Package csb :: Package bio :: Package fragments :: Class Target

Class Target

            object --+        
                     |        
core.AbstractContainer --+    
                         |    
  core.AbstractNIContainer --+
                             |
                            Target

Known Subclasses:

ChemShiftTarget

Represents a protein structure prediction target.

Nested Classes
Inherited from `core.AbstractContainer`: `__metaclass__`

Instance Methods

__init__(self, id, length, residues, overlap=None, factory=<csb.bio.fragments.AssignmentFactory object at 0x7fe0c5616390>)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

assign(self, fragment)
Add a new fragment match.

source code

assignall(self, fragments)
Assign a bunch of fragments at once.

source code

Target

clone(self)
Returns: a deep copy of the target

source code

Target

filter(self, threshold=1.5, extend=False)
Filter the current fragment map using a FragmentCluster.

source code

Inherited from core.AbstractNIContainer: __getitem__

Inherited from core.AbstractContainer: __bool__, __iter__, __len__, __nonzero__

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

Static Methods

deserialize(pickle)

source code

Target

from_profile(hmm)
Factory, which builds Target objects from an HMM profile.

source code

Target

from_sequence(id, sequence)
Factory, which builds Target objects from a bare sequence.

source code

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
	accession
	chain_id
	errors
	id
	length
	matches
	max_overlap
	residues
	sequence
Inherited from `object`: `__class__`

Method Details

init(self, id, length, residues, overlap=None, factory=<csb.bio.fragments.AssignmentFactory object at 0x7fe0c5616390>)
(Constructor)

source code

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

Parameters:

id (str) - target sequence ID, in PDB accnC format
length (int) - total target sequence length
residues (iterable of csb.bio.structure.ProteinResidues) - a list, containing target's residues. See also Target.from_sequence

Overrides: object.__init__

(inherited documentation)

assign(self, fragment)

source code

Add a new fragment match.

Parameters:

fragment (Assignment) - fragment to assign

assignall(self, fragments)

source code

Assign a bunch of fragments at once.

Parameters:

fragments (iterable of Assignments)

clone(self)

source code

Returns: Target: a deep copy of the target

filter(self, threshold=1.5, extend=False)

source code

Filter the current fragment map using a FragmentCluster.

Parameters:

threshold (float) - cluster RMSD threshold (see FragmentCluster)
extend (bool) - pick extended alternatives where possible (default=False)

Returns: Target

a new target, containing only cluster centroids/reps

from_profile(hmm)
Static Method

source code

Factory, which builds Target objects from an HMM profile.

Parameters:

hmm (csb.bio.hmm.ProfileHMM) - target's HMM

Returns: Target

from_sequence(id, sequence)
Static Method

source code

Factory, which builds Target objects from a bare sequence.

Parameters:

sequence (csb.bio.sequence.AbstractSequence, str or iterable) - target's sequence

Returns: Target

Property Details

accession

Get Method:: unreachable.accession(self)

chain_id

Get Method:: unreachable.chain_id(self)

errors

Get Method:: unreachable.errors(self)

id

Get Method:: unreachable.id(self)

length

Get Method:: unreachable.length(self)

matches

Get Method:: unreachable.matches(self)

max_overlap

Get Method:: unreachable.max_overlap(self)

residues

Get Method:: unreachable.residues(self)

sequence

Get Method:: unreachable.sequence(self)

Class Target

__init__(self, id, length, residues, overlap=None, factory=<csb.bio.fragments.AssignmentFactory object at 0x7fe0c5616390>) (Constructor)

assign(self, fragment)

assignall(self, fragments)

clone(self)

filter(self, threshold=1.5, extend=False)

from_profile(hmm) Static Method

from_sequence(id, sequence) Static Method

accession

chain_id

errors

id

length

matches

max_overlap

residues

sequence

init(self, id, length, residues, overlap=None, factory=<csb.bio.fragments.AssignmentFactory object at 0x7fe0c5616390>)
(Constructor)

from_profile(hmm)
Static Method

from_sequence(id, sequence)
Static Method