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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)
bool is_modified
Return True id this is a modified residue
iterator of AbstractEntity items
Iterator over all immediate children of the entity
str label
Original residue label (different from Residue.type for modified residues)
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

is_modified

Return True id this is a modified residue

Get Method:
unreachable.is_modified(self) - Return True id this is a modified residue
Type:
bool

items

Iterator over all immediate children of the entity

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

label

Original residue label (different from Residue.type for modified residues)

Get Method:
unreachable.label(self) - Original residue label (different from Residue.type for modified residues)
Set Method:
unreachable.label(self, value)
Type:
str

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

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