Add support for N-terminal, protonated, disulfide-bonded cysteine (branch form of #2194)#2195
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) * fix(proteins): generate n-terminal disulfide cysteine templates * chore(proteins): update cysteine substructure data * test(proteins): cover n-terminal cysteine disulfide ingestion * docs: note n-terminal cysteine disulfide support * fix(utils): use reachable wwPDB CIF endpoint * chore(proteins): align cysteine data with full regeneration
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j-wags
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This looks flawless to me. Thanks @joelaforet!
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(not blocking) Reviewing this made me realize that our CYX loading test files don't have CONECT records for the disulfide bond. So right now we only test the case where there are disulfide bonds without CONECT records, but maybe it'd be good to add variants of the test inputs to exercise the explicit-CONECT case as well. This isn't something that should be handled here but I may make a separate issue for this.
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This is the continuation of the changeset in #2194
The following is copied from @joelaforet's original PR body:
Fixes #2191.
This PR adds support for loading N-terminal, protonated, disulfide-bonded cysteine residues from PDB files.
Specifically, this covers a
CYSresidue with:NH3+SGHGSG-SGdisulfide connectivityChanges made:
utilities/make_substructure_dict/_cif_to_substructure_dict.py.aa_residues_substructures_with_caps.jsonaa_residues_substructures_explicit_bond_orders_with_caps.jsonaa_residues_substructures_explicit_bond_orders_with_caps_explicit_connectivity.jsonMolecule.from_polymer_pdb.docs/releasehistory.md.ftp.wwpdb.orgtofiles.wwpdb.org, sinceftp.wwpdb.orgdid not resolve locally but the same wwPDB file was available fromfiles.wwpdb.org.Validation run locally:
mamba run -n openff-toolkit-ncy pytest openff/toolkit/_tests/test_molecule.py -k "cys_disulfide or mainchain_cyx_dipeptide or mainchain_cys_dipeptide or mainchain_cym_dipeptide"Result:
4 passed
Additional checks:
The regenerated explicit-connectivity SMARTS library validates successfully.
The motivating protein, PDB=4CHA, now loads with Topology.from_pdb, giving 3519 atoms and 1 molecule.