KO
|
EN
gitlite โ search
Search
#typescript
#ai-agents
#ai
#dsh-plugin
#deepseek-harness
#open-source
#claude-code
#codex
#cli
#developer-tools
#react
#windows
spyrmsd
โ 119
Open GitHub โ
๐ Symmetry-corrected RMSD in Python
Download README (.md)
Explore Similar Repositories
litefy
:
a lightweight spotify client
smix-eleventy-starter
:
A standards-respecting starter kit for Eleventy. Go Indie.
deep_autoviml
:
Build tensorflow keras model pipelines in a single line of code. Now with mlflow tracking. Created by Ram Seshadri. Collaborators welcome. Permission granted upon request.
fastify-schedule
:
Fastify plugin for scheduling periodic jobs
fastify-sse-v2
:
Provide Server-Sent Events to Fastify
// repository documentation
Was this content helpful?
โ 0
(0 ratings)
Select Rating:
โ
โ
โ
โ
โ
Submit Feedback
Recent Feedback
×
Download README
Do you want to download the
README.md
file for
spyrmsd
?
Download (.md)
# sPyRMSD [](https://github.com/RMeli/spyrmsd/actions/workflows/pytest.yml)   [](https://codecov.io/gh/RMeli/spyrmsd/branch/master) [](https://spyrmsd.readthedocs.io) [](https://spyrmsd.readthedocs.io/en/develop/?badge=develop) [](https://opensource.org/licenses/MIT) [](https://pypi.org/project/spyrmsd/) [](https://anaconda.org/conda-forge/spyrmsd) [](https://doi.org/10.1186/s13321-020-00455-2) [](https://zenodo.org/badge/latestdoi/214157073) Python tool for symmetry-corrected RMSD calculations. --- If you find `spyrmsd` useful, please consider citing the following paper: ```text @article{spyrmsd2020, Author = {Meli, Rocco and Biggin, Philip C.}, Journal = {Journal of Cheminformatics}, Number = {1}, Pages = {49}, Title = {spyrmsd: symmetry-corrected RMSD calculations in Python}, Volume = {12}, Year = {2020} } ``` ## Installation `spyrmsd` is available on [PyPI](https://pypi.org/project/spyrmsd/) and [conda-forge](https://github.com/conda-forge/spyrmsd-feedstock) and can be easily installed from source. See [Dependencies](###Dependencies) for a description of all the dependencies. > [!NOTE] > `spyrmsd` will install [rustworkx] (multi-platform) when using `pip` or `conda`. You can install other backends manually. > [!WARNING] > If `spyrmsd` is used as a standalone tool, it is required to install [RDKit](https://rdkit.org/). It is not automatically installed with `pip` nor `conda`. ### PyPI ```bash pip install spyrmsd ``` ### conda ```bash conda install spyrmsd -c conda-forge ``` ### GitHub ```bash git clone https://github.com/RMeli/spyrmsd.git cd spyrmsd pip install . ``` ### Dependencies `spyrmsd` can be used both as a module or as a standalone tool. #### Module The following packages are required to use `spyrmsd` as a module: * [numpy](https://numpy.org/) * [scipy](https://www.scipy.org/) One of the following graph libraries is required: * [graph-tool] * [rustworkx] * [NetworkX] > [!NOTE] > `spyrmsd` uses the following priority when multiple graph libraries are present: [graph-tool], [rustworkx], [NetworkX]. *This order might change. Use `set_backend` to ensure you are always using the same backend, if needed.* #### Standalone Tool Additionally, the following package is required to use `spyrmsd` as a standalone tool: * [RDKit](https://rdkit.org/) ## Usage ### Standalone Tool `spyrmsd` provides a convenient CLI tool. See `spyrmsd`'s `--help` for the usage: ```bash python -m spyrmsd -h ``` ### Module ```python from spyrmsd import rmsd ``` #### RMSD The function `rmsd.rmsd` computes RMSD without symmetry correction. The atoms are expected to be in the same order for both molecules being compared (no atom matching is performed). ```python def rmsd( coords1: np.ndarray, # Coordinates of molecule 1 coords2: np.ndarray, # Coordinates of molecule 2 aprops1: np.ndarray, # Atomic properties of molecule 1 aprops2: np.ndarray, # Atomic properties of molecule 2 center: bool = False, # Flag to center molecules at origin minimize: bool = False, # Flag to compute minimum RMSD atol: float = 1e-9, # Numerical tolerance for QCP method ) ``` > [!NOTE] > Atomic properties (`aprops`) can be any Python object when using [NetworkX] and [rustworkx], or integers, floats, or strings when using [graph-tool]. #### Symmetry-Corrected RMSD The function `rmsd.symmrmsd` computes symmetry-corrected RMSD using molecular graph isomorphisms. Symmetry correction requires molecular adjacency matrices describing the connectivity but needs not the atoms to be in the same order. Atom matching is performed according to the molecular graph. This function should also be used when atoms in the molecules being compared are not in the same order (even if there is not symmetry to be accounted for). ```python def symmrmsd( coordsref: np.ndarray, # Reference coordinated coords: Union[np.ndarray, List[np.ndarray]], # Coordinates (one set or multiple sets) apropsref: np.ndarray, # Reference atomic properties aprops: np.ndarray, # Atomic properties amref: np.ndarray, # Reference adjacency matrix am: np.ndarray, # Adjacency matrix center: bool = False, # Flag to center molecules at origin minimize: bool = False, # Flag to compute minimum RMSD cache: bool = True, # Cache graph isomorphisms atol: float = 1e-9, # Numerical tolerance for QCP method ) ``` > [!NOTE] > Atomic properties (`aprops`) can be any Python object when using [NetworkX] and [rustworkx], or integers, floats, or strings when using [graph-tool](https://graph-tool.skewed.de/). #### Select Backend `spyrmsd` supports the following graph libraries for the calculation of graph isomorphisms: * [graph-tool] * [NetworkX] * [rustworkx] You can check which backend is being used with ```python spyrmsd.get_backend() ``` You can also manually select your preferred backend with ```python spyrmsd.set_backend("networkx") # spyrmsd uses NetworkX spyrmsd.set_backend("graph_tool") # spyrmsd uses graph_tool ``` The available backends (which depend on the installed dependencies) are stored in `spyrmsd.available_backends`. ## Development > [!WARNING] > Please check out our [AI policy](AI.md) for the use of AI tools in development. To ensure code quality and consistency the following tools are used during development: * [black](https://black.readthedocs.io/en/stable/) * [Flake 8](http://flake8.pycqa.org/en/latest/) (CI) * [isort](https://pycqa.github.io/isort/) * [mypy](http://mypy-lang.org/) (CI) Pre-commit `git` hooks can be installed with [pre-commit]. ## Copyright Copyright (c) 2019-2024, Rocco Meli. ## References References are tracked with [duecredit](https://github.com/duecredit/duecredit/). Run the `credits.sh` script in order to print up-to-date references. ### Acknowledgements Project based on the [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version `1.1`. [rustworkx]: https://www.rustworkx.org [NetworkX]: https://networkx.github.io/ [graph-tool]: https://graph-tool.skewed.de/ [pre-commit]: https://pre-commit.com/
