Source code for MDAnalysisData.ifabp_water

# -*- coding: utf-8 -*-

"""MD simulation of I-FABP with water.

https://figshare.com/articles/Molecular_dynamics_trajectory_of_I-FABP_for_testing_and_benchmarking_solvent_dynamics_analysis/7058030
"""

from os.path import dirname, exists, join
from os import makedirs, remove

import logging

from .base import get_data_home
from .base import _fetch_remote, _read_description
from .base import RemoteFileMetadata
from .base import Bunch

NAME = "ifabp_water"
DESCRIPTION = "ifabp_water.rst"
# The original data can be found at the figshare URL.
# The SHA256 checksum of the zip file changes with every download so we
# cannot check its checksum. Instead we download individual files.
# separately. The keys of this dict are also going to be the keys in the
# Bunch that is returned.
ARCHIVE = {
    'topology': RemoteFileMetadata(
        filename='ifabp_water.psf',
        url='https://ndownloader.figshare.com/files/12980639',
        checksum='ba40714318aabec537015dc550fe5bd5ac1ac0b853f5abdd2f0ae63af9cfcafa',
    ),
    'structure': RemoteFileMetadata(
        filename='ifabp_water_0.pdb',
        url='https://ndownloader.figshare.com/files/12980636',
        checksum='8ccf5f75fd85385921c0cb77f00281a93b933fc1261c42fc9492f43983448a72',
    ),
    'trajectory':  RemoteFileMetadata(
        filename='rmsfit_ifabp_water_1.dcd',
        url='https://ndownloader.figshare.com/files/12980642',
        checksum='cebb48e58015abc8ff2f5bb7ba3eb7a289047f256351a8252bf1f29f9aaacf0e',
    ),
}



logger = logging.getLogger(__name__)


[docs]def fetch_ifabp_water(data_home=None, download_if_missing=True): """Load the I-FABP with water 0.5 ns equilibrium trajectory Parameters ---------- data_home : optional, default: None Specify another download and cache folder for the datasets. By default all MDAnalysisData data is stored in '~/MDAnalysis_data' subfolders. This dataset is stored in ``<data_home>/ifabp_water``. download_if_missing : optional, default=True If ``False``, raise a :exc:`IOError` if the data is not locally available instead of trying to download the data from the source site. Returns ------- dataset : dict-like object with the following attributes: dataset.topology : filename Filename of the topology file dataset.trajectory : filename Filename of the trajectory file dataset.structure : filename Filename of a structure file in PDB format dataset.DESCR : string Description of the trajectory. See :ref:`ifabp-water-dataset` for description. """ name = NAME data_location = join(get_data_home(data_home=data_home), name) if not exists(data_location): makedirs(data_location) records = Bunch() for file_type, meta in ARCHIVE.items(): local_path = join(data_location, meta.filename) records[file_type] = local_path if not exists(local_path): if not download_if_missing: raise IOError("Data {0}={1} not found and `download_if_missing` is " "False".format(file_type, local_path)) logger.info("Downloading {0}: {1} -> {2}...".format( file_type, meta.url, local_path)) archive_path = _fetch_remote(meta, dirname=data_location) records.DESCR = _read_description(DESCRIPTION) return records