Package csb :: Package bio :: Package fragments :: Module isites :: Class RepStructureFragment
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Class RepStructureFragment

source code

object --+
         |
        RepStructureFragment

Container class which describes an I-Sites paradigm structure for a cluster.

Instance Methods
 
__init__(self, accession, chain, start, angles=None, source=None, struct=None)
x.__init__(...) initializes x; see help(type(x)) for signature
source code

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

Properties
  angles
  source
  structure

Inherited from object: __class__

Method Details

__init__(self, accession, chain, start, angles=None, source=None, struct=None)
(Constructor)

source code 

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

Parameters:
  • accession (str) - paradigm's accession number
  • chain (str) - chain ID
  • start (int) - the start position in the paradigm's chain where the fragment instance is located (including the overhangs). In the original library this is a PDB sequence number, not a SEQRES rank. The residue rank can be retrieved from the structure instead:
    >>> cluster.representative.structure.find(start).rank
    residue rank
  • angles (structure.TorsionAnglesCollection) - torsion angles of the paradigm, in degrees
  • source (ChainSequence) - the entire paradigm chain with pre-computed torsion angles
  • struct (structure.Chain) - a segment of the paradigm's structure.Chain which contains the I-Site. Residue ranks and IDs are preserved as they were in the original chain (no shifting)
Overrides: object.__init__
(inherited documentation)

Property Details

angles

Get Method:
unreachable.angles(self)
Set Method:
unreachable.angles(self, angles)

source

Get Method:
unreachable.source(self)
Set Method:
unreachable.source(self, chain)

structure

Get Method:
unreachable.structure(self)
Set Method:
unreachable.structure(self, chain_fragment)