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)