def test_topology(self): frame = Frame() frame.resize(2) topology = Topology() topology.atoms.append(Atom("Zn")) topology.atoms.append(Atom("Ar")) frame.topology = topology self.assertEqual(frame.atoms[0].name, "Zn") self.assertEqual(frame.atoms[1].name, "Ar")
def test_topology(self): frame = Frame() frame.resize(2) topology = Topology() topology.atoms.append(Atom("Zn")) topology.atoms.append(Atom("Ar")) frame.topology = topology self.assertEqual(frame.topology.atoms[0].name, "Zn") self.assertEqual(frame.topology.atoms[1].name, "Ar") self.assertEqual(frame.atoms[0].name, "Zn") self.assertEqual(frame.atoms[1].name, "Ar")
# http://creativecommons.org/publicdomain/zero/1.0/ #!/usr/bin/env python import numpy as np from chemfiles import Topology, Frame, Atom, UnitCell, Trajectory topology = Topology() topology.atoms.append(Atom("H")) topology.atoms.append(Atom("O")) topology.atoms.append(Atom("H")) topology.add_bond(0, 1) topology.add_bond(2, 1) frame = Frame() frame.resize(3) frame.topology = topology frame.positions[0, :] = np.array([1.0, 0.0, 0.0]) frame.positions[1, :] = np.array([0.0, 0.0, 0.0]) frame.positions[2, :] = np.array([0.0, 1.0, 0.0]) frame.add_atom(Atom("O"), [5.0, 0.0, 0.0]) frame.add_atom(Atom("C"), [6.0, 0.0, 0.0]) frame.add_atom(Atom("O"), [7.0, 0.0, 0.0]) frame.add_bond(3, 4) frame.add_bond(4, 5) frame.cell = UnitCell(10, 10, 10) with Trajectory("water-co2.pdb", 'w') as trajectory: trajectory.write(frame)