Science Score: 36.0%
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○Scientific vocabulary similarity
Low similarity (15.9%) to scientific vocabulary
Repository
[FI]tti[N]g 13[C] 1[H] hsqc nmr
Basic Info
- Host: GitHub
- Owner: mahynski
- License: other
- Language: Python
- Default Branch: main
- Size: 105 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 1
Metadata Files
README.md
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FINCHnmr : [FI]tti[N]g 13[C] 1[H] HSQC [NMR]
FINCHnmr is lightweight toolkit for fitting 2D heteronuclear single-quantum coherence nuclear magnetic resonance (HSQC NMR) data to a known library of substances. This predicts the presence and relative concentration of these compounds, and the residual (error) can be interpreted as the sum of the remaining unknown compounds present. For a live demonstration, visit our HuggingFace space or try it out on streamlit's community cloud. Although originally designed to work with (1H-13C) data, FINCHnmr will work with any 2D NMR as long as the library used matches the sample being predicted / analyzed.
There are two approaches to generating the spectral libraries. Both methods are demonstrated in the documentation.
- Library spectra are taken directly from the Biological Magnetic Resonance Bank (BMRB). These spectra are automatically padded and resized so that they match the extent (2D grid) and resolution of the wild spectra being fit.
- Library spectra are reconstructed from a feature list of peak locations by placing bivariate Gaussians at these locations; assumptions must be made about the spread of these distributions in both dimentions of frequency shift space.
Installation
We recommend creating a virtual environment or, e.g., a conda environment then installing finchnmr with pip:
~~~bash $ conda create -n finchnmr-env python=3.10 $ conda activate finchnmr-env $ pip install finchnmr ~~~
You can also install from this GitHub repo source:
~~~bash $ git clone git@github.com:mahynski/finchnmr.git $ cd finchnmr $ conda create -n finchnmr-env python=3.10 $ conda activate finchnmr-env $ pip install . $ python -m pytest # Optional unittests ~~~
To install this into a Jupyter kernel:
~~~bash $ conda activate finchnmr-env $ python -m ipykernel install --user --name finchnmr-kernel --display-name "finchnmr-kernel" ~~~
Documentation
Documentation is hosted at https://finchnmr.readthedocs.io/ via readthedocs.
The logo was generated using Google Gemini (Imagen 3) with the prompt "Design a logo involving a finch and NMR" on Nov. 9, 2024.
License Information
- See LICENSE.md for more information.
- Any mention of commercial products is for information only; it does not imply recommendation or endorsement by NIST.
Owner
- Name: Nathan A. Mahynski
- Login: mahynski
- Kind: user
- Location: Gaithersburg, MD
- Company: NIST
- Website: https://nathan-mahynski.github.io/
- Repositories: 4
- Profile: https://github.com/mahynski
Chemical Engineer at NIST. Interests include: machine learning, nuclear metrology, food science, thermodynamics, tiling, and crystallography.
GitHub Events
Total
- Create event: 3
- Release event: 2
- Issues event: 3
- Watch event: 1
- Delete event: 2
- Member event: 1
- Issue comment event: 1
- Public event: 1
- Push event: 159
Last Year
- Create event: 3
- Release event: 2
- Issues event: 3
- Watch event: 1
- Delete event: 2
- Member event: 1
- Issue comment event: 1
- Public event: 1
- Push event: 159
Packages
- Total packages: 1
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Total downloads:
- pypi 10 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 2
pypi.org: finchnmr
[FI]tti[N]g 13[C] 1[H] HSQC [NMR]
- Documentation: https://finchnmr.readthedocs.io/
- License: # NIST Software Licensing Statement NIST-developed software is provided by NIST as a public service. You may use, copy, and distribute copies of the software in any medium, provided that you keep intact this entire notice. You may improve, modify, and create derivative works of the software or any portion of the software, and you may copy and distribute such modifications or works. Modified works should carry a notice stating that you changed the software and should note the date and nature of any such change. Please explicitly acknowledge the National Institute of Standards and Technology as the source of the software. NIST-developed software is expressly provided "AS IS." NIST MAKES NO WARRANTY OF ANY KIND, EXPRESS, IMPLIED, IN FACT, OR ARISING BY OPERATION OF LAW, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, AND DATA ACCURACY. NIST NEITHER REPRESENTS NOR WARRANTS THAT THE OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR-FREE, OR THAT ANY DEFECTS WILL BE CORRECTED. NIST DOES NOT WARRANT OR MAKE ANY REPRESENTATIONS REGARDING THE USE OF THE SOFTWARE OR THE RESULTS THEREOF, INCLUDING BUT NOT LIMITED TO THE CORRECTNESS, ACCURACY, RELIABILITY, OR USEFULNESS OF THE SOFTWARE. You are solely responsible for determining the appropriateness of using and distributing the software and you assume all risks associated with its use, including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and the unavailability or interruption of operation. This software is not intended to be used in any situation where a failure could cause risk of injury or damage to property. The software developed by NIST employees is not subject to copyright protection within the United States.
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Latest release: 0.0.0b1
published over 1 year ago
Rankings
Maintainers (2)
Dependencies
- actions/checkout v4 composite
- actions/setup-python v2 composite
- codecov/codecov-action v4 composite
- nbsphinx ==0.9.2
- readthedocs-sphinx-search ==0.3.1
- sphinx *
- sphinx-book-theme ==1.0.1
- sphinx_gallery ==0.14.0
- sphinxcontrib-bibtex ==2.5.0
- ipykernel *
- ipython <=8.21
- matplotlib >=3.7.2
- mypy *
- nmrglue ==0.11
- numpy >= 1.23, <2.0.0
- pandas ==2.2
- pre-commit ==3.3.3
- pytest >=7.4.0
- scikit-image ==0.24.0
- scikit-learn *
- scipy ==1.11.1
- sphinx *
- tqdm >=4.66.1
- xml-python ==0.4.3
- bokeh ==2.4.3
- finchnmr *
- streamlit-drawable-canvas *
- streamlit-extras *
- 116 dependencies