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Write single bonds to chem_comp_bond as fallback #870

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Merged
padix-key merged 1 commit into from
Feb 27, 2026
Merged

Write single bonds to chem_comp_bond as fallback #870

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15 changes: 13 additions & 2 deletions src/biotite/structure/io/pdbx/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -852,6 +852,17 @@ def _get_box(block):
return vectors_from_unitcell(len_a, len_b, len_c, alpha, beta, gamma)


def _get_chem_comp_bond_type(bond_type):
try:
return COMP_BOND_TYPE_TO_ORDER[bond_type]
except KeyError:
warnings.warn(
f"Bond type '{BondType(bond_type).name}' is not recognized by "
"'chem_comp_bond', a single bond will be assigned instead"
)
return ("SING", "N")


def set_structure(
pdbx_file,
array,
Expand Down Expand Up @@ -1147,7 +1158,7 @@ def _set_intra_residue_bonds(array, atom_site):
if bond_type == BondType.ANY:
# ANY bonds will be masked anyway, no need to set the value
continue
order, aromatic = COMP_BOND_TYPE_TO_ORDER[bond_type]
order, aromatic = _get_chem_comp_bond_type(bond_type)
value_order[i] = order
aromatic_flag[i] = aromatic
any_mask = bond_array[:, 2] == BondType.ANY
Expand Down Expand Up @@ -1520,7 +1531,7 @@ def set_component(pdbx_file, array, data_block=None):
order_flags = []
aromatic_flags = []
for bond_type in bond_array[:, 2]:
order_flag, aromatic_flag = COMP_BOND_TYPE_TO_ORDER[bond_type]
order_flag, aromatic_flag = _get_chem_comp_bond_type(bond_type)
order_flags.append(order_flag)
aromatic_flags.append(aromatic_flag)

Expand Down
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