.codecov.yml
.docstr.yaml
.gitignore
.mailmap
.pylintrc
.style.yapf
CHANGELOG.md
CODE_OF_CONDUCT.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
pytest.ini
pytest.sh
scratch_install.log
setup.cfg
setup.py
.githooks/commit-msg
.github/pull_request_template.md
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/scripts/parse_pylint.py
.github/workflows/ci.yml
.github/workflows/docs.yml
.github/workflows/pr-title.yml
.github/workflows/pylint.yml
.github/workflows/release.yml
PQAnalysis/__init__.py
PQAnalysis/_lazy_import.py
PQAnalysis/_version.py
PQAnalysis/config.py
PQAnalysis/exceptions.py
PQAnalysis/formats.py
PQAnalysis/type_checking.py
PQAnalysis/types.py
PQAnalysis/version.py
PQAnalysis.egg-info/PKG-INFO
PQAnalysis.egg-info/SOURCES.txt
PQAnalysis.egg-info/dependency_links.txt
PQAnalysis.egg-info/entry_points.txt
PQAnalysis.egg-info/requires.txt
PQAnalysis.egg-info/scm_file_list.json
PQAnalysis.egg-info/scm_version.json
PQAnalysis.egg-info/top_level.txt
PQAnalysis/analysis/__init__.py
PQAnalysis/analysis/_output_header.py
PQAnalysis/analysis/_output_schemas.py
PQAnalysis/analysis/_xvg.py
PQAnalysis/analysis/output.py
PQAnalysis/analysis/momentum/__init__.py
PQAnalysis/analysis/momentum/_momentum_kernel.c
PQAnalysis/analysis/momentum/_momentum_kernel.pyx
PQAnalysis/analysis/momentum/_momentum_kernel_py.py
PQAnalysis/analysis/momentum/api.py
PQAnalysis/analysis/momentum/exceptions.py
PQAnalysis/analysis/momentum/momentum.py
PQAnalysis/analysis/momentum/momentum_output_file_writer.py
PQAnalysis/analysis/msd/__init__.py
PQAnalysis/analysis/msd/_msd_kernel.c
PQAnalysis/analysis/msd/_msd_kernel.pyx
PQAnalysis/analysis/msd/_msd_kernel_py.py
PQAnalysis/analysis/msd/api.py
PQAnalysis/analysis/msd/exceptions.py
PQAnalysis/analysis/msd/msd.py
PQAnalysis/analysis/msd/msd_input_file_reader.py
PQAnalysis/analysis/msd/msd_output_file_writer.py
PQAnalysis/analysis/rdf/__init__.py
PQAnalysis/analysis/rdf/_rdf_kernel.c
PQAnalysis/analysis/rdf/_rdf_kernel.pyx
PQAnalysis/analysis/rdf/_rdf_kernel_py.py
PQAnalysis/analysis/rdf/api.py
PQAnalysis/analysis/rdf/exceptions.py
PQAnalysis/analysis/rdf/rdf.py
PQAnalysis/analysis/rdf/rdf_input_file_reader.py
PQAnalysis/analysis/rdf/rdf_output_file_writer.py
PQAnalysis/analysis/spectrum_broadening/__init__.py
PQAnalysis/analysis/spectrum_broadening/api.py
PQAnalysis/analysis/spectrum_broadening/exceptions.py
PQAnalysis/analysis/spectrum_broadening/spectrum_broadening.py
PQAnalysis/analysis/spectrum_broadening/spectrum_broadening_output_file_writer.py
PQAnalysis/analysis/vacf/__init__.py
PQAnalysis/analysis/vacf/_raw_charge_reader.py
PQAnalysis/analysis/vacf/_vacf_kernel.c
PQAnalysis/analysis/vacf/_vacf_kernel.pyx
PQAnalysis/analysis/vacf/_vacf_kernel_py.py
PQAnalysis/analysis/vacf/api.py
PQAnalysis/analysis/vacf/exceptions.py
PQAnalysis/analysis/vacf/spectrum.py
PQAnalysis/analysis/vacf/vacf.py
PQAnalysis/analysis/vacf/vacf_input_file_reader.py
PQAnalysis/analysis/vacf/vacf_output_file_writer.py
PQAnalysis/analysis/vibrational/__init__.py
PQAnalysis/analysis/vibrational/api.py
PQAnalysis/analysis/vibrational/exceptions.py
PQAnalysis/analysis/vibrational/vibrational_analysis.py
PQAnalysis/analysis/vibrational/vibrational_input_file_reader.py
PQAnalysis/atomic_system/__init__.py
PQAnalysis/atomic_system/_decorators.py
PQAnalysis/atomic_system/_positions.py
PQAnalysis/atomic_system/_properties.py
PQAnalysis/atomic_system/_standard_properties.py
PQAnalysis/atomic_system/atomic_system.py
PQAnalysis/atomic_system/exceptions.py
PQAnalysis/cli/__init__.py
PQAnalysis/cli/_argument_parser.py
PQAnalysis/cli/_cli_base.py
PQAnalysis/cli/add_molecules.py
PQAnalysis/cli/build_nep_traj.py
PQAnalysis/cli/build_spectrum.py
PQAnalysis/cli/check_momentum.py
PQAnalysis/cli/continue_input.py
PQAnalysis/cli/convert.py
PQAnalysis/cli/gen2xyz.py
PQAnalysis/cli/main.py
PQAnalysis/cli/msd.py
PQAnalysis/cli/rdf.py
PQAnalysis/cli/rst2xyz.py
PQAnalysis/cli/traj2box.py
PQAnalysis/cli/traj2extxyz.py
PQAnalysis/cli/traj2qmcfc.py
PQAnalysis/cli/vacf.py
PQAnalysis/cli/vibrations.py
PQAnalysis/cli/xyz2gen.py
PQAnalysis/cli/xyz2rst.py
PQAnalysis/core/__init__.py
PQAnalysis/core/api.py
PQAnalysis/core/exceptions.py
PQAnalysis/core/residue.py
PQAnalysis/core/atom/__init__.py
PQAnalysis/core/atom/atom.py
PQAnalysis/core/atom/element.py
PQAnalysis/core/cell/__init__.py
PQAnalysis/core/cell/_standard_properties.py
PQAnalysis/core/cell/cell.py
PQAnalysis/grammar/PQ_inputGrammar.lark
PQAnalysis/grammar/QMCFC_inputGrammar.lark
PQAnalysis/grammar/inputGrammar.lark
PQAnalysis/grammar/rules.lark
PQAnalysis/grammar/selection.lark
PQAnalysis/grammar/terminals.lark
PQAnalysis/io/__init__.py
PQAnalysis/io/api.py
PQAnalysis/io/base.py
PQAnalysis/io/box_reader.py
PQAnalysis/io/box_writer.py
PQAnalysis/io/conversion_api.py
PQAnalysis/io/energy_file_reader.py
PQAnalysis/io/exceptions.py
PQAnalysis/io/formats.py
PQAnalysis/io/info_file_reader.py
PQAnalysis/io/moldescriptor_reader.py
PQAnalysis/io/optimizer_file_reader.py
PQAnalysis/io/write_api.py
PQAnalysis/io/gen_file/__init__.py
PQAnalysis/io/gen_file/api.py
PQAnalysis/io/gen_file/exceptions.py
PQAnalysis/io/gen_file/gen_file_reader.py
PQAnalysis/io/gen_file/gen_file_writer.py
PQAnalysis/io/input_file_reader/__init__.py
PQAnalysis/io/input_file_reader/exceptions.py
PQAnalysis/io/input_file_reader/formats.py
PQAnalysis/io/input_file_reader/input_file_parser.py
PQAnalysis/io/input_file_reader/pq/__init__.py
PQAnalysis/io/input_file_reader/pq/output_files.py
PQAnalysis/io/input_file_reader/pq/pq_input_file_reader.py
PQAnalysis/io/input_file_reader/pq_analysis/__init__.py
PQAnalysis/io/input_file_reader/pq_analysis/_file_mixin.py
PQAnalysis/io/input_file_reader/pq_analysis/_parse.py
PQAnalysis/io/input_file_reader/pq_analysis/_positions_mixin.py
PQAnalysis/io/input_file_reader/pq_analysis/_selection_mixin.py
PQAnalysis/io/input_file_reader/pq_analysis/pqanalysis_input_file_reader.py
PQAnalysis/io/nep/__init__.py
PQAnalysis/io/nep/exceptions.py
PQAnalysis/io/nep/nep_writer.py
PQAnalysis/io/restart_file/__init__.py
PQAnalysis/io/restart_file/api.py
PQAnalysis/io/restart_file/exceptions.py
PQAnalysis/io/restart_file/restart_reader.py
PQAnalysis/io/restart_file/restart_writer.py
PQAnalysis/io/topology_file/__init__.py
PQAnalysis/io/topology_file/api.py
PQAnalysis/io/topology_file/exceptions.py
PQAnalysis/io/topology_file/topology_file_reader.py
PQAnalysis/io/topology_file/topology_file_writer.py
PQAnalysis/io/traj_file/.gitignore
PQAnalysis/io/traj_file/__init__.py
PQAnalysis/io/traj_file/_process_lines_py.py
PQAnalysis/io/traj_file/_slab_parser.c
PQAnalysis/io/traj_file/_slab_parser.pyx
PQAnalysis/io/traj_file/_slab_parser_py.py
PQAnalysis/io/traj_file/api.py
PQAnalysis/io/traj_file/exceptions.py
PQAnalysis/io/traj_file/frame_reader.py
PQAnalysis/io/traj_file/process_lines.c
PQAnalysis/io/traj_file/process_lines.pyx
PQAnalysis/io/traj_file/raw_frame_reader.py
PQAnalysis/io/traj_file/trajectory_reader.py
PQAnalysis/io/traj_file/trajectory_writer.py
PQAnalysis/io/virial/__init__.py
PQAnalysis/io/virial/api.py
PQAnalysis/io/virial/virial_reader.py
PQAnalysis/physical_data/__init__.py
PQAnalysis/physical_data/energy.py
PQAnalysis/physical_data/exceptions.py
PQAnalysis/tools/__init__.py
PQAnalysis/tools/add_molecule.py
PQAnalysis/tools/traj_to_com_traj.py
PQAnalysis/topology/__init__.py
PQAnalysis/topology/api.py
PQAnalysis/topology/exceptions.py
PQAnalysis/topology/selection.py
PQAnalysis/topology/shake_topology.py
PQAnalysis/topology/topology.py
PQAnalysis/topology/bonded_topology/__init__.py
PQAnalysis/topology/bonded_topology/_topology_properties.py
PQAnalysis/topology/bonded_topology/angle.py
PQAnalysis/topology/bonded_topology/bond.py
PQAnalysis/topology/bonded_topology/bonded_topology.py
PQAnalysis/topology/bonded_topology/dihedral.py
PQAnalysis/traj/__init__.py
PQAnalysis/traj/api.py
PQAnalysis/traj/exceptions.py
PQAnalysis/traj/formats.py
PQAnalysis/traj/trajectory.py
PQAnalysis/utils/__init__.py
PQAnalysis/utils/common.py
PQAnalysis/utils/custom_logging.py
PQAnalysis/utils/decorators.py
PQAnalysis/utils/files.py
PQAnalysis/utils/math.py
PQAnalysis/utils/progress.py
PQAnalysis/utils/random.py
PQAnalysis/utils/string.py
PQAnalysis/utils/units.py
benchmarks/pytest.ini
benchmarks/analysis/benchmark_momentum.py
benchmarks/analysis/benchmark_msd.py
benchmarks/analysis/benchmark_rdf.py
benchmarks/analysis/benchmark_spectrum_broadening.py
benchmarks/analysis/benchmark_vacf.py
benchmarks/core/benchmark_cell.py
benchmarks/core/benchmark_traj_reader.py
conda-recipes/README.md
conda-recipes/pqanalysis/bld.bat
conda-recipes/pqanalysis/build.sh
conda-recipes/pqanalysis/meta.yaml
docs/Makefile
docs/make.bat
docs/source/conf.py
docs/source/examples.rst
docs/source/getting-started.rst
docs/source/index.rst
docs/source/python-api.rst
docs/source/references.rst
docs/source/workflow.rst
docs/source/_ext/pq_cli_tables.py
docs/source/_plots/_style.py
docs/source/_plots/msd.py
docs/source/_plots/rdf.py
docs/source/_plots/vacf.py
docs/source/_plots/vibrations.py
docs/source/_plots/workflow.py
docs/source/_static/css/custom.css
docs/source/_templates/module.rst
docs/source/_templates/package.rst
docs/source/analyses/index.rst
docs/source/analyses/momentum.rst
docs/source/analyses/msd-details.rst
docs/source/analyses/msd.rst
docs/source/analyses/rdf-details.rst
docs/source/analyses/rdf.rst
docs/source/analyses/vacf-details.rst
docs/source/analyses/vacf.rst
docs/source/analyses/vibrations-details.rst
docs/source/analyses/vibrations.rst
docs/source/data/index.rst
docs/source/data/selections.rst
docs/source/developerGuide/adding-analysis.rst
docs/source/developerGuide/architecture.rst
docs/source/developerGuide/developerGuide.rst
docs/source/developerGuide/release.rst
docs/source/developerGuide/validation.rst
docs/source/logo/PQAnalysis.png
docs/source/reference/api.rst
docs/source/reference/cli.rst
docs/source/reference/functions.rst
docs/source/userGuide/analysisOutputFiles.rst
docs/source/userGuide/inputFile.rst
docs/source/userGuide/userGuide.rst
examples/add_molecules/mil68ga-md-01.rst
examples/add_molecules/perylene-md-05.rst
examples/add_molecules/perylene-md-05.xyz
examples/add_molecules/shake_mil.top
examples/add_molecules/shake_perylene.top
examples/continue_input/run-01.in
examples/continue_input/pq/run-08.in
examples/continue_input/pq/run-09.in.ref
examples/continue_input/qmcfc/run-01.in
examples/continue_input/qmcfc/run-02.in.ref
examples/rdf/md.xyz
examples/rdf/rdf.in
examples/rdf/rdf.out
examples/rdf/rdf_restart.out
examples/rdf/rdf_with_restart.in
examples/rdf/restart.rst
examples/shake_topology/gen_shake.ipynb
examples/shake_topology/perylene-md-01.xyz
examples/shake_topology/perylene.png
examples/shake_topology/shake.top
examples/traj2box/.gitignore
examples/traj2box/acof_triclinic.xyz
examples/traj2box/acof_triclinic_2.xyz
examples/traj2comtraj/umcm-9-md-01.xyz
examples/vibrational/README.md
examples/vibrational/h2o.rst
examples/vibrational/hessian.dat
examples/vibrational/input.in
examples/vibrational/moldescriptor.dat
examples/water/README.md
examples/water/hessian.dat
examples/water/moldescriptor.dat
examples/water/msd.in
examples/water/rdf.in
examples/water/restart.rst
examples/water/structure.rst
examples/water/trajectory.vel
examples/water/trajectory.xyz
examples/water/vacf.in
examples/water/vibrations.in
tests/__init__.py
tests/conftest.py
tests/test_formats.py
tests/test_lazy_imports.py
tests/test_logging_env_vars.py
tests/test_type_checking.py
tests/test_version.py
tests/analysis/__init__.py
tests/analysis/test_output.py
tests/analysis/momentum/__init__.py
tests/analysis/momentum/test_api.py
tests/analysis/momentum/test_momentum.py
tests/analysis/momentum/test_momentum_dispatch.py
tests/analysis/momentum/test_momentum_kernel_fallback.py
tests/analysis/momentum/test_parity.py
tests/analysis/msd/__init__.py
tests/analysis/msd/test_api.py
tests/analysis/msd/test_exceptions.py
tests/analysis/msd/test_msd.py
tests/analysis/msd/test_msd_input_file_reader.py
tests/analysis/msd/test_msd_kernel.py
tests/analysis/msd/test_msd_kernel_fallback.py
tests/analysis/msd/test_msd_output_file_writer.py
tests/analysis/msd/test_parity.py
tests/analysis/rdf/__init__.py
tests/analysis/rdf/test_api.py
tests/analysis/rdf/test_parity.py
tests/analysis/rdf/test_rdf.py
tests/analysis/rdf/test_rdfInputFileReader.py
tests/analysis/rdf/test_rdfOutputFileReader.py
tests/analysis/rdf/test_rdf_kernel.py
tests/analysis/spectrum_broadening/__init__.py
tests/analysis/spectrum_broadening/test_api.py
tests/analysis/spectrum_broadening/test_spectrum_broadening.py
tests/analysis/vacf/__init__.py
tests/analysis/vacf/test_api.py
tests/analysis/vacf/test_exceptions.py
tests/analysis/vacf/test_parity.py
tests/analysis/vacf/test_raw_charge_reader.py
tests/analysis/vacf/test_spectrum.py
tests/analysis/vacf/test_vacf.py
tests/analysis/vacf/test_vacf_coverage.py
tests/analysis/vacf/test_vacf_input_file_reader.py
tests/analysis/vacf/test_vacf_kernel.py
tests/analysis/vacf/test_vacf_output_file_writer.py
tests/analysis/vibrational/__init__.py
tests/analysis/vibrational/test_api.py
tests/analysis/vibrational/test_vibrational_analysis.py
tests/analysis/vibrational/test_vibrational_input_file_reader.py
tests/atomicSystem/__init__.py
tests/atomicSystem/test_atomic_system.py
tests/atomicSystem/test_decorators.py
tests/atomicSystem/test_positions.py
tests/cli/__init__.py
tests/cli/test_add_molecules.py
tests/cli/test_build_spectrum.py
tests/cli/test_check_momentum.py
tests/cli/test_continue_input.py
tests/cli/test_convert.py
tests/cli/test_main.py
tests/cli/test_msd.py
tests/cli/test_rdf.py
tests/cli/test_rst2xyz.py
tests/cli/test_traj2box.py
tests/cli/test_traj2extxyz.py
tests/cli/test_traj2qmcfc.py
tests/cli/test_vacf.py
tests/cli/test_vibrations.py
tests/cli/test_xyz2gen.py
tests/cli/test_xyz2rst.py
tests/core/__init__.py
tests/core/test_cell.py
tests/core/test_residue.py
tests/core/atom/__init__.py
tests/core/atom/test_atom.py
tests/core/atom/test_element.py
tests/data/inputFileReader/input.in
tests/data/inputFileReader/input_PQ.in
tests/data/inputFileReader/PQAnalysis_input/input_PQ.in
tests/data/inputFileReader/PQ_input/n_not_matching.in
tests/data/inputFileReader/PQ_input/n_not_matching_input_file_n-08.in
tests/data/inputFileReader/PQ_input/no_output_files.in
tests/data/inputFileReader/PQ_input/no_start_file.in
tests/data/inputFileReader/PQ_input/old_n_not_less_one_than_actual_n-09.in
tests/data/inputFileReader/PQ_input/run-08.in
tests/data/inputFileReader/PQ_input/run-08.rpmd.in
tests/data/inputFileReader/PQ_input/run-09.in.ref
tests/data/inputFileReader/PQ_input/run-09.rpmd.in.ref
tests/data/inputFileReader/PQ_input/run-10.in.ref
tests/data/inputFileReader/PQ_input/run-10.rpmd.in.ref
tests/data/momentum/gas3.vel
tests/data/momentum/two_frames.vel
tests/data/msd/diffcalc_O.in
tests/data/msd/diffcalc_O_start.in
tests/data/msd/diffcalc_atom3.in
tests/data/msd/input.in
tests/data/msd/input_alias_conflict.in
tests/data/msd/input_defaults.in
tests/data/msd/input_full.in
tests/data/msd/input_missing_required.in
tests/data/msd/input_negative_start.in
tests/data/msd/input_start_alias.in
tests/data/msd/msd_ref_O.dat
tests/data/msd/msd_ref_O_start.dat
tests/data/msd/msd_ref_atom3.dat
tests/data/msd/traj.xyz
tests/data/rdf/infer.rst
tests/data/rdf/infer.xyz
tests/data/rdf/input.in
tests/data/rdf/input_moldescriptor_restart.in
tests/data/rdf/input_no_intra_molecular_empty_glob.in
tests/data/rdf/input_no_intra_molecular_false.in
tests/data/rdf/input_no_intra_molecular_infer.in
tests/data/rdf/input_no_intra_molecular_restart.in
tests/data/rdf/input_no_restart.in
tests/data/rdf/input_topology_files_default.in
tests/data/rdf/input_topology_files_false.in
tests/data/rdf/traj.xyz
tests/data/readEnergyFile/md-01.en
tests/data/readEnergyFile/md-01.info
tests/data/readEnergyFile/md-01_noinfo.en
tests/data/readEnergyFile/qmmm.en
tests/data/readEnergyFile/qmmm.info
tests/data/readInfoFile/md-01.info
tests/data/readInfoFile/md-01.qmcfc.info
tests/data/readMoldescriptor/moldescriptor.dat
tests/data/readMoldescriptor/moldescriptor_tooFewAtoms.dat
tests/data/readMoldescriptor/moldescriptor_tooFewAtoms_midFile.dat
tests/data/readMoldescriptor/moldescriptor_withError.dat
tests/data/readOptimizerFile/optimization.opt
tests/data/readRestartFile/md-01.rst
tests/data/readRestartFile/moldescriptor.dat
tests/data/rst2xyz/md-01.rst
tests/data/spectrum_broadening/lines.dat
tests/data/spectrum_broadening/spectrum.dat
tests/data/traj2box/box.dat
tests/data/traj2box/box.vmd.xyz
tests/data/traj2box/test.xyz
tests/data/traj2qmcfc/acof_triclinic.xyz
tests/data/traj2qmcfc/acof_triclinic_2.xyz
tests/data/traj2qmcfc/traj.qmcfc.xyz
tests/data/vacf/charges.dat
tests/data/vacf/flux_static_ref.dat
tests/data/vacf/flux_traj_ref.dat
tests/data/vacf/spectrum_blackman_ref.dat
tests/data/vacf/spectrum_exponential_ref.dat
tests/data/vacf/spectrum_hann_ref.dat
tests/data/vacf/spectrum_none_ref.dat
tests/data/vacf/traj_1.chrg
tests/data/vacf/traj_1.vel
tests/data/vacf/traj_2.chrg
tests/data/vacf/traj_2.vel
tests/data/vacf/vacf_ref.dat
tests/data/vacf/windowed_blackman_ref.dat
tests/data/vacf/windowed_exponential_ref.dat
tests/data/vacf/windowed_hann_ref.dat
tests/data/vibrational/h2o.rst
tests/data/vibrational/hessian.dat
tests/data/vibrational/input.in
tests/data/vibrational/invalid_unit.in
tests/data/vibrational/mode_output.in
tests/data/vibrational/moldescriptor.dat
tests/data/xyz2rst/md-01.force
tests/data/xyz2rst/md-01.vel
tests/data/xyz2rst/md-01.xyz
tests/data/xyz2rst/md-01_nobox.xyz
tests/data/xyz2rst/md-01_null.xyz
tests/data/xyz2rst/md-01_qmcfc.xyz
tests/data/xyz2rst/moldescriptor.dat
tests/integration_tests/__init__.py
tests/integration_tests/add_molecules/__init__.py
tests/integration_tests/add_molecules/test_add_molecules.py
tests/integration_tests/add_molecules/ref_data/combined.rst
tests/integration_tests/add_molecules/ref_data/mil68ga-md-01.rst
tests/integration_tests/add_molecules/ref_data/perylene-md-05.rst
tests/integration_tests/add_molecules/ref_data/perylene-md-05.xyz
tests/integration_tests/add_molecules/ref_data/shake_mil.top
tests/integration_tests/add_molecules/ref_data/shake_perylene.top
tests/integration_tests/add_molecules/ref_data/top.top
tests/io/__init__.py
tests/io/test_base.py
tests/io/test_boxReader.py
tests/io/test_boxWriter.py
tests/io/test_energyFileReader.py
tests/io/test_frameReader.py
tests/io/test_genFile.py
tests/io/test_infoFileReader.py
tests/io/test_moldescriptorReader.py
tests/io/test_nepWriter.py
tests/io/test_optimizerFileReader.py
tests/io/test_process_lines_py.py
tests/io/test_raw_frame_reader.py
tests/io/test_restartReader.py
tests/io/test_restartWriter.py
tests/io/test_slab_parser.py
tests/io/test_topology_writer.py
tests/io/test_trajectoryReader.py
tests/io/test_trajectoryWriter.py
tests/io/test_virialReader.py
tests/io/test_write_api.py
tests/io/inputFileReader/__init__.py
tests/io/inputFileReader/test_inputDictionary.py
tests/io/inputFileReader/test_inputFileParser.py
tests/io/inputFileReader/test_transformers.py
tests/io/inputFileReader/test_visitors.py
tests/io/inputFileReader/PQ/__init__.py
tests/io/inputFileReader/PQ/test_PQ_inputFileReader.py
tests/io/inputFileReader/PQAnalysis/__init__.py
tests/io/inputFileReader/PQAnalysis/test_parse.py
tests/io/inputFileReader/PQAnalysis/test_pqanalysis_input_file_reader.py
tests/physicalData/__init__.py
tests/physicalData/test_energy.py
tests/tools/__init__.py
tests/tools/test_traj_to_com_traj.py
tests/topology/__init__.py
tests/topology/test_selection.py
tests/topology/test_selectionTransformer.py
tests/topology/test_shakeTopology.py
tests/topology/test_topology.py
tests/topology/bonded_topology/__init__.py
tests/topology/bonded_topology/test_angle.py
tests/topology/bonded_topology/test_bond.py
tests/topology/bonded_topology/test_bondedTopology.py
tests/topology/bonded_topology/test_dihedral.py
tests/traj/__init__.py
tests/traj/test_api.py
tests/traj/test_formats.py
tests/traj/test_trajectory.py
tests/utils/__init__.py
tests/utils/test_common.py
tests/utils/test_custom_logging.py
tests/utils/test_decorators.py
tests/utils/test_math.py
tests/utils/test_progress.py
tests/utils/test_string.py
tests/utils/test_units.py