Add support for N-terminal, protonated, disulfide-bonded cysteine#2194
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j-wags merged 6 commits intoJun 8, 2026
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Thanks @joelaforet! This looks quite good to me, but while this is just a fork the tests won't run. I'm going to retarget this PR to put the changes from your fork into a branch, then merge it, then I'll open a second PR to merge the changes from that branch into main (which will actually run the tests).
Sorry for the runaround in this process, the tests-fail-on-forks issue is downstream of us needing to test against OpenEye.
| import requests | ||
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| r = requests.get("https://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif") | ||
| r = requests.get("https://files.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif") |
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(not blocking) Oh nice, good catch!
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) (#2195) * 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 Co-authored-by: Joe Laforet Jr. <76799675+joelaforet@users.noreply.github.com>
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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.