besmarts.core.primitives module

besmarts.core.primitives

Standard definitions of SMARTS primitives.

class besmarts.core.primitives.primitive_codec(implements, smarts_prefix)

Bases: object

decode_int(x: int) → int

Transform a decoded integer into its value for SMARTS/SMILES. The default behavior is a passthrough and works for most primitives, such as element and hydrogen. Special behavior for certain primitives e.g. formal charge, must be handled by subclassing.

Parameters:

x (int) – The integer to decode

Returns:

The decoded integer

Return type:

int

decode_smarts(dtype, obj) → bitvec

Parse and decode a SMARTS atom or bond for a primitive.

Parameters:

• dtype (array) – The class used to store the decoded values

• obj (str) – The atom or bond string to parse and decode

Returns:

The decoded SMARTS as an array of bits

Return type:

bitvec

decode_smiles(dtype: bitvec, obj) → bitvec

decode_supersmarts(dtype, obj) → bitvec

encode_int(x: int) → int

Transform an integer parsed from a SMILES or SMARTS representation to a valid value for storing in a bit array. The default behavior is a passthrough and works for most primitives, such as element and hydrogen. Special behavior for certain primitives e.g. formal charge, must be handled by subclassing.

Parameters:

x (int) – The integer to encode

Returns:

The encoded integer

Return type:

int

encode_smarts(arr: bitvec) → str

Transform a primitive as a bit array to a SMARTS string.

Parameters:

arr (array) – The primitive in the form of a bit array

Returns:

The SMARTS string represented the array. Note that if the primitive has no values set, it is not a valid SMARTS string and “_” will be returned

Return type:

str

encode_smiles(arr: bitvec) → str

encode_supersmarts(dtype, obj) → bitvec

tokenize_smarts(obj) → List[str]

class besmarts.core.primitives.primitive_key(*args, **kwds)

Bases: object

AROMATIC = 'aromatic'

BOND_ORDER = 'bond_order'

BOND_RING = 'bond_ring'

CHIRALITY = 'chirality'

CONNECTIVITY_RING = 'connectivity_ring'

CONNECTIVITY_TOTAL = 'connectivity_total'

ELEMENT = 'element'

FORMAL_CHARGE = 'formal_charge'

HYDROGEN = 'hydrogen'

LINK_DST = 'link_dst'

LINK_SRC = 'link_src'

RING_SMALLEST = 'ring_smallest'

UNIT = 'unit'

UNIT_INDEX = 'unit_index'

VALENCE = 'valence'

VARIABLE = 'variable'