├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── devtools ├── conda-recipe │ ├── README.md │ ├── build.sh │ └── meta.yaml └── travis-ci │ ├── after_success.sh │ ├── index.html │ ├── install.sh │ └── push-docs-to-s3.py ├── dist └── smarty-0.1.0-py2.7.egg ├── examples ├── README.md ├── parm@frosst │ ├── README.md │ ├── atomtypes │ │ ├── README.md │ │ ├── basetypes-elemental.smarts │ │ ├── basetypes.smarts │ │ ├── decorators-simple.smarts │ │ ├── decorators.smarts │ │ └── substitutions.smarts │ ├── make_subset.py │ ├── molecules │ │ ├── zinc-subset-500-parm@frosst.mol2.gz │ │ ├── zinc-subset-500-tripos.mol2.gz │ │ ├── zinc-subset-parm@frosst.mol2.gz │ │ └── zinc-subset-tripos.mol2.gz │ └── scripts │ │ ├── README.md │ │ └── convert-atom-names-to-tripos.py ├── smarty_simulations │ ├── AlkEthOH.csv │ ├── AlkEthOH.log │ ├── AlkEthOH.pdf │ ├── Hydrogen.csv │ ├── Hydrogen.log │ ├── Hydrogen.pdf │ ├── README.md │ ├── Simple-Decorators.csv │ ├── Simple-Decorators.log │ └── Simple-Decorators.pdf └── smirky │ ├── README.md │ ├── atom_AND_decorators.smarts │ ├── atom_OR_bases.smarts │ ├── atom_OR_decorators.smarts │ ├── atom_odds_forTorsions.smarts │ ├── bond_AND_decorators.smarts │ ├── bond_OR_bases.smarts │ ├── bond_odds_forTorsions.smarts │ ├── initial_Torsions.smarts │ ├── output.csv │ ├── output.log │ ├── output.pdf │ ├── output_results.smarts │ └── substitutions.smarts ├── oe_license.txt.enc ├── setup.py ├── smarty ├── __init__.py ├── atomtyper.py ├── cli_smarty.py ├── cli_smirky.py ├── data │ ├── README.md │ ├── __init__.py │ ├── atomtypes │ │ ├── README.md │ │ ├── basetypes.smarts │ │ ├── decorators-simple.smarts │ │ ├── decorators.smarts │ │ ├── initial_AlkEthOH.smarts │ │ ├── initialtypes.smarts │ │ ├── new-decorators.smarts │ │ └── replacements.smarts │ └── odds_files │ │ ├── atom_OR_bases.smarts │ │ ├── atom_decorators.smarts │ │ ├── atom_index_odds.smarts │ │ ├── bond_AND_decorators.smarts │ │ ├── bond_OR_bases.smarts │ │ ├── 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