Package csb :: Package bio :: Package structure :: Class AbstractEntity

Class AbstractEntity

object --+
         |
        AbstractEntity

Known Subclasses:

Base class for all protein structure entities.

This class defines uniform interface of all entities (e.g. Structure, Chain, Residue) according to the Composite pattern.

Nested Classes
	__metaclass__ Metaclass for defining Abstract Base Classes (ABCs).

Instance Methods

components(self, klass=None)
Return an iterator over all descendants of the entity.

source code

list

get_coordinates(self, what=None, skip=False)
Extract the coordinates of the specified kind(s) of atoms and return them as a list.

source code

transform(self, rotation, translation)
Apply in place RotationMatrix and translation Vector to all atoms.

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables
	__abstractmethods__ = `frozenset(['items'])`

Properties
iterator of AbstractEntity	items Iterator over all immediate children of the entity
Inherited from `object`: `__class__`

Method Details

components(self, klass=None)

source code

Return an iterator over all descendants of the entity.

Parameters:

klass - return entities of the specified AbstractEntity subclass only. If None, traverse the hierarchy down to the lowest level.
klass - class

get_coordinates(self, what=None, skip=False)

source code

Extract the coordinates of the specified kind(s) of atoms and return them as a list.

Parameters:

what (list or None) - a list of atom kinds, e.g. ['N', 'CA', 'C']

Returns: list

a list of lists, each internal list corresponding to the coordinates of a 3D vector

Raises:

Broken3DStructureError - if a specific atom kind cannot be retrieved from a residue

transform(self, rotation, translation)

source code

Apply in place RotationMatrix and translation Vector to all atoms.

Parameters:

rotation (numpy array)
translation (numpy array)

Property Details

items

Iterator over all immediate children of the entity

Get Method:: unreachable.items(self) - Iterator over all immediate children of the entity
Type:: iterator of AbstractEntity