def _add_bonds_to_plot(axes, acids):
"""Add certain bonds in a folding to the plot."""
bonds = Algorithms.find_bonds(acids)
linestyle = 'dotted'
for bond_type in bonds:
for bond in bond_type:
x = []
y = []
z = []
for acid in bond:
x.append(acid['x'])
y.append(acid['y'])
z.append(acid['z'])
axes.plot3D(x, y, z, color='black', linestyle=linestyle)
linestyle = 'dashed'
return axes
def test_find_bonds(protein):
weak_bonds, _ = Algorithms.find_bonds(protein.acids)
assert len(weak_bonds) == 1
