mythos.energy.martini.m3

Martini2 energy functions.

Submodules

mythos.energy.martini.m3.angle

Classes

`AngleConfiguration`	Configuration for Martini angle energy function.
`Bond`	Bond potential energy function for Martini 2.
`BondConfiguration`	Configuration for Martini bond energy function.
`Angle`	Angle energy function for Martini3.

Package Contents

class mythos.energy.martini.m3.AngleConfiguration(couplings: dict[str, list[str]] | None = None, **kwargs)[source]

Bases: mythos.energy.martini.base.MartiniEnergyConfiguration

Configuration for Martini angle energy function.

Angle params must be provided as “angle_k_I_J_K” and “angle_theta0_I_J_K” in corresponding pairs for each angle name in the system. NAME should be in the format of “MOLTYPE_ATOMNAME1_ATOMNAME2_ATOMNAME3”, e.g., “DMPC_NC3_PO4_GL1”.

__post_init__() → None[source]: Hook for additional initialization in subclasses.

class mythos.energy.martini.m3.Bond[source]

Bases: mythos.energy.martini.base.MartiniEnergyFunction

Bond potential energy function for Martini 2.

params: BondConfiguration

__post_init__(topology: None = None) → None[source]

compute_energy(trajectory: mythos.simulators.io.SimulatorTrajectory) → float[source]: Compute the energy of the system given the nucleotide.

class mythos.energy.martini.m3.BondConfiguration(couplings: dict[str, list[str]] | None = None, **kwargs)[source]

Bases: mythos.energy.martini.base.MartiniEnergyConfiguration

Configuration for Martini bond energy function.

Bond params must be provided as “bond_k_NAME” and “bond_r0_NAME” in corresponding pairs for each bond name in the system. NAME should be in the format of “MOLTYPE_ATOMNAME1_ATOMNAME2”, e.g., “DMPC_NC3_PO4”.

__post_init__() → None[source]: Hook for additional initialization in subclasses.

class mythos.energy.martini.m3.Angle[source]

Bases: mythos.energy.martini.m2.angle.Angle

Angle energy function for Martini3.

use_G96: ClassVar[bool] = False