def _seed_alignment(self):
# Build a Seed Alignment
from hpf.pdb import get_seq, get_crystal
#kdrew: this gets the atom record sequence and not the full sequence
pdb_seq = get_seq(get_crystal(self._pdbid))
#print "_seed_alignment pdb sequence: ", pdb_seq
from hpf.amnh.align import SeedAlignmentFactory
from Bio.SeqRecord import SeqRecord
#kdrew: might change this to be pairwise2 alignment
factory = SeedAlignmentFactory()
alignment = factory.create(self._alignment,
[SeqRecord(pdb_seq,self._pdbid+"_atom_record")])
return alignment
def __init__(self, prediction, experiment, mapping):
self.prediction = prediction
self.experiment = experiment
self.mapping = mapping
self.pred_seq = get_seq(self.prediction)
self.exp_seq = get_seq(self.experiment)
