def to_molsysmt_MolSys(item,
selection='all',
structure_indices='all',
syntaxis='MolSysMT'):
if check:
digest_item(item, 'openmm.GromacsGroFile')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from molsysmt.native.molsys import MolSys
from .to_molsysmt_Topology import to_molsysmt_Topology
from .to_molsysmt_Structures import to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
tmp_item.structures = to_molsysmt_Structures(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
return tmp_item
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 to_molsysmt_MolSys(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'pytraj.Trajectory')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from molsysmt.native.molsys import MolSys
from . import to_molsysmt_Topology
from . import to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(item,
atom_indices=atom_indices,
check=False)
tmp_item.structures = to_molsysmt_Structures(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
return tmp_item
def to_molsysmt_MolSys(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'openmm.Modeller')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from molsysmt.native.molsys import MolSys
from . import to_molsysmt_Topology
from . import to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(item, atom_indices=atom_indices)
tmp_item.structures = to_molsysmt_Structures(
item, atom_indices=atom_indices, structure_indices=structure_indices)
return tmp_item
def to_molsysmt_MolSys(item, atom_indices='all', check=True):
if check:
digest_item(item, 'pdbfixer.PDBFixer')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from molsysmt.native.molsys import MolSys
from . import to_molsysmt_Topology
from . import to_molsysmt_Structures as pdbfixer_PDBFixer_to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(item,
atom_indices=atom_indices,
check=False)
tmp_item.structures = pdbfixer_PDBFixer_to_molsysmt_Structures(
item, atom_indices=atom_indices, check=False)
return tmp_item
def to_molsysmt_MolSys(item,
selection='all',
structure_indices='all',
syntaxis='MolSysMT'):
if check:
try:
is_openmm_PDBFile(item)
except:
raise WrongFormError('openmm.PDBFile')
try:
atom_indices = digest_atom_indices(atom_indices)
except:
raise WrongAtomIndicesError()
try:
structure_indices = digest_structure_indices(structure_indices)
except:
raise WrongStructureIndicesError()
from molsysmt.native.molsys import MolSys
from .to_molsysmt_Topology import to_molsysmt_Topology
from .to_molsysmt_Structures import to_molsysmt_Structures
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
tmp_item.structures = to_molsysmt_Structures(
item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
return tmp_item
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
def to_molsysmt_MolSys(item, atom_indices='all', coordinates=None, box=None, check=True):
if check:
try:
is_openmm_Topology(item)
except:
raise WrongFormError('openmm.Topology')
try:
atom_indices = digest_atom_indices(atom_indices)
except:
raise WrongAtomIndicesError()
try:
coordinates = digest_coordinates(coordinates)
except:
raise WrongCoordinatesError()
try:
box = digest_box(box)
except:
raise WrongBoxError()
from molsysmt.native.molsys import MolSys
from molsysmt.native.structures import Structures
from . import to_molsysmt_Topology as to_molsysmt_Topology
from . import get_box_from_system
tmp_item = MolSys()
tmp_item.topology = to_molsysmt_Topology(item, atom_indices=atom_indices, check=False)
tmp_item.structures = Structures()
if box is None:
box = get_box_from_system(item)
tmp_item.structures.append_structures(coordinates=coordinates, box=box)
return tmp_item