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src/c/o/cogent-1.5.3/cogent/struct/rna2d.py   cogent(Download)
"""
from numpy import zeros, put
from cogent.util.transform import make_trans, float_from_string
from cogent.core.tree import TreeNode, TreeError
from cogent.util.misc import not_none, flatten
 
 
wuss_to_vienna_table = make_trans('<([{>)]} ', '(((()))) ', '.')
 
def wuss_to_vienna(data):

src/p/y/pycogent-HEAD/cogent/struct/rna2d.py   pycogent(Download)
"""
from numpy import zeros, put
from cogent.util.transform import make_trans, float_from_string
from cogent.core.tree import TreeNode, TreeError
from cogent.util.misc import not_none, flatten
 
 
wuss_to_vienna_table = make_trans('<([{>)]} ', '(((()))) ', '.')
 
def wuss_to_vienna(data):

src/c/o/cogent-1.5.3/cogent/parse/pknotsrg.py   cogent(Download)
 
from string                import strip,split,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
from cogent.struct.knots   import opt_single_random
    return result
 
primary_table = make_trans('{[]}','....')
first_table   = make_trans('({[]})','..()..')
second_table  = make_trans('([{}])','..()..')

src/c/o/cogent-1.5.3/cogent/parse/nupack.py   cogent(Download)
#!/usr/bin/env python
 
from string                import strip,split,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
    return result
 
curly_to_dots_table = make_trans('{}','..')
bracket_to_dots_table = make_trans('()','..')
curly_to_bracket_table = make_trans('{}','()')

src/p/y/pycogent-HEAD/cogent/parse/pknotsrg.py   pycogent(Download)
 
from string                import strip,split,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
from cogent.struct.knots   import opt_single_random
    return result
 
primary_table = make_trans('{[]}','....')
first_table   = make_trans('({[]})','..()..')
second_table  = make_trans('([{}])','..()..')

src/p/y/pycogent-HEAD/cogent/parse/nupack.py   pycogent(Download)
#!/usr/bin/env python
 
from string                import strip,split,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
    return result
 
curly_to_dots_table = make_trans('{}','..')
bracket_to_dots_table = make_trans('()','..')
curly_to_bracket_table = make_trans('{}','()')

src/c/o/cogent-1.5.3/cogent/parse/consan.py   cogent(Download)
#!/usr/bin/env python
 
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna
from cogent.util.transform import make_trans
 
__status__ = "Development"
 
to_vienna_table = make_trans('><','()')
 
def consan_parser(lines):

src/p/y/pycogent-HEAD/cogent/parse/consan.py   pycogent(Download)
#!/usr/bin/env python
 
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna
from cogent.util.transform import make_trans
 
__status__ = "Development"
 
to_vienna_table = make_trans('><','()')
 
def consan_parser(lines):

src/c/o/cogent-1.5.3/cogent/parse/cove.py   cogent(Download)
#!/usr/bin/env python
 
from string                import split,strip
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna
    return result
 
cove_to_vienna_table = make_trans('><','()')
 
def remove_gaps(struct,seq):

src/p/y/pycogent-HEAD/cogent/parse/cove.py   pycogent(Download)
#!/usr/bin/env python
 
from string                import split,strip
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import ViennaStructure,wuss_to_vienna
    return result
 
cove_to_vienna_table = make_trans('><','()')
 
def remove_gaps(struct,seq):

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