def setUp(self):
self.cistrans = CisTrans(index=1,
atom_indices=[1, 2, 3],
dihedral=60.0,
reaction_center=True,
stero='str',
mask=[True, True, True])
def get_cistrans(self):
"""
A method for identifying all possible cistrans bonds in a molecule
"""
torsion_list = []
cistrans_list = []
for bond1 in self.rdkit_molecule.GetBonds():
atom1 = bond1.GetBeginAtom()
atom2 = bond1.GetEndAtom()
if atom1.IsInRing() or atom2.IsInRing():
# Making sure that bond1 we're looking at are not in a ring
continue
bond_list1 = list(atom1.GetBonds())
bond_list2 = list(atom2.GetBonds())
if not len(bond_list1) > 1 and not len(bond_list2) > 1:
# Making sure that there are more than one bond attached to
# the atoms we're looking at
continue
# Getting the 0th and 3rd atom and insuring that atoms
# attached to the 1st and 2nd atom are not terminal hydrogens
# We also make sure that all of the atoms are properly bound
# together
# If the above are satisfied, we append a tuple of the torsion our
# torsion_list
got_atom0 = False
got_atom3 = False
for bond0 in bond_list1:
atomX = bond0.GetOtherAtom(atom1)
# if atomX.GetAtomicNum() == 1 and len(atomX.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# NOTE: for H_abstraction TSs, a non teminal H should exist
# continue
if atomX.GetIdx() != atom2.GetIdx():
got_atom0 = True
atom0 = atomX
for bond2 in bond_list2:
atomY = bond2.GetOtherAtom(atom2)
# if atomY.GetAtomicNum() == 1 and len(atomY.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# continue
if atomY.GetIdx() != atom1.GetIdx():
got_atom3 = True
atom3 = atomY
if not (got_atom0 and got_atom3):
# Making sure atom0 and atom3 were not found
continue
# Looking to make sure that all of the atoms are properly bonded to
# eached
if (
"DOUBLE" in str(
self.rdkit_molecule.GetBondBetweenAtoms(
atom1.GetIdx(),
atom2.GetIdx()).GetBondType()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom0.GetIdx(),
atom1.GetIdx()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom1.GetIdx(),
atom2.GetIdx()) and self.rdkit_molecule.GetBondBetweenAtoms(
atom2.GetIdx(),
atom3.GetIdx())):
torsion_tup = (atom0.GetIdx(), atom1.GetIdx(),
atom2.GetIdx(), atom3.GetIdx())
already_in_list = False
for torsion_entry in torsion_list:
a, b, c, d = torsion_entry
e, f, g, h = torsion_tup
if (b, c) == (f, g) or (b, c) == (g, f):
already_in_list = True
if not already_in_list:
cistrans_list.append(torsion_tup)
cistrans = []
for ct_index, indices in enumerate(cistrans_list):
i, j, k, l = indices
b0 = self.rdkit_molecule.GetBondBetweenAtoms(i, j)
b1 = self.rdkit_molecule.GetBondBetweenAtoms(j, k)
b2 = self.rdkit_molecule.GetBondBetweenAtoms(k, l)
b0.SetBondDir(Chem.BondDir.ENDUPRIGHT)
b2.SetBondDir(Chem.BondDir.ENDDOWNRIGHT)
Chem.AssignStereochemistry(self.rdkit_molecule, force=True)
if "STEREOZ" in str(b1.GetStereo()):
if round(self.ase_molecule.get_dihedral(i, j, k, l), -1) == 0:
atom = self.rdkit_molecule.GetAtomWithIdx(k)
bonds = atom.GetBonds()
for bond in bonds:
indexes = [
bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx()]
if not ((sorted([j, k]) == sorted(indexes)) or (
sorted([k, l]) == sorted(indexes))):
break
for index in indexes:
if not (index in indices):
l = index
break
indices = [i, j, k, l]
stero = "Z"
else:
if round(
self.ase_molecule.get_dihedral(
i, j, k, l), -1) == 180:
atom = self.rdkit_molecule.GetAtomWithIdx(k)
bonds = atom.GetBonds()
for bond in bonds:
indexes = [
bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx()]
if not ((sorted([j, k]) == sorted(indexes)) or (
sorted([k, l]) == sorted(indexes))):
break
for index in indexes:
if not (index in indices):
l = index
break
indices = [i, j, k, l]
stero = "E"
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = CisTrans(index=ct_index,
atom_indices=indices,
dihedral=dihedral,
mask=[],
stero=stero)
mask = self.get_mask(tor)
reaction_center = False
cistrans.append(CisTrans(index=ct_index,
atom_indices=indices,
dihedral=dihedral,
mask=mask,
stero=stero
)
)
self.cistrans = cistrans
return self.cistrans
def get_torsions(self):
rdmol_copy = self.rdkit_molecule
torsion_list = []
cistrans_list = []
for bond1 in rdmol_copy.GetBonds():
atom1 = bond1.GetBeginAtom()
atom2 = bond1.GetEndAtom()
if atom1.IsInRing() or atom2.IsInRing():
# Making sure that bond1 we're looking at are not in a ring
continue
bond_list1 = list(atom1.GetBonds())
bond_list2 = list(atom2.GetBonds())
if not len(bond_list1) > 1 and not len(bond_list2) > 1:
# Making sure that there are more than one bond attached to
# the atoms we're looking at
continue
# Getting the 0th and 3rd atom and insuring that atoms
# attached to the 1st and 2nd atom are not terminal hydrogens
# We also make sure that all of the atoms are properly bound together
# If the above are satisfied, we append a tuple of the torsion our torsion_list
got_atom0 = False
got_atom3 = False
for bond0 in bond_list1:
atomX = bond0.GetOtherAtom(atom1)
# if atomX.GetAtomicNum() == 1 and len(atomX.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# NOTE: for H_abstraction TSs, a non teminal H should exist
# continue
if atomX.GetIdx() != atom2.GetIdx():
got_atom0 = True
atom0 = atomX
for bond2 in bond_list2:
atomY = bond2.GetOtherAtom(atom2)
# if atomY.GetAtomicNum() == 1 and len(atomY.GetBonds()) == 1:
# This means that we have a terminal hydrogen, skip this
# continue
if atomY.GetIdx() != atom1.GetIdx():
got_atom3 = True
atom3 = atomY
if not (got_atom0 and got_atom3):
# Making sure atom0 and atom3 were not found
continue
# Looking to make sure that all of the atoms are properly bonded to eached
if ("SINGLE" in str(
rdmol_copy.GetBondBetweenAtoms(
atom1.GetIdx(), atom2.GetIdx()).GetBondType())
and rdmol_copy.GetBondBetweenAtoms(atom0.GetIdx(),
atom1.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom1.GetIdx(),
atom2.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom2.GetIdx(),
atom3.GetIdx())):
torsion_tup = (atom0.GetIdx(), atom1.GetIdx(), atom2.GetIdx(),
atom3.GetIdx())
already_in_list = False
for torsion_entry in torsion_list:
a, b, c, d = torsion_entry
e, f, g, h = torsion_tup
if (b, c) == (f, g) or (b, c) == (g, f):
already_in_list = True
if not already_in_list:
torsion_list.append(torsion_tup)
if ("DOUBLE" in str(
rdmol_copy.GetBondBetweenAtoms(
atom1.GetIdx(), atom2.GetIdx()).GetBondType())
and rdmol_copy.GetBondBetweenAtoms(atom0.GetIdx(),
atom1.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom1.GetIdx(),
atom2.GetIdx())
and rdmol_copy.GetBondBetweenAtoms(atom2.GetIdx(),
atom3.GetIdx())):
torsion_tup = (atom0.GetIdx(), atom1.GetIdx(), atom2.GetIdx(),
atom3.GetIdx())
already_in_list = False
for torsion_entry in torsion_list:
a, b, c, d = torsion_entry
e, f, g, h = torsion_tup
if (b, c) == (f, g) or (b, c) == (g, f):
already_in_list = True
if not already_in_list:
cistrans_list.append(torsion_tup)
torsions = []
cistrans = []
for indices in torsion_list:
i, j, k, l = indices
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = Torsion(indices=indices,
dihedral=dihedral,
left_mask=[],
right_mask=[])
left_mask = self.get_left_mask(tor)
right_mask = self.get_right_mask(tor)
reaction_center = "No"
torsions.append(
Torsion(indices, dihedral, left_mask, right_mask,
reaction_center))
for indices in cistrans_list:
i, j, k, l = indices
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = CisTrans(indices=indices,
dihedral=dihedral,
left_mask=[],
right_mask=[])
left_mask = self.get_left_mask(tor)
right_mask = self.get_right_mask(tor)
reaction_center = "No"
cistrans.append(
CisTrans(indices, dihedral, left_mask, right_mask,
reaction_center))
self.torsions = torsions
self.cistrans = cistrans
return self.torsions