def test_print_xyz():
"""Tests that xyz files are printed correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
with open(local("test.pos_1.pdb"), "w") as out:
for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)):
assert(len(atoms) == 3)
assert_equal(pos*(num+1), atoms.q)
io_pdb.print_pdb(atoms, Cell(h=np.identity(3, float)), filedesc=out)
assert(filecmp.cmp(local("test.pos_0.pdb"), local("test.pos_1.pdb")))
os.unlink(local("test.pos_1.pdb"))
def test_print_xyz():
"""Tests that xyz files are printed correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
with open(local("test.pos_1.pdb"), "w") as out:
for num, ret in enumerate(iter_file("pdb", f)):
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos * (num + 1), atoms.q)
print_file("pdb", atoms, ret["cell"], filedesc=out)
assert filecmp.cmp(local("test.pos_0.pdb"), local("test.pos_1.pdb"))
os.unlink(local("test.pos_1.pdb"))
def test_print_xyz():
"""Tests that xyz files are printed correctly."""
with open(local("test.pos_0.xyz"), "r") as f:
with open(local("test.pos_1.xyz"), "w") as out:
for num, ret in enumerate(iter_file("xyz", f)):
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_xyz * (num + 1), atoms.q)
print_file("xyz", atoms, ret["cell"], filedesc=out)
assert filecmp.cmp(local("test.pos_0.xyz"), local("test.pos_1.xyz"))
os.unlink(local("test.pos_1.xyz"))
def test_iter_pdb():
"""Tests that pdb files with multiple frames are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
for num, (atoms, cell) in enumerate(io_pdb.iter_pdb(f)):
assert(len(atoms) == 3)
assert_equal(pos*(num+1), atoms.q)
def test_read_pdb():
"""Tests that pdb files are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
atoms, cell = io_pdb.read_pdb(f)
assert(len(atoms) == 3)
assert_equal(pos, atoms.q)
def test_iter_xyz():
"""Tests that xyz files with multiple frames are read correctly."""
with open(local("test.pos_0.xyz"), "r") as f:
for num, atoms in enumerate(io_xyz.iter_xyz(f)):
assert(len(atoms) == 3)
assert_equal(pos*(num+1), atoms.q)
def test_read_xyz():
"""Tests that xyz files are read correctly."""
with open(local("test.pos_0.xyz"), "r") as f:
atoms = io_xyz.read_xyz(f)
assert(len(atoms) == 3)
assert_equal(pos, atoms.q)
def index(reqClass=None, reqAction=None, reqData=None):
comReturn = common.local()
if comReturn:
return comReturn
if (reqClass == None):
reqClass = 'index'
pageFile = ('config', 'control', 'crontab', 'files', 'firewall', 'index',
'plugins', 'login', 'system', 'site', 'ssl', 'task', 'soft')
if not reqClass in pageFile:
return redirect('/')
if reqAction == None:
if not isLogined():
return redirect('/login')
import config_api
data = config_api.config_api().get()
return render_template(reqClass + '.html', data=data)
classFile = ('config_api', 'crontab_api', 'files_api', 'firewall_api',
'plugins_api', 'system_api', 'site_api', 'task_api')
className = reqClass + '_api'
if not className in classFile:
return "error"
eval_str = "__import__('" + className + "')." + className + '()'
newInstance = eval(eval_str)
return publicObject(newInstance, reqAction)
def test_read_xyz2():
"""Tests that mode/xyz files are read correctly."""
with open(local("test.pos_0.xyz"), "r") as f:
ret = read_file("xyz", f)
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos, atoms.q)
def test_iter_pdb():
"""Tests that pdb files with multiple frames are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
for num, ret in enumerate(iter_file("pdb", f)):
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos * (num + 1), atoms.q)
def test_read_pdb():
"""Tests that pdb files are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
ret = read_file("pdb", f)
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos, atoms.q)
def test_read_xyz2():
"""Tests that mode/xyz files are read correctly."""
with open(local("test.pos_0.xyz"), "r") as f:
ret = read_file("xyz", f)
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_xyz, atoms.q)
def test_iter_pdb():
"""Tests that pdb files with multiple frames are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
for num, ret in enumerate(iter_file("pdb", f)):
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_pdb * (num + 1), atoms.q)
def test_read_pdb():
"""Tests that pdb files are read correctly."""
with open(local("test.pos_0.pdb"), "r") as f:
ret = read_file("pdb", f)
atoms = ret["atoms"]
assert len(atoms) == 3
assert_equal(pos_pdb, atoms.q)
def get_atoms(fin):
"""Reads atoms object from file @fin."""
with open(local(fin), "r") as f:
ret = read_file("xyz", f)
return ret["atoms"]
def get_atoms(fin):
"""Reads atoms object from file @fin."""
with open(local(fin), "r") as f:
ret = read_file("xyz", f)
return ret["atoms"]