From c1f9612b59567a5c99592d94c8bf75a58a2ef1de Mon Sep 17 00:00:00 2001 From: Matt Johnson Date: Wed, 8 Jan 2025 16:53:28 -0800 Subject: [PATCH] fix brackets in get_bond calls --- pynta/main.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pynta/main.py b/pynta/main.py index 60f042f9..49bf2b8b 100644 --- a/pynta/main.py +++ b/pynta/main.py @@ -711,7 +711,7 @@ def setup_active_learning_loop(self): if bd.atom1.is_surface_site() or bd.atom2.is_surface_site(): keep_binding_vdW_bonds_in_reactants = True m = mol.copy(deep=True) - b = m.get_bond(m.atoms(mol.atoms.index(bd.atom1)),m.atoms[mol.atoms.index(bd.atom2)]) + b = m.get_bond(m.atoms[mol.atoms.index(bd.atom1)],m.atoms[mol.atoms.index(bd.atom2)]) m.remove_bond(b) out = m.split() if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface @@ -724,7 +724,7 @@ def setup_active_learning_loop(self): if bd.atom1.is_surface_site() or bd.atom2.is_surface_site(): keep_binding_vdW_bonds_in_products = True m = mol.copy(deep=True) - b = m.get_bond(m.atoms(mol.atoms.index(bd.atom1)),m.atoms[mol.atoms.index(bd.atom2)]) + b = m.get_bond(m.atoms[mol.atoms.index(bd.atom1)],m.atoms[mol.atoms.index(bd.atom2)]) m.remove_bond(b) out = m.split() if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface @@ -759,7 +759,7 @@ def setup_active_learning_loop(self): if bd.atom1.is_surface_site() or bd.atom2.is_surface_site(): keep_binding_vdW_bonds = True m = mol.copy(deep=True) - b = m.get_bond(m.atoms(mol.atoms.index(bd.atom1)),m.atoms[mol.atoms.index(bd.atom2)]) + b = m.get_bond(m.atoms[mol.atoms.index(bd.atom1)],m.atoms[mol.atoms.index(bd.atom2)]) m.remove_bond(b) out = m.split() if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface