This example leads to the following error as of now:
from irmsd import read_structures, sorter_irmsd_molecule
# read an xyz file with multiple frames and return a list of irmsd.Molecule objects
molecules = read_structures('/PATH/TO/YOUR/input.xyz')
# Analyze the structure list and assign each molecule to a group (simple list of integers)
# as well as the aligned molecules
groups,aligned_molecules = sorter_irmsd_molecule(molecules)
Traceback (most recent call last):
File "/Users/marcelmueller/projects/irmsd/script.py", line 8, in <module>
groups,aligned_molecules = sorter_irmsd_molecule(molecules)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
TypeError: sorter_irmsd_molecule() missing 1 required positional argument: 'rthr'
I suggest giving a sensible default here:
def sorter_irmsd_molecule(
molecule_list: Sequence[Molecule],
rthr: float,
iinversion: int = 0,
allcanon: bool = True,
printlvl: int = 0,
ethr: float | None = None,
ewin: float | None = None,
) -> Tuple[np.ndarray, List[Molecule]]:
This example leads to the following error as of now:
I suggest giving a sensible default here: