kinoml.utils

Miscellaneous utilities

Module Contents

kinoml.utils.APPDIR
kinoml.utils.PACKAGE_ROOT
class kinoml.utils.FromDistpatcherMixin
classmethod _from_dispatcher(value, handler, handler_argname, prefix)
class kinoml.utils.LocalFileStorage

Generate standardized paths for storing and reading data locally.

DIRECTORY
static rcsb_structure_pdb(pdb_id, directory=DIRECTORY)
static rcsb_structure_cif(pdb_id, directory=DIRECTORY)
static rcsb_ligand_sdf(pdb_id, chain_id, expo_id, altloc, directory=DIRECTORY)
static rcsb_electron_density_mtz(pdb_id, directory=DIRECTORY)
static klifs_ligand_mol2(structure_id, directory=DIRECTORY)
static klifs_structure_db(directory=DIRECTORY)
static klifs_kinase_db(directory=DIRECTORY)
static featurizer_result(featurizer_name, result_details, file_format, directory=DIRECTORY)
static pdb_smiles_json(directory=DIRECTORY)
class kinoml.utils.FileDownloader

Download and store files locally.

DIRECTORY
static rcsb_structure_pdb(pdb_id, directory=DIRECTORY)
static rcsb_structure_cif(pdb_id, directory=DIRECTORY)
static rcsb_electron_density_mtz(pdb_id, directory=DIRECTORY)
kinoml.utils.datapath(path: str) → pathlib.Path

Return absolute path to a file contained in this package’s data directory.

Parameters

path (str) – Relative path to file in data.

Returns

Absolute path to the file in the KinoML data directory. Existence is not checked or guaranteed.

Return type

path pathlib.Path

kinoml.utils.grouper(iterable: Iterable, n: int, fillvalue: Any = None) → Iterable

Given an iterable, consume it in n-sized groups, filling it with fillvalue if needed.

Parameters

  • iterable (list, tuple, str or iterable) – Something that can be split in sub-items and grouped.

  • n (int) – Size of the group

  • fillvalue (object) – Last group will be padded with this object until len(group)==n

class kinoml.utils.defaultdictwithargs(call: Callable)

Bases: collections.defaultdict

A defaultdict that will create new values based on the missing value

Parameters

call (class or callable) – Factory to be called on missing key

__missing__(key)
kinoml.utils.download_file(url: str, path: str)

Download a file and save it locally.

Parameters

  • url (str) – URL for downloading data.

  • path (str) – Path to save downloaded data.

Returns

True if successful, else False.

Return type

bool

kinoml.utils.seed_everything(seed=1234)

Fix the random number generator seed in several pieces of the Python runtime: Python itself, NumPy, Torch.

Parameters

seed (int, optional=1234) –

kinoml.utils.watermark()

Check and log versions and environment details of the execution context. We currently check for:

  • Whatever watermark (the library) returns

  • The output of nvidia-smi, if available

  • The output of conda info, if available

  • The output of conda list, if available

Note

This assumes you are running the function inside a Jupyter notebook.

kinoml.utils.collapsible(function, *args, **kwargs)

An IPython widget that can collapse its contents.

Parameters

function (callable) – A function that generates some kind of output (print, plots, etc). Args and kwargs will be forwarded here.

Return type

ipywidgets.Accordion

kinoml.utils.fill_until_next_multiple(container, multiple_of: int, factory)

Fill container with instances of factory until its length reaches the next multiple of multiple_of.

container gets modified in place and returned.

Parameters

  • container (list or set) – Extendable container

  • multiple_of (int) – The final size of container will match the next multiple of this number.

  • factory (callable) – This callable will be run to produce the filler elements used to extend container

Returns

Modified in place

Return type

container

kinoml.utils.import_object(import_path: str)

Import an object using its full import path

Parameters

import_path (str) – Full import path to object, like kinoml.core.measurements.MeasurementType.

Return type

object

kinoml.utils.sha256_objects(objects_to_hash: Iterable[object]) → str

Generate a SHA256 hash of pickable objects.

Parameters

objects_to_hash (Iterable of object) – Objects that should be hashed.

Returns

The SHA256 of given objects.

Return type

str