def to_mdtraj_Trajectory(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from openmm.unit import nanometers
from mdtraj.core.trajectory import Trajectory as mdtraj_Trajectory
tmp_topology, _ = to_mdtraj_Topology(item,
molecular_system,
atom_indices=atom_indices,
structure_indices=structure_indices)
coordinates = get_coordinates_from_atom(
item, indices=atom_indices, structure_indices=structure_indices)
coordinates = coordinates.in_units_of(nanometers)._value
tmp_item = mdtraj_Trajectory(coordinates, tmp_topology)
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_mdtraj_Trajectory(item, atom_indices='all', check=True):
if check:
try:
is_pdbfixer_PDBFixer(item)
except:
raise WrongFormError('pdbfixer.PDBFixer')
try:
atom_indices = digest_atom_indices(atom_indices)
except:
raise WrongAtomIndicesError()
try:
from mdtraj.core.trajectory import Trajectory as mdtraj_Trajectory
except:
raise LibraryNotFoundError('MDTraj')
from molsysmt import puw
from . import to_mdtraj_Topology
from . import get_coordinates_from_atom
tmp_item = to_mdtraj_Topology(item, atom_indices=atom_indices, check=False)
coordinates = get_coordinates_from_atom(tmp_item,
indices=atom_indices,
check=False)
coordinates = puw.convert(coordinates,
to_units='nanometer',
to_form='openmm.unit')
tmp_item = mdtraj_Trajectory(coordinates, tmp_item)
return tmp_item
def to_mdtraj_Trajectory(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)
try:
from mdtraj.core.trajectory import Trajectory as mdtraj_Trajectory
except:
raise LibraryNotFound('MDTraj')
from . import to_mdtraj_Topology
from ..mdtraj_Trajectory import extract as extract_mdtraj_Trajectory
from molsysmt import puw
tmp_topology = to_mdtraj_Topology(item, check=False)
positions = puw.get_value(item.positions, to_unit='nanometers')
tmp_item = mdtraj_Trajectory(positions, tmp_topology)
tmp_item = extract_mdtraj_Trajectory(tmp_item, atom_indices=atom_indices,
structure_indices=structure_indices, copy_if_all=False,
check=False)
return tmp_item
def to_mdtraj_Trajectory(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'molsysmt.MolSys')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from molsysmt import puw
from . import to_mdtraj_Topology
from . import get_box_lengths_from_system, get_box_angles_from_system, get_coordinates_from_atom, get_time_from_system
try:
from mdtraj.core.trajectory import Trajectory as mdtraj_Trajectory
except:
raise LibraryNotFound('mdtraj')
tmp_item_topology = to_mdtraj_Topology(item,
atom_indices=atom_indices,
check=False)
tmp_box_lengths = get_box_lengths_from_system(
item, structure_indices=structure_indices, check=False)
if tmp_box_lengths is not None:
tmp_box_lengths = puw.get_value(tmp_box_lengths, to_unit='nm')
tmp_box_angles = get_box_angles_from_system(
item, structure_indices=structure_indices, check=False)
if tmp_box_angles is not None:
tmp_box_angles = puw.get_value(tmp_box_angles, to_unit='degrees')
tmp_coordinates = get_coordinates_from_atom(
item,
indices=atom_indices,
structure_indices=structure_indices,
check=False)
tmp_coordinates = puw.get_value(tmp_coordinates, to_unit='nm')
tmp_time = get_time_from_system(item,
structure_indices=structure_indices,
check=False)
if tmp_time is not None:
tmp_time = puw.get_value(tmp_time, to_unit='ps')
tmp_item = mdtraj_Trajectory(tmp_coordinates,
tmp_item_topology,
tmp_time,
unitcell_lengths=tmp_box_lengths,
unitcell_angles=tmp_box_angles)
return tmp_item
def to_mdtraj_Trajectory(item,
atom_indices='all',
structure_indices='all',
check=True):
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 .to_mdtraj_Topology import to_mdtraj_Topology
from .get import get_coordinates_from_atom
try:
from mdtraj.core.trajectory import Trajectory as mdtraj_Trajectory
except:
raise LibraryNotFoundError()
topology = to_mdtraj_Topology(item, atom_indices=atom_indices)
coordinates = get_coordinates_from_atom(
item,
indices=atom_indices,
structure_indices=structure_indices,
check=False)
tmp_item = mdtraj_Trajectory(positions, topology)
return tmp_item