spyrmsd 0.3.0

Python RMSD tool with symmetry correction.

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:

• graph-tool or NetworkX
• numpy
• scipy
• qcelemental

Standalone Tool

Additionally, one of the following packages are required to use spyrmsd as a standalone tool:

• Open Babel
• RDKit

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:

• black
• Flake 8 (CI)
• mypy (CI)

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)
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) 2019-2020, Rocco Meli.

Acknowledgements

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