CIFTools

ECMAScript modules for manipulating Crystallographic Information File (CIF).

Currently, following functionalities are implemented:

• reading (from a CIF 1.1 or CIF2.0 string to a CIF object)
• translation of a data value by using DDL1 dictionaries

New functionalities, for example,

• writing (from a CIF object to a CIF string)
• validation
• support for DDL2, DDLm and dREL

may be added on (author's) demand in future.

Instllation

npm install @kkitahara/cif-tools

Examples

import { CIF, Dict } from '@kkitahara/cif-tools'

Construct a CIF object from a string

let cif = CIF.fromCIFString(`#\\#CIF_2.0
    data_my_awesome_crystal
      _cell_length_a 1.00(1)
      _cell_length_b 2.00(2)
      _cell_length_c 3.00(3)

    data_My_Ordinary_Crystal
      _cell_length_a 1.0(1)
      _cell_length_b 2.0(2)
      _cell_length_c 3.0(3)

    data_MY_AWFUL_CRYSTAL
      _CELL_LENGTH_A 1.0(10)
      _CELL_LENGTH_B 2.0(20)
      _CELL_LENGTH_C 3.0(30)
`)
cif instanceof CIF // true

Extract block codes from a CIF object

let blockCodes = CIF.getBlockCodes(cif)

blockCodes[0] // 'my_awesome_crystal'
blockCodes[1] // 'my_ordinary_crystal'
blockCodes[2] // 'my_awful_crystal'

:memo: block codes are case folded

Extract a data block from a CIF object

let block = CIF.getBlock(cif, 'my_awful_crystal')

Extract a raw data value from a block

let val = CIF.getDataValue(block, '_cell_length_a')

// A raw data value is contained in an array
val.length // 1
val[0] // '1.0(10)'

:memo: tag (data name) is case-insensitive

Get dictionaries to which blocks in a given cif corform

let dicts = Dict.getConformDicts(cif)

// A dictionary for a block
let dict = dicts['my_awful_crystal']

Translate a data value by using a dictionary

let translated = Dict.translate(dict, '_cell_length_a', val[0])
translated.value // 1
translated.su // 1

The data structure of CIF objects conforms to JSON representation of CIF information (DRAFT)

cif['CIF-JSON']['my_awesome_crystal']['_cell_length_a'][0] // '1.00(1)'

JSON.stringify

let str = JSON.stringify(cif)

JSON.parse

cif = JSON.parse(str, CIF.reviver)
cif instanceof CIF // true

ESDoc documents

For more examples, see ESDoc documents:

cd node_modules/@kkitahara/cif-tools
npm install --only=dev
npm run doc

and open doc/index.html in your browser.

Deviations from specs

• CIF 1.1 (specification)
  • A <WhiteSpace> is inserted before the first <value> of <LoopBody>, otherwise the first <value> cannot be distinguished from the last <Tag> in loops by the lexer.
• CIF 2.0 (specification)
  • Sequences [wspace], [comment] appear in the productions CIF2-file and wspace-data-value are replaced by [wspace [comment]], otherwise comments can follow the preceding token without any white spaces.
  • The specification does not mention the uniqueness of table keys. As for the CIF-JSON object, the keys must be unique. Therefore, the uniqueness (case sensitive manner) of the keys is required in this software.

LICENSE

© 2019 Koichi Kitahara
Apache 2.0