Commit for public release

.gitattributes

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+*.dx text eol=crlf

.gitignore

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+**/__pycache__/
+**/.cache
+*.ipynb_checkpoints
+**/.vscode
+
+build/
+*.egg-info/
+*.egg
+.tox/
+.coverage
+
+tests/
+wheels/

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/econchick/interrogate
+    rev: 237be78f9c6135fc1a620d211cdfdc5d3885082b
+    hooks:
+      - id: interrogate
+        args: [--config=pyproject.toml]
+        pass_filenames: true
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 5c52d752e64f210369b37654e7b26ce25e2266d6
+    hooks:
+      - id: flake8 # E***, W***, F***
+        additional_dependencies:
+          - dlint # DUO***
+          - flake8-2020 # YTT***
+          - flake8-bugbear # B***
+          - flake8-builtins # A***
+          - flake8-comprehensions # C4**
+          - flake8-deprecated # D***
+          - mccabe # C9**
+          - pep8-naming # N8**
+
+  - repo: https://github.com/pycqa/isort
+    rev: 7de182933fd50e04a7c47cc8be75a6547754b19c
+    hooks:
+      - id: isort
+        # args: ["--profile", "black", "--filter-files"]
+
+  - repo: https://github.com/PyCQA/docformatter
+    rev: 504107bdc4618f83a3378faac610e02cd62ef5f9
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --pre-summary-newline, --blank, --diff]
+
+  - repo: https://github.com/psf/black
+    rev: 8fe602b1fa91dc6db682d1dba79a8a7341597271
+    hooks:
+      - id: black
+        args: [--line-length=79]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.8.0
+    hooks:
+      - id: mypy

LICENSE

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+MIT License
+
+Copyright (c) 2024 AIC Group
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# Main workflow code for Synthesis Bots (A.I.C. Group)
+
+## Requirements and installation
+
+### System requirements and dependencies
+
+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](https://www.jstatsoft.org/article/view/v031i07))
+- `matplotlib` (v3.8.2, [ref](https://doi.org/10.1109/MCSE.2007.55))
+- `numpy` (v1.26.3, [ref](https://www.nature.com/articles/s41586-020-2649-2))
+- `pandas` (v2.2.0, [ref](https://doi.org/10.5281/zenodo.3509134))
+- `pyserial` (v3.5, [ref](https://github.com/pyserial/pyserial/))
+- `scipy` (v1.12, [ref](https://doi.org/10.1038/s41592-019-0686-2))
+- `pyzmq` (v25.1.2, [ref](https://github.com/zeromq/pyzmq))
+
+which can all be obtained directly from the Python Package Index (PyPI) with `pip` package installer.
+
+### LC-MS System
+
+LC-MS parser requires DLL driver files from Waters, packaged as `masslynx`: [masslynx_sdk](https://github.com/cooper-group-uol-robotics/masslynx_sdk_public) (see on [Zenodo](https://zenodo.org/doi/10.5281/zenodo.11174322)).
+
+### NMR System
+
+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.
+
+### Installation
+
+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
+
+Examples with minimum input files and expected output can be found on [Zenodo](https://doi.org/10.5281/zenodo.11197260) 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.
+
+## References
+
+The exact mass calculator file (to be replaced in the future versions) is taken directly from [pyISOPACh](https://github.com/AberystwythSystemsBiology/pyISOPACh), which has been published under the MIT License.

pyproject.toml

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+[build-system]
+requires = [
+    "setuptools",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "synthesis_bots"
+description = "Main control for the Synthesis Bots project (A.I.C. Group)"
+version = "0.3.0"
+requires-python = ">=3.12"
+authors = [
+    { name = "Filip T. Szczypiński", email = "[email protected]" },
+    { name = "Jean-François Ayme", email = "[email protected]" },
+    { name = "Tianwei Dai", email = "[email protected]" },
+    { name = "Sriram Vijayakrishnan", email = "[email protected]" },
+]
+dependencies = [
+    "dtw-python",
+    "matplotlib",
+    "numpy",
+    "pandas",
+    "pyserial",
+    "scipy",
+    "zmq",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+
+    [project.optional-dependencies]
+    dev = [
+        "pre-commit",
+        "black",
+        "docformatter",
+        "interrogate",
+        "ipython",
+        "isort",
+        "pandas-stubs",
+        "pycodestyle",
+        "pydocstyle",
+        "pytest",
+        "pytest-cov",
+        "flake8",
+    ]
+    lcms = [
+        "lcms_parser@git+https://github.com/cooper-group-uol-robotics/lcms_parser",
+    ]
+    nmr = [
+        "fourier_nmr_driver@git+https://github.com/cooper-group-uol-robotics/fourier_nmr_driver",
+    ]
+
+    [project.scripts]
+    synthesis_bots = "synthesis_bots.utils.__main__:main"
+    connect_nmr    = "synthesis_bots.utils.connect:connect_nmr"
+    connect_lcms   = "synthesis_bots.utils.connect:connect_lcms"
+
+[tool.setuptools]
+include-package-data = true
+
+    [tool.setuptools.packages.find]
+    where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["py.typed", "*.mplstyle"]
+
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]
+
+[tool.interrogate]
+exclude = [
+    "setup.py",
+]
+verbose = 2
+ignore-init-method = true
+ignore-init-module = true
+ignore-setters = true
+ignore-property-decorators = true
+ignore-magic = true
+
+[[tool.mypy.overrides]]
+module = [
+    'scipy.signal',
+    'masslynx',
+    'serial',
+    'bruker.api.topspin',
+    'dtw',
+]
+ignore_missing_imports = true
+
+[tool.isort]
+profile         = "black"
+force_grid_wrap = 2
+line_length     = 79

settings.toml

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+[dry]
+
+dry = false
+
+[tcp]
+
+HOST      = "tcp://172.31.1.17:5558"
+NMR       = "tcp://172.31.1.15:5552"
+CHEMSPEED = "tcp://172.31.1.16:5553"
+LCMS      = "tcp://172.31.1.18:5554"
+
+[paths]
+
+LCMS_archive   = "D:/synthesis_bots"
+LCMS_queue     = "D:/Queue"
+LCMS_data      = "D:/Projects/SynthesisBotsSuprachem.PRO/Data"
+LCMS_to_NMR    = "Y:/synthesis_bots"
+NMR_data       = "C:/synthesis_bots"
+NMR_archive    = "Y:/synthesis_bots"
+CS_csv_supra   = "C:/synthesis-bot/Import_CSV.csv"
+CS_csv_medchem = "C:/synthesis-bot/Medchem.csv"
+
+[defaults.NMR]
+
+num_scans    = 64
+pp_threshold = 0.02
+field_presat = 10
+l30          = 2
+parameters   = "MULTISUPPDC_f"
+solvent      = "CH3CN"
+wait_time    = 120
+shim_time    = 1200
+reshim_time  = 14400
+shim_sample  = 1
+rack_layout  = "KUKA"
+owner        = "Filip T. Szczypinski"
+origin       = "AIC Group, University of Liverpool"
+
+[defaults.MS]
+injection_volume      = 0.5
+peak_match_tolerance  = 0.4
+analog_peak_threshold = 0.3
+tic_peak_params       = { "height" = 0.2, "distance" = 50 }
+analog_peaks_params   = { "height" = 0.1, "distance" = 50 }
+ms_peak_params        = { "height" = 0.15, "distance" = 10 }
+solvent_front         = 0.4
+lc_run_end            = 3.0
+integral_rel_height   = 0.95
+# Time (s) for sample to reach MS after LC detector
+lc_ms_flowpath = 2.84
+
+[workflows.PREFIX]
+
+Supramol_Screening   = "SUPRAMOL-SCREENING"
+Supramol_Replication = "SUPRAMOL-REPLICATION"
+Supramol_HostGuest   = "SUPRAMOL-HOST-GUEST"
+Medchem_Screening    = "MEDCHEM-SCREENING"
+Medchem_Scaleup      = "MEDCHEM-SCALEUP"
+Medchem_Diversity    = "MEDCHEM-DIVERSITY"
+Photocat             = "PHOTOCATALYSIS"
+
+[workflows.NMR]
+
+Supramol_Screening   = "synthesis_bots.workflows.nmr.supramol.screening"
+Supramol_Replication = "synthesis_bots.workflows.nmr.supramol.replication"
+Supramol_HostGuest   = "synthesis_bots.workflows.nmr.supramol.host_guest"
+Medchem_Screening    = "synthesis_bots.workflows.nmr.medchem.screening"
+Medchem_Scaleup      = "synthesis_bots.workflows.nmr.medchem.scaleup"
+Medchem_Diversity    = "synthesis_bots.workflows.nmr.medchem.diversity"
+
+[workflows.LCMS]
+InsertRack1  = "synthesis_bots.workflows.ms.insert_rack_one"
+InsertRack2  = "synthesis_bots.workflows.ms.insert_rack_two"
+ExtractRack1 = "synthesis_bots.workflows.ms.eject_rack_one"
+ExtractRack2 = "synthesis_bots.workflows.ms.eject_rack_two"
+Supra1       = "synthesis_bots.workflows.ms.supramol.screening"
+Supra2       = "synthesis_bots.workflows.ms.supramol.replication"
+Medchem1     = "synthesis_bots.workflows.ms.medchem.screening"
+Medchem2     = "synthesis_bots.workflows.ms.medchem.scaleup"
+Medchem3     = "synthesis_bots.workflows.ms.medchem.diversity"
+Photochem    = "synthesis_bots.workflows.ms.photocat.photocat"
+
+[workflows.decision]
+
+peak_number = 3 # How many peaks different from SM allowed.
+shifted_proportion = 0.5 # What proportion of peaks needs to have shifted.
+metals_mz = [
+    3,
+    2,
+] # [x, y] if x metals, required at least y m/z peaks.
+dtw_threshold = 20.0 # Distance threshold for dynamic time warp.
+ppm_range = [11, 6] # PPM range of interest
+hg_shift = 0.02 # PPM shift to trigget host-guest identification
+hg_lb = 1.8 # Hz exponential multiplication line broadening

setup.py

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+#!/usr/bin/env python
+"""Install package."""
+
+import setuptools
+
+if __name__ == "__main__":
+    setuptools.setup()

src/synthesis_bots/__init__.py

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+"""Synthesis Bots (AIC Group)."""
+
+__version__ = "0.3.0"