API documentation

Submodules

• site_analysis.atom
  • Atom
    • Atom.index
    • Atom.in_site
    • Atom.trajectory
    • Atom.as_dict()
    • Atom.assign_coords()
    • Atom.frac_coords
    • Atom.from_dict()
    • Atom.from_file()
    • Atom.from_str()
    • Atom.most_recent_site
    • Atom.reset()
    • Atom.to()
    • Atom.update_recent_site()
  • atoms_from_indices()
  • atoms_from_species_string()
  • atoms_from_structure()
• site_analysis.builders
  • TrajectoryBuilder
    • TrajectoryBuilder.build()
    • TrajectoryBuilder.reset()
    • TrajectoryBuilder.with_dynamic_voronoi_sites()
    • TrajectoryBuilder.with_existing_atoms()
    • TrajectoryBuilder.with_existing_sites()
    • TrajectoryBuilder.with_min_atom_distance()
    • TrajectoryBuilder.with_mobile_species()
    • TrajectoryBuilder.with_polyhedral_sites()
    • TrajectoryBuilder.with_reference_structure()
    • TrajectoryBuilder.with_site_mapping()
    • TrajectoryBuilder.with_spherical_sites()
    • TrajectoryBuilder.with_structure()
    • TrajectoryBuilder.with_structure_alignment()
    • TrajectoryBuilder.with_voronoi_sites()
  • create_trajectory_with_dynamic_voronoi_sites()
  • create_trajectory_with_polyhedral_sites()
  • create_trajectory_with_spherical_sites()
  • create_trajectory_with_voronoi_sites()
• site_analysis.dynamic_voronoi_site
  • DynamicVoronoiSite
    • DynamicVoronoiSite.reference_indices
    • DynamicVoronoiSite.centre_coords
    • DynamicVoronoiSite.as_dict()
    • DynamicVoronoiSite.calculate_centre()
    • DynamicVoronoiSite.centre
    • DynamicVoronoiSite.cn
    • DynamicVoronoiSite.contains_point()
    • DynamicVoronoiSite.coordination_number
    • DynamicVoronoiSite.from_dict()
    • DynamicVoronoiSite.reset()
    • DynamicVoronoiSite.sites_from_reference_indices()
• site_analysis.dynamic_voronoi_site_collection
  • DynamicVoronoiSiteCollection
    • DynamicVoronoiSiteCollection.sites
    • DynamicVoronoiSiteCollection.analyse_structure()
    • DynamicVoronoiSiteCollection.assign_site_occupations()
    • DynamicVoronoiSiteCollection.reset()
• site_analysis.pbc_utils
  • apply_legacy_pbc_correction()
  • correct_pbc()
  • unwrap_vertices_to_reference_center()
  • update_pbc_shifts()
• site_analysis.polyhedral_site
  • FaceTopologyCache
    • FaceTopologyCache.face_simplices
    • FaceTopologyCache.contains_point()
    • FaceTopologyCache.update()
  • PolyhedralSite
    • PolyhedralSite.vertex_indices
    • PolyhedralSite.vertex_coords
    • PolyhedralSite.reference_center
    • PolyhedralSite.as_dict()
    • PolyhedralSite.assign_vertex_coords()
    • PolyhedralSite.centre
    • PolyhedralSite.cn
    • PolyhedralSite.contains_atom()
    • PolyhedralSite.contains_point()
    • PolyhedralSite.coordination_number
    • PolyhedralSite.delaunay
    • PolyhedralSite.from_dict()
    • PolyhedralSite.get_vertex_species()
    • PolyhedralSite.notify_structure_changed()
    • PolyhedralSite.reset()
    • PolyhedralSite.sites_from_vertex_indices()
• site_analysis.polyhedral_site_collection
  • PolyhedralSiteCollection
    • PolyhedralSiteCollection.sites
    • PolyhedralSiteCollection.analyse_structure()
    • PolyhedralSiteCollection.assign_site_occupations()
    • PolyhedralSiteCollection.neighbouring_sites()
    • PolyhedralSiteCollection.sites_contain_points()
  • construct_neighbouring_sites()
• site_analysis.reference_workflow
  • ReferenceBasedSites
    • ReferenceBasedSites.reference_structure
    • ReferenceBasedSites.target_structure
    • ReferenceBasedSites.aligned_structure
    • ReferenceBasedSites.translation_vector
    • ReferenceBasedSites.alignment_metrics
    • ReferenceBasedSites.create_dynamic_voronoi_sites()
    • ReferenceBasedSites.create_polyhedral_sites()
  • StructureAligner
    • StructureAligner.align()
  • CoordinationEnvironmentFinder
    • CoordinationEnvironmentFinder.find_environments()
  • IndexMapper
    • IndexMapper.map_coordinating_atoms()
  • SiteFactory
    • SiteFactory.structure
    • SiteFactory.create_dynamic_voronoi_sites()
    • SiteFactory.create_polyhedral_sites()
• site_analysis.site
  • Site
    • Site.index
    • Site.contains_atoms
    • Site.trajectory
    • Site.points
    • Site.transitions
    • Site.as_dict()
    • Site.average_occupation
    • Site.centre
    • Site.contains_atom()
    • Site.contains_point()
    • Site.coordination_number
    • Site.from_dict()
    • Site.most_frequent_transitions()
    • Site.reset()
    • Site.reset_index()
    • Site.residence_times()
    • Site.summary()
• site_analysis.site_collection
  • PriorityAssignmentMixin
  • SiteCollection
    • SiteCollection.sites
    • SiteCollection.analyse_structure()
    • SiteCollection.assign_site_occupations()
    • SiteCollection.neighbouring_sites()
    • SiteCollection.reset()
    • SiteCollection.reset_site_occupations()
    • SiteCollection.site_by_index()
    • SiteCollection.sites_contain_points()
    • SiteCollection.summaries()
    • SiteCollection.update_occupation()
• site_analysis.spherical_site
  • SphericalSite
    • SphericalSite.frac_coords
    • SphericalSite.rcut
    • SphericalSite.as_dict()
    • SphericalSite.centre
    • SphericalSite.contains_atom()
    • SphericalSite.contains_point()
    • SphericalSite.from_dict()
• site_analysis.spherical_site_collection
  • SphericalSiteCollection
    • SphericalSiteCollection.analyse_structure()
    • SphericalSiteCollection.assign_site_occupations()
• site_analysis.tools
  • calculate_species_distances()
  • get_coordination_indices()
  • get_nearest_neighbour_indices()
  • get_vertex_indices()
  • indices_for_species()
  • site_index_mapping()
  • species_string_from_site()
  • x_pbc()
• site_analysis.trajectory
  • Trajectory
    • Trajectory.analyse_structure()
    • Trajectory.append_timestep()
    • Trajectory.assign_site_occupations()
    • Trajectory.at
    • Trajectory.atom_by_index()
    • Trajectory.atom_sites
    • Trajectory.atoms_trajectory
    • Trajectory.reset()
    • Trajectory.site_by_index()
    • Trajectory.site_coordination_numbers()
    • Trajectory.site_labels()
    • Trajectory.site_occupations
    • Trajectory.site_summaries()
    • Trajectory.sites_trajectory
    • Trajectory.st
    • Trajectory.trajectory_from_structures()
    • Trajectory.transition_counts_by_label()
    • Trajectory.transition_counts_by_site()
    • Trajectory.transition_probabilities_by_label()
    • Trajectory.transition_probabilities_by_site()
    • Trajectory.write_site_summaries()
  • update_occupation()
• site_analysis.transition_table
  • TransitionTable
    • TransitionTable.filter()
    • TransitionTable.get()
    • TransitionTable.keys
    • TransitionTable.matrix
    • TransitionTable.reorder()
    • TransitionTable.to_dict()
• site_analysis.voronoi_site
  • VoronoiSite
    • VoronoiSite.frac_coords
    • VoronoiSite.as_dict()
    • VoronoiSite.centre
    • VoronoiSite.contains_point()
    • VoronoiSite.from_dict()
• site_analysis.voronoi_site_collection
  • VoronoiSiteCollection
    • VoronoiSiteCollection.analyse_structure()
    • VoronoiSiteCollection.assign_site_occupations()