njzjz / comparemol

Compare whether two molecules are equivalent.

comparemol

This package is used to compare if two molecules are equivalent.

Installation

This package requires Python 3.8.

pip install comparemol

Usage

Compare if two molecules are equivalent

from comparemol import Mol
# define types and coordinates
types1 = [0, 0]
types2 = [0, 0]
coords1 = [[0.0, 0.0, 0.0], [1.0, 1.0, 1.0]]
coords2 = [[0.0, 0.0, 0.0], [1.73205081, 0.0, 0.0]]
# define two molecules
mol1 = Mol(types1, coords1)
mol2 = Mol(types2, coords2)
# compare whether they are equivalent
assert mol1 == mol2

Rotate forces to match coordinates

from comparemol import get_rotation
# define rotation: mol2 -> mol1
r = get_rotation(mol1, mol2)
# rotate forces
force2 = [[1.73205081, 0.0, 0.0]]
force1 = r.apply(force2)

Load from a dpdata System

Load a molecule from a dpdata System:

from comparemol import Mol
# system: dpdata.System
mol = Mol.load_from_dpdata(system)

Note that only the first frame is loaded.