def testCenterOfMass(self):
""" Tests the center-of-mass calculator """
almost_equal = np.testing.assert_array_almost_equal
# Make some systems we know the answer for
array = np.asarray([[1, 0, 0], [-1, 0, 0]])
masses = np.asarray([1, 1])
self.assertTrue(np.all(geo.center_of_mass(array, masses) == 0))
# Change masses
masses = np.asarray([2, 1])
almost_equal(geo.center_of_mass(array, masses), np.array([1/3, 0, 0]))
def _imaging_atom(res):
"""
Determines the imaging atom for the residue. If all atoms are hydrogen
except 1, it is the heavy atom. Otherwise, it is the atom *closest* to the
COM of the residue
"""
from parmed.geometry import center_of_mass
#TODO implement the docstring
found_heavy = False
heavy_idx = -1
for i, atom in enumerate(res):
if atom.atomic_number > 1:
heavy_idx = i
if found_heavy: break
found_heavy = True
else:
if heavy_idx != -1:
return heavy_idx
return 0 # No heavy atoms?? No imaging atom, then.
# Now pick the atom closest to COM (if numpy is available)
if np is None:
warnings.warn('numpy not available. imaging atom set to 0')
return 0
coords = res.coordinates.reshape((len(res), 3))
masses = np.zeros(len(res))
for i, atom in enumerate(res):
if atom.mass == 0:
masses[i] = pt.Mass[pt.Element[atom.atomic_number]]
else:
masses[i] = atom.mass
com = center_of_mass(coords, masses)
diff = coords - com
return np.argmin((diff * diff).sum(axis=1)) + 1
def _imaging_atom(res):
"""
Determines the imaging atom for the residue. If all atoms are hydrogen
except 1, it is the heavy atom. Otherwise, it is the atom *closest* to the
COM of the residue
"""
from parmed.geometry import center_of_mass
#TODO implement the docstring
found_heavy = False
heavy_idx = -1
for i, atom in enumerate(res):
if atom.atomic_number > 1:
heavy_idx = i
if found_heavy: break
found_heavy = True
else:
if heavy_idx != -1:
return heavy_idx
return 0 # No heavy atoms?? No imaging atom, then.
coords = res.coordinates.reshape((len(res), 3))
masses = np.zeros(len(res))
for i, atom in enumerate(res):
if atom.mass == 0:
masses[i] = pt.Mass[pt.Element[atom.atomic_number]]
else:
masses[i] = atom.mass
com = center_of_mass(coords, masses)
diff = coords - com
return np.argmin((diff * diff).sum(axis=1))