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)