DrelTools: A dREL to Julia translator

Introduction

dREL (J. Chem. Inf. Model., 2012, 52 (8), pp 1917–1925 DOI: 10.1021/ci300076w) is a machine-readable language for describing the relationships between data names defined in a CIF (Crystallographic Information Framework) dictionary. Examples of dREL use can be found in the latest CIF core dictionary.

This package is experimental. Method and type names are subject to change. Suggestions on speed improvement and new functionality are welcome.

Installation

Install Julia. At the Pkg prompt (ie after entering ]) type add DrelTools. Simply put using DrelTools at the top of any Julia code that uses methods from this package.

Note that CIF support is provided by the CrystalInfoFramework package, which you will probably also need to install in order to read in CIF files.

Please advise of any difficulties in installation so that either these instructions or the installation setup can be improved.

Documentation

Documentation is available here.

Usage

1. define_dict_funcs(c::Cifdic) will process all dREL functions found in the dictionary. This must be called if the dictionary contains a Function category that defines functions used in other dREL fragments. Note that dREL functions are like library functions that are not associated with data names, unlike the methods found inside definitions.
2. A DynamicDDLmRC is a container that holds relations (ie tables), whose contents are described by a DDLm dictionary. It takes any DataSource, including CIF data blocks. It is dynamic because it can derive missing values using dREL fragments in the dictionary. The resulting values are not stored in the block, but are cached. The example below shows how a DynamicDDLmRC is created from a data block and a dictionary.
3. derive(d::DynamicDDLmRC,s::String) will derive the value of dataname s based on other values in the block and dREL code found in the dictionary associated with d.
4. empty_cache!(d::dynamic_block) clears cached values from previous derivations.

    p = DDLm_Dictionary("cif_core.dic")
    define_dict_funcs(p)    #add dREL Functions to dictionary
    n = NativeCif("nick1.cif") #Read in a CIF file
    b = n["saly2_all_aniso"] #select a data block
    t = TypedDataSource(b,p) #p describes the data in b
    db = DynamicDDLmRC(t,p) #create a dynamic block
    # 
    # (Re)evaluate an item
    #
    s = derive(db,"_cell.atomic_mass") #derive value

test/drel_exec.jl contains simple demonstrations of how to make use of dREL scripts found in dictionaries.

Note

The deps directory contains a short script to pre-build the dREL grammar. When changing the grammar this should be re-run.