The following table shows arguments that are required when scripting a local Nova application prediction. Only a subset of these arguments is required, depending on the application. The three rightmost columns show whether the argument applies to NF (NovaFold), NFA (NovaFold Antibody) or ND (NovaDock).
| Name | Definition | Arguments and Defaults | NF | NFA | ND |
|---|---|---|---|---|---|
| --datadir DATADIR | The path to the location where output/results will be written. | ✔ | ✔ | ||
| --seqname SEQNAME | The unique name of the query sequence. | ✔ | ✔ | ||
| --output-dir OUTPUT, -o OUTPUT | The path to the result output directory. | ✔ | |||
| --name NAME | The name for this complex prediction. | ✔ | |||
| --lfile LFILE | Path to a ligand PDB file that includes all chains. The ligand is often, though not always, smaller than the receptor. | ✔ | |||
| --rfile RFILE | Path to a receptor PDB file that includes all chains. The receptor is often, though not always, larger than the ligand. | ✔ |
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