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src/b/i/biopython-HEAD/Bio/SeqUtils/__init__.py   biopython(Download)
            tmp_type = 'protein'
            # Convert to one-letter sequence. Have to use a string for seq1  
            seq = Seq(seq1(str(seq)), alphabet=Alphabet.ProteinAlphabet())
        elif not isinstance(base_alphabet, Alphabet.Alphabet):
            raise TypeError("%s is not a valid alphabet for mass calculations"

src/b/i/biopython-1.63/Scripts/xbbtools/nextorf.py   biopython(Download)
class ProteinX(Alphabet.ProteinAlphabet):
    letters = IUPACData.extended_protein_letters + "X"
 
proteinX = ProteinX()
 

src/b/i/biopython-HEAD/Scripts/xbbtools/nextorf.py   biopython(Download)
class ProteinX(Alphabet.ProteinAlphabet):
    letters = IUPACData.extended_protein_letters + "X"
 
proteinX = ProteinX()
 

src/b/i/biopython-1.63/Bio/Alphabet/Reduced.py   biopython(Download)
class Murphy15(Alphabet.ProteinAlphabet):
    letters = "LCAGSTPFWEDNQKH"
    size = 15
murphy_15 = Murphy15()
 
class Murphy10(Alphabet.ProteinAlphabet):
    letters = "LCAGSPFEKH"
    size = 10
murphy_10 = Murphy10()
 
class Murphy8(Alphabet.ProteinAlphabet):
    letters = "LASPFEKH"
    size = 8
murphy_8 = Murphy8()
 
class Murphy4(Alphabet.ProteinAlphabet):
    letters = "LAFE"
    size = 4
murphy_4 = Murphy4()
 
class HPModel(Alphabet.ProteinAlphabet):
    letters = "HP"
    size = 2
hp_model = HPModel()
 

src/b/i/biopython-HEAD/Bio/Alphabet/Reduced.py   biopython(Download)
class Murphy15(Alphabet.ProteinAlphabet):
    letters = "LCAGSTPFWEDNQKH"
    size = 15
murphy_15 = Murphy15()
 
class Murphy10(Alphabet.ProteinAlphabet):
    letters = "LCAGSPFEKH"
    size = 10
murphy_10 = Murphy10()
 
class Murphy8(Alphabet.ProteinAlphabet):
    letters = "LASPFEKH"
    size = 8
murphy_8 = Murphy8()
 
class Murphy4(Alphabet.ProteinAlphabet):
    letters = "LAFE"
    size = 4
murphy_4 = Murphy4()
 
class HPModel(Alphabet.ProteinAlphabet):
    letters = "HP"
    size = 2
hp_model = HPModel()
 

src/b/i/biopython-1.63/Bio/Alphabet/IUPAC.py   biopython(Download)
class ExtendedIUPACProtein(Alphabet.ProteinAlphabet):
    """Extended uppercase IUPAC protein single letter alphabet including X etc.
 
    In addition to the standard 20 single letter protein codes, this includes:
 

src/b/i/biopython-HEAD/Bio/Alphabet/IUPAC.py   biopython(Download)
class ExtendedIUPACProtein(Alphabet.ProteinAlphabet):
    """Extended uppercase IUPAC protein single letter alphabet including X etc.
 
    In addition to the standard 20 single letter protein codes, this includes:
 

src/b/i/biopython-HEAD/Bio/CodonAlign/__init__.py   biopython(Download)
    # add an option to allow the user to specify the returned object?
 
    from Bio.Alphabet import ProteinAlphabet
    from Bio.Align import MultipleSeqAlignment
 

src/b/i/biopython-HEAD/Tests/test_GenBank.py   biopython(Download)
from Bio.GenBank import utils
 
from Bio.Alphabet import _get_base_alphabet, ProteinAlphabet
 
gb_file_dir = os.path.join(os.getcwd(), 'GenBank')

src/b/i/biopython-1.63/Tests/test_GenBank.py   biopython(Download)
from Bio.GenBank import utils
 
from Bio.Alphabet import _get_base_alphabet, ProteinAlphabet
 
#TODO - Test we get the warnings we expect on the bad input files