├── .gitattributes ├── .gitignore ├── .travis.yml ├── CHANGELOG ├── LICENCE.txt ├── MANIFEST.in ├── README.md ├── devtools ├── conda-recipe │ ├── build.sh │ └── meta.yaml └── travis-ci │ └── install.sh ├── examples ├── example.py └── example_radial_graph.py ├── lomap ├── __init__.py ├── _version.py ├── dbmol.py ├── fp.py ├── graphgen.py └── mcs.py ├── setup.cfg ├── setup.py ├── test ├── basic │ ├── 1,3,7-trimethylnaphthalene.mol2 │ ├── 1-butyl-4-methylbenzene.mol2 │ ├── 2,6-dimethylnaphthalene.mol2 │ ├── 2-methyl-6-propylnaphthalene.mol2 │ ├── 2-methylnaphthalene.mol2 │ ├── 2-naftanol.mol2 │ ├── MCS.pickle │ ├── chlorophenyl.sdf │ ├── methylcyclohexane.mol2 │ ├── molecules.gpickle │ ├── toluene.mol2 │ └── toluyl.sdf ├── chiral │ ├── Chiral1R.sdf │ ├── Chiral1S.sdf │ ├── Chiral2R.sdf │ ├── Chiral3RS.sdf │ ├── Chiral3SR.sdf │ ├── Chiral3SS.sdf │ ├── Chiral4RR.sdf │ ├── Chiral4RS.sdf │ ├── RingChiralR.sdf │ ├── RingChiralS.sdf │ ├── SpiroR.sdf │ ├── SpiroS.sdf │ ├── bace_cat_13d.sdf │ ├── bace_cat_13d_inverted.sdf │ ├── bace_cat_13d_perm1.sdf │ ├── bace_cat_13d_perm2.sdf │ ├── bace_cat_13d_perm3.sdf │ ├── bace_cat_13d_perm4.sdf │ ├── bace_cat_13d_perm5.sdf │ ├── bace_mk1.sdf │ ├── tpbs2_lig1.sdf │ ├── tpbs2_lig1a.sdf │ └── tpbs2_lig2.sdf ├── linksfile │ ├── links1.txt │ ├── links2.txt │ ├── links3.txt │ ├── phenyl.sdf │ ├── phenylcyclobutyl.sdf │ ├── phenylfuran.sdf │ └── toluyl.sdf ├── radial │ ├── ejm_31.mol2 │ ├── ejm_42.mol2 │ ├── ejm_43.mol2 │ ├── ejm_44.mol2 │ ├── ejm_45.mol2 │ ├── ejm_46.mol2 │ ├── ejm_47.mol2 │ ├── ejm_48.mol2 │ ├── ejm_49.mol2 │ ├── ejm_50.mol2 │ ├── ejm_54.mol2 │ ├── ejm_55.mol2 │ ├── jmc_23.mol2 │ ├── jmc_27.mol2 │ ├── jmc_28.mol2 │ ├── jmc_30.mol2 │ ├── molecules.gpickle │ ├── radial.gpickle │ ├── radial_hub.gpickle │ ├── radial_hub_fingerprint.gpickle │ └── radial_hub_fingerprint_fast.gpickle ├── test_lomap.py └── transforms │ ├── bromophenyl.sdf │ ├── cdk2_lig1.sdf │ ├── cdk2_lig11.sdf │ ├── cdk2_lig13.sdf │ ├── cdk2_lig14.sdf │ ├── cdk2_lig14_translated.sdf │ ├── cdk2_lig15.sdf │ ├── cdk2_lig16.sdf │ ├── cdk2_lig2.sdf │ ├── chlorophenol.sdf │ ├── chlorophenyl.sdf │ ├── chlorophenyl2.sdf │ ├── chlorotoluyl1.sdf │ ├── chlorotoluyl2.sdf │ ├── fluorophenyl.sdf │ ├── iodophenyl.sdf │ ├── methoxyphenyl.sdf │ ├── napthyl.sdf │ ├── napthyl2.sdf │ ├── napthyl3.sdf │ ├── phenyl.sdf │ ├── phenylamide.sdf │ ├── phenylcyclobutyl.sdf │ ├── phenylcyclononyl.sdf │ ├── phenylcyclopentyl.sdf │ ├── phenylcyclopentylmethyl1.sdf │ ├── phenylcyclopentylmethyl2.sdf │ ├── phenylcyclopropyl.sdf │ ├── phenylethyl.sdf │ ├── phenylfuran.sdf │ ├── phenylimidazole.sdf │ ├── phenylisoxazole.sdf │ ├── phenylmethylamino.sdf │ ├── phenyloxazole.sdf │ ├── phenylphenyl.sdf │ ├── phenylpyrazole.sdf │ ├── phenylpyridine1.sdf │ ├── phenylpyridine2.sdf │ ├── phenylpyrimidine.sdf │ ├── phenylpyrrole.sdf │ ├── phenylsulfonamide.sdf │ ├── sulfonamide.sdf │ ├── sulfone.sdf │ ├── test.py │ ├── tetrahydronaphthyl.sdf │ ├── toluyl.sdf │ ├── toluyl2.sdf │ └── 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