.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/__init__.py
bin/polyply
polyply/__init__.py
polyply.egg-info/PKG-INFO
polyply.egg-info/SOURCES.txt
polyply.egg-info/dependency_links.txt
polyply.egg-info/not-zip-safe
polyply.egg-info/pbr.json
polyply.egg-info/requires.txt
polyply.egg-info/top_level.txt
polyply/data/__init__.py
polyply/data/gromos_2016H66_polymers/CH3.ff
polyply/data/gromos_2016H66_polymers/PEG.gromos.2016.itp
polyply/data/gromos_2016H66_polymers/PMMA.gromos.2016.itp
polyply/data/gromos_2016H66_polymers/links.ff
polyply/data/martini2_polymers/P3HT.martini.2.itp
polyply/data/martini2_polymers/PDADMA.martini.2.itp
polyply/data/martini2_polymers/PE.martini.2.itp
polyply/data/martini2_polymers/PEO.martini.2.itp
polyply/data/martini2_polymers/PP.martini.2.itp
polyply/data/martini2_polymers/PS.martini.2.itp
polyply/data/martini2_polymers/PSS.martini.2.itp
polyply/data/martini2_polymers/links.ff
polyply/data/martini3_beta_polymers/PEO.martini.3.itp
polyply/src/__init__.py
polyply/src/annotate_ligands.py
polyply/src/apply_links.py
polyply/src/apply_modifications.py
polyply/src/backmap.py
polyply/src/build_file_parser.py
polyply/src/build_system.py
polyply/src/gen_coords.py
polyply/src/gen_itp.py
polyply/src/gen_seq.py
polyply/src/generate_templates.py
polyply/src/graph_utils.py
polyply/src/linalg_functions.py
polyply/src/load_library.py
polyply/src/map_to_molecule.py
polyply/src/meta_molecule.py
polyply/src/minimizer.py
polyply/src/nonbond_engine.py
polyply/src/polyply_parser.py
polyply/src/processor.py
polyply/src/random_walk.py
polyply/src/top_parser.py
polyply/src/topology.py
polyply/src/virtual_site_builder.py
polyply/tests/.coverage
polyply/tests/__init__.py
polyply/tests/example_fixtures.py
polyply/tests/test_annotate_lingads.py
polyply/tests/test_apply_links.py
polyply/tests/test_backmap.py
polyply/tests/test_build_file_parser.py
polyply/tests/test_build_system.py
polyply/tests/test_gen_coords.py
polyply/tests/test_gen_seq.py
polyply/tests/test_generate_templates.py
polyply/tests/test_graph_utils.py
polyply/tests/test_itp_files.py
polyply/tests/test_itp_gen.py
polyply/tests/test_linalg.py
polyply/tests/test_load_library.py
polyply/tests/test_map_to_molecule.py
polyply/tests/test_meta_molecule.py
polyply/tests/test_nb_engine.py
polyply/tests/test_optimize_geometry.py
polyply/tests/test_polyply_input.py
polyply/tests/test_random_walk.py
polyply/tests/test_top_parser.py
polyply/tests/test_topology.py
polyply/tests/test_vs_builder.py
polyply/tests/test_data/ff/aminoacids.ff
polyply/tests/test_data/gen_itp/input/P3HT.martini.2.itp
polyply/tests/test_data/gen_itp/input/PEO.martini.3.itp
polyply/tests/test_data/gen_itp/input/PPI.ff
polyply/tests/test_data/gen_itp/input/PPI.json
polyply/tests/test_data/gen_itp/input/PS.json
polyply/tests/test_data/gen_itp/input/PS.martini.2.itp
polyply/tests/test_data/gen_itp/input/test.ff
polyply/tests/test_data/gen_itp/output/P3HT_out.itp
polyply/tests/test_data/gen_itp/output/PEO_out.itp
polyply/tests/test_data/gen_itp/output/PPI_out.itp
polyply/tests/test_data/gen_itp/output/PS_out.itp
polyply/tests/test_data/gen_itp/ref/G3.itp
polyply/tests/test_data/gen_itp/ref/P3HT_10.itp
polyply/tests/test_data/gen_itp/ref/PEO_10.itp
polyply/tests/test_data/gen_itp/ref/PS_10.itp
polyply/tests/test_data/gen_itp/ref/end.itp
polyply/tests/test_data/gen_itp/ref/test_rev.itp
polyply/tests/test_data/gen_seq/input/molecule_0.itp
polyply/tests/test_data/gen_seq/output/PEO_PS.json
polyply/tests/test_data/gen_seq/output/PPI.json
polyply/tests/test_data/gen_seq/output/lysoPEG.json
polyply/tests/test_data/gen_seq/output/lyso_PEG.json
polyply/tests/test_data/gen_seq/output/rand_PEG_PPO.json
polyply/tests/test_data/gen_seq/ref/PEO_PS_ref.json
polyply/tests/test_data/gen_seq/ref/PPI_ref.json
polyply/tests/test_data/gen_seq/ref/lyso_PEG.json
polyply/tests/test_data/itp/PEO.itp
polyply/tests/test_data/json/double_branch.json
polyply/tests/test_data/json/hyperbranched.json
polyply/tests/test_data/json/linear.json
polyply/tests/test_data/json/linear_rev.json
polyply/tests/test_data/json/single_branch.json
polyply/tests/test_data/polyply/P3HT.martini.2.itp
polyply/tests/test_data/polyply/PDADMA.martini.2.itp
polyply/tests/test_data/polyply/PE.martini.2.itp
polyply/tests/test_data/polyply/PEL_lipid.martini.2.itp
polyply/tests/test_data/polyply/PEO.martini.2.itp
polyply/tests/test_data/polyply/PEO.martini.3.itp
polyply/tests/test_data/polyply/PP.martini.2.itp
polyply/tests/test_data/polyply/PS.martini.2.itp
polyply/tests/test_data/polyply/PSS.martini.2.itp
polyply/tests/test_data/struc_build/PEO.itp
polyply/tests/test_data/struc_build/martini_PEO_PS_CNP.itp
polyply/tests/test_data/struc_build/system.top
polyply/tests/test_data/topology_test/W.itp
polyply/tests/test_data/topology_test/ffnonbonded.itp
polyply/tests/test_data/topology_test/molecule_0.itp
polyply/tests/test_data/topology_test/pdb.top
polyply/tests/test_data/topology_test/system.top
polyply/tests/test_data/topology_test/test.gro
polyply/tests/test_data/topology_test/test.itp
polyply/tests/test_data/topology_test/test.pdb