Quick Start Guide¶

This Quick Start Guide provides simple examples to help you begin using mofstructure for working with metal-organic frameworks (MOFs). We’ll cover basic command-line usage and how to use mofstructure as a Python library.

Running on the Command Line¶

Example 1: Deconstructing a MOF into Building Units¶

To deconstruct a MOF from a CIF file into its building units, run the following command:

mofstructure example_mof.cif

This command processes the example_mof.cif file and saves the output in a folder named MOF_building_units within the current directory.

Example 2: Specifying an Output Directory¶

If you want to save the deconstructed MOF in a specific folder, use this command:

mofstructure example_mof.cif /path/to/output_folder

Replace /path/to/output_folder with your desired output directory.

Example 3: Creating a Database from Multiple CIF Files¶

To create a database from a folder containing multiple CIF files, use the following command:

mofstructure_database /path/to/cif_folder

The database will be saved in a folder named MOFDb in the current directory.

Using mofstructure as a Library¶

Example 1: Importing the Module and Reading a CIF File¶

Start by importing the necessary modules and reading a CIF file using ASE:

from mofstructure import mofdeconstructor
from ase.io import read

ase_atom = read('example_mof.cif')

Example 2: Removing Unbound Guest Molecules¶

To remove unbound guest molecules from the structure, use:

no_guest_indices = mofdeconstructor.remove_unbound_guest(ase_atom)
no_guest_atom = ase_atom[no_guest_indices]

Example 3: Computing Porosity¶

To compute the porosity of the MOF, run:

from mofstructure import porosity

pores = porosity.zeo_calculation(ase_atom, probe_radius=1.86)
print(pores)

Example 4: Deconstructing MOFs into SBUs and linkers¶

To identify and extract SBUs and linkers from the MOF:

connected_components, atoms_indices_at_breaking_point, porpyrin_checker, all_regions = MOF_deconstructor.secondary_building_units(ase_atom)

 metal_sbus, organic_sbus, _ = MOF_deconstructor.find_unique_building_units(
             connected_components,
             atoms_indices_at_breaking_point,
             ase_atom, porpyrin_checker,
             all_regions,
             cheminfo=True,
             add_dummy=True
         )

This code will output the SBUs and linkers along with their cheminformatic information.