Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W A add_ring_bonds_for_lammps_full() (in module topo_metrics.io.lmp) adjacency_to_ase_bonds_array() (in module topo_metrics.io.lmp) angle (topo_metrics.rings.Ring attribute) apply_image_shift() (topo_metrics.topology.Node method) Array (in module topo_metrics.knots) ase_atoms (topo_metrics.io.lammps_data.LammpsDataComponents attribute) asphericity (topo_metrics.ring_geometry.RingGeometry property) atoms (topo_metrics.io.lmp.PackedRings attribute) autoreduce_neighborlist() (in module topo_metrics.neighbours) B box_size (topo_metrics.io.conflink.Configuration attribute) C cart_coord (topo_metrics.topology.Node attribute) cart_coords (topo_metrics.io.lammps_data.LammpsDataComponents attribute) cartesian_coordinates (topo_metrics.topology.Topology property) CARVS (class in topo_metrics.symbols) central_node_id (topo_metrics.clusters.Cluster attribute) Cluster (class in topo_metrics.clusters) clusters (topo_metrics.topology.RingsResults attribute) Configuration (class in topo_metrics.io.conflink) connections (topo_metrics.io.conflink.Configuration attribute) counts (topo_metrics.rings.RingSizeCounts attribute) cycle_edges() (in module topo_metrics.io.lmp) D depth (topo_metrics.topology.RingsResults attribute) E edges (topo_metrics.io.lammps_data.LammpsDataComponents attribute) (topo_metrics.topology.Topology attribute) F frac_coord (topo_metrics.topology.Node attribute) frac_coords (topo_metrics.io.lammps_data.LammpsDataComponents attribute) fractional_coordinates (topo_metrics.topology.Topology property) from_ase() (topo_metrics.topology.Topology class method) from_cgd() (topo_metrics.topology.Topology class method) from_conflink() (topo_metrics.topology.Topology class method) from_lammps_data() (topo_metrics.topology.Topology class method) from_list() (topo_metrics.symbols.CARVS class method) G geometric_centroid (topo_metrics.ring_geometry.RingGeometry property) geometry() (topo_metrics.rings.Ring method) get_all_node_frac_coords() (in module topo_metrics.topology) get_all_topological_distances() (in module topo_metrics.symbols) get_carvs_std_dev() (in module topo_metrics.clusters) get_carvs_vector() (in module topo_metrics.clusters) get_clusters() (in module topo_metrics.clusters) (topo_metrics.topology.Topology method) get_coordination_sequences() (topo_metrics.topology.Topology method) get_data_dir() (in module topo_metrics.paths) get_opposite_angles() (in module topo_metrics.clusters) get_ordered_node_list() (in module topo_metrics.rings) get_project_root() (in module topo_metrics.paths) get_project_src() (in module topo_metrics.paths) get_ring_size_by_angle() (in module topo_metrics.clusters) get_ring_sizes() (in module topo_metrics.clusters) get_rings() (topo_metrics.topology.Topology method) get_topological_genome() (topo_metrics.topology.Topology method) get_unique_angles() (in module topo_metrics.clusters) get_vertex_symbol() (in module topo_metrics.clusters) GlobalLink (in module topo_metrics.io.lmp) graph_edges_by_cutoff() (in module topo_metrics.neighbours) gyration_tensor (topo_metrics.ring_geometry.RingGeometry property) H hushed (class in topo_metrics.utils) I instantiate_julia() (in module topo_metrics.paths) is_linked_from_lk() (in module topo_metrics.knots) is_linked_to() (topo_metrics.ring_geometry.RingGeometry method) is_shifted (topo_metrics.topology.Node attribute) is_single_node (topo_metrics.symbols.CARVS attribute), [1] J jl (in module topo_metrics.paths) L LammpsDataComponents (class in topo_metrics.io.lammps_data) largest_ring_size() (in module topo_metrics.clusters) lattice (topo_metrics.topology.Topology attribute) linking_number() (topo_metrics.ring_geometry.RingGeometry method) linking_number_int() (in module topo_metrics.knots) linking_number_method_1a() (in module topo_metrics.knots) linking_number_method_1b() (in module topo_metrics.knots) linking_number_pbc() (in module topo_metrics.knots) lk_round() (in module topo_metrics.knots) load_lammps_data() (in module topo_metrics.io.lammps_data) M min_count() (in module topo_metrics.utils) module topo_metrics topo_metrics.analysis topo_metrics.clusters topo_metrics.io topo_metrics.io.cgd topo_metrics.io.conflink topo_metrics.io.lammps_data topo_metrics.io.lmp topo_metrics.knots topo_metrics.neighbours topo_metrics.paths topo_metrics.ring_geometry topo_metrics.rings topo_metrics.symbols topo_metrics.topology topo_metrics.utils N nb (in module topo_metrics.knots) Node (class in topo_metrics.topology) node_id (topo_metrics.topology.Node attribute) node_list_to_ring() (in module topo_metrics.rings) node_type (topo_metrics.topology.Node attribute) nodes (topo_metrics.ring_geometry.RingGeometry attribute) (topo_metrics.rings.Ring attribute) (topo_metrics.topology.Topology attribute) number_of_angles() (in module topo_metrics.clusters) number_of_rings() (in module topo_metrics.clusters) O only_smallest_ring_size() (in module topo_metrics.clusters) P pack_rings_to_ase() (in module topo_metrics.io.lmp) PackedRings (class in topo_metrics.io.lmp) pad_carvs() (in module topo_metrics.symbols) pad_carvs_per_atom() (in module topo_metrics.symbols) parse_cgd() (in module topo_metrics.io.cgd) parse_conflink() (in module topo_metrics.io.conflink) positions (topo_metrics.io.conflink.Configuration attribute) (topo_metrics.ring_geometry.RingGeometry property) principal_moments (topo_metrics.ring_geometry.RingGeometry property) process_neighbour_list() (in module topo_metrics.io.cgd) properties (topo_metrics.topology.Topology attribute) R radius_of_gyration (topo_metrics.ring_geometry.RingGeometry property) Ring (class in topo_metrics.rings) ring_list_to_cluster() (in module topo_metrics.clusters) ring_ranges (topo_metrics.io.lmp.PackedRings attribute) ring_size_count (topo_metrics.topology.RingsResults attribute) ring_species (topo_metrics.io.lmp.PackedRings attribute) RingGeometry (class in topo_metrics.ring_geometry) RingLocalLink (in module topo_metrics.io.lmp) rings (topo_metrics.clusters.Cluster attribute) rings_are_strong (topo_metrics.topology.RingsResults attribute) RingSizeCounts (class in topo_metrics.rings) RingsResults (class in topo_metrics.topology) RingStatistics (in module topo_metrics.paths) S set_types_by_ring_and_element() (in module topo_metrics.io.lmp) shares_edge() (in module topo_metrics.clusters) size (topo_metrics.rings.Ring property) sizes (topo_metrics.rings.RingSizeCounts attribute) smallest_ring_size() (in module topo_metrics.clusters) species (topo_metrics.ring_geometry.RingGeometry property) spread (topo_metrics.symbols.CARVS attribute), [1] symbols (topo_metrics.io.lammps_data.LammpsDataComponents attribute) T to_nodes_edges_lattice() (topo_metrics.io.conflink.Configuration method) to_str() (topo_metrics.symbols.VertexSymbol method) to_tuple() (in module topo_metrics.utils) to_xyz() (topo_metrics.ring_geometry.RingGeometry method) topo_metrics module topo_metrics.analysis module topo_metrics.clusters module topo_metrics.io module topo_metrics.io.cgd module topo_metrics.io.conflink module topo_metrics.io.lammps_data module topo_metrics.io.lmp module topo_metrics.knots module topo_metrics.neighbours module topo_metrics.paths module topo_metrics.ring_geometry module topo_metrics.rings module topo_metrics.symbols module topo_metrics.topology module topo_metrics.utils module Topology (class in topo_metrics.topology) U uniform_repr() (in module topo_metrics.utils) V vector (topo_metrics.symbols.CARVS attribute), [1] (topo_metrics.symbols.VertexSymbol attribute), [1] vector_all_rings (topo_metrics.symbols.VertexSymbol attribute), [1] VertexSymbol (class in topo_metrics.symbols) W write_rings_lammps_full() (in module topo_metrics.io.lmp) writhe_and_acn() (topo_metrics.ring_geometry.RingGeometry method) writhe_method_1a() (in module topo_metrics.knots) writhe_method_1b() (in module topo_metrics.knots) writhe_method_2a() (in module topo_metrics.knots) writhe_method_2b() (in module topo_metrics.knots)