def _read(self, name):
rmf = RMF.open_rmf_file_read_only(name)
rt = rmf.get_root_node()
print("children", rt.get_children())
c = rt.get_children()
print(-1, c)
c0 = c[0]
print(0, c0.get_children())
ref0 = c0.get_children()[0]
print("r0", ref0)
print(1, c0.get_children(), ref0)
print(rt.get_children()[0].get_children())
print(2)
ref1 = rt.get_children()[1].get_children()[0]
print("factory")
ef = RMF.ExternalFactory(rmf)
ref0d = ef.get(ref0)
path0 = ref0d.get_path()
print(path0)
self.assert_(os.path.exists(path0))
path1 = ref0d.get_path()
self.assert_(os.path.exists(path1))
self.assertEqual(path0, path1)
simple0 = open(path0, "r").read()
input = RMF._get_test_input_file_path("simple.pdb")
inputpdb = open(input, "r").read()
self.assertEqual(simple0, inputpdb)
def _read(self, name):
rmf = RMF.open_rmf_file_read_only(name)
rt = rmf.get_root_node()
print("children", rt.get_children())
c = rt.get_children()
print(-1, c)
c0 = c[0]
print(0, c0.get_children())
ref0 = c0.get_children()[0]
print("r0", ref0)
print(1, c0.get_children(), ref0)
print(rt.get_children()[0].get_children())
print(2)
ref1 = rt.get_children()[1].get_children()[0]
print("factory")
ef = RMF.ExternalFactory(rmf)
ref0d = ef.get(ref0)
path0 = ref0d.get_path()
print(path0)
# API should return an absolute path
self.assertTrue(os.path.isabs(path0))
# Internally, the path should be relative to that of the RMF
key = self.get_path_key(rmf)
# On Windows the path is stored unchanged
if sys.platform == 'win32':
self.assertEqual(ref0.get_value(key), path0)
else:
self.assertEqual(ref0.get_value(key), 'simple.pdb')
self.assertTrue(os.path.exists(path0))
path1 = ref0d.get_path()
self.assertTrue(os.path.exists(path1))
self.assertEqual(path0, path1)
simple0 = open(path0, "r").read()
input = RMF._get_test_input_file_path("simple.pdb")
inputpdb = open(input, "r").read()
self.assertEqual(simple0, inputpdb)
def _create(self, name, pdb_fname):
rmf = RMF.create_rmf_file(name)
rmf.add_frame("zero", RMF.FRAME)
rt = rmf.get_root_node()
# now make hierarchy
rff = RMF.ReferenceFrameFactory(rmf)
ef = RMF.ExternalFactory(rmf)
# add a couple transformed copies of simple
c0 = rt.add_child("copy0", RMF.REPRESENTATION)
rb0 = rff.get(c0)
rb0.set_translation(RMF.Vector3(100, 0, 0))
rb0.set_rotation(RMF.Vector4(1, 0, 0, 0))
external = c0.add_child("simple.pdb", RMF.REPRESENTATION)
ed = ef.get(external)
ed.set_path(pdb_fname)
c1 = rt.add_child("copy1", RMF.REPRESENTATION)
rb1 = rff.get(c1)
rb1.set_translation(RMF.Vector3(0, 0, 0))
rb1.set_rotation(RMF.Vector4(0, 1, 0, 0))
external = c1.add_child("simple.pdb", RMF.REPRESENTATION)
ed = ef.get(external)
ed.set_path(pdb_fname)
import sys
input_pdb = os.path.join(os.path.split(sys.argv[0])[0], "simple.pdb")
rmf_name = RMF._get_temporary_file_path("externals.rmf")
output_pdb = RMF._get_temporary_file_path("simple.pdb")
print("file name is", rmf_name)
rmf = RMF.create_rmf_file(rmf_name)
rmf.add_frame("root", RMF.FRAME)
# copy simple.pdb to output dir
open(output_pdb, "w").write(open(input_pdb, "r").read())
pdb_relpath = "./simple.pdb"
rpf = RMF.ReferenceFrameFactory(rmf)
ef = RMF.ExternalFactory(rmf)
# add a couple transformed copies of simple
c0 = rmf.get_root_node().add_child("copy0", RMF.REPRESENTATION)
rb0 = rpf.get(c0)
rb0.set_translation(RMF.Vector3(0, 0, 0))
rb0.set_rotation(RMF.Vector4(1, 0, 0, 0))
external = c0.add_child("simple.pdb", RMF.REPRESENTATION)
ed = ef.get(external)
ed.set_path(pdb_relpath)
# add another, reusing the same reference node
c1 = rmf.get_root_node().add_child("copy1", RMF.REPRESENTATION)
rb1 = rpf.get(c1)
rb1.set_translation(RMF.Vector3(20, 0, 0))
rb1.set_rotation(RMF.Vector4(.5, .5, .5, .5))
c1.add_child(external)
