├── .gitignore ├── .pre-commit-config.yaml ├── AUTHORS.md ├── CMakeLists.txt ├── INSTALL.md ├── README.md ├── dev └── conda_envs │ └── combiff.yml ├── doc ├── CombiFF.pdf ├── enu.pdf └── tex │ ├── CombiFF.tex │ ├── enu.tex │ ├── references.bib │ └── tbl.tex ├── license.txt ├── scr ├── clean.py ├── compile.py ├── compile_documentation.py ├── draw_isomers.py ├── helper_functions.py ├── run_enu.py └── run_tbl.py ├── src ├── CMakeLists.txt ├── cnv │ ├── CMakeLists.txt │ ├── lib │ │ ├── AdjacencyMatrixCnv.h │ │ ├── AdjacencyMatrixHandler.cpp │ │ ├── AdjacencyMatrixHandler.h │ │ ├── CMakeLists.txt │ │ ├── FamilyIdentifierHandler.cpp │ │ ├── FamilyIdentifierHandler.h │ │ ├── FormulaHandler.cpp │ │ ├── FormulaHandler.h │ │ ├── Handler.cpp │ │ ├── Handler.h │ │ ├── InputOutput.cpp │ │ ├── InputOutput.h │ │ ├── NameHandler.cpp │ │ ├── NameHandler.h │ │ ├── SmilesHandler.cpp │ │ └── SmilesHandler.h │ └── main.cpp ├── enu │ ├── CMakeLists.txt │ ├── lib │ │ ├── AdjacencyMatrixEnu.h │ │ ├── Alias.cpp │ │ ├── Alias.h │ │ ├── CMakeLists.txt │ │ ├── EnumRun.cpp │ │ ├── EnumRun.h │ │ ├── EnumSpecification.cpp │ │ ├── EnumSpecification.h │ │ ├── Enumerator.cpp │ │ ├── Enumerator.h │ │ ├── Family.cpp │ │ ├── Family.h │ │ ├── FamilySpecifications.cpp │ │ ├── FamilySpecifications.h │ │ ├── HydrogenDistribution.cpp │ │ ├── HydrogenDistribution.h │ │ ├── InputFiles.h │ │ ├── InputOutput.cpp │ │ ├── InputOutput.h │ │ ├── MaxFillAlg.cpp │ │ ├── MaxFillAlg.h │ │ ├── Pseudoatom.cpp │ │ ├── Pseudoatom.h │ │ ├── StereoGenerator.cpp │ │ ├── StereoGenerator.h │ │ ├── Substructure.cpp │ │ ├── Substructure.h │ │ ├── matchingEnu.cpp │ │ ├── matchingEnu.h │ │ ├── printInfo.cpp │ │ ├── printInfo.h │ │ ├── readLambdas.cpp │ │ └── readLambdas.h │ └── main.cpp ├── shared │ ├── Atom.cpp │ ├── Atom.h │ ├── CMakeLists.txt │ ├── ContainerOperators.h │ ├── ElementTypes.h │ ├── LambdaVector.h │ ├── Matrix.cpp │ ├── Matrix.h │ ├── Permutation.cpp │ ├── Permutation.h │ ├── Range.cpp │ ├── Range.h │ ├── SmilesGenerator.h │ ├── StringVector.h │ ├── Time.h │ ├── XmlParser.cpp │ ├── XmlParser.h │ ├── exceptions.cpp │ ├── exceptions.h │ ├── smilesToMatrix.cpp │ ├── smilesToMatrix.h │ └── version.h └── tbl │ ├── CMakeLists.txt │ ├── lib │ ├── AdjMatrixTBL.h │ ├── AtomTypes.cpp │ ├── AtomTypes.h │ ├── CMakeLists.txt │ ├── InputFiles.h │ ├── InputOutput.cpp │ ├── InputOutput.h │ ├── Link.cpp │ ├── Link.h │ ├── Linkage.h │ ├── MatrixTbl.h │ ├── MoleculeDecomposer.cpp │ ├── MoleculeDecomposer.h │ ├── TblAtom.cpp │ ├── TblAtom.h │ ├── TblFragment.cpp │ ├── TblFragment.h │ ├── TblRun.cpp │ ├── TblRun.h │ ├── TopologicalProperty.cpp │ ├── TopologicalProperty.h │ ├── moleculeMacros.cpp │ ├── moleculeMacros.h │ ├── mtb.cpp │ ├── mtb.h │ ├── replacement.cpp │ └── replacement.h │ └── main.cpp └── use ├── global_settings.py ├── input_files ├── README ├── aliases │ ├── README │ ├── aliases.dtd │ └── aliases.xml ├── atomtypes │ ├── README │ ├── atomtypes.dtd │ └── atomtypes.xml ├── family_definitions │ ├── README │ ├── family_definitions.dtd │ ├── family_definitions_01xx.xml │ ├── family_definitions_02xx.xml │ ├── family_definitions_03xx.xml │ ├── family_definitions_04xx.xml │ ├── family_definitions_05xx.xml │ ├── family_definitions_06xx.xml │ ├── family_definitions_07xx.xml │ ├── family_definitions_08xx.xml │ ├── family_definitions_09xx.xml │ ├── family_definitions_10xx.xml │ ├── family_definitions_11xx.xml │ ├── family_definitions_12xx.xml │ ├── family_definitions_13xx.xml │ ├── family_definitions_14xx.xml │ ├── family_definitions_intro.xml │ └── family_definitions_tests.xml ├── fragments │ ├── README │ ├── fragments.dtd │ ├── fragments.xml │ └── united_atom_fragments.xml ├── macro_replacements │ ├── replacements.dtd │ └── replacements.xml ├── pseudoatoms │ ├── README │ ├── pseudoatoms.dtd │ └── pseudoatoms.xml ├── smiles_list └── substructures │ ├── README │ ├── substructures.dtd │ └── substructures.xml └── output_files ├── family_isomer_enumerations └── 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