.gitignore
CONTRIBUTE.md
LICENSE
README.md
environment.yml
pyproject.toml
.githooks/pre-push
.github/workflows/cicd.yml
assets/ptm_example.png
assets/viennaptm_logo.png
assets/viennaptm_logo.xcf
assets/viennaptm_logo_c.png
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/scripts/list_ptms_from_library.py
docs/scripts/ptms_to_rst_table.py
docs/source/api.rst
docs/source/citation.rst
docs/source/conf.py
docs/source/entrypoint.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/introduction.rst
docs/source/list_of_ptms.rst
docs/source/references.bib
docs/source/tutorial.rst
docs/source/_static/config.png
docs/source/_static/custom.css
docs/source/_static/debug_mode.png
docs/source/_static/example.png
docs/source/_static/finished_run.png
docs/source/_static/help.png
docs/source/_static/logger_override.png
docs/source/_static/logo.png
docs/source/_static/parameter_console_input.png
docs/source/_templates/autosummary/class.rst
docs/source/_templates/autosummary/functions.rst
notebooks/visualization.ipynb
tests/__init__.py
tests/file_paths.py
tests/helper_functions.py
tests/data/1vii.cif
tests/data/1vii.pdb
tests/data/example_config.yaml
tests/test_entrypoints/__init__.py
tests/test_entrypoints/test_entrypoint_validation.py
tests/test_entrypoints/test_viennaptm.py
tests/test_modification_log/__init__.py
tests/test_modification_log/test_modification_log.py
tests/tests_gromacs/__init__.py
tests/tests_gromacs/test_minimzation_pipeline.py
tests/tests_gromacs/test_pdb2gmx.py
tests/tests_io/__init__.py
tests/tests_io/test_iostructure.py
tests/tests_io/test_resources.py
tests/tests_modification/__init__.py
tests/tests_modification/test_modification_all.py
tests/tests_modification/test_modification_general.py
viennaptm/__init__.py
viennaptm.egg-info/PKG-INFO
viennaptm.egg-info/SOURCES.txt
viennaptm.egg-info/dependency_links.txt
viennaptm.egg-info/entry_points.txt
viennaptm.egg-info/requires.txt
viennaptm.egg-info/top_level.txt
viennaptm/dataclasses/annotatedstructure.py
viennaptm/dataclasses/parameters/modifier_parameters.py
viennaptm/entrypoints/viennaptm.py
viennaptm/gromacs/editconf.py
viennaptm/gromacs/gromacs_command.py
viennaptm/gromacs/grompp.py
viennaptm/gromacs/mdrun.py
viennaptm/gromacs/minimization_pipeline.py
viennaptm/gromacs/pdb2gmx.py
viennaptm/gromacs/trjconv.py
viennaptm/modification/modification_library.py
viennaptm/modification/application/modifier.py
viennaptm/modification/calculation/align.py
viennaptm/resources/LICENSE
viennaptm/resources/gromacs/minim.mdp
viennaptm/resources/libraries/library.json
viennaptm/resources/metadata/annotations.json
viennaptm/resources/pdbs_minimized/ALA.pdb
viennaptm/resources/pdbs_minimized/ARG.pdb
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viennaptm/utils/logger.py
viennaptm/utils/paths.py
viennaptm/utils/unit_test_utils.py
viennaptm/utils/visualizer.py