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! — Reply to this email directly, view it on GitHub <#139>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA76LAXDYBFS53QXVREOXBTXFPN7LANCNFSM6AAAAAAX5DAT34> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>