.codecov.yml
.coveragerc
.pylintrc
.travis.yml
LICENSE
README.md
pyproject.toml
requirements-docs.txt
requirements-tests.txt
run_pylint.py
setup.cfg
setup.py
bin/embed_test.py
bin/martinize2
bin/run_martinize2.py
doc/Makefile
doc/source/conf.py
doc/source/index.rst
doc/source/_static/.empty_for_git
doc/source/_templates/layout.html
maintainers/head_template_data
maintainers/head_template_py
maintainers/releasing.md
maintainers/vim/syntax/README.md
maintainers/vim/syntax/ff.vim
vermouth/__init__.py
vermouth/edge_tuning.py
vermouth/ffinput.py
vermouth/forcefield.py
vermouth/geometry.py
vermouth/graph_utils.py
vermouth/ismags.py
vermouth/log_helpers.py
vermouth/map_input.py
vermouth/map_parser.py
vermouth/molecule.py
vermouth/parser_utils.py
vermouth/selectors.py
vermouth/system.py
vermouth/truncating_formatter.py
vermouth/utils.py
vermouth.egg-info/PKG-INFO
vermouth.egg-info/SOURCES.txt
vermouth.egg-info/dependency_links.txt
vermouth.egg-info/not-zip-safe
vermouth.egg-info/pbr.json
vermouth.egg-info/requires.txt
vermouth.egg-info/top_level.txt
vermouth/data/quotes.txt
vermouth/data/force_fields/elnedyn/aminoacids.ff
vermouth/data/force_fields/elnedyn/general.ff
vermouth/data/force_fields/elnedyn22/aminoacids.ff
vermouth/data/force_fields/elnedyn22/general.ff
vermouth/data/force_fields/elnedyn22p/aminoacids.ff
vermouth/data/force_fields/elnedyn22p/general.ff
vermouth/data/force_fields/martini22/aminoacids.ff
vermouth/data/force_fields/martini22/general.ff
vermouth/data/force_fields/martini22/modifications.ff
vermouth/data/force_fields/martini22p/aminoacids.ff
vermouth/data/force_fields/martini22p/general.ff
vermouth/data/force_fields/martini30b32/aminoacids.ff
vermouth/data/force_fields/martini30dev/aminoacids.ff
vermouth/data/force_fields/universal/aminoacids.rtp
vermouth/data/force_fields/universal/modifications.ff
vermouth/data/mappings/ala.charmm36.map
vermouth/data/mappings/arg.charmm36.map
vermouth/data/mappings/arg.charmm36.martini22p.map
vermouth/data/mappings/asn.charmm36.map
vermouth/data/mappings/asn.charmm36.martini22p.map
vermouth/data/mappings/asp.charmm36.map
vermouth/data/mappings/asp.charmm36.martini22p.map
vermouth/data/mappings/chol.charmm36.map
vermouth/data/mappings/cys.charmm36.map
vermouth/data/mappings/dmpc.charmm36.map
vermouth/data/mappings/dopc.charmm36.map
vermouth/data/mappings/dppc.charmm36.map
vermouth/data/mappings/dppg.charmm36.map
vermouth/data/mappings/gln.charmm36.map
vermouth/data/mappings/gln.charmm36.martini22p.map
vermouth/data/mappings/glu.charmm36.map
vermouth/data/mappings/glu.charmm36.martini22p.map
vermouth/data/mappings/gly.charmm36.map
vermouth/data/mappings/his.charmm36.map
vermouth/data/mappings/ile.charmm36.map
vermouth/data/mappings/leu.charmm36.map
vermouth/data/mappings/lys.charmm36.map
vermouth/data/mappings/lys.charmm36.martini22p.map
vermouth/data/mappings/met.charmm36.map
vermouth/data/mappings/modifications.mapping
vermouth/data/mappings/phe.charmm36.map
vermouth/data/mappings/popc.charmm36.map
vermouth/data/mappings/pope.charmm36.map
vermouth/data/mappings/popg.charmm36.map
vermouth/data/mappings/pops.charmm36.map
vermouth/data/mappings/pro.charmm36.map
vermouth/data/mappings/ser.charmm36.map
vermouth/data/mappings/ser.charmm36.martini22p.map
vermouth/data/mappings/thr.charmm36.map
vermouth/data/mappings/thr.charmm36.martini22p.map
vermouth/data/mappings/trp.charmm36.map
vermouth/data/mappings/tyr.charmm36.map
vermouth/data/mappings/val.charmm36.map
vermouth/data/mappings/elnedyn/ala.charmm36.map
vermouth/data/mappings/elnedyn/arg.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/arg.charmm36.map
vermouth/data/mappings/elnedyn/asn.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/asn.charmm36.map
vermouth/data/mappings/elnedyn/asp.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/asp.charmm36.map
vermouth/data/mappings/elnedyn/chol.charmm36.map
vermouth/data/mappings/elnedyn/cys.charmm36.map
vermouth/data/mappings/elnedyn/dmpc.charmm36.map
vermouth/data/mappings/elnedyn/dopc.charmm36.map
vermouth/data/mappings/elnedyn/dppc.charmm36.map
vermouth/data/mappings/elnedyn/dppg.charmm36.map
vermouth/data/mappings/elnedyn/gln.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/gln.charmm36.map
vermouth/data/mappings/elnedyn/glu.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/glu.charmm36.map
vermouth/data/mappings/elnedyn/gly.charmm36.map
vermouth/data/mappings/elnedyn/his.charmm36.map
vermouth/data/mappings/elnedyn/ile.charmm36.map
vermouth/data/mappings/elnedyn/leu.charmm36.map
vermouth/data/mappings/elnedyn/lys.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/lys.charmm36.map
vermouth/data/mappings/elnedyn/met.charmm36.map
vermouth/data/mappings/elnedyn/phe.charmm36.map
vermouth/data/mappings/elnedyn/popc.charmm36.map
vermouth/data/mappings/elnedyn/pope.charmm36.map
vermouth/data/mappings/elnedyn/popg.charmm36.map
vermouth/data/mappings/elnedyn/pops.charmm36.map
vermouth/data/mappings/elnedyn/pro.charmm36.map
vermouth/data/mappings/elnedyn/ser.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/ser.charmm36.map
vermouth/data/mappings/elnedyn/thr.charmm36.elnedyn22p.map
vermouth/data/mappings/elnedyn/thr.charmm36.map
vermouth/data/mappings/elnedyn/trp.charmm36.map
vermouth/data/mappings/elnedyn/tyr.charmm36.map
vermouth/data/mappings/elnedyn/val.charmm36.map
vermouth/data/mappings/martini30/ala.charmm36.map
vermouth/data/mappings/martini30/arg.charmm36.map
vermouth/data/mappings/martini30/asn.charmm36.map
vermouth/data/mappings/martini30/asp.charmm36.map
vermouth/data/mappings/martini30/cys.charmm36.map
vermouth/data/mappings/martini30/gln.charmm36.map
vermouth/data/mappings/martini30/glu.charmm36.map
vermouth/data/mappings/martini30/gly.charmm36.map
vermouth/data/mappings/martini30/his.charmm36.map
vermouth/data/mappings/martini30/ile.charmm36.map
vermouth/data/mappings/martini30/leu.charmm36.map
vermouth/data/mappings/martini30/lys.charmm36.map
vermouth/data/mappings/martini30/met.charmm36.map
vermouth/data/mappings/martini30/phe.charmm36.map
vermouth/data/mappings/martini30/pro.charmm36.map
vermouth/data/mappings/martini30/ser.charmm36.map
vermouth/data/mappings/martini30/thr.charmm36.map
vermouth/data/mappings/martini30/trp.charmm36.map
vermouth/data/mappings/martini30/tyr.charmm36.map
vermouth/data/mappings/martini30/val.charmm36.map
vermouth/dssp/__init__.py
vermouth/dssp/dssp.py
vermouth/gmx/__init__.py
vermouth/gmx/gro.py
vermouth/gmx/itp.py
vermouth/gmx/rtp.py
vermouth/graphing/grappa.py
vermouth/pdb/__init__.py
vermouth/pdb/pdb.py
vermouth/processors/__init__.py
vermouth/processors/add_molecule_edges.py
vermouth/processors/apply_posres.py
vermouth/processors/apply_rubber_band.py
vermouth/processors/attach_mass.py
vermouth/processors/average_beads.py
vermouth/processors/canonicalize_modifications.py
vermouth/processors/do_links.py
vermouth/processors/do_mapping.py
vermouth/processors/go_vs_includes.py
vermouth/processors/gro_reader.py
vermouth/processors/locate_charge_dummies.py
vermouth/processors/make_bonds.py
vermouth/processors/merge_all_molecules.py
vermouth/processors/merge_chains.py
vermouth/processors/name_moltype.py
vermouth/processors/neutral_termini.py
vermouth/processors/pdb_reader.py
vermouth/processors/processor.py
vermouth/processors/quote.py
vermouth/processors/rename_modified_residues.py
vermouth/processors/repair_graph.py
vermouth/processors/set_molecule_meta.py
vermouth/processors/sort_molecule_atoms.py
vermouth/processors/tune_cystein_bridges.py
vermouth/redistributed/LICENSE
vermouth/redistributed/__init__.py
vermouth/redistributed/kdtree.py
vermouth/tests/__init__.py
vermouth/tests/datafiles.py
vermouth/tests/helper_functions.py
vermouth/tests/molecule_strategies.py
vermouth/tests/test_add_molecule_edges.py
vermouth/tests/test_average_beads.py
vermouth/tests/test_do_mapping.py
vermouth/tests/test_dssp.py
vermouth/tests/test_edge_tuning.py
vermouth/tests/test_ff_files.py
vermouth/tests/test_ffinput.py
vermouth/tests/test_forcefield.py
vermouth/tests/test_geometry.py
vermouth/tests/test_go_vs_includes.py
vermouth/tests/test_graph_utils.py
vermouth/tests/test_grappa.py
vermouth/tests/test_ismags.py
vermouth/tests/test_links.py
vermouth/tests/test_logging.py
vermouth/tests/test_map_input.py
vermouth/tests/test_map_parser.py
vermouth/tests/test_mapping_integrative.py
vermouth/tests/test_molecule.py
vermouth/tests/test_name_moltype.py
vermouth/tests/test_native_forcefield.py
vermouth/tests/test_neutral_termini.py
vermouth/tests/test_ptm_detection.py
vermouth/tests/test_redistributed_kdtree.py
vermouth/tests/test_repair_graph.py
vermouth/tests/test_selectors.py
vermouth/tests/test_set_molecule_meta.py
vermouth/tests/test_sort_molecule_atoms.py
vermouth/tests/test_tune_cystein_bridges.py
vermouth/tests/test_utils.py
vermouth/tests/test_version.py
vermouth/tests/data/1bta.pdb
vermouth/tests/data/1bta_mutated.pdb
vermouth/tests/data/2QWO.pdb
vermouth/tests/data/2dn2.pdb
vermouth/tests/data/ala5.pdb
vermouth/tests/data/ala5_cg.pdb
vermouth/tests/data/dna-short.pdb
vermouth/tests/data/dssp_1bta.ssd
vermouth/tests/data/heme.pdb
vermouth/tests/data/force_fields/martini-test/aminoacids.ff
vermouth/tests/data/force_fields/pepplane/ala.ff
vermouth/tests/data/force_fields/pepplane/general.ff
vermouth/tests/data/force_fields/pepplane/modifications.ff
vermouth/tests/data/force_fields/universal-test/aminoacids.rtp
vermouth/tests/data/force_fields/universal-test/modifications.ff
vermouth/tests/data/mappings/universal-test/martini-test/ser.mapping
vermouth/tests/data/mappings/universal-test/pepplane/ala.mapping
vermouth/tests/data/mappings/universal-test/pepplane/modifications.mapping
vermouth/tests/gmx/test_gro.py
vermouth/tests/gmx/test_itp.py
vermouth/tests/pdb/test_write_pdb.py