def test_angle_between(self):
for _ in range(10):
v1 = np.random.rand(3, )
v2 = np.random.rand(3, )
angle = angle_between(v1, v2)
self.assertLessEqual(angle, np.pi)
self.assertGreaterEqual(angle, 0.0)
self.assertAlmostEqual(angle_between(v1, v1), 0.0)
self.assertAlmostEqual(angle_between(v1, -v1), np.pi)
def is_pi_parallel(ring1_center: np.ndarray,
ring1_normal: np.ndarray,
ring2_center: np.ndarray,
ring2_normal: np.ndarray,
dist_cutoff: float = 8.0,
angle_cutoff: float = 30.0) -> bool:
"""Check if two aromatic rings form a parallel pi-pi contact.
Parameters
----------
ring1_center, ring2_center: np.ndarray
Positions of centers of the two rings. Can be computed with the
compute_ring_center function.
ring1_normal, ring2_normal: np.ndarray
Normals of the two rings. Can be computed with the compute_ring_normal
function.
dist_cutoff: float
Distance cutoff. Max allowed distance between the ring center (Angstroms).
angle_cutoff: float
Angle cutoff. Max allowed deviation from the ideal (0deg) angle between
the rings (in degrees).
Returns
-------
bool
True if two aromatic rings form a parallel pi-pi.
"""
dist = np.linalg.norm(ring1_center - ring2_center)
angle = angle_between(ring1_normal, ring2_normal) * 180 / np.pi
if ((angle < angle_cutoff or angle > 180.0 - angle_cutoff) and
dist < dist_cutoff):
return True
return False
def is_pi_t(ring1_center,
ring1_normal,
ring2_center,
ring2_normal,
dist_cutoff=5.5,
angle_cutoff=30.0):
"""Check if two aromatic rings form a T-shaped pi-pi contact.
Parameters:
-----------
ring1_center, ring2_center: np.ndarray
Positions of centers of the two rings. Can be computed with the
compute_ring_center function.
ring1_normal, ring2_normal: np.ndarray
Normals of the two rings. Can be computed with the compute_ring_normal
function.
dist_cutoff: float
Distance cutoff. Max allowed distance between the ring center (Angstroms).
angle_cutoff: float
Angle cutoff. Max allowed deviation from the ideal (90deg) angle between
the rings (in degrees).
"""
dist = np.linalg.norm(ring1_center - ring2_center)
angle = angle_between(ring1_normal, ring2_normal) * 180 / np.pi
if ((90.0 - angle_cutoff < angle < 90.0 + angle_cutoff) and
dist < dist_cutoff):
return True
return False
def is_cation_pi(cation_position,
ring_center,
ring_normal,
dist_cutoff=6.5,
angle_cutoff=30.0):
"""Check if a cation and an aromatic ring form contact.
Parameters:
-----------
ring_center: np.ndarray
Positions of ring center. Can be computed with the compute_ring_center
function.
ring_normal: np.ndarray
Normal of ring. Can be computed with the compute_ring_normal function.
dist_cutoff: float
Distance cutoff. Max allowed distance between ring center
and cation (in Angstroms).
angle_cutoff: float
Angle cutoff. Max allowed deviation from the ideal (0deg)
angle between ring normal and vector pointing from ring
center to cation (in degrees).
"""
cation_to_ring_vec = cation_position - ring_center
dist = np.linalg.norm(cation_to_ring_vec)
angle = angle_between(cation_to_ring_vec, ring_normal) * 180. / np.pi
if ((angle < angle_cutoff or angle > 180.0 - angle_cutoff) and
(dist < dist_cutoff)):
return True
return False