Cage Isomer Builder¶
A Python library for building, enumerating, and functionalising metal-organic cages and framework (MOF) isomers. It can also be used as a lightweight tool for generating host-guest docked complexes for finite cages.
Main functionalities¶
- Build any of the 29 most common metal-organic cage topologies from a simple node and linker input
- Optimise cage structures with UFF4MOF using real bond orders, or with GFN-xTB, while preserving the shape of nodes and linkers through rigid-body relaxation
- Generate symmetry-unique isomers for finite cages using point-group methods, and for periodic MOFs using space-group methods based on spglib
- Find the point group of a finite cage from its atoms, so it works for any topology, including Ih and D5h cages
- Count and enumerate isomers with two or more different functional groups (R1, R2, ...)
- Functionalise cages and MOFs by attaching real fragments to one, several, or all active sites, with control over the distribution by ratio
- Dock guest molecules into finite cages, including mixed-guest systems and capacity checks
- Place guests at their lowest-energy sites, scored with DFT-D4 dispersion
- Calculate cage-level statistics such as isomer counts, functional-group-to-functional-group distance distributions, and endo/exo classifications
- Describe pores and guests by feature-site pair distributions (functional groups, aromatic rings, H-bond sites, open metal sites), averaged exactly over multivariate, defective and flexible ensembles, and match guests to pores (see Descriptors)
Where to start¶
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Install from PyPI or from source.
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The whole workflow on one page: build a pore, count and write its isomers, attach groups, compute descriptors and dock a guest.
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One page per workflow, every example runnable as it is.
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Look up which builder class matches your node/linker topicity.
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Every public class and function, each with a runnable example.
License¶
This project is released under the MIT License.