Python get_root_node Examples

Example #1

File: test_geometry.py Project: andreyto/imp-fork-proddl

 def _do_test_round_trip(self, g):
     gg= IMP.display.create_geometry(g)
     nm=self.get_tmp_file_name("round_trip_g.rmf")
     rmf= RMF.create_rmf_file(nm)
     IMP.rmf.add_geometries(rmf.get_root_node(), [gg])
     IMP.rmf.save_frame(rmf, 0)
     del rmf
     rmf=RMF.open_rmf_file_read_only(nm)
     ggb= IMP.rmf.create_geometries(rmf)
     IMP.rmf.load_frame(rmf, 0)
     ggbt= gg.get_from(gg)
     self.assertEqual(type(ggbt.get_geometry()), type(g))

Example #2

 def _do_test_round_trip(self, g, suffix):
     gg = IMP.display.create_geometry(g)
     nm = self.get_tmp_file_name("round_trip_g" + suffix)
     print(nm)
     rmf = RMF.create_rmf_file(nm)
     IMP.rmf.add_geometries(rmf.get_root_node(), [gg])
     IMP.rmf.save_frame(rmf, "zero")
     del rmf
     rmf = RMF.open_rmf_file_read_only(nm)
     ggb = IMP.rmf.create_geometries(rmf)
     IMP.rmf.load_frame(rmf, RMF.FrameID(0))
     ggbt = gg.get_from(gg)
     self.assertEqual(type(ggbt.get_geometry()), type(g))

Example #3

File: medium_test_too_many_terms.py Project: drussel/imp

 def test_round_trip(self):
     """Test that restraints with a zillion terms are squashed"""
     for suffix in RMF.suffixes:
         m= IMP.Model()
         l0= IMP.atom.read_pdb(self.get_input_file_name("simple.pdb"), m)
         l1= IMP.atom.read_pdb(self.get_input_file_name("simple.pdb"), m)
         cpc= IMP.container.CloseBipartitePairContainer(IMP.atom.get_leaves(l0), IMP.atom.get_leaves(l1), 15, 1)
         r= IMP.container.PairsRestraint(IMP.core.HarmonicDistancePairScore(10, 10), cpc)
         rmf= RMF.create_rmf_file(self.get_tmp_file_name("zillion."+suffix))
         IMP.rmf.add_hierarchies(rmf, [l0, l1])
         IMP.rmf.add_restraints(rmf, [r])
         IMP.rmf.set_maximum_number_of_terms(rmf, 10)
         IMP.rmf.save_frame(rmf, 0)
         num_nodes= self._get_num_nodes(rmf.get_root_node())
         print num_nodes
         self.assertEqual(num_nodes,
                          m.get_number_of_particles()+1+1+2*len(IMP.atom.get_leaves(l0)))

Example #4

 def test_round_trip(self):
     """Test that restraints with a zillion terms are squashed"""
     for suffix in IMP.rmf.suffixes:
         m = IMP.Model()
         l0 = IMP.atom.read_pdb(self.get_input_file_name("simple.pdb"), m)
         l1 = IMP.atom.read_pdb(self.get_input_file_name("simple.pdb"), m)
         cpc = IMP.container.CloseBipartitePairContainer(
             IMP.atom.get_leaves(l0), IMP.atom.get_leaves(l1), 15, 1)
         r = IMP.container.PairsRestraint(
             IMP.core.HarmonicDistancePairScore(10, 10), cpc)
         rmf = RMF.create_rmf_file(
             self.get_tmp_file_name("zillion" + suffix))
         IMP.rmf.add_hierarchies(rmf, [l0, l1])
         IMP.rmf.add_restraints(rmf, [r])
         IMP.rmf.set_maximum_number_of_terms(rmf, 10)
         IMP.rmf.save_frame(rmf)
         num_nodes = self._get_num_nodes(rmf.get_root_node())
         print(num_nodes)
         self.assertEqual(num_nodes, len(m.get_particle_indexes()) + 1 + 1)

Example #5

slabss= IMP.npctransport.SlabSingletonScore(height, radius, 1)
r= IMP.core.SingletonRestraint(slabss, p, "slab")
r.set_log_level(IMP.WARNING)
nm=IMP.base.create_temporary_file_name("display_slab", ".pym")
w= IMP.display.create_writer(nm)
if use_rmf:
    rnm=IMP.base.create_temporary_file_name("display_slab", ".rmf")
    rmf= RMF.create_rmf_file(rnm)
    #IMP.rmf.add_hierarchies(rmf, [p])
sg= IMP.npctransport.SlabWireGeometry(height, radius, 100)
sg.set_was_used(True);
if use_rmf:
    sg.set_color(IMP.display.Color(0,1,0))
    sgs= sg.get_components()
    nh= rmf.get_root_node().add_child("slab", RMF.GEOMETRY)
    IMP.rmf.add_geometries(nh, sgs)
    #[sc.show() for sc in sgs]
w.add_geometry(sg)

bb=IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0),
                             IMP.algebra.Vector3D(sz, sz, sz))

#nh= rmf.get_root_node().add_child("derivatives", RMF.GEOMETRY)

gs=[]
if use_rmf:
    nh= rmf.get_root_node().add_child("deriv", RMF.GEOMETRY)
for c in IMP.algebra.get_grid_interior_cover_by_spacing(bb, 5):
    #print c
    d.set_coordinates(c)

Example #6

slabss = IMP.npctransport.SlabSingletonScore(height, radius, 1)
r = IMP.core.SingletonRestraint(slabss, p, "slab")
r.set_log_level(IMP.WARNING)
nm = IMP.base.create_temporary_file_name("display_slab", ".pym")
w = IMP.display.create_writer(nm)
if use_rmf:
    rnm = IMP.base.create_temporary_file_name("display_slab", ".rmf")
    rmf = RMF.create_rmf_file(rnm)
    #IMP.rmf.add_hierarchies(rmf, [p])
sg = IMP.npctransport.SlabWireGeometry(height, radius, 100)
sg.set_was_used(True)
if use_rmf:
    sg.set_color(IMP.display.Color(0, 1, 0))
    sgs = sg.get_components()
    nh = rmf.get_root_node().add_child("slab", RMF.GEOMETRY)
    IMP.rmf.add_geometries(nh, sgs)
    #[sc.show() for sc in sgs]
w.add_geometry(sg)

bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0),
                               IMP.algebra.Vector3D(sz, sz, sz))

#nh= rmf.get_root_node().add_child("derivatives", RMF.GEOMETRY)

gs = []
if use_rmf:
    nh = rmf.get_root_node().add_child("deriv", RMF.GEOMETRY)
for c in IMP.algebra.get_grid_interior_cover_by_spacing(bb, 5):
    #print c
    d.set_coordinates(c)