Python RMSD tool with symmetry correction.
Project description
sPyRMSD
Python-first tool for symmetry-corrected RMSD calculations.
Installation
PyPI
pip install spyrmsd
This install spyrmsd
as a library. In order to use the standalone RMSD calculation tool, you will need to install Open Babel or RDKit.
GitHub
git clone https://github.com/RMeli/spyrmsd.git
cd spyrmsd
pip install .
conda
Usage
Standalone
python -m spyrmsd.spyrmsd -h
usage: spyrmsd.py [-h] [-m] [-c] [--hydrogens] [-n]
reference molecules [molecules ...]
Python RMSD tool.
positional arguments:
reference Reference file
molecules Input file(s)
optional arguments:
-h, --help show this help message and exit
-m, --minimize Minimize (fit)
-c, --center Center molecules at origin
--hydrogens Keep hydrogen atoms
-n, --nosymm No graph isomorphism
Module
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 molecule being compared (no atom matching is performed).
Symmetric RMSD
The function rmsd.rmsd_isomorphic
computes symmetry-corrected RMSD, using molecular graph isomorphisms. Symmetry correction requires molecular adjacency matrices but needs not the atoms to be in the same order.
Contributions
List of Contributors
Name | GitHub |
---|---|
Rocco Meli | @RMeli |
Tools
Formatting
The code is automatically formatted using black:
black .
Style
Code style is enforced using Flake 8
flake8
Static Checks
Static checks are performed using mypy
mypy
Deployment
PyPI
Build wheel and sdist:
flit build
Upload wheel and sdist on PyPI:
flit publish
References
Copyright
Copyright (c) 2019-2020, Rocco Meli.
Acknowledgements
Project based on the Computational Molecular Science Python Cookiecutter version 1.1
.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.