Package csb :: Package bio :: Package fragments :: Class Assignment |
[frames] | no frames]

# Class Assignment

source code

       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)