CrystalInfoFramework.jl

Julia tools for working with the Crystallographic Information Framework, including reading data files in Crystallographic Information Format (CIF) versions 1 and 2 (this includes mmCIF files from the PDB). As CIF format is a significant subset of STAR format, files in STAR format are likely to read in without problems. The tools also understand dictionaries written in DDLm and DDL2, which can be used to return correct types and find aliased datanames (note that this includes the PDB mmCIF dictionaries).

Warning: pre-1.0 release

Types, method names, and method signatures may change in later versions.

If you see ways to improve the naming or architecture, now is the time to raise an issue.

Installation

Once Julia is installed, it is sufficient to add CrystalInfoFramework at the Pkg prompt (accessed by the ] character in the REPL).

Documentation

Detailed documentation is becoming progressively available here.

Getting started

Type Cif is like a Dict{String,Block}. A Block works like a Dict{String,Array{Any,1}}. All returned values are Arrays, even if the data name appears as a key-value pair in the file. Primitive values are always Strings. CIF2 Tables become julia Dict types, and CIF2 lists are julia Array types.

Even in the presence of a dictionary, DDLm Set category values are returned as 1-element Arrays. This may change in the future

Reading

Cif objects are created by calling the Cif constructor with a file name. File names should be provided as FilePaths paths. These can be produced from strings be prepending the letter p once FilePaths is added. If a String is provided to the Cif constructor it will be interpreted as the contents of a CIF file. The optional argument native switches between the C cif_api parser (native=false, not currently available for Windows) and a native Julia parser (native=true, the default).

To open a file, and read _cell.length_a from block only_block, returning a one-element Array{String,1}:

julia> using CrystalInfoFramework, FilePaths

julia> nc = Cif(p"my_cif.cif")
...
julia> my_block = nc["only_block"]  #could also use first(nc).second
...
julia> l = my_block["_cell.length_a"]
1-element Array{Any,1}:
 "11.520(12)"

get_loop returns a DataFrame object that can be manipulated using the methods of that package, most obviously, eachrow to iterate over the packets in a loop:

julia> l = get_loop(my_block,"_atom_site.label")
...
julia> for r in eachrow(l)
    println("$(r[Symbol("_atom_site.fract_x")])")
end

Updating

Values are added in the same way as for a normal dictionary.

my_block["_new_item"] = [1,2,3]

If the dataname belongs to a loop, following assignment of the value the new dataname can be added to a previously-existing loop. The following call adds _new_item to the loop containing _old_item:

add_to_loop(my_block,"_old_item","_new_item")

The number of values in the array assigned to _new_item must match the length of the loop - this is checked.

Dictionaries and DataSources

CIF dictionaries are created by passing the dictionary file name to DDLm_Dictionary or DDL2_Dictionary. Either a FilePath or String may be used to specify the file location.

DataSources

A DataSource is any data source returning an array of values when supplied with a string. A CIF Block conforms to this specification. DataSources are defined in submodule CrystalInfoFramework.DataContainer.

A CIF dictionary can be used to obtain data with correct Julia type from a DataSource that uses data names defined in the dictionary by creating a TypedDataSource:

julia> using CrystalInfoFramework.DataContainer
julia> my_dict = DDLm_Dictionary("cif_core.dic")
julia> bd = TypedDataSource(my_block,my_dict)
julia> l = bd["_cell.length_a"]
1-element Array{Float64,1}:
 11.52
julia> l = bd["_cell_length_a"] #understand aliases
1-element Array{Float64,1}:
 11.52

Writing

Use show(io::IO,::MIME"text/cif",d) to produce correctly-formatted dictionaries or data files.

Architecture

The C cif_api library parsing callbacks are used to construct a Cif object during file traversal. The Julia parser uses a pre-built parser generated by Lerche using a CIF EBNF to produce a parse tree that is then transformed into a Cif object.

Further information

Read the tests in the tests directory for typical usage examples.

Contributing

Contributions, suggestions, and bug reports are welcome! Please use Github issues and pull requests to do this.