def to_pairs(struct=None):
"""
Converts structure string in to a pairs object.
Starts by checking for pseudoknots if pseudoknotted it translates each
steam in to vienna notation and from there makes a pairs object.
Each pairs object is then joined to form the final pairs object of
the entire structure
Returns a tuple of the pairs object and the energy
"""
primary = first = second = struct.split(None,2)[0]
energy = atof(struct.split(None,2)[1].strip('()'))
if struct.__contains__('['): #Checks for first pseudoknot steam
primary = ViennaStructure(primary.translate(primary_table))
first = ViennaStructure(first.translate(first_table))
pairs = primary.toPairs()
pairs.extend(first.toPairs()) #Adds the first steam to pairs object
if struct.__contains__('{'): #Checks for second pseudo steam
second = ViennaStructure(second.translate(second_table))
pairs.extend(second.toPairs())
else:
primary = ViennaStructure(primary.translate(primary_table))
pairs = primary.toPairs()
return pairs,energy
def to_pairs(struct=None):
"""
Converts structure string in to a pairs object.
Starts by checking for pseudoknots if pseudoknotted it translates each
steam in to vienna notation and from there makes a pairs object.
Each pairs object is then joined to form the final pairs object of
the entire structure
Returns a tuple of the pairs object and the energy
"""
primary = first = second = struct.split(None, 2)[0]
energy = atof(struct.split(None, 2)[1].strip('()'))
if struct.__contains__('['): #Checks for first pseudoknot steam
primary = ViennaStructure(primary.translate(primary_table))
first = ViennaStructure(first.translate(first_table))
pairs = primary.toPairs()
pairs.extend(first.toPairs()) #Adds the first steam to pairs object
if struct.__contains__('{'): #Checks for second pseudo steam
second = ViennaStructure(second.translate(second_table))
pairs.extend(second.toPairs())
else:
primary = ViennaStructure(primary.translate(primary_table))
pairs = primary.toPairs()
return pairs, energy
def to_pairs(list=None,pseudo=True):
"""
Converts nupack structure string into pairs object
pseudoknotted and not pseudoknotted.
"""
tmp = list[1]
pairs = []
if list.__contains__('pseudoknotted!'):
#since pseudoknotted is denoted by {} it divides into {} and () string
#they are then turned into pairs lists seperatly and then the lists are
#joined to form the complete set of pairs
first = second = tmp
first = ViennaStructure(first.translate(curly_to_dots_table))
second = second.translate(bracket_to_dots_table)
second = ViennaStructure(second.translate(curly_to_bracket_table))
pairs = first.toPairs()
pairs.extend(second.toPairs())
pairs.sort()
if not pseudo:
pairs = opt_single_random(pairs)
pairs.sort()
else:
structure = ViennaStructure(tmp.translate(curly_to_bracket_table))
pairs = structure.toPairs()
pairs.sort()
return pairs
def to_Pairs(struct=None):
"""
Converts a vienna structure into a pairs object
Returns pairs object
"""
struct = ViennaStructure(struct)
pairs = struct.toPairs()
return pairs
def to_Pairs(struct=None):
"""
Converts a vienna structure into a pairs object
Returns pairs object
"""
struct = ViennaStructure(struct)
pairs = struct.toPairs()
return pairs
def to_pairs(struct):
"""
Takes a structure in dot-bracket notation and converts it to pairs notation
functions tested in rna2d.py
"""
struct = ViennaStructure(struct)
struct = struct.toPairs()
return struct
def to_pairs(struct):
"""
Takes a structure in dot-bracket notation and converts it to pairs notation
functions tested in rna2d.py
"""
struct = ViennaStructure(struct)
struct = struct.toPairs()
return struct
def to_pairs(struct=None):
"""
Converts a vienna structure into a pairs object
Returns pairs object
pairs functions tested in test for rna2d.py
"""
struct = ViennaStructure(struct)
pairs = struct.toPairs()
return pairs
def to_pairs(struct=None):
"""
Converts a vienna structure into a pairs object
Returns pairs object
pairs functions tested in test for rna2d.py
"""
struct = ViennaStructure(struct)
pairs = struct.toPairs()
return pairs
