.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/data.rst
doc/source/file_formats.rst
doc/source/general_overview.rst
doc/source/graph_algorithms.rst
doc/source/index.rst
doc/source/martinize2_workflow.rst
doc/source/processors.rst
doc/source/technical_background.rst
doc/source/_static/.empty_for_git
doc/source/_templates/layout.html
doc/source/tutorials/index.rst
doc/source/tutorials/1_simple_protein_aa/index.rst
doc/source/tutorials/2_simple_protein_cg/index.rst
doc/source/tutorials/3_membrane_protein/index.rst
doc/source/tutorials/4_branched_polymer/index.rst
doc/source/tutorials/5_glycosylated_protein/index.rst
doc/source/tutorials/6_adding_residues_links/index.rst
doc/source/tutorials/7_adding_modifications/index.rst
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/file_writer.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
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vermouth/data/force_fields/elnedyn/modifications.ff
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vermouth/data/force_fields/elnedyn22/general.ff
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vermouth/data/force_fields/elnedyn22p/aminoacids.ff
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vermouth/data/force_fields/martini22/aminoacids.ff
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vermouth/data/force_fields/martini30dev/aminoacids.ff
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vermouth/data/force_fields/universal/aminoacids.rtp
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vermouth/data/mappings/ala.charmm36.map
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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/modifications.mapping
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/elnedyn/elnedyn22/modifications.mapping
vermouth/data/mappings/elnedyn/elnedyn22p/modifications.mapping
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
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vermouth/data/mappings/martini30/lys.charmm36.map
vermouth/data/mappings/martini30/met.charmm36.map
vermouth/data/mappings/martini30/modifications.mapping
vermouth/data/mappings/martini30/phe.charmm36.map
vermouth/data/mappings/martini30/pro.charmm36.map
vermouth/data/mappings/martini30/ser.charmm36.map
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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/itp_read.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/annotate_mut_mod.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/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_annotate_mut_mod.py
vermouth/tests/test_apply_rubber_band.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_file_writer.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_itp_files.py
vermouth/tests/test_links.py
vermouth/tests/test_logging.py
vermouth/tests/test_make_bonds.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_ptm_detection.py
vermouth/tests/test_redistributed_kdtree.py
vermouth/tests/test_repair_graph.py
vermouth/tests/test_section_parser.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/6E8W.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/integration_tests/tier-0/mini-protein1_betasheet/README
vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/aa.pdb
vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/cg.pdb
vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/chain_A.ssd
vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command
vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/molecule_0.itp
vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/screen.output
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vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/README
vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/aa.pdb
vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/cg.pdb
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vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/topol.top
vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/README
vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/aa.pdb
vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/cg.pdb
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vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/topol.top
vermouth/tests/data/integration_tests/tier-1/bpti/README
vermouth/tests/data/integration_tests/tier-1/bpti/aa.pdb
vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/cg.pdb
vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/chain_A.ssd
vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command
vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/molecule_0.itp
vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/screen.output
vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/topol.top
vermouth/tests/data/integration_tests/tier-1/lysozyme/README
vermouth/tests/data/integration_tests/tier-1/lysozyme/aa.pdb
vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/cg.pdb
vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/chain_A.ssd
vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command
vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/molecule_0.itp
vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/screen.output
vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/test.itp
vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/topol.top
vermouth/tests/data/integration_tests/tier-1/villin/README
vermouth/tests/data/integration_tests/tier-1/villin/aa.pdb
vermouth/tests/data/integration_tests/tier-1/villin/martinize2/cg.pdb
vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command
vermouth/tests/data/integration_tests/tier-1/villin/martinize2/molecule_0.itp
vermouth/tests/data/integration_tests/tier-1/villin/martinize2/screen.output
vermouth/tests/data/integration_tests/tier-1/villin/martinize2/topol.top
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/integration_tests/__init__.py
vermouth/tests/integration_tests/test_integration.py
vermouth/tests/pdb/test_read_pdb.py
vermouth/tests/pdb/test_write_pdb.py