From 48c46e42909ed380cfd3485625e3118a527d8477 Mon Sep 17 00:00:00 2001 From: haokun-zhao Date: Thu, 23 Jul 2026 00:41:58 -0700 Subject: [PATCH] Fix config path in V2 de novo generation command 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. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index df2102d..e227455 100644 --- a/README.md +++ b/README.md @@ -247,7 +247,7 @@ The training used 8 NVIDIA A100 GPUs. ### *De Novo* Generation Run the following command to perform *de novo* generation using GenMol V2: ```bash -python scripts/exps/denovo/run.py -c scripts/exps/frag/hparams_v2.yaml +python scripts/exps/denovo/run.py -c hparams_v2.yaml ``` ### Fragment-constrained Generation