from molsysmt._private.argdigest import arg_digest
[docs]
@arg_digest()
def get_chain_name(
molecular_system,
element="atom",
selection="all",
redefine_indices=False,
redefine_ids=False,
redefine_names=False,
syntax="MolSysMT",
skip_digestion=False,
):
"""
Getting chain names from a molecular system.
Parameters
----------
molecular_system : molecular system
Molecular system in any supported MolSysMT format.
element : str, default='atom'
Structural element level to query ('atom', 'group', 'component', 'molecule', 'chain', 'entity').
selection : str, list, tuple, or numpy.ndarray, default='all'
Selection string or boolean/integer array specifying elements.
redefine_indices : bool, default=False
Whether to reassign contiguous 0-based indices.
redefine_ids : bool, default=False
Whether to assign sequential string identifiers.
redefine_names : bool, default=False
Whether to assign normalized element names.
syntax : str, default='MolSysMT'
Selection syntax used to evaluate `selection` (e.g., 'MolSysMT', 'MDTraj').
skip_digestion : bool, default=False
Whether to skip MolSysMT's internal argument digestion mechanism.
Returns
-------
list of str
List of chain names.
.. versionadded:: 1.0.0
"""
if isinstance(selection, str) and selection == "all":
from molsysmt.native import MolSys, Topology
from molsysmt.native._topology_infer import project_chain_name_from_topology
if isinstance(molecular_system, Topology):
return project_chain_name_from_topology(
molecular_system,
element=element,
redefine_indices=redefine_indices,
redefine_names=redefine_names,
)
if isinstance(molecular_system, MolSys):
return project_chain_name_from_topology(
molecular_system.topology,
element=element,
redefine_indices=redefine_indices,
redefine_names=redefine_names,
)
if redefine_names:
from .chain_names import all_chain_names
from .get_chain_index import get_chain_index
chain_indices = get_chain_index(
molecular_system,
element=element,
selection=selection,
syntax=syntax,
redefine_indices=redefine_indices,
skip_digestion=True,
)
chain_names = [all_chain_names[ii] for ii in chain_indices]
if element == "chain":
return chain_names
else:
raise NotImplementedError
else:
from molsysmt import get
output = get(
molecular_system,
element=element,
selection=selection,
syntax=syntax,
chain_name=True,
skip_digestion=True,
)
return output
