def test_circular(self):
u = mda.Universe.empty(6, trajectory=True)
# circular structure
bondlist = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 0)]
u.add_TopologyAttr(Bonds(bondlist))
with pytest.raises(ValueError) as ex:
polymer.sort_backbone(u.atoms)
assert 'cyclical' in str(ex.value)
def test_sortbb(self, u):
# grab backbone atoms out of order
# 0 1 4 6 8 - correct
ag = u.atoms[[4, 1, 0, 8, 6]]
s_ag = polymer.sort_backbone(ag)
assert_equal(s_ag.ids, [0, 1, 4, 6, 8])
def test_branches(self, u):
# includes side branches, can't sort
bad_ag = u.atoms[:10] # include -H etc
with pytest.raises(ValueError):
polymer.sort_backbone(bad_ag)
def test_not_fragment(self, u):
# two fragments don't work
bad_ag = u.residues[0].atoms[:2] + u.residues[1].atoms[:2]
with pytest.raises(ValueError):
polymer.sort_backbone(bad_ag)
def test_missing_bonds(self):
u = mda.Universe(Plength)
with pytest.raises(NoDataError):
polymer.sort_backbone(u.atoms[:10])
def PersistenceL(trajFile,
top,
backboneAtoms,
NP,
coef=1. / 10.,
stride=1.,
chain0Id=0,
firstpoint=2):
"""
get persistence length of chains of indices from chain0Id to chain0Id+NP-1
coef: divide results by 10. to convert to nm since MDAnalysis uses Angstrom
"""
from MDAnalysis.lib.mdamath import make_whole
import MDAnalysis as mda
from MDAnalysis.analysis import polymer
u = mda.Universe(top, trajFile)
for frag in u.atoms.fragments:
make_whole(frag)
molecules = u.atoms.fragments
filter = 'name {}'.format(*backboneAtoms)
backbones = [mol.select_atoms(filter)
for mol in molecules][chain0Id:chain0Id + NP]
sorted_backbones = [polymer.sort_backbone(bb) for bb in backbones]
persistence_length = polymer.PersistenceLength(sorted_backbones)
persistence_length.run()
LB = persistence_length.lb * coef
if firstpoint == 0:
LP = persistence_length.lp * coef
else:
LP = polymer.fit_exponential_decay(
persistence_length.x[firstpoint:],
persistence_length.results[firstpoint:])
persistence_length.fit = np.exp(-persistence_length.x[firstpoint:] /
LP)
LP *= coef
fig, ax = plt.subplots(nrows=1, ncols=1, figsize=[3, 2])
ax.plot(persistence_length.x * coef,
persistence_length.results,
'ro',
label='Result')
ax.plot(persistence_length.x[firstpoint:] * coef,
persistence_length.fit,
label='Fit')
ax.vlines(LP, 0., 1, ls=':', lw=0.75)
plt.text(2. * LP,
0.5 * max(persistence_length.fit),
'$<cos\\theta> = exp(-n*{}/{})$'.format(round(LB, 3),
round(LP, 3)),
size=7)
ax.set_xlim(-0.1, 1.1 * max(persistence_length.x * coef))
ax.set_xlabel(r'$n*l_b$')
ax.set_ylabel(r'$C(n*l_b)$')
plt.savefig('persistenceL.png',
dpi=500,
transparent=True,
bbox_inches="tight")
return LP, LB, len(sorted_backbones[0])
