mofstructure documentation

Introduction

mofstructure is a powerful and user-friendly Python module designed for the manipulation and analysis of metal-organic frameworks (MOFs) and other porous materials, including covalent organic frameworks (COFs) and zeolites. The module offers a range of functions that streamline complex tasks related to the study and modification of these structures. Whether you are a researcher, scientist, or student working in the field of materials science, mofstructure provides the tools you need to efficiently analyze and manipulate these intricate frameworks.

Key Features of mofstructure

The mofstructure module includes a variety of features that simplify common operations and enhance the workflow for users working with MOFs and similar materials. Some of the key functionalities include:

1. Computation of Geometric Properties of MOFs: - mofstructure integrates seamlessly with the zeo++ software in the background to enable quick and accurate computation of all porosity-related properties. Users can easily obtain essential metrics such as Pore Limiting Diameter (PLD), Largest Cavity Diameter (LCD), Accessible Surface Area (ASA), and other geometric characteristics critical to the analysis of MOFs.

2. Automated Removal of Unbound Guest Molecules: - The module offers an automated process for identifying and removing unbound guest molecules from the framework. This feature is particularly useful when preparing structures for simulations or other computational analyses where the presence of unbound molecules could skew results.

3. Deconstruction of Metal-Organic Frameworks into Building Units: - mofstructure allows users to deconstruct MOFs into their constituent building units, including organic ligands, metal clusters, organic secondary building units (SBUs), and metal SBUs. For each building unit, the module computes important cheminformatic identifiers such as SMILES strings, InChI, and InChIKey. Additionally, it identifies the type of metal SBU and determines the coordination number of the central metal atom, which is crucial for understanding the structural properties of the framework.

4. Wrapping Systems Around Unit Cells to Remove the Effect of Periodic Boundary Conditions (PBC): - When visualizing CIF files or converting CIF files to XYZ format, systems may appear uncoordinated due to the effects of periodic boundary conditions. mofstructure provides a solution by wrapping systems around their unit cells, ensuring a more accurate and visually coherent representation of the structure.

5. Separation of Building Units into Regions: - This feature is essential for users who need to substitute specific ligands or building units within a framework. By separating building units into distinct regions, mofstructure enables targeted modifications, allowing for precise customization of the framework’s properties.

Contents:

• Installation
  • Option 1: Installing via pip
  • Option 2: Installing via GitHub Repository
• Quick Start Guide
• Running on the Command Line
  • Example 1: Deconstructing a MOF into Building Units
  • Example 2: Specifying an Output Directory
  • Example 3: Creating a Database from Multiple CIF Files
• Using mofstructure as a Library
  • Example 1: Importing the Module and Reading a CIF File
    • Example 2: Removing Unbound Guest Molecules
  • Example 3: Computing Porosity
  • Example 4: Deconstructing MOFs into SBUs and linkers
• How to Guide
• Run on the Command Line
  • Building Units
  • Custom Output Directory
• Processing Multiple CIF Files
  • Creating a Database
  • Custom Database Output Directory
• Use as a Library
  • Extracting Cheminformatic Information
• API Reference
  • MOF Deconstructions
    • all_ferrocene_metals()
    • angle_tolerance_to_rad()
    • ase_2_pybel()
    • ase_2_xyz()
    • check_planarity()
    • compute_ase_neighbour()
    • compute_cheminformatic_from_rdkit()
    • compute_inchis()
    • compute_openbabel_cheminformatic()
    • compute_smi()
    • connected_components()
    • covalent_radius()
    • dfsutil_graph_method()
    • find_COS()
    • find_carbonyl_sulphate()
    • find_carboxylates()
    • find_key_or_value()
    • find_phosphate()
    • find_phosphite()
    • find_sulfides()
    • find_unique_building_units()
    • inter_atomic_distance_check()
    • is_ferrocene()
    • is_irmof()
    • is_mof32()
    • is_paddlewheel()
    • is_paddlewheel_with_water()
    • is_rodlike()
    • is_uio66()
    • ligands_and_metal_clusters()
    • longest_list()
    • matrix2dict()
    • max_index()
    • metal_coordination_enviroment()
    • metal_coordination_number()
    • metal_in_porphyrin()
    • metal_in_porphyrin2()
    • mof_regions()
    • move2front()
    • obmol_2_rdkit()
    • remove_unbound_guest()
    • remove_unbound_guest_and_return_unique()
    • rod_manipulation()
    • secondary_building_units()
    • transition_metals()
    • wrap_systems_in_unit_cell()
  • Computing Porosity
    • ase_to_zeoobject()
    • zeo_calculation()
  • Computing stacking in 2D systems and inter-layer height
    • compute_cof_stacking()
• Updates Version 0.1.4
• Updates Version 0.1.5
• Updates Version 0.1.6
  • Compute Only Deconstruction
  • Compute Only Porosity
  • Compute Only Open Metal Sites
• Updates Version 0.1.7
• Updates Version 0.1.8
• Updates Version 0.1.8.1
• Updates Version 0.1.8.2

Support

The module contains much more functionalities. If you are struggling or wish to compute a new quantity that is not yet present, feel free to send me an email: bafgreat@gamil.com.

Roadmap

In the future, the code should be able to:

1. Compute RCSR topological code

2. Substitute building units in a MOF to enable framework functionalization

3. Automatically curate CIFs

4. Deconstruct COFs into their building units

• Index

• Module Index

• Search Page