Simplify _construct_atom_map for protein mutations
#860
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
| @@ -336,6 +337,71 @@ def test_mutate_from_alanine(): | |||
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| _ = generate_dipeptide_top_pos_sys(ala.topology, amino, ala.system, ala.positions, system_generator, conduct_geometry_prop=False) | |||
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| def test_protein_atom_maps(): | |||
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it looks like you hardcoded some specific mutations. is this robust enough? i guess you can augment this test as/if you encounter problems in future?
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I think this is robust enough, as the test cases are representative of the different cases handled by the code:
- mutations where the old or new residue is GLY
- mutations where the old or new residue is in ['THR', 'ILE', 'VAL'] -- these contain HB atoms whereas all other non GLY amino acids contain HB1/HB2/HB3
- all other mutations
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| # Define function for checking that the atom map is correct | ||
| def check_atom_map(topology_proposal, reference_map): |
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can this be a utility outside the test fn?
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It will never be used outside of test_protein_atom_maps, so there's no need to move it outside
| new_oemol_res_copy : openeye.oechem.oemol object | ||
| copy of modified new oemol | ||
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| local_atom_map : dict, key: int, value int |
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i vaguely remember there being a reason we make a deepcopy of the oemol to append to the Topology object. can we keep that?
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scratch this. i dont think we need to keep deepcopy anymore.
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agreed. the deepcopy was necessary before because we were deleting backbone atoms from the original oemol (which would then be inputted to AtomMapper). However, we are no longer using the oemol for generating the map.
| current_oemol = PolymerProposalEngine.generate_oemol_from_pdb_template(current_residue_pdb_filename) | ||
| proposed_oemol = PolymerProposalEngine.generate_oemol_from_pdb_template(proposed_residue_pdb_filename) | ||
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| old_oemol_res_copy = copy.deepcopy(current_oemol) |
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reference to the oemol deepcopy is here.
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@jchodera Could you review this and let us know if its ok to merge? |
…eralab/perses into simplify-protein-atom-mapping
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@jchodera : Could you review this and let us know if its ok to merge? |
ijpulidos
modified the milestones:
0.10.0 Featurepalooza: Improved automated geometric mapping, new hybrid topology factory, improved support for charge changes, and protein mutations,
0.10.1 Bugfixes and More
Description
I've simplified the code for generating protein mutation atom mappings by generating the mapping directly from the old/new residue topologies. Generating the atom mapping no longer involves using
AtomMapperor oemols, but oemols are still generated and attached to the outputTopologyProposalbecause they are needed as input to the geometry engine.By default, we map backbone atoms and CB atoms (except for GLY, where we map CA but not HA2 or HA3).
Motivation and context
Resolves #857
How has this been tested?
I added
test_protein_atom_maps()totest_topology_proposal.py, which tests the generation of atom maps for some representative transformations.Change log