chemprop.featurizers.bond#

Classes#

`MultiHotBondFeaturizer`	A `MultiHotBondFeaturizer` feauturizes bonds based on the following attributes:
`RIGRBondFeaturizer`	A `RIGRBondFeaturizer` featurizes bonds using resonance-invariant features [1]_.

Module Contents#

class chemprop.featurizers.bond.MultiHotBondFeaturizer(bond_types=None, stereos=None)[source]#

Bases: chemprop.featurizers.base.VectorFeaturizer[rdkit.Chem.rdchem.Bond]

A MultiHotBondFeaturizer feauturizes bonds based on the following attributes:

null-ity (i.e., is the bond None?)
bond type
conjugated?
in ring?
stereochemistry

The feature vectors produced by this featurizer have the following (general) signature:

slice [start, stop)	subfeature	unknown pad?
0-1	null?	N
1-5	bond type	N
5-6	conjugated?	N
6-8	in ring?	N
7-14	stereochemistry	Y

NOTE: the above signature only applies for the default arguments, as the bond type and sterochemistry slices can increase in size depending on the input arguments.

Parameters:

bond_types (Sequence[BondType] | None, default=[SINGLE, DOUBLE, TRIPLE, AROMATIC]) – the known bond types
stereos (Sequence[int] | None, default=[0, 1, 2, 3, 4, 5]) – the known bond stereochemistries. See [1]_ for more details

References

bond_types#

stereo#

__len__()[source]#

__call__(b)[source]#

Parameters:: b (rdkit.Chem.rdchem.Bond)
Return type:: numpy.ndarray

classmethod one_hot_index(x, xs)[source]#

Returns a tuple of the index of x in xs and len(xs) + 1 if x is in xs. Otherwise, returns a tuple with len(xs) and len(xs) + 1.

Parameters:: xs (Sequence)
Return type:: tuple[int, int]

class chemprop.featurizers.bond.RIGRBondFeaturizer[source]#

Bases: chemprop.featurizers.base.VectorFeaturizer[rdkit.Chem.rdchem.Bond]

A RIGRBondFeaturizer featurizes bonds using resonance-invariant features [1]_.

The generated bond features include: * null-ity (i.e., whether the bond is None) * in ring?

References

__len__()[source]#

__call__(b)[source]#

Parameters:: b (rdkit.Chem.rdchem.Bond)
Return type:: numpy.ndarray

classmethod one_hot_index(x, xs)[source]#

Returns a tuple of the index of x in xs and len(xs) + 1 if x is in xs. Otherwise, returns a tuple with len(xs) and len(xs) + 1.

Parameters:: xs (Sequence)
Return type:: tuple[int, int]