Fix SIGSEGV with unsupported atom types in SDF ligands#180
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…ron) Add atom type validation to parse_sdf_atom_string() matching the existing check in parse_pdbqt_atom_string(). Without this, unsupported elements like boron return AD_TYPE_SIZE (sentinel value 35) from string_to_ad_type(), leading to out-of-bounds grid access and a segfault. Now the parser throws a struct_parse_error so the ligand is skipped gracefully. Also adds the is_non_ad_metal_name() check for non-AD metal types, which was similarly missing from the SDF parser. Fixes dptech-corp#138 Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
Miniforge 26.x (released Feb 2026) ships Python 3.13 by default, but the openbabel conda-forge package only has builds up to Python 3.12. This caused the "install tools" step to fail for all PRs. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>
This reverts commit ab6103c.
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Summary
parse_sdf_atom_string()inparse_pdbqt.cpp, matching the existing check inparse_pdbqt_atom_string()AD_TYPE_SIZEsentinel, causing out-of-bounds grid accessis_non_ad_metal_name()check for non-AD metal types in SDF parserRoot Cause
parse_sdf_atom_string()did not validate atom types. When an SDF contains boron or other unsupported elements,string_to_ad_type("B")returnsAD_TYPE_SIZE(35). The atom was added to the model without validation, and later grid evaluation accessedm_grids[35]out of bounds, causing a segfault.The PDBQT parser already had this validation via
acceptable_type()+struct_parse_error, but the SDF parser was missing it entirely.Test plan
Fixes #138
🤖 Generated with Claude Code