Fix bugs and improve robustness of ROCS scoring#19
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fulopjoz wants to merge 4 commits intoCDDLeiden:devfrom
Open
Fix bugs and improve robustness of ROCS scoring#19fulopjoz wants to merge 4 commits intoCDDLeiden:devfrom
fulopjoz wants to merge 4 commits intoCDDLeiden:devfrom
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Tutorial scripts used Path.cwd() to build paths, causing failures when invoked from a different directory. Now resolve paths relative to the script file location via Path(__file__).resolve().parent.
Add docstring to _score_single_reference explaining Gaussian shape overlay, the opt_param choices, and benchmarking results showing that optimization objective has no effect on final TanimotoCombo scores when sufficient conformer pairs are sampled.
Add configurable per-isomer timeout (default 120s) for ETKDGv3 embedding to prevent pathological molecules from blocking the conformer generation pipeline indefinitely.
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Summary
Follow-up fixes for the ROCS scoring module merged in #15. Addresses several bugs found during production use of the OpenEye ROCS scorer and improves robustness of conformer generation.
Changes
OpenEye ROCS scorer (
rocs_openeye.py):-shapeonlyflag always passing"false"instead of"true"when enabledcolor_optimizeparameter to the-optchemCLI flag (was silently ignored)OMP_NUM_THREADS="1"environment override from subprocess callRDKit conformer generator (
conformer_generators.py):timeoutparameter for ETKDGv3 embedding to prevent pathological molecules from blocking the pipelineTutorial scripts (
tutorial/advanced/rocs/):__file__) instead of current working directory so scripts work when invoked from any directoryRDKit ROCS scorer (
rocs_rdkit.py):_score_single_reference(Gaussian shape overlay vs graph-based ROCS)@martin-sicho