README.md

Gromacs Metadata Extractor

This is the script that extracts the metadata from the molecular dynamics simulations.

This code is also deployed at https://gmxmetadump.biodata.ceitec.cz/, where it is possible to obtain metadata after uploading a TPR file without need to install or run local scripts.

Dependencies

• Gromacs software with dump utility (gmx dump)
• Python 3.8 and greater

Usage

How to use the Gromacs Metadata Extractor software.

Basic usage from CLI

pytohn3 extract.py --tpr_file <path to TPR file>

Available Arguments

Argument	Description	Example
--tpr_file	Path to the TPR file	--tpr_file <path_to_TPR_file>
--cpt_file	Path to the CPT file	Unnused at the moment
--gro_file	Path to the GRO file	Unnused at the moment
--format	Format of output metadata <json/yaml>	--format json
--debug	Print debug information <true/false>	--debug true

As Python module

Use for automatization from own Python scripts.

from GromacsMetadataExtractor import MetadataExtractor

extractor_object = MetadataExtractor(tpr_file[, gro_file[, cpt_file[, debug]]])
metadata = extractor_object.run().export()
# Print `metadata` dictionary
print(metadata)

Methods

Method	Description
run()	Runs the metadata parser
print(format=<json/yaml>)	Prints the metadata to STDOUT
export()	Returns dictionary with metadata

Example of advanced usage

See paralel_run.py

Authors

Adrián Rošinec - adrian@ics.muni.cz
Ondřej Schindler - ondrej.schindler@mail.muni.cz

License

BSD 3-Clause License, see LICESNE file

Copyright (c) 2023, CEITEC and CERIT-SC, Masaryk University. All rights reserved.