Package csb :: Package bio :: Package structure :: Class SecondaryStructureElement |
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# Class SecondaryStructureElement

source code

    object --+
             |
            SecondaryStructureElement

Describes a Secondary Structure Element.

Instance Methods
__eq__(self, other) | source code
__init__(self, start, end, type, score=None) x.__init__(...) initializes x; see help(type(x)) for signature | source code
__lt__(self, other) | source code
__repr__(self) repr(x) | source code
__str__(self) str(x) | source code
SecondaryStructureElement |
merge(self, other) Merge `self` and `other`. | source code
bool |
overlaps(self, other) Return True if `self` overlaps with `other`. | source code
simplify(self) Convert to three-state secondary structure (Helix, Strand, Coil). | source code
str |
to_string(self) Dump the element as a string. | source code
Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__setattr__`, `__sizeof__`, `__subclasshook__`

Properties
int | end End position (1-based)
int | length Number of residues covered by this element
CollectionContainer | score Secondary structure confidence values for each residue
int | start Start position (1-based)
enum item | type Secondary structure type - a member of SecStructures
Inherited from `object`: `__class__`

Method Details

### __init__(self, start, end, type, score=None) (Constructor) | source code
x.__init__(...) initializes x; see help(type(x)) for signature Parameters: `start` (float) - start position with reference to the chain `end` (float) - end position with reference to the chain `type` (csb.core.EnumItem) - element type - a member of the SecStructures enum `score` (int) - secondary structure prediction confidence, if available Raises: `IndexError` - if start/end positions are out of range Overrides: object.__init__ (inherited documentation)

### __repr__(self) (Representation operator) | source code
repr(x) Overrides: object.__repr__ (inherited documentation)

### __str__(self) (Informal representation operator) | source code
str(x) Overrides: object.__str__ (inherited documentation)

### merge(self, other) | source code
Merge `self` and `other`. Parameters: `other` (SecondaryStructureElement) Returns: SecondaryStructureElement a new secondary structure element Bug: confidence scores are lost

### overlaps(self, other) | source code
Return True if `self` overlaps with `other`. Parameters: `other` (SecondaryStructureElement) Returns: bool

### to_string(self) | source code
Dump the element as a string. Returns: str string representation of the element

Property Details

### end End position (1-based) Get Method: unreachable.end(self) - End position (1-based) Set Method: unreachable.end(self, value) Type: int

### length Number of residues covered by this element Get Method: unreachable.length(self) - Number of residues covered by this element Type: int

### score Secondary structure confidence values for each residue Get Method: unreachable.score(self) - Secondary structure confidence values for each residue Set Method: unreachable.score(self, scores) Type: CollectionContainer

### start Start position (1-based) Get Method: unreachable.start(self) - Start position (1-based) Set Method: unreachable.start(self, value) Type: int

### type Secondary structure type - a member of SecStructures Get Method: unreachable.type(self) - Secondary structure type - a member of SecStructures Set Method: unreachable.type(self, value) Type: enum item