def test_convertToMolecule(self):
from moleculekit.molecule import mol_equal
sm = SmallMol(self.benzamidine_mol2)
mol = sm.toMolecule(formalcharges=False)
assert mol_equal(sm, mol, exceptFields=['serial', 'name'], _logger=False)
def test_align(self):
from moleculekit.util import rotationMatrix
import numpy as np
sm = SmallMol(self.benzamidine_mol2)
mol = sm.toMolecule()
mol.rotateBy(rotationMatrix([1, 0, 0], 3.14))
sm.align(mol)
assert (np.abs(sm._coords) - np.abs(mol.coords)).max() # I need to do the abs of the coords since it's a symmetrical molecule
def test_convertToMolecule(self):
from moleculekit.molecule import mol_equal
sm = SmallMol(self.benzamidine_mol2)
mol = sm.toMolecule()
assert mol_equal(sm,
mol,
exceptFields=["serial", "name"],
_logger=False)
