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Fix/merge conflicts openmm #2

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Fix/merge conflicts openmm #2

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5a5cb4a
fix import issues
KyuJungJun Oct 24, 2025
bd48677
add tetraorion
KyuJungJun Oct 28, 2025
9bd4707
updates to include tetrameric anion support
KyuJungJun Oct 28, 2025
24239d5
Merge remote-tracking branch 'origin/main'
KyuJungJun Feb 4, 2026
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22 changes: 20 additions & 2 deletions builder_ligpargen_openmm_from_molality_multi_system.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,8 @@ def run(
salt_type:str,
molality:float,
charges:str,
polynames:list,
lit_charges_save_path:str,
system:str,
simu_temp:float,
atom_count:int,
Expand Down Expand Up @@ -188,7 +190,8 @@ def run(
atom_names_short=atom_names_short_list,
atom_names_long=atom_names_long_list,
param_dict=param_dict_list,
lit_charges_save_path=None,
lit_charges_save_path=lit_charges_save_path,
polynames=polynames,
charges=charges,
charge_scale=charge_scale,
salt_smiles=salt_smiles,
Expand Down Expand Up @@ -364,8 +367,18 @@ def run(
ratios_type = 'mol'
assert len(smiles) == len(ratios)
else:
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@JurgisR JurgisR Feb 9, 2026

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You haven't properly done a previous merge, fix this please

mol_ratios = None
if len(lines) == 3:
"""
3rd line is the DFT charge CSV file name for each molecule.
This line is optional.
"""
polynames = lines[2].split(",")
=======
ratios = None
ratios_type = None
>>>>>>> origin/main

if args.atom_count == "None":
atom_count = None
Expand All @@ -376,7 +389,10 @@ def run(
polymer_chain_length = None
else:
polymer_chain_length = int(args.polymer_chain_length)

if args.charge_type == "LIT":
print("polynames: ", polynames)
else:
polynames = None

run(
save_path=args.save_path,
Expand All @@ -386,6 +402,8 @@ def run(
salt_type=args.salt_type,
molality=float(args.molality_salt),
charges=args.charge_type,
polynames=polynames,
lit_charges_save_path=args.lit_charges_save_path,
system=args.system,
atom_count=atom_count,
md_save_time=int(args.md_save_time),
Expand Down
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