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Allow loading computationally predicted cif files, which may not have certain custom annotations #670

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merged 3 commits into from
Oct 19, 2024
Merged

Allow loading computationally predicted cif files, which may not have certain custom annotations #670

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69cbe87
feat: allow missing extra fields when reading cif files; warn user if…
Croydon-Brixton Oct 4, 2024
6718b1d
fix: explicitly note that masked values are set to 0
Croydon-Brixton Oct 9, 2024
9b235e1
chore: ruff
Croydon-Brixton Oct 16, 2024
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45 changes: 41 additions & 4 deletions src/biotite/structure/io/pdbx/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -480,16 +480,53 @@ def _fill_annotations(array, atom_site, extra_fields, use_author_fields):
array.set_annotation("element", atom_site["type_symbol"].as_array(str))

if "atom_id" in extra_fields:
array.set_annotation("atom_id", atom_site["id"].as_array(int))
if "id" in atom_site:
array.set_annotation("atom_id", atom_site["id"].as_array(int))
else:
warnings.warn(
"Missing 'id' in 'atom_site' category. 'atom_id' generated automatically.",
UserWarning,
)
array.set_annotation("atom_id", np.arange(array.array_length()))
extra_fields.remove("atom_id")
if "b_factor" in extra_fields:
array.set_annotation("b_factor", atom_site["B_iso_or_equiv"].as_array(float))
if "B_iso_or_equiv" in atom_site:
array.set_annotation(
"b_factor", atom_site["B_iso_or_equiv"].as_array(float)
)
else:
warnings.warn(
"Missing 'B_iso_or_equiv' in 'atom_site' category. 'b_factor' will be set to `nan`.",
UserWarning,
)
array.set_annotation("b_factor", np.full(array.array_length(), np.nan))
extra_fields.remove("b_factor")
if "occupancy" in extra_fields:
array.set_annotation("occupancy", atom_site["occupancy"].as_array(float))
if "occupancy" in atom_site:
array.set_annotation("occupancy", atom_site["occupancy"].as_array(float))
else:
warnings.warn(
"Missing 'occupancy' in 'atom_site' category. 'occupancy' will be assumed to be 1.0",
UserWarning,
)
array.set_annotation(
"occupancy", np.ones(array.array_length(), dtype=float)
)
extra_fields.remove("occupancy")
if "charge" in extra_fields:
array.set_annotation("charge", atom_site["pdbx_formal_charge"].as_array(int, 0))
if "pdbx_formal_charge" in atom_site:
array.set_annotation(
"charge",
atom_site["pdbx_formal_charge"].as_array(
int, 0
), # masked values are set to 0
)
else:
warnings.warn(
"Missing 'pdbx_formal_charge' in 'atom_site' category. 'charge' will be set to 0",
UserWarning,
)
array.set_annotation("charge", np.zeros(array.array_length(), dtype=int))
extra_fields.remove("charge")

# Handle all remaining custom fields
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