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Fix FrozenInstanceError when discarding non-reactant monomers #43

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Merged
janitha-mahanthe merged 2 commits into from
Mar 3, 2026
+19 −9
Merged

Fix FrozenInstanceError when discarding non-reactant monomers #43

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Copilot Mar 3, 2026
4258427
Fix FrozenInstanceError: use dataclasses.replace instead of direct at…
Copilot Mar 3, 2026
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28 changes: 19 additions & 9 deletions AutoREACTER/detectors/non_monomer_detector.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
from dataclasses import replace
from typing import List
from rdkit import Chem
from rdkit.Chem import rdmolops, Draw
Expand Down Expand Up @@ -243,7 +244,8 @@ def non_reactant_selection(self, simulation_setup: SimulationSetup, non_reactant
either retained or marked as discarded based on user input.

Note:
- This method modifies the status attribute of MonomerEntry objects in place.
- This method replaces MonomerEntry objects in simulation_setup.monomers with
updated copies (via dataclasses.replace) to reflect 'discarded' status.
- For single non-reactant monomers, only N and A options are presented.
- The status values follow the StatusType convention: 'active' or 'discarded'.
"""
Expand Down Expand Up @@ -279,7 +281,11 @@ def non_reactant_selection(self, simulation_setup: SimulationSetup, non_reactant
continue
if user_input == 'N':
# Mark single monomer as discarded
non_reactants_list[0].status = 'discarded'
target_id = non_reactants_list[0].id
simulation_setup.monomers = [
replace(m, status='discarded') if m.id == target_id else m
for m in simulation_setup.monomers
]
break
elif user_input == 'A':
# Keep the single monomer (retain)
Expand All @@ -292,9 +298,12 @@ def non_reactant_selection(self, simulation_setup: SimulationSetup, non_reactant
continue

if user_input == 'N':
# Discard all non-reactants: mark each as 'discarded'
for monomer in non_reactants_list:
monomer.status = 'discarded'
# Discard all non-reactants: replace each with 'discarded' status
discard_ids = {m.id for m in non_reactants_list}
simulation_setup.monomers = [
replace(m, status='discarded') if m.id in discard_ids else m
for m in simulation_setup.monomers
]
break
elif user_input == 'A':
# Retain all non-reactants: do nothing (keep 'active' status)
Expand All @@ -305,10 +314,11 @@ def non_reactant_selection(self, simulation_setup: SimulationSetup, non_reactant
selected_ids = input("Enter the IDs of the monomers you want to retain, separated by commas: ")
# Parse input into list of integers ( monomer IDs)
selected_ids = [int(id.strip()) for id in selected_ids.split(',')]
for monomer in non_reactants_list:
# Discard monomers NOT in the selected list
if monomer.id not in selected_ids:
monomer.status = 'discarded'
discard_ids = {m.id for m in non_reactants_list if m.id not in selected_ids}
simulation_setup.monomers = [
replace(m, status='discarded') if m.id in discard_ids else m
for m in simulation_setup.monomers
]
break

# Return the modified simulation setup
Expand Down