Package csb :: Package bio :: Package structure :: Class DisorderedAtom

Class DisorderedAtom

              object --+            
                       |            
    core.AbstractIndexer --+        
                           |        
core.BaseCollectionContainer --+    
                               |    
        core.CollectionContainer --+
                                   |
                  object --+       |
                           |       |
              AbstractEntity --+   |
                               |   |
                            Atom --+
                                   |
                                  DisorderedAtom

A wobbling atom, which has alternative locations. Each alternative is represented as a 'normal' Atom. The atom with a highest occupancy is selected as a representative, hence a DisorderedAtom behaves as a regular Atom (proxy of the representative) as well as a collection of Atoms.

Nested Classes
Inherited from `AbstractEntity`: `__metaclass__`

Instance Methods

__getattr__(self, name)

source code

__init__(self, atom)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

__repr__(self)
repr(x)

source code

int

append(self, atom)
Append a new atom to the collection of alternatives.

source code

Atom

find(self, altloc)
Retrieve a specific atom by its altloc identifier.

source code

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

source code

Inherited from core.BaseCollectionContainer: __bool__, __contains__, __getitem__, __iter__, __len__, __nonzero__

Inherited from Atom: __lt__, clone, get_coordinates

Inherited from AbstractEntity: components

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

Class Variables
Inherited from `Atom`: `__abstractmethods__`

Properties

Inherited from core.BaseCollectionContainer: last_index, length, start_index

Inherited from Atom: alternate, bfactor, charge, element, items, name, occupancy, residue, serial_number, vector

Inherited from object: __class__

Method Details

init(self, atom)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

atom (Atom) - the first atom to be appended to the collection of alternatives. It is automatically defined as a representative, until a new atom with higher occupancy is appended to the collection

Overrides: object.__init__

(inherited documentation)

repr(self)
(Representation operator)

source code

repr(x)

Overrides: object.__repr__: (inherited documentation)

append(self, atom)

source code

Append a new atom to the collection of alternatives.

Parameters:

atom (Atom) - the new alternative

Returns: int

the index of the new element

Raises:

TypeError - when the container is type-safe and item has an incorrect type

Overrides: core.CollectionContainer.append

find(self, altloc)

source code

Retrieve a specific atom by its altloc identifier.

Parameters:

altloc (str) - alternative location identifier

Returns: Atom

transform(self, rotation, translation)

source code

Apply in place RotationMatrix and translation Vector to all atoms.

Overrides: AbstractEntity.transform: (inherited documentation)

Class DisorderedAtom

__init__(self, atom) (Constructor)

__repr__(self) (Representation operator)

append(self, atom)

find(self, altloc)

transform(self, rotation, translation)

init(self, atom)
(Constructor)

repr(self)
(Representation operator)