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Fix atom37_to_atom14 tensor shape errors in all_atom_multimer.py #430

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Fix atom37_to_atom14 tensor shape errors in all_atom_multimer.py #430

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30 changes: 17 additions & 13 deletions openfold/utils/all_atom_multimer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,28 +56,32 @@ def atom14_to_atom37(


def atom37_to_atom14(aatype, all_atom_pos, all_atom_mask):
"""Convert Atom37 positions to Atom14 positions."""
"""Convert atom37 positions to atom14 positions."""
residx_atom14_to_atom37 = get_rc_tensor(
rc.RESTYPE_ATOM14_TO_ATOM37, aatype
)
no_batch_dims = len(aatype.shape)
rc.RESTYPE_ATOM14_TO_ATOM37,
aatype # (..., num_residues)
) # (..., num_residues, 14)
no_batch_dims = len(aatype.shape) - 1
atom14_mask = tensor_utils.batched_gather(
all_atom_mask,
residx_atom14_to_atom37,
all_atom_mask, # (..., num_residues, 37)
residx_atom14_to_atom37, # (..., num_residues, 14)
dim=no_batch_dims + 1,
no_batch_dims=no_batch_dims + 1,
).to(all_atom_pos.dtype)
).to(all_atom_pos.dtype) # (..., num_residues, 14)
# create a mask for known groundtruth positions
atom14_mask *= get_rc_tensor(rc.RESTYPE_ATOM14_MASK, aatype)
atom14_mask *= get_rc_tensor(rc.RESTYPE_ATOM14_MASK, aatype)
# gather the groundtruth positions
atom14_positions = tensor_utils.batched_gather(
all_atom_pos,
residx_atom14_to_atom37,
all_atom_pos, # (..., num_residues, 37, 3)
residx_atom14_to_atom37,
dim=no_batch_dims + 1,
no_batch_dims=no_batch_dims + 1,
),
atom14_positions = atom14_mask * atom14_positions
return atom14_positions, atom14_mask
)
atom14_positions = atom14_mask[..., None] * atom14_positions
return (
atom14_positions, # (..., num_residues, 14, 3)
atom14_mask # (..., num_residues, 14)
)


def get_alt_atom14(aatype, positions: torch.Tensor, mask):
Expand Down