def setup(self, args):
protsel = self.processor.universe.select_atoms(args.pmask)
self.uselib = args.uselib
if self.uselib == "no":
self.atm2 = protsel.select_atoms("name " + args.atoms[1])
self.atm1 = protsel.select_atoms("name " + args.atoms[0] +
" and byres name " +
args.atoms[1])
elif self.uselib in resanallib:
lib = resanallib[self.uselib]
atm1 = []
atm2 = []
for res in self.processor.universe.select_atoms(
"protein").residues:
if res.name not in lib:
continue
for atompairs in lib[res.name]:
atm1.append(res[atompairs[0]])
atm2.append(res[atompairs[1]])
self.atm2 = AtomGroup.AtomGroup(atm2)
self.atm1 = AtomGroup.AtomGroup(atm1)
self.mat = np.zeros([len(self.atm1), len(self.atm1)])
self.s2list = []
self.outname = args.out
self.dosubsample = True
self.resoffset = args.resoffset
def test_merge_without_topology(self):
# This shouldn't have topology as we merged single atoms
ag1 = AtomGroup([self.u.atoms[1]])
ag2 = AtomGroup([self.u.atoms[10]])
u2 = MDAnalysis.Merge(ag1, ag2)
assert_(len(u2.atoms) == 2)
assert_(len(u2.bonds) == 0)
assert_(len(u2.angles) == 0)
assert_(len(u2.dihedrals) == 0)
assert_(len(u2.impropers) == 0)
def test_emptyAG_ValueError(self):
a = AtomGroup([])
b = AtomGroup([])
assert_raises(ValueError, Merge, a, b)
def test_pickle_unpickle_empty(self):
"""Test that an empty AtomGroup can be pickled/unpickled (Issue 293)"""
ag = AtomGroup([])
pickle_str = cPickle.dumps(ag, protocol=cPickle.HIGHEST_PROTOCOL)
newag = cPickle.loads(pickle_str)
assert_equal(len(newag), 0)