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Support ARCSpecies in to_Rdkit_mol #782

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Support ARCSpecies in to_Rdkit_mol #782

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bb18f1c
Added support to the ARCSpecies object in to_rdkit_mol
kfir4444 Feb 12, 2025
a3e23e3
Test: to_rdkit_mol with ARCSpecies
kfir4444 Feb 12, 2025
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4 changes: 3 additions & 1 deletion arc/species/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1730,13 +1730,15 @@ def to_rdkit_mol(mol, remove_h=False, sanitize=True):
Adopted from rmgpy/molecule/converter.py

Args:
mol (Molecule): An RMG Molecule object for the conversion.
mol (Molecule, ARCSpecies): An ARCSpecies or RMG Molecule object for the conversion.
remove_h (bool, optional): Whether to remove hydrogen atoms from the molecule, ``True`` to remove.
sanitize (bool, optional): Whether to sanitize the RDKit molecule, ``True`` to sanitize.

Returns:
RDMol: An RDKit molecule object corresponding to the input RMG Molecule object.
"""
if type(mol) == ARCSpecies:
mol = mol.mol
atom_id_map = dict()

# only manipulate a copy of ``mol``
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5 changes: 5 additions & 0 deletions arc/species/converter_test.py
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Expand Up @@ -3643,6 +3643,11 @@ def test_to_rdkit_mol(self):
rd_mol_block = Chem.MolToMolBlock(rd_mol).splitlines()
self._check_atom_connectivity_in_rd_mol_block(spc1.mol, rd_mol_block)

rd_mol = converter.to_rdkit_mol(spc1)
self.assertIsInstance(rd_mol, rdchem.Mol)
rd_mol_block = Chem.MolToMolBlock(rd_mol).splitlines()
self._check_atom_connectivity_in_rd_mol_block(spc1.mol, rd_mol_block)

xyz = {'symbols': ('O', 'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'),
'isotopes': (16, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
'coords': ((-1.3435816539552077, -1.2858724378615196, 1.2807152578949395),
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