def align_to(self, target, selection='', template_aligned=None):
if not template_aligned:
if not selection:
selection = 'chain ' + ','.join(target.list_chains().keys())
aligned = self.template.select(selection)
else:
aligned = template_aligned
pieces = ranges([self.template.atoms.index(a) for a in aligned])
t = target.to_matrix()
t_com = np.average(t, 0)
t = np.subtract(t, t_com)
shape = self.coordinates.shape
for model in self.coordinates.reshape(-1, len(self.template), 3):
query = np.concatenate(
[model[piece[0]:piece[1]] for piece in pieces])
q_com = np.average(query, 0)
q = np.subtract(query, q_com)
np.copyto(
model,
np.add(
np.dot(np.subtract(model, q_com),
kabsch(t, q, concentric=True)), t_com))
def test_can_generate_ranges_from_several_ranges(self):
val = self.simpilfy(u.ranges({
'units': '2GOZ|1|A|A|3:2GOZ|1|A|A|5,2GOZ|1|B|A|8:2GOZ|1|B|A|50'
}))
ans = ('2GOZ', 1, [('A', 3, 5), ('B', 8, 50)])
self.assertEquals(ans, val)
def test_can_generate_ranges_from_a_range(self):
val = self.simpilfy(u.ranges({'units': '2GOZ|1|A|A|3:2GOZ|1|A|A|5'}))
ans = ('2GOZ', 1, [('A', 3, 5)])
self.assertEquals(ans, val)
def test_can_generate_ranges_from_several_single(self):
val = self.simpilfy(u.ranges({
'units': '2GOZ|1|A|A|3,2GOZ|1|A|A|4,2GOZ|1|A|A|5'
}))
ans = ('2GOZ', 1, [('A', 3, 3), ('A', 4, 4), ('A', 5, 5)])
self.assertEquals(ans, val)
def test_can_generate_range_from_one_single(self):
val = self.simpilfy(u.ranges({'units': '2GOZ|1|A|A|3'}))
ans = ('2GOZ', 1, [('A', 3, 3)])
self.assertEquals(ans, val)