mythos.energy.martini.base

Common Martini Energy Utilities.

Classes

MartiniTopology	Class representing the topology of a Martini system.
MartiniEnergyFunction	Base class for Martini energy functions.
MartiniEnergyConfiguration	Base class for Martini energy function configurations.

Functions

get_periodic(→ callable)	Return displacement function given box_size.
derive_bond_names(→ tuple[str, Ellipsis])	Derive bond names aligned with bonded_neighbors.
derive_angle_names(→ tuple[str, Ellipsis])	Derive angle names aligned with angles.

Module Contents

mythos.energy.martini.base.get_periodic(box_size: mythos.utils.types.Vector3D) → callable

Return displacement function given box_size.

mythos.energy.martini.base.derive_bond_names(residue_names: tuple[str, Ellipsis], atom_names: tuple[str, Ellipsis], bonded_neighbors: mythos.utils.types.Arr_N) → tuple[str, Ellipsis]

Derive bond names aligned with bonded_neighbors.

Each name has the form RESIDUE_BEAD1_BEAD2, e.g. DMPC_GL1_GL2.

mythos.energy.martini.base.derive_angle_names(residue_names: tuple[str, Ellipsis], atom_names: tuple[str, Ellipsis], angles: mythos.utils.types.Arr_N) → tuple[str, Ellipsis]

Derive angle names aligned with angles.

Each name has the form RESIDUE_BEAD1_BEAD2_BEAD3, e.g. DMPC_NC3_PO4_GL1.

class mythos.energy.martini.base.MartiniTopology

Class representing the topology of a Martini system.

This class contains information about the atom types, bonded interactions, and angles in the system. It can be used to construct energy functions and to interpret simulation results.

atom_types

A tuple of atom type names.

atom_names

A tuple of atom names.

residue_names

A tuple of residue names.

angles

An array of shape (n_angles, 3) containing the indices of the atoms involved in each angle.

bonded_neighbors

An array of shape (n_bonds, 2) containing the indices of the bonded pairs of atoms.

atom_types: tuple[str, Ellipsis]

atom_names: tuple[str, Ellipsis]

residue_names: tuple[str, Ellipsis]

angles: mythos.utils.types.Arr_N

bonded_neighbors: mythos.utils.types.Arr_N

classmethod from_universe(universe: MDAnalysis.Universe) → MartiniTopology

Create a MartiniTopology from a Universe object.

classmethod from_tpr(tpr_file: pathlib.Path) → MartiniTopology

Create a MartiniTopology from a TPR format topology file.

property bond_names: tuple[str, Ellipsis]

Return bond names based on atom names and bonded neighbors.

property angle_names: tuple[str, Ellipsis]

Return angle names based on atom names and angles.

class mythos.energy.martini.base.MartiniEnergyFunction

Bases: mythos.energy.base.BaseEnergyFunction

Base class for Martini energy functions.

atom_types: tuple[str, Ellipsis]

atom_names: tuple[str, Ellipsis]

residue_names: tuple[str, Ellipsis]

angles: mythos.utils.types.Arr_N

displacement_fn: callable

__post_init__(topology: None = None) → None

classmethod from_topology(topology: MartiniTopology, **kwargs) → MartiniEnergyFunction

Create an energy function from a MartiniTopology.

property bond_names: tuple[str, Ellipsis]

Return bond names based on atom names and bonded neighbors.

property angle_names: tuple[str, Ellipsis]

Return angle names based on atom names and angles.

class mythos.energy.martini.base.MartiniEnergyConfiguration(couplings: dict[str, list[str]] | None = None, **kwargs)

Base class for Martini energy function configurations.

Given the large size and sparse inclusion of parameters in Martini models, this class implements parameters as a dictionary while supporting operations of configuration classes used in EnergyFunction.

This class also supports parameter coupling, where a single proxy parameter controls multiple underlying parameters. Couplings should be provided as a dictionary of lists, where each key is a proxy parameter name and the value is a list of target parameter names that it controls. The params field of this will be populated with the expanded parameters.

Subclasses can override __post_init__ for additional initialization logic. Parameters will be available in self.params after initialization.

couplings

reversed_couplings

params

__post_init__() → None

Hook for additional initialization in subclasses.

init_params() → MartiniEnergyConfiguration

Dependent params initialization. Default to no-op.

property opt_params: dict[str, any]

Returns the parameters to optimize.

__getitem__(key: str) → any

__contains__(key: str) → bool

__or__(other: MartiniEnergyConfiguration) → MartiniEnergyConfiguration

Merge two configurations, with other taking precedence.