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pad short lines when reading from non-file io #24

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Merged
padix-key merged 2 commits into from
May 27, 2025
Merged

pad short lines when reading from non-file io #24

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1ec1a2b
add test for reading from lines not padded to 80 chars
kleinhenz May 21, 2025
b329533
pad to 80 characters
kleinhenz May 21, 2025
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2 changes: 1 addition & 1 deletion python-src/fastpdb/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def read(file):
else:
if not is_text(file):
raise TypeError("A file opened in 'text' mode is required")
pdb_file._pdb_file = RustPDBFile(file.read().splitlines())
pdb_file._pdb_file = RustPDBFile([s.ljust(80) for s in file.read().splitlines()])

# Synchronize with PDB file representation in Rust
pdb_file.lines = pdb_file._pdb_file.lines
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12 changes: 11 additions & 1 deletion tests/test_fastpdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,4 +194,14 @@ def test_inferred_elements(tmp_path):
guessed_pdb_file = fastpdb.PDBFile.read(temp)
atoms_guessed_elements = guessed_pdb_file.get_structure()

assert atoms_guessed_elements.element.tolist() == atoms.element.tolist()
assert atoms_guessed_elements.element.tolist() == atoms.element.tolist()


def test_non_80_char_columns():
with open(DATA_PATH / "1l2y.pdb") as f:
lines = list(map(lambda s: s.rstrip(), f.readlines()))

pdb_file = fastpdb.PDBFile.read(StringIO(str.join("\n", lines)))
atoms = pdb_file.get_structure()

assert atoms is not None
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