MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
ParmEd.egg-info/PKG-INFO
ParmEd.egg-info/SOURCES.txt
ParmEd.egg-info/dependency_links.txt
ParmEd.egg-info/entry_points.txt
ParmEd.egg-info/top_level.txt
examples/amber/ala2_solv.parm7
examples/amber/ala2_solv.rst7
examples/amber/ala5_gas.parm7
examples/amber/ala5_gas.rst7
examples/amber/simulate_amber_gb.py
examples/amber/simulate_amber_pme.py
examples/charmm/ala2_charmmgui.crd
examples/charmm/ala2_charmmgui.psf
examples/charmm/ala5_autopsf.pdb
examples/charmm/ala5_autopsf.psf
examples/charmm/simulate_charmm_gb.py
examples/charmm/simulate_charmm_gui.py
examples/charmm/toppar/par_all36_prot.prm
examples/charmm/toppar/toppar_water_ions.str
examples/gromacs/dhfr_gas.gro
examples/gromacs/dhfr_gas.top
examples/gromacs/dhfr_pme.gro
examples/gromacs/dhfr_pme.top
examples/gromacs/simulate_gromacs_gb.py
examples/gromacs/simulate_gromacs_pme.py
examples/rosetta/simulate_ala12_mutant.py
parmed/__init__.py
parmed/_version.py
parmed/constants.py
parmed/exceptions.py
parmed/geometry.py
parmed/parameters.py
parmed/periodic_table.py
parmed/residue.py
parmed/scripts.py
parmed/structure.py
parmed/symmetry.py
parmed/topologyobjects.py
parmed/vec3.py
parmed/amber/__init__.py
parmed/amber/_amberparm.py
parmed/amber/_chamberparm.py
parmed/amber/_tinkerparm.py
parmed/amber/amberformat.py
parmed/amber/asciicrd.py
parmed/amber/mask.py
parmed/amber/netcdffiles.py
parmed/amber/offlib.py
parmed/amber/parameters.py
parmed/amber/readparm.py
parmed/amber/titratable_residues.py
parmed/amber/mdin/__init__.py
parmed/amber/mdin/cntrl.py
parmed/amber/mdin/ewald.py
parmed/amber/mdin/mdin.py
parmed/amber/mdin/pb.py
parmed/amber/mdin/qmmm.py
parmed/charmm/__init__.py
parmed/charmm/_charmmfile.py
parmed/charmm/charmmcrds.py
parmed/charmm/parameters.py
parmed/charmm/psf.py
parmed/formats/__init__.py
parmed/formats/mol2.py
parmed/formats/pdb.py
parmed/formats/pqr.py
parmed/formats/psf.py
parmed/formats/registry.py
parmed/formats/sdf.py
parmed/formats/pdbx/PdbxContainers.py
parmed/formats/pdbx/PdbxReader.py
parmed/formats/pdbx/PdbxWriter.py
parmed/formats/pdbx/__init__.py
parmed/gromacs/__init__.py
parmed/gromacs/_cpp.py
parmed/gromacs/_gromacsfile.py
parmed/gromacs/gromacsgro.py
parmed/gromacs/gromacstop.py
parmed/modeller/__init__.py
parmed/modeller/residue.py
parmed/modeller/standardtemplates.py
parmed/modeller/data/standard_residues.lib
parmed/namd/__init__.py
parmed/namd/namdbinfiles.py
parmed/openmm/__init__.py
parmed/openmm/parameters.py
parmed/openmm/reporters.py
parmed/openmm/topsystem.py
parmed/openmm/utils.py
parmed/openmm/xmlfile.py
parmed/rdkit/__init__.py
parmed/rdkit/rdkit.py
parmed/rosetta/__init__.py
parmed/rosetta/pose.py
parmed/tinker/__init__.py
parmed/tinker/parameterfile.py
parmed/tinker/system.py
parmed/tinker/tinkerfiles.py
parmed/tinker/topologyobjects.py
parmed/tools/__init__.py
parmed/tools/actions.py
parmed/tools/add1264.py
parmed/tools/addljtype.py
parmed/tools/argumentlist.py
parmed/tools/changeradii.py
parmed/tools/checkvalidity.py
parmed/tools/coarsegrain.py
parmed/tools/exceptions.py
parmed/tools/logos.py
parmed/tools/parmed_cmd.py
parmed/tools/parmlist.py
parmed/tools/gui/__init__.py
parmed/tools/gui/_guiactions.py
parmed/tools/gui/_guiwidgets.py
parmed/tools/gui/guiactions.py
parmed/tools/gui/guifiletools.py
parmed/tools/gui/guitools.py
parmed/tools/simulations/__init__.py
parmed/tools/simulations/openmm.py
parmed/tools/simulations/sanderapi.py
parmed/unit/__init__.py
parmed/unit/basedimension.py
parmed/unit/baseunit.py
parmed/unit/constants.py
parmed/unit/mymatrix.py
parmed/unit/prefix.py
parmed/unit/quantity.py
parmed/unit/standard_dimensions.py
parmed/unit/unit.py
parmed/unit/unit_definitions.py
parmed/unit/unit_math.py
parmed/unit/unit_operators.py
parmed/utils/__init__.py
parmed/utils/decorators.py
parmed/utils/io.py
parmed/utils/netcdf.py
parmed/utils/pairlist.py
parmed/utils/pandautils.py
parmed/utils/six.py
parmed/utils/timer.py
parmed/utils/fortranformat/FortranRecordReader.py
parmed/utils/fortranformat/FortranRecordWriter.py
parmed/utils/fortranformat/__init__.py
parmed/utils/fortranformat/_edit_descriptors.py
parmed/utils/fortranformat/_exceptions.py
parmed/utils/fortranformat/_input.py
parmed/utils/fortranformat/_lexer.py
parmed/utils/fortranformat/_misc.py
parmed/utils/fortranformat/_output.py
parmed/utils/fortranformat/_parser.py
parmed/utils/fortranformat/check_version.txt
parmed/utils/fortranformat/config.py
src/CompatibilityMacros.h
src/_rdparm.cpp
src/main.cpp
src/readparm.cpp
src/readparm.h
test/test_format_conversions.py
test/test_openmm_amber.py
test/test_openmm_amber_forces.py
test/test_openmm_charmm.py
test/test_openmm_gromacs.py
test/test_openmm_reporters.py
test/test_parmed_amber.py
test/test_parmed_charmm.py
test/test_parmed_cif.py
test/test_parmed_formats.py
test/test_parmed_genopen.py
test/test_parmed_geometry.py
test/test_parmed_gromacs.py
test/test_parmed_gromacs_cpp.py
test/test_parmed_misc.py
test/test_parmed_modeller.py
test/test_parmed_namd.py
test/test_parmed_netcdf.py
test/test_parmed_openmm.py
test/test_parmed_pandas.py
test/test_parmed_parameterset.py
test/test_parmed_rdkit.py
test/test_parmed_residue.py
test/test_parmed_rosetta.py
test/test_parmed_serialization.py
test/test_parmed_structure.py
test/test_parmed_structure_slicing.py
test/test_parmed_tinker.py
test/test_parmed_topologyobjects.py
test/test_parmed_unit.py
test/test_parmed_visualization.py
test/test_parmedtools_actions.py
test/test_parmedtools_parmlist.py