def __init__(self, fh, diameter):
self.atom_factory = RMF.AtomFactory(fh)
self.bond_factory = RMF.BondFactory(fh)
self.particle_factory = RMF.ParticleFactory(fh)
self.ball_factory = RMF.BallFactory(fh)
self.segment_factory = RMF.SegmentFactory(fh)
self.cylinder_factory = RMF.CylinderFactory(fh)
self.diameter = diameter * 1.5
def create_hierarchy(file):
cf = RMF.ChainFactory(file)
af = RMF.AtomFactory(file)
rf = RMF.ResidueFactory(file)
pf = RMF.ParticleFactory(file)
n = file.get_root_node()
for i in range(0, 3 * scale):
child = n.add_child(str(i), RMF.REPRESENTATION)
cf.get(child).set_chain_id(str(i))
create_chain(child, rf, af, pf)
prev)
return prev
fh = RMF.open_rmf_file_read_only(RMF.get_example_path("3U7W.rmf"))
fh.set_current_frame(RMF.FrameID(0))
outpath = RMF._get_temporary_file_path("3U7W-residues.rmf")
out = RMF.create_rmf_file(outpath)
out.add_frame("nothing", RMF.FRAME)
print("file is", outpath)
bf = RMF.BondFactory(out)
rcf = RMF.ResidueFactory(fh)
rf = RMF.ResidueFactory(out)
pcf = RMF.ParticleFactory(fh)
pf = RMF.ParticleFactory(out)
acf = RMF.AtomFactory(fh)
af = RMF.AtomFactory(out)
ccf = RMF.ChainFactory(fh)
cf = RMF.ChainFactory(out)
bf = RMF.BondFactory(out)
copy_to_residues(
fh.get_root_node(),
out.get_root_node(),
rcf,
rf,
pcf,
pf,
acf,
af,
ccf,
cf,
