def plot(ax, systems):
for system, path in systems.items():
for rank, flexname, protname in list_poses(system, path):
print(flexname, protname)
flex = mda.Universe(flexname)
prot = mda.Universe(protname)
sel = select_flexres(flex, prot)
J = Janin(sel).run()
J.plot(ax=ax, color=colors[rank], ref=False)
def test_janin_single_frame(self, universe, janin_ref_array):
janin = Janin(universe.select_atoms("protein")).run(start=5, stop=6)
assert_almost_equal(janin.angles[0],
janin_ref_array[5],
3,
err_msg="error: dihedral angles should "
"match test values")
def test_janin_residue_selections(self, universe):
janin = Janin(universe.select_atoms("resname LYS")).run()
test_janin = np.load(LYSJaninArray)
assert_almost_equal(janin.angles,
test_janin,
3,
err_msg="error: dihedral angles should "
"match test values")
def test_janin(self, universe, janin_ref_array):
janin = Janin(universe.select_atoms("protein")).run()
# Test precision lowered to account for platform differences with osx
assert_almost_equal(janin.angles,
janin_ref_array,
3,
err_msg="error: dihedral angles should "
"match test values")
def mda_janin_with_CSTV(u, selection):
"""
Takes in a MDAnalysis universe and a selection of that universe that contains
one or several aminoacids sharing resid and resname. It calculates the regular
Janin angles but if it is a CSTV it gives out only chi1 if it is a GAP it returns
none.
Parameters
----------
u: MDAnalysis universe.
selection: selection of the universe containing one or several aminoacids
sharing resid and resname.
Returns
-------
output_angles: numpy array of angles, shape[n_frames, n_dihedrals, n_subunits]
"""
import numpy as np
from MDAnalysis import Universe
from MDAnalysis.analysis.dihedrals import Janin
substitute = {
"CYS": "SG",
"SER": "OG",
"THR": "CG2",
"VAL": "CG1",
}
resname = np.unique(selection.resnames)
resid = np.unique(selection.resids)
assert resname.shape[0] != 1 or resid.shape[0] == 1, "more than one resid"
assert isinstance(u, Universe), "u should be a MDAnlaysis universe."
if resname[0] in ["CYS", "SER", "THR", "VAL"]:
my_list = []
for res in selection.residues:
my_list0 = []
for ts in u.trajectory:
chi1 = res.chi1_selection(
cg_name=substitute[resname[0]]).dihedral.value()
my_list0.append(chi1)
my_list.append(my_list0)
output_angles = np.array(my_list)
output_angles = output_angles.reshape(
[output_angles.shape[0], output_angles.shape[1], 1])
output_angles = output_angles + 180.0
else:
try:
output_angles = Janin(selection).run().angles
except:
output_angles = None
return output_angles
def test_plot(self, universe):
ax = Janin(universe.select_atoms("resid 5-10")).run().plot(ref=True)
assert isinstance(ax, matplotlib.axes.Axes), \
"Ramachandran.plot() did not return and Axes instance"
def test_atom_selection(self):
with pytest.raises(ValueError):
u = mda.Universe(PDB_janin)
janin = Janin(
u.select_atoms("protein and not resname ALA CYS GLY "
"PRO SER THR VAL"))
def test_remove_residues(self, universe):
with pytest.warns(UserWarning):
janin = Janin(universe.select_atoms("protein")).run()
def test_outside_protein_length(self, universe):
with pytest.raises(ValueError):
janin = Janin(universe.select_atoms("resid 220")).run()