mythos.input.oxdna_input

oxDNA input file parser.

Attributes

INVALID_DICT_LINE

Classes

oxDNAInputData

Data loaded from an oxDNA input directory.

Functions

`_parse_numeric`(→ tuple[float \| int, bool])
`_parse_boolean`(→ tuple[bool, bool])
`_parse_value`(→ str \| float \| int \| bool)
`_parse_dict`(→ tuple[dict[str, ...)
`read`(→ dict[str, str \| float \| int \| bool])	Read an oxDNA input file.
`write_to`(→ None)	Write an oxDNA input file.
`read_box_size`(→ jax.numpy.ndarray)	Read the box size from an oxDNA configuration file.
`read_input_dir`(→ oxDNAInputData)	Load topology, temperature and box size from an oxDNA input directory.
`write`(→ None)	Write an oxDNA input file.

Module Contents

mythos.input.oxdna_input.INVALID_DICT_LINE = 'Invalid dictionary line: {}'

mythos.input.oxdna_input._parse_numeric(value: str) → tuple[float | int, bool][source]

mythos.input.oxdna_input._parse_boolean(value: str) → tuple[bool, bool][source]

mythos.input.oxdna_input._parse_value(value: str) → str | float | int | bool[source]

mythos.input.oxdna_input._parse_dict(in_line: str, lines: Iterable[str]) → tuple[dict[str, str | float | int | bool], Iterable[str]][source]

mythos.input.oxdna_input.read(input_file: pathlib.Path) → dict[str, str | float | int | bool][source]: Read an oxDNA input file.

mythos.input.oxdna_input.write_to(input_config: dict, f: io.TextIOWrapper) → None[source]: Write an oxDNA input file.

mythos.input.oxdna_input.read_box_size(conf_file: pathlib.Path) → jax.numpy.ndarray[source]

Read the box size from an oxDNA configuration file.

Parses the b = ... line from the configuration file header.

Parameters:: conf_file – Path to the oxDNA configuration (.conf / .dat) file.
Returns:: A JAX array of shape (3,) with the box dimensions.
Raises:: ValueError – If no b = ... line is found in the file.

class mythos.input.oxdna_input.oxDNAInputData[source]

Data loaded from an oxDNA input directory.

topology: The parsed topology.

kT: The simulation temperature in oxDNA energy units.

box_size: Box dimensions as a JAX array of shape (3,).

config: The full parsed input-file dictionary.

topology: mythos.input.topology.Topology

kT: float

box_size: jax.numpy.ndarray

config: dict[str, Any]

mythos.input.oxdna_input.read_input_dir(input_dir: pathlib.Path, input_file: str = 'input') → oxDNAInputData[source]

Load topology, temperature and box size from an oxDNA input directory.

Reads the oxDNA input file (or the name given by input_file), extracts the topology, simulation temperature (kT), and box dimensions from the configuration files referenced therein.

Parameters:

input_dir – Directory containing the oxDNA input files.
input_file – Name of the input file inside input_dir.

Returns:

An oxDNAInputData with the parsed values.

mythos.input.oxdna_input.write(input_config: dict, input_file: pathlib.Path) → None[source]: Write an oxDNA input file.