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:
objectA 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