Usage

Command Line

The biosim-extractor CLI supports both local schema files and auto-fetched schema bundles.

Basic log-file extraction:

biosim-extractor mappings.json --engine gromacs --logfile md.log --output metadata.json

The mappings.json file used is created from biosim-schema here.

Using an explicit biosim schema file for validation:

biosim-extractor mappings.json \
  --biosimschema biosim_schema.yaml \
  --engine amber \
  --logfile md.log \
  --output metadata.json

Using fetched schema bundle (no local schema paths required):

biosim-extractor \
  --schema-version latest \
  --schema-cache-dir /tmp/biosim-schema-cache \
  --engine gromacs \
  --logfile md.log

Force refresh of cached schema bundle:

biosim-extractor --update-schema --engine gromacs --logfile md.log

Topology/trajectory mode via biosim-extractor:

biosim-extractor mappings.json --top topology.top --traj traj1.xtc traj2.xtc --output metadata.json

Control file metadata inclusion:

biosim-extractor mappings.json --engine gromacs --logfile md.log --no-file-metadata
biosim-extractor mappings.json --engine gromacs --logfile md.log --file-metadata

Other available options:

• --config: path to configuration file.

• -o, --output: output file path (prints to stdout when omitted).

Toptraj standalone parser:

python -m biosim_extractor.mdanalysis.toptraj topology.top trajectory.xtc --output toptraj.json

Python API

You can also use the API directly in your own scripts.

Log-file mode (Amber/GROMACS):

from biosim_extractor.metadata.populatemetadata import MetadataPopulator

populator = MetadataPopulator(
    schema_path="mappings.json",
    log_file="md.log",
    engine="gromacs",
    store_file_metadata=True,  # set False to skip file hash/size collection
)

metadata = populator.populate()
populator.validate(metadata, biosimschema_path="biosim_schema.yaml")
print(metadata)

Topology/trajectory mode:

from biosim_extractor.metadata.populatemetadata import MetadataPopulator

populator = MetadataPopulator(
    schema_path="mappings.json",
    top_file="topology.top",
    traj_file=["traj1.xtc", "traj2.xtc"],
    store_file_metadata=False,
)

metadata = populator.populate()
print(metadata)