# Identify various components. solvated_topology_mdtraj = mdtraj.Topology.from_openmm(solvated_topology_openmm) atom_indices = dict() for component in components: atom_indices[component] = solvated_topology_mdtraj.select(component_dsl[component]) # DEBUG print "Atom indices of ligand:" print atom_indices[phase]['ligand'] alchemical_phases.append(AlchemicalPhase(phase, solvated_system, solvated_topology_openmm, solvated_positions, atom_indices, protocols[phase_prefix])) # Create reference thermodynamic state. from yank.repex import ThermodynamicState # TODO: Fix this weird import path to something more sane, like 'from yank.repex import ThermodynamicState' if is_periodic: thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure) else: thermodynamic_state = ThermodynamicState(temperature=temperature) # TODO: Select protocols. # Create new simulation. yank = Yank(store_dir, **options) yank.create(thermodynamic_state, *alchemical_phases) # TODO: Write PDB files
# Identify various components. solvated_topology_mdtraj = mdtraj.Topology.from_openmm(solvated_topology_openmm) atom_indices[phase] = dict() for component in components: atom_indices[phase][component] = solvated_topology_mdtraj.select(component_dsl[component]) # DEBUG print "Atom indices of ligand:" print atom_indices[phase]['ligand'] # Create list of phase names. phases = systems.keys() # Create reference thermodynamic state. from yank.repex import ThermodynamicState # TODO: Fix this weird import path to something more sane, like 'from yank.repex import ThermodynamicState' if is_periodic: thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure) else: thermodynamic_state = ThermodynamicState(temperature=temperature) # TODO: Select protocols. # Turn off MC ligand displacement. yank.mc_displacement_sigma = None # Create new simulation. yank.create(phases, systems, positions, atom_indices, thermodynamic_state, options=options) # TODO: Write PDB files
# DEBUG print "Atom indices of ligand:" print atom_indices[phase]['ligand'] # Create list of phase names. phases = systems.keys() # Create reference thermodynamic state. from yank.repex import ThermodynamicState # TODO: Fix this weird import path to something more sane, like 'from yank.repex import ThermodynamicState' if is_periodic: thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure) else: thermodynamic_state = ThermodynamicState(temperature=temperature) # TODO: Select protocols. # Turn off MC ligand displacement. yank.mc_displacement_sigma = None # Create new simulation. yank.create(phases, systems, positions, atom_indices, thermodynamic_state, options=options) # TODO: Write PDB files