[sukhmansaran]

Code of Conduct

OK

Description

PandasMol2._get_atomsection() only sets last_idx_plus1 when it finds a blank line or another @<TRIPOS> record after the ATOM section. If the ATOM section is the last thing in the input, that variable is never set, and reading the molecule fails:

from biopandas.mol2 import PandasMol2

lines = [
    "@<TRIPOS>MOLECULE\n", "sodium\n", "1 0 0 0 0\n", "SMALL\n", "USER_CHARGES\n", "\n",
    "@<TRIPOS>ATOM\n",
    "1 Na 0.0000 0.0000 0.0000 Na 1 NA 1.0000\n",
]
PandasMol2().read_mol2_from_list(lines, "sodium")
# UnboundLocalError: cannot access local variable 'last_idx_plus1' where it is not associated with a value

read_mol2() hits the same error for a file that ends with its ATOM section, with or without a trailing newline. This happens for molecules without bonds (e.g. a single ion), where some tools write no BOND section.

The fix sets last_idx_plus1 = len(mol2_lst) before the loop, so in that case the ATOM section runs to the end of the input. When a blank line or @<TRIPOS> record follows the section, it still ends there as before, and the ValueError for input without an ATOM section is unchanged.

This is a different case from #136, which was fixed by #140 (blank lines between sections).

Tests (tests/mol2/test_pandas_mol2.py):

• test_read_mol2_atom_section_at_end_of_input reads a molecule whose ATOM section is last via read_mol2_from_list, with and without a newline after the last atom.
• test_read_mol2_file_atom_section_at_end_of_file reads a single-ion .mol2 file that ends with its ATOM section via read_mol2.

Both fail on main with the UnboundLocalError above and pass with this change.

Related issues or pull requests

Related to #170 (Mol2 BOND parsing). The two PRs touch different parts of pandas_mol2.py, the tests file and the changelog, and merge with each other without conflicts.

Pull Request Checklist

• Added a note about the modification or contribution to the ./docs/sources/CHANGELOG.md file (if applicable) (added to docs/CHANGELOG.md, where the current "Unreleased" section is)
• Added appropriate unit test functions in the ./biopandas/*/tests directories (if applicable) (in tests/mol2/)
• Modify documentation in the corresponding Jupyter Notebook under biopandas/docs/sources/ (if applicable) (not needed, no API change)
• Ran PYTHONPATH='.' pytest ./biopandas -sv and make sure that all unit tests pass (full tests/ suite: 129 passed, 7 skipped, 13 xfailed with pandas 3.1.1; tests/mol2 also passes with pandas 2.3.3. tests/pdb/test_read_pdb.py was deselected locally because it needs network access to RCSB.)
• Checked for style issues by running flake8 ./biopandas (no warnings on the changed files)

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