besmarts.codecs.codec_rdkit module

besmarts.besmarts_rdkit.codecs

BESMARTS graph encoding using the RDKit perception model

besmarts.codecs.codec_rdkit.get_indices(mol)[source]
besmarts.codecs.codec_rdkit.get_tags(mol)[source]
class besmarts.codecs.codec_rdkit.graph_codec_rdkit(atom_primitives=None, bond_primitives=None)[source]

Bases: graph_codec

static list_implemented_atom_primitives() → Sequence[primitive_key][source]
static list_implemented_bond_primitives() → Sequence[primitive_key][source]
rdmol_decode(mol: Mol) → graph[source]

Build a graph directly from an RDKit molecule. This sidesteps all sanitization and manipulation; the graph is built by directly querying the molecule for primmitives. Make sure the aromaticity model is compatible!

Parameters:

mol (Chem.Mol) – The RDKit molecule to parse

Return type:

graphs.graph

sdf_decode(sdf) → graph_assignment[source]
smarts_decode(sma) → graph[source]

Transform a SMARTS string into a subgraph or structure depending if there are mapped atoms present.

Paramters

smartsstr

The SMARTS string to decode

returns:

The graph representation of the SMILES string. If the SMARTS has mapped atoms, then a substructure will be returned instead.

rtype:

graphs.graph

smiles_decode(smi) → graph[source]

Transform a SMILES string into a graph

Parameters:

smiles (str) – The SMILES string to decode

Returns:

The graph representation of the SMILES string

Return type:

graph

xyz_decode(smi, xyz) → graph_assignment[source]
besmarts.codecs.codec_rdkit.list_atom_primitives() → Sequence[primitive_key][source]
besmarts.codecs.codec_rdkit.list_bond_primitives() → Sequence[primitive_key][source]
besmarts.codecs.codec_rdkit.parse_atom(codecs, arr, atom) → Dict[primitive_key, bitvec][source]
besmarts.codecs.codec_rdkit.parse_bond(codecs, arr: bitvec, bond) → Dict[primitive_key, bitvec][source]
besmarts.codecs.codec_rdkit.parse_chem(codecs, arr: bitvec, chem) → Dict[primitive_key, bitvec][source]
class besmarts.codecs.codec_rdkit.primitive_codec_aromatic_rdkit[source]

Bases: primitive_codec_aromatic

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_bond_order_rdkit[source]

Bases: primitive_codec_bond_order

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_bond_ring_rdkit[source]

Bases: primitive_codec_bond_ring

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_chirality_rdkit[source]

Bases: primitive_codec_chirality

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_connectivity_ring_rdkit[source]

Bases: primitive_codec_connectivity_ring

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_connectivity_total_rdkit[source]

Bases: primitive_codec_connectivity_total

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_element_rdkit[source]

Bases: primitive_codec_element

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_formal_charge_rdkit[source]

Bases: primitive_codec_formal_charge

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_hydrogen_rdkit[source]

Bases: primitive_codec_hydrogen

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_ring_smallest_rdkit[source]

Bases: primitive_codec_ring_smallest

decode_smiles(dtype: type, obj) → bitvec[source]
class besmarts.codecs.codec_rdkit.primitive_codec_valence_rdkit[source]

Bases: primitive_codec_valence

decode_smiles(dtype: type, obj) → bitvec[source]
besmarts.codecs.codec_rdkit.primitive_codecs_get() → Dict[primitive_key, primitive_codec][source]
besmarts.codecs.codec_rdkit.rdkit_mol_decode(pcp, codecs, arr: bitvec, atom_primitives, bond_primitives, mol) → graph[source]
besmarts.codecs.codec_rdkit.rdkit_sdf_to_smiles_assignment(sdf) → Tuple[smiles_assignment, Dict][source]
besmarts.codecs.codec_rdkit.rdkit_smarts_decode(codecs, arr: bitvec, atom_primitives, bond_primitives, sma) → graph[source]
besmarts.codecs.codec_rdkit.rdkit_smiles_decode(pcp, codecs, arr: bitvec, atom_primitives, bond_primitives, smi) → graph[source]
besmarts.codecs.codec_rdkit.rdkit_xyz_to_smiles_assignment(smiles, xyz) → Tuple[smiles_assignment, Dict][source]