openmmio.py File Reference

Go to the source code of this file.

Namespaces
	src.openmmio
	forcebalance.openmmio
	OpenMM input/output.

Functions
def	src.openmmio.get_mask (grps)
	Given a list of booleans [1, 0, 1] return the bitmask that sets these force groups appropriately in Context.getState(). More...
def	src.openmmio.energy_components (Sim, verbose=False)
def	src.openmmio.get_multipoles (simulation, q=None, mass=None, positions=None, rmcom=True)
	Return the current multipole moments in Debye and Buckingham units. More...
def	src.openmmio.get_dipole (simulation, q=None, mass=None, positions=None)
	Return the current dipole moment in Debye. More...
def	src.openmmio.PrepareVirtualSites (system)
	Prepare a list of function wrappers and vsite parameters from the system. More...
def	src.openmmio.ResetVirtualSites_fast (positions, vsinfo)
	Given a set of OpenMM-compatible positions and a System object, compute the correct virtual site positions according to the System. More...
def	src.openmmio.ResetVirtualSites (positions, system)
	Given a set of OpenMM-compatible positions and a System object, compute the correct virtual site positions according to the System. More...
def	src.openmmio.GetVirtualSiteParameters (system)
	Return an array of all virtual site parameters in the system. More...
def	src.openmmio.CopyAmoebaBondParameters (src, dest)
def	src.openmmio.CopyAmoebaOutOfPlaneBendParameters (src, dest)
def	src.openmmio.CopyAmoebaAngleParameters (src, dest)
def	src.openmmio.CopyAmoebaInPlaneAngleParameters (src, dest)
def	src.openmmio.CopyAmoebaVdwParameters (src, dest)
def	src.openmmio.CopyAmoebaMultipoleParameters (src, dest)
def	src.openmmio.CopyHarmonicBondParameters (src, dest)
def	src.openmmio.CopyHarmonicAngleParameters (src, dest)
def	src.openmmio.CopyPeriodicTorsionParameters (src, dest)
def	src.openmmio.CopyNonbondedParameters (src, dest)
def	src.openmmio.CopyGBSAOBCParameters (src, dest)
def	src.openmmio.CopyCustomNonbondedParameters (src, dest)
	copy whatever updateParametersInContext can update: per-particle parameters More...
def	src.openmmio.do_nothing (src, dest)
def	src.openmmio.CopySystemParameters (src, dest)
	Copy parameters from one system (i.e. More...
def	src.openmmio.UpdateSimulationParameters (src_system, dest_simulation)
def	src.openmmio.SetAmoebaVirtualExclusions (system)
def	src.openmmio.AddVirtualSiteBonds (mod, ff)
def	src.openmmio.SetAmoebaNonbondedExcludeAll (system, topology)
	Manually set the AmoebaVdwForce, AmoebaMultipoleForce to exclude all atoms belonging to the same residue. More...
def	src.openmmio.MTSVVVRIntegrator (temperature, collision_rate, timestep, system, ninnersteps=4)
	Create a multiple timestep velocity verlet with velocity randomization (VVVR) integrator. More...

Variables
	src.openmmio.logger = getLogger(__name__)