Package csb :: Package bio :: Package structure :: Class SecondaryStructure

Class SecondaryStructure

              object --+            
                       |            
    core.AbstractIndexer --+        
                           |        
core.BaseCollectionContainer --+    
                               |    
        core.CollectionContainer --+
                                   |
                                  SecondaryStructure

Describes the secondary structure of a chain. Provides an index-based access to the secondary structure elements of the chain.

Instance Methods

__init__(self, string=None, conf_string=None)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

__str__(self)
str(x)

source code

int

append(self, element)
Add a new SecondaryStructureElement.

source code

tuple of SecondaryStructureElements

at(self, rank, type=None)
Returns: all secondary structure elements covering the specifid position

source code

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

source code

float

q3(self, reference, relaxed=True)
Compute Q3 score.

source code

tuple of SecondaryStructureElements

scan(self, start, end, filter=None, loose=True, cut=True)
Get all secondary structure elements within the specified [start, end] region.

source code

SecondaryStructure

subregion(self, start, end)
Same as ss.scan(...cut=True), but also shift the start-end positions of all motifs and return a SecondaryStructure instance instead of a list. source code

str

to_string(self, chain_length=None)
Get back the string representation of the secondary structure.

source code

to_three_state(self)
Convert to three-state secondary structure (Helix, Strand, Coil).

source code

Inherited from core.BaseCollectionContainer: __bool__, __contains__, __getitem__, __iter__, __len__, __nonzero__, __repr__

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

Static Methods

list

parse(string, conf_string=None)
Parse secondary structure from DSSP/PSI-PRED output string.

source code

Properties
int	end End position of the rightmost element
int	start Start position of the leftmost element
Inherited from `core.BaseCollectionContainer`: `last_index`, `length`, `start_index` Inherited from `object`: `__class__`

Method Details

init(self, string=None, conf_string=None)
(Constructor)

source code

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

Parameters:

string (str) - a secondary structure string (e.g. a PSI-PRED output)
conf_string (str) - secondary structure prediction confidence values, if available

Overrides: object.__init__

(inherited documentation)

str(self)
(Informal representation operator)

source code

str(x)

Overrides: object.__str__: (inherited documentation)

append(self, element)

source code

Add a new SecondaryStructureElement. Then sort all elements by their start position.

Parameters:

item - the new item to append

Returns: int

the index of the new element

Raises:

TypeError - when the container is type-safe and item has an incorrect type

Overrides: core.CollectionContainer.append

at(self, rank, type=None)

source code

Returns: tuple of SecondaryStructureElements: all secondary structure elements covering the specifid position

clone(self)

source code

Returns:: a deep copy of the object

parse(string, conf_string=None)
Static Method

source code

Parse secondary structure from DSSP/PSI-PRED output string.

Parameters:

string (str) - a secondary structure string (e.g. a PSI-PRED output)
conf_string (str) - secondary structure prediction confidence values, if available

Returns: list

a list of SecondaryStructureElements.

Raises:

ValueError - if the confidence string is not of the same length

q3(self, reference, relaxed=True)

source code

Compute Q3 score.

Parameters:

reference (SecondaryStructure) - reference secondary structure
relaxed (bool) - if True, treat gaps as coils

Returns: float

the percentage of reference residues with identical 3-state secondary structure.

scan(self, start, end, filter=None, loose=True, cut=True)

source code

Get all secondary structure elements within the specified [start, end] region.

Parameters:

start (int) - the start position of the region, 1-based, inclusive
end (int) - the end position of the region, 1-based, inclusive
filter (csb.core.EnumItem) - return only elements of the specified SecStructures kind
loose (bool) - grab all fully or partially matching elements within the region. if False, return only the elements which strictly reside within the region
cut (bool) - if an element is partially overlapping with the start..end region, cut its start and/or end to make it fit into the region. If False, return the elements with their real lengths

Returns: tuple of SecondaryStructureElements

a list of deep-copied SecondaryStructureElements, sorted by their start position

subregion(self, start, end)

source code

Same as ss.scan(...cut=True), but also shift the start-end positions of all motifs and return a SecondaryStructure instance instead of a list.

Parameters:

start (int) - start position of the subregion, with reference to the chain
end (int) - start position of the subregion, with reference to the chain

Returns: SecondaryStructure

a deep-copy sub-fragment of the original SecondaryStructure

to_string(self, chain_length=None)

source code

Get back the string representation of the secondary structure.

Returns: str: a string of secondary structure elements

Bug: [CSB 0000003] If conflicting elements are found at a given rank, this position is represented as a coil.

Property Details

end

End position of the rightmost element

Get Method:: unreachable.end(self) - End position of the rightmost element
Type:: int

start

Start position of the leftmost element

Get Method:: unreachable.start(self) - Start position of the leftmost element
Type:: int

Class SecondaryStructure

__init__(self, string=None, conf_string=None) (Constructor)

__str__(self) (Informal representation operator)

append(self, element)

at(self, rank, type=None)

clone(self)

parse(string, conf_string=None) Static Method

q3(self, reference, relaxed=True)

scan(self, start, end, filter=None, loose=True, cut=True)

subregion(self, start, end)

to_string(self, chain_length=None)

end

start

init(self, string=None, conf_string=None)
(Constructor)

str(self)
(Informal representation operator)

parse(string, conf_string=None)
Static Method