Fix segfault when ligands fail to parse in batch mode#181
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caic99 wants to merge 2 commits intodptech-corp:mainfrom
Open
Fix segfault when ligands fail to parse in batch mode#181caic99 wants to merge 2 commits intodptech-corp:mainfrom
caic99 wants to merge 2 commits intodptech-corp:mainfrom
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When using --ligand_index, ligands that fail to parse return an empty model with an empty ligands vector. Accessing ligands[0] on that empty vector causes a segfault. Add a guard to check for empty ligands and skip them with a warning instead of crashing. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
--ligand_indexwith ligands that fail to parseparse_ligand_from_file_no_failure()returns an empty model (with emptyligandsvector) when parsing fails, butmain.cppaccessesligands[0]without checking, causing a crashligandsvector before accessing it, skipping failed ligands with a warning instead of crashingTest plan
--ligand_indexcontaining a mix of valid and intentionally malformed ligand files🤖 Generated with Claude Code