spyrmsd 0.1.2

Python RMSD tool with symmetry correction.

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_qcpcomputes 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

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

Copyright

Copyright (c) 2019, Rocco Meli.

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.