Package csb :: Package bio :: Package structure :: Class ProteinResidue |
[frames] | no frames]

# Class ProteinResidue

source code

                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