cgexplore.forcefields.AssignedSystem¶

class cgexplore.forcefields.AssignedSystem(molecule, forcefield_terms, system_xml, topology_xml, bead_set, vdw_bond_cutoff, mass=10)[source]¶

Bases: object

A system with forces assigned.

Methods

`get_openmm_system`	Return OpenMM.System object.
`get_openmm_topology`	Return OpenMM.Topology object.

Attributes

`molecule`
`forcefield_terms`
`system_xml`
`topology_xml`
`bead_set`
`vdw_bond_cutoff`
`mass`

Parameters:

molecule (Molecule)
forcefield_terms (dict[str, Sequence[Bond | Angle | CosineAngle | Torsion | Nonbonded]])
system_xml (Path)
topology_xml (Path)
bead_set (BeadLibrary)
vdw_bond_cutoff (int)
mass (float)

get_openmm_system()[source]¶

Return OpenMM.System object.

Return type:: System

get_openmm_topology()[source]¶

Return OpenMM.Topology object.

Return type:: Topology

bead_set: BeadLibrary¶

forcefield_terms: dict[str, Sequence[Bond | Angle | CosineAngle | Torsion | Nonbonded]]¶

mass: float¶

molecule: Molecule¶

system_xml: Path¶

topology_xml: Path¶

vdw_bond_cutoff: int¶