def recenter(self, selection=None, weights=None, syntaxis='mdtraj'):
from molsysmt import select as _select
from molsysmt import get as _get
if selection is not None:
atom_indices = _select(self.topology_mdtraj, selection, syntaxis)
else:
atom_indices = _np.arange(self.n_atoms, dtype=int)
if weights == 'masses':
weights_array = _get(self.topology_mdtraj,
atom_indices,
masses=True)
elif weights is None:
weights_array = _np.ones(atom_indices.shape[0], dtype=int)
self.coordinates = _np.asfortranarray(self.coordinates,
dtype='float64')
_libcom.recenter(self.coordinates, atom_indices, weights_array,
self.n_structures, self.n_atoms,
atom_indices.shape[0])
self.coordinates = _np.ascontiguousarray(self.coordinates)
pass
def unwrap(self,
selection=None,
minimum_image_reference=None,
syntaxis='mdtraj'):
from molsysmt import select as _select
from molsysmt import get as _get
from molsysmt.utils.fortran import listoflists2fortran as _listoflists2fortran
molecules, bonds = _get(self.topology_mdtraj,
molecules=True,
bonded_atoms=True)
if selection is not None:
atom_indices = _select(self.topology_mdtraj, selection, syntaxis)
molecules2unwrap = []
for molecule in molecules:
if len(_np.intersect1d(molecule, atom_indices)):
molecules2unwrap.append(molecule)
molecules = molecules2unwrap
molecules_array_all, molecules_array_starts = _listoflists2fortran(
molecules, dtype='int64')
bonds_array_all, bonds_array_starts = _listoflists2fortran(
bonds, dtype='int64')
self.coordinates = _np.asfortranarray(self.coordinates,
dtype='float64')
self.box = _np.asfortranarray(self.box, dtype='float64')
self.invbox = _np.asfortranarray(self.invbox, dtype='float64')
_libbox.unwrap(self.coordinates, molecules_array_all,
molecules_array_starts, bonds_array_all,
bonds_array_starts, self.box, self.invbox,
self.orthogonal, self.n_structures, self.n_atoms,
molecules_array_all.shape[0],
molecules_array_starts.shape[0],
bonds_array_all.shape[0], bonds_array_starts.shape[0])
self.coordinates = _np.ascontiguousarray(self.coordinates)
self.box = _np.ascontiguousarray(self.box)
self.invbox = _np.ascontiguousarray(self.invbox)
pass
def get_n_degrees_of_freedom_from_system(item,
indices='all',
structure_indices='all'):
from molsysmt import get_degrees_of_freedom as _get
return _get(item, indices=indices)
def get_n_atoms_from_system(item, indices='all', structure_indices='all'):
from .api_openmm_Topology import get_n_atoms_from_system as _get
return _get(item, indices=indices)
def get_net_charge_from_system(item, indices='all', structure_indices='all'):
from molsysmt import get_net_charge as _get
return _get(item, indices=indices)
def get_molecule_type_from_chain(item, indices='all', structure_indices='all'):
from .api_openmm_Topology import get_molecule_type_from_chain as _get
return _get(item, indices=indices)
def get_chain_id_from_group(item, indices='all', structure_indices='all'):
from .api_openmm_Topology import get_chain_id_from_group as _get
return _get(item, indices=indices)
def get_coordinates_from_atom(item, indices='all', structure_indices='all'):
from .api_openmm_Positions import get_coordinates_from_atom as _get
return _get(item, indices=indices)
def get_net_mass_from_atom(item, indices='all', structure_indices='all'):
from molsysmt import get_net_mass as _get
return _get(item, indices=indices)
def get_n_ions_from_atom(item, indices='all', structure_indices='all'):
from .api_openmm_Topology import get_n_ions_from_atom as _get
_get(item.topology, indices=indices)
