Package csb :: Package bio :: Package fragments :: Class RosettaFragsetFactory

Class RosettaFragsetFactory

object --+
         |
        RosettaFragsetFactory

Simplifies the construction of fragment libraries.

Instance Methods

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

source code

RosettaFragmentMap

make_chopped(self, fragments, window)
Build a fixed-length fragment library from a list of variable-length Assignments.

source code

RosettaFragmentMap

make_combined(self, target, filling, threshold=0.5, callback=None)
Complement target's assignments with filling (e.g. source code

RosettaFragmentMap

make_filtered(self, target, extend=False, callback=None)
Builed a filtered fragment library (by clustering), containing only representative fragments (cluster centroids).

source code

RosettaFragmentMap

make_fragset(self, target)
Build a fragment library given a Target and its Assignments.

source code

RosettaFragmentMap

mix(self, *fragsets)
Mix fragments from multiple libraries.

source code

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

Properties
Inherited from `object`: `__class__`

Method Details

init(self)
(Constructor)

source code

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

Overrides: object.__init__: (inherited documentation)

make_chopped(self, fragments, window)

source code

Build a fixed-length fragment library from a list of variable-length Assignments.

Parameters:

fragments (iterable of RosettaFragments) - source fragments
window (int) - fixed-length fragment size (for classic Rosetta: choose 9)

Returns: RosettaFragmentMap

fixed-length fragment library

make_combined(self, target, filling, threshold=0.5, callback=None)

source code

Complement target's assignments with filling (e.g. rosetta fragments). The regions to be complemented are determined by calculating the confidence at each residue (by filtering).

Parameters:

target (Target) - target protein
filling (RosettaFragmentMap or iterable of RosettaFragment) - additional fragments to place in the low-conf regions
threshold (float) - confidence threshold

Returns: RosettaFragmentMap

complemented fragment library