Python RMSD tool with symmetry correction.
Project description
sPyRMSD
Python-first tool for symmetry-corrected RMSD calculations.
Installation
GitHub
git clone https://github.com/RMeli/spyrmsd.git
cd spyrmsd
pip install .
pip
conda
Usage
Standalone
python -m spyrmsd.spyrmsd -h
usage: spyrmsd.py [-h] [-m] [-c] [-s] [-n] [-v]
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
-s, --strip Strip H atoms
-n, --nosymm No graph isomorphism
-v, --verbose Verbose output
Module
from spyrmsd import rmsd
Standard RMSD
The function rmsd.rmsd_standard
computes the standard RMSD without symmetry correction or minimization. The atoms are expected to be in the same order for both molecule being compared.
Minimized RMSD
The function rmsd.rmsd_qcp
computes the minimised RMSD without symmetry correction, using the quaternion characteristic polynomial method. The atoms are expected to be in the same order for both molecule being compared.
Symmetric RMSD
The function rmsd.rmsd_isomorphic
computes the symmetry-corrected RMSD, using molecular graph isomorphisms. Symmetry correction requires molecular adjacency matrices.
Minimized Symmetric RMSD
The function rmsd.rmsd_qcp_isomorphic
computes the minimized and symmetry-corrected RMSD, using molecular graph isomorphisms and the characteristic polynomial method. Symmetry correction requires molecular adjacency matrices.
Contributions
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
References
Copyright
Copyright (c) 2019, Rocco Meli.
Acknowledgements
Project based on the Computational Molecular Science Python Cookiecutter version 1.1
.
Project details
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