def test_parse():
#from PDB file
my_emap = pyemap.parse(os.path.join(sys.path[0],"pyemap/tests/test_pdbs/1u3d.pdb"))
assert len(list(my_emap.structure.get_residues()))==577
#from CIF file
my_emap = pyemap.parse(os.path.join(sys.path[0],"pyemap/tests/test_pdbs/1u3d.cif"))
assert len(list(my_emap.structure.get_residues()))==577
def test_save_functions():
my_emap = pyemap.parse(
os.path.join(sys.path[0], "pyemap/tests/test_pdbs/4DJA.pdb"))
#cluster
fout = tempfile.NamedTemporaryFile(suffix=".png")
''' commented out for now until we can find a solution with newer RDKit
#aromatic eta moiety
my_emap.residue_to_Image("SF4603(A)")
my_emap.residue_to_file("SF4603(A)",dest=fout.name)
my_emap.residue_to_Image("FAD601(A)-1")
my_emap.residue_to_file("FAD601(A)-1",dest=fout.name)
'''
#after file is processed
pyemap.process(my_emap)
#standard residue
''' commented out for now until we can find a solution with newer RDKit
my_emap.residue_to_Image("Y443(A)")
my_emap.residue_to_file("Y443(A)",dest=fout.name)
'''
#init graph
my_emap.init_graph_to_Image()
my_emap.init_graph_to_file(dest=fout.name)
pyemap.find_paths(my_emap, "Y443(A)")
#paths graph
my_emap.paths_graph_to_Image()
my_emap.paths_graph_to_file(dest=fout.name)
#check that report does something
assert my_emap.report() != None
def setUpClass(cls):
cls.my_emap = pyemap.parse(
os.path.join(sys.path[0], "pyemap/tests/test_pdbs/2oal.pdb"))
if platform == "linux":
pyemap.process(cls.my_emap, sdef=0)
elif platform == "darwin":
pyemap.process(cls.my_emap)
def setUpClass(cls):
cls.my_emap = pyemap.parse(os.path.join(sys.path[0],"pyemap/tests/test_pdbs/2oal.pdb"))
pyemap.process(cls.my_emap)
def setUpClass(cls):
cls.my_emap = pyemap.parse(os.path.join(sys.path[0],"pyemap/tests/test_pdbs/1u3d.pdb"))