def test_structure_reproducibility(self):
from mbuild.lib.recipes import Alkane
filename = 'decane-tmp.xyz'
decane = Alkane(10)
decane.save(filename)
with open(get_fn('decane.xyz')) as file1:
with open(filename) as file2:
diff = difflib.ndiff(file1.readlines(), file2.readlines())
changes = [l for l in diff if l.startswith('+ ') or l.startswith('- ')]
assert not changes
def __init__(self, chain_length, terminal_group):
super(Alkylsilane, self).__init__()
terminal_group_dict = {"methyl":Methyl}
tgroup = terminal_group_dict[terminal_group]()
alkane = Alkane(chain_length, cap_front=False, cap_end=False)
self.add(alkane, 'alkane')
self.add(tgroup, 'terminal_group')
mb.force_overlap(self['alkane'], self['alkane']['up'],
self['terminal_group']['down'])
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(self['silane'], self['silane']['up'], self['alkane']['down'])
self.add(silane['down'], 'down', containment=False)
def __init__(self, chain_length, terminal_group):
super(Alkylsilane, self).__init__()
module = __import__('atools.lib.moieties.one_port.'+terminal_group)
class_ = getattr(module.lib.moieties.one_port, terminal_group.title())
tgroup = class_()
alkane = Alkane(chain_length, cap_front=False, cap_end=False)
self.add(alkane, 'alkane')
self.add(tgroup, 'terminal_group')
mb.force_overlap(self['alkane'], self['alkane']['up'],
self['terminal_group']['down'])
silane = Silane()
self.add(silane, 'silane')
mb.force_overlap(self['silane'], self['silane']['up'], self['alkane']['down'])
self.add(silane['down'], 'down', containment=False)
def test_remove_port(self):
from mbuild.lib.recipes import Alkane
butane = Alkane(n=4)
butane.remove(butane[-1])
box = mb.fill_box(butane, n_compounds=10, density=1)
def octane(self):
from mbuild.lib.recipes import Alkane
return Alkane(8, cap_front=True, cap_end=True)
def propyl(self):
from mbuild.lib.recipes import Alkane
return Alkane(3, cap_front=True, cap_end=False)