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Change hydrogen on hydrogen mapping default to True #69

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Change hydrogen on hydrogen mapping default to True #69

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a764bd4
only map H on H
jthorton Nov 22, 2024
76c4c9c
Merge branch 'main' into atom_mapping_default
jthorton Nov 26, 2024
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6 changes: 4 additions & 2 deletions src/kartograf/atom_mapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ def __init__(
*,
atom_max_distance: float = 0.95,
atom_map_hydrogens: bool = True,
map_hydrogens_on_hydrogens_only: bool = False,
map_hydrogens_on_hydrogens_only: bool = True,
map_exact_ring_matches_only: bool = True,
allow_partial_fused_rings: bool = True,
additional_mapping_filter_functions: Optional[Iterable[Callable[[
Expand All @@ -87,8 +87,10 @@ def __init__(
atom_max_distance : float, optional
geometric criteria for two atoms, how far their distance
can be maximal (in Angstrom). Default 0.95
atom_map_hydrogens : bool, optional
If hydrogens should be included in the atom mapping. Default True
map_hydrogens_on_hydrogens_only : bool, optional
map hydrogens only on hydrogens. Default False
map hydrogens only on hydrogens. Default True
map_exact_ring_matches_only : bool, optional
if true, only rings with matching ringsize and same bond-orders
will be mapped. Additionally no ring-breaking is permitted. default
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2 changes: 1 addition & 1 deletion src/kartograf/tests/conftest.py
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Expand Up @@ -44,7 +44,7 @@ def stereco_chem_molecules():
@pytest.fixture(scope="session")
def stereo_chem_mapping():
mols = stereo_chem_mols()
expected_mapping = {2: 7, 4: 4, 5: 5, 6: 6, 7: 2, 0: 0, 1: 1, 3: 3}
expected_mapping = {4: 4, 5: 5, 6: 6, 0: 0, 1: 1, 3: 3}

return LigandAtomMapping(mols[0], mols[1], expected_mapping)

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