The following table shows optional arguments when scripting a local Nova application prediction. Only a subset of these arguments is available, 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 |
|---|---|---|---|---|---|
| --force | Performs these two functions: * Deletes any existing Docker container sharing the same --seqname or --name as the current prediction input. * After the current run has finished, deletes the Docker container for that run. The --force command has additional functionality related to reinstallation. |
✔ | ✔ | ✔ | |
| -h, --help | To display a list containing a subset of options and then to exit. | ✔ | ✔ | ✔ | |
| --log [CRITICAL, ERROR, WARNING, INFO, DEBUG, NOTSET] | To enable specific types of logging. | default: [INFO] | ✔ | ✔ | ✔ |
| --lshost LSHOST | To define the network license server, where value is the IP address (or hostname) of the DNASTAR License Server. For capitalization rules, see Set up and run a prediction. Note: This parameter is not required if the environment variable has already been set. |
✔ | ✔ | ✔ | |
| --recover | To recover results from a stopped Docker container. | ✔ | ✔ | ✔ | |
| --version | To output the NovaFold version and exit. | ✔ | ✔ | ✔ | |
| --supplemental-help | To display a list containing additional NovaFold options and exit. An argument shown without brackets is required. The use of brackets signifies that the argument is optional. | ✔ | |||
| --library LIBRARY | The version of library volume for prediction. | default: [latest novafold-antibody-library] | ✔ | ✔ | |
| --seqfile SEQFILE | To designate a local FASTA file as the query. SEQFILE represents the local path and filename of the query sequence, which must be in FASTA format. If you provide a path with no filename, NovaFold Local will look for a file named seq.fasta located in the specified directory. | ✔ | ✔ | ||
| --lcontacts LCONTACTS | To specify a file listing proposed contact residues for the ligand. Each line represents one contact residue using the format: [CHAIN ID] [RESIDUE NUMBER] * The CHAIN ID is case sensitive and is typically a single character. * The RESIDUE NUMBER is an integer and may include an insertion code. Examples: L 15 L 15A |
✔ | |||
| --rcontacts RCONTACTS | To specify a file listing proposed contact residues for the receptor. Using this argument causes NovaDock to focus docking around the specified contacts, reducing computation time. Each line represents one contact residue using the format: [CHAIN ID][RESIDUE NUMBER] * The CHAIN ID is case sensitive and is typically a single character. * The RESIDUE NUMBER is an integer and may include an insertion code. Examples: R 15 R 15A |
✔ | |||
| --lmodes LMODES | Number of normal modes of motion to explore for the ligand. We suggest using the default to model large, concerted conformational changes and using a higher number (e.g. 20) to model more localized fluctuations, such as within antibody interfaces. | default: 5 | ✔ | ||
| --rmodes RMODES | Number of normal modes of motion to explore for the receptor. We suggest using the default to model large, concerted conformational changes and using a higher number (e.g. 20) to model more localized fluctuations, such as within antibody interfaces. | default: 5 | ✔ | ||
| --ncopies NCOPIES | Number of copies of each swarm point to run. | range: [1,50] default: 4 | ✔ |
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