Package csb :: Package bio :: Package fragments :: Class RosettaFragsetFactory |
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# Class RosettaFragsetFactory

source code

    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

### make_filtered(self, target, extend=False, callback=None) | source code
Builed a filtered fragment library (by clustering), containing only representative fragments (cluster centroids). Parameters: `target` (Target) - target protein `extend` (bool) - if True, pick alternative reps if available Returns: RosettaFragmentMap filtered fragment library

### make_fragset(self, target) | source code
Build a fragment library given a Target and its Assignments. Parameters: `target` (Target) - target protein Returns: RosettaFragmentMap

### mix(self, *fragsets) | source code
Mix fragments from multiple libraries. Parameters: `fragsets` (RosettaFragmentMap) Returns: RosettaFragmentMap mixed fragment library