jax_dna.simulators.oxdna

oxDNA simulator module.

Submodules

• jax_dna.simulators.oxdna.oxdna
• jax_dna.simulators.oxdna.utils

Attributes

BIN_PATH_ENV_VAR
BUILD_PATH_ENV_VAR
CMAKE_BIN_ENV_VAR
ERR_BIN_PATH_NOT_SET
ERR_BUILD_PATH_NOT_SET
ERR_BUILD_SETUP_FAILED
ERR_INPUT_FILE_NOT_FOUND
ERR_MISSING_REQUIRED_KEYS
MAKE_BIN_ENV_VAR

Classes

oxDNABinarySemaphore	A semaphore for the oxDNA binary.
oxDNABinarySemaphoreActor	A ray actor wrapped oxDNA binary semaphore.
oxDNASimulator	A sampler base on running an oxDNA simulation.

Functions

_guess_binary_location(→ pathlib.Path | None)

Guess the location of a binary.

Package Contents

jax_dna.simulators.oxdna.BIN_PATH_ENV_VAR = 'OXDNA_BIN_PATH'

jax_dna.simulators.oxdna.BUILD_PATH_ENV_VAR = 'OXDNA_BUILD_PATH'

jax_dna.simulators.oxdna.CMAKE_BIN_ENV_VAR = 'CMAKE_BIN_PATH'

jax_dna.simulators.oxdna.ERR_BIN_PATH_NOT_SET = 'OXDNA_BIN_PATH environment variable not set'

jax_dna.simulators.oxdna.ERR_BUILD_PATH_NOT_SET = 'OXDNA_BUILD_PATH environment variable not set'

jax_dna.simulators.oxdna.ERR_BUILD_SETUP_FAILED = 'OXDNA build setup failed wiht return code: {}'

jax_dna.simulators.oxdna.ERR_INPUT_FILE_NOT_FOUND = 'Input file not found: {}'

jax_dna.simulators.oxdna.ERR_MISSING_REQUIRED_KEYS = 'Missing required keys: {}'

jax_dna.simulators.oxdna.MAKE_BIN_ENV_VAR = 'MAKE_BIN_PATH'

jax_dna.simulators.oxdna._guess_binary_location(bin_name: str, env_var: str) → pathlib.Path | None

Guess the location of a binary.

class jax_dna.simulators.oxdna.oxDNABinarySemaphore

A semaphore for the oxDNA binary.

_ready = False

check() → bool

Check if the semaphore is ready.

set(ready: bool) → None

Set the value of the semaphore.

class jax_dna.simulators.oxdna.oxDNABinarySemaphoreActor

Bases: oxDNABinarySemaphore

A ray actor wrapped oxDNA binary semaphore.

class jax_dna.simulators.oxdna.oxDNASimulator

Bases: jax_dna.simulators.base.BaseSimulation

A sampler base on running an oxDNA simulation.

input_dir: str

sim_type: jax_dna.utils.types.oxDNASimulatorType

energy_configs: list[jax_dna.energy.configuration.BaseConfiguration] | None = None

n_build_threads: int = 4

logger_config: dict[str, Any] | None = None

disable_build: bool = False

check_build_ready: collections.abc.Callable[[None], bool]

set_build_ready: collections.abc.Callable[[bool], None]

build_wait_interval: int = 15

__post_init__(*args, **kwds) → None

Check the validity of the configuration.

_initialize_logger() → None

run(opt_params: list[jax_dna.utils.types.Params] | None = None, seed: numpy.ndarray | None = None, **kwargs) → jax_dna.input.trajectory.Trajectory

Run an oxDNA simulation.

_update_params(*, new_params: list[dict]) → None

Update the simulation.

This function will recompile the oxDNA binary with the new parameters.

_restore_params() → None

Restore the original parameters.