Source code for MDAnalysis.fetch.pdb

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# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
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# doi: 10.25080/majora-629e541a-00e
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# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#

"""
PDB Fetchers --- :mod:`MDAnalysis.fetch.pdb`
============================================

This suite of functions download structure files from the Research
Collaboratory for Structural Bioinformatics (RCSB)
`Protein Data Batabank`_ (PDB).

.. _Protein Data Batabank: https://www.rcsb.org/

Variables
---------

.. autodata:: DEFAULT_CACHE_NAME_DOWNLOADER

Functions
---------

.. autofunction:: from_PDB

"""

import re
import warnings

from .fetchers import StaticFetcher

#: Alias to fetchers/DEFAULT_CACHE_NAME_DOWNLOADER
#:
#: Maintained for backwards compatiblity
#:
from .fetchers import DEFAULT_CACHE_NAME_DOWNLOADER

# These file formats are here https://www.rcsb.org/docs/programmatic-access/file-download-services#pdb-entry-files"
_SUPPORTED_FILE_FORMATS_PDB = (
    "cif",
    "cif.gz",
    "bcif",
    "bcif.gz",
    "xml",
    "xml.gz",
    "pdb",
    "pdb.gz",
    "pdb1",
    "pdb1.gz",
)


def from_PDB(
    pdb_ids,
    cache_path=None,
    progressbar=False,
    file_format="cif.gz",
):
    """
    Download one or more PDB files from the RCSB Protein Data Bank and cache
    them locally.

    Given one or multiple PDB IDs, downloads the corresponding structure files
    format and stores them in a local cache directory. If files are cached on
    disk, *from_PDB* will skip the download and use the cached version instead.

    Returns the path(s) as a :class:`~pathlib.Path` to the downloaded file(s).

    Parameters
    ----------
    pdb_ids : str or sequence of str
        A single PDB ID as a string, or a sequence of PDB IDs to fetch.
    cache_path : str or pathlib.Path
        Directory where downloaded file(s) will be cached.
        The default ``None`` argument uses the :mod:`pooch` default cache with
        project name :data:`DEFAULT_CACHE_NAME_DOWNLOADER`.
    file_format : str
        The file extension/format to download (e.g., "cif", "pdb").
        See the Notes section below for a list of all supported file formats.
    progressbar : bool
        If True, display a progress bar during file downloads. Default
        is False.

    Returns
    -------
    :class:`~pathlib.Path` or list of :class:`~pathlib.Path`
        The path(s) to the downloaded file(s). Returns a single
        :class:`~pathlib.Path` if a single pdb id is given, or a list of
        :class:`~pathlib.Path` if multiple pdb ids are provided.

    Raises
    ------
    ValueError
        For an invalid file format. Supported file formats are under Notes.

    :class:`requests.exceptions.HTTPError`
        If an invalid PDB code is specified.

    Notes
    -----
    This function uses the `RCSB File Download Services`_ for directly
    downloading structure files via https.

    .. _`RCSB File Download Services`:
       https://www.rcsb.org/docs/programmatic-access/file-download-services

    The RCSB currently provides data in ``'cif'`` , ``'cif.gz'`` , ``'bcif'`` ,
    ``'bcif.gz'`` , ``'xml'`` , ``'xml.gz'`` , ``'pdb'`` , ``'pdb.gz'``,
    ``'pdb1'``, ``'pdb1.gz'`` file formats and can therefore be downloaded.
    Not all of these formats can be currently read with MDAnalysis.

    Caching, controlled by the `cache_path` parameter, is handled internally by
    :mod:`pooch`. The default cache name is taken from
    :data:`DEFAULT_CACHE_NAME_DOWNLOADER`. To clear cache (and subsequently
    force re-fetching), it is required to delete the cache folder
    as specified by `cache_path`.

    Examples
    --------
    Download a single PDB file:

    >>> mda.fetch.from_PDB("1AKE", file_format="cif")
    './MDAnalysis_pdbs/1AKE.cif'

    Download multiple PDB files with a progress bar:

    >>> mda.fetch.from_PDB(["1AKE", "4BWZ"], progressbar=True)
    ['./MDAnalysis_pdbs/1AKE.pdb.gz', './MDAnalysis_pdbs/4BWZ.pdb.gz']

    Download a single PDB file and convert it to a universe:

    >>> mda.Universe(mda.fetch.from_PDB("1AKE"), file_format="pdb.gz")
    <Universe with 3816 atoms>

    Download multiple PDB files and convert each of them into a universe:

    >>> [mda.Universe(pdb) for pdb in mda.fetch.from_PDB(["1AKE", "4BWZ"], progressbar=True)]
    [<Universe with 3816 atoms>, <Universe with 2824 atoms>]


    .. versionadded:: 2.11.0
    """

    if file_format not in _SUPPORTED_FILE_FORMATS_PDB:
        raise ValueError(
            "Invalid file format. Supported file formats "
            f"are {_SUPPORTED_FILE_FORMATS_PDB}"
        )

    if isinstance(pdb_ids, str):
        _pdb_ids = (pdb_ids + "." + file_format,)
    else:
        _pdb_ids = [pdb + "." + file_format for pdb in pdb_ids]

    fetcher = StaticFetcher(cache_path=cache_path)
    return fetcher.fetch(
        file_name=_pdb_ids,
        base_url="https://files.wwpdb.org/download/",
        progressbar=progressbar,
        append_db=True,
    )


def from_DOI(doi, file_name, cache_path=None, remove_prefix=True):
    """
    Download one or more files given the Digital Object Identifier (DOI).
    them locally.

    Given one DOI, this function downloads one or multiple file names from
    the repository and stores them in a local cache directory. If files
    are cached on disk, *from_DOI* will skip the download and use the
    cached version instead.

    Returns the path(s) as a :class:`~pathlib.Path` to the downloaded file(s).

    Parameters
    ----------
    doi: str
        the name of a links o
    file_name, : str
        The file extension/format to download (e.g., "cif", "pdb").
        See the Notes section below for a list of all supported file formats.
    cache_path : str or pathlib.Path
        Directory where downloaded file(s) will be cached.
        The default ``None`` argument uses the :mod:`pooch` default cache with
        project name :data:`DEFAULT_CACHE_NAME_DOWNLOADER`.
    remove_prefix : bool
        If True, display a progress bar during file downloads. Default
        is False.

    Returns
    -------
    :class:`~pathlib.Path` or list of :class:`~pathlib.Path`
        The path(s) to the downloaded file(s). Returns a single
        :class:`~pathlib.Path` if a single pdb id is given, or a list of
        :class:`~pathlib.Path` if multiple pdb ids are provided.

    Raises
    ------
    ValueError
        For an invalid file format. Supported file formats are under Notes.

    :class:`requests.exceptions.HTTPError`
        If an invalid PDB code is specified.

    Notes
    -----
    This function uses the `RCSB File Download Services`_ for directly
    downloading structure files via https.

    .. _`RCSB File Download Services`:
       https://www.rcsb.org/docs/programmatic-access/file-download-services

    The RCSB currently provides data in ``'cif'`` , ``'cif.gz'`` , ``'bcif'`` ,
    ``'bcif.gz'`` , ``'xml'`` , ``'xml.gz'`` , ``'pdb'`` , ``'pdb.gz'``,
    ``'pdb1'``, ``'pdb1.gz'`` file formats and can therefore be downloaded.
    Not all of these formats can be currently read with MDAnalysis.

    Caching, controlled by the `cache_path` parameter, is handled internally by
    :mod:`pooch`. The default cache name is taken from
    :data:`DEFAULT_CACHE_NAME_DOWNLOADER`. To clear cache (and subsequently
    force re-fetching), it is required to delete the cache folder
    as specified by `cache_path`.

    Examples
    --------
    Download a single PDB file:

    >>> mda.fetch.from_PDB("1AKE", file_format="cif")
    './MDAnalysis_pdbs/1AKE.cif'

    Download multiple PDB files with a progress bar:

    >>> mda.fetch.from_PDB(["1AKE", "4BWZ"], progressbar=True)
    ['./MDAnalysis_pdbs/1AKE.pdb.gz', './MDAnalysis_pdbs/4BWZ.pdb.gz']

    Download a single PDB file and convert it to a universe:

    >>> mda.Universe(mda.fetch.from_PDB("1AKE"), file_format="pdb.gz")
    <Universe with 3816 atoms>

    Download multiple PDB files and convert each of them into a universe:

    >>> [mda.Universe(pdb) for pdb in mda.fetch.from_PDB(["1AKE", "4BWZ"], progressbar=True)]
    [<Universe with 3816 atoms>, <Universe with 2824 atoms>]


    .. versionadded:: 2.11.0
    """

    # Suppress Figshare warning of getting most current
    # repository if none is provided
    warnings.filterwarnings("ignore", category=UserWarning)

    if remove_prefix:
        # Captures https:// and ftp://
        match = re.match(r"^(.*?:\/\/)", doi)

        if match is not None:
            start, end = match.span()
            doi = doi[end:]

    # In format of doi.org/stuff/stuff
    # Need to massage into pooch-compataible syntax
    doi = doi.replace("doi.org/", "doi:")

    fetcher = StaticFetcher(cache_path=cache_path)
    return fetcher.fetch(
        base_url=doi, file_name=file_name, append_db=True, downloader="doi"
    )


##