import numpy as np
from molsysmt._private.argdigest import arg_digest
[docs]
@arg_digest()
def get_molecule_id(
molecular_system,
element="molecule",
selection="all",
redefine_indices=False,
redefine_ids=False,
syntax="MolSysMT",
skip_digestion=False,
):
"""
Getting molecule identifier strings from a molecular system.
Parameters
----------
molecular_system : molecular system
Molecular system in any supported MolSysMT format.
element : str, default='molecule'
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.
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 molecule IDs.
.. versionadded:: 1.0.0
"""
if isinstance(selection, str) and selection == "all":
from molsysmt.native import MolSys, Topology
topology = None
if isinstance(molecular_system, Topology):
topology = molecular_system
elif isinstance(molecular_system, MolSys):
topology = molecular_system.topology
if topology is not None:
if redefine_indices or redefine_ids:
from .get_molecule_index import get_molecule_index
output = get_molecule_index(
molecular_system,
element=element,
selection=selection,
redefine_indices=redefine_indices or redefine_ids,
syntax=syntax,
skip_digestion=True,
)
else:
from molsysmt.basic import get
output = get(
molecular_system,
element=element,
selection=selection,
syntax=syntax,
molecule_id=True,
)
elif redefine_indices:
from .get_molecule_index import get_molecule_index
output = get_molecule_index(
molecular_system,
element=element,
selection=selection,
redefine_indices=True,
syntax=syntax,
)
elif redefine_ids:
from .get_molecule_index import get_molecule_index
output = get_molecule_index(
molecular_system,
element=element,
selection=selection,
redefine_indices=False,
syntax=syntax,
)
else:
from molsysmt.basic import get
output = get(
molecular_system,
element=element,
selection=selection,
syntax=syntax,
molecule_id=True,
)
elif redefine_indices:
from .get_molecule_index import get_molecule_index
output = get_molecule_index(
molecular_system,
element=element,
selection=selection,
redefine_indices=True,
syntax=syntax,
)
elif redefine_ids:
from .get_molecule_index import get_molecule_index
output = get_molecule_index(
molecular_system,
element=element,
selection=selection,
redefine_indices=False,
syntax=syntax,
)
else:
from molsysmt.basic import get
output = get(
molecular_system,
element=element,
selection=selection,
syntax=syntax,
molecule_id=True,
)
if output is not None:
arr = np.asarray(output)
if arr.shape == ():
output = [str(arr.astype(str))]
else:
output = arr.astype(str)
output = output.tolist()
return output
