The International Union of Crystallography has approved two standards for writing CIF dictionaries (ontologies), DDL2 and DDLm. DDL2 dictionaries for macromolecular crystallography are developed and supported by the wwPDB. DDLm dictionaries cover the remainder of crystallographic disciplines. Some dictionaries are relevant to both areas, such as the image CIF dictionary. Ideally it should be possible to automatically transform between DDL2 and DDLm versions of this dictionary so that only one canonical version needs to be supported. This project implements such automatic translation.

1. Install Julia
2. After starting Julia, install the DrelTools package:

using Pkg
Pkg.add("DrelTools")

3. Exit from the Julia interactive prompt
4. Copy the contents of the distribution directory (easy with git): git clone https://github.com/jamesrhester/ddl_to_ddl

From the command line, and located in the distribution directory copied above, run:

julia ddl_to_ddl.jl <source_dictionary> <source_ddl>

This will convert <source_dictionary> written in DDL variant <source_ddl> (which must be either ddl2 or ddlm) to a version written in the other variant. The new dictionary will have to_<target_ddl>.dic appended. Note that this conversion is currently very slow (several minutes for the imgCIF dictionary).

Program compare.jl is also included. This compares two DDL2 dictionaries to find differences:

julia compare.jl <ddl> <first_dictionary> <second_dictionary>

where <ddl> is ddl2 (DDLm not yet supported).

The specifications for translating the dictionary attributes are entirely expressed in dREL. dREL is a language for manipulating relationally-organised data. The files ddl2_in_ddlm.dic, ddl2_extra_ddlm.dic and ddl2_with_methods.dic contain these dREL methods in the appropriate places.

In order to use dREL the relational organisation of the dictionaries themselves must be described. In other words, the save frame contents must be combined to form a set of tables. DDL2 is rigorously relational in its organisation and requires no further clarification; in the case of DDLm, master_id is added to all categories to refer to the definition.id to which a given attribute value relates. This is the only addition to the DDLm attribute set and only appears in the dREL methods.

ddl2_extra_ddlm.dic contains additional DDLm attribute definitions for describing construction of text values. The detailed descriptions found in DDL2 are not present in DDLm.