/C=C\I 2 44 | C(=C\F)/C=C\I 2 45 | C(=C\F)/C=C\I 2 46 | C(=C\F)/C=C\I 2 47 | C(=C(\Cl)/F)(/Br)\I 3 48 | C(=C(\Cl)/F)(/Br)\I 3 49 | C(=C(\Cl)/F)(/Br)\I 3 50 | C(=C(\Cl)/F)(/Br)\I 3 51 | C(=C(\Cl)/F)(/Br)\I 3 52 | C(=C(\Cl)/F)(/Br)\I 3 53 | C(=C(\Cl)/F)(/Br)\I 3 54 | C(=C(\Cl)/F)(/Br)\I 3 55 | C(=C(\Cl)/F)(/Br)\I 3 56 | C(=C(\Cl)/F)(/Br)\I 3 57 | C(=C(\Cl)/F)(/Br)\I 3 58 | C(=C(\Cl)/F)(/Br)\I 3 59 | C(=C(\Cl)/F)(/Br)\I 3 60 | C(=C(\Cl)/F)(/Br)\I 3 61 | C(=C(\Cl)/F)(/Br)\I 3 62 | C(=C(\Cl)/F)(/Br)\I 3 63 | C(=C(\Cl)/F)(/Br)\I 3 64 | C(=C(\Cl)/F)(/Br)\I 3 65 | C(=C(\Cl)/F)(/Br)\I 3 66 | C(=C(\Cl)/F)(/Br)\I 3 67 | C(=C(\Cl)/F)(/Br)\I 3 68 | C(=C(\Cl)/F)(/Br)\I 3 69 | C(=C(\Cl)/F)(/Br)\I 3 70 | C(=C(\Cl)/F)(/Br)\I 3 71 | C(=C(\Cl)/F)(/Br)\I 3 72 | C(=C(\Cl)/F)(/Br)\I 3 73 | C(=C(\Cl)/F)(/Br)\I 3 74 | C(=C(\Cl)/F)(/Br)\I 3 75 | C(=C(\Cl)/F)(/Br)\I 3 76 | C(=C(\Cl)/F)(/Br)\I 3 77 | C(=C(\Cl)/F)(/Br)\I 3 78 | C(=C(\Cl)/F)(/Br)\I 3 79 | C(=C(\Cl)/F)(/Br)\I 3 80 | C(=C(\Cl)/F)(/Br)\I 3 81 | C(=C(\Cl)/F)(/Br)\I 3 82 | C(=C(\Cl)/F)(/Br)\I 3 83 | C(=C(\Cl)/F)(/Br)\I 3 84 | C(=C(\Cl)/F)(/Br)\I 3 85 | C(=C(\Cl)/F)(/Br)\I 3 86 | C(=C(\Cl)/F)(/Br)\I 3 87 | C(=C(\Cl)/F)(/Br)\I 3 88 | C(=C(\Cl)/F)(/Br)\I 3 89 | C(=C(\Cl)/F)(/Br)\I 3 90 | C(=C(\Cl)/F)(/Br)\I 3 91 | C(=C(\Cl)/F)(/Br)\I 3 92 | C(=C(\Cl)/F)(/Br)\I 3 93 | C(=C(\Cl)/F)(/Br)\I 3 94 | C(=C(\Cl)/F)(/Br)\I 3 95 | C(=C(\Cl)/F)(/Br)\I 3 96 | C(=C(\Cl)/F)(/Br)\I 3 97 | C(=C(\Cl)/F)(/Br)\I 3 98 | C(=C(\Cl)/F)(/Br)\I 3 99 | C(=C(\Cl)/F)(/Br)\I 3 100 | C(=C(\Cl)/F)(/Br)\I 3 101 | C(=C(\Cl)/F)(/Br)\I 3 102 | C(=C(\Cl)/F)(/Br)\I 3 103 | C(=C(\Cl)/F)(/Br)\I 3 104 | C(=C(\Cl)/F)(/Br)\I 3 105 | C(=C(\Cl)/F)(/Br)\I 3 106 | C(=C(\Cl)/F)(/Br)\I 3 107 | C(=C(\Cl)/F)(/Br)\I 3 108 | C(=C(\Cl)/F)(/Br)\I 3 109 | C(=C(\Cl)/F)(/Br)\I 3 110 | C(=C(\Cl)/F)(/Br)\I 3 111 | C(=C(\Cl)/F)(/Br)\I 3 112 | C(=C(\Cl)/F)(/Br)\I 3 113 | C(=C(\Cl)/F)(/Br)\I 3 114 | C(=C(\Cl)/F)(/Br)\I 3 115 | C(=C(\Cl)/F)(/Br)\I 3 116 | C(=C(\Cl)/F)(/Br)\I 3 117 | C(=C(\Cl)/F)(/Br)\I 3 118 | C(=C(\Cl)/F)(/Br)\I 3 119 | C(=C(\Cl)/F)(/Br)\I 3 120 | C(=C(\Cl)/F)(/Br)\I 3 121 | C(=C(\Cl)/F)(/Br)\I 3 122 | C(=C(\Cl)/F)(/Br)\I 3 123 | C(=C(\Cl)/F)(/Br)\I 3 124 | C(=C(\Cl)/F)(/Br)\I 3 125 | C(=C(\Cl)/F)(/Br)\I 3 126 | C(=C(\Cl)/F)(/Br)\I 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/indigo_1.3.0b.r16.smi: -------------------------------------------------------------------------------- 1 | F/C=C/I 1 2 | F/C=C/I 1 3 | F/C=C/I 1 4 | F/C=C/I 1 5 | F/C=C/I 1 6 | F/C=C/I 1 7 | F/C=C/I 1 8 | F/C=C/I 1 9 | F/C=C/I 1 10 | F/C=C/I 1 11 | F/C=C/I 1 12 | F/C=C/I 1 13 | F/C=C/I 1 14 | F/C=C/I 1 15 | F/C=C/I 1 16 | F/C=C/I 1 17 | F/C=C/I 1 18 | F/C=C/I 1 19 | F/C=C/I 1 20 | F/C=C/I 1 21 | F/C=C/I 1 22 | F/C=C/I 1 23 | F/C=C/C=C\I 2 24 | F/C=C/C=C\I 2 25 | F/C=C/C=C\I 2 26 | F/C=C/C=C\I 2 27 | F/C=C/C=C\I 2 28 | F/C=C/C=C\I 2 29 | F/C=C/C=C\I 2 30 | F/C=C/C=C\I 2 31 | F/C=C/C=C\I 2 32 | F/C=C/C=C\I 2 33 | F/C=C/C=C\I 2 34 | F/C=C/C=C\I 2 35 | F/C=C/C=C\I 2 36 | F/C=C/C=C\I 2 37 | F/C=C/C=C\I 2 38 | F/C=C/C=C\I 2 39 | F/C=C/C=C\I 2 40 | F/C=C/C=C\I 2 41 | F/C=C/C=C\I 2 42 | F/C=C/C=C\I 2 43 | F/C=C/C=C\I 2 44 | F/C=C/C=C\I 2 45 | F/C=C/C=C\I 2 46 | F/C=C/C=C\I 2 47 | F/C(/Cl)=C(\Br)/I 3 48 | F/C(/Cl)=C(\Br)/I 3 49 | F/C(/Cl)=C(\Br)/I 3 50 | F/C(/Cl)=C(\Br)/I 3 51 | F/C(/Cl)=C(\Br)/I 3 52 | F/C(/Cl)=C(\Br)/I 3 53 | F/C(/Cl)=C(\Br)/I 3 54 | F/C(/Cl)=C(\Br)/I 3 55 | F/C(/Cl)=C(\Br)/I 3 56 | F/C(/Cl)=C(\Br)/I 3 57 | F/C(/Cl)=C(\Br)/I 3 58 | F/C(/Cl)=C(\Br)/I 3 59 | F/C(/Cl)=C(\Br)/I 3 60 | F/C(/Cl)=C(\Br)/I 3 61 | F/C(/Cl)=C(\Br)/I 3 62 | F/C(/Cl)=C(\Br)/I 3 63 | F/C(/Cl)=C(\Br)/I 3 64 | F/C(/Cl)=C(\Br)/I 3 65 | F/C(/Cl)=C(\Br)/I 3 66 | F/C(/Cl)=C(\Br)/I 3 67 | F/C(/Cl)=C(\Br)/I 3 68 | F/C(/Cl)=C(\Br)/I 3 69 | F/C(/Cl)=C(\Br)/I 3 70 | F/C(/Cl)=C(\Br)/I 3 71 | F/C(/Cl)=C(\Br)/I 3 72 | F/C(/Cl)=C(\Br)/I 3 73 | F/C(/Cl)=C(\Br)/I 3 74 | F/C(/Cl)=C(\Br)/I 3 75 | F/C(/Cl)=C(\Br)/I 3 76 | F/C(/Cl)=C(\Br)/I 3 77 | F/C(/Cl)=C(\Br)/I 3 78 | F/C(/Cl)=C(\Br)/I 3 79 | F/C(/Cl)=C(\Br)/I 3 80 | F/C(/Cl)=C(\Br)/I 3 81 | F/C(/Cl)=C(\Br)/I 3 82 | F/C(/Cl)=C(\Br)/I 3 83 | F/C(/Cl)=C(\Br)/I 3 84 | F/C(/Cl)=C(\Br)/I 3 85 | F/C(/Cl)=C(\Br)/I 3 86 | F/C(/Cl)=C(\Br)/I 3 87 | F/C(/Cl)=C(\Br)/I 3 88 | F/C(/Cl)=C(\Br)/I 3 89 | F/C(/Cl)=C(\Br)/I 3 90 | F/C(/Cl)=C(\Br)/I 3 91 | F/C(/Cl)=C(\Br)/I 3 92 | F/C(/Cl)=C(\Br)/I 3 93 | F/C(/Cl)=C(\Br)/I 3 94 | F/C(/Cl)=C(\Br)/I 3 95 | F/C(/Cl)=C(\Br)/I 3 96 | F/C(/Cl)=C(\Br)/I 3 97 | F/C(/Cl)=C(\Br)/I 3 98 | F/C(/Cl)=C(\Br)/I 3 99 | F/C(/Cl)=C(\Br)/I 3 100 | F/C(/Cl)=C(\Br)/I 3 101 | F/C(/Cl)=C(\Br)/I 3 102 | F/C(/Cl)=C(\Br)/I 3 103 | F/C(/Cl)=C(\Br)/I 3 104 | F/C(/Cl)=C(\Br)/I 3 105 | F/C(/Cl)=C(\Br)/I 3 106 | F/C(/Cl)=C(\Br)/I 3 107 | F/C(/Cl)=C(\Br)/I 3 108 | F/C(/Cl)=C(\Br)/I 3 109 | F/C(/Cl)=C(\Br)/I 3 110 | F/C(/Cl)=C(\Br)/I 3 111 | F/C(/Cl)=C(\Br)/I 3 112 | F/C(/Cl)=C(\Br)/I 3 113 | F/C(/Cl)=C(\Br)/I 3 114 | F/C(/Cl)=C(\Br)/I 3 115 | F/C(/Cl)=C(\Br)/I 3 116 | F/C(/Cl)=C(\Br)/I 3 117 | F/C(/Cl)=C(\Br)/I 3 118 | F/C(/Cl)=C(\Br)/I 3 119 | F/C(/Cl)=C(\Br)/I 3 120 | F/C(/Cl)=C(\Br)/I 3 121 | F/C(/Cl)=C(\Br)/I 3 122 | F/C(/Cl)=C(\Br)/I 3 123 | F/C(/Cl)=C(\Br)/I 3 124 | F/C(/Cl)=C(\Br)/I 3 125 | F/C(/Cl)=C(\Br)/I 3 126 | F/C(/Cl)=C(\Br)/I 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/iwtoolkit_1.0.smi: -------------------------------------------------------------------------------- 1 | I/C=C/F 1 2 | I/C=C/F 1 3 | I/C=C/F 1 4 | I/C=C/F 1 5 | I/C=C/F 1 6 | I/C=C/F 1 7 | I/C=C/F 1 8 | I/C=C/F 1 9 | I/C=C/F 1 10 | I/C=C/F 1 11 | I/C=C/F 1 12 | I/C=C/F 1 13 | I/C=C/F 1 14 | I/C=C/F 1 15 | I/C=C/F 1 16 | I/C=C/F 1 17 | I/C=C/F 1 18 | I/C=C/F 1 19 | I/C=C/F 1 20 | I/C=C/F 1 21 | I/C=C/F 1 22 | I/C=C/F 1 23 | I/C=C\C=C\F 2 24 | I/C=C\C=C\F 2 25 | I/C=C\C=C\F 2 26 | I/C=C\C=C\F 2 27 | I/C=C\C=C\F 2 28 | I/C=C\C=C\F 2 29 | I/C=C\C=C\F 2 30 | I/C=C\C=C\F 2 31 | I/C=C\C=C\F 2 32 | I/C=C\C=C\F 2 33 | I/C=C\C=C\F 2 34 | I/C=C\C=C\F 2 35 | I/C=C\C=C\F 2 36 | I/C=C\C=C\F 2 37 | I/C=C\C=C\F 2 38 | I/C=C\C=C\F 2 39 | I/C=C\C=C\F 2 40 | I/C=C\C=C\F 2 41 | I/C=C\C=C\F 2 42 | I/C=C\C=C\F 2 43 | I/C=C\C=C\F 2 44 | I/C=C\C=C\F 2 45 | I/C=C\C=C\F 2 46 | I/C=C\C=C\F 2 47 | I/C(=C(\Cl)/F)/Br 3 48 | I/C(=C(\Cl)/F)/Br 3 49 | I/C(=C(\Cl)/F)/Br 3 50 | I/C(=C(\Cl)/F)/Br 3 51 | I/C(=C(\Cl)/F)/Br 3 52 | I/C(=C(\Cl)/F)/Br 3 53 | I/C(=C(\Cl)/F)/Br 3 54 | I/C(=C(\Cl)/F)/Br 3 55 | I/C(=C(\Cl)/F)/Br 3 56 | I/C(=C(\Cl)/F)/Br 3 57 | I/C(=C(\Cl)/F)/Br 3 58 | I/C(=C(\Cl)/F)/Br 3 59 | I/C(=C(\Cl)/F)/Br 3 60 | I/C(=C(\Cl)/F)/Br 3 61 | I/C(=C(\Cl)/F)/Br 3 62 | I/C(=C(\Cl)/F)/Br 3 63 | I/C(=C(\Cl)/F)/Br 3 64 | I/C(=C(\Cl)/F)/Br 3 65 | I/C(=C(\Cl)/F)/Br 3 66 | I/C(=C(\Cl)/F)/Br 3 67 | I/C(=C(\Cl)/F)/Br 3 68 | I/C(=C(\Cl)/F)/Br 3 69 | I/C(=C(\Cl)/F)/Br 3 70 | I/C(=C(\Cl)/F)/Br 3 71 | I/C(=C(\Cl)/F)/Br 3 72 | I/C(=C(\Cl)/F)/Br 3 73 | I/C(=C(\Cl)/F)/Br 3 74 | I/C(=C(\Cl)/F)/Br 3 75 | I/C(=C(\Cl)/F)/Br 3 76 | I/C(=C(\Cl)/F)/Br 3 77 | I/C(=C(\Cl)/F)/Br 3 78 | I/C(=C(\Cl)/F)/Br 3 79 | I/C(=C(\Cl)/F)/Br 3 80 | I/C(=C(\Cl)/F)/Br 3 81 | I/C(=C(\Cl)/F)/Br 3 82 | I/C(=C(\Cl)/F)/Br 3 83 | I/C(=C(\Cl)/F)/Br 3 84 | I/C(=C(\Cl)/F)/Br 3 85 | I/C(=C(\Cl)/F)/Br 3 86 | I/C(=C(\Cl)/F)/Br 3 87 | I/C(=C(\Cl)/F)/Br 3 88 | I/C(=C(\Cl)/F)/Br 3 89 | I/C(=C(\Cl)/F)/Br 3 90 | I/C(=C(\Cl)/F)/Br 3 91 | I/C(=C(\Cl)/F)/Br 3 92 | I/C(=C(\Cl)/F)/Br 3 93 | I/C(=C(\Cl)/F)/Br 3 94 | I/C(=C(\Cl)/F)/Br 3 95 | I/C(=C(\Cl)/F)/Br 3 96 | I/C(=C(\Cl)/F)/Br 3 97 | I/C(=C(\Cl)/F)/Br 3 98 | I/C(=C(\Cl)/F)/Br 3 99 | I/C(=C(\Cl)/F)/Br 3 100 | I/C(=C(\Cl)/F)/Br 3 101 | I/C(=C(\Cl)/F)/Br 3 102 | I/C(=C(\Cl)/F)/Br 3 103 | I/C(=C(\Cl)/F)/Br 3 104 | I/C(=C(\Cl)/F)/Br 3 105 | I/C(=C(\Cl)/F)/Br 3 106 | I/C(=C(\Cl)/F)/Br 3 107 | I/C(=C(\Cl)/F)/Br 3 108 | I/C(=C(\Cl)/F)/Br 3 109 | I/C(=C(\Cl)/F)/Br 3 110 | I/C(=C(\Cl)/F)/Br 3 111 | I/C(=C(\Cl)/F)/Br 3 112 | I/C(=C(\Cl)/F)/Br 3 113 | I/C(=C(\Cl)/F)/Br 3 114 | I/C(=C(\Cl)/F)/Br 3 115 | I/C(=C(\Cl)/F)/Br 3 116 | I/C(=C(\Cl)/F)/Br 3 117 | I/C(=C(\Cl)/F)/Br 3 118 | I/C(=C(\Cl)/F)/Br 3 119 | I/C(=C(\Cl)/F)/Br 3 120 | I/C(=C(\Cl)/F)/Br 3 121 | I/C(=C(\Cl)/F)/Br 3 122 | I/C(=C(\Cl)/F)/Br 3 123 | I/C(=C(\Cl)/F)/Br 3 124 | I/C(=C(\Cl)/F)/Br 3 125 | I/C(=C(\Cl)/F)/Br 3 126 | I/C(=C(\Cl)/F)/Br 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/oechem_Feb2018.smi: -------------------------------------------------------------------------------- 1 | C(=C/I)\F 1 2 | C(=C/I)\F 1 3 | C(=C/I)\F 1 4 | C(=C/I)\F 1 5 | C(=C/I)\F 1 6 | C(=C/I)\F 1 7 | C(=C/I)\F 1 8 | C(=C/I)\F 1 9 | C(=C/I)\F 1 10 | C(=C/I)\F 1 11 | C(=C/I)\F 1 12 | C(=C/I)\F 1 13 | C(=C/I)\F 1 14 | C(=C/I)\F 1 15 | C(=C/I)\F 1 16 | C(=C/I)\F 1 17 | C(=C/I)\F 1 18 | C(=C/I)\F 1 19 | C(=C/I)\F 1 20 | C(=C/I)\F 1 21 | C(=C/I)\F 1 22 | C(=C/I)\F 1 23 | C(=C/F)\C=C/I 2 24 | C(=C/F)\C=C/I 2 25 | C(=C/F)\C=C/I 2 26 | C(=C/F)\C=C/I 2 27 | C(=C/F)\C=C/I 2 28 | C(=C/F)\C=C/I 2 29 | C(=C/F)\C=C/I 2 30 | C(=C/F)\C=C/I 2 31 | C(=C/F)\C=C/I 2 32 | C(=C/F)\C=C/I 2 33 | C(=C/F)\C=C/I 2 34 | C(=C/F)\C=C/I 2 35 | C(=C/F)\C=C/I 2 36 | C(=C/F)\C=C/I 2 37 | C(=C/F)\C=C/I 2 38 | C(=C/F)\C=C/I 2 39 | C(=C/F)\C=C/I 2 40 | C(=C/F)\C=C/I 2 41 | C(=C/F)\C=C/I 2 42 | C(=C/F)\C=C/I 2 43 | C(=C/F)\C=C/I 2 44 | C(=C/F)\C=C/I 2 45 | C(=C/F)\C=C/I 2 46 | C(=C/F)\C=C/I 2 47 | C(=C(\Br)/I)(\F)/Cl 3 48 | C(=C(\Br)/I)(\F)/Cl 3 49 | C(=C(\Br)/I)(\F)/Cl 3 50 | C(=C(\Br)/I)(\F)/Cl 3 51 | C(=C(\Br)/I)(\F)/Cl 3 52 | C(=C(\Br)/I)(\F)/Cl 3 53 | C(=C(\Br)/I)(\F)/Cl 3 54 | C(=C(\Br)/I)(\F)/Cl 3 55 | C(=C(\Br)/I)(\F)/Cl 3 56 | C(=C(\Br)/I)(\F)/Cl 3 57 | C(=C(\Br)/I)(\F)/Cl 3 58 | C(=C(\Br)/I)(\F)/Cl 3 59 | C(=C(\Br)/I)(\F)/Cl 3 60 | C(=C(\Br)/I)(\F)/Cl 3 61 | C(=C(\Br)/I)(\F)/Cl 3 62 | C(=C(\Br)/I)(\F)/Cl 3 63 | C(=C(\Br)/I)(\F)/Cl 3 64 | C(=C(\Br)/I)(\F)/Cl 3 65 | C(=C(\Br)/I)(\F)/Cl 3 66 | C(=C(\Br)/I)(\F)/Cl 3 67 | C(=C(\Br)/I)(\F)/Cl 3 68 | C(=C(\Br)/I)(\F)/Cl 3 69 | C(=C(\Br)/I)(\F)/Cl 3 70 | C(=C(\Br)/I)(\F)/Cl 3 71 | C(=C(\Br)/I)(\F)/Cl 3 72 | C(=C(\Br)/I)(\F)/Cl 3 73 | C(=C(\Br)/I)(\F)/Cl 3 74 | C(=C(\Br)/I)(\F)/Cl 3 75 | C(=C(\Br)/I)(\F)/Cl 3 76 | C(=C(\Br)/I)(\F)/Cl 3 77 | C(=C(\Br)/I)(\F)/Cl 3 78 | C(=C(\Br)/I)(\F)/Cl 3 79 | C(=C(\Br)/I)(\F)/Cl 3 80 | C(=C(\Br)/I)(\F)/Cl 3 81 | C(=C(\Br)/I)(\F)/Cl 3 82 | C(=C(\Br)/I)(\F)/Cl 3 83 | C(=C(\Br)/I)(\F)/Cl 3 84 | C(=C(\Br)/I)(\F)/Cl 3 85 | C(=C(\Br)/I)(\F)/Cl 3 86 | C(=C(\Br)/I)(\F)/Cl 3 87 | C(=C(\Br)/I)(\F)/Cl 3 88 | C(=C(\Br)/I)(\F)/Cl 3 89 | C(=C(\Br)/I)(\F)/Cl 3 90 | C(=C(\Br)/I)(\F)/Cl 3 91 | C(=C(\Br)/I)(\F)/Cl 3 92 | C(=C(\Br)/I)(\F)/Cl 3 93 | C(=C(\Br)/I)(\F)/Cl 3 94 | C(=C(\Br)/I)(\F)/Cl 3 95 | C(=C(\Br)/I)(\F)/Cl 3 96 | C(=C(\Br)/I)(\F)/Cl 3 97 | C(=C(\Br)/I)(\F)/Cl 3 98 | C(=C(\Br)/I)(\F)/Cl 3 99 | C(=C(\Br)/I)(\F)/Cl 3 100 | C(=C(\Br)/I)(\F)/Cl 3 101 | C(=C(\Br)/I)(\F)/Cl 3 102 | C(=C(\Br)/I)(\F)/Cl 3 103 | C(=C(\Br)/I)(\F)/Cl 3 104 | C(=C(\Br)/I)(\F)/Cl 3 105 | C(=C(\Br)/I)(\F)/Cl 3 106 | C(=C(\Br)/I)(\F)/Cl 3 107 | C(=C(\Br)/I)(\F)/Cl 3 108 | C(=C(\Br)/I)(\F)/Cl 3 109 | C(=C(\Br)/I)(\F)/Cl 3 110 | C(=C(\Br)/I)(\F)/Cl 3 111 | C(=C(\Br)/I)(\F)/Cl 3 112 | C(=C(\Br)/I)(\F)/Cl 3 113 | C(=C(\Br)/I)(\F)/Cl 3 114 | C(=C(\Br)/I)(\F)/Cl 3 115 | C(=C(\Br)/I)(\F)/Cl 3 116 | C(=C(\Br)/I)(\F)/Cl 3 117 | C(=C(\Br)/I)(\F)/Cl 3 118 | C(=C(\Br)/I)(\F)/Cl 3 119 | C(=C(\Br)/I)(\F)/Cl 3 120 | C(=C(\Br)/I)(\F)/Cl 3 121 | C(=C(\Br)/I)(\F)/Cl 3 122 | C(=C(\Br)/I)(\F)/Cl 3 123 | C(=C(\Br)/I)(\F)/Cl 3 124 | C(=C(\Br)/I)(\F)/Cl 3 125 | C(=C(\Br)/I)(\F)/Cl 3 126 | C(=C(\Br)/I)(\F)/Cl 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/openbabel.smi: -------------------------------------------------------------------------------- 1 | F/C=C/I 1 2 | F/C=C/I 1 3 | F/C=C/I 1 4 | F/C=C/I 1 5 | F/C=C/I 1 6 | F/C=C/I 1 7 | F/C=C/I 1 8 | F/C=C/I 1 9 | F/C=C/I 1 10 | F/C=C/I 1 11 | F/C=C/I 1 12 | F/C=C/I 1 13 | F/C=C/I 1 14 | F/C=C/I 1 15 | F/C=C/I 1 16 | F/C=C/I 1 17 | F/C=C/I 1 18 | F/C=C/I 1 19 | F/C=C/I 1 20 | F/C=C/I 1 21 | F/C=C/I 1 22 | F/C=C/I 1 23 | F/C=C/C=C\I 2 24 | F/C=C/C=C\I 2 25 | F/C=C/C=C\I 2 26 | F/C=C/C=C\I 2 27 | F/C=C/C=C\I 2 28 | F/C=C/C=C\I 2 29 | F/C=C/C=C\I 2 30 | F/C=C/C=C\I 2 31 | F/C=C/C=C\I 2 32 | F/C=C/C=C\I 2 33 | F/C=C/C=C\I 2 34 | F/C=C/C=C\I 2 35 | F/C=C/C=C\I 2 36 | F/C=C/C=C\I 2 37 | F/C=C/C=C\I 2 38 | F/C=C/C=C\I 2 39 | F/C=C/C=C\I 2 40 | F/C=C/C=C\I 2 41 | F/C=C/C=C\I 2 42 | F/C=C/C=C\I 2 43 | F/C=C/C=C\I 2 44 | F/C=C/C=C\I 2 45 | F/C=C/C=C\I 2 46 | F/C=C/C=C\I 2 47 | F/C(=C(/I)\Br)/Cl 3 48 | F/C(=C(/I)\Br)/Cl 3 49 | F/C(=C(/I)\Br)/Cl 3 50 | F/C(=C(/I)\Br)/Cl 3 51 | F/C(=C(/I)\Br)/Cl 3 52 | F/C(=C(/I)\Br)/Cl 3 53 | F/C(=C(/I)\Br)/Cl 3 54 | F/C(=C(/I)\Br)/Cl 3 55 | F/C(=C(/I)\Br)/Cl 3 56 | F/C(=C(/I)\Br)/Cl 3 57 | F/C(=C(/I)\Br)/Cl 3 58 | F/C(=C(/I)\Br)/Cl 3 59 | F/C(=C(/I)\Br)/Cl 3 60 | F/C(=C(/I)\Br)/Cl 3 61 | F/C(=C(/I)\Br)/Cl 3 62 | F/C(=C(/I)\Br)/Cl 3 63 | F/C(=C(/I)\Br)/Cl 3 64 | F/C(=C(/I)\Br)/Cl 3 65 | F/C(=C(/I)\Br)/Cl 3 66 | F/C(=C(/I)\Br)/Cl 3 67 | F/C(=C(/I)\Br)/Cl 3 68 | F/C(=C(/I)\Br)/Cl 3 69 | F/C(=C(/I)\Br)/Cl 3 70 | F/C(=C(/I)\Br)/Cl 3 71 | F/C(=C(/I)\Br)/Cl 3 72 | F/C(=C(/I)\Br)/Cl 3 73 | F/C(=C(/I)\Br)/Cl 3 74 | F/C(=C(/I)\Br)/Cl 3 75 | F/C(=C(/I)\Br)/Cl 3 76 | F/C(=C(/I)\Br)/Cl 3 77 | F/C(=C(/I)\Br)/Cl 3 78 | F/C(=C(/I)\Br)/Cl 3 79 | F/C(=C(/I)\Br)/Cl 3 80 | F/C(=C(/I)\Br)/Cl 3 81 | F/C(=C(/I)\Br)/Cl 3 82 | F/C(=C(/I)\Br)/Cl 3 83 | F/C(=C(/I)\Br)/Cl 3 84 | F/C(=C(/I)\Br)/Cl 3 85 | F/C(=C(/I)\Br)/Cl 3 86 | F/C(=C(/I)\Br)/Cl 3 87 | F/C(=C(/I)\Br)/Cl 3 88 | F/C(=C(/I)\Br)/Cl 3 89 | F/C(=C(/I)\Br)/Cl 3 90 | F/C(=C(/I)\Br)/Cl 3 91 | F/C(=C(/I)\Br)/Cl 3 92 | F/C(=C(/I)\Br)/Cl 3 93 | F/C(=C(/I)\Br)/Cl 3 94 | F/C(=C(/I)\Br)/Cl 3 95 | F/C(=C(/I)\Br)/Cl 3 96 | F/C(=C(/I)\Br)/Cl 3 97 | F/C(=C(/I)\Br)/Cl 3 98 | F/C(=C(/I)\Br)/Cl 3 99 | F/C(=C(/I)\Br)/Cl 3 100 | F/C(=C(/I)\Br)/Cl 3 101 | F/C(=C(/I)\Br)/Cl 3 102 | F/C(=C(/I)\Br)/Cl 3 103 | F/C(=C(/I)\Br)/Cl 3 104 | F/C(=C(/I)\Br)/Cl 3 105 | F/C(=C(/I)\Br)/Cl 3 106 | F/C(=C(/I)\Br)/Cl 3 107 | F/C(=C(/I)\Br)/Cl 3 108 | F/C(=C(/I)\Br)/Cl 3 109 | F/C(=C(/I)\Br)/Cl 3 110 | F/C(=C(/I)\Br)/Cl 3 111 | F/C(=C(/I)\Br)/Cl 3 112 | F/C(=C(/I)\Br)/Cl 3 113 | F/C(=C(/I)\Br)/Cl 3 114 | F/C(=C(/I)\Br)/Cl 3 115 | F/C(=C(/I)\Br)/Cl 3 116 | F/C(=C(/I)\Br)/Cl 3 117 | F/C(=C(/I)\Br)/Cl 3 118 | F/C(=C(/I)\Br)/Cl 3 119 | F/C(=C(/I)\Br)/Cl 3 120 | F/C(=C(/I)\Br)/Cl 3 121 | F/C(=C(/I)\Br)/Cl 3 122 | F/C(=C(/I)\Br)/Cl 3 123 | F/C(=C(/I)\Br)/Cl 3 124 | F/C(=C(/I)\Br)/Cl 3 125 | F/C(=C(/I)\Br)/Cl 3 126 | F/C(=C(/I)\Br)/Cl 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/openchemlib_2018.7.0.smi: -------------------------------------------------------------------------------- 1 | F/C=C/I 1 2 | F/C=C/I 1 3 | F/C=C/I 1 4 | F/C=C/I 1 5 | F/C=C/I 1 6 | F/C=C/I 1 7 | F/C=C/I 1 8 | F/C=C/I 1 9 | F/C=C/I 1 10 | F/C=C/I 1 11 | F/C=C/I 1 12 | F/C=C/I 1 13 | FC=CI 1 14 | F/C=C\I 1 15 | FC=CI 1 16 | F/C=C\I 1 17 | FC=CI 1 18 | F/C=C\I 1 19 | FC=CI 1 20 | F/C=C/I 1 21 | F/C=C/I 1 22 | FC=CI 1 23 | F/C=C/C=C\I 2 24 | F/C=C/C=C\I 2 25 | F/C=C/C=C\I 2 26 | F/C=C/C=C\I 2 27 | F/C=C/C=C\I 2 28 | F/C=C/C=C\I 2 29 | F/C=C/C=C\I 2 30 | F/C=C/C=C\I 2 31 | F/C=C/C=C\I 2 32 | F/C=C/C=C\I 2 33 | F/C=C/C=C\I 2 34 | F/C=C/C=C\I 2 35 | F/C=C/C=C\I 2 36 | F/C=C/C=C\I 2 37 | F/C=C/C=C\I 2 38 | F/C=C/C=C\I 2 39 | F/C=C/C=C\I 2 40 | F/C=C/C=C\I 2 41 | F/C=C/C=C\I 2 42 | F/C=C/C=C\I 2 43 | F/C=C/C=CI 2 44 | F/C=C/C=C/I 2 45 | FC=C/C=C\I 2 46 | F/C=C\C=C/I 2 47 | F/C(/Cl)=C(\Br)/I 3 48 | F/C(/Cl)=C(\Br)/I 3 49 | F/C(/Cl)=C(\Br)/I 3 50 | F/C(/Cl)=C(\Br)/I 3 51 | F/C(/Cl)=C(\Br)/I 3 52 | F/C(/Cl)=C(\Br)/I 3 53 | F/C(/Cl)=C(\Br)/I 3 54 | F/C(/Cl)=C(\Br)/I 3 55 | F/C(/Cl)=C(\Br)/I 3 56 | F/C(/Cl)=C(\Br)/I 3 57 | F/C(/Cl)=C(\Br)/I 3 58 | F/C(/Cl)=C(\Br)/I 3 59 | F/C(/Cl)=C(\Br)/I 3 60 | F/C(/Cl)=C(\Br)/I 3 61 | F/C(/Cl)=C(\Br)/I 3 62 | F/C(/Cl)=C(\Br)/I 3 63 | F/C(/Cl)=C(\Br)/I 3 64 | F/C(/Cl)=C(\Br)/I 3 65 | F/C(/Cl)=C(\Br)/I 3 66 | F/C(/Cl)=C(\Br)/I 3 67 | F/C(/Cl)=C(\Br)/I 3 68 | F/C(/Cl)=C(\Br)/I 3 69 | F/C(/Cl)=C(\Br)/I 3 70 | F/C(/Cl)=C(\Br)/I 3 71 | F/C(/Cl)=C(\Br)/I 3 72 | F/C(/Cl)=C(\Br)/I 3 73 | F/C(/Cl)=C(\Br)/I 3 74 | F/C(/Cl)=C(\Br)/I 3 75 | F/C(/Cl)=C(\Br)/I 3 76 | F/C(/Cl)=C(\Br)/I 3 77 | F/C(/Cl)=C(\Br)/I 3 78 | F/C(/Cl)=C(\Br)/I 3 79 | F/C(/Cl)=C(\Br)/I 3 80 | F/C(/Cl)=C(\Br)/I 3 81 | F/C(/Cl)=C(\Br)/I 3 82 | F/C(/Cl)=C(\Br)/I 3 83 | F/C(/Cl)=C(\Br)/I 3 84 | F/C(/Cl)=C(\Br)/I 3 85 | F/C(/Cl)=C(\Br)/I 3 86 | F/C(/Cl)=C(\Br)/I 3 87 | F/C(/Cl)=C(\Br)/I 3 88 | F/C(/Cl)=C(\Br)/I 3 89 | F/C(/Cl)=C(\Br)/I 3 90 | F/C(/Cl)=C(\Br)/I 3 91 | F/C(/Cl)=C(\Br)/I 3 92 | F/C(/Cl)=C(\Br)/I 3 93 | F/C(/Cl)=C(\Br)/I 3 94 | F/C(/Cl)=C(\Br)/I 3 95 | F/C(/Cl)=C(\Br)/I 3 96 | F/C(/Cl)=C(\Br)/I 3 97 | F/C(/Cl)=C(\Br)/I 3 98 | F/C(/Cl)=C(\Br)/I 3 99 | F/C(/Cl)=C(\Br)/I 3 100 | F/C(/Cl)=C(\Br)/I 3 101 | F/C(/Cl)=C(\Br)/I 3 102 | F/C(/Cl)=C(\Br)/I 3 103 | F/C(/Cl)=C(\Br)/I 3 104 | F/C(/Cl)=C(\Br)/I 3 105 | F/C(/Cl)=C(\Br)/I 3 106 | F/C(/Cl)=C(\Br)/I 3 107 | F/C(/Cl)=C(\Br)/I 3 108 | F/C(/Cl)=C(\Br)/I 3 109 | F/C(/Cl)=C(\Br)/I 3 110 | F/C(/Cl)=C(\Br)/I 3 111 | F/C(/Cl)=C(\Br)/I 3 112 | F/C(/Cl)=C(\Br)/I 3 113 | F/C(/Cl)=C(\Br)/I 3 114 | F/C(/Cl)=C(\Br)/I 3 115 | F/C(/Cl)=C(\Br)/I 3 116 | F/C(/Cl)=C(\Br)/I 3 117 | F/C(/Cl)=C(\Br)/I 3 118 | F/C(/Cl)=C(\Br)/I 3 119 | F/C(/Cl)=C(\Br)/I 3 120 | F/C(/Cl)=C(\Br)/I 3 121 | F/C(/Cl)=C(\Br)/I 3 122 | F/C(/Cl)=C(\Br)/I 3 123 | F/C(/Cl)=C(\Br)/I 3 124 | F/C(/Cl)=C(\Br)/I 3 125 | F/C(/Cl)=C(\Br)/I 3 126 | F/C(/Cl)=C(\Br)/I 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans/rdkit_2018.03.1.smi: -------------------------------------------------------------------------------- 1 | F/C=C/I 1 2 | F/C=C/I 1 3 | F/C=C/I 1 4 | F/C=C/I 1 5 | F/C=C/I 1 6 | F/C=C/I 1 7 | F/C=C/I 1 8 | F/C=C/I 1 9 | F/C=C/I 1 10 | F/C=C/I 1 11 | F/C=C/I 1 12 | F/C=C/I 1 13 | F/C=C/I 1 14 | F/C=C/I 1 15 | F/C=C/I 1 16 | F/C=C/I 1 17 | F/C=C/I 1 18 | F/C=C/I 1 19 | F/C=C/I 1 20 | F/C=C/I 1 21 | F/C=C/I 1 22 | F/C=C/I 1 23 | F/C=C/C=C\I 2 24 | F/C=C/C=C\I 2 25 | F/C=C/C=C\I 2 26 | F/C=C/C=C\I 2 27 | F/C=C/C=C\I 2 28 | F/C=C/C=C\I 2 29 | F/C=C/C=C\I 2 30 | F/C=C/C=C\I 2 31 | F/C=C/C=C\I 2 32 | F/C=C/C=C\I 2 33 | F/C=C/C=C\I 2 34 | F/C=C/C=C\I 2 35 | F/C=C/C=C\I 2 36 | F/C=C/C=C\I 2 37 | F/C=C/C=C\I 2 38 | F/C=C/C=C\I 2 39 | F/C=C/C=C\I 2 40 | F/C=C/C=C\I 2 41 | F/C=C/C=C\I 2 42 | F/C=C/C=C\I 2 43 | F/C=C/C=C\I 2 44 | F/C=C/C=C\I 2 45 | F/C=C/C=C\I 2 46 | F/C=C/C=C\I 2 47 | F/C(Cl)=C(\Br)I 3 48 | F/C(Cl)=C(\Br)I 3 49 | F/C(Cl)=C(\Br)I 3 50 | F/C(Cl)=C(\Br)I 3 51 | F/C(Cl)=C(\Br)I 3 52 | F/C(Cl)=C(\Br)I 3 53 | F/C(Cl)=C(\Br)I 3 54 | F/C(Cl)=C(\Br)I 3 55 | F/C(Cl)=C(\Br)I 3 56 | F/C(Cl)=C(\Br)I 3 57 | F/C(Cl)=C(\Br)I 3 58 | F/C(Cl)=C(\Br)I 3 59 | F/C(Cl)=C(\Br)I 3 60 | F/C(Cl)=C(\Br)I 3 61 | F/C(Cl)=C(\Br)I 3 62 | F/C(Cl)=C(\Br)I 3 63 | F/C(Cl)=C(\Br)I 3 64 | F/C(Cl)=C(\Br)I 3 65 | F/C(Cl)=C(\Br)I 3 66 | F/C(Cl)=C(\Br)I 3 67 | F/C(Cl)=C(\Br)I 3 68 | F/C(Cl)=C(\Br)I 3 69 | F/C(Cl)=C(\Br)I 3 70 | F/C(Cl)=C(\Br)I 3 71 | F/C(Cl)=C(\Br)I 3 72 | F/C(Cl)=C(\Br)I 3 73 | F/C(Cl)=C(\Br)I 3 74 | F/C(Cl)=C(\Br)I 3 75 | F/C(Cl)=C(\Br)I 3 76 | F/C(Cl)=C(\Br)I 3 77 | F/C(Cl)=C(\Br)I 3 78 | F/C(Cl)=C(\Br)I 3 79 | F/C(Cl)=C(\Br)I 3 80 | F/C(Cl)=C(\Br)I 3 81 | F/C(Cl)=C(\Br)I 3 82 | F/C(Cl)=C(\Br)I 3 83 | F/C(Cl)=C(\Br)I 3 84 | F/C(Cl)=C(\Br)I 3 85 | F/C(Cl)=C(\Br)I 3 86 | F/C(Cl)=C(\Br)I 3 87 | F/C(Cl)=C(\Br)I 3 88 | F/C(Cl)=C(\Br)I 3 89 | F/C(Cl)=C(\Br)I 3 90 | F/C(Cl)=C(\Br)I 3 91 | F/C(Cl)=C(\Br)I 3 92 | F/C(Cl)=C(\Br)I 3 93 | F/C(Cl)=C(\Br)I 3 94 | F/C(Cl)=C(\Br)I 3 95 | F/C(Cl)=C(\Br)I 3 96 | F/C(Cl)=C(\Br)I 3 97 | F/C(Cl)=C(\Br)I 3 98 | F/C(Cl)=C(\Br)I 3 99 | F/C(Cl)=C(\Br)I 3 100 | F/C(Cl)=C(\Br)I 3 101 | F/C(Cl)=C(\Br)I 3 102 | F/C(Cl)=C(\Br)I 3 103 | F/C(Cl)=C(\Br)I 3 104 | F/C(Cl)=C(\Br)I 3 105 | F/C(Cl)=C(\Br)I 3 106 | F/C(Cl)=C(\Br)I 3 107 | F/C(Cl)=C(\Br)I 3 108 | F/C(Cl)=C(\Br)I 3 109 | F/C(Cl)=C(\Br)I 3 110 | F/C(Cl)=C(\Br)I 3 111 | F/C(Cl)=C(\Br)I 3 112 | F/C(Cl)=C(\Br)I 3 113 | F/C(Cl)=C(\Br)I 3 114 | F/C(Cl)=C(\Br)I 3 115 | F/C(Cl)=C(\Br)I 3 116 | F/C(Cl)=C(\Br)I 3 117 | F/C(Cl)=C(\Br)I 3 118 | F/C(Cl)=C(\Br)I 3 119 | F/C(Cl)=C(\Br)I 3 120 | F/C(Cl)=C(\Br)I 3 121 | F/C(Cl)=C(\Br)I 3 122 | F/C(Cl)=C(\Br)I 3 123 | F/C(Cl)=C(\Br)I 3 124 | F/C(Cl)=C(\Br)I 3 125 | F/C(Cl)=C(\Br)I 3 126 | F/C(Cl)=C(\Br)I 3 127 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/BIOVIADraw_2018.smi: -------------------------------------------------------------------------------- 1 | F\C=N\I 1 2 | F\C=N\I 1 3 | F\C=N\I 1 4 | F\C=N\I 1 5 | F\C=N\I 1 6 | F\C=N\I 1 7 | F\C=N\I 1 8 | F\C=N\I 1 9 | F\C=N\I 1 10 | F\C=N\I 1 11 | F\C=N\I 1 12 | F\C=N\I 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/ChemDraw_17.1.smi: -------------------------------------------------------------------------------- 1 | I/N=C/F 1 2 | I/N=C/F 1 3 | I/N=C/F 1 4 | I/N=C/F 1 5 | I/N=C/F 1 6 | I/N=C/F 1 7 | I/N=C/F 1 8 | I/N=C/F 1 9 | I/N=C/F 1 10 | I/N=C/F 1 11 | I/N=C/F 1 12 | I/N=C/F 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/KnowItAll_2018.smi: -------------------------------------------------------------------------------- 1 | F\C=N\I 1 2 | F\C=N\I 1 3 | F\C=N\I 1 4 | F\C=N\I 1 5 | F\C=N\I 1 6 | F\C=N\I 1 7 | F\C=N\I 1 8 | F\C=N\I 1 9 | F\C=N\I 1 10 | F\C=N\I 1 11 | F\C=N\I 1 12 | F\C=N\I 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/avalon_1.2.0.smi: -------------------------------------------------------------------------------- 1 | I/N=C/F 1 2 | I/N=C/F 1 3 | F\C=N\I 1 4 | F\C=N\I 1 5 | F\C=N\I 1 6 | F\C=N\I 1 7 | I\N=C\F 1 8 | I\N=C\F 1 9 | F/C=N/I 1 10 | F/C=N/I 1 11 | I\N=C\F 1 12 | I\N=C\F 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/cdk_2.1.smi: -------------------------------------------------------------------------------- 1 | C(=N\I)/F 1 2 | C(=N\I)/F 1 3 | C(=N\I)/F 1 4 | C(=N\I)/F 1 5 | C(=N\I)/F 1 6 | C(=N\I)/F 1 7 | C(=N\I)/F 1 8 | C(=N\I)/F 1 9 | C(=N\I)/F 1 10 | C(=N\I)/F 1 11 | C(=N\I)/F 1 12 | C(=N\I)/F 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/indigo_1.3.0b.r16.smi: -------------------------------------------------------------------------------- 1 | F/C=N/I 1 2 | F/C=N/I 1 3 | F/C=N/I 1 4 | F/C=N/I 1 5 | F/C=N/I 1 6 | F/C=N/I 1 7 | F/C=N/I 1 8 | F/C=N/I 1 9 | F/C=N/I 1 10 | F/C=N/I 1 11 | F/C=N/I 1 12 | F/C=N/I 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/iwtoolkit_1.0.smi: -------------------------------------------------------------------------------- 1 | I/N=C/F 1 2 | I/N=C/F 1 3 | I/N=C/F 1 4 | I/N=C/F 1 5 | I/N=C/F 1 6 | I/N=C/F 1 7 | I/N=C/F 1 8 | I/N=C/F 1 9 | I/N=C/F 1 10 | I/N=C/F 1 11 | I/N=C/F 1 12 | I/N=C/F 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/oechem_Feb2018.smi: -------------------------------------------------------------------------------- 1 | C(=N/I)\F 1 2 | C(=N/I)\F 1 3 | C(=N/I)\F 1 4 | C(=N/I)\F 1 5 | C(=N/I)\F 1 6 | C(=N/I)\F 1 7 | C(=N/I)\F 1 8 | C(=N/I)\F 1 9 | C(=N/I)\F 1 10 | C(=N/I)\F 1 11 | C(=N/I)\F 1 12 | C(=N/I)\F 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/openbabel.smi: -------------------------------------------------------------------------------- 1 | F/C=N/I 1 2 | F/C=N/I 1 3 | F/C=N/I 1 4 | F/C=N/I 1 5 | F/C=N/I 1 6 | F/C=N/I 1 7 | F/C=N/I 1 8 | F/C=N/I 1 9 | F/C=N/I 1 10 | F/C=N/I 1 11 | F/C=N/I 1 12 | F/C=N/I 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/openchemlib_2018.7.0.smi: -------------------------------------------------------------------------------- 1 | F/C=N/I 1 2 | F/C=N/I 1 3 | F/C=N/I 1 4 | F/C=N/I 1 5 | F/C=N/I 1 6 | F/C=N/I 1 7 | F/C=N/I 1 8 | F/C=N/I 1 9 | F/C=N/I 1 10 | F/C=N/I 1 11 | F/C=N/I 1 12 | F/C=N/I 1 13 | -------------------------------------------------------------------------------- /5-results/cistrans_nitrogen/rdkit_2018.03.1.smi: -------------------------------------------------------------------------------- 1 | F/C=N/I 1 2 | F/C=N/I 1 3 | F/C=N/I 1 4 | F/C=N/I 1 5 | F/C=N/I 1 6 | F/C=N/I 1 7 | F/C=N/I 1 8 | F/C=N/I 1 9 | F/C=N/I 1 10 | F/C=N/I 1 11 | F/C=N/I 1 12 | F/C=N/I 1 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral/BIOVIADraw_2018.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@](Cl)(Br)I 1 9 | F[C@](Cl)(Br)I 1 10 | F[C@](Cl)(Br)I 1 11 | F[C@](Cl)(Br)I 1 12 | F[C@](Cl)(Br)I 1 13 | F[C@](Cl)(Br)I 1 14 | F[C@](Cl)(Br)I 1 15 | F[C@](Cl)(Br)I 1 16 | F[C@](Cl)(Br)I 1 17 | F[C@](Cl)(Br)I 1 18 | F[C@](Cl)(Br)I 1 19 | F[C@](Cl)(Br)I 1 20 | F[C@](Cl)(Br)I 1 21 | F[C@](Cl)(Br)I 1 22 | F[C@](Cl)(Br)I 1 23 | F[C@](Cl)(Br)I 1 24 | F[C@](Cl)(Br)I 1 25 | F[C@](Cl)(Br)I 1 26 | F[C@](Cl)(Br)I 1 27 | F[C@](Cl)(Br)I 1 28 | F[C@](Cl)(Br)I 1 29 | F[C@](Cl)(Br)I 1 30 | F[C@](Cl)(Br)I 1 31 | F[C@](Cl)(Br)I 1 32 | F[C@](Cl)(Br)I 1 33 | F[C@](Cl)(Br)I 1 34 | F[C@](Cl)(Br)I 1 35 | F[C@](Cl)(Br)I 1 36 | F[C@](Cl)(Br)I 1 37 | F[C@](Cl)(Br)I 1 38 | F[C@](Cl)(Br)I 1 39 | F[C@](Cl)(Br)I 1 40 | F[C@](Cl)(Br)I 1 41 | F[C@](Cl)(Br)I 1 42 | F[C@](Cl)(Br)I 1 43 | F[C@](Cl)(Br)I 1 44 | F[C@](Cl)(Br)I 1 45 | F[C@](Cl)(Br)I 1 46 | F[C@](Cl)(Br)I 1 47 | F[C@](Cl)(Br)I 1 48 | F[C@](Cl)(Br)I 1 49 | F[C@](Cl)(Br)I 1 50 | F[C@](Cl)(Br)I 1 51 | F[C@](Cl)(Br)I 1 52 | F[C@H](Br)I 2 53 | F[C@H](Br)I 2 54 | F[C@H](Br)I 2 55 | F[C@H](Br)I 2 56 | F[C@H](Br)I 2 57 | F[C@H](Br)I 2 58 | F[C@H](Br)I 2 59 | F[C@H](Br)I 2 60 | F[C@H](Br)I 2 61 | F[C@H](Br)I 2 62 | F[C@H](Br)I 2 63 | F[C@H](Br)I 2 64 | F[C@H](Br)I 2 65 | F[C@H](Br)I 2 66 | F[C@H](Br)I 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/ChemDraw_17.1.smi: -------------------------------------------------------------------------------- 1 | Br[C@](I)(F)Cl 1 2 | Br[C@](I)(F)Cl 1 3 | Br[C@](I)(F)Cl 1 4 | Br[C@](I)(F)Cl 1 5 | Br[C@](I)(F)Cl 1 6 | Br[C@](I)(F)Cl 1 7 | Br[C@](I)(F)Cl 1 8 | Br[C@](I)(F)Cl 1 9 | Br[C@](I)(F)Cl 1 10 | Br[C@](I)(F)Cl 1 11 | Br[C@](I)(F)Cl 1 12 | Br[C@](I)(F)Cl 1 13 | Br[C@](I)(F)Cl 1 14 | Br[C@](I)(F)Cl 1 15 | Br[C@](I)(F)Cl 1 16 | Br[C@](I)(F)Cl 1 17 | Br[C@](I)(F)Cl 1 18 | Br[C@](I)(F)Cl 1 19 | Br[C@](I)(F)Cl 1 20 | Br[C@](I)(F)Cl 1 21 | Br[C@](I)(F)Cl 1 22 | Br[C@](I)(F)Cl 1 23 | Br[C@](I)(F)Cl 1 24 | Br[C@](I)(F)Cl 1 25 | Br[C@](I)(F)Cl 1 26 | Br[C@](I)(F)Cl 1 27 | Br[C@](I)(F)Cl 1 28 | Br[C@](I)(F)Cl 1 29 | Br[C@](I)(F)Cl 1 30 | Br[C@](I)(F)Cl 1 31 | Br[C@](I)(F)Cl 1 32 | Br[C@](I)(F)Cl 1 33 | Br[C@](I)(F)Cl 1 34 | Br[C@](I)(F)Cl 1 35 | Br[C@](I)(F)Cl 1 36 | Br[C@](I)(F)Cl 1 37 | Br[C@](I)(F)Cl 1 38 | Br[C@](I)(F)Cl 1 39 | Br[C@](I)(F)Cl 1 40 | Br[C@](I)(F)Cl 1 41 | Br[C@](I)(F)Cl 1 42 | Br[C@](I)(F)Cl 1 43 | Br[C@](I)(F)Cl 1 44 | Br[C@](I)(F)Cl 1 45 | Br[C@](I)(F)Cl 1 46 | Br[C@](I)(F)Cl 1 47 | Br[C@](I)(F)Cl 1 48 | Br[C@](I)(F)Cl 1 49 | Br[C@](I)(F)Cl 1 50 | Br[C@](I)(F)Cl 1 51 | Br[C@](I)(F)Cl 1 52 | Br[C@H](I)F 2 53 | Br[C@H](I)F 2 54 | Br[C@H](I)F 2 55 | Br[C@H](I)F 2 56 | Br[C@H](I)F 2 57 | Br[C@H](I)F 2 58 | Br[C@H](I)F 2 59 | Br[C@H](I)F 2 60 | Br[C@H](I)F 2 61 | Br[C@H](I)F 2 62 | Br[C@H](I)F 2 63 | Br[C@H](I)F 2 64 | Br[C@H](I)F 2 65 | Br[C@H](I)F 2 66 | Br[C@H](I)F 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/KnowItAll_2018.smi: -------------------------------------------------------------------------------- 1 | [C@](F)(Cl)(Br)I 1 2 | [C@](F)(Cl)(Br)I 1 3 | [C@](F)(Cl)(Br)I 1 4 | [C@](F)(Cl)(Br)I 1 5 | [C@](F)(Cl)(Br)I 1 6 | [C@](F)(Cl)(Br)I 1 7 | [C@](F)(Cl)(Br)I 1 8 | [C@](F)(Cl)(Br)I 1 9 | [C@](F)(Cl)(Br)I 1 10 | [C@](F)(Cl)(Br)I 1 11 | [C@](F)(Cl)(Br)I 1 12 | [C@](F)(Cl)(Br)I 1 13 | [C@](F)(Cl)(Br)I 1 14 | [C@](F)(Cl)(Br)I 1 15 | [C@](F)(Cl)(Br)I 1 16 | [C@](F)(Cl)(Br)I 1 17 | [C@](F)(Cl)(Br)I 1 18 | [C@](F)(Cl)(Br)I 1 19 | [C@](F)(Cl)(Br)I 1 20 | [C@](F)(Cl)(Br)I 1 21 | [C@](F)(Cl)(Br)I 1 22 | [C@](F)(Cl)(Br)I 1 23 | [C@](F)(Cl)(Br)I 1 24 | [C@](F)(Cl)(Br)I 1 25 | [C@](F)(Cl)(Br)I 1 26 | [C@](F)(Cl)(Br)I 1 27 | [C@](F)(Cl)(Br)I 1 28 | [C@](F)(Cl)(Br)I 1 29 | [C@](F)(Cl)(Br)I 1 30 | [C@](F)(Cl)(Br)I 1 31 | [C@](F)(Cl)(Br)I 1 32 | [C@](F)(Cl)(Br)I 1 33 | [C@](F)(Cl)(Br)I 1 34 | [C@](F)(Cl)(Br)I 1 35 | [C@](F)(Cl)(Br)I 1 36 | [C@](F)(Cl)(Br)I 1 37 | [C@](F)(Cl)(Br)I 1 38 | [C@](F)(Cl)(Br)I 1 39 | [C@](F)(Cl)(Br)I 1 40 | [C@](F)(Cl)(Br)I 1 41 | [C@](F)(Cl)(Br)I 1 42 | [C@](F)(Cl)(Br)I 1 43 | [C@](F)(Cl)(Br)I 1 44 | [C@](F)(Cl)(Br)I 1 45 | [C@](F)(Cl)(Br)I 1 46 | [C@](F)(Cl)(Br)I 1 47 | [C@](F)(Cl)(Br)I 1 48 | [C@](F)(Cl)(Br)I 1 49 | [C@](F)(Cl)(Br)I 1 50 | [C@](F)(Cl)(Br)I 1 51 | [C@](F)(Cl)(Br)I 1 52 | [C@](F)(Br)(I)[H] 2 53 | [C@](F)(Br)(I)[H] 2 54 | [C@](F)(Br)(I)[H] 2 55 | [C@](F)(Br)(I)[H] 2 56 | [C@](F)(Br)(I)[H] 2 57 | [C@](F)(Br)(I)[H] 2 58 | [C@](F)(Br)(I)[H] 2 59 | [C@](F)(Br)(I)[H] 2 60 | [C@](F)(Br)(I)[H] 2 61 | [C@](F)(Br)(I)[H] 2 62 | [C@](F)(Br)(I)[H] 2 63 | [C@](F)(Br)(I)[H] 2 64 | [C@](F)(Br)(I)[H] 2 65 | [C@](F)(Br)(I)[H] 2 66 | [C@](F)(Br)(I)[H] 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/avalon_1.2.0.smi: -------------------------------------------------------------------------------- 1 | Br[C@@](Cl)(F)I 1 2 | Br[C@@](F)(I)Cl 1 3 | Br[C@@](I)(Cl)F 1 4 | Br[C@](Cl)(I)F 1 5 | Br[C@](F)(Cl)I 1 6 | Br[C@](I)(F)Cl 1 7 | Br[C@@](Cl)(F)I 1 8 | Br[C@](Cl)(I)F 1 9 | Br[C@](F)(Cl)I 1 10 | Br[C@@](F)(I)Cl 1 11 | Br[C@@](I)(Cl)F 1 12 | Br[C@](I)(F)Cl 1 13 | Cl[C@](Br)(F)I 1 14 | Cl[C@@](Br)(I)F 1 15 | Cl[C@@](F)(Br)I 1 16 | Cl[C@](F)(I)Br 1 17 | Cl[C@](I)(Br)F 1 18 | Cl[C@@](I)(F)Br 1 19 | F[C@@](Br)(Cl)I 1 20 | F[C@](Br)(I)Cl 1 21 | F[C@](Cl)(Br)I 1 22 | F[C@@](Cl)(I)Br 1 23 | F[C@@](I)(Br)Cl 1 24 | F[C@](I)(Cl)Br 1 25 | I[C@](Br)(Cl)F 1 26 | I[C@@](Br)(F)Cl 1 27 | I[C@@](Cl)(Br)F 1 28 | I[C@](Cl)(F)Br 1 29 | I[C@](F)(Br)Cl 1 30 | I[C@@](F)(Cl)Br 1 31 | Cl[C@@](Br)(I)F 1 32 | Cl[C@@](F)(Br)I 1 33 | Cl[C@@](I)(F)Br 1 34 | Cl[C@](Br)(F)I 1 35 | Cl[C@](F)(I)Br 1 36 | Cl[C@](I)(Br)F 1 37 | F[C@@](Br)(Cl)I 1 38 | F[C@@](Cl)(I)Br 1 39 | F[C@@](I)(Br)Cl 1 40 | F[C@](Br)(I)Cl 1 41 | F[C@](Cl)(Br)I 1 42 | F[C@](I)(Cl)Br 1 43 | I[C@@](Br)(F)Cl 1 44 | I[C@@](Cl)(Br)F 1 45 | I[C@@](F)(Cl)Br 1 46 | I[C@](Br)(Cl)F 1 47 | I[C@](Cl)(F)Br 1 48 | I[C@](F)(Br)Cl 1 49 | # Parse_error 1 50 | # Parse_error 1 51 | Br[C@](F)(Cl)I 1 52 | Br[C@@]([H])(F)I 2 53 | Br[C@]([H])(I)F 2 54 | [H][C@](Br)(F)I 2 55 | [H][C@@](Br)(I)F 2 56 | [H][C@@](F)(Br)I 2 57 | [H][C@](F)(I)Br 2 58 | [H][C@](I)(Br)F 2 59 | [H][C@@](I)(F)Br 2 60 | F[C@@]([H])(I)Br 2 61 | F[C@]([H])(Br)I 2 62 | I[C@@]([H])(Br)F 2 63 | I[C@]([H])(F)Br 2 64 | # Parse_error 2 65 | Br[C@@]([H])(F)I 2 66 | Br[C@]([H])(I)F 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/cactvs_3_426.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@](Cl)(Br)I 1 9 | F[C@](Cl)(Br)I 1 10 | F[C@](Cl)(Br)I 1 11 | F[C@](Cl)(Br)I 1 12 | F[C@](Cl)(Br)I 1 13 | F[C@](Cl)(Br)I 1 14 | F[C@](Cl)(Br)I 1 15 | F[C@](Cl)(Br)I 1 16 | F[C@](Cl)(Br)I 1 17 | F[C@](Cl)(Br)I 1 18 | F[C@](Cl)(Br)I 1 19 | F[C@](Cl)(Br)I 1 20 | F[C@](Cl)(Br)I 1 21 | F[C@](Cl)(Br)I 1 22 | F[C@](Cl)(Br)I 1 23 | F[C@](Cl)(Br)I 1 24 | F[C@](Cl)(Br)I 1 25 | F[C@](Cl)(Br)I 1 26 | F[C@](Cl)(Br)I 1 27 | F[C@](Cl)(Br)I 1 28 | F[C@](Cl)(Br)I 1 29 | F[C@](Cl)(Br)I 1 30 | F[C@](Cl)(Br)I 1 31 | F[C@](Cl)(Br)I 1 32 | F[C@](Cl)(Br)I 1 33 | F[C@](Cl)(Br)I 1 34 | F[C@](Cl)(Br)I 1 35 | F[C@](Cl)(Br)I 1 36 | F[C@](Cl)(Br)I 1 37 | F[C@](Cl)(Br)I 1 38 | F[C@](Cl)(Br)I 1 39 | F[C@](Cl)(Br)I 1 40 | F[C@](Cl)(Br)I 1 41 | F[C@](Cl)(Br)I 1 42 | F[C@](Cl)(Br)I 1 43 | F[C@](Cl)(Br)I 1 44 | F[C@](Cl)(Br)I 1 45 | F[C@](Cl)(Br)I 1 46 | F[C@](Cl)(Br)I 1 47 | F[C@](Cl)(Br)I 1 48 | F[C@](Cl)(Br)I 1 49 | F[C@](Cl)(Br)I 1 50 | F[C@](Cl)(Br)I 1 51 | F[C@](Cl)(Br)I 1 52 | F[C@H](Br)I 2 53 | F[C@H](Br)I 2 54 | F[C@H](Br)I 2 55 | F[C@H](Br)I 2 56 | F[C@H](Br)I 2 57 | F[C@H](Br)I 2 58 | F[C@H](Br)I 2 59 | F[C@H](Br)I 2 60 | F[C@H](Br)I 2 61 | F[C@H](Br)I 2 62 | F[C@H](Br)I 2 63 | F[C@H](Br)I 2 64 | F[C@H](Br)I 2 65 | F[C@H](Br)I 2 66 | F[C@H](Br)I 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/cdk_2.1.smi: -------------------------------------------------------------------------------- 1 | [C@@](Br)(Cl)(F)I 1 2 | [C@@](Br)(Cl)(F)I 1 3 | [C@@](Br)(Cl)(F)I 1 4 | [C@@](Br)(Cl)(F)I 1 5 | [C@@](Br)(Cl)(F)I 1 6 | [C@@](Br)(Cl)(F)I 1 7 | [C@@](Br)(Cl)(F)I 1 8 | [C@@](Br)(Cl)(F)I 1 9 | [C@@](Br)(Cl)(F)I 1 10 | [C@@](Br)(Cl)(F)I 1 11 | [C@@](Br)(Cl)(F)I 1 12 | [C@@](Br)(Cl)(F)I 1 13 | [C@@](Br)(Cl)(F)I 1 14 | [C@@](Br)(Cl)(F)I 1 15 | [C@@](Br)(Cl)(F)I 1 16 | [C@@](Br)(Cl)(F)I 1 17 | [C@@](Br)(Cl)(F)I 1 18 | [C@@](Br)(Cl)(F)I 1 19 | [C@@](Br)(Cl)(F)I 1 20 | [C@@](Br)(Cl)(F)I 1 21 | [C@@](Br)(Cl)(F)I 1 22 | [C@@](Br)(Cl)(F)I 1 23 | [C@@](Br)(Cl)(F)I 1 24 | [C@@](Br)(Cl)(F)I 1 25 | [C@@](Br)(Cl)(F)I 1 26 | [C@@](Br)(Cl)(F)I 1 27 | [C@@](Br)(Cl)(F)I 1 28 | [C@@](Br)(Cl)(F)I 1 29 | [C@@](Br)(Cl)(F)I 1 30 | [C@@](Br)(Cl)(F)I 1 31 | [C@@](Br)(Cl)(F)I 1 32 | [C@@](Br)(Cl)(F)I 1 33 | [C@@](Br)(Cl)(F)I 1 34 | [C@@](Br)(Cl)(F)I 1 35 | [C@@](Br)(Cl)(F)I 1 36 | [C@@](Br)(Cl)(F)I 1 37 | [C@@](Br)(Cl)(F)I 1 38 | [C@@](Br)(Cl)(F)I 1 39 | [C@@](Br)(Cl)(F)I 1 40 | [C@@](Br)(Cl)(F)I 1 41 | [C@@](Br)(Cl)(F)I 1 42 | [C@@](Br)(Cl)(F)I 1 43 | [C@@](Br)(Cl)(F)I 1 44 | [C@@](Br)(Cl)(F)I 1 45 | [C@@](Br)(Cl)(F)I 1 46 | [C@@](Br)(Cl)(F)I 1 47 | [C@@](Br)(Cl)(F)I 1 48 | [C@@](Br)(Cl)(F)I 1 49 | [C@@](Br)(Cl)(F)I 1 50 | [C@@](Br)(Cl)(F)I 1 51 | [C@@](Br)(Cl)(F)I 1 52 | [C@H](Br)(F)I 2 53 | [C@H](Br)(F)I 2 54 | [C@H](Br)(F)I 2 55 | [C@H](Br)(F)I 2 56 | [C@H](Br)(F)I 2 57 | [C@H](Br)(F)I 2 58 | [C@H](Br)(F)I 2 59 | [C@H](Br)(F)I 2 60 | [C@H](Br)(F)I 2 61 | [C@H](Br)(F)I 2 62 | [C@H](Br)(F)I 2 63 | [C@H](Br)(F)I 2 64 | [C@H](Br)(F)I 2 65 | [C@H](Br)(F)I 2 66 | [C@H](Br)(F)I 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/indigo_1.3.0b.r16.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@](Cl)(Br)I 1 9 | F[C@](Cl)(Br)I 1 10 | F[C@](Cl)(Br)I 1 11 | F[C@](Cl)(Br)I 1 12 | F[C@](Cl)(Br)I 1 13 | F[C@](Cl)(Br)I 1 14 | F[C@](Cl)(Br)I 1 15 | F[C@](Cl)(Br)I 1 16 | F[C@](Cl)(Br)I 1 17 | F[C@](Cl)(Br)I 1 18 | F[C@](Cl)(Br)I 1 19 | F[C@](Cl)(Br)I 1 20 | F[C@](Cl)(Br)I 1 21 | F[C@](Cl)(Br)I 1 22 | F[C@](Cl)(Br)I 1 23 | F[C@](Cl)(Br)I 1 24 | F[C@](Cl)(Br)I 1 25 | F[C@](Cl)(Br)I 1 26 | F[C@](Cl)(Br)I 1 27 | F[C@](Cl)(Br)I 1 28 | F[C@](Cl)(Br)I 1 29 | F[C@](Cl)(Br)I 1 30 | F[C@](Cl)(Br)I 1 31 | F[C@](Cl)(Br)I 1 32 | F[C@](Cl)(Br)I 1 33 | F[C@](Cl)(Br)I 1 34 | F[C@](Cl)(Br)I 1 35 | F[C@](Cl)(Br)I 1 36 | F[C@](Cl)(Br)I 1 37 | F[C@](Cl)(Br)I 1 38 | F[C@](Cl)(Br)I 1 39 | F[C@](Cl)(Br)I 1 40 | F[C@](Cl)(Br)I 1 41 | F[C@](Cl)(Br)I 1 42 | F[C@](Cl)(Br)I 1 43 | F[C@](Cl)(Br)I 1 44 | F[C@](Cl)(Br)I 1 45 | F[C@](Cl)(Br)I 1 46 | F[C@](Cl)(Br)I 1 47 | F[C@](Cl)(Br)I 1 48 | F[C@](Cl)(Br)I 1 49 | F[C@](Cl)(Br)I 1 50 | F[C@](Cl)(Br)I 1 51 | F[C@](Cl)(Br)I 1 52 | F[C@H](Br)I 2 53 | F[C@H](Br)I 2 54 | F[C@H](Br)I 2 55 | F[C@H](Br)I 2 56 | F[C@H](Br)I 2 57 | F[C@H](Br)I 2 58 | F[C@H](Br)I 2 59 | F[C@H](Br)I 2 60 | F[C@H](Br)I 2 61 | F[C@H](Br)I 2 62 | F[C@H](Br)I 2 63 | F[C@H](Br)I 2 64 | F[C@H](Br)I 2 65 | F[C@H](Br)I 2 66 | F[C@H](Br)I 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/iwtoolkit_1.0.smi: -------------------------------------------------------------------------------- 1 | I[C@](Br)(Cl)F 1 2 | I[C@](Br)(Cl)F 1 3 | I[C@](Br)(Cl)F 1 4 | I[C@](Br)(Cl)F 1 5 | I[C@](Br)(Cl)F 1 6 | I[C@](Br)(Cl)F 1 7 | I[C@](Br)(Cl)F 1 8 | I[C@](Br)(Cl)F 1 9 | I[C@](Br)(Cl)F 1 10 | I[C@](Br)(Cl)F 1 11 | I[C@](Br)(Cl)F 1 12 | I[C@](Br)(Cl)F 1 13 | I[C@](Br)(Cl)F 1 14 | I[C@](Br)(Cl)F 1 15 | I[C@](Br)(Cl)F 1 16 | I[C@](Br)(Cl)F 1 17 | I[C@](Br)(Cl)F 1 18 | I[C@](Br)(Cl)F 1 19 | I[C@](Br)(Cl)F 1 20 | I[C@](Br)(Cl)F 1 21 | I[C@](Br)(Cl)F 1 22 | I[C@](Br)(Cl)F 1 23 | I[C@](Br)(Cl)F 1 24 | I[C@](Br)(Cl)F 1 25 | I[C@](Br)(Cl)F 1 26 | I[C@](Br)(Cl)F 1 27 | I[C@](Br)(Cl)F 1 28 | I[C@](Br)(Cl)F 1 29 | I[C@](Br)(Cl)F 1 30 | I[C@](Br)(Cl)F 1 31 | I[C@](Br)(Cl)F 1 32 | I[C@](Br)(Cl)F 1 33 | I[C@](Br)(Cl)F 1 34 | I[C@](Br)(Cl)F 1 35 | I[C@](Br)(Cl)F 1 36 | I[C@](Br)(Cl)F 1 37 | I[C@](Br)(Cl)F 1 38 | I[C@](Br)(Cl)F 1 39 | I[C@](Br)(Cl)F 1 40 | I[C@](Br)(Cl)F 1 41 | I[C@](Br)(Cl)F 1 42 | I[C@](Br)(Cl)F 1 43 | I[C@](Br)(Cl)F 1 44 | I[C@](Br)(Cl)F 1 45 | I[C@](Br)(Cl)F 1 46 | I[C@](Br)(Cl)F 1 47 | I[C@](Br)(Cl)F 1 48 | I[C@](Br)(Cl)F 1 49 | I[C@](Br)(Cl)F 1 50 | I[C@](Br)(Cl)F 1 51 | I[C@](Br)(Cl)F 1 52 | I[C@@H](Br)F 2 53 | I[C@@H](Br)F 2 54 | I[C@@H](Br)F 2 55 | I[C@@H](Br)F 2 56 | I[C@@H](Br)F 2 57 | I[C@@H](Br)F 2 58 | I[C@@H](Br)F 2 59 | I[C@@H](Br)F 2 60 | I[C@@H](Br)F 2 61 | I[C@@H](Br)F 2 62 | I[C@@H](Br)F 2 63 | I[C@@H](Br)F 2 64 | I[C@@H](Br)F 2 65 | I[C@@H](Br)F 2 66 | I[C@@H](Br)F 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/oechem_Feb2018.smi: -------------------------------------------------------------------------------- 1 | [C@](F)(Cl)(Br)I 1 2 | [C@](F)(Cl)(Br)I 1 3 | [C@](F)(Cl)(Br)I 1 4 | [C@](F)(Cl)(Br)I 1 5 | [C@](F)(Cl)(Br)I 1 6 | [C@](F)(Cl)(Br)I 1 7 | [C@](F)(Cl)(Br)I 1 8 | [C@](F)(Cl)(Br)I 1 9 | [C@](F)(Cl)(Br)I 1 10 | [C@](F)(Cl)(Br)I 1 11 | [C@](F)(Cl)(Br)I 1 12 | [C@](F)(Cl)(Br)I 1 13 | [C@](F)(Cl)(Br)I 1 14 | [C@](F)(Cl)(Br)I 1 15 | [C@](F)(Cl)(Br)I 1 16 | [C@](F)(Cl)(Br)I 1 17 | [C@](F)(Cl)(Br)I 1 18 | [C@](F)(Cl)(Br)I 1 19 | [C@](F)(Cl)(Br)I 1 20 | [C@](F)(Cl)(Br)I 1 21 | [C@](F)(Cl)(Br)I 1 22 | [C@](F)(Cl)(Br)I 1 23 | [C@](F)(Cl)(Br)I 1 24 | [C@](F)(Cl)(Br)I 1 25 | [C@](F)(Cl)(Br)I 1 26 | [C@](F)(Cl)(Br)I 1 27 | [C@](F)(Cl)(Br)I 1 28 | [C@](F)(Cl)(Br)I 1 29 | [C@](F)(Cl)(Br)I 1 30 | [C@](F)(Cl)(Br)I 1 31 | [C@](F)(Cl)(Br)I 1 32 | [C@](F)(Cl)(Br)I 1 33 | [C@](F)(Cl)(Br)I 1 34 | [C@](F)(Cl)(Br)I 1 35 | [C@](F)(Cl)(Br)I 1 36 | [C@](F)(Cl)(Br)I 1 37 | [C@](F)(Cl)(Br)I 1 38 | [C@](F)(Cl)(Br)I 1 39 | [C@](F)(Cl)(Br)I 1 40 | [C@](F)(Cl)(Br)I 1 41 | [C@](F)(Cl)(Br)I 1 42 | [C@](F)(Cl)(Br)I 1 43 | [C@](F)(Cl)(Br)I 1 44 | [C@](F)(Cl)(Br)I 1 45 | [C@](F)(Cl)(Br)I 1 46 | [C@](F)(Cl)(Br)I 1 47 | [C@](F)(Cl)(Br)I 1 48 | [C@](F)(Cl)(Br)I 1 49 | [C@](F)(Cl)(Br)I 1 50 | [C@](F)(Cl)(Br)I 1 51 | [C@](F)(Cl)(Br)I 1 52 | [C@@H](F)(Br)I 2 53 | [C@@H](F)(Br)I 2 54 | [C@@H](F)(Br)I 2 55 | [C@@H](F)(Br)I 2 56 | [C@@H](F)(Br)I 2 57 | [C@@H](F)(Br)I 2 58 | [C@@H](F)(Br)I 2 59 | [C@@H](F)(Br)I 2 60 | [C@@H](F)(Br)I 2 61 | [C@@H](F)(Br)I 2 62 | [C@@H](F)(Br)I 2 63 | [C@@H](F)(Br)I 2 64 | [C@@H](F)(Br)I 2 65 | [C@@H](F)(Br)I 2 66 | [C@@H](F)(Br)I 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/openbabel.smi: -------------------------------------------------------------------------------- 1 | F[C@@](I)(Br)Cl 1 2 | F[C@@](I)(Br)Cl 1 3 | F[C@@](I)(Br)Cl 1 4 | F[C@@](I)(Br)Cl 1 5 | F[C@@](I)(Br)Cl 1 6 | F[C@@](I)(Br)Cl 1 7 | F[C@@](I)(Br)Cl 1 8 | F[C@@](I)(Br)Cl 1 9 | F[C@@](I)(Br)Cl 1 10 | F[C@@](I)(Br)Cl 1 11 | F[C@@](I)(Br)Cl 1 12 | F[C@@](I)(Br)Cl 1 13 | F[C@@](I)(Br)Cl 1 14 | F[C@@](I)(Br)Cl 1 15 | F[C@@](I)(Br)Cl 1 16 | F[C@@](I)(Br)Cl 1 17 | F[C@@](I)(Br)Cl 1 18 | F[C@@](I)(Br)Cl 1 19 | F[C@@](I)(Br)Cl 1 20 | F[C@@](I)(Br)Cl 1 21 | F[C@@](I)(Br)Cl 1 22 | F[C@@](I)(Br)Cl 1 23 | F[C@@](I)(Br)Cl 1 24 | F[C@@](I)(Br)Cl 1 25 | F[C@@](I)(Br)Cl 1 26 | F[C@@](I)(Br)Cl 1 27 | F[C@@](I)(Br)Cl 1 28 | F[C@@](I)(Br)Cl 1 29 | F[C@@](I)(Br)Cl 1 30 | F[C@@](I)(Br)Cl 1 31 | F[C@@](I)(Br)Cl 1 32 | F[C@@](I)(Br)Cl 1 33 | F[C@@](I)(Br)Cl 1 34 | F[C@@](I)(Br)Cl 1 35 | F[C@@](I)(Br)Cl 1 36 | F[C@@](I)(Br)Cl 1 37 | F[C@@](I)(Br)Cl 1 38 | F[C@@](I)(Br)Cl 1 39 | F[C@@](I)(Br)Cl 1 40 | F[C@@](I)(Br)Cl 1 41 | F[C@@](I)(Br)Cl 1 42 | F[C@@](I)(Br)Cl 1 43 | F[C@@](I)(Br)Cl 1 44 | F[C@@](I)(Br)Cl 1 45 | F[C@@](I)(Br)Cl 1 46 | F[C@@](I)(Br)Cl 1 47 | F[C@@](I)(Br)Cl 1 48 | F[C@@](I)(Br)Cl 1 49 | F[C@@](I)(Br)Cl 1 50 | F[C@@](I)(Br)Cl 1 51 | F[C@@](I)(Br)Cl 1 52 | F[C@@H](I)Br 2 53 | F[C@@H](I)Br 2 54 | F[C@@H](I)Br 2 55 | F[C@@H](I)Br 2 56 | F[C@@H](I)Br 2 57 | F[C@@H](I)Br 2 58 | F[C@@H](I)Br 2 59 | F[C@@H](I)Br 2 60 | F[C@@H](I)Br 2 61 | F[C@@H](I)Br 2 62 | F[C@@H](I)Br 2 63 | F[C@@H](I)Br 2 64 | F[C@@H](I)Br 2 65 | F[C@@H](I)Br 2 66 | F[C@@H](I)Br 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/openchemlib_2018.7.0.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@](Cl)(Br)I 1 9 | F[C@](Cl)(Br)I 1 10 | F[C@](Cl)(Br)I 1 11 | F[C@](Cl)(Br)I 1 12 | F[C@](Cl)(Br)I 1 13 | F[C@](Cl)(Br)I 1 14 | F[C@](Cl)(Br)I 1 15 | F[C@](Cl)(Br)I 1 16 | F[C@](Cl)(Br)I 1 17 | F[C@](Cl)(Br)I 1 18 | F[C@](Cl)(Br)I 1 19 | F[C@](Cl)(Br)I 1 20 | F[C@](Cl)(Br)I 1 21 | F[C@](Cl)(Br)I 1 22 | F[C@](Cl)(Br)I 1 23 | F[C@](Cl)(Br)I 1 24 | F[C@](Cl)(Br)I 1 25 | F[C@](Cl)(Br)I 1 26 | F[C@](Cl)(Br)I 1 27 | F[C@](Cl)(Br)I 1 28 | F[C@](Cl)(Br)I 1 29 | F[C@](Cl)(Br)I 1 30 | F[C@](Cl)(Br)I 1 31 | F[C@](Cl)(Br)I 1 32 | F[C@](Cl)(Br)I 1 33 | F[C@](Cl)(Br)I 1 34 | F[C@](Cl)(Br)I 1 35 | F[C@](Cl)(Br)I 1 36 | F[C@](Cl)(Br)I 1 37 | F[C@](Cl)(Br)I 1 38 | F[C@](Cl)(Br)I 1 39 | F[C@](Cl)(Br)I 1 40 | F[C@](Cl)(Br)I 1 41 | F[C@](Cl)(Br)I 1 42 | F[C@](Cl)(Br)I 1 43 | F[C@](Cl)(Br)I 1 44 | F[C@](Cl)(Br)I 1 45 | F[C@](Cl)(Br)I 1 46 | F[C@](Cl)(Br)I 1 47 | F[C@](Cl)(Br)I 1 48 | F[C@](Cl)(Br)I 1 49 | F[C@](Cl)(Br)I 1 50 | F[C@](Cl)(Br)I 1 51 | F[C@](Cl)(Br)I 1 52 | F[C@H](Br)I 2 53 | F[C@H](Br)I 2 54 | F[C@H](Br)I 2 55 | F[C@H](Br)I 2 56 | F[C@H](Br)I 2 57 | F[C@H](Br)I 2 58 | F[C@H](Br)I 2 59 | F[C@H](Br)I 2 60 | F[C@H](Br)I 2 61 | F[C@H](Br)I 2 62 | F[C@H](Br)I 2 63 | F[C@H](Br)I 2 64 | F[C@H](Br)I 2 65 | F[C@H](Br)I 2 66 | F[C@H](Br)I 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral/rdkit_2018.03.1.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@](Cl)(Br)I 1 9 | F[C@](Cl)(Br)I 1 10 | F[C@](Cl)(Br)I 1 11 | F[C@](Cl)(Br)I 1 12 | F[C@](Cl)(Br)I 1 13 | F[C@](Cl)(Br)I 1 14 | F[C@](Cl)(Br)I 1 15 | F[C@](Cl)(Br)I 1 16 | F[C@](Cl)(Br)I 1 17 | F[C@](Cl)(Br)I 1 18 | F[C@](Cl)(Br)I 1 19 | F[C@](Cl)(Br)I 1 20 | F[C@](Cl)(Br)I 1 21 | F[C@](Cl)(Br)I 1 22 | F[C@](Cl)(Br)I 1 23 | F[C@](Cl)(Br)I 1 24 | F[C@](Cl)(Br)I 1 25 | F[C@](Cl)(Br)I 1 26 | F[C@](Cl)(Br)I 1 27 | F[C@](Cl)(Br)I 1 28 | F[C@](Cl)(Br)I 1 29 | F[C@](Cl)(Br)I 1 30 | F[C@](Cl)(Br)I 1 31 | F[C@](Cl)(Br)I 1 32 | F[C@](Cl)(Br)I 1 33 | F[C@](Cl)(Br)I 1 34 | F[C@](Cl)(Br)I 1 35 | F[C@](Cl)(Br)I 1 36 | F[C@](Cl)(Br)I 1 37 | F[C@](Cl)(Br)I 1 38 | F[C@](Cl)(Br)I 1 39 | F[C@](Cl)(Br)I 1 40 | F[C@](Cl)(Br)I 1 41 | F[C@](Cl)(Br)I 1 42 | F[C@](Cl)(Br)I 1 43 | F[C@](Cl)(Br)I 1 44 | F[C@](Cl)(Br)I 1 45 | F[C@](Cl)(Br)I 1 46 | F[C@](Cl)(Br)I 1 47 | F[C@](Cl)(Br)I 1 48 | F[C@](Cl)(Br)I 1 49 | F[C@](Cl)(Br)I 1 50 | F[C@](Cl)(Br)I 1 51 | F[C@](Cl)(Br)I 1 52 | F[C@H](Br)I 2 53 | F[C@H](Br)I 2 54 | F[C@H](Br)I 2 55 | F[C@H](Br)I 2 56 | F[C@H](Br)I 2 57 | F[C@H](Br)I 2 58 | F[C@H](Br)I 2 59 | F[C@H](Br)I 2 60 | F[C@H](Br)I 2 61 | F[C@H](Br)I 2 62 | F[C@H](Br)I 2 63 | F[C@H](Br)I 2 64 | F[C@H](Br)I 2 65 | F[C@H](Br)I 2 66 | F[C@H](Br)I 2 67 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/BIOVIADraw_2018.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@H](Br)I 2 9 | F[C@H](Br)I 2 10 | F[C@H](Br)I 2 11 | F[C@H](Br)I 2 12 | F[C@H](Br)I 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/ChemDraw_17.1.smi: -------------------------------------------------------------------------------- 1 | Br[C@](I)(F)Cl 1 2 | Br[C@](I)(F)Cl 1 3 | Br[C@](I)(F)Cl 1 4 | Br[C@](I)(F)Cl 1 5 | Br[C@](I)(F)Cl 1 6 | Br[C@](I)(F)Cl 1 7 | Br[C@](I)(F)Cl 1 8 | Br[C@H](I)F 2 9 | Br[C@H](I)F 2 10 | Br[C@H](I)F 2 11 | Br[C@H](I)F 2 12 | Br[C@H](I)F 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/KnowItAll_2018.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@](Br)(I)[H] 2 9 | F[C@](Br)(I)[H] 2 10 | F[C@](Br)(I)[H] 2 11 | F[C@](Br)(I)[H] 2 12 | F[C@](Br)(I)[H] 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/avalon_1.2.0.smi: -------------------------------------------------------------------------------- 1 | # Parse_error 1 2 | # Parse_error 1 3 | # Parse_error 1 4 | # Parse_error 1 5 | Br[C@](F)(Cl)I 1 6 | Br[C@@](Cl)(F)I 1 7 | Br[C@](Cl)(I)F 1 8 | # Parse_error 2 9 | # Parse_error 2 10 | # Parse_error 2 11 | Br[C@]([H])(I)F 2 12 | Br[C@@]([H])(F)I 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/cactvs_3_426.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@H](Br)I 2 9 | F[C@H](Br)I 2 10 | F[C@H](Br)I 2 11 | F[C@H](Br)I 2 12 | F[C@H](Br)I 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/cdk_2.1.smi: -------------------------------------------------------------------------------- 1 | [C@@](Br)(Cl)(F)I 1 2 | [C@@](Br)(Cl)(F)I 1 3 | [C@@](Br)(Cl)(F)I 1 4 | # Parse_error 1 5 | [C@@](Br)(Cl)(F)I 1 6 | [C@@](Br)(Cl)(F)I 1 7 | # Parse_error 1 8 | [C@H](Br)(F)I 2 9 | [C@H](Br)(F)I 2 10 | [C@H](Br)(F)I 2 11 | [C@H](Br)(F)I 2 12 | [C@H](Br)(F)I 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/indigo_1.3.0b.r16.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@H](Br)I 2 9 | F[C@H](Br)I 2 10 | F[C@H](Br)I 2 11 | F[C@H](Br)I 2 12 | F[C@H](Br)I 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/iwtoolkit_1.0.smi: -------------------------------------------------------------------------------- 1 | I[C@](Br)(Cl)F 1 2 | I[C@](Br)(Cl)F 1 3 | I[C@](Br)(Cl)F 1 4 | I[C@](Br)(Cl)F 1 5 | I[C@](Br)(Cl)F 1 6 | I[C@](Br)(Cl)F 1 7 | I[C@](Br)(Cl)F 1 8 | I[C@@H](Br)F 2 9 | I[C@@H](Br)F 2 10 | I[C@@H](Br)F 2 11 | I[C@@H](Br)F 2 12 | I[C@@H](Br)F 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/oechem_Feb2018.smi: -------------------------------------------------------------------------------- 1 | [C@](F)(Cl)(Br)I 1 2 | [C@](F)(Cl)(Br)I 1 3 | [C@](F)(Cl)(Br)I 1 4 | [C@](F)(Cl)(Br)I 1 5 | [C@](F)(Cl)(Br)I 1 6 | [C@](F)(Cl)(Br)I 1 7 | [C@](F)(Cl)(Br)I 1 8 | [C@@H](F)(Br)I 2 9 | [C@@H](F)(Br)I 2 10 | [C@@H](F)(Br)I 2 11 | [C@@H](F)(Br)I 2 12 | [C@@H](F)(Br)I 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/openbabel.smi: -------------------------------------------------------------------------------- 1 | F[C@@](I)(Br)Cl 1 2 | F[C@@](I)(Br)Cl 1 3 | F[C@@](I)(Br)Cl 1 4 | F[C@@](I)(Br)Cl 1 5 | F[C@@](I)(Br)Cl 1 6 | F[C@@](I)(Br)Cl 1 7 | F[C@@](I)(Br)Cl 1 8 | F[C@@H](I)Br 2 9 | F[C@@H](I)Br 2 10 | F[C@@H](I)Br 2 11 | F[C@@H](I)Br 2 12 | F[C@@H](I)Br 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/openchemlib_2018.7.0.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | FC(Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | FC(Cl)(Br)I 1 8 | F[C@H](Br)I 2 9 | F[C@H](Br)I 2 10 | FC(Br)I 2 11 | F[C@H](Br)I 2 12 | FC(Br)I 2 13 | -------------------------------------------------------------------------------- /5-results/tetrahedral_distantbcdigit/rdkit_2018.03.1.smi: -------------------------------------------------------------------------------- 1 | F[C@](Cl)(Br)I 1 2 | F[C@](Cl)(Br)I 1 3 | F[C@](Cl)(Br)I 1 4 | F[C@@](Cl)(Br)I 1 5 | F[C@](Cl)(Br)I 1 6 | F[C@](Cl)(Br)I 1 7 | F[C@](Cl)(Br)I 1 8 | F[C@H](Br)I 2 9 | F[C@H](Br)I 2 10 | F[C@H](Br)I 2 11 | F[C@H](Br)I 2 12 | F[C@H](Br)I 2 13 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 2-Clause License 2 | 3 | Copyright (c) 2017, NextMove Software 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | * Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | * Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 17 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 18 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 19 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 20 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 21 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 22 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 23 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 24 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 25 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 26 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # SMILES reading benchmark 2 | 3 | I call this a benchmark, but it is primarily a means to identify ambiguities in the spec and highlight cornercases, with the goal of ensuring that SMILES are transferred between different programs without any loss or corruption of information. 4 | 5 | This benchmark focuses exclusively on whether different programs can agree on the identity of a molecule as read from a SMILES string, particularly an aromatic SMILES string. For each benchmark SMILES string, the result is the number of implicit hydrogens on each atom of the molecule (in the order in which they appear in the SMILES string). 6 | 7 | If you are interested in looking at the results, unzip some of the entries in the results folder and diff them. Note that it only makes sense to compare entries where they are reading the same SMILES string, i.e. ProgramA-reading-ProgramC.txt and ProgramB-reading-ProgramC.txt. 8 | 9 | If you are interested in adding results for a new toolkit, unzip everything (keeping the originals*) and create a new script in the scripts directory that does the conversion, first from the benchmark Kekule SMILES to aromatic SMILES, and then counting the number of implicit hydrogens in each of the aromatic SMILES strings. 10 | 11 | * Note: "gunzip -k" will do this, but is not available on some platforms. Otherwise, "for d in *.gz; do gunzip -c $d > ${d%.smi.gz}.smi; done". 12 | 13 | 14 | -------------------------------------------------------------------------------- /scripts/BIOVIADirect.py: -------------------------------------------------------------------------------- 1 | # set PATH=C:\Tools\Oracle\product\11.2.0\client_1\BIN;%PATH% 2 | # ...for OCI.dll 3 | 4 | import cx_Oracle as cx 5 | 6 | import my_oracle 7 | con = cx.connect(my_oracle.details) 8 | c = con.cursor() 9 | 10 | import common 11 | 12 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 13 | def getoutput(self, smi): 14 | c.execute("select smiles(mol('%s')) from dual" % smi) 15 | smi = next(c)[0] 16 | return smi 17 | 18 | class MyHydrogenCounter(common.HydrogenCounter): 19 | def getoutput(self, smi): 20 | c.execute("select molfile(mol('%s')) from dual" % smi) 21 | try: 22 | results = next(c) 23 | except cx.DatabaseError: 24 | return None, "Parse_error" 25 | molfile = results[0].read() 26 | return None, "MOLFILE:%s" % molfile.replace("\n", "!!") 27 | 28 | if __name__ == "__main__": 29 | myname = "BIOVIADirect_2017" 30 | # MyAromaticSmilesWriter(myname).main() 31 | MyHydrogenCounter(myname).main() 32 | -------------------------------------------------------------------------------- /scripts/BIOVIADraw.py: -------------------------------------------------------------------------------- 1 | # IronPython 2 | import clr 3 | clr.AddReferenceToFileAndPath(r"D:\Program Files\BIOVIA\BIOVIA Draw 2018\lib\MDL.Draw.Foundation.dll") 4 | 5 | from MDL.Draw.StructureConversion import StructureConverter 6 | sc = StructureConverter() 7 | 8 | import common 9 | import urllib 10 | import urllib2 11 | 12 | import json 13 | 14 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 15 | def getoutput(self, smi): 16 | sc.Smiles = smi 17 | return sc.Smiles 18 | 19 | class MyHydrogenCounter(common.HydrogenCounter): 20 | def getoutput(self, smi): 21 | try: 22 | sc.Smiles = smi 23 | molfile = sc.MolfileString 24 | except StandardError as e: 25 | msg = e.message 26 | if "Failed to get a molfile string" in msg: 27 | return None, "Parse_error" 28 | print "%s gives %s" % (smi, msg) 29 | return None, "MOLFILE:%s" % molfile.replace("\r\n", "!!") 30 | 31 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 32 | def getoutput(self, smi): 33 | sc.Smiles = smi 34 | return sc.Smiles 35 | 36 | if __name__ == "__main__": 37 | myname = "BIOVIADraw_2018" 38 | # MyAromaticSmilesWriter(myname).main() 39 | # MyHydrogenCounter(myname).main() 40 | MyStereoSmilesWriter(myname).main() 41 | -------------------------------------------------------------------------------- /scripts/CDK.py: -------------------------------------------------------------------------------- 1 | # Jython 2 | import org.openscience.cdk as cdk 3 | import java 4 | 5 | import common 6 | 7 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 8 | def getoutput(self, smi): 9 | sp = cdk.smiles.SmilesParser(cdk.silent.SilentChemObjectBuilder.getInstance()) 10 | mol = sp.parseSmiles(smi) 11 | 12 | aromaticity = cdk.aromaticity.Aromaticity(cdk.aromaticity.ElectronDonation.daylight(), cdk.graph.Cycles.or(cdk.graph.Cycles.all(),cdk.graph.Cycles.all(6))) 13 | aromaticity.apply(mol) 14 | sg = cdk.smiles.SmilesGenerator(cdk.smiles.SmiFlavor.UseAromaticSymbols) 15 | msmi = sg.create(mol) 16 | return msmi 17 | 18 | class MyHydrogenCounter(common.HydrogenCounter): 19 | def getoutput(self, smi): 20 | sp = cdk.smiles.SmilesParser(cdk.silent.SilentChemObjectBuilder.getInstance()) 21 | try: 22 | mol = sp.parseSmiles(smi) 23 | except cdk.exception.InvalidSmilesException as e: 24 | msg = e.message 25 | if "kekul" in msg.lower(): 26 | return None, "Kekulization_failure" 27 | if "could not parse" in msg: 28 | return None, "Parse_error" 29 | print "%s gives %s" % (smi, msg) 30 | return 31 | 32 | N = mol.getAtomCount() 33 | hcounts = [mol.getAtom(i).getImplicitHydrogenCount() for i in range(N)] 34 | return hcounts, None 35 | 36 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 37 | def getoutput(self, smi): 38 | sp = cdk.smiles.SmilesParser(cdk.silent.SilentChemObjectBuilder.getInstance()) 39 | try: 40 | mol = sp.parseSmiles(smi) 41 | except cdk.exception.InvalidSmilesException as e: 42 | return "# Parse_error" 43 | 44 | sg = cdk.smiles.SmilesGenerator(cdk.smiles.SmiFlavor.Absolute) 45 | msmi = sg.create(mol) 46 | return msmi 47 | 48 | if __name__ == "__main__": 49 | myname = "cdk_2.1" 50 | # MyAromaticSmilesWriter(myname).main() 51 | # MyHydrogenCounter(myname).main() 52 | MyStereoSmilesWriter(myname).main() 53 | -------------------------------------------------------------------------------- /scripts/Cactvs.py: -------------------------------------------------------------------------------- 1 | """ 2 | Run this as follows: 3 | start D:\Program Files (x86)\cactvs3_426\lib\pycactvs 4 | > import os, sys 5 | > os.chdir("D:\Work\smilesreading\scripts") 6 | > sys.path.append("D:\Work\smilesreading\scripts") 7 | > import Cactvs 8 | > Cactvs.MyAromaticSmilesWriter("cactvs_3_426").main() 9 | > Cactvs.MyHydrogenCounter("cactvs_3_426").main() 10 | > Cactvs.MyStereoSmilesWriter("cactvs_3_426").main() 11 | > import importlib 12 | > importlib.reload(Cactvs) 13 | or on Linux 14 | $ export PYTHONPATH=/home/noel/Tools/Cactvs/python3.6 15 | $ export LD_LIBRARY_PATH=/home/noel/Tools/Cactvs/lib 16 | $ /home/noel/Tools/Cactvs/python3 17 | ...as above 18 | """ 19 | 20 | import common 21 | import pycactvs as cs 22 | 23 | # cs.Prop.Setparam('E_SMILES', {'usearo':True}) # Create aromatic SMILES 24 | cs.Prop.Setparam('E_SMILES', {'unique':True}) # Create canonical SMILES 25 | 26 | cs.cactvs['aromaticity_model'] = 'daylight' 27 | # Turn off the following to get the default behaviour 28 | cs.cactvs['smiles_hypervalent_hydrogen_addition'] = 1 29 | 30 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 31 | def getoutput(self, smi): 32 | mol = cs.Ens(smi) 33 | aromsmi = mol.new("E_SMILES") 34 | mol.delete() 35 | return aromsmi 36 | 37 | class MyHydrogenCounter(common.HydrogenCounter): 38 | def getoutput(self, smi): 39 | mol = cs.Ens(smi) 40 | hcounts = [atom.A_HCOUNT for atom in mol.atoms() if atom.A_ELEMENT != 1] 41 | mol.delete() 42 | return hcounts, None 43 | 44 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 45 | def getoutput(self, smi): 46 | try: 47 | mol = cs.Ens(smi) 48 | except RuntimeError: 49 | return "# Parse_error" 50 | aromsmi = mol.new("E_SMILES") 51 | mol.delete() 52 | return aromsmi 53 | 54 | if __name__ == "__main__": 55 | myname = "Cactvs_3.4.6.19" 56 | # MyAromaticSmilesWriter(myname).main() 57 | # MyHydrogenCounter(myname).main() 58 | MyStereoSmilesWriter(myname).main() 59 | 60 | -------------------------------------------------------------------------------- /scripts/ChemDoodle.py: -------------------------------------------------------------------------------- 1 | # Jython 2 | import main 3 | main.ChemDoodle.setup() 4 | 5 | import com.iChemLabs.api.io as io 6 | import com.iChemLabs.api.informatics as informatics 7 | 8 | import java.io 9 | 10 | import common 11 | 12 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 13 | def getoutput(self, smi): 14 | reader = io.SMILESInterpreter() 15 | reader.read(smi) 16 | mols = reader.molecules 17 | if len(mols) == 0: 18 | return "" 19 | 20 | delocalizer = informatics.Delocalizer() 21 | delocalizer.delocalize(mols[0]) 22 | 23 | smilesout = io.SMILESInterpreter() 24 | smilesout.setWriteAromatics(True) 25 | return smilesout.generateString(mols, java.util.ArrayList(0)) 26 | 27 | class MyHydrogenCounter(common.HydrogenCounter): 28 | def getoutput(self, smi): 29 | if smi == "b1cccc[n+]1C": 30 | return None, "Parse_error" 31 | reader = io.SMILESInterpreter() 32 | reader.read(smi) 33 | mols = reader.molecules 34 | N = len(mols) 35 | if N == 0: 36 | return None, "Failed to parse SMILES" 37 | elif N > 1: 38 | return None, "Parsed %d molecules" % N 39 | mol = reader.superMolecule 40 | hcounts = [atom.implicitHydrogenCount + atom.explicitHydrogenCount for atom in mol.atoms] 41 | # Kekulization failure is not detectable 42 | return hcounts, None 43 | 44 | if __name__ == "__main__": 45 | myname = "ChemDoodleAPI_2.3.0" 46 | # MyAromaticSmilesWriter(myname).main() 47 | MyHydrogenCounter(myname).main() 48 | -------------------------------------------------------------------------------- /scripts/ChemDraw.py: -------------------------------------------------------------------------------- 1 | """ 2 | Python 3 3 | 4 | Note that there is a memory leak which hits the 2GB limit every 2.5 input 5 | files. It's probably best to run it one file at a time and capture the stdout 6 | so we can look for kekulization failures afterwards: 7 | 8 | py -3.2 -u ChemDraw.py > rdkit.out 2>&1 9 | """ 10 | 11 | import common 12 | import sys 13 | sys.path.append(r"D:\Program Files (x86)\PerkinElmerInformatics\ChemOffice2017\ChemScript\Lib") 14 | import ChemScript17 as cs 15 | import opsin 16 | 17 | op = cs.NormOptions() 18 | 19 | op.AnonList = False 20 | op.Azide = False 21 | op.CleaveIntoSalts = False 22 | op.CreatedDelRep_1 = False 23 | op.CreatedDelRep_2 = False 24 | op.CollapseZwitterion = False 25 | op.Dative = False 26 | op.DativeToDouble = False 27 | op.Dekekulize = True 28 | op.Delrep = False 29 | op.Diazo_a = False 30 | op.Diazo_b = False 31 | op.FeaturelessHydrogens = False 32 | op.Isonitrile_fg = False 33 | op.MergeCharges = False 34 | op.MergeMetalSalts = False 35 | op.MoveChargeFromCarbon = False 36 | op.NeutralDiazo_fg = False 37 | op.RemoveIsotopy = False 38 | op.RemoveLabel = False 39 | op.RemoveNonGraphStereo = False 40 | op.RemoveRTable = False 41 | op.RemoveRxnCenters = False 42 | op.RemoveTextAtoms = False 43 | op.RemoveValence = False 44 | op.RemoveWedge = False 45 | op.StripEitherDoubleBond = False 46 | op.StripEitherSingleBond = False 47 | op.R3NO_b = False 48 | op.ProvideMissingCoords = False 49 | op.Thiazole = False 50 | op.XMinusToX_fg = False 51 | op.ExpandStoichiometry = False 52 | op.ConsolidateStoichiometry = False 53 | 54 | print(op) # Prints out the values of the options 55 | 56 | class MyHydrogenCounter(common.HydrogenCounter): 57 | def getoutput(self, smi): 58 | print(smi) # We use this to detect kekulization errors written to stdout 59 | mol = cs.StructureData.LoadData(smi) 60 | if mol is None: 61 | return None, "Parse_error" 62 | ok = mol.NormalizeStructure(op) 63 | if not ok: 64 | # never happens - warning to stdout but I can't capture it 65 | return None, "Kekulization error" 66 | mol.ConvertTo3DStructure() # adds hydrogens by default 67 | numHs = [] 68 | for atom in mol.Atoms: 69 | if atom.Element != "H": 70 | numH = sum([1 for x in mol.BondedAtomsOf(atom) if x.Element == "H"]) 71 | numHs.append(numH) 72 | return numHs, None 73 | 74 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 75 | def getoutput(self, smi): 76 | mol = cs.StructureData.LoadData(smi) 77 | name = mol.ChemicalName() 78 | return opsin.read(name) 79 | 80 | if __name__ == "__main__": 81 | myname = "ChemDraw_17.1" 82 | MyHydrogenCounter(myname).main() 83 | # MyStereoSmilesWriter(myname).main() 84 | -------------------------------------------------------------------------------- /scripts/ChemDraw_FindKekuleFailures.py: -------------------------------------------------------------------------------- 1 | """ 2 | 1. Copy the original results into 3-results/ChemDraw_orig 3 | 2. Ensure that all of the input smiles files are unzipped 4 | 3. The files chemdraw/avalon_1.2.0.out, etc. should exist containing a list of SMILES along with any 5 | error messages 6 | 7 | Run this script. The output is written to chemdraw. 8 | 9 | """ 10 | import os 11 | import glob 12 | 13 | def geterrors(logfile): 14 | errors = [] 15 | with open(logfile) as inp: 16 | old = None 17 | for line in inp: 18 | line = line.strip() 19 | if "MF changed" in line: 20 | if "ChemCentral" in line: 21 | errors.append( old ) 22 | continue 23 | old = line 24 | return errors 25 | 26 | if __name__ == "__main__": 27 | inputfiles = glob.glob(os.path.join("..", "3-results", "chembl", "ChemDraw_17.1_reading*.txt")) 28 | for inputfile in inputfiles: 29 | program = os.path.basename(inputfile)[22:-4] 30 | print(program) 31 | errors = geterrors(os.path.join("chemdraw", "%s.out" % program)) 32 | print(len(errors)) 33 | with open(os.path.join("chemdraw", "%s.errors.smi" % program), "w") as out: 34 | for error in errors: 35 | out.write("%s %s\n" % (error, error)) 36 | errorno = 0 37 | finished = False 38 | with open(os.path.join("..", "2-aromaticsmiles", "chembl", "%s.smi" % program)) as inp: 39 | with open(os.path.join("..", "3-results", "chembl", "ChemDraw_orig", "ChemDraw_17.1_reading_%s.txt" % program)) as result: 40 | with open(os.path.join("chemdraw", "ChemDraw_17.1_reading_%s.txt" % program), "w") as out: 41 | for smi, hcounts in zip(inp, result): 42 | if finished or smi.split()[0] != errors[errorno]: 43 | out.write(hcounts) 44 | else: 45 | out.write("# Kekulization_failure\n") 46 | errorno += 1 47 | if errorno == len(errors): 48 | finished = True 49 | 50 | -------------------------------------------------------------------------------- /scripts/ConvertMolfiles.py: -------------------------------------------------------------------------------- 1 | import common_molfile 2 | from openeye import oechem as oe 3 | 4 | class MyHydrogenCounterFromMolfile(common_molfile.HydrogenCounterFromMolfile): 5 | def getoutput(self, molfile): 6 | istream = oe.oemolistream() 7 | istream.SetFormat(oe.OEFormat_MDL) 8 | ok = istream.openstring(molfile) 9 | assert ok 10 | mol = oe.OEGraphMol() 11 | ok = oe.OEReadMDLFile(istream, mol) 12 | assert ok 13 | return [x.GetImplicitHCount() for x in mol.GetAtoms()] 14 | 15 | if __name__ == "__main__": 16 | myname = "BIOVIADraw_2018" 17 | MyHydrogenCounterFromMolfile(myname).main() 18 | -------------------------------------------------------------------------------- /scripts/Indigo.py: -------------------------------------------------------------------------------- 1 | import sys 2 | from indigo import Indigo, IndigoException 3 | indigo = Indigo() 4 | 5 | import common 6 | 7 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 8 | def getoutput(self, smi): 9 | mol = indigo.loadMolecule(smi) 10 | mol.aromatize() 11 | return mol.smiles() 12 | 13 | class MyHydrogenCounter(common.HydrogenCounter): 14 | def getoutput(self, smi): 15 | # Don't require that the input has the same aromaticity model as Indigo 16 | indigo.setOption("dearomatize-verification", False) 17 | try: 18 | mol = indigo.loadMolecule(smi) 19 | except IndigoException as e: 20 | if "unrecognized lowercase symbol" in e.value: 21 | return None, "Parse_error" 22 | elif "probably pending bond" in e.value: 23 | return None, "Parse_error" 24 | else: 25 | print smi 26 | print e.value 27 | fd 28 | kekulization_failure = mol.dearomatize() 29 | if kekulization_failure==0: 30 | return None, "Kekulization_failure" 31 | try: 32 | hcounts = [atom.countImplicitHydrogens() for atom in mol.iterateAtoms()] 33 | except IndigoException as e: 34 | if "can not calculate implicit hydrogens" in e.value: 35 | return None, "Kekulization_failure" 36 | elif "bad valence on" in e.value: 37 | return None, "Bad_valence" 38 | else: 39 | print smi 40 | print e.value 41 | fd 42 | 43 | return hcounts, None 44 | 45 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 46 | def getoutput(self, smi): 47 | mol = indigo.loadMolecule(smi) 48 | return mol.canonicalSmiles() 49 | 50 | if __name__ == "__main__": 51 | myname = "indigo_1.3.0b.r16" 52 | # MyAromaticSmilesWriter(myname).main() 53 | # MyHydrogenCounter(myname).main() 54 | MyStereoSmilesWriter(myname).main() 55 | 56 | -------------------------------------------------------------------------------- /scripts/JChem.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env jython 2 | 3 | import os 4 | import sys 5 | 6 | # Add all JChem jars to path 7 | JCHEM_LIB = '/Applications/ChemAxon/JChemSuite/lib' 8 | JCHEM_LIB = r"D:\Program Files\ChemAxon\JChemSuite\lib" 9 | for f in os.listdir(JCHEM_LIB): 10 | sys.path.append(os.path.join(JCHEM_LIB, f)) 11 | 12 | from chemaxon.formats import MolImporter, MolExporter, MolFormatException 13 | from chemaxon.marvin.io import MolExportException 14 | 15 | import common 16 | 17 | 18 | # SMILES import/export options: https://docs.chemaxon.com/display/docs/SMILES+and+SMARTS+import+and+export+options 19 | # Aromatization and hydrogen export options: https://docs.chemaxon.com/display/docs/Basic+export+options 20 | 21 | 22 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 23 | def getoutput(self, smi): 24 | try: 25 | mol = MolImporter.importMol(smi, 'smiles') 26 | except MolFormatException as e: 27 | return '' 28 | try: 29 | # a - General (Daylight) aromatization. (Alternatives: a_bas, a_loose, a_ambig, etc.) 30 | # u - Write "unique" smiles (include chirality into graph invariants, slower) 31 | msmi = MolExporter.exportToFormat(mol, 'smiles:a') 32 | except MolExportException as e: 33 | # return ' '.join(str(e).split('\n')) # Write error message to a single line 34 | return '' 35 | return msmi 36 | 37 | 38 | class MyHydrogenCounter(common.HydrogenCounter): 39 | def getoutput(self, smi): 40 | try: 41 | mol = MolImporter.importMol(smi, 'smiles') 42 | except MolFormatException as e: 43 | return (None, 'Parse_error') 44 | success = mol.dearomatize() 45 | if not success: 46 | return (None, 'Kekulization_failure') 47 | N = mol.getAtomCount() 48 | hcounts = [atom.getImplicitHcount() for atom in mol.getAtomIterator()] 49 | return hcounts, None 50 | 51 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 52 | def getoutput(self, smi): 53 | try: 54 | mol = MolImporter.importMol(smi, 'smiles') 55 | except MolFormatException as e: 56 | return '' 57 | try: 58 | # a - General (Daylight) aromatization. (Alternatives: a_bas, a_loose, a_ambig, etc.) 59 | # u - Write "unique" smiles (include chirality into graph invariants, slower) 60 | msmi = MolExporter.exportToFormat(mol, 'smiles:u') 61 | except MolExportException as e: 62 | # return ' '.join(str(e).split('\n')) # Write error message to a single line 63 | return '' 64 | return msmi 65 | 66 | if __name__ == "__main__": 67 | myname = "jchem_18.18" 68 | # MyAromaticSmilesWriter(myname).main() 69 | MyHydrogenCounter(myname).main() 70 | # MyStereoSmilesWriter(myname).main() 71 | 72 | -------------------------------------------------------------------------------- /scripts/OEChem.py: -------------------------------------------------------------------------------- 1 | import sys 2 | from openeye import oechem as oe 3 | 4 | import common 5 | 6 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 7 | def getoutput(self, smi): 8 | mol = oe.OEGraphMol() 9 | ok = oe.OEParseSmiles(mol, smi) 10 | assert ok 11 | oe.OEAssignAromaticFlags(mol) 12 | return oe.OECreateSmiString(mol, 0) 13 | 14 | msgstream = oe.oeosstream() 15 | oe.OEThrow.SetOutputStream(msgstream) 16 | 17 | class MyHydrogenCounter(common.HydrogenCounter): 18 | def getoutput(self, smi): 19 | mol = oe.OEGraphMol() 20 | msgstream.clear() 21 | ok = oe.OEParseSmiles(mol, smi) 22 | if not ok: 23 | msg = msgstream.str().decode("utf-8") 24 | if "Kekul" in msg: 25 | return None, "Kekulization_failure" 26 | else: 27 | return None, "Parse_error" 28 | 29 | return [atom.GetImplicitHCount() for atom in mol.GetAtoms()], None 30 | 31 | flags = oe.OESMILESFlag_BondStereo ^ oe.OESMILESFlag_AtomStereo ^ oe.OESMILESFlag_Canonical 32 | 33 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 34 | def getoutput(self, smi): 35 | mol = oe.OEGraphMol() 36 | ok = oe.OEParseSmiles(mol, smi) 37 | assert ok 38 | return oe.OECreateSmiString(mol, flags) 39 | 40 | if __name__ == "__main__": 41 | myname = "oechem_Feb2018" 42 | # MyAromaticSmilesWriter(myname).main() 43 | # MyHydrogenCounter(myname).main() 44 | MyStereoSmilesWriter(myname).main() 45 | -------------------------------------------------------------------------------- /scripts/OpenBabel.py: -------------------------------------------------------------------------------- 1 | import common 2 | 3 | import pybel 4 | ob = pybel.ob 5 | 6 | # Changed smilesformat to return false for kekulization errors 7 | 8 | class MyHydrogenCounter(common.HydrogenCounter): 9 | def getoutput(self, smi): 10 | try: 11 | mol = pybel.readstring("smi", smi) 12 | except IOError: 13 | return None, "Kekulization_failure" 14 | return [atom.OBAtom.GetImplicitHCount() for atom in mol], None 15 | 16 | if __name__ == "__main__": 17 | myname = "openbabel_dev9May18" 18 | MyHydrogenCounter(myname).main() 19 | -------------------------------------------------------------------------------- /scripts/OpenChemLib.py: -------------------------------------------------------------------------------- 1 | # Jython 2 | import java 3 | import com.actelion.research.chem as chem 4 | 5 | import common 6 | 7 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 8 | def getoutput(self, smi): 9 | parser = chem.SmilesParser() 10 | mol = chem.StereoMolecule() 11 | parser.parse(mol, smi, java.lang.Boolean(False), java.lang.Boolean(False)) 12 | 13 | isc = chem.IsomericSmilesCreator(mol) 14 | return isc.getSmiles() 15 | 16 | class MyHydrogenCounter(common.HydrogenCounter): 17 | def getoutput(self, smi): 18 | parser = chem.SmilesParser() 19 | mol = chem.StereoMolecule() 20 | try: 21 | parser.parse(mol, smi, java.lang.Boolean(False), java.lang.Boolean(False)) 22 | except java.lang.Exception, e: 23 | if "Assignment of aromatic double bonds" in e.message: 24 | return None, "Kekulization_failure" 25 | else: 26 | raise e 27 | N = mol.getAllAtoms() 28 | hcounts = [mol.getImplicitHydrogens(i) for i in range(N)] 29 | return hcounts, None 30 | 31 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 32 | def getoutput(self, smi): 33 | parser = chem.SmilesParser() 34 | mol = chem.StereoMolecule() 35 | parser.parse(mol, smi) 36 | 37 | isc = chem.IsomericSmilesCreator(mol) 38 | return isc.getSmiles() 39 | 40 | if __name__ == "__main__": 41 | myname = "openchemlib_2018.7.0" 42 | # MyAromaticSmilesWriter(myname).main() 43 | # MyHydrogenCounter(myname).main() 44 | MyStereoSmilesWriter(myname).main() 45 | 46 | -------------------------------------------------------------------------------- /scripts/RDKit.py: -------------------------------------------------------------------------------- 1 | # At the 64-bit Anaconda prompt, "activate my-rdkit-env" first. 2 | 3 | import sys 4 | from rdkit import Chem 5 | from io import StringIO 6 | 7 | import common 8 | 9 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 10 | def getoutput(self, smi): 11 | m = Chem.MolFromSmiles(smi) 12 | if m is None: 13 | return "" 14 | return Chem.MolToSmiles(m, canonical=False) 15 | 16 | class MyHydrogenCounter(common.HydrogenCounter): 17 | def __init__(self, name): 18 | super(MyHydrogenCounter, self).__init__(name) 19 | Chem.WrapLogs() 20 | old_stderr = sys.stderr 21 | self.sio = sys.stderr = StringIO() 22 | 23 | def getoutput(self, smi): 24 | m = Chem.MolFromSmiles(smi) 25 | err = self.sio.getvalue() 26 | if err: 27 | self.sio = sys.stderr = StringIO() 28 | if "Can't kekulize" in err: 29 | return None, "Kekulization_failure" 30 | elif "Explicit valence" in err: 31 | return None, "Bad_valence" 32 | elif "SMILES Parse Error" in err: 33 | return None, "SMILES_parse_error" 34 | elif "Aromatic bonds on non aromatic atom" in err: 35 | return None, "Aromatic_bonds_on_non_aromatic_atom" 36 | elif "non-ring" in err and "marked aromatic" in err: 37 | return None, "Non_ring_atom_marked_aromatic" 38 | print("**ERROR NOT CAPTURED from %s\n%s " % (smi, err)) 39 | if m is None: 40 | return None, "No_output" 41 | return [atom.GetTotalNumHs(False) for atom in m.GetAtoms()], None 42 | 43 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 44 | def getoutput(self, smi): 45 | m = Chem.MolFromSmiles(smi) 46 | if m is None: 47 | return "" 48 | return Chem.MolToSmiles(m, canonical=True) 49 | 50 | if __name__ == "__main__": 51 | myname = "rdkit_2018.03.1" 52 | # MyAromaticSmilesWriter(myname).main() 53 | # MyHydrogenCounter(myname).main() 54 | MyStereoSmilesWriter(myname).main() 55 | 56 | -------------------------------------------------------------------------------- /scripts/WeiningerCEX.py: -------------------------------------------------------------------------------- 1 | import subprocess 2 | 3 | import common 4 | 5 | cex = """$D 6 | /_P 7 | /_V 8 | /_S<1M> 9 | /_L 10 | /_X 11 | | 12 | $MOL<%s> 13 | | 14 | """ 15 | 16 | def isAromaticSmiles(smi): 17 | N = len(smi) 18 | for i in range(N): 19 | x = smi[i] 20 | if x == ":": return True 21 | if x>='a' and x<='z': 22 | if i==0 or smi[i-1]=='[' or x in "bcnsopfi" or smi[i-1:i+1] in ["cl", "br"]: 23 | return True 24 | return False 25 | 26 | class MyHydrogenCounter(common.HydrogenCounter): 27 | def getoutput(self, smi): 28 | if isAromaticSmiles(smi): 29 | return None, "Aromatic_smiles_not_supported" 30 | # Neither are up/down bond symbols 31 | command = ["/home/noel/Tools/tmp/cex132/src/applics/mol/printmol"] 32 | proc = subprocess.Popen(command, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE) 33 | stdout, stderr = proc.communicate(cex % smi) 34 | out = stdout.split("\n") 35 | if stderr: 36 | return None, stderr.replace(" ", "_") 37 | for line in out: 38 | if "Implicit hcount" in line: 39 | idx = line.find('"') 40 | hcounts = map(int, line[idx+1:line.find('"', idx+1)].split(";")) 41 | return hcounts, None 42 | 43 | return None, "No_hcounts" 44 | 45 | if __name__ == "__main__": 46 | myname = "WeiningerCEX_132" 47 | MyHydrogenCounter(myname).main() 48 | 49 | -------------------------------------------------------------------------------- /scripts/avalon.c: -------------------------------------------------------------------------------- 1 | #include "reaccs.h" 2 | #include "smi2mol.h" 3 | #include 4 | 5 | int main(int argc, char** argv) 6 | { 7 | struct reaccs_molecule_t *mol; 8 | struct reaccs_atom_t atom; 9 | char* ans; 10 | int i; 11 | int N; 12 | int* H_counts; 13 | int kekulization_failure; 14 | 15 | if (argc != 3) { 16 | printf("Usage: NUM SMILES\n where NUM is 0 for aromatic SMILES\n and 1 for a list of H counts\n and 2 for unique SMILES\n"); 17 | return 1; 18 | } 19 | 20 | switch(argv[1][0]) { 21 | case '0': 22 | mol = SMIToMOL(argv[2], 0); 23 | ans = MOLToSMI(mol, DY_AROMATICITY); 24 | printf("%s\n", ans); 25 | break; 26 | 27 | case '1': 28 | mol = SMIToMOL(argv[2], 0); 29 | if (!mol) { 30 | fprintf(stderr, "Parse_error\n"); 31 | return 0; 32 | } 33 | kekulization_failure = 0; 34 | for (i=0; in_bonds; i++) { 35 | if (mol->bond_array[i].bond_type == AROMATIC) 36 | kekulization_failure = 1; 37 | } 38 | if (kekulization_failure) { 39 | fprintf(stderr, "Kekulization_failure\n"); 40 | return 0; 41 | } 42 | H_counts = TypeAlloc(mol->n_atoms+1, int); 43 | for (i=0; i<=mol->n_atoms; i++) 44 | H_counts[i] = 0; 45 | ComputeImplicitH(mol, H_counts); 46 | /* Take care of already fixed hydrogen counts */ 47 | /* Note: Index origin of H_counts is 1 */ 48 | for (i=0; in_atoms; i++) 49 | if (mol->atom_array[i].query_H_count != NONE) 50 | H_counts[i+1] = mol->atom_array[i].query_H_count-ZERO_COUNT; 51 | 52 | for(i=1; i<=mol->n_atoms; i++) { 53 | printf(" %d", H_counts[i]); 54 | } 55 | printf("\n"); 56 | break; 57 | 58 | case '2': 59 | mol = SMIToMOL(argv[2], 0); 60 | ans = MOLToSMI(mol, DY_AROMATICITY | CANONICAL_ORDER); 61 | printf("%s\n", ans); 62 | break; 63 | 64 | case '3': 65 | mol = SMIToMOL(argv[2], TRUE_DB_STEREO|DO_LAYOUT); 66 | if (!mol) { 67 | fprintf(stderr, "Parse_error\n"); 68 | return 0; 69 | } 70 | ans = MOLToSMI(mol, ISOMERIC_SMILES|CANONICAL_ORDER); 71 | printf("%s\n", ans); 72 | break; 73 | } 74 | 75 | return 0; 76 | } 77 | 78 | -------------------------------------------------------------------------------- /scripts/avalon.py: -------------------------------------------------------------------------------- 1 | import subprocess 2 | 3 | import common 4 | 5 | class MyAromaticSmilesWriter(common.AromaticSmilesWriter): 6 | def getoutput(self, smi): 7 | command = ["/home/noel/Tools/Avalon/SourceDistribution/common/build/noel", "0", smi] 8 | proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE) 9 | stdout, stderr = proc.communicate() 10 | msmi = stdout.rstrip() 11 | if stderr: 12 | print "%s gives %s\n" % (smi, stderr) 13 | return msmi 14 | 15 | class MyHydrogenCounter(common.HydrogenCounter): 16 | def getoutput(self, smi): 17 | command = ["/home/noel/Tools/Avalon/SourceDistribution/common/build/noel", "1", smi] 18 | proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE) 19 | stdout, stderr = proc.communicate() 20 | hcounts = map(int, stdout.strip().split()) 21 | if stderr: 22 | if "Kekulization" in stderr: 23 | return None, "Kekulization_failure" 24 | elif "Parse_error" in stderr: 25 | return None, "Parse_error" 26 | #if "illegal character" in stderr and "before ring in SMILES" in stderr: 27 | # return None, "Illegal_character_before_ring" 28 | else: 29 | print "%s gives\n%s\n%s\n" % (smi, hcounts, stderr) 30 | fd 31 | return hcounts, None 32 | 33 | class MyStereoSmilesWriter(common.StereoSmilesWriter): 34 | def getoutput(self, smi): 35 | command = ["/home/noel/Tools/Avalon/SourceDistribution/common/build/noel", "3", smi] 36 | proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE) 37 | stdout, stderr = proc.communicate() 38 | msmi = stdout.rstrip() 39 | if stderr: 40 | print "%s gives %s\n" % (smi, stderr) 41 | return "# Parse_error" 42 | return msmi 43 | 44 | if __name__ == "__main__": 45 | myname = "avalon_1.2.0" 46 | # MyAromaticSmilesWriter(myname).main() 47 | # MyHydrogenCounter(myname).main() 48 | MyStereoSmilesWriter(myname).main() 49 | 50 | -------------------------------------------------------------------------------- /scripts/common.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | import glob 4 | 5 | class AromaticSmilesWriter(object): 6 | def __init__(self, name): 7 | self.name = name 8 | def main(self): 9 | for benchmark in glob.glob(os.path.join("..", "1-benchmarks", "*.smi")): 10 | dirname = os.path.basename(benchmark).split(".")[0] 11 | outdirname = os.path.join("..", "2-aromaticsmiles", dirname) 12 | if not os.path.isdir(outdirname): 13 | os.mkdir(outdirname) 14 | outfname = os.path.join(outdirname, "%s.smi" % self.name) 15 | with open(outfname, "w") as out: 16 | for line in open(benchmark): 17 | smi, title = line.rstrip().split() 18 | output = self.getoutput(smi) 19 | out.write("%s %s\n" % (output, title)) 20 | 21 | class StereoSmilesWriter(object): 22 | def __init__(self, name): 23 | self.name = name 24 | def main(self): 25 | for benchmark in glob.glob(os.path.join("..", "4-stereosmiles", "*.smi")): 26 | dirname = os.path.basename(benchmark).split(".")[0] 27 | outdirname = os.path.join("..", "5-results", dirname) 28 | if not os.path.isdir(outdirname): 29 | os.mkdir(outdirname) 30 | outfname = os.path.join(outdirname, "%s.smi" % self.name) 31 | with open(outfname, "w") as out: 32 | for line in open(benchmark): 33 | smi, title = line.rstrip().split() 34 | output = self.getoutput(smi) 35 | out.write("%s %s\n" % (output, title)) 36 | 37 | class HydrogenCounter(object): 38 | def __init__(self, name): 39 | self.name = name 40 | def main(self): 41 | for aromsmidir in glob.glob(os.path.join("..", "2-aromaticsmiles", "*")): 42 | dirname = os.path.basename(aromsmidir) 43 | outdirname = os.path.join("..", "3-results", dirname) 44 | if not os.path.isdir(outdirname): 45 | os.mkdir(outdirname) 46 | for inputfile in glob.glob(os.path.join("..", "2-aromaticsmiles", dirname, "*.smi")): 47 | inputprogram = os.path.splitext(os.path.basename(inputfile))[0] 48 | outfname = os.path.join(outdirname, "%s_reading_%s.txt" % (self.name, inputprogram)) 49 | with open(outfname, "w") as out: 50 | for line in open(inputfile): 51 | tmp = line.rstrip().split() 52 | if len(tmp) == 1: 53 | out.write("# %s No_input\n" % tmp[0]) 54 | continue 55 | elif len(tmp) == 2: 56 | smi, title = tmp 57 | elif len(tmp) == 3: 58 | smi, cxn, title = tmp 59 | hcounts, error = self.getoutput(smi) 60 | if error: 61 | out.write("# %s %s\n" % (title, error)) 62 | else: 63 | out.write("%s %s\n" % (title, " ".join(str(x) for x in hcounts))) 64 | -------------------------------------------------------------------------------- /scripts/common_molfile.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | import glob 4 | import re 5 | 6 | pat = re.compile(" 4 0\s*!!") 7 | 8 | class HydrogenCounterFromMolfile(object): 9 | def __init__(self, name): 10 | self.name = name 11 | def main(self): 12 | fname = os.path.join("..", "3-results", "*", "%s_*.txt" % self.name) 13 | filenames = glob.glob(os.path.join("..", "3-results", "*", "%s_*.txt" % self.name)) 14 | for results in filenames: 15 | dirname = os.path.dirname(results) 16 | basename = os.path.basename(results) 17 | tmpfile = os.path.join(dirname, "%s.tmp" % basename) 18 | with open(tmpfile, "w") as out: 19 | for line in open(results): 20 | if line[0] != '#': 21 | out.write(line) 22 | continue 23 | _, title, data = line.rstrip().split(" ", 2) 24 | if not data.startswith("MOLFILE:"): 25 | out.write(line) 26 | continue 27 | if pat.search(data): # aromatic bond 28 | out.write("# %s Kekulization_failure\n" % title) 29 | continue 30 | molfile = "\n".join(data[8:].split("!!")) 31 | hcounts = self.getoutput(molfile) 32 | out.write("%s %s\n" % (title, " ".join(str(x) for x in hcounts))) 33 | if os.path.isfile("%s.orig" % results): 34 | os.remove("%s.orig" % results) 35 | os.rename(results, "%s.orig" % results) 36 | os.rename(tmpfile, results) 37 | -------------------------------------------------------------------------------- /scripts/iwtoolkit.cpp: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include "molecule.h" 4 | #include "smiles.h" 5 | #include "aromatic.h" 6 | 7 | int main(int argc, char** argv) 8 | { 9 | if (argc != 3) { 10 | printf("Usage: NUM SMILES\n where NUM is 0 for aromatic SMILES\n and 1 for a list of H counts\n and 2 for unique SMILES\n"); 11 | exit(0); 12 | } 13 | 14 | IWString smi(argv[2]); 15 | Molecule m; 16 | m.build_from_smiles(smi); 17 | 18 | switch(argv[1][0]) { 19 | case '0': { 20 | set_global_aromaticity_type(Daylight); 21 | set_include_aromaticity_in_smiles(1); 22 | IWString ans = m.smiles(); 23 | printf("%s\n", ans.c_str()); 24 | break; 25 | } 26 | 27 | case '1': { 28 | /* Uncomment the following to try to get behaviour closer to Daylight (on average) */ 29 | //set_four_connected_neutral_nitrogen_has_h(1); // add a H to N(C)(C)(C)C 30 | //set_alternate_valences_give_hcount(0); // don't round up to the next valence 31 | const int N = m.natoms(); 32 | for(int i=0; i