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src/c/o/cogent-1.5.3/cogent/parse/pknotsrg.py   cogent(Download)
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
from cogent.struct.knots   import opt_single_random
 
__author__ = "Shandy Wikman"
    tmp_pairs.sort()
    if not pseudo:
        tmp_pairs = opt_single_random(tmp_pairs)
        tmp_pairs.sort()
    result.append([seq,tmp_pairs,energy])

src/c/o/cogent-1.5.3/cogent/parse/nupack.py   cogent(Download)
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
from cogent.struct.knots   import opt_single_random
 
__author__ = "Shandy Wikman"
 
        if not pseudo:
            pairs = opt_single_random(pairs)
            pairs.sort()
    else:

src/c/o/cogent-1.5.3/cogent/parse/ilm.py   cogent(Download)
#!/usr/bin/env python
 
from cogent.struct.rna2d      import Pairs
from cogent.struct.knots      import opt_single_random
from cogent.struct.pairs_util import adjust_base
    tmp.sort()
    if not pseudo:
        tmp = opt_single_random(tmp)
        tmp.sort()
    result = []

src/c/o/cogent-1.5.3/cogent/parse/comrna.py   cogent(Download)
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs
from cogent.struct.knots   import opt_single_random
from string                import index
 
        tmp = []
        for block in result:
            tmp.append([block[0],opt_single_random(block[-1])])
        result = tmp
    return result

src/p/y/pycogent-HEAD/cogent/parse/pknotsrg.py   pycogent(Download)
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
from cogent.struct.knots   import opt_single_random
 
__author__ = "Shandy Wikman"
    tmp_pairs.sort()
    if not pseudo:
        tmp_pairs = opt_single_random(tmp_pairs)
        tmp_pairs.sort()
    result.append([seq,tmp_pairs,energy])

src/p/y/pycogent-HEAD/cogent/parse/nupack.py   pycogent(Download)
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs,ViennaStructure
from cogent.struct.knots   import opt_single_random
 
__author__ = "Shandy Wikman"
 
        if not pseudo:
            pairs = opt_single_random(pairs)
            pairs.sort()
    else:

src/p/y/pycogent-HEAD/cogent/parse/ilm.py   pycogent(Download)
#!/usr/bin/env python
 
from cogent.struct.rna2d      import Pairs
from cogent.struct.knots      import opt_single_random
from cogent.struct.pairs_util import adjust_base
    tmp.sort()
    if not pseudo:
        tmp = opt_single_random(tmp)
        tmp.sort()
    result = []

src/p/y/pycogent-HEAD/cogent/parse/comrna.py   pycogent(Download)
from cogent.util.transform import make_trans
from cogent.struct.rna2d   import Pairs
from cogent.struct.knots   import opt_single_random
from string                import index
 
        tmp = []
        for block in result:
            tmp.append([block[0],opt_single_random(block[-1])])
        result = tmp
    return result

src/c/o/cogent-1.5.3/tests/test_struct/test_knots.py   cogent(Download)
from cogent.util.dict2d import Dict2D
from cogent.struct.rna2d import Pairs
from cogent.struct.knots import PairedRegion, PairedRegionFromPairs,\
    PairedRegions, PairedRegionsFromPairs, ConflictMatrix,\
    opt_all, contains_true, empty_matrix,\
        exp1, exp_rem1 = [(10,20),(11,19)], [(15,25),(16,24)]
        exp2, exp_rem2 = [(15,25),(16,24)], [(10,20),(11,19)]
        obs = opt_single_random(p)
        self.failUnless(obs == exp1 or obs == exp2)
        obs = opt_single_random(p, return_removed=True)

src/p/y/pycogent-HEAD/tests/test_struct/test_knots.py   pycogent(Download)
from cogent.util.dict2d import Dict2D
from cogent.struct.rna2d import Pairs
from cogent.struct.knots import PairedRegion, PairedRegionFromPairs,\
    PairedRegions, PairedRegionsFromPairs, ConflictMatrix,\
    opt_all, contains_true, empty_matrix,\
        exp1, exp_rem1 = [(10,20),(11,19)], [(15,25),(16,24)]
        exp2, exp_rem2 = [(15,25),(16,24)], [(10,20),(11,19)]
        obs = opt_single_random(p)
        self.failUnless(obs == exp1 or obs == exp2)
        obs = opt_single_random(p, return_removed=True)

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