Index

A

a_star() (Path method) add_conformation() (Assembly method) add_deformation() (Polyhedron method) add_xyz() (Structure method) align_axes() (Structure method) append() (Assembly method) apply_biomatrix() (Molecule method) apply_symmetry() (Molecule method)

apply_transformation() (Structure method) assembly module Assembly (class in assembly) assign_atomtype() (Molecule method) atomignore() (Molecule method) atomselect() (Molecule method) (Multimer method)

B

best_threshold() (Density method) beta_factor_from_rmsf() (Molecule method) biobox.measures.calculators module

biobox.measures.interaction module biobox.measures.path module blur() (Density method)

C

ccs() (Cone method) (Cylinder method) (Ellipsoid method) (in module biobox.measures.calculators) (Prism method) (Sphere method) center_assembly() (Assembly method) center_subunit() (Assembly method) center_to_origin() (Structure method) check_inclusion() (Ellipsoid method) (Sphere method)

clear() (Assembly method) (Structure method) Cone (class in convex) contact_ratio() (Assembly method) convex module convex_hull() (Structure method) coordinates (Structure attribute) current (Structure attribute) Cylinder (class in convex)

D

data (Structure attribute) delete_xyz() (Polyhedron method) (Structure method) density module

Density (class in density) distance_matrix() (in module biobox.measures.interaction) (Xlink method)

E

Ellipsoid (class in convex)

export_as_pdb() (Density method)

F

find_data_from_ccs() (Density method)

find_data_from_sigma() (Density method) find_data_from_volume() (Density method)

G

generate_polyhedron() (Polyhedron method) get_all_xyz() (Assembly method) get_atoms_ccs() (Molecule method) get_buried() (Assembly method) get_center() (Structure method) get_couples() (Molecule method) get_data() (Molecule method) (Multimer method) get_density() (Structure method) get_dipole_density() (Molecule method) get_dipole_map() (Molecule method) get_electrostatics() (Molecule method) get_mass_by_atom() (Molecule method) get_mass_by_residue() (Molecule method) get_neighbors() (in module biobox.measures.interaction) (Polyhedron method) get_oversampled_points() (Density method) get_pdb_data() (Molecule method) get_polyhedron_properties() (Polyhedron method) get_principal_axes() (Structure method) get_secondary_structure() (Molecule method)

get_sigma_from_thresh() (Density method) get_size() (Assembly method) (Structure method) get_sphericity() (Ellipsoid method) (Sphere method) get_subset() (Molecule method) get_surface() (Cone method) (Cylinder method) (Ellipsoid method) (Prism method) (Sphere method) get_thresh_from_sigma() (Density method) get_uxyz() (Assembly method) get_vdw_density() (Molecule method) get_volume() (Cone method) (Cylinder method) (Density method) (Ellipsoid method) (Prism method) (Sphere method) get_xyz() (Structure method) guess_chain_split() (Molecule method)

I

import_gro() (Molecule method) import_map() (Density method)

import_numpy() (Density method) import_pdb() (Molecule method) import_pqr() (Molecule method)

K

know() (Molecule method)

L

lazy_theta_star() (Path method) lennard_jones() (in module biobox.measures.interaction)

load() (Assembly method) load_list() (Assembly method)

M

make_circular_symmetry() (Assembly method) make_curved_chain() (Assembly method) make_fiber() (Assembly method) make_molecule() (Multimer method) make_prism() (Assembly method) make_stacked_rings() (Assembly method) make_structure() (Assembly method) match_residue() (Molecule method) merge() (Assembly method) module assembly biobox.measures.calculators biobox.measures.interaction biobox.measures.path convex density molecule multimer polyhedron structure

molecule module Molecule (class in molecule) multimer module Multimer (class in multimer)

N

num_units_fiber() (Assembly static method)

P

Path (class in biobox.measures.path) pca() (Structure method) pdb2pqr() (Molecule method) place_points() (Density method) points (Structure attribute)

polyhedron module Polyhedron (class in polyhedron) Prism (class in convex) properties (Structure attribute)

Q

query() (Molecule method) (Multimer method)

R

return_density_map() (Density method) rgyr() (in module biobox.measures.calculators) rmsd() (Structure method) rmsd_distance_matrix() (Polyhedron method) (Structure method)

rmsd_one_vs_all() (Structure method) rmsf() (Structure method) rmsf_from_beta_factor() (Molecule method) rotate() (Assembly method) (Structure method) rotation_matrix() (Structure method)

S

s2() (Molecule method) same_residue() (Molecule method) same_residue_unique() (Molecule method) sasa() (in module biobox.measures.calculators) saxs() (in module biobox.measures.calculators) scan_threshold() (Density method) search_path() (Path method) set_clashing_atoms() (Xlink method) set_current() (Polyhedron method) (Structure method) set_data() (Molecule method)

set_xyz() (Structure method) setup_global_search() (Path method) (Xlink method) setup_local_search() (Path method) (Xlink method) setup_polyhedron() (Polyhedron method) smooth() (Path method) Sphere (class in convex) squeeze() (Sphere method) structure module Structure (class in structure)

T

theta_star() (Path method) threshold_vol_ccs() (Density method)

translate() (Assembly method) (Structure method)

W

write_dx() (Density method) write_grid() (Path method) write_gro() (Molecule method) write_pdb() (Assembly method) (Molecule method) (Multimer method) (Structure method)

write_poly_architecture() (Polyhedron method) write_pqr() (Molecule method) write_protein_points() (Xlink method)

X

Xlink (class in biobox.measures.path)