This code has been used and tested on Windows 10 (UPLC-MS and NMR control PCs) and Windows 11 (development). The package makes use of the following dependencies and was tested with the following versions:
dtw-python(v1.3.1, ref)matplotlib(v3.8.2, ref)numpy(v1.26.3, ref)pandas(v2.2.0, ref)pyserial(v3.5, ref)scipy(v1.12, ref)pyzmq(v25.1.2, ref)
which can all be obtained directly from the Python Package Index (PyPI) with pip package installer.
LC-MS parser requires DLL driver files from Waters, packaged as masslynx: masslynx_sdk (see on Zenodo).
The NMR driver requires official Bruker TopSpin 4.3.0 Python API. Assuming the default TopSpin installation folder, you can use:
conda create -n synthesis-bots-nmr python=3.12
conda activate synthesis-bots-nmr
python -I -m pip install --find-links 'C:\Bruker\TopSpin4.3.0\python\examples' .[nmr]
on a different system you need to replace 'C:\Bruker\TopSpin4.3.0\python\examples' with a path to wherever the official Bruker TopSpin API can be found.
Easiest and recommended approach is to dedicate an isolated conda environment for the package:
conda create -n synthesis_bots python>=3.12
conda activate synthesis_bots
then - provided all the non-pip dependencies for NMR and UPLC-MS are present, the package can easily be installed with:
python -m pip install .
On a typical desktop computer with fast internet connection, the installation should take a couple of minutes (depending on how many dependencies have already been satisfied).
Examples with minimum input files and expected output can be found on Zenodo and include all reproduction instructions:
- Medicinal Chemistry example data and analysis
- Supramolecular Chemistry example data and analysis
- Photocatalysis example data and analysis
- Workflow instrument integration example
The run time for the code examples on a typical desktop computers is minutes.
The exact mass calculator file (to be replaced in the future versions) is taken directly from pyISOPACh, which has been published under the MIT License.