This was a large part of my PhD work. It is a framework for programming chemistry in an XML-based markup language. The purpose is so that chemical procedures can be compiled to run on different platforms, similar to computer code being written once and compiled to different processor architectures. The hierarchical component-based architecture is similar in some ways to frontend frameworks such as React.
This project played a major role in spawning the startup Chemify, and led to a paper published in the journal Science: A universal system for digitization and automatic execution of the chemical synthesis literature.
Forked from this repository to snapshot the state of the code when I stopped working on it: https://gitlab.com/croningroup/chemputer/xdl
XDL is a chemical description language for representing chemical procedures in a machine and human-readable way. This package provides an abstract framework for linking this representation to execution on automated synthesis platforms.
git clone https://gitlab.com/croningroup/chemputer/xdl.git
pip install -e xdl
This is a basic usage example. For more detailed usage instructions, see the documentation.
from xdl import XDL
# Load XDL procedure
x = XDL('procedure.xdl')
# Compile XDL procedure to run on specific platform graph
x.prepare_for_execution('procedure_graph.json')
# This line depends which platform you are doing so is just written here as pseudocode.
platform_controller = instantiate_platform_controller(**params)
# Execute XDL procedure on automated platform
x.execute(platform_controller)If you wish to contribute a change to XDL, please follow this process.
- Submit an issue describing the proposed change and reasons for the change.
- Discuss with the project maintainers until an agreement is reached on the proposed implementation.
- Fork the repo and make your change.
- Add new tests as appropriate, make sure all tests still pass, and make sure the
flake8lint still passes. - Submit a merge request back to the main repo, and reference the corresponding issue in the merge request.