DatabankLib CLI

The NMRlipids Databank includes several standalone programs that are used to add simulation, pair them with experiments, evaluate quality and process ranking.

nml_initialize_data

Initializes NMRlipids Databank data folder for further work and creates databank_env.rc file.

Usage:

nml_initialize_data [toy|stable|dev|-h]
source databank_env.rc

  • toy: copies ToyData from the package data. This Databank contains only 4 very small systems

  • stable: download stable release from github.com/NMRlipids/BilayerData (even without git)

  • dev: clone NMRlipids/BilayerData (requires git)

nml_add_simulation

Add new simulation into the NMRlipids Databank.

The script adds a simulation into the Databank based on info.yaml file.

Usage:

nml_add_simulation [-h] [-f FILE] [-d] [-n] [-w WORK_DIR] [–dry-run]

-h, --help

Show this help message and exit

-f FILE, --file=FILE

Input config file in yaml format.

-d, --debug

Enable debug logging output

-n, --no-cache

Always redownload repository files

-w WORK_DIR, --work-dir=WORK_DIR

Set custom temporary working directory [not set = read from YAML]

Returns error codes:

  • 0 - success

  • 1 - input YAML parsing errors

  • 2 - filesystem writting errors

  • 3 - network accessing errors

nml_compute_databank

Compute properties for systems of the databank.

Script can compute selected set of properties for selected range of systems of the databank. Properties available: APL, thickness, PCA relaxation times, MAICOS (density profiles, water orientation, dielectric profiles, X-ray form factor).

Usage:

nml_compute_databank [--apl] [--nmrpca] [--maicos] [--thickness] \
    [--OP] [--range 0-1000] [--debug] [-h]

Command line arguments:

--range=ID_RANGE

Range of system IDs to analyze, e.g. 0-1000. The interval ID_RANGE can be opened at either end, e.g. *-50 or 25-*. Use *-0 to analyze all just-added systems.

--apl

Compute APL (Area Per Lipid) for all systems.

--nmrpca

Compute NMR PCA for all systems.

--ff

Compute MAICOS electron density and form-factor for all systems.

--maicos

Compute MAICOS profiles for all systems.

--thickness

Compute Thickness for all systems.

--OP

Compute Order Parameter for all systems.

--debug

Enable debug logging.

--help

Show this help message and exit.

nml_match_experiments

Match simulations with experiments in the databank.

Script goes through all simulations and experiments in the databank and finds pairs of simulations and experiments that match in composition, temperature and other conditions. The found pairs are written into the simulation README.yaml files and into a log file.

Usage:

nml_match_experiments

No arguments are needed.

nml_evaluate_quality

Perform comparison of experiments and simulations.

The script compares according to EXPERIMENT field inside the simulation README.yaml file. In the standard protocol, it should be run after nml_match_experiments.

Usage:

nml_evaluate_quality

No arguments are needed.

nml_make_ranking

Creates different types of ranking lists inside the Databank.

It ranks simulations based on their quality against experiments. The ranking lists are stored in {NMLDB_DATA_PATH}/Ranking/ folder in JSON format. The lists can be shown with the DatabankLib.plottings module.

Usage:

nml_make_ranking

No arguments are needed.