comparemol
This package is used to compare if two molecules are equivalent.
Installation
This package requires Python 3.8.
pip install comparemolUsage
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 == mol2Rotate 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.
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