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Fix bug sometimes skipping peptide bond when using bio ccd to infer bonds. #203

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Fix bug sometimes skipping peptide bond when using bio ccd to infer bonds. #203

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12 changes: 7 additions & 5 deletions src/chilife/Topology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -422,10 +422,8 @@ def bonds_from_ccd_data(molsys, ccd_data):

if "chem_comp" in ccd_data[res.resname]:
res_ccd_data = ccd_data[res.resname]["chem_comp"]
if (
pres := res.previous_residue()
) is not None and "link type" in res_ccd_data:
link_type = res_ccd_data["link type"]
if (pres := res.previous_residue()) is not None and "type" in res_ccd_data:
link_type = res_ccd_data["type"].lower()
if link_type in POLYMER_LINKAGE_TYPES:
a1, a2, btype, bchiral = POLYMER_LINKAGE_TYPES[link_type]
i1 = pres.ix[pres.names == a1].flat[0]
Expand Down Expand Up @@ -477,4 +475,8 @@ def numpyify_ccd(ccd_data):


# Linkage data is atom name of the previous residue followed by atom name of the current residue followed by bond type
POLYMER_LINKAGE_TYPES = {"L-peptide linking": ["C", "N", BondType.SINGLE, "N"]}
POLYMER_LINKAGE_TYPES = {
"l-peptide linking": ["C", "N", BondType.SINGLE, "N"],
"peptide linking": ["C", "N", BondType.SINGLE, "N"],
"d-peptide linking": ["C", "N", BondType.SINGLE, "N"],
}
2 changes: 1 addition & 1 deletion src/chilife/__init__.py
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Expand Up @@ -44,4 +44,4 @@
# SpinLabel = SpinLabel.SpinLabel
# dSpinLabel = dSpinLabel.dSpinLabel

__version__ = "1.2.1"
__version__ = "1.2.2"
2 changes: 1 addition & 1 deletion tests/test_MolSys.py
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Expand Up @@ -707,5 +707,5 @@ def test_write_sdf():

def test_use_ccd():
mol = MolSys.from_pdb("test_data/7o1o.pdb", use_ccd=chilife.bio_ccd)
assert len(mol.bonds) == 5508
assert len(mol.bonds) == 5863
assert chilife.BondType.DOUBLE in mol.bond_types
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