.codecov.yml
.coveragerc
.pylintrc
.travis.yml
AUTHORS
ChangeLog
LIBRARY.md
LICENSE
README.md
pyproject.toml
requirements-docs.txt
requirements-tests.txt
run_pylint.py
setup.cfg
setup.py
.github/CONTRIBUTING.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/parameter-submission.md
.github/workflows/pypi_deploy.yml
.github/workflows/python-app.yml
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/2016H66/chiral_links.ff
polyply/data/2016H66/citation.bib
polyply/data/2016H66/polyether_blocks.ff
polyply/data/2016H66/polyether_links.ff
polyply/data/2016H66/polyether_polyvinyl_links.ff
polyply/data/2016H66/polyvinyl_blocks.ff
polyply/data/2016H66/polyvinyl_links.ff
polyply/data/2016H66/terminal_blocks.ff
polyply/data/gromos53A6/Hter.ff
polyply/data/gromos53A6/P3HT.gromos.53A6.ff
polyply/data/gromos53A6/citations.bib
polyply/data/gromos53A6/links.ff
polyply/data/martini2/DNA_M2.ff
polyply/data/martini2/P3HT.martini.2.itp
polyply/data/martini2/PDADMA.martini.2.itp
polyply/data/martini2/PE.martini.2.itp
polyply/data/martini2/PEO.martini.2.itp
polyply/data/martini2/PP.martini.2.itp
polyply/data/martini2/PS.martini.2.itp
polyply/data/martini2/PSS.martini.2.itp
polyply/data/martini2/citations.bib
polyply/data/martini2/links.ff
polyply/data/martini3/P3HT.martini3.ff
polyply/data/martini3/PDMS.martini3.ff
polyply/data/martini3/PE.martini3.ff
polyply/data/martini3/PEL_link.ff
polyply/data/martini3/PEO.martini3.ff
polyply/data/martini3/PMA.martini3.ff
polyply/data/martini3/PMMA.martini3.ff
polyply/data/martini3/PPE.martini3.ff
polyply/data/martini3/PS.martini3.ff
polyply/data/martini3/PSS.martini3.ff
polyply/data/martini3/PS_PEO_link.ff
polyply/data/martini3/PTMA.martini3.ff
polyply/data/martini3/PVA.martini3.ff
polyply/data/martini3/aminoacids.ff
polyply/data/martini3/cellulose.martini3.ff
polyply/data/martini3/citations.bib
polyply/data/martini3/dextran.martini3.ff
polyply/data/martini3_beta/PEO.martini.3.itp
polyply/data/martini3_beta/citations.bib
polyply/data/oplsaaLigParGen/OHter.ff
polyply/data/oplsaaLigParGen/PEO.oplsaa.LigParGen.ff
polyply/data/oplsaaLigParGen/citations.bib
polyply/data/oplsaaLigParGen/links.ff
polyply/data/parmbsc1/citations.bib
polyply/data/parmbsc1/dna_final.ff
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/check_residue_equivalence.py
polyply/src/ff_parser_sub.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/logging.py
polyply/src/map_to_molecule.py
polyply/src/meta_molecule.py
polyply/src/minimizer.py
polyply/src/nonbond_engine.py
polyply/src/persistence.py
polyply/src/polyply_parser.py
polyply/src/processor.py
polyply/src/random_walk.py
polyply/src/restraints.py
polyply/src/simple_seq_parsers.py
polyply/src/top_parser.py
polyply/src/topology.py
polyply/src/virtual_site_builder.py
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_ff_parser.py
polyply/tests/test_gen_coords.py
polyply/tests/test_gen_coords_logic.py
polyply/tests/test_gen_params.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_lib_files.py
polyply/tests/test_linalg.py
polyply/tests/test_load_library.py
polyply/tests/test_logging.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_persistence.py
polyply/tests/test_polyply_input.py
polyply/tests/test_random_walk.py
polyply/tests/test_residue_check.py
polyply/tests/test_restraints.py
polyply/tests/test_simple_seq_parsers.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_params/input/P3HT.martini.2.itp
polyply/tests/test_data/gen_params/input/PEO.martini.3.itp
polyply/tests/test_data/gen_params/input/PPI.ff
polyply/tests/test_data/gen_params/input/PPI.json
polyply/tests/test_data/gen_params/input/PS.json
polyply/tests/test_data/gen_params/input/PS.martini.2.itp
polyply/tests/test_data/gen_params/input/removal.ff
polyply/tests/test_data/gen_params/input/test.ff
polyply/tests/test_data/gen_params/input/test_edge_attr.ff
polyply/tests/test_data/gen_params/input/test_edge_attr.json
polyply/tests/test_data/gen_params/logging/ERROR_block.ff
polyply/tests/test_data/gen_params/logging/ERROR_link.ff
polyply/tests/test_data/gen_params/logging/INFO_block.ff
polyply/tests/test_data/gen_params/logging/INFO_link.ff
polyply/tests/test_data/gen_params/logging/WARNING_block.ff
polyply/tests/test_data/gen_params/logging/WARNING_link.ff
polyply/tests/test_data/gen_params/output/P3HT_out.itp
polyply/tests/test_data/gen_params/output/PEO_out.itp
polyply/tests/test_data/gen_params/output/PPI_out.itp
polyply/tests/test_data/gen_params/output/PS_out.itp
polyply/tests/test_data/gen_params/output/removal.itp
polyply/tests/test_data/gen_params/output/test_edge_attr_out.itp
polyply/tests/test_data/gen_params/output/test_out.itp
polyply/tests/test_data/gen_params/ref/G3.itp
polyply/tests/test_data/gen_params/ref/P3HT_10.itp
polyply/tests/test_data/gen_params/ref/PEO_10.itp
polyply/tests/test_data/gen_params/ref/PS_10.itp
polyply/tests/test_data/gen_params/ref/end.itp
polyply/tests/test_data/gen_params/ref/removal.itp
polyply/tests/test_data/gen_params/ref/test_edge_attr_ref.itp
polyply/tests/test_data/gen_params/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/fail.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/library_tests/2016H66/C12E4/polyply/C12E4.itp
polyply/tests/test_data/library_tests/2016H66/C12E4/polyply/command
polyply/tests/test_data/library_tests/2016H66/PE/PE.json
polyply/tests/test_data/library_tests/2016H66/PE/polyply/PE.itp
polyply/tests/test_data/library_tests/2016H66/PE/polyply/command
polyply/tests/test_data/library_tests/2016H66/PMA/PMA.json
polyply/tests/test_data/library_tests/2016H66/PMA/polyply/PMA.itp
polyply/tests/test_data/library_tests/2016H66/PMA/polyply/command
polyply/tests/test_data/library_tests/2016H66/PP/PP.json
polyply/tests/test_data/library_tests/2016H66/PP/polyply/PP.itp
polyply/tests/test_data/library_tests/2016H66/PP/polyply/command
polyply/tests/test_data/library_tests/2016H66/PS/PS.json
polyply/tests/test_data/library_tests/2016H66/PS/polyply/PS.itp
polyply/tests/test_data/library_tests/2016H66/PS/polyply/command
polyply/tests/test_data/library_tests/2016H66/PVA/PVA.json
polyply/tests/test_data/library_tests/2016H66/PVA/polyply/PVA.itp
polyply/tests/test_data/library_tests/2016H66/PVA/polyply/command
polyply/tests/test_data/library_tests/gromos53A6/P3HT/polyply/P3HT.itp
polyply/tests/test_data/library_tests/gromos53A6/P3HT/polyply/command
polyply/tests/test_data/library_tests/martini2/PEL/DPPC.itp
polyply/tests/test_data/library_tests/martini2/PEL/polyply/PEL.itp
polyply/tests/test_data/library_tests/martini2/PEL/polyply/command
polyply/tests/test_data/library_tests/martini2/PEO/polyply/PEO.itp
polyply/tests/test_data/library_tests/martini2/PEO/polyply/command
polyply/tests/test_data/library_tests/martini2/PEO_PE/PEO_PE.json
polyply/tests/test_data/library_tests/martini2/PEO_PE/polyply/PEO_PE.itp
polyply/tests/test_data/library_tests/martini2/PEO_PE/polyply/command
polyply/tests/test_data/library_tests/martini2/PS/polyply/PS.itp
polyply/tests/test_data/library_tests/martini2/PS/polyply/command
polyply/tests/test_data/library_tests/martini2/ssDNA/ssDNA.itp
polyply/tests/test_data/library_tests/martini2/ssDNA/ssDNA.json
polyply/tests/test_data/library_tests/martini2/ssDNA/polyply/command
polyply/tests/test_data/library_tests/martini2/ssDNA/polyply/ssDNA.itp
polyply/tests/test_data/library_tests/martini3/CEL/polyply/CEL.itp
polyply/tests/test_data/library_tests/martini3/CEL/polyply/command
polyply/tests/test_data/library_tests/martini3/DEX/polyply/DEX.itp
polyply/tests/test_data/library_tests/martini3/DEX/polyply/command
polyply/tests/test_data/library_tests/martini3/P3HT/polyply/P3HT.itp
polyply/tests/test_data/library_tests/martini3/P3HT/polyply/command
polyply/tests/test_data/library_tests/martini3/PDMS/polyply/PDMS.itp
polyply/tests/test_data/library_tests/martini3/PDMS/polyply/command
polyply/tests/test_data/library_tests/martini3/PE/polyply/PE.itp
polyply/tests/test_data/library_tests/martini3/PE/polyply/command
polyply/tests/test_data/library_tests/martini3/PEO/polyply/PEO.itp
polyply/tests/test_data/library_tests/martini3/PEO/polyply/command
polyply/tests/test_data/library_tests/martini3/PPE/polyply/PPE.itp
polyply/tests/test_data/library_tests/martini3/PPE/polyply/command
polyply/tests/test_data/library_tests/martini3/PROT/init.itp
polyply/tests/test_data/library_tests/martini3/PROT/lysozyme_seq.json
polyply/tests/test_data/library_tests/martini3/PROT/polyply/PROT.itp
polyply/tests/test_data/library_tests/martini3/PROT/polyply/command
polyply/tests/test_data/library_tests/martini3/PS/polyply/PS.itp
polyply/tests/test_data/library_tests/martini3/PS/polyply/command
polyply/tests/test_data/library_tests/martini3/PTMA/polyply/PTMA.itp
polyply/tests/test_data/library_tests/martini3/PTMA/polyply/command
polyply/tests/test_data/library_tests/oplsaaLigParGen/PEO/polyply/PEO.itp
polyply/tests/test_data/library_tests/oplsaaLigParGen/PEO/polyply/command
polyply/tests/test_data/library_tests/parmbsc1/DNA/DNA.itp
polyply/tests/test_data/library_tests/parmbsc1/DNA/ref.json
polyply/tests/test_data/library_tests/parmbsc1/DNA/polyply/DNA.itp
polyply/tests/test_data/library_tests/parmbsc1/DNA/polyply/command
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/simple_seq_files/test.fasta
polyply/tests/test_data/simple_seq_files/test.ig
polyply/tests/test_data/simple_seq_files/test.txt
polyply/tests/test_data/simple_seq_files/test_RNA.fasta
polyply/tests/test_data/simple_seq_files/test_RNA.ig
polyply/tests/test_data/simple_seq_files/test_circle.ig
polyply/tests/test_data/simple_seq_files/test_fail.ig
polyply/tests/test_data/simple_seq_files/test_protein.fasta
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/cog.gro
polyply/tests/test_data/topology_test/cog_missing.gro
polyply/tests/test_data/topology_test/complete.gro
polyply/tests/test_data/topology_test/fail.gro
polyply/tests/test_data/topology_test/ffnonbonded.itp
polyply/tests/test_data/topology_test/meta.gro
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