Index

_

__call__() (pressomancy.helper_functions.RoutineWithArgs method) __init__() (pressomancy.simulation.Simulation method) __name__ (pressomancy.helper_functions.ManagedSimulation attribute)

__qualname__ (pressomancy.helper_functions.ManagedSimulation attribute) _espressomd_system (pressomancy.helper_functions.ManagedSimulation attribute) _global_registry (pressomancy.helper_functions.SinglePairDict attribute)

A

aClass (pressomancy.helper_functions.ManagedSimulation attribute) add_anchors() (pressomancy.object_classes.filament_class.Filament method) add_bending_potential() (pressomancy.object_classes.filament_class.Filament method) (pressomancy.object_classes.quadriplex_class.Quadriplex method) add_dipole_to_embedded_virt() (pressomancy.object_classes.filament_class.Filament method)

add_dipole_to_type() (pressomancy.object_classes.filament_class.Filament method) add_particle() (pressomancy.object_classes.object_class.Simulation_Object method) add_patches_triples() (pressomancy.object_classes.quadriplex_class.Quadriplex method) align_vectors() (in module pressomancy.helper_functions) avoid_explosion() (pressomancy.simulation.Simulation method), [1]

B

bond_center_to_center() (pressomancy.object_classes.filament_class.Filament method) bond_nearest_part() (pressomancy.object_classes.filament_class.Filament method) bond_overlapping_virtualz() (pressomancy.object_classes.filament_class.Filament method) bond_owned_part_pair() (pressomancy.object_classes.object_class.Simulation_Object method)

bond_quadriplexes() (pressomancy.object_classes.filament_class.Filament method) bond_quartets_center_to_center() (pressomancy.object_classes.quadriplex_class.Quadriplex method) bond_quartets_corner_to_corner() (pressomancy.object_classes.quadriplex_class.Quadriplex method) BondWrapper (class in pressomancy.helper_functions) build_grid_and_adjacent() (in module pressomancy.helper_functions)

C

calculate_pair_distances() (in module pressomancy.helper_functions) center_filament() (pressomancy.object_classes.filament_class.Filament method) change_part_type() (pressomancy.object_classes.object_class.Simulation_Object method) collect_instances_recursively() (pressomancy.simulation.Simulation method) common_keys (pressomancy.object_classes.object_class.ObjectConfigParams attribute), [1] config (pressomancy.object_classes.crowder_class.Crowder attribute) (pressomancy.object_classes.egg_model_part.EGGPart attribute) (pressomancy.object_classes.filament_class.Filament attribute) (pressomancy.object_classes.otp_molecule_class.OTP attribute) (pressomancy.object_classes.quadriplex_class.Quadriplex attribute) (pressomancy.object_classes.quadriplex_class.Quartet attribute) (pressomancy.object_classes.raspberry_sphere.RaspberrySphere attribute) (pressomancy.object_classes.stoner_wohlfarth_part.SWPart attribute) (pressomancy.object_classes.tel_sequence.TelSeq attribute)

create_flow_channel() (pressomancy.simulation.Simulation method), [1] Crowder (class in pressomancy.object_classes.crowder_class)

D

default_factory (pressomancy.helper_functions.PartDictSafe attribute) delete_objects() (pressomancy.simulation.Simulation method)

delete_owned_parts() (pressomancy.object_classes.object_class.Simulation_Object method) dump_to_init() (pressomancy.simulation.Simulation method), [1]

E

EGGPart (class in pressomancy.object_classes.egg_model_part)

F

fcc_lattice() (in module pressomancy.helper_functions)

Filament (class in pressomancy.object_classes.filament_class) func (pressomancy.helper_functions.RoutineWithArgs attribute)

G

generate_positions() (in module pressomancy.helper_functions) generate_positions_directed_triples() (in module pressomancy.helper_functions) generate_random_unit_vectors() (in module pressomancy.helper_functions) generic_modify_system_attribute() (in module pressomancy.object_classes.object_class) generic_routine_per_volume() (pressomancy.helper_functions.RoutineWithArgs method) (pressomancy.helper_functions.RoutineWithArgs static method) generic_type_exception() (in module pressomancy.object_classes.object_class) generic_type_exception_inst() (in module pressomancy.object_classes.object_class) get_all_pairs() (pressomancy.helper_functions.SinglePairDict class method) get_child_ids() (pressomancy.analysis.data_analysis.H5DataSelector method)

get_connectivity_map() (pressomancy.analysis.data_analysis.H5DataSelector method) get_connectivity_values() (pressomancy.analysis.data_analysis.H5DataSelector method) get_cross_lattice_nonintersecting_volumes() (in module pressomancy.helper_functions) get_H_ext() (pressomancy.simulation.Simulation method), [1] get_neighbours() (in module pressomancy.helper_functions) get_neighbours_cross_lattice() (in module pressomancy.helper_functions) get_orientation_vec() (in module pressomancy.helper_functions) get_owned_part() (pressomancy.object_classes.object_class.Simulation_Object method) get_parent_ids() (pressomancy.analysis.data_analysis.H5DataSelector method) get_property() (pressomancy.analysis.data_analysis.H5DataSelector method) get_raw_handle() (pressomancy.helper_functions.BondWrapper method)

H

H5DataSelector (class in pressomancy.analysis.data_analysis)

helper_set_attribute() (in module pressomancy.object_classes.object_class)

I

init_args (pressomancy.helper_functions.ManagedSimulation attribute) init_kwargs (pressomancy.helper_functions.ManagedSimulation attribute) init_lb() (pressomancy.simulation.Simulation method), [1]

init_magnetic_inter() (pressomancy.simulation.Simulation method), [1] init_pickle_dump() (pressomancy.simulation.Simulation method), [1] inscribe_part_group_to_h5() (pressomancy.simulation.Simulation method) instance (pressomancy.helper_functions.ManagedSimulation attribute)

K

key (pressomancy.helper_functions.SinglePairDict property)

L

load_coord_file() (in module pressomancy.helper_functions)

load_pickle_dump() (pressomancy.simulation.Simulation method), [1]

M

magnetize() (pressomancy.simulation.Simulation method), [1] make_centered_rand_orient_point_array() (in module pressomancy.helper_functions) ManagedSimulation (class in pressomancy.helper_functions) ManagedSimulation() (in module pressomancy.simulation) mark_covalent_bonds() (pressomancy.object_classes.quadriplex_class.Quadriplex method) mark_covalent_corner() (pressomancy.object_classes.quadriplex_class.Quartet method) mark_for_collision_detection() (pressomancy.simulation.Simulation method), [1] min_img_dist() (in module pressomancy.helper_functions) MissingFeature modify_system_attribute() (pressomancy.simulation.Simulation method), [1] module pressomancy pressomancy.analysis, [1] pressomancy.analysis.data_analysis pressomancy.helper_functions pressomancy.object_classes pressomancy.object_classes.crowder_class pressomancy.object_classes.egg_model_part pressomancy.object_classes.filament_class pressomancy.object_classes.object_class pressomancy.object_classes.otp_molecule_class pressomancy.object_classes.quadriplex_class pressomancy.object_classes.raspberry_sphere pressomancy.object_classes.stoner_wohlfarth_part pressomancy.object_classes.tel_sequence pressomancy.simulation

N

no_objects (pressomancy.simulation.Simulation attribute) num_monomers (pressomancy.helper_functions.RoutineWithArgs attribute) numInstances (pressomancy.object_classes.crowder_class.Crowder attribute) (pressomancy.object_classes.egg_model_part.EGGPart attribute) (pressomancy.object_classes.filament_class.Filament attribute) (pressomancy.object_classes.otp_molecule_class.OTP attribute) (pressomancy.object_classes.quadriplex_class.Quadriplex attribute) (pressomancy.object_classes.quadriplex_class.Quartet attribute) (pressomancy.object_classes.raspberry_sphere.RaspberrySphere attribute) (pressomancy.object_classes.stoner_wohlfarth_part.SWPart attribute) (pressomancy.object_classes.tel_sequence.TelSeq attribute)

O

object_permissions (pressomancy.simulation.Simulation attribute) ObjectConfigParams (class in pressomancy.object_classes.object_class)

objects (pressomancy.simulation.Simulation attribute) OTP (class in pressomancy.object_classes.otp_molecule_class)

P

part_positions (pressomancy.simulation.Simulation attribute) part_types (pressomancy.object_classes.crowder_class.Crowder attribute) (pressomancy.object_classes.egg_model_part.EGGPart attribute) (pressomancy.object_classes.filament_class.Filament attribute) (pressomancy.object_classes.otp_molecule_class.OTP attribute) (pressomancy.object_classes.quadriplex_class.Quadriplex attribute) (pressomancy.object_classes.quadriplex_class.Quartet attribute) (pressomancy.object_classes.raspberry_sphere.RaspberrySphere attribute) (pressomancy.object_classes.stoner_wohlfarth_part.SWPart attribute) (pressomancy.object_classes.tel_sequence.TelSeq attribute) (pressomancy.simulation.Simulation attribute) PartDictSafe (class in pressomancy.helper_functions) ParticleAccessor (class in pressomancy.analysis.data_analysis) particles (pressomancy.analysis.data_analysis.H5DataSelector property) partition_cubic_volume() (in module pressomancy.helper_functions) partition_cubic_volume_oriented_rectangles() (in module pressomancy.helper_functions) partitioned (pressomancy.simulation.Simulation attribute) pressomancy module pressomancy.analysis module, [1] pressomancy.analysis.data_analysis module pressomancy.helper_functions module

pressomancy.object_classes module pressomancy.object_classes.crowder_class module pressomancy.object_classes.egg_model_part module pressomancy.object_classes.filament_class module pressomancy.object_classes.object_class module pressomancy.object_classes.otp_molecule_class module pressomancy.object_classes.quadriplex_class module pressomancy.object_classes.raspberry_sphere module pressomancy.object_classes.stoner_wohlfarth_part module pressomancy.object_classes.tel_sequence module pressomancy.simulation module Properties() (pressomancy.helper_functions.SinglePairDict method)

Q

Quadriplex (class in pressomancy.object_classes.quadriplex_class)

Quartet (class in pressomancy.object_classes.quadriplex_class)

R

RaspberrySphere (class in pressomancy.object_classes.raspberry_sphere) reinitialize_instance() (pressomancy.helper_functions.ManagedSimulation method) required_features (pressomancy.object_classes.crowder_class.Crowder attribute) (pressomancy.object_classes.egg_model_part.EGGPart attribute) (pressomancy.object_classes.filament_class.Filament attribute) (pressomancy.object_classes.otp_molecule_class.OTP attribute) (pressomancy.object_classes.quadriplex_class.Quadriplex attribute) (pressomancy.object_classes.quadriplex_class.Quartet attribute) (pressomancy.object_classes.raspberry_sphere.RaspberrySphere attribute) (pressomancy.object_classes.stoner_wohlfarth_part.SWPart attribute) (pressomancy.object_classes.tel_sequence.TelSeq attribute)

RoutineWithArgs (class in pressomancy.helper_functions) rule_maker() (in module pressomancy.object_classes.tel_sequence)

S

sanity_check() (pressomancy.analysis.data_analysis.H5DataSelector method) (pressomancy.helper_functions.PartDictSafe method) (pressomancy.simulation.Simulation method) seed (pressomancy.simulation.Simulation attribute) select_particles_by_object() (pressomancy.analysis.data_analysis.H5DataSelector method) set_default_factory() (pressomancy.helper_functions.PartDictSafe method) set_H_ext() (pressomancy.simulation.Simulation method), [1] set_hydrod_props() (pressomancy.object_classes.raspberry_sphere.RaspberrySphere method) set_object() (pressomancy.object_classes.crowder_class.Crowder method) (pressomancy.object_classes.egg_model_part.EGGPart method) (pressomancy.object_classes.filament_class.Filament method) (pressomancy.object_classes.object_class.Simulation_Object method) (pressomancy.object_classes.otp_molecule_class.OTP method) (pressomancy.object_classes.quadriplex_class.Quadriplex method) (pressomancy.object_classes.quadriplex_class.Quartet method) (pressomancy.object_classes.raspberry_sphere.RaspberrySphere method) (pressomancy.object_classes.stoner_wohlfarth_part.SWPart method) (pressomancy.object_classes.tel_sequence.TelSeq method) set_objects() (pressomancy.simulation.Simulation method), [1] set_steric() (pressomancy.simulation.Simulation method), [1]

set_steric_custom() (pressomancy.simulation.Simulation method), [1] set_sys() (pressomancy.simulation.Simulation method), [1] set_vdW() (pressomancy.simulation.Simulation method), [1] set_vdW_custom() (pressomancy.simulation.Simulation method), [1] Simulation (class in pressomancy.simulation) Simulation_Object (class in pressomancy.object_classes.object_class) simulation_type (pressomancy.object_classes.crowder_class.Crowder attribute) (pressomancy.object_classes.egg_model_part.EGGPart attribute) (pressomancy.object_classes.filament_class.Filament attribute) (pressomancy.object_classes.otp_molecule_class.OTP attribute) (pressomancy.object_classes.quadriplex_class.Quadriplex attribute) (pressomancy.object_classes.quadriplex_class.Quartet attribute) (pressomancy.object_classes.raspberry_sphere.RaspberrySphere attribute) (pressomancy.object_classes.stoner_wohlfarth_part.SWPart attribute) (pressomancy.object_classes.tel_sequence.TelSeq attribute) SimulationExistsException SinglePairDict (class in pressomancy.helper_functions) specify() (pressomancy.object_classes.object_class.ObjectConfigParams method) store_objects() (pressomancy.simulation.Simulation method), [1] SWPart (class in pressomancy.object_classes.stoner_wohlfarth_part)

T

TelSeq (class in pressomancy.object_classes.tel_sequence)

timestep (pressomancy.analysis.data_analysis.H5DataSelector property) TimestepAccessor (class in pressomancy.analysis.data_analysis)

U

unstore_objects() (pressomancy.simulation.Simulation method)

update() (pressomancy.helper_functions.PartDictSafe method)

V

value (pressomancy.helper_functions.SinglePairDict property)

volume_centers (pressomancy.simulation.Simulation attribute) volume_size (pressomancy.simulation.Simulation attribute)

W

wrap_into_Tel() (pressomancy.object_classes.tel_sequence.TelSeq method)

write_part_group_to_h5() (pressomancy.simulation.Simulation method)