kermt-embed

Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint. The skill is the workflow orchestrator: validate ckpt, validate CSV, clean SMILES, launch the runner blocking, return the per-readout .npy files.

Hardware requirements

• GPUs: 1 (single-GPU).
• VRAM: ≥ 4 GB for the default batch_size 64.
• Disk: depends on output size — roughly a few MB per 1k molecules at hidden 800 per readout, so ~10–20 MB per 1k molecules across the 4 readouts. Plus a small canonical_smiles.npy + validity.npy per run.
• Driver / CUDA: any host supporting CUDA 12.6.

Inputs

Required: