Source code for MDAnalysisData.PEG_1chain

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

"""Molecular dynamics trajectory of a single PEG chain in TIP3P water.

https://doi.org/10.6084/m9.figshare.7325774
"""

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 = "PEG_1chain"
DESCRIPTION = "PEG_1chain.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='PEG.prmtop',
        url='https://ndownloader.figshare.com/files/13532462',
        checksum='2d7955b9a8cb6e008171e0c5a1c31e3e458246ea3ee7302281eafefafa7cede9',
    ),
    'trajectory':  RemoteFileMetadata(
        filename='PEG_03_prod.nc',
        url='https://ndownloader.figshare.com/files/13532465',
        checksum='b978714ec2f93d1cbe99564cb257959f0cb38872359aa745c8eba720a7d85225',
    ),
}

logger = logging.getLogger(__name__)


[docs]def fetch_PEG_1chain(data_home=None, download_if_missing=True): """Load the PEG polymer 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>/CG_fiber``. 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.DESCR : string Description of the trajectory. See :ref:`PEG_1chain-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