from molsysmt._private.digestion import digest
from molsysmt._private.variables import is_all
from molsysmt import pyunitwizard as puw
import numpy as np
###### Set
## Atom
[docs]
@digest(form='molsysmt.Structures')
def set_coordinates_to_atom(item, indices='all', structure_indices='all', value=None, skip_digestion=False):
if is_all(indices):
if is_all(structure_indices):
item.coordinates = value
item.n_structures = value.shape[0]
item.n_atoms = value.shape[1]
if item.box is not None:
if item.box.shape[0]!=item.n_structures:
if item.box.shape[0]==1:
item.box = puw.utils.numpy.repeat(item.box, item.n_structures, axis=0,
value_type='numpy.ndarray')
else:
raise ValueError("The number of boxes is different than the number of frames")
else:
item.coordinates[structure_indices,:,:] = value[:,:,:]
else:
if is_all(structure_indices):
item.coordinates[:,indices,:] = value[:,:,:]
else:
item.coordinates[np.ix_(structure_indices, indices)]=value[:,:,:]
pass
[docs]
@digest(form='molsysmt.Structures')
def set_velocities_to_atom(item, indices='all', structure_indices='all', value=None, skip_digestion=False):
if is_all(indices):
if is_all(structure_indices):
item.velocities = value
item.n_structures = value.shape[0]
item.n_atoms = value.shape[1]
else:
item.velocities[structure_indices,:,:] = value[:,:,:]
else:
if is_all(structure_indices):
item.velocities[:,indices,:] = value[:,:,:]
else:
item.velocities[np.ix_(structure_indices, indices)]=value[:,:,:]
pass
[docs]
@digest(form='molsysmt.Structures')
def set_occupancy_to_atom(item, indices='all', structure_indices='all', value=None, skip_digestion=False):
if is_all(indices):
if is_all(structure_indices):
item.occupancy = value
else:
item.occupancy[structure_indices,:] = value[:,:]
else:
if is_all(structure_indices):
item.occupancy[:,indices] = value[:,:]
else:
item.occupancy[np.ix_(structure_indices, indices)]=value[:,:]
pass
[docs]
@digest(form='molsysmt.Structures')
def set_b_factor_to_atom(item, indices='all', structure_indices='all', value=None, skip_digestion=False):
if is_all(indices):
if is_all(structure_indices):
item.b_factor = value
else:
item.b_factor[structure_indices,:] = value[:,:]
else:
if is_all(structure_indices):
item.b_factor[:,indices] = value[:,:]
else:
item.b_factor[np.ix_(structure_indices, indices)]=value[:,:]
pass
## System
[docs]
@digest(form='molsysmt.Structures')
def set_structure_id_to_system(item, structure_indices='all', value=None, skip_digestion=False):
if is_all(structure_indices):
item.structure_id = value
else:
item.structure_id[structure_indices,:,:] = value[:,:,:]
pass
[docs]
@digest(form='molsysmt.Structures')
def set_time_to_system(item, structure_indices='all', value=None, skip_digestion=False):
if is_all(structure_indices):
item.time = value
else:
item.time[structure_indices,:,:] = value[:,:,:]
pass
[docs]
@digest(form='molsysmt.Structures')
def set_box_to_system(item, structure_indices='all', value=None, skip_digestion=False):
if is_all(structure_indices):
item.box = value
else:
item.box[structure_indices,:,:] = value[:,:,:]
pass
[docs]
@digest(form='molsysmt.Structures')
def set_coordinates_to_system(item, indices='all', structure_indices='all', value=None, skip_digestion=False):
return set_coordinates_to_atom(item, indices='all', structure_indices=structure_indices,
value=value, skip_digestion=True)
[docs]
@digest(form='molsysmt.Structures')
def set_velocities_to_system(item, indices='all', structure_indices='all', value=None, skip_digestion=False):
return set_velocities_to_atom(item, indices='all', structure_indices=structure_indices,
value=value, skip_digestion=True)
