Package Bio :: Package PDB :: Module Polypeptide :: Class _PPBuilder

Class _PPBuilder

Known Subclasses:

Base class to extract polypeptides.

It checks if two consecutive residues in a chain are connected.
The connectivity test is implemented by a subclass.

This assumes you want both standard and non-standard amino acids.

Instance Methods

[hide private]

__init__(self, radius)
@param radius: distance...

source code

_accept(self, residue, standard_aa_only)
Check if the residue is an amino acid (PRIVATE).

source code

build_peptides(self, entity, aa_only=1)
Build and return a list of Polypeptide objects.

source code

Method Details

[hide private]

init(self, radius)
(Constructor)

source code


@param radius: distance
@type radius: float

build_peptides(self, entity, aa_only=1)

source code

Build and return a list of Polypeptide objects.

@param entity: polypeptides are searched for in this object
@type entity: L{Structure}, L{Model} or L{Chain}

@param aa_only: if 1, the residue needs to be a standard AA
@type aa_only: int

Class _PPBuilder

__init__(self, radius) (Constructor)

build_peptides(self, entity, aa_only=1)

init(self, radius)
(Constructor)