def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
return None
def set_coordinates_to_system(item, indices='all', structure_indices='all', value=None, check=True):
if check:
_digest_item(item, 'molsysmt.MolSys')
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
return set_coordinates_to_atom(item, indices='all', structure_indices=structure_indices,
value=value, check=False)
def set_box_to_system(item, indices='all', structure_indices='all', value=None, check=True):
if check:
_digest_item(item, 'molsysmt.MolSys')
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
item.trajectory.box = value
pass
def set_atom_name_to_atom(item, indices='all', structure_indices='all', value=None, check=True):
if check:
_digest_item(item, 'molsysmt.MolSys')
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from ..molsysmt_Topology import set_atom_name_to_atom as aux_set
return aux_set(item.topology, indices=indices, structure_indices=structure_indices, value=value, check=True)
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
if structure_indices is 'all':
output = item.step
else:
output = item.step[structure_indices]
return output
def get_coordinates_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
if structure_indices is 'all':
output = item.coordinates
else:
output = item.coordinates[structure_indices, :, :]
return output
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
raise NotImplementedMethodError()
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
box = item.getPeriodicBoxVectors()
unit = _puw.get_unit(box)
box = _np.expand_dims(puw.get_value(box), axis=0)
box = _puw.standardize(box * unit)
return box
def get_box_angles_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
tmp_box_angles = item.get_box_angles()
if structure_indices is 'all':
output = tmp_box_angles
else:
output = tmp_box_angles[structure_indices, :]
return output
def get_time_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
output = _puw.quantity(item.time, unit='ps')
if structure_indices is not 'all':
output = output[structure_indices]
return output
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
box = getBoxVectors(asNumpy=True)
unit = _puw.get_unit(box)
box = _np.expand_dims(box, axis=0)
box = _puw.standardize(box * unit)
return box
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from .to_molsysmt_MolSys import to_molsysmt_MolSys
from ..molsysmt_MolSys import get_step_from_system as aux_get
tmp_item = to_molsysmt_MolSys(item, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_openmm_AmberInpcrdFile
from ..openmm_AmberInpcrdFile import get_step_from_system as aux_get
tmp_item = to_openmm_AmberInpcrdFile(item, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_openmm_Topology
from ..openmm_Topology import get_box_from_system as aux_get
tmp_item = to_openmm_Topology(item, structure_indices=structure_indices, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_string_pdb_text
from ..string_pdb_text import get_step_from_system as aux_get
tmp_item = to_string_pdb_text(item, check=False)
output = aux_get(tmp_item, check=False)
return output
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
output = None
if item.box is not None:
if structure_indices is 'all':
output = item.box
else:
output = item.box[structure_indices, :, :]
return output
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_mdtraj_XTCTrajectoryFile
from ..mdtraj_XTCTrajectoryFile import get_step_from_system as aux_get
tmp_item = to_mdtraj_XTCTrajectoryFile(item, check=False)
output = aux_get(tmp_item, structure_indices=structure_indices, check=False)
return output
def set_atom_name_to_atom(item,
indices='all',
structure_indices='all',
value=None,
check=True):
if check:
_digest_item(item, 'molsysmt.Topology')
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
item.atoms_dataframe.loc[indices, 'atom_name'] = value
pass
def get_box_shape_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt.pbc import box_shape_from_box_vectors
output = None
box = get_box_from_system(item,
structure_indices=structure_indices,
check=False)
if box is not None:
output = box_shape_from_box_vectors(box)
return output
def get_coordinates_from_atom(item, indices='all', structure_indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
coordinates= _puw.quantity(item.xyz * 0.1, unit='nm')
if indices is not 'all':
coordinates = coordinates[:, atom_indices, :]
if structure_indices is not 'all':
coordinates = coordinates[structure_indices,:,:]
return coordinates
def get_step_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(indices)
from . import to_mmtf_MMTFDecoder
from ..mmtf_MMTFDecoder import get_step_from_system as aux_get
tmp_item = to_mmtf_MMTFDecoder(item, check=False)
output = aux_get(tmp_item,
structure_indices=structure_indices,
check=False)
return output
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from .to_molsysmt_MolSys import to_molsysmt_MolSys
from ..molsysmt_MolSys import get_coordinates_from_atom as aux_get
tmp_item = to_molsysmt_MolSys(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt.pbc import box_vectors_from_box_lengths_and_angles
lengths = _puw.quantity(item.unitcells[:,0:3]*0.1, unit='nm')
angles = _puw.quantity(item.unitcells[:,3:6], unit='degrees')
if structure_indices is not 'all':
lengths = lengths[structure_indices,:]
angles = angles[structure_indices,:]
output = box_vectors_from_box_lengths_and_angles(lengths, angles)
return output
def get_box_from_system(item, structure_indices='all', check=True):
if check:
_digest_item(item, _form)
structure_indices = _digest_structure_indices(structure_indices)
box = item.getPeriodicBoxVectors()
output = None
if box is not None:
unit = _puw.get_unit(box)
box = _np.array(_puw.get_value(box))
box = box.reshape(1, box.shape[0], box.shape[1])
box = box * unit
output = _puw.standardize(box)
return output
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
tmp_coordinates = item.coordinates
if structure_indices is not 'all':
tmp_coordinates = tmp_coordinates[structure_indices, :, :]
if indices is not 'all':
tmp_coordinates = tmp_coordinates[:, indices, :]
return tmp_coordinates
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_openmm_GromacsGroFile
from ..openmm_GromacsGroFile import get_coordinates_from_atom as aux_get
tmp_item = to_openmm_GromacsGroFile(item, check=False)
output = aux_get(tmp_item,
indices=indices,
structure_indices=structure_indices,
check=False)
return output
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from . import to_mdtraj_Trajectory
from ..mdtraj_Trajectory import get_coordinates_from_atom as aux_get
tmp_item = to_mdtraj_Trajectory(item, check=False)
output = aux_get(tmp_item,
indices=indices,
structure_indices=structure_indices,
check=False)
return output
def get_coordinates_from_atom(item,
indices='all',
structure_indices='all',
check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
from molsysmt._private.math import serie_to_chunks
if structure_indices is 'all':
n_structures = get_n_structures_from_system(item)
structure_indices = _np.arange(n_structures)
starts_serie_frames, size_serie_frames = serie_to_chunks(structure_indices)
xyz_list = []
for start, size in zip(starts_serie_frames, size_serie_frames):
item.seek(start)
if indices is 'all':
xyz, _, _, _ = item.read(n_structures=size)
else:
xyz, _, _, _ = item.read(n_structures=size, atom_indices=indices)
xyz_list.append(xyz)
xyz = _np.concatenate(xyz_list)
del (xyz_list)
xyz = xyz.astype('float64')
xyz = xyz * _puw.unit(item.distance_unit)
xyz = _puw.standardize(xyz)
return xyz
def get_coordinates_from_atom(item, indices='all', structure_indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
structure_indices = _digest_structure_indices(structure_indices)
unit = _puw.get_unit(item.positions)
coordinates = _np.array(_puw.get_value(item.getPositions(asNumpy=True)))
coordinates = coordinates.reshape(1, coordinates.shape[0], coordinates.shape[1])
if structure_indices is not 'all':
coordinates = coordinates[structure_indices,:,:]
if indices is not 'all':
coordinates = coordinates[:,indices,:]
coordinates = coordinates * unit
coordinates = _puw.standardize(coordinates)
return coordinates
def set_box_to_system(item, structure_indices='all', value=None, check=True):
if check:
_digest_item(item, 'openmm.Topology')
structure_indices = _digest_structure_indices(structure_indices)
box = _digest_box(value)
box = _puw.convert(value, to_unit='nanometers', to_form='openmm.unit')
n_structures = box.shape[0]
if n_structures == 1:
item.setPeriodicBoxVectors(box[0])
else:
raise ValueError(
"The box to set in to a openmm.Topology has more than a frame")
pass
