This repository contains all code related to the analysis, design, and synthesis of metal-organic polyhedra (MOPs), a class of discrete reticular materials, within The World Avatar (TWA).
The folder "MOP_Discovery" contains all software agents and tools used for the rational design of novel MOP structures based on known MOPs, their building units, and assembly models. This work was published in the Journal of the American Chemical Society, where the described algorithms were used to generate over 1,500 novel MOP structures based on 151 known MOPs.
The folder "MOPs_Assembler" contains all software to run the geometry assembler for newly suggested MOPs described in preprint 329. This geometry assembler was used to generate geometries for the ~1500 novel MOPs suggested earlier, curated data for reproduction can be found in a separate repository.
The folder "twa_mops" contains all code of MOPs-related applications used in preprint 335 to illustrate the capabilities of the TWA Python package. The newly developed object-graph mapper (OGM) was used to simplify rational design and geometry assembly of novel MOPs, highlighted by the incorporation of additional structures and building units. The underlying codes of the TWA Python package can be found in a separate repository.
The folder "MOP_Literature_Extraction" contains all code and embedded LLM prompts used for an automated pipeline that extracts reported MOP synthesis descriptions from the literature. As described in preprint 336, this pipeline was used to extract nearly 300 synthesis procedures related to the original 151 known MOPs and integrate within TWA for analysis and retrosynthetic efforts.
- In twa_mops/mops.env, instead of using hard-coded IP addresses, we should aim to use an alias such as
mops.theworldavatar.io(whilst removing any custom port numbers). In order to make that work, at a minimum, the following would be required: Spin up an nginx container that forwards ports 80/443 to 3838 (or wherever the local stack is hosted, and don't forget to configure the firewall appropriately). Enablehttps(not justhttp). Otherwise, cloudflare will block any forwarded requests.