improve error handling for failed paddings

[diogomart]

Currently, an error is thrown but it does not state which residues cause the problem.

bad_clash.pdb.txt

[ghliu521]

matched with excess inter-residue bond(s): S:101
Traceback (most recent call last):
File "/home/ghliu/miniconda3/envs/dockenv/bin/mk_prepare_receptor.py", line 9, in
sys.exit(main())
^^^^^^
File "/home/ghliu/miniconda3/envs/dockenv/lib/python3.11/site-packages/meeko/cli/mk_prepare_receptor.py", line 610, in main
polymer = Polymer.from_prody(
^^^^^^^^^^^^^^^^^^^
File "/home/ghliu/miniconda3/envs/dockenv/lib/python3.11/site-packages/meeko/polymer.py", line 1331, in from_prody
polymer = cls(
^^^^
File "/home/ghliu/miniconda3/envs/dockenv/lib/python3.11/site-packages/meeko/polymer.py", line 931, in init
padded_mols = self._build_padded_mols(self.monomers, bonds, padders)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ghliu/miniconda3/envs/dockenv/lib/python3.11/site-packages/meeko/polymer.py", line 1801, in _build_padded_mols
raise RuntimeError(err_msg)
RuntimeError: Expected 4 paddings for (B:2, S:101) with bonds [(28, 40), (28, 42)], but got 2

Maybe this error happened to me might help identify which residues are causing the issue. The PDB ID is 7ELP; the file can be downloaded from the RCSB.

[diogomart]

@ghliu521 please open new issues for new issues, and don't repeat the same issue. This is a case of a standard residue (GTP) having a covalent bond to other residues. GTP is not expected to have bonds to other residues (although it does sometimes). Meeko does not handle this situation currently. If the tri-phosphate isn't in the binding site of interest, you could delete two phosphates and model GTP as standard G.

[ghliu521]

Sorry I was expecting to find similar issues as mine.

You're right, in most cases GTP exist as standalone ligand. Thank you very much for your advice.

[diogomart]

We will work on this eventually, but there's other things we need to get done before we get to it. Sorry for not handling your system properly.

[ghliu521]

Thank you very much anyway. It still helps me a lot.