Validating NEF file

[kumar-physics]

How to validate a NEF file and make sure it is consistent with NEF dictionary? Will NEF developers provide validation tools?

[rhfogh]

There are two main issues here:

• Is the file formally correct? That should be possible to test using the specification .dic and the standard tools for validating cif files, which deal with mandatory fields, data types, etc.
• Are data consistent? The one issue that can be checked formally is whether a given chain code and sequence code consistently use the same residue type ('name') throughout.

The biggest practical problem is whether atom names (especially) can be mapped correctly to IUPAC naming. This is not really susceptible to validation, since just about any atom name is legal - assignments that cannot be matched to the structure and sequence are simply interpreted as anonymous, unassigned atoms. And which atoms can be matched to the sequence and structure can, of course, only be determined by comparing with the known sequence and structure.

The most practical approach might be a reference imlementation for converting atoms to IUPAC names given a known sequence.