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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
 
 
    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()
 

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
 
 
    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()
 

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
        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.sort()
    else:
        structure = ViennaStructure(tmp.translate(curly_to_bracket_table))
        pairs = structure.toPairs()
        pairs.sort()

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
        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.sort()
    else:
        structure = ViennaStructure(tmp.translate(curly_to_bracket_table))
        pairs = structure.toPairs()
        pairs.sort()

src/c/o/cogent-1.5.3/cogent/parse/rnashapes.py   cogent(Download)
from string                import split,strip,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
 
__author__ = "Shandy Wikman"
    Returns pairs object
    """
    struct = ViennaStructure(struct)
    pairs = struct.toPairs()
 

src/c/o/cogent-1.5.3/cogent/parse/rnaforester.py   cogent(Download)
#!/usr/bin/env python
 
from string import strip,split
from cogent.struct.rna2d import Pairs,ViennaStructure
 
    functions tested in rna2d.py
    """
    struct = ViennaStructure(struct)
    struct = struct.toPairs()
 

src/c/o/cogent-1.5.3/cogent/parse/rnaalifold.py   cogent(Download)
#!/usr/bin/env python
 
from string                import strip,split,atof
from cogent.struct.rna2d   import ViennaStructure,Pairs
 
    pairs functions tested in test for rna2d.py
    """
    struct = ViennaStructure(struct)
    pairs = struct.toPairs()
 

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
    """
    try:
        return toPairs(ViennaStructure(data.translate(cove_to_vienna_table)))
    except IndexError:
        return ''

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
 
    """
    try:
        vienna = ViennaStructure(data.translate(to_vienna_table))
        return toPairs(vienna)
    except IndexError:

src/p/y/pycogent-HEAD/cogent/parse/rnashapes.py   pycogent(Download)
from string                import split,strip,atof
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
 
__author__ = "Shandy Wikman"
    Returns pairs object
    """
    struct = ViennaStructure(struct)
    pairs = struct.toPairs()
 

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