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Python RMSD tool with symmetry correction.

Project description

sPyRMSD

Travis Build Status Build status codecov Language grade: Python Documentation Status

DOI Docs PyPI License

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

Method Reference DOI
QCP D. L. Theobald, Acta Crys. A61, 478-480 (2005) doi
Hungarian W. J. Allen and R. C. Rizzo, J. Chem. Inf. Model. 54, 518-529 (2014) doi
Connectivity E. C. Meng and R. A. Lewis, J. Comp. Chem. 12, 891-898 (1991) doi

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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