Fix config path in V2 de novo generation command in README - #30
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haokun-zhao wants to merge 1 commit into
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Fix config path in V2 de novo generation command in README#30haokun-zhao wants to merge 1 commit into
haokun-zhao wants to merge 1 commit into
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The README's GenMol V2 de novo command passes `-c scripts/exps/frag/hparams_v2.yaml`, which fails two ways: 1. `denovo/run.py` resolves the `-c` path relative to the script's own directory (os.path.dirname(os.path.realpath(__file__))), so the argument expands to scripts/exps/denovo/scripts/exps/frag/hparams_v2.yaml -> FileNotFoundError. 2. Even by absolute path, frag/hparams_v2.yaml nests its parameters under per-task keys (linker_design, motif_extension, ...), whereas denovo/run.py reads flat top-level keys, so it raises KeyError: 'softmax_temp'. The correct config is denovo/hparams_v2.yaml, which is flat and already present. Since run.py resolves relative to its own dir, the argument is just `-c hparams_v2.yaml` (matching the V1 de novo command above). Verified: the fixed command runs cleanly on GenMol V2, producing metrics consistent with the paper's de novo benchmark table.
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The GenMol V2 De Novo Generation command in the README currently reads:
This fails for two independent reasons:
Wrong relative path.
denovo/run.pyresolves the-cargument relative to the script's own directory:So
scripts/exps/frag/hparams_v2.yamlexpands toscripts/exps/denovo/scripts/exps/frag/hparams_v2.yamland raisesFileNotFoundError.Wrong config schema. Even when pointed at
frag/hparams_v2.yamlby absolute path, that file nests its hyperparameters under per-task keys (linker_design,motif_extension,scaffold_decoration, ...).denovo/run.pyreads flat top-level keys (config['softmax_temp'],config['randomness'],config['min_add_len']), so it raisesKeyError: 'softmax_temp'.The intended config is
denovo/hparams_v2.yaml, which is flat and already in the repo. Becauserun.pyresolves relative to its own directory, the argument is simply-c hparams_v2.yaml— consistent with the V1 De Novo command earlier in the README.I verified the fixed command runs cleanly on GenMol V2 and produces metrics consistent with the de novo benchmark table in the README (validity 1.0, uniqueness ~0.95, diversity ~0.83, quality ~0.86).
The Fragment-constrained command below is unchanged —
frag/run.pycorrectly consumes the nestedfrag/hparams_v2.yaml.