def test_contact_matrix():
d = np.arange(5)
radius = np.ones(5) * 2.5
out = contacts.contact_matrix(d, radius)
assert_array_equal(out, [True, True, True, False, False])
# check in-place update
out = np.empty(out.shape)
contacts.contact_matrix(d, radius, out=out)
assert_array_equal(out, [True, True, True, False, False])
def test_contact_matrix():
d = np.arange(5)
radius = np.ones(5) * 2.5
out = contacts.contact_matrix(d, radius)
assert_array_equal(out, [True, True, True, False, False])
# check in-place update
out = np.empty(out.shape)
contacts.contact_matrix(d, radius, out=out)
assert_array_equal(out, [True, True, True, False, False])
def __init__(self,
mobiles,
refs,
method="hard_cut",
radius=4.5,
kwargs=None):
"""
Parameters
----------
mobiles : tuple(AtomGroup, AtomGroup)
two contacting groups that change over time
refs : tuple(AtomGroup, AtomGroup)
two contacting atomgroups in their reference conformation. This
can also be a list of tuples containing different atom groups
radius : float, optional (4.5 Angstroms)
radius within which contacts exist in refgroup
method : string | callable (optional)
Can either be one of ``['hard_cut' , 'soft_cut']`` or a callable
with call signature ``func(r, r0, **kwargs)`` (the "Contacts API").
kwargs : dict, optional
dictionary of additional kwargs passed to `method`. Check
respective functions for reasonable values.
"""
universe = mobiles[0].universe
super(Contacts, self).__init__(universe, mobiles)
if method == 'hard_cut':
self.fraction_contacts = hard_cut_q
elif method == 'soft_cut':
self.fraction_contacts = soft_cut_q
else:
if not callable(method):
raise ValueError("method has to be callable")
self.fraction_contacts = method
# contacts formed in reference
self.r0 = []
self.initial_contacts = []
if isinstance(refs[0], mda.core.groups.AtomGroup):
refA, refB = refs
self.r0.append(distance_array(refA.positions, refB.positions))
self.initial_contacts.append(contact_matrix(self.r0[-1], radius))
else:
for refA, refB in refs:
self.r0.append(distance_array(refA.positions, refB.positions))
self.initial_contacts.append(
contact_matrix(self.r0[-1], radius))
self.fraction_kwargs = kwargs if kwargs is not None else {}
def contact_maps_from_traj(pdb_file,
traj_file,
contact_cutoff=8.0,
savefile=None):
"""
Get contact map from trajectory.
"""
mda_traj = mda.Universe(pdb_file, traj_file)
traj_length = len(mda_traj.trajectory)
ca = mda_traj.select_atoms('name CA')
if savefile:
savefile = os.path.abspath(savefile)
outfile = tables.open_file(savefile, 'w')
atom = tables.Float64Atom()
cm_table = outfile.create_earray(outfile.root,
'contact_maps',
atom,
shape=(traj_length, 0))
contact_matrices = []
for frame in mda_traj.trajectory:
cm_matrix = contacts.contact_matrix(distances.self_distance_array(
ca.positions),
radius=contact_cutoff) * 1.0
contact_matrices.append(cm_matrix)
if savefile:
cm_table.append(contact_matrices)
outfile.close()
return contact_matrices
def test_radius_cut_method(self, universe):
acidic = universe.select_atoms(self.sel_acidic)
basic = universe.select_atoms(self.sel_basic)
r = contacts.distance_array(acidic.positions, basic.positions)
initial_contacts = contacts.contact_matrix(r, 6.0)
expected = []
for ts in universe.trajectory:
r = contacts.distance_array(acidic.positions, basic.positions)
expected.append(contacts.radius_cut_q(r[initial_contacts], None, radius=6.0))
ca = self._run_Contacts(universe, method='radius_cut')
assert_array_equal(ca.timeseries[:, 1], expected)
def report(self, simulation, state):
ca_indices = []
for atom in simulation.topology.atoms():
if atom.name == 'CA':
ca_indices.append(atom.index)
positions = np.array(state.getPositions().value_in_unit(u.angstrom))
time = int(np.round(state.getTime().value_in_unit(u.picosecond)))
positions_ca = positions[ca_indices].astype(np.float32)
distance_matrix = distances.self_distance_array(positions_ca)
contact_map = contacts.contact_matrix(distance_matrix,
radius=8.0) * 1.0
self._out.create_dataset(str(time), data=contact_map)