Package csb :: Package bio :: Package structure :: Class ProteinResidue

Class ProteinResidue

            object --+            
                     |            
core.AbstractContainer --+        
                         |        
  core.AbstractNIContainer --+    
                             |    
                object --+   |    
                         |   |    
            AbstractEntity --+    
                             |    
                       Residue --+
                                 |
                                ProteinResidue

Represents a single amino acid residue.

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

TorsionAngles

compute_torsion(self, prev_residue, next_residue, strict=True)
Compute the torsion angles of the current residue with neighboring residues prev_residue and next_residue. source code

Inherited from Residue: __repr__, clone, get_coordinates

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
Inherited from `Residue`: `create`

Class Variables
Inherited from `Residue`: `__abstractmethods__`

Properties

Inherited from Residue: atoms, has_structure, id, insertion_code, is_modified, items, label, rank, secondary_structure, sequence_number, torsion, type

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 csb.bio.sequence.SequenceAlphabets.Protein
sequence_number (str) - PDB sequence number of the residue
insertion_code (str) - PDB insertion code, if any

Overrides: object.__init__

(inherited documentation)

compute_torsion(self, prev_residue, next_residue, strict=True)

source code

Compute the torsion angles of the current residue with neighboring residues prev_residue and next_residue.

Parameters:

prev_residue (Residue) - the previous residue in the chain
next_residue (Residue) - the next residue in the chain
strict (bool) - if True, Broken3DStructureError is raised if either prev_residue or next_residue has a broken structure, else the error is silently ignored and an empty TorsionAngles instance is created

Returns: TorsionAngles

a TorsionAngles object, holding the phi, psi and omega values

Raises:

Broken3DStructureError - when a specific atom cannot be found

Class ProteinResidue

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

compute_torsion(self, prev_residue, next_residue, strict=True)

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