Package csb :: Package bio :: Package fragments :: Class Assignment

Class Assignment

   object --+    
            |    
FragmentMatch --+
                |
               Assignment

Known Subclasses:

ChemShiftAssignment

Represents a match between a fragment and its target.

Instance Methods

__init__(self, source, start, end, qstart, qend, id=None, probability=None, rmsd=None, tm_score=None, score=None, neff=None, internal_id=None)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

bool

anchored_around(self, rank)
Returns: True if the fragment is centered around position=rank source code

list

backbone_at(self, qstart, qend)
Returns: the CA coordinates of the fragment at the specified subregion.

source code

float

mda_to(self, other, min_overlap=5)
Returns: the MDA (maximum deviation in torsion angles) between self and other. source code

float

nrmsd_to(self, other, min_overlap=5)
Returns: the normalized CA RMSD between self and other. source code

set of int

overlap(self, other)
Returns: target positions, covered by both self and other source code

float

rmsd_to(self, other, min_overlap=5)
Returns: the CA RMSD between self and other. source code

list

sec_structure_at(self, qstart, qend)
Returns: secondary structure of the fragment at the specified subregion

source code

list

torsion_at(self, qstart, qend)
Returns: torsion angles of the fragment at the specified subregion

source code

transform(self, rotation, translation)
Apply rotation/translation to fragment's coordinates in place

source code

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

Static Methods

Assignment

from_fragment(fragment, provider)
Create a new Assignment given a source rosetta fragment.

source code

Properties
	backbone
	end
	neff
	score
	secondary_structure
	sequence
	source_id
	start
	torsion
Inherited from `FragmentMatch`: `id`, `length`, `probability`, `qend`, `qlength`, `qstart`, `rmsd`, `tm_score` Inherited from `object`: `__class__`

Method Details

init(self, source, start, end, qstart, qend, id=None, probability=None, rmsd=None, tm_score=None, score=None, neff=None, internal_id=None)
(Constructor)

source code

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

Parameters:

source (csb.bio.structure.Chain) - source structure (must have torsion angles precomputed)
start (int) - start position in source (rank)
end (int) - end position in source (rank)
id (str) - fragment ID
qstart (int) - start position in target (rank)
qend (int) - end position in target (rank)
probability (float) - probability of assignment
rmsd (float) - RMSD of the fragment, compared to target's native structure

Overrides: object.__init__

(inherited documentation)

anchored_around(self, rank)

source code

Returns: bool: True if the fragment is centered around position=rank

backbone_at(self, qstart, qend)

source code

Returns: list: the CA coordinates of the fragment at the specified subregion.

from_fragment(fragment, provider)
Static Method

source code

Create a new Assignment given a source rosetta fragment.

Parameters:

fragment (RosettaFragment) - rosetta fragment
provider (StructureProvider) - PDB database provider

Returns: Assignment

mda_to(self, other, min_overlap=5)

source code

Parameters:

other (Assignment) - another fragment
min_overlap (int) - require at least that number of overlapping residues (return None if not satisfied)

Returns: float

the MDA (maximum deviation in torsion angles) between self and other.

nrmsd_to(self, other, min_overlap=5)

source code

Parameters:

other (Assignment) - another fragment
min_overlap (int) - require at least that number of overlapping residues (return None if not satisfied)

Returns: float

the normalized CA RMSD between self and other.

overlap(self, other)

source code

Parameters:

other (Assignment)

Returns: set of int

target positions, covered by both self and other

rmsd_to(self, other, min_overlap=5)

source code

Parameters:

other (Assignment) - another fragment
min_overlap (int) - require at least that number of overlapping residues (return None if not satisfied)

Returns: float

the CA RMSD between self and other.

sec_structure_at(self, qstart, qend)

source code

Returns: list: secondary structure of the fragment at the specified subregion

torsion_at(self, qstart, qend)

source code

Returns: list: torsion angles of the fragment at the specified subregion

Property Details

backbone

Get Method:: unreachable.backbone(self)

end

Get Method:: unreachable.end(self)

neff

Get Method:: unreachable.neff(self)

score

Get Method:: unreachable.score(self)

secondary_structure

Get Method:: unreachable.secondary_structure(self)
Set Method:: unreachable.secondary_structure(self, value)

sequence

Get Method:: unreachable.sequence(self)

source_id

Get Method:: unreachable.source_id(self)

start

Get Method:: unreachable.start(self)

torsion

Get Method:: unreachable.torsion(self)

Class Assignment

__init__(self, source, start, end, qstart, qend, id=None, probability=None, rmsd=None, tm_score=None, score=None, neff=None, internal_id=None) (Constructor)

anchored_around(self, rank)

backbone_at(self, qstart, qend)

from_fragment(fragment, provider) Static Method

mda_to(self, other, min_overlap=5)

nrmsd_to(self, other, min_overlap=5)

overlap(self, other)

rmsd_to(self, other, min_overlap=5)

sec_structure_at(self, qstart, qend)

torsion_at(self, qstart, qend)

backbone

end

neff

score

secondary_structure

sequence

source_id

start

torsion

init(self, source, start, end, qstart, qend, id=None, probability=None, rmsd=None, tm_score=None, score=None, neff=None, internal_id=None)
(Constructor)

from_fragment(fragment, provider)
Static Method