meld.system.builders.spec.SystemSpec

class meld.system.builders.spec.SystemSpec(solvation, system, topology, integrator, barostat, coordinates, velocities, box_vectors, builder_info=None)[source]

Bases: object

A system specification.

solvation

implicit or explicit

Type

str

system

the system to be modeled

Type

openmm.openmm.System

topology

the topology of the system

Type

openmm.app.topology.Topology

integrator

the integrator to be used

Type

openmm.openmm.LangevinIntegrator

barostat

the barostat to be used

Type

Optional[openmm.openmm.MonteCarloBarostat]

coordinates

the initial coordinates of the system

Type

numpy.ndarray

velocities

the initial velocities of the system

Type

numpy.ndarray

box_vectors

the box vectors of the system

Type

Optional[numpy.ndarray]

builder_info

extra information about how the system was built

Type

dict

__init__(solvation, system, topology, integrator, barostat, coordinates, velocities, box_vectors, builder_info=None)[source]

Methods

__init__(solvation, system, topology, ...[, ...])

finalize()

Finalize the system specification.

Attributes

solvation

system

topology

integrator

barostat

coordinates

velocities

box_vectors

builder_info

finalize()[source]

Finalize the system specification.

Return type

System

Returns

The system described by this specification.