cellpack.autopack.interface_objects package

Submodules

cellpack.autopack.interface_objects.database_ids module

class cellpack.autopack.interface_objects.database_ids.DATABASE_IDS(value)[source]

Bases: MetaEnum

AWS = 'aws'
FIREBASE = 'firebase'
GITHUB = 'github'
classmethod handlers()[source]
classmethod with_colon()[source]

cellpack.autopack.interface_objects.default_values module

cellpack.autopack.interface_objects.ingredient_types module

class cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE(value)[source]

Bases: MetaEnum

GROW = 'grow'
MESH = 'mesh'
MULTI_CYLINDER = 'multi_cylinder'
MULTI_SPHERE = 'multi_sphere'
SINGLE_CUBE = 'single_cube'
SINGLE_CYLINDER = 'single_cylinder'
SINGLE_SPHERE = 'single_sphere'

cellpack.autopack.interface_objects.meta_enum module

class cellpack.autopack.interface_objects.meta_enum.MetaEnum(value)[source]

Bases: str, Enum

classmethod is_member(item)[source]
classmethod values()[source]

cellpack.autopack.interface_objects.packed_objects module

class cellpack.autopack.interface_objects.packed_objects.PackedObject(position, rotation, radius, pt_index, ingredient=None, is_compartment=False)[source]

Bases: object

class cellpack.autopack.interface_objects.packed_objects.PackedObjects[source]

Bases: object

add(new_object: PackedObject)[source]
get_all()[source]
get_compartment()[source]
get_encapsulating_radii()[source]
get_ingredients()[source]
get_positions()[source]
get_positions_for_ingredient(ingredient_name)[source]
get_radii()[source]
get_rotations_for_ingredient(ingredient_name)[source]

cellpack.autopack.interface_objects.partners module

class cellpack.autopack.interface_objects.partners.Partner(name, position, weight, binding_probability)[source]

Bases: object

distanceFunction(d, expression=None, function=None)[source]
get_point(index)[source]
set_ingredient(ingredient)[source]
class cellpack.autopack.interface_objects.partners.Partners(partners)[source]

Bases: object

__init__(partners)[source]

This object holds the partner data

add_partner(ingredient, probability_binding=0.5)[source]
get_partner_by_ingr_name(name)[source]
is_partner(full_ingredient_name)[source]

cellpack.autopack.interface_objects.representations module

class cellpack.autopack.interface_objects.representations.Representations(mesh=None, atomic=None, packing=None)[source]

Bases: object

DATABASE = 'https://raw.githubusercontent.com/mesoscope/cellPACK_data/master/cellPACK_database_1.1.0'
__init__(mesh=None, atomic=None, packing=None)[source]

This object holds the different representation types for an ingredient

mesh : OBJ file info atomic : PDB or ciff file info packing: Sphere tree file or sphere tree data

get_active()[source]
get_active_data()[source]
get_adjusted_position(position, rotation)[source]
get_deepest_level()[source]
get_mesh_format()[source]
get_mesh_name()[source]
get_mesh_path()[source]
get_min_max_radius()[source]
get_pdb_path()[source]
get_positions()[source]
get_radii()[source]
has_mesh()[source]
has_pdb()[source]
set_active(type='atomic')[source]
set_sphere_positions()[source]

Module contents

Interface classes for cellpack. These are to establish data structures.