Getting started

The functions that help analyzing data in the FAIRMD Lipids are described here. These functions are located in the fairmd.lipids module. To get started using these functions, first set up the package and initialize the databank:

pip install nmrlipids_databank fmdl_initialize_data toy source databank_env.rc

“Toy” is a small test databank which is useful for testing and learning the package. You can then start to work with the template or write a code from the scratch. The minimum python code to intialize FAIRMD Lipids is

from fairmd.lipids.core import initialize_databank

systems = initialize_databank()

After running this, systems is an instance of fairmd.lipids.core.SystemsCollection which works like a list but with added functionality and contains dictionaries where each dictionary is a simulation in the FAIRMD Lipids. A simulation dictionary contains the content of the README.yaml for that simulation. The content of README.yaml files is described in Simulation metadata. systems can be then used to loop over all simulations:

for system in systems:
    print(system)

Examples on analyses over FAIRMD Lipids can be found from the template and codes used to analyze the results for the FAIRMD Lipids manuscript.

The core functionality of the fairmd-lipids including initializing the database and the definition of main data models is provided by fairmd.lipids.core. Some useful functions for analysis of the simulations can be found in the fairmd.lipids.databankLibrary module.

• Examples and tutorials