BioSim Extractor Documentation

biosim-extractor is available at http://github.com/CCPBioSim/biosim-extractor

A toolkit for extracting standardised metadata from molecular dynamics (MD) simulations.

Overview

BioSim Extractor provides tools to parse, extract, and standardize metadata from MD simulation outputs (AMBER, GROMACS, etc.), and validate against biosim-schema.

Features

• Parse log files from multiple MD engines

• Extract topology and trajectory metadata

• Standardise units and schema

• Validate metadata against biosim-schema biosim-schema

Getting Started

See Installation for setup instructions and Usage for examples.

API Reference

The full API documentation is available in API Reference.

Contents

Contents:

• Installation
• Usage
  • Command Line
  • Python API
• Contributing
  • Setting up for development
  • Running the tests
  • Linting and formatting
  • Pre-commit hooks
  • Continuous integration
  • Building the documentation
  • Submitting changes
• API Reference
  • MetadataPopulator
  • add_to_path()
  • assign_by_path()
  • flatten_dict()
  • get_by_path()
  • is_numeric()
  • main()
  • normalize_key()
  • parse_args()
  • remove_null_parents()
  • resolve_schema_inputs()
  • transform_value()
  • extract_schema_version()
  • validate_extracted()
  • validate_metadata()
  • convert_populated_metadata_units()
  • TopTrajParser
  • classify_box()
  • get_nucleic_sequence()
  • get_protein_sequence()
  • main()
  • parse_args()
  • safe_extract()
  • GromacsLogParser
  • main()
  • parse_args()
  • AmberLogParser
  • main()
  • parse_args()
  • UnitConverter

Funding

Contributors to biosim-extractor were supported by

Indices and tables

• Index

• Module Index