def get_truncated_ts(reaction, bond_rearr):
"""Get the TS of a truncated reactant and product complex"""
# Truncate the reactant and product complex to the core atoms so the full
# TS can be template-d
f_reactant = reaction.reactant.copy()
f_product = reaction.product.copy()
# Set the truncated reactant and product for this reaction
reaction.reactant = get_truncated_complex(f_reactant, bond_rearr)
reaction.product = get_truncated_complex(f_product, bond_rearr)
# Re-find the bond rearrangements, which should exist
reaction.name += '_truncated'
bond_rearrangs = get_bond_rearrangs(reaction.reactant,
reaction.product,
name=reaction.name)
if bond_rearrangs is None:
logger.error('Truncation generated a complex with 0 rearrangements')
return None
# Find all the possible TSs
for bond_rearr in bond_rearrangs:
get_ts(reaction, reaction.reactant, bond_rearr, is_truncated=True)
# Reset the reactant, product and name of the full reaction
reaction.reactant = f_reactant
reaction.product = f_product
reaction.name = reaction.name.rstrip('_truncated')
logger.info('Done with truncation')
return None
def test_enone_truncation():
enone = Reactant(name='enone', smiles='CC(O)=CC(=O)OC')
reactant = ReactantComplex(enone)
bond_rearr = BondRearrangement(breaking_bonds=[(2, 11)],
forming_bonds=[(11, 5)])
truncated = get_truncated_complex(reactant, bond_rearr)
assert truncated.n_atoms == 10
assert truncated.graph.number_of_edges() == 9
def test_product_complex_truncation():
# H atom transfer from methane to ethene
bond_rearr = BondRearrangement(breaking_bonds=[(0, 1)], forming_bonds=[(1, 5)])
methane_ethene = ReactantComplex(methane, ethene, name='product_complex')
# Should retain all atoms
truncated = get_truncated_complex(methane_ethene, bond_rearr)
assert truncated.n_atoms == 11
def test_reactant_complex_truncation():
# Non-sensical bond rearrangement
bond_rearr = BondRearrangement(forming_bonds=[(0, 1)], breaking_bonds=[(0, 5)])
methane_dimer = ReactantComplex(methane, methane)
# Should not truncate methane dimer at all
truncated = get_truncated_complex(methane_dimer, bond_rearr)
assert truncated.n_atoms == 10
def test_two_component_truncation():
propylbromide = Reactant(name='RBr', atoms=xyz_file_to_atoms('RBr.xyz'))
chloride = Reactant(name='Cl', smiles='[Cl-]')
mol = ReactantComplex(chloride, propylbromide)
bond_rearr = BondRearrangement(forming_bonds=[(0, 3)],
breaking_bonds=[(3, 4)])
truncated = get_truncated_complex(r_complex=mol,
bond_rearrangement=bond_rearr)
# Should truncate to ethylbromide + Cl-
assert truncated.n_atoms == 9
def test_large_truncation():
mol = ReactantComplex(
Reactant(name='product', atoms=xyz_file_to_atoms('product.xyz')))
bond_rearr = BondRearrangement(breaking_bonds=[(7, 8), (14, 18)])
assert mol.n_atoms == 50
truncated = get_truncated_complex(r_complex=mol,
bond_rearrangement=bond_rearr)
assert truncated.n_atoms == 27
assert truncated.graph.number_of_edges() == 28
def test_core_strip():
bond_rearr = BondRearrangement()
bond_rearr.active_atoms = [0]
stripped = get_truncated_complex(methane, bond_rearr)
# Should not strip any atoms if the carbon is designated as active
assert stripped.n_atoms == 5
stripped = get_truncated_complex(ethene, bond_rearr)
assert stripped.n_atoms == 6
bond_rearr.active_atoms = [1]
# Propene should strip to ethene if the terminal C=C is the active atom
stripped = get_truncated_complex(propene, bond_rearr)
assert stripped.n_atoms == 6
assert is_isomorphic(stripped.graph, ethene.graph)
# But-1-ene should strip to ethene if the terminal C=C is the active atom
stripped = get_truncated_complex(but1ene, bond_rearr)
assert stripped.n_atoms == 6
assert is_isomorphic(stripped.graph, ethene.graph)
# Benzene shouldn't be truncated at all
stripped = get_truncated_complex(benzene, bond_rearr)
assert stripped.n_atoms == 12
bond_rearr.active_atoms = [0]
# Ethanol with the terminal C as the active atom should not replace the OH
# with a H
stripped = get_truncated_complex(ethanol, bond_rearr)
assert stripped.n_atoms == 9
# Ether with the terminal C as the active atom should replace the OMe with
# OH
stripped = get_truncated_complex(methlyethylether, bond_rearr)
assert stripped.n_atoms == 9
assert is_isomorphic(stripped.graph, ethanol.graph)
