def from_openmm_Simulation(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from molsysmt.native.molsys import MolSys
from molsysmt.native.io.topology import from_openmm_Simulation as molsysmt_Topology_from_openmm_Simulation
from molsysmt.native.io.trajectory import from_openmm_Simulation as molsysmt_Structures_from_openmm_Simulation
tmp_item = MolSys()
tmp_item.topology, _ = molsysmt_Topology_from_openmm_Simulation(
item,
molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices)
tmp_item.trajectory, _ = molsysmt_Structures_from_openmm_Simulation(
item,
molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices)
if tmp_molecular_system is not None:
tmp_molecular_system = molecular_system.combine_with_items(
tmp_item,
atom_indices=atom_indices,
structure_indices=structure_indices)
else:
tmp_molecular_system = None
return tmp_item, tmp_molecular_system
def from_pytraj_Trajectory(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from molsysmt.native.molsys import MolSys
from molsysmt.native.io.topology import from_pytraj_Trajectory as pytraj_Trajectory_to_molsysmt_Topology
from molsysmt.native.io.trajectory import from_pytraj_Trajectory as pytraj_Trajectory_to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology, _ = pytraj_Trajectory_to_molsysmt_Topology(
item, atom_indices=atom_indices, structure_indices=structure_indices)
tmp_item.trajectory, _ = pytraj_Trajectory_to_molsysmt_Structures(
item, atom_indices=atom_indices, structure_indices=structure_indices)
if molecular_system is not None:
tmp_molecular_system = molecular_system.combine_with_items(
tmp_item,
atom_indices=atom_indices,
structure_indices=structure_indices)
else:
tmp_molecular_system = None
return tmp_item, tmp_molecular_system