def test_bond_guessing():
from chemlab.core.molecule import guess_bonds
from chemlab.db import ChemlabDB, CirDB
from chemlab.graphics import display_molecule
from chemlab.io import datafile
#mol = ChemlabDB().get('molecule', 'example.norbornene')
import time
#mol = CirDB().get('molecule', 'caffeine')
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
t = time.time()
bonds = guess_bonds(mol.r_array, mol.type_array)
print 'elapsed', time.time() - t
mol.bonds = bonds
display_molecule(mol)
def test_read_cml():
from chemlab.graphics import display_molecule
df = datafile('tests/data/mol.cml')
mol = df.read("molecule")
display_molecule(mol)
def test_cir():
db = CirDB()
bz = db.get("molecule", "norbornene")
display_molecule(bz)
