check for adsorbates in resonance

ReactionMechanismGenerator · Sep 23, 2024 · fed408f · fed408f
1 parent a2e1e60
commit fed408f
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/rmgpy/molecule/resonance.py b/rmgpy/molecule/resonance.py
@@ -96,9 +96,9 @@ def populate_resonance_algorithms(features=None):
  method_list.append(generate_allyl_delocalization_resonance_structures)
  if features['is_cyclic']:
  method_list.append(generate_aryne_resonance_structures)
- if features['hasNitrogenVal5']:
+ if features['hasNitrogenVal5'] and not features['is_adsorbate']:
  method_list.append(generate_N5dc_radical_resonance_structures)
- if features['hasLonePairs']:
+ if features['hasLonePairs'] and not features['is_adsorbate']:
  method_list.append(generate_adj_lone_pair_radical_resonance_structures)
  method_list.append(generate_adj_lone_pair_multiple_bond_resonance_structures)
  method_list.append(generate_adj_lone_pair_radical_multiple_bond_resonance_structures)
@@ -130,6 +130,7 @@ def analyze_molecule(mol, save_order=False):
  'is_aryl_radical': False,
  'hasNitrogenVal5': False,
  'hasLonePairs': False,
+ 'is_adsorbate':mol.contains_surface_site(),
  }
 
  if features['is_cyclic']: