Index _ | A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | U | V | W _ __init__() (AFBuilder method) (CSHBuilder method) (GlassBuilder method) (SolutionBuilder method) (Splitter method) (SurfaceBuilder method) A add_angle() (AtomicSystem method) add_atom() (AtomicSystem method) add_atoms() (AtomicSystem method) add_bond() (AtomicSystem method) add_dihedral() (AtomicSystem method) add_droplet() (AtomicSystem method) add_improper() (AtomicSystem method) add_liquid_layer() (AtomicSystem method) add_solution() (Splitter method) add_structure() (AtomicSystem method) AFBuilder (class in cemd.build) analyze() (CSHBuilder method) analyze_silicates() (in module cemd.analysis) angle_types (AtomicSystem property) apply_pair_mixing_rules() (AtomicSystem method) atom_types (AtomicSystem property) AtomicSystem (class in cemd.core.atomic_system) B best_coordinate() (Splitter method) bond_types (AtomicSystem property) bondcorr() (in module cemd.analysis.tcf) box (AtomicSystem property) build() (AFBuilder method) (CSHBuilder method) (GlassBuilder method) (SolutionBuilder method) (Splitter method) (SurfaceBuilder method) build_afm() (AFBuilder method) build_aft() (AFBuilder method) build_hemisphere() (SolutionBuilder method) C center_on_com() (AtomicSystem method) charges (AtomicSystem property) compute_rdf() (in module cemd.analysis) copy() (AtomicSystem method) count_broken_bonds() (Splitter method) count_broken_ionic() (Splitter method) CSHBuilder (class in cemd.build) D density (AtomicSystem property) density_map() (in module cemd.analysis) density_profile() (in module cemd.analysis) diffusion_coefficient() (in module cemd.analysis) diffusion_coefficient_profile() (in module cemd.analysis.diffusion) dihedral_types (AtomicSystem property) E electrostatic_potential() (in module cemd.analysis) elements (AtomicSystem property) explore() (SurfaceBuilder method) explore_ff_database() (AtomicSystem method) F ff_keys (AtomicSystem property) ff_params (AtomicSystem property) find_broken_bonds() (Splitter method) find_interfaces_coordinates() (in module cemd.analysis.density) from_cod() (AtomicSystem class method) from_elements() (GlassBuilder class method) from_file() (AtomicSystem class method) from_mda() (AtomicSystem class method) from_oxides() (GlassBuilder class method) from_pmg() (AtomicSystem class method) from_pubchem() (AtomicSystem class method) from_smiles() (AtomicSystem class method) from_stoichiometry() (GlassBuilder class method) from_system() (CSHBuilder class method) from_water() (SolutionBuilder class method) G get_actual_density() (GlassBuilder method) get_center_of_mass() (AtomicSystem method) get_coefficient() (GlassBuilder method) get_components() (GlassBuilder method) get_count() (AtomicSystem method) get_elemental_composition() (GlassBuilder method) get_mass_per_formula_unit() (GlassBuilder method) get_num_formula_units() (GlassBuilder method) get_solute_mass() (SolutionBuilder method) get_total_charge() (GlassBuilder method) get_water_count() (SolutionBuilder method) GlassBuilder (class in cemd.build) guess_angles() (AtomicSystem method) guess_connections() (AtomicSystem method) guess_dihedrals() (AtomicSystem method) guess_impropers() (AtomicSystem method) I improper_types (AtomicSystem property) is_pure() (GlassBuilder method) K keep_connection_types() (AtomicSystem method) L lifetime() (in module cemd.analysis.tcf) M masses (AtomicSystem property) msd() (in module cemd.analysis) msd_profile() (in module cemd.analysis) N neutralize_charge() (AtomicSystem method) normalize() (GlassBuilder method) num_angle_types (AtomicSystem property) num_angles (AtomicSystem property) num_atom_types (AtomicSystem property) num_atoms (AtomicSystem property) num_bond_types (AtomicSystem property) num_bonds (AtomicSystem property) num_dihedral_types (AtomicSystem property) num_dihedrals (AtomicSystem property) num_improper_types (AtomicSystem property) num_impropers (AtomicSystem property) O orthogonalize() (AtomicSystem method) P plot_diffusion_profile() (in module cemd.analysis.diffusion) plot_msd() (in module cemd.analysis.diffusion) protonate_atom() (AtomicSystem method) protonate_atoms() (AtomicSystem method) R remove_all_connections() (AtomicSystem method) remove_atom() (AtomicSystem method) remove_atoms() (AtomicSystem method) remove_connection_types() (AtomicSystem method) replicate() (AtomicSystem method) S scan_broken_bonds() (Splitter method) set_angle_ff_keys() (AtomicSystem method) set_angle_params() (AtomicSystem method) set_atom_ff_keys() (AtomicSystem method) set_atom_position() (AtomicSystem method) set_bond_ff_keys() (AtomicSystem method) set_bond_params() (AtomicSystem method) set_box() (AtomicSystem method) set_charges() (AtomicSystem method) set_dihedral_ff_keys() (AtomicSystem method) set_dihedral_params() (AtomicSystem method) set_ff_from_database() (AtomicSystem method) set_ff_keys() (AtomicSystem method) set_improper_ff_keys() (AtomicSystem method) set_improper_params() (AtomicSystem method) set_masses() (AtomicSystem method) set_pair_params() (AtomicSystem method) set_topology() (AtomicSystem method) set_type2atoms() (AtomicSystem method) set_types() (AtomicSystem method) set_types_from_elements() (AtomicSystem method) shift_profile() (in module cemd.analysis.density) side_mask() (Splitter method) SolutionBuilder (class in cemd.build) split() (Splitter method) Splitter (class in cemd.build) summary() (AtomicSystem method) SurfaceBuilder (class in cemd.build) T to_cash() (CSHBuilder method) to_counts() (SolutionBuilder method) to_mda() (AtomicSystem method) to_pmg() (AtomicSystem method) total_charge (AtomicSystem property) total_mass (AtomicSystem property) U unskew() (AtomicSystem method) V view() (AtomicSystem method) volume (AtomicSystem property) W with_coordinate() (Splitter method) wrap() (AtomicSystem method) write() (AtomicSystem method)
