Skip to content

Convert CIF to BinaryCIF

BinaryCIF is an efficient, binary flavor of the CIF format. See specification and publication for further details.

This script reads data in CIF format and converts it lossless to a BinaryCIF file that can be read by Mol* or other applications.

Example

node lib/commonjs/cli/cif2bcif/index.js file.cif file.bcif

Usage

Argument Description
src Source CIF to convert (can be gzipped)
out Generated BinaryCIF output path
-c Path to optional config file
-f Path to optional filter file 
index.js [-h] [-c CONFIG] [-f FILTER] src out

Config file

Controls how certain columns will be encoded. This is a JSON array of instructions: 

interface EncodingStrategyHint {
    categoryName: string,
    columnName: string,
    encoding: 'pack' | 'rle' | 'delta' | 'delta-rle',
    precision?: number
}
Identify a particular CIF columns by its name and override the encoding by Integer Packing, Run-Length Encoding, Delta Encoding, or Delta & Run-Length Encoding. You can optionally control the precision if dealing with float values.

Filter file

Specifies which categories and columns will be written. This is a plain text file, each line represents one entry. You can specify explicitly which categories or columns to include by adding category_name or category_name.field_name. You can also choose to ignore some categories or columns by adding !category_name or !category_name.field_name.