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

source code

        object --+
                 |
    AbstractEntity --+
                     |
                    Atom

Known Subclasses:
  - DisorderedAtom

Represents a single atom in space.

Nested Classes
Inherited from `AbstractEntity`: `__metaclass__`

Instance Methods
__init__(self, serial_number, name, element, vector, alternate=False) x.__init__(...) initializes x; see help(type(x)) for signature | source code
__lt__(self, other) | source code
__repr__(self) repr(x) | source code
clone(self) | 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 `AbstractEntity`: `components` Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Class Variables
| __abstractmethods__ = ``frozenset([``])``

Properties
str | alternate Alternative location flag
float | bfactor Temperature factor
int | charge Charge
enum item | element Chemical element - a member of ChemElements
iterator of AbstractEntity | items Iterator over all immediate children of the entity
str | name PDB atom name (trimmed)
float | occupancy Occupancy number
Residue | residue Residue instance that owns this atom (if available)
int | serial_number PDB serial number
numpy.array | vector Atom's 3D coordinates (x, y, z)
Inherited from `object`: `__class__`

Method Details

### __init__(self, serial_number, name, element, vector, alternate=False) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `serial_number` (int) - atom's UID `name` (str) - atom's name `element` (csb.core.EnumItem) - corresponding ChemElements `vector` (numpy array) - atom's coordinates `alternate` (bool) - if True, means that this is a wobbling atom with multiple alternative locations Overrides: object.__init__ (inherited documentation)

### __repr__(self) (Representation operator) | source code
repr(x) Overrides: object.__repr__ (inherited documentation)

### 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` - 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 Overrides: AbstractEntity.get_coordinates (inherited documentation)

### transform(self, rotation, translation) | source code
Apply in place RotationMatrix and translation Vector to all atoms. Overrides: AbstractEntity.transform (inherited documentation)

Property Details

### alternate Alternative location flag Get Method: unreachable.alternate(self) - Alternative location flag Set Method: unreachable.alternate(self, value) Type: str

### bfactor Temperature factor Get Method: unreachable.bfactor(self) - Temperature factor Set Method: unreachable.bfactor(self, value) Type: float

### charge Charge Get Method: unreachable.charge(self) - Charge Set Method: unreachable.charge(self, value) Type: int

### element Chemical element - a member of ChemElements Get Method: unreachable.element(self) - Chemical element - a member of ChemElements Type: enum item

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

### name PDB atom name (trimmed) Get Method: unreachable.name(self) - PDB atom name (trimmed) Type: str

### occupancy Occupancy number Get Method: unreachable.occupancy(self) - Occupancy number Set Method: unreachable.occupancy(self, value) Type: float

### residue Residue instance that owns this atom (if available) Get Method: unreachable.residue(self) - Residue instance that owns this atom (if available) Set Method: unreachable.residue(self, residue) Type: Residue

### serial_number PDB serial number Get Method: unreachable.serial_number(self) - PDB serial number Set Method: unreachable.serial_number(self, number) Type: int

### vector Atom's 3D coordinates (x, y, z) Get Method: unreachable.vector(self) - Atom's 3D coordinates (x, y, z) Set Method: unreachable.vector(self, vector) Type: numpy.array