def get_angles(self):
rdmol_copy = self.rdkit_molecule
angle_list = []
for atom1 in rdmol_copy.GetAtoms():
for atom2 in atom1.GetNeighbors():
for atom3 in atom2.GetNeighbors():
if atom1.GetIdx() == atom3.GetIdx():
continue
to_add = (atom1.GetIdx(), atom2.GetIdx(), atom3.GetIdx())
if (to_add in angle_list) or (tuple(reversed(to_add))
in angle_list):
continue
angle_list.append(to_add)
angles = []
for indices in angle_list:
i, j, k = indices
degree = self.ase_molecule.get_angle(i, j, k)
ang = Angle(indices=indices,
degree=degree,
left_mask=[],
right_mask=[])
left_mask = self.get_left_mask(ang)
right_mask = self.get_right_mask(ang)
reaction_center = "No"
angles.append(
Angle(indices, degree, left_mask, right_mask, reaction_center))
self.angles = angles
return self.angles
def get_ts_angles(self):
rdmol_copy = self.create_pseudo_geometry()
angle_list = []
for atom1 in rdmol_copy.GetAtoms():
for atom2 in atom1.GetNeighbors():
for atom3 in atom2.GetNeighbors():
if atom1.GetIdx() == atom3.GetIdx():
continue
to_add = (atom1.GetIdx(), atom2.GetIdx(), atom3.GetIdx())
if (to_add in angle_list) or (tuple(reversed(to_add))
in angle_list):
continue
angle_list.append(to_add)
angles = []
for indices in angle_list:
i, j, k = indices
degree = self.ase_ts.get_angle(i, j, k)
ang = Angle(indices=indices,
degree=degree,
left_mask=[],
right_mask=[])
left_mask = self.get_ts_left_mask(ang)
right_mask = self.get_ts_right_mask(ang)
reaction_center = "No"
if (self.rmg_ts.atoms[i].label != ""
and self.rmg_ts.atoms[j].label != ""
and self.rmg_ts.atoms[k].label != ""):
reaction_center = "Yes"
elif ((self.rmg_ts.atoms[i].label != ""
and self.rmg_ts.atoms[j].label != "")
or (self.rmg_ts.atoms[j].label != ""
and self.rmg_ts.atoms[k].label != "")):
reaction_center = "Close"
angles.append(
Angle(indices, degree, left_mask, right_mask, reaction_center))
self.angles = angles
return self.angles
def get_angles(self, rdkit_molecule=None, ase_molecule=None):
"""
A method for identifying all of the angles in a conforemr
"""
if not rdkit_molecule:
rdkit_molecule = self.rdkit_molecule
rdmol_copy = rdkit_molecule
if not ase_molecule:
ase_molecule = self.ase_molecule
angle_list = []
for atom1 in rdmol_copy.GetAtoms():
for atom2 in atom1.GetNeighbors():
for atom3 in atom2.GetNeighbors():
if atom1.GetIdx() == atom3.GetIdx():
continue
to_add = (atom1.GetIdx(), atom2.GetIdx(), atom3.GetIdx())
if (to_add in angle_list) or (tuple(reversed(to_add))
in angle_list):
continue
angle_list.append(to_add)
angles = []
for index, indices in enumerate(angle_list):
i, j, k = indices
degree = ase_molecule.get_angle(i, j, k)
ang = Angle(index=index,
atom_indices=indices,
degree=degree,
mask=[])
mask = self.get_mask(ang, rdmol_copy, ase_molecule)
reaction_center = False
angles.append(
Angle(index=index,
atom_indices=indices,
degree=degree,
mask=mask,
reaction_center=reaction_center))
self.angles = angles
return self.angles
def setUp(self):
self.angle = Angle(index=1,
atom_indices=[1, 2],
degree=90.0,
reaction_center=True,
mask=[True, True, True])