├── .coveragerc ├── .github └── workflows │ ├── publish.yml │ └── python-package.yml ├── .gitignore ├── .readthedocs.yml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── arguments.md ├── conf.py ├── file-formats.md ├── index.md ├── make.bat ├── mapping-only.md ├── tutorial.md └── tutorial_files │ ├── Makefile │ ├── atenolol.bnd │ ├── atenolol.map │ ├── average_columns.py │ ├── em.mdp │ ├── md.mdp │ ├── npt.mdp │ ├── ref-for-rgyr.tpr │ ├── ref.gro │ ├── ref.xtc │ └── template.top ├── poetry.lock ├── pycgtool ├── __init__.py ├── __main__.py ├── bondset.py ├── data │ ├── martini_v2.2.itp │ ├── w.itp │ ├── water.gro │ └── watermodels.dat ├── forcefield.py ├── frame.py ├── functionalforms.py ├── mapping.py ├── parsers │ ├── __init__.py │ ├── cfg.py │ └── itp.py └── util.py ├── pyproject.toml ├── sanitize.py ├── tests ├── __init__.py ├── data │ ├── ALLA_angle.dat │ ├── ALLA_angle_one.dat │ ├── ALLA_dihedral.dat │ ├── ALLA_dihedral_one.dat │ ├── ALLA_length.dat │ ├── ALLA_length_one.dat │ ├── dppc.gro │ ├── dppc.map │ ├── duplicate_atoms.bnd │ ├── ffout.ff │ │ ├── atomtypes.atp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── martini_v2.2.itp │ │ ├── out.r2b │ │ ├── out.rtp │ │ ├── w.itp │ │ └── watermodels.dat │ ├── martini.map │ ├── martini3 │ │ ├── four.gro │ │ ├── four.itp │ │ ├── four.map │ │ ├── naphthalene.bnd │ │ ├── naphthalene.gro │ │ ├── naphthalene.map │ │ └── naphthalene_out.itp │ ├── martini_aminoacids.map │ ├── martini_lipids.map │ ├── membrane │ │ ├── AT_AA_POPE.itp │ │ ├── AT_AA_POPG.itp │ │ ├── PII_charmm36.itp │ │ ├── TOCL2.itp │ │ ├── membrane.gro │ │ ├── membrane.map │ │ ├── membrane.top │ │ └── twice.itp │ ├── nosections.cfg │ ├── pbcpolyethene.gro │ ├── pbcwater.gro │ ├── polyethene.bnd │ ├── polyethene.gro │ ├── polyethene.map │ ├── sugar-cg.gro │ ├── sugar.bnd │ ├── sugar.gro │ ├── sugar.map │ ├── sugar.xtc │ ├── sugar_only.map │ ├── sugar_out.gro │ ├── sugar_out.itp │ ├── sugar_out.xtc │ ├── triangle.bnd │ ├── 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