mmCIF File Script

This Python script provides command line interface to read, write, and manipulate mmCIF files using the py-mmcif library.

Installation

You need Python 3.6 or later to run this script. The py-mmcif library can be installed via pip:

pip install py-mmcif

Run the script with the -h or --help option to view the help message:

python sffile.py --help

Here are the available command line arguments:

-r or --read: Read from an mmCIF file. Provide the filename as an argument. Example: python sffile.py --read myfile.cif
-w or --write: Write to an mmCIF file. Provide the filename as an argument. Example: python sffile.py --write myfile.cif
-b or --block: Get a block by its name. Provide the block name as an argument. Example: python sffile.py --read myfile.cif --block myblock
-o or --object: Get an object from a block by its category. Provide the block name and category as arguments. Example: python sffile.py --read myfile.cif --object myblock mycategory
-d or --default: Set a block as the default block. Provide the block name as an argument. Example: python sffile.py --read myfile.cif --default myblock
-g or --get: Get an object from the default block by its category. Provide the category as an argument. Example: python sffile.py --read myfile.cif --default myblock --get mycategory
-ob or --objblock: Get an object from a block. This is similar to the --object argument. Provide the block name and category as arguments. Example: python sffile.py --read myfile.cif --objblock myblock mycategory
-l or --list: List the names of all blocks in the file. Example: python sffile.py --read myfile.cif --list
-c or --categories: List all categories in a block. Provide the block name as an argument. Example: python sffile.py --read myfile.cif --categories myblock

You can also combine these arguments. For example, you can read from a file, list the blocks, get an object from a block, and then write to a file:

python sffile.py --read myfile.cif --list --object myblock mycategory --write myfile.cif