Package csb :: Package bio :: Package structure :: Class DisorderedAtom |
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# Class DisorderedAtom

source code

                  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)