@ccp-nc/crystcif-parse

crystcif-parse

A JavaScript parser for Crystallographic Information File (CIF) files. This module provides a barebone structure to parse the CIF data format and interpret some basic keywords in order to retrieve a crystal structure.

Supported:

• parsing of CIF 1.1 syntax
• partial interpretation of structural core dictionary keywords (position, cell parameters, labels)
• basic treatment of symmetry (symmetry operations)
• spacegroup symbols

Not supported yet:

• CIF 2.0 syntax
• non-essential atomic properties (masses, charges, bonds, etc.)

Module contents

The module exposes to the user a few core methods and classes that are useful for the sake of parsing CIF files and handling the resulting structures.

parseCifStructures(ciftext);

Parses the file passed as ciftext in form of string and returns a dictionary of Atoms classes, with the names of the corresponding data blocks as keys.

parseCif(ciftext)

Parses the file passed as ciftext in form of string and returns a dictionary with data block names as keys. The blocks contain in turn the tags for any data items, each corresponding to a full data item entry and corresponding value (represented by specific classes).

Atoms(elems, positions, cell, info, scaled, tolerant)

A class defining a single crystal structure. Inspired by the Python class of the same name in the Atomic Simulation Environment. It is created by passing the following arguments:

• elems: Array of element symbols of atomic numbers
• positions: Array of xyz coordinates for each atom
• cell: unit cell for the structure. If not passed, the structure will not be considered periodic. Can be an Array of three numbers (treated as orthorombic cell with sides [a,b,c]), an Array of two Arrays of three for lengths and angles, or an Array of three Arrays of three for cartesian components
• info: a dictionary of any additional information necessary
• scaled: if true, the coordinates are considered fractional instead of absolute
• tolerant: if true, any unknown chemical symbols are accepted instead of causing an exception. Unknown atomic numbers will still fail

The Atoms class also provide the following methods to access its various properties:

• .length()
• .get_positions()
• .get_scaled_positions()
• .get_chemical_symbols()
• .get_atomic_numbers()
• .get_cell()
• .get_pbc() (return periodic boundary conditions in X, Y, Z as an array of Boolean)
• .get_array(name) and .set_array(name, array) for getting and setting additional custom properties