def get_complexes(self, rmg_reaction=None):
"""
A method to create a forward and reverse TS complexes used to initialize transition state geometries
"""
if not rmg_reaction:
rmg_reaction = self.rmg_reaction
reactant_complex = RMGMolecule()
for react in rmg_reaction.reactants:
if isinstance(react, RMGMolecule):
reactant_complex = reactant_complex.merge(react)
elif isinstance(react, RMGSpecies):
reactant_complex = reactant_complex.merge(react.molecule[0])
product_complex = RMGMolecule()
for prod in rmg_reaction.products:
if isinstance(prod, RMGMolecule):
product_complex = product_complex.merge(prod)
elif isinstance(prod, RMGSpecies):
product_complex = product_complex.merge(prod.molecule[0])
reactant_complex.updateMultiplicity()
product_complex.updateMultiplicity()
self.complexes = {
"forward": reactant_complex,
"reverse": product_complex
}
return self.complexes
def get_rmg_complexes(self):
"""
A method to create a forward and reverse TS complexes used to initialize transition state geometries
Variables:
- rmg_reaction (RMGReaction): The RMGReaction of interest
Returns:
- complexes (dict): a dictionary containing RMGMolecules of the forward and reverse reaction complexes
"""
if self.rmg_reaction is None:
self.get_labeled_reaction()
reactant_complex = RMGMolecule()
for react in self.rmg_reaction.reactants:
if isinstance(react, RMGMolecule):
reactant_complex = reactant_complex.merge(react)
elif isinstance(react, RMGSpecies):
for mol in react.molecule:
if len(mol.getLabeledAtoms()) > 0:
reactant_complex = reactant_complex.merge(mol)
product_complex = RMGMolecule()
for prod in self.rmg_reaction.products:
if isinstance(prod, RMGMolecule):
product_complex = product_complex.merge(prod)
elif isinstance(prod, RMGSpecies):
for mol in prod.molecule:
if len(mol.getLabeledAtoms()) > 0:
product_complex = product_complex.merge(mol)
reactant_complex.updateMultiplicity()
product_complex.updateMultiplicity()
if len(reactant_complex.getLabeledAtoms()) == 0 or len(
product_complex.getLabeledAtoms()) == 0:
logging.warning(
"REACTING ATOMS LABELES NOT PROVIDED. Please call `Reaction.get_labeled_reaction` to generate labeled complexes"
)
self.complexes = {
"forward": reactant_complex,
"reverse": product_complex
}
return self.complexes
def get_complexes(self, rmg_reaction=None):
"""
A method to create a forward and reverse TS complexes used to initialize transition state geometries
Variables:
- rmg_reaction (RMGReaction): The RMGReaction of interest
Returns:
- complexes (dict): a dictionary containing RMGMolecules of the forward and reverse reaction complexes
"""
if not rmg_reaction:
rmg_reaction = self.rmg_reaction
reactant_complex = RMGMolecule()
for react in rmg_reaction.reactants:
if isinstance(react, RMGMolecule):
reactant_complex = reactant_complex.merge(react)
elif isinstance(react, RMGSpecies):
for mol in react.molecule:
if len(mol.getLabeledAtoms()) > 0:
reactant_complex = reactant_complex.merge(mol)
product_complex = RMGMolecule()
for prod in rmg_reaction.products:
if isinstance(prod, RMGMolecule):
product_complex = product_complex.merge(prod)
elif isinstance(prod, RMGSpecies):
for mol in prod.molecule:
if len(mol.getLabeledAtoms()) > 0:
product_complex = product_complex.merge(mol)
reactant_complex.updateMultiplicity()
product_complex.updateMultiplicity()
self.complexes = {
"forward": reactant_complex,
"reverse": product_complex}
return self.complexes
class Conformer():
"""
A class for generating and editing 3D conformers of molecules
"""
def __init__(self, smiles=None, rmg_molecule=None, index=0):
self.energy = None
self.index = index
if (smiles or rmg_molecule):
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(RMGMolecule(
SMILES=smiles)), "SMILES string did not match RMG Molecule object"
self.smiles = smiles
self.rmg_molecule = rmg_molecule
elif rmg_molecule:
self.rmg_molecule = rmg_molecule
self.smiles = rmg_molecule.toSMILES()
else:
self.smiles = smiles
self.rmg_molecule = RMGMolecule(SMILES=smiles)
self.rmg_molecule.updateMultiplicity()
self.get_molecules()
self.get_geometries()
self._symmetry_number = None
else:
self.smiles = None
self.rmg_molecule = None
self.rdkit_molecule = None
self.ase_molecule = None
self.bonds = []
self.angles = []
self.torsions = []
self.cistrans = []
self.chiral_centers = []
self._symmetry_number = None
def __repr__(self):
return '<Conformer "{}">'.format(self.smiles)
def copy(self):
copy_conf = Conformer()
copy_conf.smiles = self.smiles
copy_conf.rmg_molecule = self.rmg_molecule.copy()
copy_conf.rdkit_molecule = self.rdkit_molecule.__copy__()
copy_conf.ase_molecule = self.ase_molecule.copy()
copy_conf.get_geometries()
copy_conf.energy = self.energy
return copy_conf
@property
def symmetry_number(self):
if not self._symmetry_number:
self._symmetry_number = self.calculate_symmetry_number()
return self._symmetry_number
def get_rdkit_mol(self):
"""
A method for creating an rdkit geometry from an rmg mol
"""
assert self.rmg_molecule, "Cannot create an RDKit geometry without an RMG molecule object"
RDMol = self.rmg_molecule.toRDKitMol(removeHs=False)
rdkit.Chem.AllChem.EmbedMolecule(RDMol)
self.rdkit_molecule = RDMol
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
for i, atom in enumerate(self.rmg_molecule.atoms):
j = i + 4
coords = mol_list[j].split()[:3]
for k, coord in enumerate(coords):
coords[k] = float(coord)
atom.coords = np.array(coords)
return self.rdkit_molecule
def get_ase_mol(self):
"""
A method for creating an ase atoms object from an rdkit mol
"""
if not self.rdkit_molecule:
self.get_rdkit_mol()
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
ase_atoms = []
for i, line in enumerate(mol_list):
if i > 3:
try:
atom0, atom1, bond, rest = line
atom0 = int(atom0)
atom0 = int(atom1)
bond = float(bond)
except ValueError:
try:
x, y, z, symbol = line.split()[0:4]
x = float(x)
y = float(y)
z = float(z)
ase_atoms.append(
Atom(symbol=symbol, position=(x, y, z)))
except BaseException:
continue
self.ase_molecule = Atoms(ase_atoms)
return self.ase_molecule
def get_molecules(self):
if not self.rmg_molecule:
self.rmg_molecule = RMGMolecule(SMILES=self.smiles)
self.rdkit_molecule = self.get_rdkit_mol()
self.ase_molecule = self.get_ase_mol()
self.get_geometries()
return self.rdkit_molecule, self.ase_molecule
def view(self):
"""
A method designed to create a 3D figure of the AutoTST_Molecule with py3Dmol from the rdkit_molecule
"""
mb = Chem.MolToMolBlock(self.rdkit_molecule)
p = py3Dmol.view(width=600, height=600)
p.addModel(mb, "sdf")
p.setStyle({'stick': {}})
p.setBackgroundColor('0xeeeeee')
p.zoomTo()
return p.show()
def get_bonds(self):
"""
A method for identifying all of the bonds in a conformer
"""
bond_list = []
for bond in self.rdkit_molecule.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for index, indices in enumerate(bond_list):
i, j = indices
length = self.ase_molecule.get_distance(i, j)
center = False
if ((self.rmg_molecule.atoms[i].label) and (
self.rmg_molecule.atoms[j].label)):
center = True
bond = Bond(index=index,
atom_indices=indices,
length=length,
reaction_center=center)
mask = self.get_mask(bond)
bond.mask = mask
bonds.append(bond)
self.bonds = bonds
return self.bonds
def get_angles(self):
"""
A method for identifying all of the angles in a conformer
"""
angle_list = []
for atom1 in self.rdkit_molecule.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 = self.ase_molecule.get_angle(i, j, k)
ang = Angle(index=index,
atom_indices=indices,
degree=degree,
mask=[])
mask = self.get_mask(ang)
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 get_torsions(self):
"""
A method for identifying all of the torsions in a conformer
"""
torsion_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 (
"SINGLE" 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:
torsion_list.append(torsion_tup)
torsions = []
for index, indices in enumerate(torsion_list):
i, j, k, l = indices
dihedral = self.ase_molecule.get_dihedral(i, j, k, l)
tor = Torsion(index=index,
atom_indices=indices,
dihedral=dihedral,
mask=[])
mask = self.get_mask(tor)
reaction_center = False
torsions.append(Torsion(index=index,
atom_indices=indices,
dihedral=dihedral,
mask=mask,
reaction_center=reaction_center))
self.torsions = torsions
return self.torsions
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_mask(self, geometry):
"""
Getting the right hand mask for a geometry object:
- self: an AutoTST Conformer object
- geometry: a Bond, Angle, Dihedral, or Torsion object
"""
rdkit_atoms = self.rdkit_molecule.GetAtoms()
if (isinstance(geometry, autotst.geometry.Torsion) or
isinstance(geometry, autotst.geometry.CisTrans)):
L1, L0, R0, R1 = geometry.atom_indices
# trying to get the left hand side of this torsion
LHS_atoms_index = [L0, L1]
RHS_atoms_index = [R0, R1]
elif isinstance(geometry, autotst.geometry.Angle):
a1, a2, a3 = geometry.atom_indices
LHS_atoms_index = [a2, a1]
RHS_atoms_index = [a2, a3]
elif isinstance(geometry, autotst.geometry.Bond):
a1, a2 = geometry.atom_indices
LHS_atoms_index = [a1]
RHS_atoms_index = [a2]
complete_RHS = False
i = 0
atom_index = RHS_atoms_index[0]
while complete_RHS is False:
try:
RHS_atom = rdkit_atoms[atom_index]
for neighbor in RHS_atom.GetNeighbors():
if (neighbor.GetIdx() in RHS_atoms_index) or (
neighbor.GetIdx() in LHS_atoms_index):
continue
else:
RHS_atoms_index.append(neighbor.GetIdx())
i += 1
atom_index = RHS_atoms_index[i]
except IndexError:
complete_RHS = True
mask = [index in RHS_atoms_index for index in range(
len(self.ase_molecule))]
return mask
def get_chiral_centers(self):
"""
A method to identify
"""
centers = rdkit.Chem.FindMolChiralCenters(
self.rdkit_molecule, includeUnassigned=True)
chiral_centers = []
for index, center in enumerate(centers):
atom_index, chirality = center
chiral_centers.append(
ChiralCenter(
index=index,
atom_index=atom_index,
chirality=chirality))
self.chiral_centers = chiral_centers
return self.chiral_centers
def get_geometries(self):
"""
A helper method to obtain all geometry things
"""
self.bonds = self.get_bonds()
self.angles = self.get_angles()
self.torsions = self.get_torsions()
self.cistrans = self.get_cistrans()
self.chiral_centers = self.get_chiral_centers()
return (
self.bonds,
self.angles,
self.torsions,
self.cistrans,
self.chiral_centers)
def update_coords(self):
"""
A function that creates distance matricies for the RMG, ASE, and RDKit molecules and finds which
(if any) are different. If one is different, this will update the coordinates of the other two
with the different one. If all three are different, nothing will happen. If all are the same,
nothing will happen.
"""
rdkit_dm = rdkit.Chem.rdmolops.Get3DDistanceMatrix(self.rdkit_molecule)
ase_dm = self.ase_molecule.get_all_distances()
l = len(self.rmg_molecule.atoms)
rmg_dm = np.zeros((l, l))
for i, atom_i in enumerate(self.rmg_molecule.atoms):
for j, atom_j in enumerate(self.rmg_molecule.atoms):
rmg_dm[i][j] = np.linalg.norm(atom_i.coords - atom_j.coords)
d1 = round(abs(rdkit_dm - ase_dm).max(), 3)
d2 = round(abs(rdkit_dm - rmg_dm).max(), 3)
d3 = round(abs(ase_dm - rmg_dm).max(), 3)
if np.all(np.array([d1, d2, d3]) > 0):
return False, None
if np.any(np.array([d1, d2, d3]) > 0):
if d1 == 0:
diff = "rmg"
self.update_coords_from("rmg")
elif d2 == 0:
diff = "ase"
self.update_coords_from("ase")
else:
diff = "rdkit"
self.update_coords_from("rdkit")
return True, diff
else:
return True, None
def update_coords_from(self, mol_type="ase"):
"""
A method to update the coordinates of the RMG, RDKit, and ASE objects with a chosen object.
"""
possible_mol_types = ["ase", "rmg", "rdkit"]
assert (mol_type.lower() in possible_mol_types), "Please specifiy a valid mol type. Valid types are {}".format(
possible_mol_types)
if mol_type.lower() == "rmg":
conf = self.rdkit_molecule.GetConformers()[0]
ase_atoms = []
for i, atom in enumerate(self.rmg_molecule.atoms):
x, y, z = atom.coords
symbol = atom.symbol
conf.SetAtomPosition(i, [x, y, z])
ase_atoms.append(Atom(symbol=symbol, position=(x, y, z)))
self.ase_molecule = Atoms(ase_atoms)
# self.calculate_symmetry_number()
elif mol_type.lower() == "ase":
conf = self.rdkit_molecule.GetConformers()[0]
for i, position in enumerate(self.ase_molecule.get_positions()):
self.rmg_molecule.atoms[i].coords = position
conf.SetAtomPosition(i, position)
# self.calculate_symmetry_number()
elif mol_type.lower() == "rdkit":
mol_list = AllChem.MolToMolBlock(self.rdkit_molecule).split('\n')
for i, atom in enumerate(self.rmg_molecule.atoms):
j = i + 4
coords = mol_list[j].split()[:3]
for k, coord in enumerate(coords):
coords[k] = float(coord)
atom.coords = np.array(coords)
self.get_ase_mol()
# self.calculate_symmetry_number()
def set_bond_length(self, bond_index, length):
"""
This is a method to set bond lengths
Variabels:
- bond_index (int): the index of the bond you want to edit
- length (float, int): the distance you want to set the bond (in angstroms)
"""
assert isinstance(length, (float, int))
matched = False
for bond in self.bonds:
if bond.index == bond_index:
matched = True
break
if not matched:
logging.info("Angle index provided is out of range. Nothing was changed.")
return self
i, j = bond.atom_indices
self.ase_molecule.set_distance(
a0=i,
a1=j,
distance=length,
mask=bond.mask,
fix=0
)
bond.length = length
self.update_coords_from(mol_type="ase")
return self
def set_angle(self, angle_index, angle):
"""
A method that will set the angle of an Angle object accordingly
"""
assert isinstance(
angle, (int, float)), "Plese provide a float or an int for the angle"
matched = False
for a in self.angles:
if a.index == angle_index:
matched = True
break
if not matched:
logging.info("Angle index provided is out of range. Nothing was changed.")
return self
i, j, k = a.atom_indices
self.ase_molecule.set_angle(
a1=i,
a2=j,
a3=k,
angle=angle,
mask=a.mask
)
a.degree = angle
self.update_coords_from(mol_type="ase")
return self
def set_torsion(self, torsion_index, dihedral):
"""
A method that will set the diehdral angle of a Torsion object accordingly.
"""
assert isinstance(
dihedral, (int, float)), "Plese provide a float or an int for the diehdral angle"
matched = False
for torsion in self.torsions:
if torsion.index == torsion_index:
matched = True
break
if not matched:
logging.info("Torsion index provided is out of range. Nothing was changed.")
return self
i, j, k, l = torsion.atom_indices
self.ase_molecule.set_dihedral(
a1=i,
a2=j,
a3=k,
a4=l,
angle=dihedral,
mask=torsion.mask
)
torsion.dihedral = dihedral
self.update_coords_from(mol_type="ase")
return self
def set_cistrans(self, cistrans_index, stero="E"):
"""
A module that will set a corresponding cistrans bond to the proper E/Z config
"""
assert stero.upper() in [
"E", "Z"], "Please specify a valid stero direction."
matched = False
for cistrans in self.cistrans:
if cistrans.index == cistrans_index:
matched = True
break
if not matched:
logging.info("CisTrans index provided is out of range. Nothing was changed.")
return self
if cistrans.stero == stero.upper():
self.update_coords_from("ase")
return self
else:
cistrans.stero = stero.upper()
i, j, k, l = cistrans.atom_indices
self.ase_molecule.rotate_dihedral(
a1=i,
a2=j,
a3=k,
a4=l,
angle=float(180),
mask=cistrans.mask
)
cistrans.stero = stero.upper()
self.update_coords_from(mol_type="ase")
return self
def set_chirality(self, chiral_center_index, stero="R"):
"""
A module that can set the orientation of a chiral center.
"""
assert stero.upper() in ["R", "S"], "Specify a valid stero orientation"
centers_dict = {
'R': Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW,
'S': Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW
}
assert isinstance(chiral_center_index,
int), "Please provide an integer for the index"
rdmol = self.rdkit_molecule.__copy__()
match = False
for chiral_center in self.chiral_centers:
if chiral_center.index == chiral_center_index:
match = True
break
if not match:
logging.info("ChiralCenter index provided is out of range. Nothing was changed")
return self
rdmol.GetAtomWithIdx(chiral_center.atom_index).SetChiralTag(
centers_dict[stero.upper()])
rdkit.Chem.rdDistGeom.EmbedMolecule(rdmol)
old_torsions = self.torsions[:] + self.cistrans[:]
self.rdkit_molecule = rdmol
self.update_coords_from(mol_type="rdkit")
# Now resetting dihedral angles in case if they changed.
for torsion in old_torsions:
i, j, k, l = torsion.atom_indices
self.ase_molecule.set_dihedral(
a1=i,
a2=j,
a3=k,
a4=l,
mask=torsion.mask,
angle=torsion.dihedral,
)
self.update_coords_from(mol_type="ase")
return self
def calculate_symmetry_number(self):
from rmgpy.qm.symmetry import PointGroupCalculator
from rmgpy.qm.qmdata import QMData
atom_numbers = self.ase_molecule.get_atomic_numbers()
coordinates = self.ase_molecule.get_positions()
qmdata = QMData(
groundStateDegeneracy=1, # Only needed to check if valid QMData
numberOfAtoms=len(atom_numbers),
atomicNumbers=atom_numbers,
atomCoords=(coordinates, str('angstrom')),
energy=(0.0, str('kcal/mol')) # Only needed to avoid error
)
settings = type(str(''), (), dict(symmetryPath=str(
'symmetry'), scratchDirectory="."))() # Creates anonymous class
pgc = PointGroupCalculator(settings, self.smiles, qmdata)
pg = pgc.calculate()
#os.remove("{}.symm".format(self.smiles))
if pg is not None:
symmetry_number = pg.symmetryNumber
else:
symmetry_number = 1
return symmetry_number
class TS(Conformer):
"""
A class that defines the 3D geometry of a transition state (TS)
"""
def __init__(self,
smiles=None,
reaction_label=None,
rmg_molecule=None,
reaction_family="H_Abstraction",
distance_data=None,
index=0):
self.energy = None
#####################################################
#####################################################
assert reaction_label, "A reaction label needs to be provided in addition to a smiles or rmg_molecule"
self.reaction_label = reaction_label
self._rdkit_molecule = None
self._ase_molecule = None
self.reaction_family = reaction_family
self.distance_data = distance_data
self.index = index
if (smiles or rmg_molecule):
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(
RMGMolecule(SMILES=smiles)
), "SMILES string did not match RMG Molecule object"
self.smiles = smiles
self.rmg_molecule = rmg_molecule
elif rmg_molecule:
self.rmg_molecule = rmg_molecule
self.smiles = rmg_molecule.toSMILES()
else:
self.smiles = smiles
self.rmg_molecule = RMGMolecule(SMILES=smiles)
self.rmg_molecule.updateMultiplicity()
self.get_mols()
self.get_geometries()
else:
self.smiles = None
self.rmg_molecule = None
self.rdkit_molecule = None
self._pseudo_geometry = None
self.ase_molecule = None
self.bonds = []
self.angles = []
self.torsions = []
self.cistrans = []
self.chiral_centers = []
def __repr__(self):
return '<TS "{}">'.format(self.smiles)
def copy(self):
copy_conf = TS(reaction_label=self.reaction_label,
reaction_family=self.reaction_family)
copy_conf.smiles = self.smiles
copy_conf.rmg_molecule = self.rmg_molecule.copy()
copy_conf.rdkit_molecule = self.rdkit_molecule.__copy__()
copy_conf._pseudo_geometry = self._pseudo_geometry.__copy__()
copy_conf.ase_molecule = self.ase_molecule.copy()
copy_conf.get_geometries()
return copy_conf
@property
def rdkit_molecule(self):
if (self._rdkit_molecule is None) and self.distance_data:
self._rdkit_molecule = self.get_rdkit_mol(self.rmg_molecule,
self.reaction_family,
self.distance_data)[0]
return self._rdkit_molecule
@property
def ase_molecule(self):
if (self._ase_molecule is None):
self._ase_molecule = self.get_ase_mol()
return self._ase_molecule
def get_rdkit_mol(self,
rmg_molecule=None,
reaction_family="H_Abstraction",
distance_data=None):
"""
A method to create an rdkit geometry... slightly different than that of the conformer method
returns both the rdkit_molecule and the bm
"""
if not rmg_molecule:
rmg_molecule = self.rmg_molecule
rdkit_molecule = Chem.RWMol(
Conformer().get_rdkit_mol(rmg_molecule=rmg_molecule))
labels, atom_match = self.get_labels(rmg_molecule, reaction_family)
for i, atom in enumerate(rmg_molecule.atoms):
assert atom.number == rdkit_molecule.GetAtoms()[i].GetAtomicNum()
if len(labels) == 3:
rd_copy = rdkit_molecule.__copy__()
lbl1, lbl2, lbl3 = labels
if not rd_copy.GetBondBetweenAtoms(lbl1, lbl2):
rd_copy.AddBond(lbl1,
lbl2,
order=rdkit.Chem.rdchem.BondType.SINGLE)
else:
rd_copy.AddBond(lbl2,
lbl3,
order=rdkit.Chem.rdchem.BondType.SINGLE)
self._pseudo_geometry = rd_copy
logging.info("Initially embedded molecule")
bm = None
if distance_data:
logging.info("Getting bounds matrix")
bm = self.get_bounds_matrix(rdkit_molecule=rdkit_molecule)
if len(labels) > 0:
logging.info("Editing bounds matrix")
bm = self.edit_matrix(rmg_molecule, bm, labels, distance_data)
logging.info("Performing triangle smoothing on bounds matrix.")
DistanceGeometry.DoTriangleSmoothing(bm)
logging.info("Now attempting to embed using edited bounds matrix.")
rdkit_molecule = self.rd_embed(rdkit_molecule,
10000,
bm=bm,
match=atom_match)[0]
return rdkit_molecule, bm
def get_bounds_matrix(self, rmg_molecule=None, rdkit_molecule=None):
"""
A method to obtain the bounds matrix
"""
if not rmg_molecule:
try:
rmg_molecule = self.rmg_molecule
except BaseException:
return None
if not rdkit_molecule:
try:
rdkit_molecule = self.get_rdkit_mol(rmg_molecule=rmg_molecule)
except BaseException:
return None
logging.info("before")
bm = rdDistGeom.GetMoleculeBoundsMatrix(rdkit_molecule)
logging.info("Got bounds matrix")
return bm
def set_limits(self, bm, lbl1, lbl2, value, uncertainty):
"""
A method to set the limits of a particular distance between two atoms
:param bm: an array of arrays corresponding to the bounds matrix
:param lbl1: the label of one atom
:param lbl2: the label of another atom
:param value: the distance from a distance data object (float)
:param uncertainty: the uncertainty of the `value` distance (float)
:return bm: an array of arrays corresponding to the edited bounds matrix
"""
logging.info(
"For atoms {0} and {1} we have a distance of: \t {2}".format(
lbl1, lbl2, value))
if lbl1 > lbl2:
bm[lbl2][lbl1] = value + uncertainty / 2
bm[lbl1][lbl2] = max(0, value - uncertainty / 2)
else:
bm[lbl2][lbl1] = max(0, value - uncertainty / 2)
bm[lbl1][lbl2] = value + uncertainty / 2
return bm
def bm_pre_edit(self, bm, sect):
"""
Clean up some of the atom distance limits before attempting triangle smoothing.
This ensures any edits made do not lead to unsolvable scenarios for the molecular
embedding algorithm.
sect is the list of atom indices belonging to one species.
"""
others = range(len(bm))
for idx in sect:
others.remove(idx)
for i in range(len(bm)): # sect:
for j in range(i): # others:
if i < j:
continue
for k in range(len(bm)):
if k == i or k == j or i == j:
continue
Uik = bm[i, k] if k > i else bm[k, i]
Ukj = bm[j, k] if k > j else bm[k, j]
maxLij = Uik + Ukj - 0.1
if bm[i, j] > maxLij:
logging.info("Changing lower limit {0} to {1}".format(
bm[i, j], maxLij))
bm[i, j] = maxLij
return bm
def get_labels(self, rmg_molecule, reaction_family):
"""
A method to get the labeled atoms from a reaction
:param reactants: a combined rmg_molecule object
:return labels: the atom labels corresponding to the reaction center
:return atomMatch: a tuple of tuples the atoms labels corresponding to the reaction center
"""
if len(rmg_molecule.getLabeledAtoms()) == 0:
labeles = []
atomMatch = ()
if reaction_family.lower() in [
'h_abstraction', 'r_addition_multiplebond', 'intra_h_migration'
]:
# for i, atom in enumerate(reactants.atoms):
lbl1 = rmg_molecule.getLabeledAtoms()["*1"].sortingLabel
lbl2 = rmg_molecule.getLabeledAtoms()["*2"].sortingLabel
lbl3 = rmg_molecule.getLabeledAtoms()["*3"].sortingLabel
labels = [lbl1, lbl2, lbl3]
atomMatch = ((lbl1, ), (lbl2, ), (lbl3, ))
elif reaction_family.lower() in ['disproportionation']:
lbl1 = rmg_molecule.getLabeledAtoms()["*2"].sortingLabel
lbl2 = rmg_molecule.getLabeledAtoms()["*4"].sortingLabel
lbl3 = rmg_molecule.getLabeledAtoms()["*1"].sortingLabel
labels = [lbl1, lbl2, lbl3]
atomMatch = ((lbl1, ), (lbl2, ), (lbl3, ))
#logging.info("The labled atoms are {}.".format(labels))
return labels, atomMatch
def edit_matrix(self, rmg_molecule, bm, labels, distance_data):
"""
A method to edit the bounds matrix using labels and distance data
"""
lbl1, lbl2, lbl3 = labels
sect = []
for atom in rmg_molecule.split()[0].atoms:
sect.append(atom.sortingLabel)
uncertainties = {'d12': 0.02, 'd13': 0.02, 'd23': 0.02}
bm = self.set_limits(bm, lbl1, lbl2, distance_data.distances['d12'],
uncertainties['d12'])
bm = self.set_limits(bm, lbl2, lbl3, distance_data.distances['d23'],
uncertainties['d23'])
bm = self.set_limits(bm, lbl1, lbl3, distance_data.distances['d13'],
uncertainties['d13'])
bm = self.bm_pre_edit(bm, sect)
return bm
def optimize(self, rdmol, boundsMatrix=None, atomMatch=None):
"""
Optimizes the rdmol object using UFF.
Determines the energy level for each of the conformers identified in rdmol.GetConformer.
:param rdmol:
:param boundsMatrix:
:param atomMatch:
:return rdmol, minEid (index of the lowest energy conformer)
"""
energy = 0.0
minEid = 0
lowestE = 9.999999e99 # start with a very high number, which would never be reached
for conf in rdmol.GetConformers():
if (boundsMatrix is None) or (atomMatch is None):
AllChem.UFFOptimizeMolecule(rdmol, confId=conf.GetId())
energy = AllChem.UFFGetMoleculeForceField(
rdmol, confId=conf.GetId()).CalcEnergy()
else:
_, energy = EmbedLib.OptimizeMol(rdmol,
boundsMatrix,
atomMatches=atomMatch,
forceConstant=100000.0)
if energy < lowestE:
minEid = conf.GetId()
lowestE = energy
return rdmol, minEid
def rd_embed(self, rdmol, numConfAttempts, bm=None, match=None):
"""
This portion of the script is literally taken from rmgpy but hacked to work without defining a geometry object
Embed the RDKit molecule and create the crude molecule file.
"""
if (bm is None) or (match is None):
AllChem.EmbedMultipleConfs(rdmol, numConfAttempts, randomSeed=1)
rdmol, minEid = self.optimize(rdmol)
else:
"""
Embed the molecule according to the bounds matrix. Built to handle possible failures
of some of the embedding attempts.
"""
rdmol.RemoveAllConformers()
for i in range(0, numConfAttempts):
try:
EmbedLib.EmbedMol(rdmol, bm, atomMatch=match)
break
except ValueError:
logging.info(
"RDKit failed to embed on attempt {0} of {1}".format(
i + 1, numConfAttempts))
except RuntimeError:
logging.info("RDKit failed to embed.")
else:
logging.error("RDKit failed all attempts to embed")
return None, None
"""
RDKit currently embeds the conformers and sets the id as 0, so even though multiple
conformers have been generated, only 1 can be called. Below the id's are resolved.
"""
for i in range(len(rdmol.GetConformers())):
rdmol.GetConformers()[i].SetId(i)
rdmol, minEid = self.optimize(rdmol,
boundsMatrix=bm,
atomMatch=match)
return rdmol, minEid
def get_bonds(self):
return Conformer().get_bonds(self._pseudo_geometry, self.ase_molecule,
self.rmg_molecule)
def get_torsions(self):
return Conformer().get_torsions(self._pseudo_geometry,
self.ase_molecule)
def get_angles(self):
return Conformer().get_angles(self._pseudo_geometry, self.ase_molecule)