rna_library.structure.helix

Module Contents

Classes

Helix

Represents a helix or stack in an RNA structure. Inherits from Motif().

class rna_library.structure.helix.Helix(**kwargs)

Bases: rna_library.structure.motif.Motif

Represents a helix or stack in an RNA structure. Inherits from Motif().

size(self)

Returns the size of the Helix() which is just the number of pairs in the stack.

Returns

size

Return type

int

size(self, val)

Sets the current size for the Helix().

Parameters

val (int) – the new size of the helix.

buffer(self)

Returns the buffer of the Helix() which is just the number of pairs in the stack.

Returns

buffer

Return type

int

pairs(self)

Returns the basepairs in the stack as a list of strings of length 2. Pairs are returned in order of lowest 3 prime starting index.

Returns

pairs

Return type

List[str]

is_helix(self)

Indicates that the Motif() is of type Helix().

Returns

is_helix

Return type

bool

recursive_structure(self)

Builds and returns the continguous sequence of the structure viewing the current Motif() as the root of the structure. The returned sequence will be part of the main sequence.

Returns

sequence

Return type

str

recursive_sequence(self)

Builds and returns the continguous structure of the structure viewing the current Motif() as the root of the structure. The returned structure will be part of the main structure.

Returns

structure

Return type

str

has_non_canonical(self)

Checks if any of the basepairs are non-canonical (i.e. non- AU/UA, GU/UG, GC/CG).

Returns

has_non_canonical

Return type

bool

generate_sequences(self)

Generates all possible sequences for the Helix() that are compatible with the constraints for the motif.