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Improve IMGT numbering #76

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210671f
Rework annotations
benjiemc Jun 5, 2025
aea2ddc
Fix issue with PLIP renumbering
benjiemc Jun 6, 2025
cef106a
Silence BioPythonWarnings
benjiemc Jun 6, 2025
358a20c
Improve error message on failed annotation
benjiemc Jun 19, 2025
567f6c9
Fix bug where startFlag was not being unset
benjiemc Jun 23, 2025
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37 changes: 22 additions & 15 deletions stcrpy/tcr_interactions/TCRpMHC_PLIP_Model_Parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
)

from rdkit import Chem
from Bio import PDB
from Bio import BiopythonWarning, PDB
from Bio.PDB.PDBParser import PDBParser

from ..tcr_processing.TCRParser import TCRParser
Expand Down Expand Up @@ -71,13 +71,16 @@ def parse_tcr_pmhc_complex(
]
if renumber:
# renumber each chain from one to N to avoid automated renumbering issues related to plip and openbabel
renumbering = {}
for chain in tcr_and_mhc_chains:
renumbering[chain.id] = {}
for new_idx, res in enumerate(chain.get_residues()):
new_id = (" ", new_idx + 1, " ")
renumbering[chain.id][new_id] = res.id
res.id = new_id
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonWarning)

renumbering = {}
for chain in tcr_and_mhc_chains:
renumbering[chain.id] = {}
for new_idx, res in enumerate(chain.get_residues()):
new_id = (" ", new_idx + 1, " ")
renumbering[chain.id][new_id] = res.id
res.id = new_id
domain_assignment = tcr_pmhc_complex.get_domain_assignment()

TCR_MHC_FILE = os.path.join(self.tmp_dir, "tcr_mhc.pdb")
Expand All @@ -88,13 +91,17 @@ def parse_tcr_pmhc_complex(
io.set_structure(ligand)
io.save(PEPTIDE_PDB_FILE)

tcr_mhc_struct = PDB.Model.Model(id=0)
# add TCR chains to protein structure
for chain in tcr_pmhc_complex.get_chains():
tcr_mhc_struct.add(chain)
# add MHC chain to protein structure
for chain in tcr_pmhc_complex.get_MHC()[0].get_chains():
tcr_mhc_struct.add(chain)
tcr_mhc_struct = PDB.Structure.Structure('')
new_model = PDB.Model.Model(id=0)
for tcr_chain in tcr_and_mhc_chains:
new_chain = PDB.Chain.Chain(tcr_chain.id)

for residue in tcr_chain:
new_chain.add(residue.copy())

new_model.add(new_chain)

tcr_mhc_struct.add(new_model)

io = PDB.PDBIO()
io.set_structure(tcr_mhc_struct)
Expand Down
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