Python RMSD tool with symmetry correction.
Project description
sPyRMSD
Python tool for symmetry-corrected RMSD calculations.
Installation
PyPI
pip install spyrmsd
GitHub
git clone https://github.com/RMeli/spyrmsd.git
cd spyrmsd
pip install .
conda
Dependencies
spyrmsd
can be used both as a module or a standalone tool.
Module
The following packages are required to use spyrmsd
as a module:
Standalone Tool
Additionally, one of the following packages are required to use spyrmsd
as a standalone tool:
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 molecules being compared (no atom matching is performed).
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. Therefore, this function should be used when atoms in the molecules being compared are not in the same order (even if there is not symmetry).
Development
To ensure code quality and consistency the following tools are used during development:
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
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