"""oxDNA1 energy implementation in mythos."""
import functools
from types import MappingProxyType
from mythos.energy import DEFAULT_DISPLACEMENT
from mythos.energy.base import BaseEnergyFunction, ComposedEnergyFunction, EnergyFunction
from mythos.energy.configuration import BaseConfiguration
from mythos.energy.dna1.bonded_excluded_volume import BondedExcludedVolume, BondedExcludedVolumeConfiguration
from mythos.energy.dna1.coaxial_stacking import CoaxialStacking, CoaxialStackingConfiguration
from mythos.energy.dna1.cross_stacking import CrossStacking, CrossStackingConfiguration
from mythos.energy.dna1.fene import Fene, FeneConfiguration
from mythos.energy.dna1.hydrogen_bonding import HydrogenBonding, HydrogenBondingConfiguration
from mythos.energy.dna1.nucleotide import Nucleotide
from mythos.energy.dna1.stacking import Stacking, StackingConfiguration
from mythos.energy.dna1.unbonded_excluded_volume import UnbondedExcludedVolume, UnbondedExcludedVolumeConfiguration
from mythos.energy.utils import default_configs_for
from mythos.input.topology import Topology
from mythos.utils.types import PyTree
[docs]
def default_configs() -> tuple[PyTree, PyTree]:
"""Return the default simulation and energy configurations for dna1."""
return default_configs_for("dna1")
def default_energy_configs(
overrides: dict = MappingProxyType({}), opts: dict = MappingProxyType({})
) -> list[BaseConfiguration]:
"""Return the default configurations for the energy functions."""
default_sim_config, default_config = default_configs()
def get_param(x: str) -> dict:
return default_config[x] | overrides.get(x, {})
def get_opts(x: str, defaults: tuple[str] = BaseConfiguration.OPT_ALL) -> tuple[str]:
return opts.get(x, defaults)
default_stacking_opts = tuple(set(default_config["stacking"].keys()) - {"kT", "ss_stack_weights"})
return [
FeneConfiguration.from_dict(get_param("fene"), get_opts("fene")),
BondedExcludedVolumeConfiguration.from_dict(
get_param("bonded_excluded_volume"), get_opts("bonded_excluded_volume")
),
StackingConfiguration.from_dict(
get_param("stacking") | {"kt": overrides.get("kT", default_sim_config["kT"])},
get_opts("stacking", default_stacking_opts),
),
UnbondedExcludedVolumeConfiguration.from_dict(
get_param("unbonded_excluded_volume"), get_opts("unbonded_excluded_volume")
),
HydrogenBondingConfiguration.from_dict(get_param("hydrogen_bonding"), get_opts("hydrogen_bonding")),
CrossStackingConfiguration.from_dict(get_param("cross_stacking"), get_opts("cross_stacking")),
CoaxialStackingConfiguration.from_dict(get_param("coaxial_stacking"), get_opts("coaxial_stacking")),
]
[docs]
def default_energy_fns() -> list[BaseEnergyFunction]:
"""Return the default energy functions."""
return [
Fene,
BondedExcludedVolume,
Stacking,
UnbondedExcludedVolume,
HydrogenBonding,
CrossStacking,
CoaxialStacking,
]
def default_transform_fn() -> callable:
"""Return the default transform function for dna1 simulations."""
_, default_config = default_configs()
geometry = default_config["geometry"]
return functools.partial(
Nucleotide.from_rigid_body,
com_to_backbone=geometry["com_to_backbone"],
com_to_hb=geometry["com_to_hb"],
com_to_stacking=geometry["com_to_stacking"],
)
def create_default_energy_fn(topology: Topology, displacement_fn: callable = DEFAULT_DISPLACEMENT) -> EnergyFunction:
"""Create the default oxDNA1 energy function.
This creates the composed energy function from the default set of function
classes, associated configs, and the default transform function - built for
the provided topology and displacement function.
Args:
topology: The topology of the system.
displacement_fn: The displacement function to use. defaults to
DEFAULT_DISPLACEMENT.
"""
return ComposedEnergyFunction.from_lists(
energy_fns=default_energy_fns(),
energy_configs=default_energy_configs(),
transform_fn=default_transform_fn(),
displacement_fn=displacement_fn,
topology=topology,
)
__all__ = [
"Nucleotide",
"Fene",
"FeneConfiguration",
"HydrogenBonding",
"HydrogenBondingConfiguration",
"Stacking",
"StackingConfiguration",
"CoaxialStacking",
"CoaxialStackingConfiguration",
"CrossStacking",
"CrossStackingConfiguration",
"BondedExcludedVolume",
"BondedExcludedVolumeConfiguration",
"UnbondedExcludedVolume",
"UnbondedExcludedVolumeConfiguration",
"default_configs",
"default_energy_fns",
]