#######################################################################################
########### THE FOLLOWING LINES NEED TO BE CUSTOMIZED FOR EVERY CLASS ################
#######################################################################################
from molsysmt._private.execfile import execfile
from molsysmt._private.exceptions import NotImplementedMethodError, NotWithThisFormError
from molsysmt._private.digestion import digest
form='openmm.AmberPrmtopFile'
## From atom
[docs]
@digest(form=form)
def get_atom_id_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_atom_id_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_atom_name_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_atom_name_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_atom_type_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_atom_type_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_group_index_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_group_index_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_component_index_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_component_index_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_chain_index_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_chain_index_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_molecule_index_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_molecule_index_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_entity_index_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_entity_index_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_inner_bonded_atoms_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_inner_bonded_atoms_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_n_inner_bonds_from_atom(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_inner_bonds_from_atom as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
## From group
[docs]
@digest(form=form)
def get_group_id_from_group(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_group_id_from_group as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_group_name_from_group(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_group_name_from_group as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_group_type_from_group(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_group_type_from_group as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
## From component
[docs]
@digest(form=form)
def get_component_id_from_component(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_component_id_from_component as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_component_name_from_component(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_component_name_from_component as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_component_type_from_component(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_component_type_from_component as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
## From molecule
[docs]
@digest(form=form)
def get_molecule_id_from_molecule(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_molecule_id_from_molecule as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_molecule_name_from_molecule(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_molecule_name_from_molecule as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_molecule_type_from_molecule(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_molecule_type_from_molecule as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
## From chain
[docs]
@digest(form=form)
def get_chain_id_from_chain(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_chain_id_from_chain as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_chain_name_from_chain(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_chain_name_from_chain as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_chain_type_from_chain(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_chain_type_from_chain as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
## From entity
[docs]
@digest(form=form)
def get_entity_id_from_entity(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_entity_id_from_entity as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_entity_name_from_entity(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_entity_name_from_entity as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_entity_type_from_entity(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_entity_type_from_entity as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
## From system
[docs]
@digest(form=form)
def get_n_atoms_from_system(item, skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_atoms_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_n_groups_from_system(item, skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_groups_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_n_components_from_system(item, skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_components_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_n_chains_from_system(item, skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_chains_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_n_molecules_from_system(item, skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_molecules_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_n_entities_from_system(item, skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_entities_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_n_bonds_from_system(item, skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_n_bonds_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_box_from_system(item, structure_indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_box_from_system as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, structure_indices=structure_indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_time_from_system(item, structure_indices='all', skip_digestion=False):
raise NotImplementedMethodError()
[docs]
@digest(form=form)
def get_structure_id_from_system(item, structure_indices='all', skip_digestion=False):
raise NotImplementedMethodError()
## From bond
[docs]
@digest(form=form)
def get_bond_order_from_bond(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_bond_order_from_bond as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_bond_type_from_bond(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_bond_type_from_bond as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
[docs]
@digest(form=form)
def get_bonded_atoms_from_bond(item, indices='all', skip_digestion=False):
from . import to_openmm_Topology
from ..openmm_Topology import get_bonded_atoms_from_bond as aux_get
tmp_item = to_openmm_Topology(item, skip_digestion=True)
output = aux_get(tmp_item, indices=indices, skip_digestion=True)
return output
#######################################################################################
######### DO NOT TOUCH THE FOLLOWING LINES, JUST INCLUDE THEM AS THEY ARE #############
#######################################################################################
from os import path
this_folder = path.dirname(path.abspath(__file__))
common_get = path.join(this_folder, '../../_private/common_get.py')
execfile(common_get, globals(), locals())
del(path, this_folder, common_get)
