Source code for molsysmt.form.file_pdb.to_openmm_Simulation

from molsysmt._private.digestion import digest



@digest(form='file:pdb')
def to_openmm_Simulation(item, atom_indices='all', structure_indices='all',
                     forcefield=None, non_bonded_method='no_cutoff', non_bonded_cutoff='1.0 nm', constraints=None,
                     rigid_water=True, remove_cm_motion=True, hydrogen_mass=None, switch_distance=None,
                     flexible_constraints=False, integrator='Langevin', temperature='300.0 K',
                     collisions_rate='1.0 1/ps', integration_timestep='2.0 fs', platform='CUDA', skip_digestion=False):

    from . import to_openmm_Modeller
    from ..openmm_Modeller import to_openmm_Simulation as openmm_Modeller_to_openmm_Simulation

    tmp_item = to_openmm_Modeller(item, atom_indices=atom_indices, structure_indices=structure_indices,
                                  skip_digestion=True)
    tmp_item = openmm_Modeller_to_openmm_Simulation(tmp_item,
                         forcefield=forcefield, non_bonded_method=non_bonded_method,
                         non_bonded_cutoff=non_bonded_cutoff, constraints=constraints,
                         rigid_water=rigid_water, remove_cm_motion=remove_cm_motion,
                         hydrogen_mass=hydrogen_mass, switch_distance=switch_distance,
                         flexible_constraints=flexible_constraints, integrator=integrator,
                         temperature=temperature, collisions_rate=collisions_rate,
                         integration_timestep=integration_timestep, platform=platform, skip_digestion=True)

    return tmp_item