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fix: Use get_motif_features() for is_motif_atom lookup #378

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Merged
r-krishna merged 2 commits into from
Sep 2, 2026
Merged

fix: Use get_motif_features() for is_motif_atom lookup #378

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40f5c47
Use get_motif_features() for is_motif_atom lookup
rclune Aug 24, 2026
1c8886f
Use get_motif_features() for is_motif_atom lookup
rclune Aug 25, 2026
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12 changes: 8 additions & 4 deletions models/rfd3/src/rfd3/transforms/hbonds_hbplus.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
from atomworks.ml.transforms.base import Transform
from biotite.structure import AtomArray
from biotite.structure.io.pdb import PDBFile
from rfd3.transforms.conditioning_base import get_motif_features


def save_atomarray_to_pdb(atom_array, output_path):
Expand Down Expand Up @@ -133,6 +134,8 @@ def calculate_hbonds(
donor_mask = np.bool_(donor_array)
acceptor_mask = np.bool_(acceptor_array)

is_motif_atom = get_motif_features(atom_array)["is_motif_atom"]

motif_hbonds = []
for item in hbonds:
current_donor_mask = (
Expand All @@ -156,8 +159,8 @@ def calculate_hbonds(
f"Unable to uniquely identify an acceptor atom with chain_iid={item['a_chain']}, res_id={item['a_resi']}, atom_name={item['a_atom']}."
)

current_donor_is_motif = atom_array.is_motif_atom[current_donor_mask][0]
current_acceptor_is_motif = atom_array.is_motif_atom[current_acceptor_mask][0]
current_donor_is_motif = is_motif_atom[current_donor_mask][0]
current_acceptor_is_motif = is_motif_atom[current_acceptor_mask][0]

# Only keep hbonds between the motif and diffused regions
if current_donor_is_motif != current_acceptor_is_motif:
Expand Down Expand Up @@ -205,9 +208,10 @@ def forward(self, data: dict) -> dict:

hbond_types = np.vstack((atom_array.active_donor, atom_array.active_acceptor)).T

is_motif_atom = np.array(get_motif_features(atom_array)["is_motif_atom"])
final_hbond_types = hbond_types
final_hbond_types[:, 0] *= np.array(atom_array.is_motif_atom)
final_hbond_types[:, 1] *= np.array(atom_array.is_motif_atom)
final_hbond_types[:, 0] *= is_motif_atom
final_hbond_types[:, 1] *= is_motif_atom
log_dict["hbond_total_count"] = np.sum(final_hbond_types)

if data["conditions"]["hbond_subsample"] and np.sum(final_hbond_types) > 3:
Expand Down
12 changes: 8 additions & 4 deletions models/rfd3na/src/rfd3na/transforms/hbonds_hbplus.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
from atomworks.ml.transforms.base import Transform
from biotite.structure import AtomArray
from biotite.structure.io.pdb import PDBFile
from rfd3na.transforms.conditioning_base import get_motif_features


def save_atomarray_to_pdb(atom_array, output_path):
Expand Down Expand Up @@ -133,6 +134,8 @@ def calculate_hbonds(
donor_mask = np.bool_(donor_array)
acceptor_mask = np.bool_(acceptor_array)

is_motif_atom = get_motif_features(atom_array)["is_motif_atom"]

motif_hbonds = []
for item in hbonds:
current_donor_mask = (
Expand All @@ -156,8 +159,8 @@ def calculate_hbonds(
f"Unable to uniquely identify an acceptor atom with chain_iid={item['a_chain']}, res_id={item['a_resi']}, atom_name={item['a_atom']}."
)

current_donor_is_motif = atom_array.is_motif_atom[current_donor_mask][0]
current_acceptor_is_motif = atom_array.is_motif_atom[current_acceptor_mask][0]
current_donor_is_motif = is_motif_atom[current_donor_mask][0]
current_acceptor_is_motif = is_motif_atom[current_acceptor_mask][0]

# Only keep hbonds between the motif and diffused regions
if current_donor_is_motif != current_acceptor_is_motif:
Expand Down Expand Up @@ -205,9 +208,10 @@ def forward(self, data: dict) -> dict:

hbond_types = np.vstack((atom_array.active_donor, atom_array.active_acceptor)).T

is_motif_atom = np.array(get_motif_features(atom_array)["is_motif_atom"])
final_hbond_types = hbond_types
final_hbond_types[:, 0] *= np.array(atom_array.is_motif_atom)
final_hbond_types[:, 1] *= np.array(atom_array.is_motif_atom)
final_hbond_types[:, 0] *= is_motif_atom
final_hbond_types[:, 1] *= is_motif_atom
log_dict["hbond_total_count"] = np.sum(final_hbond_types)

if data["conditions"]["hbond_subsample"] and np.sum(final_hbond_types) > 3:
Expand Down
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