def models_from_pdb(fname):
"""Get models from a PDB as individual poses.
Parameters
----------
fname : str
Path to a PDB.
Yields
------
pyrosetta.Pose
The next model in the PDB.
"""
p = pyrosetta.Pose()
with open(fname, "r") as f:
model = []
for l in f:
if (l.startswith("#")):
continue
line = l.rstrip()
model.append(line)
if (line.startswith("ENDMDL")):
pose_from_pdbstring(p, pdbcontents="\n".join(model))
yield p.clone()
model = []
if (len(model)):
pose_from_pdbstring(p, pdbcontents="\n".join(model))
yield p.clone()
def pose_from_pdbstring(*args, **kwargs):
result = pose.Pose()
import_pose.pose_from_pdbstring(result, *args, **kwargs)
return result
CONECT 5 4
CONECT 6 4
CONECT 7 8
CONECT 8 7 9 12
CONECT 9 8 10 11
CONECT 10 9 13 14
CONECT 11 9 15 16
CONECT 12 8
CONECT 13 10
CONECT 14 10
CONECT 15 11
CONECT 16 11
"""
pose = Pose()
pose_from_pdbstring(pose, contents)
sc_donor = {
1: [
pick_ray(pose.residue(1), "1HD2", "ND2"),
pick_ray(pose.residue(1), "2HD2", "ND2")
],
2: [
pick_ray(pose.residue(2), "HE", "NE"),
pick_ray(pose.residue(2), "1HH1", "NH1"),
pick_ray(pose.residue(2), "2HH1", "NH1"),
pick_ray(pose.residue(2), "1HH2", "NH2"),
pick_ray(pose.residue(2), "2HH2", "NH2")
]
}
def dummy():
p = Pose()
pose_from_pdbstring(p, contents)
return p
