Index

A

AcceptanceCalculator (class in pimms.acceptance) add_derived_keywords() (pimms.keyfile_parser.KeyFileParser method) add_extra_chains() (pimms.restart.RestartObject method) alt_Markov_chain_update_move_logs() (pimms.acceptance.AcceptanceCalculator method) ANAFUNCT_acceptance() (pimms.simulation.Simulation method) ANAFUNCT_cluster_analysis() (pimms.simulation.Simulation method) ANAFUNCT_custom_stubb() (pimms.simulation.Simulation method) ANAFUNCT_distance_map() (pimms.simulation.Simulation method) ANAFUNCT_end_to_end() (pimms.simulation.Simulation method)

ANAFUNCT_internal_scaling() (pimms.simulation.Simulation method) ANAFUNCT_polymeric_properties() (pimms.simulation.Simulation method) ANAFUNCT_save_restart() (pimms.simulation.Simulation method) AnalysisSettings (class in pimms.data_structures) analyze() (in module pimms.lemonade.phase_separation) append_to_xtc_file() (in module pimms.lattice_utils) append_to_xtc_file_non_redundant() (in module pimms.lattice_utils) asphericity() (pimms.lemonade.LatticeTrajectory method) assign_default() (pimms.keyfile_parser.KeyFileParser method) auxillary_chain_update() (pimms.simulation.Simulation method)

B

bead_type_composition (pimms.lemonade.Cluster property) beads (pimms.data_structures.FreezeFile property) BinodalFit (class in pimms.lemonade.phase_separation) boltzmann_acceptance() (pimms.acceptance.AcceptanceCalculator method) build_all_envelope_pairs() (in module pimms.lattice_utils)

build_angle_interactions() (pimms.energy.Hamiltonian method) build_envelope_pairs() (in module pimms.lattice_utils) build_from_file() (pimms.restart.RestartObject method) build_from_lattice() (pimms.restart.RestartObject method) build_interaction_table() (pimms.energy.Hamiltonian method) build_R2R_distance_distribution_analysis() (pimms.simulation.Simulation method)

C

center_of_mass() (pimms.lemonade.LatticeTrajectory method) center_of_mass_from_positions() (in module pimms.lattice_utils) center_positions() (in module pimms.lattice_utils) chain_type_composition (pimms.lemonade.Cluster property) chains (pimms.data_structures.FreezeFile property) check_all_chain_connectivity() (in module pimms.lattice_utils) check_chain_connectivity() (in module pimms.lattice_utils) close_xtc_writer() (in module pimms.lattice_utils) Cluster (class in pimms.lemonade) cluster_size_distribution() (in module pimms.lemonade.phase_separation)

clusters (pimms.lemonade.Frame property) compute_cluster_gross_properties() (in module pimms.lattice_analysis_utils) compute_cluster_radial_density_profile() (in module pimms.lattice_analysis_utils) condensed_fraction() (in module pimms.lemonade.phase_separation) convert_chain_to_single_image() (in module pimms.lattice_utils) convert_sequence_to_integer_sequence() (pimms.energy.EmptyHamiltonian method) (pimms.energy.Hamiltonian method) convert_sequence_to_LR_integer_sequence() (pimms.energy.EmptyHamiltonian method) (pimms.energy.Hamiltonian method) correct_cluster_positions_to_single_image() (in module pimms.lattice_analysis_utils) correct_LR_cluster_positions_to_single_image() (in module pimms.lattice_analysis_utils)

D

delete_chain_by_ID() (in module pimms.lattice_utils) delete_chain_by_position() (in module pimms.lattice_utils) delete_residue() (in module pimms.lattice_utils) density (pimms.lemonade.Cluster property) distance_map() (pimms.lemonade.Polymer method)

DistanceMap (class in pimms.analysis_structures) do_positions_stradle_pbc_boundary() (in module pimms.lattice_utils) droplet (pimms.lemonade.Frame property) droplet_shape() (in module pimms.lemonade.phase_separation) droplet_surface_tension() (in module pimms.lemonade.surface_tension)

E

EmptyHamiltonian (class in pimms.energy) end_of_simulation_analysis() (pimms.simulation.Simulation method) end_to_end_distance() (pimms.lemonade.LatticeTrajectory method) evaluate_angle_energy() (pimms.energy.EmptyHamiltonian method) (pimms.energy.Hamiltonian method) evaluate_local_energy() (pimms.energy.EmptyHamiltonian method) (pimms.energy.Hamiltonian method)

evaluate_local_energy_LR() (pimms.energy.EmptyHamiltonian method) (pimms.energy.Hamiltonian method) evaluate_local_energy_SLR() (pimms.energy.Hamiltonian method) evaluate_total_energy() (pimms.energy.EmptyHamiltonian method) (pimms.energy.Hamiltonian method) extract_cluster_polymeric_properties() (in module pimms.lattice_analysis_utils) extract_positions_from_clusters() (in module pimms.lattice_analysis_utils)

F

filename (pimms.data_structures.FreezeFile property) find_nearest_position() (in module pimms.lattice_utils) finish_pdb_file() (in module pimms.lattice_utils) fit_radial_profile() (in module pimms.lemonade.phase_separation)

fit_scaling_exponent() (pimms.analysis_structures.InternalScalingSquared method) fit_slab_profile() (in module pimms.lemonade.phase_separation) Frame (class in pimms.lemonade) FreezeFile (class in pimms.data_structures)

G

get_adjacent_sites_2D() (in module pimms.lattice_utils) get_adjacent_sites_3D() (in module pimms.lattice_utils) get_all_chains_in_connected_component() (in module pimms.lattice_utils) get_all_chains_in_long_range_cluster() (in module pimms.lattice_utils) get_cluster_distribution() (in module pimms.lattice_analysis_utils) get_dimensions() (in module pimms.lattice_utils) get_distance_map() (pimms.analysis_structures.DistanceMap method) get_eigenvalues_of_the_T_matrix() (in module pimms.lattice_analysis_utils) get_empty_site() (in module pimms.lattice_utils) get_gridvalue() (in module pimms.lattice_utils) get_gridvalue_2D() (in module pimms.lattice_utils)

get_gridvalue_3D() (in module pimms.lattice_utils) get_indices_of_long_range_residues() (pimms.energy.EmptyHamiltonian method) (pimms.energy.Hamiltonian method) get_inter_position_distance() (in module pimms.lattice_analysis_utils) get_inter_position_distances() (in module pimms.lattice_analysis_utils) get_internal_scaling_array() (pimms.analysis_structures.InternalScaling method) (pimms.analysis_structures.InternalScalingSquared method) get_LR_cluster_distribution() (in module pimms.lattice_analysis_utils) get_polymeric_properties() (in module pimms.lattice_analysis_utils) get_real_distance() (in module pimms.lattice_utils) get_total_aux_chain_moves() (pimms.acceptance.AcceptanceCalculator method) grid (pimms.lemonade.Frame property)

H

Hamiltonian (class in pimms.energy)

I

insert_chain() (in module pimms.lattice_utils) insert_residue() (in module pimms.lattice_utils) internal_scaling() (pimms.lemonade.Polymer method)

InternalScaling (class in pimms.analysis_structures) InternalScalingSquared (class in pimms.analysis_structures) is_phase_separated (pimms.lemonade.phase_separation.PhaseSeparationResult property)

K

KeyFileParser (class in pimms.keyfile_parser)

L

largest_cluster_size() (in module pimms.lemonade.phase_separation) LatticeTrajectory (class in pimms.lemonade)

load() (in module pimms.lemonade) log_freeze_file() (pimms.data_structures.FreezeFile method)

M

make_chain_whole() (in module pimms.lattice_utils) megastep_update_move_logs() (pimms.acceptance.AcceptanceCalculator method) module pimms.acceptance pimms.analysis_IO pimms.analysis_structures pimms.chain pimms.chainTSMMC pimms.data_structures pimms.energy pimms.keyfile_parser pimms.lattice pimms.lattice_analysis_utils pimms.lattice_utils pimms.lemonade.phase_separation pimms.lemonade.surface_tension pimms.moves pimms.parameterfile_parser pimms.restart pimms.simulation

move_selector() (pimms.acceptance.AcceptanceCalculator method)

N

number_of_clusters() (in module pimms.lemonade.phase_separation)

O

open_pdb_file() (in module pimms.lattice_utils)

open_xtc_writer() (in module pimms.lattice_utils)

P

parse() (pimms.keyfile_parser.KeyFileParser method) parse_angles() (in module pimms.parameterfile_parser) parse_energy() (in module pimms.parameterfile_parser) pbc_convert() (in module pimms.lattice_utils) pbc_correct() (in module pimms.lattice_utils) PhaseSeparationResult (class in pimms.lemonade.phase_separation) pimms.acceptance module pimms.analysis_IO module pimms.analysis_structures module pimms.chain module pimms.chainTSMMC module pimms.data_structures module pimms.energy module pimms.keyfile_parser module pimms.lattice module pimms.lattice_analysis_utils module

pimms.lattice_utils module pimms.lemonade.phase_separation module pimms.lemonade.surface_tension module pimms.moves module pimms.parameterfile_parser module pimms.restart module pimms.simulation module place_chain_by_position() (in module pimms.lattice_utils) Polymer (class in pimms.lemonade) positions (pimms.lemonade.Cluster property) (pimms.lemonade.Frame property) (pimms.lemonade.LatticeTrajectory property) (pimms.lemonade.Polymer property) print_keyword_info() (in module pimms.keyfile_parser) print_status() (pimms.analysis_structures.InternalScaling method) (pimms.analysis_structures.InternalScalingSquared method) print_summary() (pimms.keyfile_parser.KeyFileParser method)

Q

quench_update() (pimms.simulation.Simulation method)

R

radial_density_profile() (in module pimms.lemonade.phase_separation) (pimms.lemonade.Cluster method) radius_of_gyration() (pimms.lemonade.LatticeTrajectory method) RestartObject (class in pimms.restart) rigid_cluster_move() (pimms.simulation.Simulation method) rigid_cluster_revert() (pimms.simulation.Simulation method)

rotate_positions_2D() (in module pimms.lattice_utils) rotate_positions_3D() (in module pimms.lattice_utils) run_all_analysis() (pimms.simulation.Simulation method) run_rotation() (in module pimms.lattice_utils) run_sanity_checks() (pimms.keyfile_parser.KeyFileParser method) run_simulation() (pimms.simulation.Simulation method)

S

same_sites() (in module pimms.lattice_utils) sanity_check_and_update_with_restart_file() (pimms.keyfile_parser.KeyFileParser method) save_out_sim() (in module pimms.lattice_utils) set_defaults() (pimms.keyfile_parser.KeyFileParser method) set_dynamic_defaults() (pimms.keyfile_parser.KeyFileParser method) set_energy() (pimms.restart.RestartObject method) set_gridvalue() (in module pimms.lattice_utils) set_hardwall() (pimms.energy.Hamiltonian method) setup_analysis() (pimms.simulation.Simulation method) Simulation (class in pimms.simulation) simulation_IO() (pimms.simulation.Simulation method)

single_chain_move() (pimms.simulation.Simulation method) single_chain_revert() (pimms.simulation.Simulation method) single_image_positions() (pimms.lemonade.Cluster method) slab_density_profile() (in module pimms.lemonade.phase_separation) slab_surface_tension() (in module pimms.lemonade.surface_tension) sphericity (pimms.lemonade.Cluster property) start_xtc_file() (in module pimms.lattice_utils) startup_analysis() (pimms.simulation.Simulation method) straddles_boundary (pimms.lemonade.Polymer property) surface_tension() (in module pimms.lemonade.surface_tension) SurfaceTension (class in pimms.lemonade.surface_tension)

T

temperature (pimms.lemonade.LatticeTrajectory property)

total_attempted_moves() (pimms.acceptance.AcceptanceCalculator method)

U

update_dimensions() (pimms.simulation.Simulation method) update_distance_map() (pimms.analysis_structures.DistanceMap method) update_internal_scaling() (pimms.analysis_structures.InternalScaling method) (pimms.analysis_structures.InternalScalingSquared method)

update_keyfile() (pimms.keyfile_parser.KeyFileParser method) update_lattice_dimensions() (pimms.restart.RestartObject method) update_master_traj() (in module pimms.lattice_utils) update_move_logs() (pimms.acceptance.AcceptanceCalculator method) update_temperature() (pimms.acceptance.AcceptanceCalculator method)

V

validate_freeze_file() (pimms.data_structures.FreezeFile method)

volume (pimms.lemonade.Cluster property)

W

whole_positions (pimms.lemonade.Polymer property) whole_positions() (pimms.lemonade.LatticeTrajectory method) write_acceptance_statistics() (in module pimms.analysis_IO) write_angle_parameter_summary() (in module pimms.parameterfile_parser) write_asphericity() (in module pimms.analysis_IO) write_cluster_properties() (in module pimms.analysis_IO) write_clusters() (in module pimms.analysis_IO) write_distance_map() (in module pimms.analysis_IO) write_end_to_end() (in module pimms.analysis_IO) write_energy() (in module pimms.analysis_IO) write_internal_scaling() (in module pimms.analysis_IO) write_keyfile() (pimms.keyfile_parser.KeyFileParser method)

write_lattice_to_pdb() (in module pimms.lattice_utils) write_LR_cluster_properties() (in module pimms.analysis_IO) write_LR_clusters() (in module pimms.analysis_IO) write_performance() (in module pimms.analysis_IO) write_quench_file() (in module pimms.analysis_IO) write_radius_of_gyration() (in module pimms.analysis_IO) write_residue_residue_distance() (in module pimms.analysis_IO) write_scaling_information() (in module pimms.analysis_IO) write_status() (pimms.analysis_structures.DistanceMap method) (pimms.analysis_structures.InternalScaling method) (pimms.analysis_structures.InternalScalingSquared method) write_to_file() (pimms.restart.RestartObject method) write_xtc_frame() (in module pimms.lattice_utils)