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)