def from_reaction_template(cls, template_smarts):
template = ReactionTemplate(template_smarts)
_rdkit_config = rdkit_config(reaction_center=template.ReactingAtomsMN,
reactant_or_product='reactant',
IsSanitized=False,
set_morgan_identifier=False)
reaction = Graph.from_rdkit(template.reactants[0],
_rdkit_config).to_networkx()
for reactant in template.reactants[1:]:
g = Graph.from_rdkit(reactant, _rdkit_config).to_networkx()
reaction = nx.disjoint_union(reaction, g)
_rdkit_config = rdkit_config(reaction_center=template.ReactingAtomsMN,
reactant_or_product='product',
IsSanitized=False,
set_morgan_identifier=False)
for product in template.products:
g = Graph.from_rdkit(product, _rdkit_config).to_networkx()
reaction = nx.disjoint_union(reaction, g)
g = _from_networkx(cls, reaction)
if g.nodes.to_pandas()['ReactingCenter'].max() <= 0:
raise RuntimeError(f'No reacting atoms are found in reactants: '
f'{template_smarts}')
if g.nodes.to_pandas()['ReactingCenter'].min() >= 0:
raise RuntimeError(f'No reacting atoms are found in products: '
f'{template_smarts}')
return g
from graphdot.kernel.marginalized.starting_probability import Uniform
from graphdot.microkernel import (Additive, Convolution as kConv, Constant as
kC, KroneckerDelta as kDelta,
SquareExponential as kSE)
from graphdot.model.gaussian_process import LowRankApproximateGPR
smiles = [
'CC', 'CCC', 'CCCC', 'CCCCC', 'CCCCCC', 'CCCCCCC', 'CCCCCCCC', 'CCCCCCCCC',
'CCCCCCCCCC', 'CCCCCCCCCCC', 'CCCCCCCCCCCC'
]
energy = [
-719.05, -1014.16, -1309.27, -1604.29, -1899.33, -2194.35, -2489.38,
-2784.41, -3079.44, -3374.47, -3669.50
]
graphs = list(map(lambda smi: Graph.from_rdkit(MolFromSmiles(smi)), smiles))
train_X = graphs[::2]
train_y = energy[::2]
test_X = graphs[1::2]
test_y = energy[1::2]
core = train_X[::2]
kernel = MarginalizedGraphKernel(
node_kernel=Additive(
aromatic=kC(0.5, (0.1, 1.0)) * kDelta(0.5, (0.1, 0.9)),
atomic_number=kC(0.5, (0.1, 1.0)) * kDelta(0.8, (0.1, 0.9)),
charge=kC(0.5, (0.1, 1.0)) * kSE(1.0),
chiral=kC(0.5, (0.1, 1.0)) * kDelta(0.5, (0.1, 0.9)),
hcount=kC(0.5, (0.1, 1.0)) * kSE(1.0),
hybridization=kC(0.5, (0.1, 1.0)) * kDelta(0.5, (0.1, 0.9)),
ring_list=kC(0.5, (0.01, 1.0)) * kConv(kDelta(0.5,