This repository implements a file converterfrom OSC-EM JSON to PDBx/mmCIF. The JSON schema is defined in OSCEM and the PDBx/mmCIF format in (PDBML Schema v50 ).
- converter executable
- with
--jsonspecify path to json file that contains metadata - with
--dicspecify path to the PDBx/mmCIF dictionary file - with
--conversionsspecify path to conversions table. This table includes correspondance in names between OSC-EM and PDBx - with
--levelspecify the json element name that contains metadata entries. For SciCat that is usually "scientificMetadata" - with
--appendspecify if the metadata should be added to existing mmCIF to later deposit it in PDB - with
--mmCIFfilespecify the path to existing mmCIF file. Throws an error if --append is false and --mmCIFfile is not specified - with
--outputspecify the file to write the newly created mmCIF with metadata entries
Converter explicitly parser through the PDBx definitions to extract as much data as possible. This allows for
- administrative categories sorted within mmCIF ( such as author information, grant, etc)
- em-related categories are sorted randomly, as there is no definitive sorting in PDB team as well
- file ends with information on atoms
- units in OSCEM definition are comared to PDBx ( converter for units will be implemented)
- numeric values are checked to be within a range allowed by PDBs
- values are checked to be within a list of attributes allowed by PDBx. This is additionally enhanced to match via regular expressions or ceratin logic.