Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W _ _written_bond_files (ArbdEngine attribute) A AbstractIBIpotential (class in arbdmodel.ibi) AbstractPotential (class in arbdmodel.interactions) add() (ArbdModel method) (Parent method) add_angle() (Parent method) add_bond() (Parent method) add_bond_angle() (Parent method) add_confinement() (ShapeCGModel method) add_diffusible_object() (StructureRigidBodyModel method) add_dihedral() (Parent method) add_exclusion() (Parent method) add_grid_potential() (ParticleType method) (PointParticle method) (PolymerGroup method) add_group_site() (ArbdModel method) add_improper() (Parent method) add_location() (PolymerSection method) add_nonbonded_interaction() (ArbdModel method) add_product_potential() (Parent method) add_protein_nb_interactions() (ShapeCGModel method) add_proteins() (ShapeCGModel method) add_restraint() (GroupSite method), [1] (PointParticle method) (RigidBody method) add_smaller_grid() (in module arbdmodel.grid) add_static_object() (StructureRigidBodyModel method) add_vector_angle() (Parent method) align_structure() (StructureProcessor method) AngleDof (class in arbdmodel.ibi) APBSRunner (class in arbdmodel.engine) apply_gaussian_smoothing() (StructureProcessor method) applyOrientation() (Transformable method) ArbdEngine (class in arbdmodel.engine) ArbdModel (class in arbdmodel.model) arbdmodel.binary_manager module arbdmodel.coords module arbdmodel.core_objects module arbdmodel.engine module arbdmodel.fjc_polymer_model module arbdmodel.grid module arbdmodel.hps_polymer_model module arbdmodel.ibi module arbdmodel.interactions module arbdmodel.kh_polymer_model module arbdmodel.logger module arbdmodel.mesh_process_surface module arbdmodel.mesh_process_volume module arbdmodel.mesh_rigidbody module arbdmodel.model module arbdmodel.mpipi_polymer module arbdmodel.onck_polymer_model module arbdmodel.parmed_bd module arbdmodel.polymer module arbdmodel.sali_polymer_model module arbdmodel.shape_cg module arbdmodel.sim_config module arbdmodel.simplearbd module arbdmodel.ssdna_two_bead module arbdmodel.structure_from_pdb module arbdmodel.structure_rigidbody module arbdmodel.version module assign_IBI_degrees_of_freedom() (ArbdModel method) attach_particle() (RigidBodyType method) average_grids() (in module arbdmodel.grid) B b (DnaStrandBeads attribute) bins (AbstractIBIpotential attribute) BondAngleDof (class in arbdmodel.ibi) BondDof (class in arbdmodel.ibi) Bound_grid() (in module arbdmodel.grid) BoundaryPotential (class in arbdmodel.interactions) C cacheUpToDate (ArbdEngine attribute) calc_atom_sasa() (ShapeCGFactory method) calculate_damping() (MeshProcessor method) (SurfaceMeshProcessor method) calculate_dimensions_from_cell_vectors() (in module arbdmodel.coords) calculate_hydrodynamic_properties() (StructureProcessor method) calculate_total_mass() (ShapeCGModel method) call_git_describe() (in module arbdmodel.version) check_git_repository() (in module arbdmodel.version) Child (class in arbdmodel.core_objects) Citation (class in arbdmodel.version) clear_all() (ArbdModel method) (Parent method) Clone (class in arbdmodel.core_objects) clone() (Group method), [1] combine() (SimConf method) compute_volume() (AngleDof method) (BondDof method) (DegreeOfFreedom method) (PairDistributionDof method) (RadiusDof method) concentration_to_debye_length() (ShapeCGModel method) configuration (ArbdEngine attribute) ConnectableElement (class in arbdmodel.polymer) Connection (class in arbdmodel.polymer) connection_locations (ConnectableElement attribute) connections (ConnectableElement attribute) constant_force() (in module arbdmodel.grid) contour_to_monomer_index() (PolymerSection method) contour_to_orientation() (PolymerSection method) contour_to_position() (PolymerSection method) contour_to_tangent() (PolymerSection method) convert_sod_to_mg() (ParmedArbd static method) convolve_kernel_truncate() (in module arbdmodel.grid) create_bounding_grid() (in module arbdmodel.grid) create_dual_topology() (ParmedArbd static method) create_dual_topology_model() (ParmedArbd class method) create_engine() (SimpleArbdConfig method) create_model() (SimpleArbdConfig method) Create_null() (in module arbdmodel.grid) D debye_length (KhNonbonded attribute) default_binary (ArbdEngine property) (NamdEngine property) (SimEngine property) DefaultSimConf (class in arbdmodel.sim_config) DegreeOfFreedom (class in arbdmodel.ibi) delete() (Connection method) DiffusiveRigidBodyType (class in arbdmodel.structure_rigidbody) DihedralDof (class in arbdmodel.ibi) dimensions_from_structure() (ArbdModel method) (PolymerGroup method) display() (Citation method) DnaModel (class in arbdmodel.ssdna_two_bead) DnaStrandBeads (class in arbdmodel.ssdna_two_bead) duplicate() (Group method), [1] (PointParticle method) (RigidBody method) E end_position (PolymerSection attribute) excludedParameters (ParticleType attribute) extend() (ArbdModel method) (PolymerGroup method) extra_bd_file_lines (ArbdEngine attribute) F filename() (AbstractIBIpotential method), [1] (AbstractPotential method) (HarmonicBondedPotential method) (NullPotential method) (ShapeCGNonbonded method) (WLCSKPotential method) fill_nans() (in module arbdmodel.grid) find_shape_based_sites() (in module arbdmodel.shape_cg) FjcBeadsFromPolymer (class in arbdmodel.fjc_polymer_model) FjcModel (class in arbdmodel.fjc_polymer_model) from_protein_list() (ShapeCGModel class method) G gaussian_kernel() (in module arbdmodel.grid) generate_beads() (PolymerModel method) (SaliModel method) generate_charge_distribution() (StructureProcessor method) Generate_coordinates() (in module arbdmodel.coords) generate_electrostatic_map() (StructureProcessor method) generate_potential_grid() (MeshProcessor method) (SurfaceMeshProcessor method) generate_protein() (ShapeCGFactory method) generate_random_protein_positions() (ShapeCGModel method) Generate_spanning_vectors() (in module arbdmodel.coords) generate_vdw_maps() (StructureProcessor method) get_angles() (Parent method) get_attached_particles() (MeshProcessor method) (SurfaceMeshProcessor method) get_binary() (SimConf method) get_bond_angles() (Parent method) get_bonds() (Parent method) get_center() (GroupSite method), [1] (Parent method) (PolymerGroup method) (PolymerSection method) get_cg_distribution() (AbstractIBIpotential method), [1] get_coarse_protein() (ShapeCGFactory method) get_coarse_types() (ShapeCGFactory method) get_collapsed_position() (Transformable method) get_connected_location() (Location method) get_connections() (PolymerGroup method) get_connections_and_locations() (ConnectableElement method), [1] get_contour_sorted_connections_and_locations() (PolymerSection method) get_default_conf() (ArbdEngine method) (NamdEngine method) (SimEngine method) get_dihedrals() (Parent method) get_exclusions() (Parent method) get_grid_files() (StructureProcessor method) get_impropers() (Parent method) get_location_at() (ConnectableElement method), [1] get_locations() (ConnectableElement method), [1] get_monomer_index() (Location method) get_original_recursively() (Clone method) get_particle_assignments() (in module arbdmodel.shape_cg) get_product_potentials() (Parent method) get_protein_types() (ShapeCGModel method) get_resource_path() (in module arbdmodel.logger) get_restraints() (GroupSite method), [1] (Parent method) (PointParticle method) (RigidBody method) get_slice_enclosing_smaller_grid() (in module arbdmodel.grid) get_target_distribution() (AbstractIBIpotential method), [1] get_values() (DegreeOfFreedom method) (PairDistributionDof method) get_vector_angles() (Parent method) get_version() (in module arbdmodel.version) getParticleTypesAndCounts() (ArbdModel method) Group (class in arbdmodel.core_objects) GroupSite (class in arbdmodel.core_objects) H HalfHarmonic (class in arbdmodel.interactions) HarmonicAngle (class in arbdmodel.interactions) HarmonicBond (class in arbdmodel.interactions) HarmonicBondedPotential (class in arbdmodel.interactions) HarmonicDihedral (class in arbdmodel.interactions) HarmonicVectorAngle (class in arbdmodel.interactions) HpsBeads (class in arbdmodel.hps_polymer_model) HpsModel (class in arbdmodel.hps_polymer_model) HpsNonbonded (class in arbdmodel.hps_polymer_model) HydroProRunner (class in arbdmodel.engine) I IBIAngle (class in arbdmodel.ibi) IBIBond (class in arbdmodel.ibi) IBIDihedral (class in arbdmodel.ibi) IBINonbonded (class in arbdmodel.ibi) index() (Parent method) initialize_binary_paths() (in module arbdmodel.binary_manager) insert() (Parent method) insert_monomers() (PolymerSection method) is_dirty() (in module arbdmodel.version) is_same_type() (ParticleType method) isotropic_kernel() (in module arbdmodel.grid) items() (SimConf method) iterate_connections_and_locations() (PolymerSection method) K KhBeads (class in arbdmodel.kh_polymer_model) KhModel (class in arbdmodel.kh_polymer_model) KhNonbonded (class in arbdmodel.kh_polymer_model) kscale (HarmonicAngle property) (HarmonicBond property) (HarmonicBondedPotential property) (HarmonicDihedral property) (HarmonicVectorAngle property) L LennardJones (class in arbdmodel.interactions) LinearBond (class in arbdmodel.sali_polymer_model) load_structure() (ParmedArbd method) load_target_IBI_distributions() (ArbdModel method) loadGrid() (in module arbdmodel.grid) Location (class in arbdmodel.polymer) locations (ConnectableElement attribute) M main() (in module arbdmodel.simplearbd) max_force (KhNonbonded attribute) MeshProcessor (class in arbdmodel.mesh_process_volume) MeshRigidBodyType (class in arbdmodel.mesh_rigidbody) MICRON_TO_ANGSTROM (MeshProcessor attribute) (SurfaceMeshProcessor attribute) minimizeRmsd() (in module arbdmodel.coords) module arbdmodel.binary_manager arbdmodel.coords arbdmodel.core_objects arbdmodel.engine arbdmodel.fjc_polymer_model arbdmodel.grid arbdmodel.hps_polymer_model arbdmodel.ibi arbdmodel.interactions arbdmodel.kh_polymer_model arbdmodel.logger arbdmodel.mesh_process_surface arbdmodel.mesh_process_volume arbdmodel.mesh_rigidbody arbdmodel.model arbdmodel.mpipi_polymer arbdmodel.onck_polymer_model arbdmodel.parmed_bd arbdmodel.polymer arbdmodel.sali_polymer_model arbdmodel.shape_cg arbdmodel.sim_config arbdmodel.simplearbd arbdmodel.ssdna_two_bead arbdmodel.structure_from_pdb arbdmodel.structure_rigidbody arbdmodel.version monomer_index_to_contour() (PolymerSection method) monomer_length (PolymerSection attribute) monomers_per_bead_group (PolymerBeads property) MpipiBeads (class in arbdmodel.mpipi_polymer) MpipiModel (class in arbdmodel.mpipi_polymer) MpipiNonbonded (class in arbdmodel.mpipi_polymer) N NamdEngine (class in arbdmodel.engine) neighborhood_average() (in module arbdmodel.grid) nt (DnaStrandBeads attribute) NullPotential (class in arbdmodel.interactions) num_bead_groups (PolymerBeads property) num_monomers (PolymerSection attribute) num_particles (ArbdEngine attribute) O OnckBeads (class in arbdmodel.onck_polymer_model) OnckModel (class in arbdmodel.onck_polymer_model) OnckNonbonded (class in arbdmodel.onck_polymer_model) other() (Connection method) P p (DnaStrandBeads attribute) PairDistributionDof (class in arbdmodel.ibi) Parent (class in arbdmodel.core_objects) ParmedArbd (class in arbdmodel.parmed_bd) parse_output() (HydroProRunner method) particles (ArbdEngine attribute) ParticleType (class in arbdmodel.core_objects) PdbModel (class in arbdmodel.model) periodic (AbstractPotential property) (HarmonicDihedral property) (IBIDihedral property) PointParticle (class in arbdmodel.core_objects) PolymerBeads (class in arbdmodel.polymer) PolymerGroup (class in arbdmodel.polymer) PolymerModel (class in arbdmodel.polymer) PolymerSection (class in arbdmodel.polymer) position_spline_params (PolymerSection attribute) potential (AbstractIBIpotential attribute) potential() (AbstractIBIpotential method), [1] (AbstractPotential method) (BoundaryPotential method) (HalfHarmonic method) (HarmonicBond method) (HarmonicBondedPotential method) (HpsNonbonded method) (KhNonbonded method), [1] (LennardJones method) (LinearBond method) (MpipiNonbonded method) (NullPotential method) (OnckNonbonded method) (SaliNonbonded method) (ShapeCGNonbonded method) (TabulatedNonbonded method) (WLCSKAngle method) (WLCSKBond method) potential_directory (ArbdEngine attribute) prepare_for_simulation() (ArbdModel method) process() (StaticObject method) process_mesh_file() (in module arbdmodel.mesh_process_volume) process_structure() (StructureProcessor method) process_surface_mesh() (in module arbdmodel.mesh_process_surface) Q quaternion_exp() (in module arbdmodel.coords) quaternion_from_matrix() (in module arbdmodel.coords) quaternion_inverse() (in module arbdmodel.coords) quaternion_product() (in module arbdmodel.coords) quaternion_slerp() (in module arbdmodel.coords) quaternion_spline_params (PolymerSection attribute) quaternion_to_matrix() (in module arbdmodel.coords) R RadiusDof (class in arbdmodel.ibi) range_ (AbstractPotential property) rb_type_dirs (ArbdEngine attribute) read_arbd_coordinates() (in module arbdmodel.coords) read_average_arbd_coordinates() (in module arbdmodel.coords) read_cg_potential() (AbstractIBIpotential method), [1] read_files() (in module arbdmodel.shape_cg) read_release_version() (in module arbdmodel.version) read_version_file() (in module arbdmodel.version) readArbdCoords() (in module arbdmodel.coords) readAvgArbdCoords() (in module arbdmodel.coords) remove() (Parent method) remove_monomers() (PolymerSection method) replace_false_with_distance() (in module arbdmodel.grid) RigidBody (class in arbdmodel.core_objects) RigidBodyType (class in arbdmodel.core_objects) rotate() (PolymerGroup method) (PolymerSection method) (Transformable method) rotationAboutAxis() (in module arbdmodel.coords) run_calculation() (APBSRunner method) (HydroProRunner method) run_from_minimized() (ShapeCGModel method) run_IBI() (ArbdModel method) run_minimization() (ShapeCGModel method) run_simulation() (SimpleArbdConfig method) (SimpleArbdEngine method) S SaliBeadsFromPolymer (class in arbdmodel.sali_polymer_model) SaliModel (class in arbdmodel.sali_polymer_model) SaliNonbonded (class in arbdmodel.sali_polymer_model) save_aligned_mesh() (MeshProcessor method) (SurfaceMeshProcessor method) save_aligned_mesh_both_formats() (SurfaceMeshProcessor method) save_as_pdb() (MeshProcessor method) (SurfaceMeshProcessor method) segname (PolymerSection attribute) sequence (PolymerSection attribute) set_binary() (SimConf method) set_connection() (Location method) set_damping_coefficient() (FjcModel method) (HpsModel method) (KhModel method) (MpipiModel method) (OnckModel method) set_orientation_splines() (PolymerSection method) set_splines() (PolymerSection method) setup_and_run() (ShapeCGModel method) setup_diffusible_objects() (SimpleArbdConfig method) setup_static_objects() (SimpleArbdConfig method) ShapeCGFactory (class in arbdmodel.shape_cg) ShapeCGModel (class in arbdmodel.shape_cg) ShapeCGNonbonded (class in arbdmodel.shape_cg) SimConf (class in arbdmodel.sim_config) SimEngine (class in arbdmodel.engine) SimpleArbdConfig (class in arbdmodel.simplearbd) SimpleArbdEngine (class in arbdmodel.structure_rigidbody) simulate() (ArbdModel method) (ParmedArbd method) (SimEngine method) slab_potential_z() (in module arbdmodel.grid) spherical_confinement() (in module arbdmodel.grid) spring_constant (HpsModel attribute) (KhModel attribute) (MpipiModel attribute) start_orientation (PolymerSection attribute) start_position (PolymerSection attribute) StaticObject (class in arbdmodel.structure_rigidbody) StructureProcessor (class in arbdmodel.structure_from_pdb) StructureRigidBodyModel (class in arbdmodel.structure_rigidbody) SurfaceMeshProcessor (class in arbdmodel.mesh_process_surface) T TabulatedNonbonded (class in arbdmodel.interactions) temperature (DefaultSimConf property) (SimConf property) test_average_grids() (TestAverageGrids method) TestAverageGrids (class in arbdmodel.grid) transform() (Transformable method) Transformable (class in arbdmodel.core_objects) translate() (PolymerGroup method) (PolymerSection method) (Transformable method) type_ (HarmonicAngle property) (HarmonicBond property) (HarmonicBondedPotential property) (HarmonicDihedral property) (HarmonicVectorAngle property) (WLCSKAngle property) (WLCSKBond property) type_counts (ArbdEngine attribute) U unit_quat_conversions() (in module arbdmodel.coords) update() (ArbdModel method) (PolymerGroup method) update_splines() (PolymerModel method) (SaliModel method) useNonbondedScheme() (ArbdModel method) V vmd_cylinder_tcl() (PolymerGroup method) vmd_tube_tcl() (PolymerGroup method) W WLCSKAngle (class in arbdmodel.interactions) WLCSKBond (class in arbdmodel.interactions) WLCSKPotential (class in arbdmodel.interactions) wrap_vector() (DegreeOfFreedom method) write_cg_potential() (AbstractIBIpotential method), [1] write_conf() (NamdEngine method) write_config() (APBSRunner method) (HydroProRunner method) write_confine_dx() (in module arbdmodel.grid) write_file() (AbstractIBIpotential method), [1] (AbstractPotential method) (BoundaryPotential method) (IBINonbonded method) (TabulatedNonbonded method) write_no_enter_potential() (MeshProcessor method) write_no_enter_potential_dx() (SurfaceMeshProcessor method) write_pdb() (PdbModel method) write_pqr() (PdbModel method) write_psf() (PdbModel method) write_release_version() (in module arbdmodel.version) write_restraint_files() (ParmedArbd method) write_simulation_files() (ArbdEngine method) (NamdEngine method) (SimEngine method) (SimpleArbdEngine method) writeDx() (in module arbdmodel.grid)