cellpack.autopack.interface_objects package

Submodules

cellpack.autopack.interface_objects.database_ids module

class cellpack.autopack.interface_objects.database_ids.DATABASE_IDS(value)

Bases: MetaEnum

An enumeration.

AWS = 'aws'

FIREBASE = 'firebase'

GITHUB = 'github'

classmethod handlers()

classmethod with_colon()

cellpack.autopack.interface_objects.default_values module

cellpack.autopack.interface_objects.gradient_data module

class cellpack.autopack.interface_objects.gradient_data.GradientData(gradient_options, gradient_name='default')

Bases: object

Takes in gradient dictionary from the recipe file to create a GradientData instance

default_values = {'description': 'Linear gradient in the X direction', 'invert': None, 'mode': 'X', 'mode_settings': {}, 'pick_mode': 'linear', 'reversed': False, 'weight_mode': 'linear', 'weight_mode_settings': {}}

set_mode_properties(gradient_data)

validate_gradient_data(gradient_data)

validate_invert_settings(invert_option)

validate_mode_settings(mode_name, mode_settings_dict)

validate_weight_mode_settings(weight_mode_name, weight_mode_settings_dict)

class cellpack.autopack.interface_objects.gradient_data.GradientModes(value)

Bases: MetaEnum

All available gradient modes

RADIAL = 'radial'

SURFACE = 'surface'

VECTOR = 'vector'

X = 'X'

Y = 'Y'

Z = 'Z'

class cellpack.autopack.interface_objects.gradient_data.InvertOptions(value)

Bases: MetaEnum

All available options for individual invert modes

distance = 'distance'

weight = 'weight'

class cellpack.autopack.interface_objects.gradient_data.ModeOptions(value)

Bases: MetaEnum

All available options for individual modes

center = 'center'

direction = 'direction'

gblob = 'gblob'

object = 'object'

radius = 'radius'

scale_distance_between = 'scale_distance_between'

class cellpack.autopack.interface_objects.gradient_data.PickModes(value)

Bases: MetaEnum

All available pick modes

BINARY = 'binary'

LINEAR = 'linear'

MAX = 'max'

MIN = 'min'

REG = 'reg'

RND = 'rnd'

SUB = 'sub'

class cellpack.autopack.interface_objects.gradient_data.WeightModeOptions(value)

Bases: MetaEnum

All available options for individual weight modes

decay_length = 'decay_length'

power = 'power'

class cellpack.autopack.interface_objects.gradient_data.WeightModes(value)

Bases: MetaEnum

All available weight modes

CUBE = 'cube'

EXPONENTIAL = 'exponential'

LINEAR = 'linear'

POWER = 'power'

SQUARE = 'square'

cellpack.autopack.interface_objects.ingredient_types module

class cellpack.autopack.interface_objects.ingredient_types.INGREDIENT_TYPE(value)

Bases: MetaEnum

An enumeration.

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)

Bases: str, Enum

An enumeration.

classmethod is_member(item)

classmethod values()

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)

Bases: object

class cellpack.autopack.interface_objects.packed_objects.PackedObjects

Bases: object

add(new_object: PackedObject)

get_all()

get_compartment()

get_encapsulating_radii()

get_ingredients()

get_positions()

get_positions_for_ingredient(ingredient_name)

get_radii()

get_rotations_for_ingredient(ingredient_name)

cellpack.autopack.interface_objects.partners module

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

Bases: object

distanceFunction(d, expression=None, function=None)

get_point(index)

set_ingredient(ingredient)

class cellpack.autopack.interface_objects.partners.Partners(partners)

Bases: object

This object holds the partner data

add_partner(ingredient, probability_binding=0.5)

get_partner_by_ingr_name(name)

is_partner(full_ingredient_name)

cellpack.autopack.interface_objects.representations module

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

Bases: object

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

DATABASE = 'https://raw.githubusercontent.com/mesoscope/cellPACK_data/master/cellPACK_database_1.1.0'

get_active()

get_active_data()

get_adjusted_position(position, rotation)

get_deepest_level()

get_mesh_format()

get_mesh_name()

get_mesh_path()

get_min_max_radius()

get_pdb_path()

get_positions()

get_radii()

has_mesh()

has_pdb()

set_active(type='atomic')

set_sphere_positions()

Module contents

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