def test_bond_guessing():
from chemlab.db import ChemlabDB, CirDB
from chemlab.graphics import display_molecule
from chemlab.io import datafile
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
print(mol.r_array)
mol.guess_bonds()
assert mol.bonds.size > 0
# We should find the bond guessing also for systems
# System Made of two benzenes
bz = datafile("tests/data/benzene.mol").read('molecule')
bzbonds = bz.bonds
bz.bonds = np.array([])
# Separating the benzenes by large amount
bz2 = bz.copy()
bz2.r_array += 2.0
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
# Separating benzenes by small amount
bz2 = bz.copy()
bz2.r_array += 0.15
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
def test_bond_guessing():
from chemlab.db import ChemlabDB, CirDB
from chemlab.graphics import display_molecule
from chemlab.io import datafile
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
print(mol.r_array)
mol.guess_bonds()
assert mol.bonds.size > 0
# We should find the bond guessing also for systems
# System Made of two benzenes
bz = datafile("tests/data/benzene.mol").read('molecule')
bzbonds = bz.bonds
bz.bonds = np.array([])
# Separating the benzenes by large amount
bz2 = bz.copy()
bz2.r_array += 2.0
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
# Separating benzenes by small amount
bz2 = bz.copy()
bz2.r_array += 0.15
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
def test_bond_guessing():
# We should find the bond guessing also for systems
# System Made of two benzenes
bz = datafile("tests/data/benzene.mol").read("molecule")
bzbonds = bz.bonds
bz.bonds = np.array([])
# Separating the benzenes by large amount
bz2 = bz.copy()
bz2.r_array += 2.0
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
# Separating benzenes by small amount
bz2 = bz.copy()
bz2.r_array += 0.15
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
