def test_set_get_angle():
"Test that set_angle() and get_angle() in Atoms are consistent"
from ase import Atoms
atoms = Atoms(
'HHCCHH',
[[-1, 1, 0], [-1, -1, 0], [0, 0, 0], [1, 0, 0], [2, 1, 0], [2, -1, 0]])
list = [2, 3, 4]
theta = 20
old_angle = atoms.get_angle(*list)
atoms.set_angle(*list, angle=old_angle + theta)
new_angle = atoms.get_angle(*list)
assert abs(new_angle - (old_angle + theta)) < 1.0e-9
def test_qmmm_acn():
import numpy as np
import ase.units as units
from ase import Atoms
from ase.calculators.acn import (ACN, m_me, r_cn, r_mec,
sigma_me, sigma_c, sigma_n,
epsilon_me, epsilon_c, epsilon_n)
from ase.calculators.qmmm import SimpleQMMM, LJInteractionsGeneral, EIQMMM
from ase.constraints import FixLinearTriatomic
from ase.optimize import BFGS
# From https://www.sciencedirect.com/science/article/pii/S0166128099002079
eref = 4.9 * units.kcal / units.mol
dref = 3.368
aref = 79.1
sigma = np.array([sigma_me, sigma_c, sigma_n])
epsilon = np.array([epsilon_me, epsilon_c, epsilon_n])
inter = LJInteractionsGeneral(sigma, epsilon, sigma, epsilon, 3)
for calc in [ACN(),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN()),
SimpleQMMM([0, 1, 2], ACN(), ACN(), ACN(), vacuum=3.0),
EIQMMM([0, 1, 2], ACN(), ACN(), inter),
EIQMMM([0, 1, 2], ACN(), ACN(), inter, vacuum=3.0),
EIQMMM([3, 4, 5], ACN(), ACN(), inter, vacuum=3.0)]:
dimer = Atoms('CCNCCN',
[(-r_mec, 0, 0),
(0, 0, 0),
(r_cn, 0, 0),
(r_mec, 3.7, 0),
(0, 3.7, 0),
(-r_cn, 3.7, 0)])
masses = dimer.get_masses()
masses[::3] = m_me
dimer.set_masses(masses)
dimer.calc = calc
fixd = FixLinearTriatomic(triples=[(0, 1, 2), (3, 4, 5)])
dimer.set_constraint(fixd)
opt = BFGS(dimer, maxstep=0.04,
trajectory=calc.name + '.traj', logfile=calc.name + 'd.log')
opt.run(0.001, steps=1000)
e0 = dimer.get_potential_energy()
d0 = dimer.get_distance(1, 4)
a0 = dimer.get_angle(2, 1, 4)
fmt = '{0:>25}: {1:.3f} {2:.3f} {3:.1f}'
print(fmt.format(calc.name, -e0, d0, a0))
assert abs(e0 + eref) < 0.013
assert abs(d0 - dref) < 0.224
assert abs(a0 - aref) < 2.9
print(fmt.format('reference', eref, dref, aref))
def test_atoms_angle():
from ase import Atoms
import numpy as np
atoms = Atoms(['O', 'H', 'H'],
positions=[[0., 0., 0.119262], [0., 0.763239, -0.477047],
[0., -0.763239, -0.477047]])
# Angle no pbc
assert abs(atoms.get_angle(1, 0, 2) - 104) < 1e-3
atoms.set_cell([2, 2, 2])
# Across different pbcs
atoms.set_pbc([True, False, True])
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Across all True pbc
atoms.set_pbc(True)
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Change Angle
old = atoms.get_angle(1, 0, 2, mic=False)
atoms.set_angle(1, 0, 2, -10, indices=[2], add=True)
new = atoms.get_angle(1, 0, 2, mic=False)
diff = old - new - 10
assert abs(diff) < 10e-3
# don't actually change angle using indices
old = atoms.get_angle(1, 0, 2, mic=False)
atoms.set_angle(1, 0, 2, -10, indices=[2, 1], add=True)
new = atoms.get_angle(1, 0, 2, mic=False)
diff = old - new
assert abs(diff) < 10e-3
# Simple tetrahedron
tetra_pos = np.array([[0, 0, 0], [1, 0, 0], [.5, np.sqrt(3) * .5, 0],
[.5, np.sqrt(1 / 3.) * .5,
np.sqrt(2 / 3.)]])
atoms = Atoms(['H', 'H', 'H', 'H'],
positions=tetra_pos - np.array([.2, 0, 0]))
angle = 70.5287793655
assert abs(atoms.get_dihedral(0, 1, 2, 3) - angle) < 1e-3
atoms.set_cell([3, 3, 3])
atoms.set_pbc(True)
atoms.wrap()
assert abs(atoms.get_dihedral(0, 1, 2, 3, mic=True) - angle) < 1e-3
from ase import Atoms
import numpy as np
atoms = Atoms(['O', 'H', 'H'], positions=[[0., 0., 0.119262],
[0., 0.763239, -0.477047],
[0., -0.763239, -0.477047]])
# Angle no pbc
assert abs(atoms.get_angle(1, 0, 2) - 104) < 1e-3
atoms.set_cell([2, 2, 2])
# Across different pbcs
atoms.set_pbc([True, False, True])
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Across all True pbc
atoms.set_pbc(True)
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Simple tetrahedron
tetra_pos = np.array([[0, 0, 0], [1, 0, 0], [.5, np.sqrt(3) * .5, 0],
[.5, np.sqrt(1/3.) * .5, np.sqrt(2/3.)]])
atoms = Atoms(['H', 'H', 'H', 'H'],
positions=tetra_pos - np.array([.2, 0, 0]))
angle = 70.5287793655
assert abs(atoms.get_dihedral(0, 1, 2, 3) - angle) < 1e-3
atoms.set_cell([3, 3, 3])
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 AutoTST_Molecule():
"""
A class that allows for one to create RMG, RDKit and ASE
molecules from a single string with identical atom indicies
Inputs:
* smiles (str): a SMILES string that describes the molecule of interest
* rmg_molecule (RMG Molecule object): an rmg molecule that we can extract information from
"""
def __init__(self, smiles=None, rmg_molecule=None):
assert (
smiles or rmg_molecule
), "Please provide a SMILES string and / or an RMG Molecule object."
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(
Molecule(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 = Molecule(SMILES=smiles)
self.get_rdkit_molecule()
self.set_rmg_coords("RDKit")
self.get_ase_molecule()
self.get_torsions()
self.get_angles()
self.get_bonds()
def __repr__(self):
return '<AutoTST Molecule "{0}">'.format(self.smiles)
def get_rdkit_molecule(self):
"""
A method to create an RDKit Molecule from the rmg_molecule.
Indicies will be the same as in the RMG Molecule
"""
RDMol = self.rmg_molecule.toRDKitMol(removeHs=False)
rdkit.Chem.AllChem.EmbedMolecule(RDMol)
self.rdkit_molecule = RDMol
def get_ase_molecule(self):
"""
A method to create an ASE Molecule from the rdkit_molecule.
Indicies will be the same as in the RMG and RDKit Molecule.
"""
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:
continue
self.ase_molecule = Atoms(ase_atoms)
return self.ase_molecule
def view_mol(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=400, height=400)
p.addModel(mb, "sdf")
p.setStyle({'stick': {}})
p.setBackgroundColor('0xeeeeee')
p.zoomTo()
return p.show()
#############################################################################
def get_bonds(self):
rdmol_copy = self.rdkit_molecule
bond_list = []
for bond in rdmol_copy.GetBonds():
bond_list.append((bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()))
bonds = []
for indices in bond_list:
i, j = indices
length = self.ase_molecule.get_distance(i, j)
reaction_center = "No"
bond = Bond(indices=indices,
length=length,
reaction_center=reaction_center)
bonds.append(bond)
self.bonds = bonds
return self.bonds
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_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
def get_right_mask(self, torsion_or_angle):
rdmol_copy = self.rdkit_molecule
rdkit_atoms = rdmol_copy.GetAtoms()
if (isinstance(torsion_or_angle, autotst.geometry.Torsion)
or isinstance(torsion_or_angle, autotst.geometry.CisTrans)):
L1, L0, R0, R1 = torsion_or_angle.indices
# trying to get the left hand side of this torsion
LHS_atoms_index = [L0, L1]
RHS_atoms_index = [R0, R1]
elif isinstance(torsion_or_angle, autotst.geometry.Angle):
a1, a2, a3 = torsion_or_angle.indices
LHS_atoms_index = [a2, a1]
RHS_atoms_index = [a2, a3]
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
right_mask = [
index in RHS_atoms_index for index in range(len(self.ase_molecule))
]
return right_mask
def get_left_mask(self, torsion_or_angle):
rdmol_copy = self.rdkit_molecule
rdkit_atoms = rdmol_copy.GetAtoms()
if (isinstance(torsion_or_angle, autotst.geometry.Torsion)
or isinstance(torsion_or_angle, autotst.geometry.CisTrans)):
L1, L0, R0, R1 = torsion_or_angle.indices
# trying to get the left hand side of this torsion
LHS_atoms_index = [L0, L1]
RHS_atoms_index = [R0, R1]
elif isinstance(torsion_or_angle, autotst.geometry.Angle):
a1, a2, a3 = torsion_or_angle.indices
LHS_atoms_index = [a2, a1]
RHS_atoms_index = [a2, a3]
complete_LHS = False
i = 0
atom_index = LHS_atoms_index[0]
while complete_LHS is False:
try:
LHS_atom = rdkit_atoms[atom_index]
for neighbor in LHS_atom.GetNeighbors():
if (neighbor.GetIdx()
in LHS_atoms_index) or (neighbor.GetIdx()
in RHS_atoms_index):
continue
else:
LHS_atoms_index.append(neighbor.GetIdx())
i += 1
atom_index = LHS_atoms_index[i]
except IndexError:
complete_LHS = True
left_mask = [
index in LHS_atoms_index for index in range(len(self.ase_molecule))
]
return left_mask
def set_rmg_coords(self, molecule_base):
if molecule_base == "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)
elif molecule_base == "ASE":
for i, position in enumerate(self.ase_molecule.get_positions()):
self.rmg_molecule.atoms[i].coords = position
def update_from_rdkit_mol(self):
# In order to update the ase molecule you simply need to rerun the get_ase_molecule method
self.get_ase_molecule()
self.set_rmg_coords("RDKit")
# Getting the new torsion angles
self.get_torsions()
def update_from_ase_mol(self):
self.set_rmg_coords("ASE")
# setting the geometries of the rdkit molecule
positions = self.ase_molecule.get_positions()
conf = self.rdkit_molecule.GetConformers()[0]
for i, atom in enumerate(self.rdkit_molecule.GetAtoms()):
conf.SetAtomPosition(i, positions[i])
# Getting the new torsion angles
self.get_torsions()
def update_from_rmg_mol(self):
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)
# Getting the new torsion angles
self.get_torsions()
mol.set_calculator(calc)
fix = {fix}
change = {change}
bonds = []
angles = []
dihedrals = []
for fi in fix:
if len(fi) == 2:
#careful: atom indices in the fix lists start at 1
bondlength = mol.get_distance(fi[0] - 1, fi[1] - 1)
bonds.append([bondlength,[fi[0] - 1, fi[1] - 1]])
if len(fi) == 3:
#careful: atom indices in the fix lists start at 1
angle = mol.get_angle(fi[0]-1,fi[1]-1,fi[2]-1) * np.pi / 180
angles.append([angle,[fi[0]-1,fi[1]-1,fi[2]-1]])
if len(fi) == 4:
#careful: atom indices in the fix lists start at 1
dihed = mol.get_dihedral(fi[0]-1,fi[1]-1,fi[2]-1,fi[3]-1) * np.pi / 180
dihedrals.append([dihed,[fi[0]-1,fi[1]-1,fi[2]-1,fi[3]-1]])
for ci in change:
if len(ci) == 3:
#careful: atom indices in the fix lists start at 1
bondlength = ci[2]
bonds.append([bondlength,[ci[0] - 1, ci[1] - 1]])
if len(ci) == 4:
#careful: atom indices in the fix lists start at 1
angle = ci[3] * np.pi / 180
angles.append([angle,[ci[0]-1,ci[1]-1,ci[2]-1]])
if len(ci) == 5:
from ase import Atoms
import numpy as np
atoms = Atoms(['O', 'H', 'H'],
positions=[[0., 0., 0.119262], [0., 0.763239, -0.477047],
[0., -0.763239, -0.477047]])
# Angle no pbc
assert abs(atoms.get_angle(1, 0, 2) - 104) < 1e-3
atoms.set_cell([2, 2, 2])
# Across different pbcs
atoms.set_pbc([True, False, True])
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Across all True pbc
atoms.set_pbc(True)
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Change Angle
old = atoms.get_angle(1, 0, 2, mic=False)
atoms.set_angle(1, 0, 2, -10, indices=[2], add=True)
new = atoms.get_angle(1, 0, 2, mic=False)
diff = old - new - 10
assert abs(diff) < 10e-3
#don't actually change angle using indices
old = atoms.get_angle(1, 0, 2, mic=False)
#apply the constraints:
fix = {fix}
change = {change}
release = {release}
bonds = []
angles = []
dihedrals = []
for f in fix:
if len(f) == 3:
dist = mol.get_distance(f[0] - 1, f[1] -
1) #ase enumerates atoms starting from zero
bonds.append([dist, [f[0] - 1, f[1] - 1]])
if len(f) == 3:
angle = mol.get_angle(f[0] - 1, f[1] - 1, f[2] -
1) #ase enumerates atoms starting from zero
angle *= pi / 180.
angles.append([angle, [f[0] - 1, f[1] - 1, f[2] - 1]])
if len(f) == 4:
dih = mol.get_dihedral(f[0] - 1, f[1] - 1, f[2] - 1, f[3] -
1) #ase enumerates atoms starting from zero
dih *= pi / 180.
dihedrals.append([dih, [f[0] - 1, f[1] - 1, f[2] - 1, f[3] - 1]])
for c in change:
if len(c) == 3:
bonds.append([c[2], [c[0] - 1, c[1] - 1]])
if len(c) == 4:
angle = c[3] * pi / 180.
angles.append([angle, [c[0] - 1, c[1] - 1, c[2] - 1]])
if len(c) == 5:
dih = c[4] * pi / 180.
def Gradient(Elements, Image, ImageNo, GuessNo, output,
dummy_variable): #output is for labeling the process
#Creates a directory for each image, at each stage
omitoutput = os.system('mkdir -p ./Molecule-%s/Image%s' %
(str(GuessNo), str(ImageNo)))
os.chdir('Molecule-%s/Image%s' % (str(GuessNo), str(ImageNo)))
#If a gradient has already been generated for a given image it will skip it
SaveGradient = 'Gradient-%s-%s' % (str(GuessNo), str(ImageNo))
os.system('ls --ignore \'INPUT*\' > CheckGradTemp')
if SaveGradient in open('CheckGradTemp').read():
os.system('rm CheckGradTemp')
f1 = open('Gradient-%s-%s' % (str(GuessNo), str(ImageNo)), 'r')
Ftemp = f1.readlines()
F = []
for i in range(0, len(Ftemp)):
force = filter(None, Ftemp[i][2:-2].split(' '))
Newline = []
for k in range(0, len(force)):
Newline.append(float(force[k]))
F.append(Newline)
print 'Gradient obtained for Guess No %s and Image No %s' % (
str(GuessNo), str(ImageNo))
else:
os.system('rm CheckGradTemp')
# Set up the molecule by specifying atomic positions and atomic number
Molecule = Atoms(numbers=Elements, positions=Image, pbc=(0, 0, 0))
write('Molecule-%s-%s-start.xyz' % (str(GuessNo), str(ImageNo)),
Molecule)
# Center the molecule in the cell with some vacuum around
Molecule.center(vacuum=6.0)
##FIX:
const = FixAtoms(mask=Molecule.positions[22, :]) #blah
Molecule.set_constraint(const) #HERE!!!
# Run the relaxation for each energy shift, and print out the
# corresponding total energy, bond length and angle
starttime = time.time()
calc = LAMMPS('Molecule',
parameters={
'pair_style': 'airebo 3.0 1 1',
'pair_coeff': ['* * ../../CH.airebo C H'],
'mass': ['1 12.0107', '2 1.00794']
},
tmp_dir='./',
keep_tmp_files=True,
no_data_file=False)
#files = ['../CH.airebo'] \n min_style fire \n unfix fix_nve','run': '1', , 'minimize': '10e-12 10e-14 100000 100000'
Molecule.set_calculator(calc)
F = Molecule.get_forces()
#print calculation_required(Molecule, 'energy')
E = Molecule.get_potential_energy()
#print 'F-%s-%s' % (str(GuessNo), str(ImageNo)), 'is', F, 'type F is; ',type(F), np.shape(F)
f2 = open(SaveGradient, 'w').write(str(F))
f3 = open('Energy', 'w').write(str(E))
AngleCNNC = Molecule.get_dihedral([3, 1, 0, 2])
AngleCCNN = Molecule.get_dihedral([7, 3, 1, 0])
AngleNNCC = Molecule.get_dihedral([1, 0, 2, 6])
AngleCNN = Molecule.get_angle([3, 1, 0])
AngleNNC = Molecule.get_angle([1, 0, 2])
AngleCCN = Molecule.get_angle([7, 3, 1])
f4 = open('CNNCandCCNNandNNCC', 'w').write(
str(AngleCNNC) + '\t' + str(AngleCCNN) + '\t' + str(AngleNNCC))
f5 = open('CNNandNNCandCCN', 'w').write(
str(AngleCNN) + '\t' + str(AngleNNC) + '\t' + str(AngleCCN))
#endtime = time.time()
#walltime = endtime - starttime
#print 'Wall time: %.5f' % walltime
#print # Make the output more readable
#client.close()
output.put((ImageNo, F))
def fix_cyclopropenyl(atoms: Atoms, mol: pybel.Molecule) -> Atoms:
"""Detect cyclopropenyl groups and assure they are planar.
Args:
atoms: Object holding the 3D positions
mol: Object holidng the bonding information
Returns:
Version of atoms with the rings flattened
"""
# Find cyclopropenyl groups
smarts = pybel.Smarts('C1=C[C+]1')
rings = smarts.findall(mol)
if len(rings) == 0:
return atoms # no changes
# For each ring, flatten it
atoms = atoms.copy()
g = get_bonding_graph(mol)
for ring in rings:
ring = tuple(x - 1 for x in rings[0]) # Pybel is 1-indexed
# Get the normal of the ring
normal = np.cross(*np.subtract(atoms.positions[ring[:2], :],
atoms.positions[ring[2], :]))
normal /= np.linalg.norm(normal)
# Adjust the groups attached to each member of the ring
for ring_atom in ring:
# Get the ID of the group bonded to it
bonded_atom = next(r for r in g[ring_atom] if r not in ring)
# Determine the atoms that are part of that functional group
h = g.copy()
h.remove_edge(ring_atom, bonded_atom)
a, b = nx.connected_components(h)
mask = np.zeros((len(atoms), ), dtype=bool)
if bonded_atom in a:
mask[list(a)] = True
else:
mask[list(b)] = True
# Get the rotation angle
bond_vector = atoms.positions[bonded_atom, :] - atoms.positions[
ring_atom, :]
angle = np.dot(bond_vector, normal) / np.linalg.norm(bond_vector)
rot_angle = np.arccos(angle) - np.pi / 2
logger.debug(f'Rotating by {rot_angle} radians')
# Perform the rotation
rotation_axis = np.cross(bond_vector, normal)
atoms._masked_rotate(atoms.positions[ring_atom], rotation_axis,
rot_angle, mask)
# make the atom at a 150 angle with the the ring too
another_ring = next(r for r in ring if r != ring_atom)
atoms.set_angle(another_ring,
ring_atom,
bonded_atom,
150,
mask=mask)
assert np.isclose(
atoms.get_angle(another_ring, ring_atom, bonded_atom),
150).all()
# Make sure it worked
bond_vector = atoms.positions[bonded_atom, :] - atoms.positions[
ring_atom, :]
angle = np.dot(bond_vector, normal) / np.linalg.norm(bond_vector)
final_angle = np.arccos(angle)
assert np.isclose(final_angle, np.pi / 2).all()
logger.info(
f'Detected {len(rings)} cyclopropenyl rings. Ensured they are planar.'
)
return atoms
"Test that set_angle() and get_angle() in Atoms are consistent"
from ase import Atoms
atoms = Atoms(
'HHCCHH',
[[-1, 1, 0], [-1, -1, 0], [0, 0, 0], [1, 0, 0], [2, 1, 0], [2, -1, 0]])
list = [2, 3, 4]
theta = 0.1
old_angle = atoms.get_angle(list)
atoms.set_angle(list, old_angle + theta)
new_angle = atoms.get_angle(list)
assert abs(new_angle - (old_angle + theta)) < 1.0e-9
"Test that set_angle() and get_angle() in Atoms are consistent"
from ase import Atoms
atoms = Atoms('HHCCHH', [[-1, 1, 0], [-1, -1, 0], [0, 0, 0],
[1, 0, 0], [2, 1, 0], [2, -1, 0]])
list = [2, 3, 4]
theta = 0.1
old_angle = atoms.get_angle(list)
atoms.set_angle(list, old_angle + theta)
new_angle = atoms.get_angle(list)
assert abs(new_angle - (old_angle + theta)) < 1.0e-9
from ase import Atoms
import numpy as np
atoms = Atoms(['O', 'H', 'H'],
positions=[[0., 0., 0.119262], [0., 0.763239, -0.477047],
[0., -0.763239, -0.477047]])
# Angle no pbc
assert abs(atoms.get_angle(1, 0, 2) - 104) < 1e-3
atoms.set_cell([2, 2, 2])
# Across different pbcs
atoms.set_pbc([True, False, True])
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Across all True pbc
atoms.set_pbc(True)
atoms.wrap()
assert abs(atoms.get_angle(1, 0, 2, mic=True) - 104) < 1e-3
# Simple tetrahedron
tetra_pos = np.array([[0, 0, 0], [1, 0, 0], [.5, np.sqrt(3) * .5, 0],
[.5, np.sqrt(1 / 3.) * .5,
np.sqrt(2 / 3.)]])
atoms = Atoms(['H', 'H', 'H', 'H'], positions=tetra_pos - np.array([.2, 0, 0]))
angle = 70.5287793655
assert abs(atoms.get_dihedral(0, 1, 2, 3) - angle) < 1e-3
atoms.set_cell([3, 3, 3])