Command Line Interface¶
After following instructions in the Installation Guide, you should be able to run ELASPIC
from the command line using the elaspic
command:
$ elaspic --help
usage: elaspic [-h] {run,database,train} ...
optional arguments:
-h, --help show this help message and exit.
command:
{run,database,train}
run run ELASPIC
database perform database maintenance tasks
train train the ELASPIC classifiers
Type --help
to see the options available for each subcommand:
elaspic run --help
elaspic database --help
elaspic database load_data --help
- etc...
elaspic run¶
Run the ELASPIC pipeline.
If you wish to mutate an existing PDB, you should specify the name of the PDB file to be mutated, and the mutation(s):
elaspic run \
--structure_file {structure_file} \
--mutations {mutations}
If you wish to first create a homology model of a protein, you should provide a fasta file containing the sequence of the protein to be modelled, a PDB file containing the structural template, and the mutation(s):
elaspic run \
--sequence_file {sequence_file} \
--structure_file {structure_file} \
--mutations {mutations}
If you wish to perform mutagenesis on a proteome-wide scale, you need to download protein domain definitions from the elaspic downloads page, and optionally a local copy of the PDB database. After saving your database information to a configuration file, you can run specify the uniprot id and mutation(s):
elaspic run \
--config_file {config_file} \
--uniprot_id {uniprot_id} \
--mutations {mutations}
elaspic train¶
Train the machine learning predictor for the ELASPIC pipeline.
This is automatically done at install time, and you do not need to do this again unless you update your scikit-learn
version.
elaspic database¶
Perform maintenance tasks on the ELASPIC database.
You must provide a configuration file containing the details of your database installation for any of these commands to work. For more information about configuration files, see Updating the configuration file.
elaspic database create¶
Create a new database schema.
elaspic database load_data¶
Load data to the database.
elaspic database delete¶
Delete the database schema.