def from_pytraj_Trajectory(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from molsysmt.native.trajectory import Trajectory
from molsysmt.api_forms.api_pytraj_Trajectory import get_frame_from_atom
tmp_item = Trajectory()
step, time, coordinates, box = get_frame_from_atom(
item, indices=atom_indices, structure_indices=structure_indices)
tmp_item.append_structures(step=step,
time=time,
coordinates=coordinates,
box=box)
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 from_XYZ(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from molsysmt.native.trajectory import Trajectory
from molsysmt.api_forms.api_XYZ import get_coordinates_from_atom
tmp_item = Trajectory()
coordinates = get_coordinates_from_atom(
item, indices=atom_indices, structure_indices=structure_indices)
tmp_item.append_structures(coordinates=coordinates)
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 from_openexplorer_OpenExplorerReporter(item,
molecular_system=None,
atom_indices='all',
structure_indices='all'):
from molsysmt import box_shape_from_box_vectors
from molsysmt.native.trajectory import Trajectory
from numpy import array
tmp_item = Trajectory()
if item.step is not None:
tmp_item.step = array(item.step, dtype=int)
units = item.coordinates.unit
tmp_item.coordinates = array(item.coordinates._value, dtype=float)
if atom_indices is not 'all':
tmp_item.coordinates = tmp_item.coordinates[:, atom_indices, :]
if structure_indices is not 'all':
tmp_item.coordinates = tmp_item.coordinates[structure_indices, :, :]
tmp_item.coordinates = tmp_item.coordinates * units
if item.box is not None:
tmp_item.box = array(item.box._value, dtype=float)
if structure_indices is not 'all':
tmp_item.box = tmp_item.box[structure_indices, :, :]
tmp_item.box = tmp_item.box * units
tmp_item.box_shape = box_shape_from_box_vectors(tmp_item.box)
tmp_item.n_structures = tmp_item.coordinates.shape[0]
tmp_item.n_atoms = tmp_item.coordinates.shape[1]
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