ensemble_hic/setup_functions.py
def make_nonbonded_prior(nb_params, bead_radii, n_structures):
    """
    Makes the default non-bonded structural prior object.

    This will either be a Boltzmann-like distribution or a
    Tsallis ensemble (currently not really supported).

    :param nonbonded_prior_params: settings for the non-bonded prior as
                                   specified in a config file
    :type nonbonded_prior_params: dict

    :param bead_radii: list of bead radii
    :type bead_radii: :class:`numpy.ndarray`

    :param n_structures: number of ensemble members
    :type n_structures: int

    :returns: the non-bonded prior object with parameters set as given
              in the settings
    :rtype: :class:`.NonbondedPrior`
    """
    from .forcefields import NBLForceField as ForceField

    forcefield = ForceField(bead_radii, float(nb_params['force_constant']))
    if not 'ensemble' in nb_params or nb_params['ensemble'] == 'boltzmann':
        from .nonbonded_prior import BoltzmannNonbondedPrior2    
        NBP = BoltzmannNonbondedPrior2('nonbonded_prior', forcefield,
                                       n_structures=n_structures, beta=1.0)
    elif nb_params['ensemble'] == 'tsallis':
        raise NotImplementedError
        from .nonbonded_prior import TsallisNonbondedPrior2
        NBP = TsallisNonbondedPrior('nonbonded_prior', bead_radii=bead_radii,
                                    force_constant=force_constant,
                                    n_structures=n_structures, q=1.0)

    return NBP

    Makes the default non-bonded structural prior object.

    This will either be a Boltzmann-like distribution or a
    Tsallis ensemble (currently not really supported).

    :param nonbonded_prior_params: settings for the non-bonded prior as
                                   specified in a config file
    :type nonbonded_prior_params: dict

    :param bead_radii: list of bead radii
    :type bead_radii: :class:`numpy.ndarray`

    :param n_structures: number of ensemble members
    :type n_structures: int

    :returns: the non-bonded prior object with parameters set as given
              in the settings
    :rtype: :class:`.NonbondedPrior`
    
Makes the default non-bonded structural prior object.
This will either be a Boltzmann-like distribution or a
Tsallis ensemble (currently not really supported).
Makes the default non - bonded structural prior object . This will either be a Boltzmann - like distribution or a Tsallis ensemble ( currently not really supported ) .
def make_nonbonded_prior(nb_params, bead_radii, n_structures):
    from .forcefields import NBLForceField as ForceField
    forcefield = ForceField(bead_radii, float(nb_params['force_constant']))
    if not 'ensemble' in nb_params or nb_params['ensemble'] == 'boltzmann':
        from .nonbonded_prior import BoltzmannNonbondedPrior2    
        NBP = BoltzmannNonbondedPrior2('nonbonded_prior', forcefield,
                                       n_structures=n_structures, beta=1.0)
    elif nb_params['ensemble'] == 'tsallis':
        raise NotImplementedError
        from .nonbonded_prior import TsallisNonbondedPrior2
        NBP = TsallisNonbondedPrior('nonbonded_prior', bead_radii=bead_radii,
                                    force_constant=force_constant,
                                    n_structures=n_structures, q=1.0)
    return NBP
def make_nonbonded_prior ( nb_params , bead_radii , n_structures ) : from . forcefields import NBLForceField as ForceField forcefield = ForceField ( bead_radii , float ( nb_params [ 'force_constant' ] ) ) if not 'ensemble' in nb_params or nb_params [ 'ensemble' ] == 'boltzmann' : from . nonbonded_prior import BoltzmannNonbondedPrior2 NBP = BoltzmannNonbondedPrior2 ( 'nonbonded_prior' , forcefield , n_structures = n_structures , beta = 1.0 ) elif nb_params [ 'ensemble' ] == 'tsallis' : raise NotImplementedError from . nonbonded_prior import TsallisNonbondedPrior2 NBP = TsallisNonbondedPrior ( 'nonbonded_prior' , bead_radii = bead_radii , force_constant = force_constant , n_structures = n_structures , q = 1.0 ) return NBP
Makes the default non-bonded structural prior object.
Makes the default non - bonded structural prior object .
"""
    Makes the default non-bonded structural prior object.

    This will either be a Boltzmann-like distribution or a
    Tsallis ensemble (currently not really supported).

    :param nonbonded_prior_params: settings for the non-bonded prior as
                                   specified in a config file
    :type nonbonded_prior_params: dict

    :param bead_radii: list of bead radii
    :type bead_radii: :class:`numpy.ndarray`

    :param n_structures: number of ensemble members
    :type n_structures: int

    :returns: the non-bonded prior object with parameters set as given
              in the settings
    :rtype: :class:`.NonbondedPrior`
    """
the non-bonded prior object with parameters set as given
in the settings
the non - bonded prior object with parameters set as given in the settings
:class:`.NonbondedPrior`
nb_params
bead_radii
list of bead radii
list of bead radii
n_structures
number of ensemble members
number of ensemble members
nonbonded_prior_params
settings for the non-bonded prior as
specified in a config file
settings for the non - bonded prior as specified in a config file