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fix: infer ori edge case #273

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Merged
RafiBrent merged 2 commits into from
Apr 23, 2026
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Merged

fix: infer ori edge case #273

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9bfbb34
fix: correct bug when inferring ori from hotspots that occurs when th…
Apr 23, 2026
fb9e594
fix:rafi hotspot fix for inference.py for rfd3na
timkartar Apr 23, 2026
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14 changes: 10 additions & 4 deletions models/rfd3/src/rfd3/utils/inference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -405,21 +405,27 @@ def infer_ori_from_hotspots(atom_array: struc.AtomArray):

# We can only perform distance computations on atoms with non-NaN coordinates
nan_coords_mask = np.any(np.isnan(atom_array.coord), axis=1)
non_nan_atom_array = atom_array[~nan_coords_mask]
motif_mask = atom_array.is_motif_atom_with_fixed_coord.astype(bool)
non_nan_motif_atom_array = atom_array[~nan_coords_mask & motif_mask]
if non_nan_motif_atom_array.array_length() == 0:
raise ValueError(
"infer_ori_from_hotspots requires at least one fixed motif atom "
"(is_motif_atom_with_fixed_coord=True) to compute nearby atoms COM."
)

# Perform the distance computation
# RFD2 used 10 Angstroms instead of 12, but was for residue-level hotspots
DISTANCE_CUTOFF = 12.0
cell_list = struc.CellList(non_nan_atom_array, cell_size=DISTANCE_CUTOFF)
cell_list = struc.CellList(non_nan_motif_atom_array, cell_size=DISTANCE_CUTOFF)
nearby_atoms_mask = get_atom_mask_from_cell_list(
hotspot_atom_array.coord,
cell_list,
len(non_nan_atom_array),
len(non_nan_motif_atom_array),
cutoff=DISTANCE_CUTOFF,
) # (n_query, n_cell_list)

nearby_atoms_mask = np.any(nearby_atoms_mask, axis=0) # (n_cell_list,)
nearby_atoms_com = non_nan_atom_array.coord[nearby_atoms_mask].mean(axis=0)
nearby_atoms_com = non_nan_motif_atom_array.coord[nearby_atoms_mask].mean(axis=0)

vector_from_core_to_hotspot = hotspot_com - nearby_atoms_com
vector_from_core_to_hotspot = vector_from_core_to_hotspot / np.linalg.norm(
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15 changes: 10 additions & 5 deletions models/rfd3na/src/rfd3na/utils/inference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -405,21 +405,26 @@ def infer_ori_from_hotspots(atom_array: struc.AtomArray):

# We can only perform distance computations on atoms with non-NaN coordinates
nan_coords_mask = np.any(np.isnan(atom_array.coord), axis=1)
non_nan_atom_array = atom_array[~nan_coords_mask]

motif_mask = atom_array.is_motif_atom_with_fixed_coord.astype(bool)
non_nan_motif_atom_array = atom_array[~nan_coords_mask & motif_mask]
if non_nan_motif_atom_array.array_length() == 0:
raise ValueError(
"infer_ori_from_hotspots requires at least one fixed motif atom "
"(is_motif_atom_with_fixed_coord=True) to compute nearby atoms COM."
)
# Perform the distance computation
# RFD2 used 10 Angstroms instead of 12, but was for residue-level hotspots
DISTANCE_CUTOFF = 12.0
cell_list = struc.CellList(non_nan_atom_array, cell_size=DISTANCE_CUTOFF)
cell_list = struc.CellList(non_nan_motif_atom_array, cell_size=DISTANCE_CUTOFF)
nearby_atoms_mask = get_atom_mask_from_cell_list(
hotspot_atom_array.coord,
cell_list,
len(non_nan_atom_array),
len(non_nan_motif_atom_array),
cutoff=DISTANCE_CUTOFF,
) # (n_query, n_cell_list)

nearby_atoms_mask = np.any(nearby_atoms_mask, axis=0) # (n_cell_list,)
nearby_atoms_com = non_nan_atom_array.coord[nearby_atoms_mask].mean(axis=0)
nearby_atoms_com = non_nan_motif_atom_array.coord[nearby_atoms_mask].mean(axis=0)

vector_from_core_to_hotspot = hotspot_com - nearby_atoms_com
vector_from_core_to_hotspot = vector_from_core_to_hotspot / np.linalg.norm(
Expand Down
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