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src/b/i/biopython-1.63/Bio/SeqIO/PdbIO.py   biopython(Download)
    """
    # Late-binding import to avoid circular dependency on SeqIO in Bio.SeqUtils
    from Bio.SeqUtils import seq1
 
    chains = collections.defaultdict(list)
            # Number of residues in the chain (repeated on every record)
            # num_res = int(line[13:17])
            residues = [seq1(res, custom_map=protein_letters_3to1) for res in line[19:].split()]
            chains[chn_id].extend(residues)
        elif rec_name == 'DBREF':
    # Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO
    from Bio.PDB import PDBParser
    from Bio.SeqUtils import seq1
 
    def restype(residue):
        """Return a residue's type as a one-letter code.
 
        Non-standard residues (e.g. CSD, ANP) are returned as 'X'.
        """
        return seq1(residue.resname, custom_map=protein_letters_3to1)
        # HETATM mod. res. policy: remove mod if in sequence, else discard
        residues = [res for res in chain.get_unpacked_list()
                    if seq1(res.get_resname().upper(),
                        custom_map=protein_letters_3to1) != "X"]
        if not residues:

src/b/i/biopython-HEAD/Bio/SeqIO/PdbIO.py   biopython(Download)
    """
    # Late-binding import to avoid circular dependency on SeqIO in Bio.SeqUtils
    from Bio.SeqUtils import seq1
 
    chains = collections.defaultdict(list)
            # Number of residues in the chain (repeated on every record)
            # num_res = int(line[13:17])
            residues = [seq1(res, custom_map=protein_letters_3to1) for res in line[19:].split()]
            chains[chn_id].extend(residues)
        elif rec_name == 'DBREF':
    # Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO
    from Bio.PDB import PDBParser
    from Bio.SeqUtils import seq1
 
    def restype(residue):
        """Return a residue's type as a one-letter code.
 
        Non-standard residues (e.g. CSD, ANP) are returned as 'X'.
        """
        return seq1(residue.resname, custom_map=protein_letters_3to1)
        # HETATM mod. res. policy: remove mod if in sequence, else discard
        residues = [res for res in chain.get_unpacked_list()
                    if seq1(res.get_resname().upper(),
                        custom_map=protein_letters_3to1) != "X"]
        if not residues:

src/b/i/biopython-1.63/Bio/SearchIO/ExonerateIO/_base.py   biopython(Download)
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
from Bio.SeqUtils import seq1
 
 
        custom_map = {'***': '*', '<->': '-'}
 
        hseq1 = seq1(str(frag.hit.seq), custom_map=custom_map)
        hstart = hsp_hstart
        hend = hstart + len(hseq1.replace('-', '')) * hstep
 
        qseq1 = seq1(str(frag.query.seq), custom_map=custom_map)

src/b/i/biopython-HEAD/Bio/SearchIO/ExonerateIO/_base.py   biopython(Download)
from Bio.SearchIO._index import SearchIndexer
from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
from Bio.SeqUtils import seq1
 
 
        custom_map = {'***': '*', '<->': '-'}
 
        hseq1 = seq1(str(frag.hit.seq), custom_map=custom_map)
        hstart = hsp_hstart
        hend = hstart + len(hseq1.replace('-', '')) * hstep
 
        qseq1 = seq1(str(frag.query.seq), custom_map=custom_map)

src/b/i/biopython-HEAD/Tests/test_SeqUtils.py   biopython(Download)
from Bio.Seq import Seq, MutableSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils import GC, seq1, seq3
from Bio.SeqUtils.lcc import lcc_simp, lcc_mult
from Bio.SeqUtils.CheckSum import crc32, crc64, gcg, seguid

src/b/i/biopython-1.63/Tests/test_SeqUtils.py   biopython(Download)
from Bio.Seq import Seq, MutableSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils import GC, quick_FASTA_reader, seq1, seq3
from Bio.SeqUtils.lcc import lcc_simp, lcc_mult
from Bio.SeqUtils.CheckSum import crc32, crc64, gcg, seguid