CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
mkdocs.yml
pyproject.toml
requirements.txt
docs/api-reference.md
docs/benchmarks.md
docs/contributing.md
docs/index.md
docs/installation.md
docs/limitations.md
docs/quickstart.md
docs/roadmap.md
docs/validation.md
docs/assets/coarsegrain/1fqy-cg-mapping-comparison.png
docs/assets/coarsegrain/1fqy-martini-mapping.png
docs/assets/contactmaps/1aml-contact-frequency.png
docs/assets/contactmaps/1fqy-ca-distance-matrix.png
docs/assets/contactmaps/1fqy-residue-contact-map.png
docs/assets/geometry/1aml-rmsf-profile.png
docs/assets/geometry/1fqy-principal-axes.png
docs/assets/graphs/1fqy-residue-contact-graph.png
docs/assets/readme/aquaporin-structure-v2.png
docs/assets/readme/coarse-grained-beads-v2.png
docs/assets/readme/residue-contact-map.png
docs/assets/readme/secondary-structure.png
docs/examples/analyze-contacts.md
docs/examples/binding-site.md
docs/examples/build-molecular-graph.md
docs/examples/coarse-grain-protein.md
docs/examples/compare-nmr-models.md
docs/examples/export-pyg.md
docs/examples/geometry-tour.md
docs/examples/index.md
docs/examples/pdb-to-graph-cg.md
docs/examples/pdb-to-pyg-ml.md
docs/examples/protein-analysis-from-scratch.md
docs/examples/residue-contact-graphs.md
docs/tutorials/index.md
docs/tutorials/pdb-to-coarse-grained-beads.md
docs/tutorials/pdb-to-descriptors.md
docs/tutorials/pdb-to-graph-gnn.md
docs/user-guide/chemical-perception.md
docs/user-guide/coarse-graining.md
docs/user-guide/contact-maps.md
docs/user-guide/coordinate-formats.md
docs/user-guide/descriptors.md
docs/user-guide/ensembles.md
docs/user-guide/geometry.md
docs/user-guide/library-selection.md
docs/user-guide/mcp-server.md
docs/user-guide/molecular-graphs.md
docs/user-guide/plotting.md
docs/user-guide/protein-analysis.md
docs/user-guide/reading-files.md
docs/user-guide/selections.md
examples/binding_site.py
examples/coarse_graining.py
examples/geometry.py
examples/graph_to_gnn.py
examples/legacy_utils.py
examples/pdb_to_pyg_ml.py
examples/protein_analysis.py
examples/residue_contact_graph.py
examples/tour.py
examples/data/1aml.pdb
examples/data/1fqy.pdb
examples/data/1shg.pdb
examples/data/1ubq.pdb
examples/data/3ptb.pdb
examples/data/helix_201.xyz
molscope/__init__.py
molscope/__main__.py
molscope/chem.py
molscope/cif.py
molscope/cli.py
molscope/coarsegrain.py
molscope/contactmap.py
molscope/contacts.py
molscope/descriptors.py
molscope/distance.py
molscope/dssp.py
molscope/elements.py
molscope/ensemble.py
molscope/graph.py
molscope/io.py
molscope/library.py
molscope/mcp_server.py
molscope/molecule.py
molscope/plotting.py
molscope.egg-info/PKG-INFO
molscope.egg-info/SOURCES.txt
molscope.egg-info/dependency_links.txt
molscope.egg-info/entry_points.txt
molscope.egg-info/requires.txt
molscope.egg-info/top_level.txt
notebooks/molscope_tour.ipynb
notebooks/pdb_to_gnn.ipynb
notebooks/protein_analysis_from_scratch.ipynb
scripts/benchmark_core.py
scripts/build_gnn_notebook.py
scripts/build_protein_analysis_notebook.py
scripts/build_user_guide_pdf.py
scripts/render_coarsegrain_images.py
scripts/render_contact_analysis_images.py
scripts/render_geometry_images.py
tests/test_cg_mapping.py
tests/test_chem.py
tests/test_cif_validation.py
tests/test_cli.py
tests/test_cli_batch.py
tests/test_clustering.py
tests/test_coarsegrain.py
tests/test_contactmap.py
tests/test_contacts.py
tests/test_descriptors.py
tests/test_dssp.py
tests/test_extras.py
tests/test_features.py
tests/test_graph.py
tests/test_io.py
tests/test_library.py
tests/test_mcp_server.py
tests/test_molecule.py
tests/test_protein_workflows.py
tests/fixtures/bad_coord.pdb
tests/fixtures/bad_coord.xyz
tests/fixtures/bad_counts.sdf
tests/fixtures/insertion_codes.cif
tests/fixtures/missing_coord_col.cif
tests/fixtures/no_atom_site.cif
tests/fixtures/no_atoms.pdb
tests/fixtures/short_atom.pdb
tests/fixtures/truncated.sdf
tests/fixtures/truncated.xyz
tests/fixtures/ugly_residue_ids.pdb
tests/fixtures/v3000.sdf
tests/fixtures/water.sdf
tests/validation/test_binding_sites_ref.py
tests/validation/test_bonds_ref.py
tests/validation/test_chem_ref.py
tests/validation/test_dssp_ref.py
tests/validation/test_geometry_ref.py
tests/validation/test_invariants.py