def get_molecule_id_from_molecule(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
raise NotImplementedMethodError()
def get_n_inner_bonds_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
raise NotImplementedMethodError()
def get_entity_name_from_entity(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
raise NotImplementedMethodError()
def get_chain_type_from_chain(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
raise NotImplementedMethodError()
def get_group_id_from_group(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
raise _NotImplementedMethodError()
def get_atom_index_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
raise NotImplementedError
def get_entity_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
return output
def get_component_type_from_component(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from molsysmt.elements.component import get_component_type_from_component as get
return get(item, indices)
def get_component_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from molsysmt.elements.component import get_component_index_from_atom as _get
return _get(item, indices=indices)
def get_entity_type_from_entity(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from molsysmt.element.entity import entity_type_from_entity as _get
return _get(item, indices)
def get_molecule_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
output = get_component_index_from_atom(item, indices=indices, check=False)
return output
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 get_atom_type_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
output = item.types.values
if indices is not 'all':
output = output[indices]
return output
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_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_atom_index_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
tmp_bonds = []
for bond in item.bonds:
tmp_bonds.append([bond.atom1.idx, bond.atom2.idx])
return tmp_bonds
def get_n_inner_bonds_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
return get_n_bonds_from_system(item)
else:
inner_bonded_atoms = get_inner_bonded_atoms_from_atom(item,
indices=indices)
return inner_bonded_atoms.shape[0]
def get_n_atoms_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
output = item.coordinates.shape[1]
else:
output = indices.shape[0]
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_openmm_Topology
from ..openmm_Topology import get_chain_index_from_atom as aux_get
tmp_item = to_openmm_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_component_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_openmm_GromacsGroFile
from ..openmm_GromacsGroFile import get_component_index_from_atom as aux_get
tmp_item = to_openmm_GromacsGroFile(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
n_atoms = get_n_atoms_from_system(item)
indices = np.arange(n_atoms)
output = item.tt.atoms2segments(indices)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
output = [atom.chain for atom in item.atoms]
else:
output = [item.atom(ii).chain for ii in indices]
output = _np.array(output)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_mmtf_MMTFDecoder
from ..mmtf_MMTFDecoder import get_chain_index_from_atom as aux_get
tmp_item = to_mmtf_MMTFDecoder(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_atom_type_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
output = [atom.type for atom in item.atoms]
else:
output = [item.atom(ii).type for ii in indices]
output = _np.array(output, dtype=object)
return output
def get_bond_type_from_bond(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_molsysmt_Topology
from ..molsysmt_Topology import get_bond_type_from_bond as aux_get
tmp_item = to_molsysmt_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_atom_id_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
if indices is 'all':
output = [None for atom in item.atoms]
else:
output = [None for ii in indices]
output = _np.array(output)
return output
def get_atom_type_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_mdtraj_Topology
from ..mdtraj_Topology import get_atom_type_from_atom as aux_get
tmp_item = to_mdtraj_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_chain_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from . import to_mdtraj_HDF5TrajectoryFile
from ..mdtraj_HDF5TrajectoryFile import get_chain_index_from_atom as aux_get
tmp_item = to_mdtraj_HDF5TrajectoryFile(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
def get_component_index_from_atom(item, indices='all', check=True):
if check:
_digest_item(item, _form)
indices = _digest_indices(indices)
from .to_molsysmt_Topology import to_molsysmt_Topology
from ..molsysmt_Topology import get_component_index_from_atom as aux_get
tmp_item = to_molsysmt_Topology(item, check=False)
output = aux_get(tmp_item, indices=indices, check=False)
return output
