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

source code

    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)