def _do_it(path):
fh = RMF.open_rmf_file_read_only(path)
mf = RMF.Molecule(fh)
cf = RMF.ChainFactory(fh)
res = RMF.get_resolutions(fh.get_root_node(), RMF.PARTICLE, .1)
if len(res) == 1:
res = [-1]
fh.set_current_frame(RMF.FrameID(0))
diameter = RMF.get_diameter(fh.get_root_node())
mydata = MyData(fh, diameter)
for f in fh.get_frames():
created = {}
fh.set_current_frame(f)
for r in res:
_create_molecules(
fh.get_root_node(),
mf,
cf,
mydata,
r,
created)
if len(created) == 0:
# fall back
_create_molecule(fh.get_root_node(), mydata, r, created)
for c in created:
cmd.load_model(created[c][1], c, f.get_index() + 1)
def test_perturbed(self):
"""Test copying an rmf file"""
# can't set index attribute any more
return
RMF.set_log_level("trace")
name = RMF._get_temporary_file_path("chain.rmf")
fh = RMF.create_rmf_file(name)
fh.set_current_frame(RMF.FrameID(0))
n = fh.get_root_node().add_child("n", RMF.REPRESENTATION)
c = fh.get_category("sequence")
k = fh.get_int_key(c, "chain id")
k2 = fh.get_int_key(c, "other")
n.set_static_value(k, 0)
n.set_static_value(k2, 8)
RMF.show_hierarchy_with_values(n)
fh.flush()
print("closing")
del n
del fh
del k
del c
fh = RMF.open_rmf_file_read_only(name)
fh.set_current_frame(RMF.FrameID(0))
cf = RMF.ChainFactory(fh)
n = fh.get_root_node().get_children()[0]
RMF.show_hierarchy_with_values(n)
self.assertTrue(cf.get_is(n))
chain = cf.get(n).get_chain_id()
self.assertEqual(chain, "A")
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)
def test_chain(self):
"""Test the Chain decorator"""
b = RMF.BufferHandle()
rmf = RMF.create_rmf_buffer(b)
rmf.add_frame('zero', RMF.FRAME)
rt = rmf.get_root_node()
cf = RMF.ChainFactory(rmf)
c0 = rt.add_child("c0", RMF.REPRESENTATION)
c1 = rt.add_child("c1", RMF.REPRESENTATION)
c = cf.get(c0)
# Check defaults
self.assertEqual(c.get_chain_type(), 'UnknownChainType')
self.assertEqual(c.get_sequence(), '')
# Check setters
c.set_chain_type('LPolypeptide')
c.set_sequence('CGY')
c.set_chain_id('X')
# Check both const and non-const getters
self.check_rmf(cf, c0, c1)
self.check_rmf(RMF.ChainConstFactory(rmf), c0, c1)
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,
bf,
None)
