"""YiiP equilibrium trajectory with water.
https://figshare.com/articles/Molecular_Dynamics_trajectories_of_membrane_protein_YiiP/8202149
"""
from os.path import dirname, exists, join
from os import makedirs, remove
import codecs
import logging
from .base import get_data_home
from .base import _fetch_remote, _read_description
from .base import RemoteFileMetadata
from .base import Bunch
NAME = "yiip_equilibrium"
DESCRIPTION = "yiip_equilibrium.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 = {
'short':{
'topology': RemoteFileMetadata(
filename='YiiP_system.pdb',
url='https://ndownloader.figshare.com/files/15286808',
checksum='3c2b96bbd2f95105e1a4f37140132ee073a947df8fe209a8170f09ca5b73e6cf',
),
'trajectory': RemoteFileMetadata(
filename='YiiP_system_9ns_center.xtc',
url='https://ndownloader.figshare.com/files/15285461',
checksum='97f6a93acc1e330915338b290625d81d84928a7e4c1e5aed63d209881fbe268b',
),
},
'long':{
'topology': RemoteFileMetadata(
filename='YiiP_system.pdb',
url='https://ndownloader.figshare.com/files/15286808',
checksum='3c2b96bbd2f95105e1a4f37140132ee073a947df8fe209a8170f09ca5b73e6cf',
),
'trajectory': RemoteFileMetadata(
filename='YiiP_system_90ns_center.xtc',
url='https://ndownloader.figshare.com/files/15294914',
checksum='de16552ad0eb46144a7fe980424b4f3b89bf6ae553512a246d5015e5a361033c',
),
},
}
logger = logging.getLogger(__name__)
[docs]
def fetch_yiip_equilibrium_short(data_home=None, download_if_missing=True):
"""Load the YiiP 9 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>/yiip_equilibrium``.
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:`yiip-equilibrium-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['short'].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
[docs]
def fetch_yiip_equilibrium_long(data_home=None, download_if_missing=True):
"""Load the YiiP 90 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>/yiip_equilibrium``.
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:`yiip-equilibrium-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['long'].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