Package csb :: Package apps :: Module csfrag :: Class CSfrag |
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# Class CSfrag

source code

    object --+
             |
            CSfrag

Instance Methods
__init__(self, query, cstable, database, window=8, logger=None) x.__init__(...) initializes x; see help(type(x)) for signature | source code
RosettaFragmentMap |
build_filtered_map(self) Build a filtered fragset of centroids. | source code
RosettaFragmentMap |
build_fragment_map(self) Build a full Rosetta fragset. | source code
tuple of ChemShiftAssignments |
extract_fragments(self, top=25, cpu=2) Extract fragments with matching chemical shifts using a sliding window. | source code
log(self, *a, **ka) | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Properties
| database
| query
| window
Inherited from `object`: `__class__`

Method Details

### __init__(self, query, cstable, database, window=8, logger=None) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `query` (str) - query FASTA sequence path and file name `cstable` (str) - file, containing the table of assigned experimental chemical shifts `database` (str) - path to the PDBS25 directory `logger` (Application) - logging client (needs to have a `log` method) Overrides: object.__init__ (inherited documentation)

### extract_fragments(self, top=25, cpu=2) | source code
Extract fragments with matching chemical shifts using a sliding window. Parameters: `top` (int) - MatchTable capacity per starting position `cpu` (int) - degree of parallelism Returns: tuple of ChemShiftAssignments

Property Details

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

### query Get Method: unreachable.query(self)

### window Get Method: unreachable.window(self) Set Method: unreachable.window(self, value)