From eb42f91fb6c6ee302fbbc63b3b5c49f87b0fe924 Mon Sep 17 00:00:00 2001 From: Marcel Mueller Date: Sat, 20 Dec 2025 21:21:58 +0100 Subject: [PATCH 1/2] fix rthr default value Signed-off-by: Marcel Mueller --- src/irmsd/interfaces/mol_interface.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/irmsd/interfaces/mol_interface.py b/src/irmsd/interfaces/mol_interface.py index c79734b..695b416 100644 --- a/src/irmsd/interfaces/mol_interface.py +++ b/src/irmsd/interfaces/mol_interface.py @@ -230,10 +230,10 @@ def get_irmsd_molecule( def sorter_irmsd_molecule( molecule_list: Sequence[Molecule], - rthr: float, iinversion: int = 0, allcanon: bool = True, printlvl: int = 0, + rthr: float = 0.125, # aligned with '--rthr' in src/irmsd/cli.py ethr: float | None = None, ewin: float | None = None, ) -> Tuple[np.ndarray, List[Molecule]]: From ea3b2da80420c1ee1df24bf441793425a53c4768 Mon Sep 17 00:00:00 2001 From: Marcel Mueller Date: Mon, 22 Dec 2025 22:23:07 +0100 Subject: [PATCH 2/2] add default value consistently; correct argument position; correct missing import Signed-off-by: Marcel Mueller --- src/irmsd/interfaces/ase_io.py | 2 +- src/irmsd/interfaces/mol_interface.py | 4 ++-- src/irmsd/interfaces/rdkit_io.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/irmsd/interfaces/ase_io.py b/src/irmsd/interfaces/ase_io.py index bd13613..482a1c9 100644 --- a/src/irmsd/interfaces/ase_io.py +++ b/src/irmsd/interfaces/ase_io.py @@ -503,7 +503,7 @@ def get_irmsd_ase( def sorter_irmsd_ase( atoms_list: Sequence["ase.Atoms"], - rthr: float, + rthr: float = 0.125, # aligned with '--rthr' in src/irmsd/cli.py iinversion: int = 0, allcanon: bool = True, printlvl: int = 0, diff --git a/src/irmsd/interfaces/mol_interface.py b/src/irmsd/interfaces/mol_interface.py index 695b416..168a000 100644 --- a/src/irmsd/interfaces/mol_interface.py +++ b/src/irmsd/interfaces/mol_interface.py @@ -1,6 +1,6 @@ from __future__ import annotations -from typing import Sequence, Tuple +from typing import Sequence, Tuple, List import numpy as np @@ -230,10 +230,10 @@ def get_irmsd_molecule( def sorter_irmsd_molecule( molecule_list: Sequence[Molecule], + rthr: float = 0.125, # aligned with '--rthr' in src/irmsd/cli.py iinversion: int = 0, allcanon: bool = True, printlvl: int = 0, - rthr: float = 0.125, # aligned with '--rthr' in src/irmsd/cli.py ethr: float | None = None, ewin: float | None = None, ) -> Tuple[np.ndarray, List[Molecule]]: diff --git a/src/irmsd/interfaces/rdkit_io.py b/src/irmsd/interfaces/rdkit_io.py index c007913..0e39937 100644 --- a/src/irmsd/interfaces/rdkit_io.py +++ b/src/irmsd/interfaces/rdkit_io.py @@ -463,7 +463,7 @@ def get_irmsd_rdkit( def sorter_irmsd_rdkit( molecules: "Mol" | Sequence["Mol"], - rthr: float, + rthr: float = 0.125, # aligned with '--rthr' in src/irmsd/cli.py iinversion: int = 0, allcanon: bool = True, printlvl: int = 0,