mythos.input.gromacs_input

GROMACS input file parser.

Handles reading and writing of GROMACS .mdp (molecular dynamics parameter) files. The format is a simple key = value format, similar to oxDNA input files.

Attributes

logger
ParamsDict
INVALID_LINE

Classes

GromacsParamsParser

Parser and parameter replacer for params in GROMACS topology files.

Functions

_parse_numeric(→ tuple[float | int, bool])	Try to parse a value as a numeric type.
_parse_boolean(→ tuple[bool, bool])	Try to parse a value as a boolean.
_parse_value(→ str | float | int | bool)	Parse a value string, handling comments and type inference.
read_mdp(→ dict[str, str | float | int | bool])	Read a GROMACS .mdp input file.
write_mdp_to(→ None)	Write a GROMACS .mdp input configuration to a file handle.
write_mdp(→ None)	Write a GROMACS .mdp input file.
update_mdp_params(→ None)	Update parameters in a GROMACS .mdp file.
read_params_from_topology(→ dict[str, ParamsDict])	Read a preprocessed GROMACS topology file.
replace_params_in_topology(→ None)	Write a modified GROMACS topology file with replaced parameters.

Module Contents

mythos.input.gromacs_input.logger

type mythos.input.gromacs_input.ParamsDict = dict[str, float]

mythos.input.gromacs_input.INVALID_LINE = 'Invalid line: {}'

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

Try to parse a value as a numeric type.

mythos.input.gromacs_input._parse_boolean(value: str) → tuple[bool, bool]

Try to parse a value as a boolean.

mythos.input.gromacs_input._parse_value(value: str) → str | float | int | bool

Parse a value string, handling comments and type inference.

mythos.input.gromacs_input.read_mdp(input_file: pathlib.Path) → dict[str, str | float | int | bool]

Read a GROMACS .mdp input file.

Parameters:

input_file – Path to the .mdp file.

Returns:

Dictionary of key-value pairs from the input file.

mythos.input.gromacs_input.write_mdp_to(input_config: dict, f: io.TextIOWrapper) → None

Write a GROMACS .mdp input configuration to a file handle.

Parameters:

• input_config – Dictionary of configuration key-value pairs.

• f – File handle to write to.

mythos.input.gromacs_input.write_mdp(input_config: dict, input_file: pathlib.Path) → None

Write a GROMACS .mdp input file.

Parameters:

• input_config – Dictionary of configuration key-value pairs.

• input_file – Path to write the .mdp file.

mythos.input.gromacs_input.update_mdp_params(mdp_file: pathlib.Path, params: dict, out_file: pathlib.Path | None = None) → None

Update parameters in a GROMACS .mdp file.

Parameters:

• mdp_file – Path to the .mdp file to update.

• params – Dictionary of parameters to update.

• out_file – Optional path to write the updated .mdp file. By default overwrites the original file.

class mythos.input.gromacs_input.GromacsParamsParser(filename: str | pathlib.Path)

Parser and parameter replacer for params in GROMACS topology files.

Reads in a preprocessed topology file, extracts parameters into structured dictionaries. When writing, it replaces parameters in the original file with values from a provided dictionary, preserving other content.

In both cases, it is important the topology file is preprocessed to in order that macros have been expanded.

file

_parser_init() → None

parse() → dict[str, ParamsDict]

Parse topology content and return structured data.

Returns:

Dictionary with keys ‘nonbond_params’, ‘bond_params’, ‘angle_params’, each mapping parameter names to values.

Raises:

ValueError – If nonbond_params references unknown atom types.

replace(params: ParamsDict, output_file: str | pathlib.Path) → None

Write topology with replaced parameters to a new file.

Reads the original topology file and writes a new file with parameters replaced from the provided dictionary.

Parameters:

• params – Dictionary mapping parameter names to new values. Keys should match the format from parse(): - “bond_k_MOLNAME_ATOMI_ATOMJ”, “bond_r0_MOLNAME_ATOMI_ATOMJ” - “angle_k_MOLNAME_ATOMI_ATOMJ_ATOMK”, “angle_theta0_MOLNAME_ATOMI_ATOMJ_ATOMK” - “lj_sigma_TYPE1_TYPE2”, “lj_epsilon_TYPE1_TYPE2”

• output_file – Path to write the modified topology.

_process_line(line: str) → None

_handle_section_header(stripped: str) → None

_handle_section_data(stripped: str, original_line: str) → None

_handle_molecule_section_data(section: str | None, parts: list[str], original_line: str) → str

_handle_nonbond_params(parts: list[str], original_line: str) → str

mythos.input.gromacs_input.read_params_from_topology(topology_file: pathlib.Path) → dict[str, ParamsDict]

Read a preprocessed GROMACS topology file.

This parses the [atomtypes] section to get bead types, the [nonbond_params] section for nonbonded parameters, and all [moleculetype] sections for bonds and angles.

Parameters are stored with descriptive keys: - Bonds: “bond_k_MOLNAME_ATOMI_ATOMJ” and “bond_r0_MOLNAME_ATOMI_ATOMJ” - Angles: “angle_k_MOLNAME_ATOMI_ATOMJ_ATOMK” and “angle_theta0_MOLNAME_ATOMI_ATOMJ_ATOMK” - Nonbonded: “lj_sigma_TYPE1_TYPE2” and “lj_epsilon_TYPE1_TYPE2”

Parameters:

topology_file – Path to the preprocessed topology file.

Returns:

Dictionary with keys ‘nonbond_params’, ‘bond_params’, ‘angle_params’.

mythos.input.gromacs_input.replace_params_in_topology(topology_file: pathlib.Path, params: ParamsDict, output_file: pathlib.Path) → None

Write a modified GROMACS topology file with replaced parameters.

Reads an existing topology file and writes a new file with parameters replaced from the provided dictionary.

Parameters:

• topology_file – Path to the input preprocessed topology file.

• params – Dictionary mapping parameter names to new values.

• output_file – Path to write the modified topology.