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CSB v1.2.5.d7fd331
Package csb :: Package bio :: Package fragments :: Class TargetResidue
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Class TargetResidue

source code

object --+
         |
        TargetResidue
Known Subclasses:

Wrapper around Target's native residues. Decorates them with additional, fragment-related methods.

Instance Methods
 
__init__(self, native_residue)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
assign(self, assignment_info) source code
Assignment
closest(self)
Returns: the fragment with the lowest RMSD at this position in the Target		 source code
ClusterRep or None
filter(self, method='rmsd_to', threshold=1.5, extend=False)
Filter all fragments, covering this position in the Target using a FragmentCluster.		 source code
Assignment
longest(self)
Returns: the longest fragment, covering the current position		 source code
float
precision(self, threshold=1.5)
Returns: the residue-wise precision of the fragment library at the current position (percentage).		 source code

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

Properties
  assignments
  native
  type

Inherited from object: __class__

Method Details

__init__(self, native_residue)
(Constructor)

source code 

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

Overrides: object.__init__
(inherited documentation)

closest(self)

source code 
Returns: Assignment
the fragment with the lowest RMSD at this position in the Target

filter(self, method='rmsd_to', threshold=1.5, extend=False)

source code 

Filter all fragments, covering this position in the Target using a FragmentCluster.

Parameters:
  • method (str) - one of the Metrics members (default=Metrics.RMSD)
  • threshold (float) - cluster RMSD threshold (see FragmentCluster)
  • extend (bool) - pick extended alternative where possible (default=False)
Returns: ClusterRep or None
cluster's representative (if converged) or None

longest(self)

source code 
Returns: Assignment
the longest fragment, covering the current position

precision(self, threshold=1.5)

source code 
Parameters:
  • threshold (float) - true-positive RMSD cutoff (default=1.5)
Returns: float
the residue-wise precision of the fragment library at the current position (percentage).

Property Details

assignments

Get Method:
unreachable.assignments(self)

native

Get Method:
unreachable.native(self)

type

Get Method:
unreachable.type(self)

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