def test_iter_matches_guaianolide():
system = System.from_file(context.get_fn('test/guaianolide.xyz'))
system.detect_bonds()
system_ref = System.from_file(context.get_fn('test/guaianolide_framework_ordered.xyz'))
system_ref.detect_bonds()
order = np.array(system.iter_matches(system_ref).next())
np.testing.assert_equal(order, [8, 9, 4, 7, 14, 12, 11, 10, 5, 6, 13, 16, 15, 2, 0, 1, 3])
def test_iter_matches_guaianolide():
system = System.from_file(context.get_fn('test/guaianolide.xyz'))
system.detect_bonds()
system_ref = System.from_file(context.get_fn('test/guaianolide_framework_ordered.xyz'))
system_ref.detect_bonds()
order = np.array(system.iter_matches(system_ref).next())
np.testing.assert_equal(order, [8, 9, 4, 7, 14, 12, 11, 10, 5, 6, 13, 16, 15, 2, 0, 1, 3])
def test_iter_matches_single_atom():
system = System.from_file(context.get_fn('test/rhodium_complex_nobornane.xyz'))
system.detect_bonds()
system_ref = System(pos=np.zeros((1, 3), float), numbers = np.array([45]))
system_ref.detect_bonds()
selected = set(system.iter_matches(system_ref).next())
reference = set([28])
np.testing.assert_equal(selected, reference)
def test_iter_matches_nobornane_rhodium():
rules = [
('H', '1'),
('C_H1', '6&=1%1'),
('C_H2', '6&=2%1'),
('C_H3', '6&=3%1'),
('C', '6'), # all remaining carbons
('P', '15'),
('Rh', '45'),
]
system = System.from_file(context.get_fn('test/rhodium_complex_nobornane.xyz'))
system.detect_bonds()
system.detect_ffatypes(rules)
system_ref = System.from_file(context.get_fn('test/nobornane.xyz'))
system_ref.detect_bonds()
system_ref.detect_ffatypes(rules)
selected = set(system.iter_matches(system_ref).next())
reference = set([77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95])
np.testing.assert_equal(selected, reference)
def run_example(workdir, command):
env = dict(os.environ)
if os.path.isfile('setup.py') and os.path.isdir('data') and os.path.isdir('yaff'):
# Needed in case the tests are executed on an in-place build:
rootdir = os.getcwd()
env['PYTHONPATH'] = rootdir + ':' + env.get('PYTHONPATH', '')
env['YAFFDATA'] = os.path.join(rootdir, 'data')
workdir = context.get_fn(workdir)
proc = subprocess.Popen(shlex.split(command), stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=workdir, env=env)
outdata, errdata = proc.communicate()
if proc.returncode != 0:
print 'Standard output'
print '+'*80
print outdata
print '+'*80
print 'Standard error'
print '+'*80
print errdata
print '+'*80
assert False
fn_clean = os.path.join(workdir, 'clean.sh')
if os.path.isfile(fn_clean):
assert os.system('cd %s; ./clean.sh &> /dev/null' % workdir) == 0
def test_context():
fn = context.get_fn('test/parameters_bks.txt')
assert os.path.isfile(fn)
fns = context.glob('test/parameters_*')
assert fn in fns
def test_context():
fn = context.get_fn('test/parameters_bks.txt')
assert os.path.isfile(fn)
fns = context.glob('test/parameters_*')
assert fn in fns
