.pylintrc
CODE_OF_CONDUCT.md
CONTRIBUTING.md
COPYING
LICENSE.md
MANIFEST.in
README.md
pdb2pka
precommit.sh
pyproject.toml
pytest.ini
setup.cfg
setup.py
docs/Makefile
docs/make.bat
docs/source/conf.py
docs/source/extending.rst
docs/source/getting.rst
docs/source/help.rst
docs/source/index.rst
docs/source/releases.rst
docs/source/supporting.rst
docs/source/api/aa.rst
docs/source/api/biomolecule.rst
docs/source/api/cells.rst
docs/source/api/cif.rst
docs/source/api/config.rst
docs/source/api/debump.rst
docs/source/api/definitions.rst
docs/source/api/forcefield.rst
docs/source/api/hydrogens.rst
docs/source/api/index.rst
docs/source/api/inputgen.rst
docs/source/api/io.rst
docs/source/api/ligand.rst
docs/source/api/main.rst
docs/source/api/na.rst
docs/source/api/pdb.rst
docs/source/api/psize.rst
docs/source/api/quatfit.rst
docs/source/api/residue.rst
docs/source/api/run.rst
docs/source/api/structures.rst
docs/source/api/topology.rst
docs/source/api/utilities.rst
docs/source/formats/dat.rst
docs/source/formats/index.rst
docs/source/formats/mol2.rst
docs/source/formats/pdb.rst
docs/source/formats/pqr.rst
docs/source/formats/xml-names.rst
docs/source/using/algorithms.rst
docs/source/using/examples.rst
docs/source/using/index.rst
docs/source/using/other-software.rst
examples/1a1p/1a1p.pdb
examples/1a1p/README
examples/graphcut/run-graphcut.sh
examples/ligands/LIG_1ABF.mol2
examples/ligands/LIG_1HPV.mol2
examples/ligands/LIG_1HPX.mol2
examples/ligands/LIG_1QBS.mol2
examples/ligands/LIG_1XL5.mol2
examples/ligands/README
pdb2pqr/__init__.py
pdb2pqr/__main__.py
pdb2pqr/_version.py
pdb2pqr/aa.py
pdb2pqr/biomolecule.py
pdb2pqr/cells.py
pdb2pqr/cif.py
pdb2pqr/config.py
pdb2pqr/debump.py
pdb2pqr/definitions.py
pdb2pqr/forcefield.py
pdb2pqr/inputgen.py
pdb2pqr/io.py
pdb2pqr/main.py
pdb2pqr/na.py
pdb2pqr/pdb.py
pdb2pqr/psize.py
pdb2pqr/quatfit.py
pdb2pqr/residue.py
pdb2pqr/run.py
pdb2pqr/structures.py
pdb2pqr/topology.py
pdb2pqr/utilities.py
pdb2pqr.egg-info/PKG-INFO
pdb2pqr.egg-info/SOURCES.txt
pdb2pqr.egg-info/dependency_links.txt
pdb2pqr.egg-info/entry_points.txt
pdb2pqr.egg-info/requires.txt
pdb2pqr.egg-info/top_level.txt
pdb2pqr/dat/AA.xml
pdb2pqr/dat/AMBER.DAT
pdb2pqr/dat/AMBER.names
pdb2pqr/dat/CHARMM.DAT
pdb2pqr/dat/CHARMM.names
pdb2pqr/dat/HYDROGENS.xml
pdb2pqr/dat/NA.xml
pdb2pqr/dat/PARSE.DAT
pdb2pqr/dat/PARSE.names
pdb2pqr/dat/PATCHES.xml
pdb2pqr/dat/PEOEPB.DAT
pdb2pqr/dat/PEOEPB.names
pdb2pqr/dat/SWANSON.DAT
pdb2pqr/dat/SWANSON.names
pdb2pqr/dat/TOPOLOGY.xml
pdb2pqr/dat/TYL06.DAT
pdb2pqr/dat/TYL06.names
pdb2pqr/hydrogens/__init__.py
pdb2pqr/hydrogens/optimize.py
pdb2pqr/hydrogens/structures.py
pdb2pqr/ligand/__init__.py
pdb2pqr/ligand/mol2.py
pdb2pqr/ligand/peoe.py
pdb2pqr/ligand/topology.py
tests/README.md
tests/common.py
tests/core_test.py
tests/io_test.py
tests/ligand_results.py
tests/ligand_test.py
tests/logging_test.py
tests/propka_test.py
tests/regression_test.py
tests/test_version.py
tests/data/1A1P.pdb
tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr
tests/data/1AFS.pdb
tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr
tests/data/1AFS_chain_whitespace_ff=AMBER.pqr
tests/data/1AFS_clean_whitespace.pqr
tests/data/1AFS_drop-water_ff=AMBER.pqr
tests/data/1AFS_ff=AMBER.pqr
tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr
tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr
tests/data/1AFS_userff_usernames_whitespace.pqr
tests/data/1AFS_whitespace_ff=AMBER.pqr
tests/data/1AFS_whitespace_ff=CHARMM.pqr
tests/data/1AFS_whitespace_ff=PARSE.pqr
tests/data/1AFS_whitespace_ff=PEOEPB.pqr
tests/data/1AFS_whitespace_ff=SWANSON.pqr
tests/data/1AFS_whitespace_ff=TYL06.pqr
tests/data/1FAS.cif
tests/data/1HPX-ligand.mol2
tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr
tests/data/1K1I.pdb
tests/data/1QBS-ligand.mol2
tests/data/1QBS.pdb
tests/data/1US0-ligand.mol2
tests/data/1US0.pdb
tests/data/3U7T.cif
tests/data/5vav_cyclic_peptide.pdb
tests/data/5vav_cyclic_peptide_out.pqr
tests/data/acetate.mol2
tests/data/acetonitrile.mol2
tests/data/acetylcholine.mol2
tests/data/adp.mol2
tests/data/anthracene.mol2
tests/data/crown-ether.mol2
tests/data/cterm_hid.pdb
tests/data/cterm_hid_out.pqr
tests/data/custom-ff.dat
tests/data/custom.names
tests/data/cyclohexane.mol2
tests/data/dummy.qcd
tests/data/dx2cube.cube
tests/data/dx2cube.dx
tests/data/dx2cube.pqr
tests/data/ethanol.mol2
tests/data/fatty-acid.mol2
tests/data/glycerol.mol2
tests/data/naphthalene.mol2
tests/data/pyrrole.mol2
tests/data/tetramethylammonium.mol2