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

Class CSfrag

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)

Class CSfrag

__init__(self, query, cstable, database, window=8, logger=None) (Constructor)

extract_fragments(self, top=25, cpu=2)

database

query

window

init(self, query, cstable, database, window=8, logger=None)
(Constructor)