rna_library.structure.junction

Module Contents

Classes

Junction

Represents a junction of any size in an RNA structure including bulges and multi-loops.

class rna_library.structure.junction.Junction(**kwargs)

Bases: rna_library.structure.motif.Motif

Represents a junction of any size in an RNA structure including bulges and multi-loops.

dms_active_idxs(self)

buffer(self)

For the Junction() type this is a list() of int()’s where the first is the size of the parent Helix() and then they are arranged in 3’ to 5’ order. Will have the same size as number of branches in the Jucntion().

Returns

buffers

Return type

List[int]

gaps(self)

Returns a list() of int()’s of gap sizes in 3’ to 5’ order. Will have the same size as number of branches in the Jucntion().

Returns

gaps

Return type

List[int]

is_junction(self)

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

Returns

is_hairpin

Return type

bool

recursive_structure(self)

Returns the owned portion of the structure. In this coding of structure it is the closing pairs as well as the child Helix()’s and their children.

Returns

recursive_structure

Return type

str

recursive_sequence(self)

Returns the owned portion of the sequence. In this coding of structure it is the closing pairs as well as the child Helix()’s and their children.

Returns

recursive_sequence

Return type

str

closing_pairs(self)

Returns a list() of str()’s that correspond to the closing pairs in the Junction() Motif.

Returns

closing_pairs

Return type

List[str]

has_non_canonical(self)

Returns whether or not any of the closing pairs are non-canonical (i.e. not AU/UA, CG/GC, GU/UG).

Returns

has_non_canonical

Return type

bool

number_branches(self)

Returns the number of branches in the current Junction().

Returns

number_branches

Return type

int

symmetric(self)

Indicates if the current Junction() is symmetric, that is the sizes of all of the gaps are the same.

Returns

is_symmetric

Return type

bool

generate_sequences(self)

Would generate all possible sequences for the Junction() that are compatible with the constraints for the motif. Not currently implemented.

Raises

TypeError