def test_ring_center_and_normal(self):
mol = parse_smiles("c1ccccc1")
R = 1.5
for i in range(6):
atom = mol.GetAtom(i+1)
atom.SetVector(R*math.cos(2*math.pi*i/6),
R*math.sin(2*math.pi*i/6),
0.0)
for ring in ob.OBMolRingIter(mol):
break
center = ob.vector3()
norm1 = ob.vector3()
norm2 = ob.vector3()
ring.findCenterAndNormal(center, norm1, norm2)
self.assertZero(center.GetX())
self.assertZero(center.GetY())
self.assertZero(center.GetZ())
self.assertZero(norm1.GetX())
self.assertZero(norm1.GetY())
self.assertClose(norm1.GetZ(), 1.0)
self.assertZero(norm2.GetX())
self.assertZero(norm2.GetY())
self.assertClose(norm2.GetZ(), -1.0)
def _compute_cation_pi(protein, ligand, protein_cation_pi, ligand_cation_pi):
for protein_ring in ob.OBMolRingIter(protein):
if protein_ring.IsAromatic():
protein_ring_center = _compute_ring_center(protein, protein_ring)
protein_ring_normal = _compute_ring_normal(protein, protein_ring)
for atom in ob.OBMolAtomIter(ligand):
if np.abs(atom.GetFormalCharge() -
1.0) < 0.01 or '+' in atom.GetType():
cation_position = np.array([atom.x(), atom.y(), atom.z()])
if _is_cation_pi(cation_position, protein_ring_center,
protein_ring_normal):
protein_cation_pi = _update_feature_dict(
protein_cation_pi, idxs=protein_ring._path)
ligand_cation_pi = _update_feature_dict(
ligand_cation_pi, indices=[atom.GetIndex()])
return protein_cation_pi, ligand_cation_pi
def _compute_pi_stack(protein_xyz,
protein,
ligand_xyz,
ligand,
pairwise_distances=None,
dist_cutoff=4.4,
angle_cutoff=30.):
'''
Pseudocode:
for each ring in ligand:
if it is aromatic:
for each ring in protein:
if it is aromatic:
compute distance between centers
compute angle.
if it counts as parallel pi-pi:
for each atom in ligand and in protein,
add to list of atom indices
if it counts as pi-T:
for each atom in ligand and in protein:
add to list of atom indices
'''
protein_pi_parallel = {}
protein_pi_t = {}
ligand_pi_parallel = {}
ligand_pi_t = {}
for protein_ring in ob.OBMolRingIter(protein):
if protein_ring.IsAromatic():
protein_ring_center = _compute_ring_center(protein, protein_ring)
protein_ring_normal = _compute_ring_normal(protein, protein_ring)
ligand_pi_parallel_idxs = set()
ligand_pi_t_idxs = set()
for ligand_ring in ob.OBMolRingIter(ligand):
if ligand_ring.IsAromatic():
ligand_ring_center = _compute_ring_center(
ligand, ligand_ring)
ligand_ring_normal = _compute_ring_normal(
ligand, ligand_ring)
if _is_pi_parallel(protein_ring_center,
protein_ring_normal, ligand_ring_center,
ligand_ring_normal):
protein_pi_parallel = _update_feature_dict(
protein_pi_parallel, idxs=protein_ring._path)
ligand_idxs_to_update = list(
set(ligand_ring._path) - ligand_pi_parallel_idxs)
ligand_pi_parallel = _update_feature_dict(
ligand_pi_parallel, idxs=ligand_idxs_to_update)
ligand_pi_parallel_idxs.update(set(ligand_ring._path))
if _is_pi_t(protein_ring_center, protein_ring_normal,
ligand_ring_center, ligand_ring_normal):
protein_pi_t = _update_feature_dict(
protein_pi_t, idxs=protein_ring._path)
ligand_idxs_to_update = list(
set(ligand_ring._path) - ligand_pi_t_idxs)
ligand_pi_t = _update_feature_dict(
ligand_pi_t, idxs=ligand_idxs_to_update)
ligand_pi_t_idxs.update(set(ligand_ring._path))
return (protein_pi_t, protein_pi_parallel, ligand_pi_t, ligand_pi_parallel)