Package csb :: Package bio :: Package structure :: Class Residue
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Class Residue

source code

            object --+        
                     |        
core.AbstractContainer --+    
                         |    
  core.AbstractNIContainer --+
                             |
                object --+   |
                         |   |
            AbstractEntity --+
                             |
                            Residue
Known Subclasses:

Base class representing a single residue. Provides a dictionary-like access to the atoms contained in the residue:

>>> residue['CA']
<Atom [3048]: CA>
>>> residue.atoms['CA']
<Atom [3048]: CA>
>>> residue.items
<iterator of Atom-s>
Nested Classes

Inherited from core.AbstractContainer: __metaclass__

Instance Methods
 
__init__(self, rank, type, sequence_number=None, insertion_code=None)
x.__init__(...) initializes x; see help(type(x)) for signature
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

Inherited from core.AbstractNIContainer: __getitem__

Inherited from core.AbstractContainer: __bool__, __iter__, __len__, __nonzero__

Inherited from AbstractEntity: components, transform

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

Static Methods
Residue subclass
create(sequence_type, *a, **k)
Residue factory method, which returns the proper Residue instance based on the specified sequence_type.
source code
Class Variables
  __abstractmethods__ = frozenset([])
Properties
ResidueAtomsTable atoms
Access residue's atoms by atom name
bool has_structure
True if this residue has any atoms
str id
PDB sequence number [+ insertion code]
str insertion_code
PDB insertion code (if defined)
iterator of AbstractEntity items
Iterator over all immediate children of the entity
int rank
Residue's position in the sequence (1-based)
SecondaryStructureElement secondary_structure
Secondary structure element this residue is part of
int sequence_number
PDB sequence number (if residue.has_structure is True)
TorsionAngles torsion
Torsion angles
enum item type
Residue type - a member of any sequence alphabet

Inherited from object: __class__

Method Details

__init__(self, rank, type, sequence_number=None, insertion_code=None)
(Constructor)

source code 

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

Parameters:
  • rank (int) - rank of the residue with respect to the chain
  • type (csb.core.EnumItem) - residue type - a member of any SequenceAlphabets
  • sequence_number (str) - PDB sequence number of the residue
  • insertion_code (str) - PDB insertion code, if any
Overrides: object.__init__
(inherited documentation)

__repr__(self)
(Representation operator)

source code 

repr(x)

Overrides: object.__repr__
(inherited documentation)

create(sequence_type, *a, **k)
Static Method

source code 

Residue factory method, which returns the proper Residue instance based on the specified sequence_type. All additional arguments are used to initialize the subclass by passing them automatically to the underlying constructor.

Parameters:
Returns: Residue subclass
a new residue of the proper subclass
Raises:
  • ValueError - if the sequence type is not known

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:
Overrides: AbstractEntity.get_coordinates
(inherited documentation)

Property Details

atoms

Access residue's atoms by atom name

Get Method:
unreachable.atoms(self) - Access residue's atoms by atom name
Type:
ResidueAtomsTable

has_structure

True if this residue has any atoms

Get Method:
unreachable.has_structure(self) - True if this residue has any atoms
Type:
bool

id

PDB sequence number [+ insertion code]

Get Method:
unreachable.id(self) - PDB sequence number [+ insertion code]
Set Method:
unreachable.id(self, value)
Type:
str

insertion_code

PDB insertion code (if defined)

Get Method:
unreachable.insertion_code(self) - PDB insertion code (if defined)
Type:
str

items

Iterator over all immediate children of the entity

Get Method:
unreachable.items(self)
Type:
iterator of AbstractEntity

rank

Residue's position in the sequence (1-based)

Get Method:
unreachable.rank(self) - Residue's position in the sequence (1-based)
Type:
int

secondary_structure

Secondary structure element this residue is part of

Get Method:
unreachable.secondary_structure(self) - Secondary structure element this residue is part of
Set Method:
unreachable.secondary_structure(self, structure)
Type:
SecondaryStructureElement

sequence_number

PDB sequence number (if residue.has_structure is True)

Get Method:
unreachable.sequence_number(self) - PDB sequence number (if residue.has_structure is True)
Type:
int

torsion

Torsion angles

Get Method:
unreachable.torsion(self) - Torsion angles
Set Method:
unreachable.torsion(self, torsion)
Type:
TorsionAngles

type

Residue type - a member of any sequence alphabet

Get Method:
unreachable.type(self) - Residue type - a member of any sequence alphabet
Set Method:
unreachable.type(self, type)
Type:
enum item