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Examples

The Pluto notebooks (.jl) containing the Julia code and the input files for all examples are in the examples directory.

Click on the images or descriptions below to see Pluto notebooks demonstrating each use case.

Example: Find substructures in a crystal

Identify the p-phenylene fragments in IRMOF-1.

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search example

Example: Generate hypothetical structures

Decorate IRMOF-1 with a functional group: ortho substitution with an acetylamido group at one quarter of the p-phenylene moieties.

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example 1

Example: Using different replacement modes

Replace BDC with nitro-BDC in IRMOF-1 using the different replacement modes to control (i) which linkers are functionalized and (ii) the substitution site on each linker.

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example1.5

Example: Insert missing hydrogen atoms

Insert missing H atoms in IRMOF-1.

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example 2

Example: Repair Disorder and Remove Adsorbates

Correct the crystallographic disorder of the PyC-2 ligands and remove guest molecules from the pores of SIFSIX-Cu-2-i.

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example 3

Example: Generate Missing-Linker Defects

Create a new channel in UiO-66 by introducing missing-linker defects and formate ion capping.

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example 4