Package csb :: Package apps :: Module hhfrag :: Class HHfrag

Class HHfrag

object --+
         |
        HHfrag

The HHfrag dynamic fragment detection protocol.

Instance Methods

__init__(self, query, binary, database, logger=None)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

RosettaFragmentMap, list of ResidueEventInfo

build_combined_map(self, fragfile, threshold=0.7, top=25)
Build a hybrid map, where low-confidence regions are complemented with the specified filling.

source code

RosettaFragmentMap, list of ResidueEventInfo

build_filtered_map(self)
Build a filtered fragset of centroids.

source code

RosettaFragmentMap

build_fragment_map(self)
Build a full Rosetta fragset.

source code

RosettaFragmentMap

build_hybrid_filtered_map(self, fragfile)
Mix the fragset with the specified (filtered)filling and then filter the mixture.

source code

tuple of Assignments

extract_fragments(self)
Extract all matching fragment instances, given the list of optimal query slices, generated during the first stage.

source code

log(self, *a, **ka)

source code

tuple of SliceContext

slice_query(self, min=6, max=21, step=3, cpu=None)
Run the query slicer and collect the optimal query segments.

source code

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

Class Variables
	PDBS = `'pdbs25.hhm'`

Properties
	aligner
	database
	pdbs25
	query
Inherited from `object`: `__class__`

Method Details

init(self, query, binary, database, logger=None)
(Constructor)

source code

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

Parameters:

query (str) - query HMM path and file name
binary (str) - the HHsearch binary
database (str) - path to the PDBS25 directory
logger (Application) - logging client (needs to have a log method)

Overrides: object.__init__

(inherited documentation)

build_combined_map(self, fragfile, threshold=0.7, top=25)

source code

Build a hybrid map, where low-confidence regions are complemented with the specified filling.

Parameters:

threshold (float) - confidence threshold
fragfile (str) - filling fragset (Rosetta fragment file)

Returns: RosettaFragmentMap, list of ResidueEventInfo

filtered fragset and a list of residue-wise predictions (centroid and torsion angles)

build_filtered_map(self)

source code

Build a filtered fragset of centroids.

Returns: RosettaFragmentMap, list of ResidueEventInfo: filtered fragset and a list of residue-wise predictions (centroid and torsion angles)

build_hybrid_filtered_map(self, fragfile)

source code

Mix the fragset with the specified (filtered)filling and then filter the mixture. If the filling is a filtered CSfrag library, this will produce a double-filtered map.

Parameters:

fragfile (str) - filtered filling (filtered CSfrag fragment file)

Returns: RosettaFragmentMap

slice_query(self, min=6, max=21, step=3, cpu=None)

source code

Run the query slicer and collect the optimal query segments.

Parameters:

min (int) - min segment length
max (int) - max segment length
step (int) - slicing step
cpu (int) - degree of parallelism

Returns: tuple of SliceContext

Property Details

aligner

Get Method:: unreachable.aligner(self)
Set Method:: unreachable.aligner(self, value)

database

Get Method:: unreachable.database(self)
Set Method:: unreachable.database(self, value)

pdbs25

Get Method:: unreachable.pdbs25(self)

query

Get Method:: unreachable.query(self)

Class HHfrag

__init__(self, query, binary, database, logger=None) (Constructor)

build_combined_map(self, fragfile, threshold=0.7, top=25)

build_filtered_map(self)

build_hybrid_filtered_map(self, fragfile)

slice_query(self, min=6, max=21, step=3, cpu=None)

aligner

database

pdbs25

query

init(self, query, binary, database, logger=None)
(Constructor)