Source code for moldesign.method

# Copyright 2016 Autodesk Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
This module contains abstract base classes for potential models, integrators, and various
associated data types (force fields, orbitals, basis sets, etc.).
import funcsigs

import moldesign as mdt
from moldesign.utils import DotDict

class _InitKeywordMeta(type):
    """ Constructs a custom call signature for __init__ based on cls.PARAMETERS.
    def __signature__(self):
        if hasattr(self, '__customsig'):
            return self.__customsig

        kwargs = []
        for param in self.PARAMETERS:

        self.__customsig = funcsigs.Signature(kwargs, __validate_parameters__=True)
        return self.__customsig

[docs]class Method(object): """Abstract Base class for energy models, integrators, and "heavy duty" simulation objects Args: **kwargs (dict): list of parameters for the method. Attributes: mol (mdt.Molecule): the molecule this method is associated with """ __metaclass__ = _InitKeywordMeta PARAMETERS = [] """ list: list of Parameters that can be used to configure this method """ PARAM_SUPPORT = {} """ Mapping(str, list): List of supported values for parameters (if a parameter is not found, it's assumed that all possible values are supported) """ def __reduce__(self): return _make_method, (self.__class__, self.params, self.mol) def __init__(self, **params): """ :param params: :return: """ # TODO: better documentation for the expected keywords self._prepped = False self.status = None self.mol = None self.params = DotDict(params) # Set default parameter values for param in self.PARAMETERS: if not in self.params: self.params[] = param.default
[docs] def to_json(self): return {'params': self.params, 'name': type(self).__name__, 'version': 'MolecularDesignToolkit-%s' % mdt.__version__}
[docs] def configure(self): from moldesign.widgets.configurator import Configurator return Configurator(self.params, self.PARAMETERS, title='Configuration for %s' % self.__class__.__name__)
[docs] def get_parameters(cls): """ This doesn't do anything right now except provide guidelines for programmers """ return cls.PARAMETERS
[docs] def get_forcefield(self): raise NotImplementedError()
[docs] def print_parameters(cls): params = cls.PARAMETERS lines = [] for obj in params: description = '' if obj.choices: description = '%s' % obj.choices if obj.types: description += ' or ' if obj.types: description += 'Type %s' % obj.types doc = '%s: %s (DEFAULT: %s)' % (, description, obj.default) lines.append(doc) return '\n'.join(lines)
def _make_method(cls, params, mol): """ Helper for serialization - allows __reduce__ to use kwargs """ obj = cls(**params) obj.mol = mol return obj