atom index in af.prep.prep_pdb

[data2code]

In the prep_pdb.py file, line 434

    im = ignore_missing[n] if isinstance(ignore_missing,list) else ignore_missing
    if im:
      r = batch["all_atom_mask"][:,0] == 1  #<===== THIS LINE
      batch = jax.tree_map(lambda x:x[r], batch)
      residue_index = batch["residue_index"] + last

Should not one use batch["all_atom_mask"][1], if we want to check if Ca is present? The 0th atom is for N according to residue_constants.atom_types.

Thanks!

[sokrypton]

🙏 thanks

On Wed, May 10, 2023, 3:37 PM Yingyao Zhou @.***> wrote:

In the prep_pdb.py file, line 434

im = ignore_missing[n] if isinstance(ignore_missing,list) else ignore_missing
if im:
  r = batch["all_atom_mask"][:,0] == 1  #<===== THIS LINE
  batch = jax.tree_map(lambda x:x[r], batch)
  residue_index = batch["residue_index"] + last

Should not one use batch["all_atom_mask"][1], if we want to check if Ca is present? The 0th atom is for N according to residue_constants.atom_types.

Thanks!

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