FPSim2.io.backends package¶

Submodules¶

FPSim2.io.backends.base module¶

class FPSim2.io.backends.base.BaseStorageBackend(fp_filename)¶

Bases: abc.ABC

abstract append_fps(io_source, mol_id_prop)¶

Appends FPs to the file.

Parameters: mols_source (str or iterable) – .smi or .sdf filename or iterable.
Returns
Return type: None

static calc_popcnt_bins(fps: numpy.ndarray) → list¶

Calcs popcount bins.

Parameters: fps (numpy array) – numpy array with the fingerprints of the database.
Returns: popcnt_bins – list with the ranges of the popcount bins.
Return type: list

abstract delete_fps(ids_list)¶

Delete FPs given a list of ids.

Parameters: ids_list (list) – ids to delete.
Returns
Return type: None

abstract get_fps_chunk(chunk_range)¶: Loads a contiguous chunk of data from the storage into memory

abstract load_fps(in_memory_fps, fps_sort) → None¶: Loads the whole fp db file into memory

abstract load_popcnt_bins()¶: Loads popcnt bins info

abstract read_parameters()¶: Reads fp file info

FPSim2.io.backends.pytables module¶

class FPSim2.io.backends.pytables.PyTablesStorageBackend(fp_filename: str, in_memory_fps: bool = True, fps_sort: bool = False)¶

Bases: FPSim2.io.backends.base.BaseStorageBackend

append_fps(mols_source: Union[str, Iterable], mol_id_prop: str = 'mol_id') → None¶

Appends FPs to the file.

Parameters: mols_source (str or iterable) – .smi or .sdf filename or iterable.
Returns
Return type: None

delete_fps(ids_list: List[int]) → None¶

Delete FPs given a list of ids.

Parameters: ids_list (list) – ids to delete.
Returns
Return type: None

get_fps_chunk(chunk_range: Tuple[int, int]) → numpy.asarray¶: Loads a contiguous chunk of data from the storage into memory

load_fps(in_memory_fps, fps_sort) → None¶

Loads FP db file into memory.

Parameters

in_memory_fps (bool) – Whether if the FPs should be loaded into memory or not.
fps_sort (bool) – Whether if the FPs should be sorted or not.

Returns

fps – Numpy array with the fingerprints.

Return type

numpy array

load_popcnt_bins(fps_sort) → None¶: Loads popcnt bins info

read_parameters() → Tuple[str, Dict[str, Dict[str, dict]], str]¶: Reads fingerprint parameters

FPSim2.io.backends.pytables.calc_popcnt_bins_pytables(fps: Any, fp_length: int) → list¶

FPSim2.io.backends.pytables.create_db_file(mols_source: Union[str, Iterable], filename: str, fp_type: str, fp_params: dict = {}, mol_id_prop: str = 'mol_id', gen_ids: bool = False, sort_by_popcnt: bool = True) → None¶

Creates FPSim2 FPs db file from .smi, .sdf files or from an iterable.