@ccp-nc/crystcif-parse v0.2.9

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