Index

_

_field_descriptors (chromo.fields.UniformDensityField attribute)

A

accept() (chromo.mc.moves.MCAdapter method) AcceptanceTracker (class in chromo.util.mc_stat) access_vols (chromo.fields.UniformDensityField attribute) all_inds (chromo.polymers.PolymerBase attribute) all_moves() (in module chromo.mc.mc_controller) (in module chromo.mc.moves)

all_moves_except_binding_state() (in module chromo.mc.mc_controller) angle_between_vectors() (in module chromo.util.linalg) arbitrary_axis_rotation() (in module chromo.util.linalg) arbitrary_path_in_x_y() (chromo.polymers.SSWLC method) arbitrary_path_in_x_y_z() (chromo.polymers.SSWLC method) assign_beads_to_bins() (in module chromo.fields)

B

Bead (class in chromo.beads) beads (chromo.polymers.PolymerBase attribute) bin_index (chromo.fields.UniformDensityField attribute) Binder (class in chromo.binders) binder_dict (chromo.fields.UniformDensityField attribute)

binder_names (chromo.beads.Bead attribute) (chromo.polymers.PolymerBase attribute) binders (chromo.fields.FieldBase attribute) Bounds (class in chromo.mc.moves) builtin_types (in module chromo.util.reproducibility)

C

calc_mean_r2() (in module chromo.util.poly_stat) calc_r2() (chromo.util.poly_stat.PolyStats method) calc_r4() (chromo.util.poly_stat.PolyStats method) change_binding_state() (in module chromo.mc.move_funcs) check_attrs() (chromo.polymers.PolymerBase method) check_steric_clashes() (chromo.polymers.DetailedChromatinWithSterics method) chemical_mod_names (chromo.polymers.PolymerBase attribute) chemical_mods (chromo.polymers.PolymerBase attribute) chi (chromo.fields.UniformDensityField attribute) Chromatin (class in chromo.polymers) chromo module chromo.beads module chromo.binders module chromo.fields module chromo.mc module chromo.mc.mc_controller module chromo.mc.mc_sim module chromo.mc.move_funcs module chromo.mc.moves module chromo.mixtures module chromo.polymers module chromo.util module chromo.util.bead_selection module chromo.util.gjk module

chromo.util.linalg module chromo.util.mc_stat module chromo.util.poly_paths module chromo.util.poly_stat module chromo.util.reproducibility module combine_repeat() (in module chromo.util) compute_dE() (chromo.polymers.DetailedChromatinWithSterics method) compute_E() (chromo.fields.UniformDensityField method) (chromo.polymers.DetailedChromatinWithSterics method) (chromo.polymers.SSTWLC method) (chromo.polymers.SSWLC method) compute_E_detailed() (chromo.polymers.DetailedChromatinWithSterics method) compute_E_detailed_reverse() (chromo.polymers.DetailedChromatinWithSterics method) compute_E_no_twist() (chromo.polymers.SSTWLC method) compute_twist_angle_omega() (in module chromo.polymers) configuration_tracker (chromo.polymers.PolymerBase attribute) ConfigurationTracker (class in chromo.util.mc_stat) confine_length (chromo.fields.UniformDensityField attribute) confine_type (chromo.fields.UniformDensityField attribute) confined_gaussian_walk() (chromo.polymers.SSWLC method) (in module chromo.util.poly_paths) confined_uniform_random_walk() (chromo.polymers.SSWLC method) (in module chromo.util.poly_paths) construct_nucleosome() (chromo.beads.Prism class method) continue_polymer_in_field_simulation() (in module chromo.mc) Controller (class in chromo.mc.mc_controller) coordinates_in_x_y() (in module chromo.util.poly_paths) coordinates_in_x_y_z() (in module chromo.util.poly_paths) count_beads() (chromo.mixtures.Mixture method) crank_shaft() (in module chromo.mc.move_funcs) create_log_file() (chromo.util.mc_stat.AcceptanceTracker method) (chromo.util.mc_stat.ConfigurationTracker method) (chromo.util.mc_stat.Tracker method)

D

densities_temp (chromo.polymers.PolymerBase attribute) DetailedChromatin (class in chromo.polymers) DetailedChromatin2 (class in chromo.polymers) DetailedChromatinWithSterics (class in chromo.polymers)

DetailedNucleosome (class in chromo.beads) dict() (chromo.binders.ReaderProtein method) dict_ (chromo.fields.UniformDensityField attribute) direction (chromo.polymers.PolymerBase attribute) dxyz (chromo.fields.UniformDensityField attribute)

E

end_pivot() (in module chromo.mc.move_funcs) estimate_tangents_from_coordinates() (in module chromo.util.poly_paths)

eval_delta_steric_clashes() (chromo.polymers.DetailedChromatinWithSterics method) eval_E_steric_clashes() (chromo.polymers.DetailedChromatinWithSterics method) evaluate_binder_interactions() (chromo.polymers.DetailedChromatinWithSterics method)

F

fast_field (chromo.fields.UniformDensityField attribute) FieldBase (class in chromo.fields) fill_missing_arguments() (chromo.polymers.PolymerBase method) finalize() (chromo.fields.Reconstructor method) find_polymers_in_output_dir() (in module chromo.util.poly_stat) from_csv() (chromo.polymers.PolymerBase method) from_dataframe() (chromo.polymers.PolymerBase method) from_file() (chromo.fields.NullField method) (chromo.fields.Reconstructor class method) (chromo.fields.UniformDensityField method) (chromo.polymers.PolymerBase method)

from_left() (in module chromo.util.bead_selection) from_point() (in module chromo.util.bead_selection) from_right() (in module chromo.util.bead_selection) full_chain_rotation() (in module chromo.mc.move_funcs) full_chain_translation() (in module chromo.mc.move_funcs)

G

gaussian_walk() (in module chromo.util.poly_paths) gaussian_walk_polymer() (chromo.polymers.SSWLC method) generate_translation_mat() (in module chromo.util.linalg) get_accessible_volumes() (chromo.fields.UniformDensityField method) get_all() (chromo.polymers.PolymerBase method) get_amplitude_bounds() (in module chromo.mc) get_arbitrary_axis_rotation_matrix() (in module chromo.util.linalg) get_blocks() (in module chromo.fields) get_by_name() (in module chromo.binders) get_delta_distances() (chromo.polymers.DetailedChromatinWithSterics method) get_dict() (chromo.fields.UniformDensityField method) get_distances() (chromo.polymers.DetailedChromatinWithSterics method) get_E_bind() (chromo.polymers.DetailedChromatinWithSterics method) get_entry_exit_orientations() (chromo.beads.DetailedNucleosome method) get_entry_exit_positions() (chromo.beads.DetailedNucleosome method) get_furthest_in_dir() (in module chromo.util.gjk)

get_latest_configuration() (in module chromo.util.poly_stat) get_latest_simulation() (in module chromo.util.poly_stat) get_neighboring_bins() (in module chromo.fields) get_neighbors() (chromo.mixtures.Mixture method) get_neighbors_at_ind() (in module chromo.fields) get_num_beads() (chromo.polymers.PolymerBase method) get_num_binders() (chromo.polymers.PolymerBase method) get_prism_verticies() (in module chromo.util.linalg) get_prop() (chromo.polymers.PolymerBase method) get_rotation_matrix() (in module chromo.util.linalg) get_tangent_vals_x_y() (in module chromo.util.poly_paths) get_tangent_vals_x_y_z() (in module chromo.util.poly_paths) get_unique_subfolder() (in module chromo.util.reproducibility) get_unique_subfolder_name() (in module chromo.util.reproducibility) get_verticies_rot_mat() (in module chromo.beads) GhostBead (class in chromo.beads) gjk_collision() (in module chromo.util.gjk)

H

half_step_xyz (chromo.fields.UniformDensityField attribute) half_width_xyz (chromo.fields.UniformDensityField attribute)

helix_parametric_x() (in module chromo.polymers) helix_parametric_y() (in module chromo.polymers) helix_parametric_z() (in module chromo.polymers)

I

id (chromo.beads.Bead attribute) in_confinement() (in module chromo.util.poly_paths) in_cubical_confinement() (in module chromo.util.poly_paths) in_spherical_confinement() (in module chromo.util.poly_paths) index_xyz (chromo.fields.UniformDensityField attribute) index_xyz_with_trial (chromo.fields.UniformDensityField attribute)

inds_xyz_to_super (chromo.fields.UniformDensityField attribute) init_field_energy_prefactors() (chromo.fields.UniformDensityField method) init_grid() (chromo.fields.UniformDensityField method) initialize_table() (in module chromo.util.mc_stat) is_field_active() (chromo.polymers.DetailedChromatinWithSterics method) (chromo.polymers.PolymerBase method)

J

jump_sample() (in module chromo.util.poly_stat)

K

kwargs (chromo.beads.GhostBead attribute)

L

last_amp_bead (chromo.polymers.PolymerBase attribute) last_amp_move (chromo.polymers.PolymerBase attribute) list_output_files() (in module chromo.util.poly_stat) load_indices() (chromo.util.poly_stat.PolyStats method) load_seqs() (chromo.polymers.PolymerBase static method) log_move() (chromo.util.mc_stat.AcceptanceTracker method) (chromo.util.mc_stat.ConfigurationTracker method) (chromo.util.mc_stat.Tracker method)

log_path (chromo.polymers.PolymerBase attribute) looped_confined_gaussian_walk() (chromo.polymers.LoopedSSTWLC method) (in module chromo.util.poly_paths) LoopedSSTWLC (class in chromo.polymers) lp (chromo.polymers.PolymerBase attribute)

M

make_binder_collection() (in module chromo.binders) max_binders (chromo.polymers.PolymerBase attribute) mc_sim() (in module chromo.mc.mc_sim) mc_step() (in module chromo.mc.mc_sim) MCAdapter (class in chromo.mc.moves) Mixture (class in chromo.mixtures) module chromo chromo.beads chromo.binders chromo.fields chromo.mc chromo.mc.mc_controller chromo.mc.mc_sim chromo.mc.move_funcs chromo.mc.moves chromo.mixtures chromo.polymers chromo.util chromo.util.bead_selection chromo.util.gjk chromo.util.linalg chromo.util.mc_stat chromo.util.poly_paths chromo.util.poly_stat chromo.util.reproducibility

N

n_binders_p1 (chromo.polymers.PolymerBase attribute) n_bins (chromo.fields.UniformDensityField attribute) n_points (chromo.fields.UniformDensityField attribute) n_polymers (chromo.fields.FieldBase attribute) n_xyz_m1 (chromo.fields.UniformDensityField attribute) name (chromo.binders.Binder attribute) (chromo.fields.FieldBase attribute) (chromo.polymers.PolymerBase attribute) nbr_indices_with_trial (chromo.fields.UniformDensityField attribute)

nbr_inds (chromo.fields.UniformDensityField attribute) NoControl (class in chromo.mc.mc_controller) nonspecific_interact_E() (chromo.fields.UniformDensityField method) Nucleosome (class in chromo.beads) NullField (class in chromo.fields) num_beads (chromo.polymers.PolymerBase attribute) num_binders (chromo.fields.UniformDensityField attribute) (chromo.polymers.PolymerBase attribute) numerical_derivative() (in module chromo.util.poly_paths)

O

only_binding_move() (in module chromo.mc.mc_controller)

overlap_sample() (in module chromo.util.poly_stat)

P

parse_type() (in module chromo.util.reproducibility) pick_line() (in module chromo.util.gjk) pick_tetrahedron() (in module chromo.util.gjk) pick_triangle() (in module chromo.util.gjk) point (chromo.polymers.PolymerBase attribute) PolymerBase (class in chromo.polymers)

polymers (chromo.fields.FieldBase attribute) PolyStats (class in chromo.util.poly_stat) print_properties() (chromo.beads.Bead method) (chromo.beads.GhostBead method) (chromo.beads.Nucleosome method) (chromo.beads.Prism method) Prism (class in chromo.beads)

R

r (chromo.beads.Bead attribute) rad (chromo.beads.GhostBead attribute) (chromo.beads.Nucleosome attribute) ReaderProtein (class in chromo.binders) Reconstructor (class in chromo.fields)

reject() (chromo.mc.moves.MCAdapter method) replicate_chromo_essentials() (in module chromo.util.reproducibility) return_arbitrary_axis_rotation() (in module chromo.util.linalg) rotation_matrix_from_vectors() (in module chromo.util.linalg) Rouse (class in chromo.polymers)

S

save_move_log() (chromo.util.mc_stat.AcceptanceTracker method) (chromo.util.mc_stat.ConfigurationTracker method) (chromo.util.mc_stat.Tracker method) save_summary_statistics() (in module chromo.util.poly_stat) shape_overlap() (in module chromo.util.gjk) SimpleControl (class in chromo.mc.mc_controller) sin_func() (in module chromo.polymers) sites_per_bead (chromo.binders.Binder attribute) slide() (in module chromo.mc.move_funcs) specific_move() (in module chromo.mc.mc_controller)

specific_moves() (in module chromo.mc.mc_controller) split_builtin_params() (in module chromo.util.reproducibility) SSTWLC (class in chromo.polymers) SSWLC (class in chromo.polymers) states (chromo.beads.Bead attribute) (chromo.polymers.PolymerBase attribute) states_trial (chromo.polymers.PolymerBase attribute) straight_line_in_x() (chromo.polymers.SSWLC method) super_ind_to_inds() (in module chromo.fields) support_function() (in module chromo.util.gjk)

T

t2 (chromo.beads.Bead attribute) t3 (chromo.beads.Bead attribute) tangent_rotation() (in module chromo.mc.move_funcs) test_collision() (chromo.beads.Bead method) (chromo.beads.GhostBead method) (chromo.beads.Nucleosome method) (chromo.beads.Prism method) to_csv() (chromo.mc.moves.Bounds method) (chromo.polymers.PolymerBase method) to_dataframe() (chromo.mc.moves.Bounds method) (chromo.polymers.PolymerBase method)

to_file() (chromo.fields.NullField method) (chromo.fields.UniformDensityField method) (chromo.mc.moves.Bounds method) (chromo.polymers.PolymerBase method) to_file_params() (in module chromo.util.reproducibility) Tracker (class in chromo.util.mc_stat) transform_r_t3_t2() (in module chromo.mc.move_funcs) transform_vertices() (chromo.beads.Prism method) transformation_mat (chromo.polymers.TransformedObject attribute) TransformedObject (class in chromo.polymers)

U

UniformDensityField (class in chromo.fields) update_acceptance_rate() (chromo.util.mc_stat.AcceptanceTracker method) update_all_densities() (chromo.fields.UniformDensityField method) update_all_densities_for_all_polymers() (chromo.fields.UniformDensityField method) update_amplitudes() (chromo.mc.mc_controller.Controller method) (chromo.mc.mc_controller.NoControl method) (chromo.mc.mc_controller.SimpleControl method) update_bead_amplitude() (chromo.mc.mc_controller.Controller method) (chromo.mc.mc_controller.NoControl method) (chromo.mc.mc_controller.SimpleControl method)

update_configuration() (chromo.beads.DetailedNucleosome method) update_log_path() (chromo.polymers.PolymerBase method) update_move_amplitude() (chromo.mc.mc_controller.Controller method) (chromo.mc.mc_controller.NoControl method) (chromo.mc.mc_controller.SimpleControl method) update_prop() (chromo.polymers.PolymerBase method)

V

vertices (chromo.beads.Prism attribute) vf_limit (chromo.fields.UniformDensityField attribute)

vol (chromo.beads.GhostBead attribute) (chromo.beads.Nucleosome attribute) vol_bin (chromo.fields.UniformDensityField attribute)

W

weight_xyz (chromo.fields.UniformDensityField attribute) weight_xyz_with_trial (chromo.fields.UniformDensityField attribute)

width_xyz (chromo.fields.UniformDensityField attribute) wt_vec (chromo.fields.UniformDensityField attribute) wt_vec_with_trial (chromo.fields.UniformDensityField attribute)

X

xyz (chromo.fields.UniformDensityField attribute)

xyz_with_trial (chromo.fields.UniformDensityField attribute)