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RelativeFEPSetup cannot handle list of smiles as input ligands #1155

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ijpulidos opened this issue Feb 7, 2023 · 0 comments · May be fixed by #1156
Open

RelativeFEPSetup cannot handle list of smiles as input ligands #1155

ijpulidos opened this issue Feb 7, 2023 · 0 comments · May be fixed by #1156
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bug 🐛 help wanted ✋ priority: high priority high
Milestone
0.11.0: New top-l...

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@ijpulidos
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According to the documentation, RelativeFEPSetup should be able to handle a list of SMILES strings as input ligands but it makes the interpreter to freeze giving the following warnings:

Warning: Unable to set unknown read format (UNDEFINED) in input stream, using existing format (Canonical stereo SMILES)
Warning: Unable to open "Oc1ccccc1" for reading molecules.

Warning: Error reading molecule "" in Canonical stereo SMILES format.

And example code to reproduce the issue is as follows (Warning, this kinda kills the python interpreter, use at your own risk):

from perses.app.relative_setup import RelativeFEPSetup
from openmm import unit
phenol_smiles = "Oc1ccccc1"
paracetamol_smiles = "CC(=O)Nc1ccc(O)cc1"
input_smiles = [phenol_smiles, paracetamol_smiles]
fe_setup = RelativeFEPSetup(
                ligand_input=input_smiles,
                old_ligand_index=0,
                new_ligand_index=1,
                forcefield_files=["amber14/tip3p.xml"],
                small_molecule_forcefield="gaff-2.11",
                phases=["solvent"],
                solvent_padding=1.1 * unit.nanometers)
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bug 🐛 help wanted ✋ priority: high priority high
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0.11.0: New top-level API
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List of input smiles as input for RelativeFEPSetup choderalab/perses
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@ijpulidos