"""Contains helper functions for initiating ``SolventConfig`` subclasses for
solvents
It has two public functions, ``get_solvent_names`` and ``get_solvent_config``,
for initating ``SolventConfig``. It has a number of private functions for
finding ``SolventConfig`` subclasses and ``WaterModel`` subclasses which can be
used as solvents."""
from glob import glob
from importlib import import_module
from inspect import isclass, isabstract, getmembers
from os.path import dirname, basename, isfile, join
from MDMC.MD import force_fields
from MDMC.MD.force_fields.ff import WaterModel
from MDMC.MD.solvents._solvent_config import SolventConfig
from MDMC.MD.solvents.SPC_config import SPCConfig
def _get_water_models():
"""
Gets a `list` of ``WaterModel`` force fields that exist
Returns
-------
list
A `list` of classes which inherit from ``WaterModel``
"""
force_fields_dir = dirname(force_fields.__file__)
modules = [import_module('.' + basename(f)[:-3], force_fields.__name__)
for f in glob(join(force_fields_dir, "*.py"))
if isfile(f) and not f.startswith('_')]
w_models = []
for module in modules:
# try/except for modules which have no subclasses of SolventConfig and
# so return an empty list
try:
w_models.append(getmembers(module,
lambda m: (isclass(m)
and not isabstract(m)
and issubclass(m,
WaterModel)
))[0][1])
except IndexError:
pass
return w_models
def _get_water_model_configs():
"""
Gets the ``SolventConfig`` for each ``WaterModel``
This is required because every water model does not have a unique
``SolventConfig``. For example, all 3 body water models use ``SPC_config``.
Returns
-------
dict
{``w_model``: ``solvent_config``} pairs, where each ``w_model`` is a
`str` specifying an available ``WaterModel``, and ``solvent_config`` is
the ``SolventConfig`` class that will be used for sovlating with that
``WaterModel``.
"""
w_model_configs = {}
for w_model in _get_water_models():
# For 3 body water models, use the SPC216 configuration. This is
# reasonable because the 3 body models are sufficiently similar that
# it is assumed that the SPC216 config will require minimal
# equilibration when used with another 3 body model.
if w_model.n_body == 3:
w_model_configs[w_model.__name__] = SPCConfig
return w_model_configs
def _get_solvent_configs():
"""
Gets a `dict` of the names of ``SolventConfig`` and their classes
Returns
-------
dict
{``name``: ``solvent_config``} pairs, where each ``name`` is a `str`
specifying an available ``SolventConfig`` subclass, and
``solvent_config`` is the corresponding class.
"""
# Import all modules in same directory, except this one
modules = [import_module('.' + basename(f)[:-3], __package__) for f
in glob(join(dirname(__file__), "*.py"))
if isfile(f) and not f.startswith('_') and f != __file__]
# Get members of all modules if they are solvent_configs (i.e. they are
# subclasses of SolventConfig)
s_configs = []
for module in modules:
# try/except for modules which have no subclasses of SolventConfig and
# so return an empty list
try:
s_configs.append(getmembers(module,
lambda m: (isclass(m)
and not isabstract(m)
and issubclass(m,
SolventConfig)
))[0][1])
except IndexError:
pass
return {s_config.__name__: s_config for s_config in s_configs}
[docs]def get_solvent_config(name):
"""
Gets the ``solvent_config`` for a solvent
Parameters
----------
name : str
The name of the solvent
Returns
-------
``SolventConfig``
An object from a subclass of ``SolventConfig`` for the specified solvent
name
"""
s_config = SOLVENT_CONFIGS.get(name+'Config', None)
if s_config is None:
try:
s_config = WATER_MODELS[name]
except KeyError as error:
raise ValueError(f"{name} is not an inbuilt solvent. The inbuilt"
f" solvents are: {get_solvent_names()}") from error
return s_config()
[docs]def get_solvent_names():
"""
Get the names of the inbuilt solvents which can be passed as parameters to
``get_solvent_config``
Returns
-------
list
A `list` of `str` with the names of the inbuilt solvents
"""
return list(set(list(WATER_MODELS.keys())
+ [name.replace('Config', '') for name
in _get_solvent_configs().keys()]))
SOLVENT_CONFIGS = _get_solvent_configs()
WATER_MODELS = _get_water_model_configs()