def from_pose(self,pose):
""" Updates the PDBMapStructure from a Rosetta::Pose object """
with tempfile.NamedTemporaryFile('wrb',suffix='.pdb',delete=False) as tf:
pose.dump_pdb(tf.name)
p = PDBParser()
with open(tf.name,'rb') as fin:
filterwarnings('ignore',category=PDBConstructionWarning)
s = p.get_structure(self.id,tf.name)
p = lib.PDBMapIO.PDBMapParser()
s = p.process_structure(s,force=True)
resetwarnings()
os.remove(tf.name)
return PDBMapStructure(s,pdb2pose={},refseq=self.refseq)
def clean(self):
p = PDBParser()
io = PDBIO()
with tempfile.NamedTemporaryFile('wrb',suffix='.pdb',delete=False) as tf:
io.set_structure(self.structure)
io.save(tf.name)
cmd = ['lib/clean_pdb.py',tf.name,'ignorechain','nopdbout']
logger.info("Shell to: %s"%' '.join(cmd))
proc = sp.Popen(cmd,stdout=sp.PIPE)
s = p.get_structure(self.get_id(),proc.stdout)
p = lib.PDBMapIO.PDBMapParser()
s = p.process_structure(s,force=True)
s = PDBMapStructure(s,pdb2pose=self._pdb2pose,refseq=self.refseq)
os.remove(tf.name)
return s
