Python System.molecules方法代码示例

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
def test_central(verbose=False):
    testsys = System(system)

    moves = RigidBodyMC(waters)
    moves.setReflectionSphere(Vector(0), radius)

    if verbose:
        print("Performing 5000 moves 10 times...")

        PDB().write(testsys.molecules(), "test_central0000.pdb")

    for i in range(1,11):
        moves.move(testsys, 5000, False)

        if verbose:
            PDB().write(testsys.molecules(), "test_central%0004d.pdb" % i)

    # the reflection sphere should ensure that none of the 
    # water molecules diffuse outside the sphere
    mols = testsys.molecules()

    for molnum in mols.molNums():
        mol = mols[molnum]

        dist = mol.evaluate().center().length()

        if verbose:
            print("%s : %s A" % (molnum.value(), dist))

        assert( dist <= radius.value() )

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
def test_local(verbose = False):
    testsys = System(system)

    moves = RigidBodyMC(waters)

    local_radius = 1 * angstrom

    if verbose:
        print("Setting local reflection spheres...")

    for molnum in waters.molNums():
        center = waters[molnum].evaluate().center()
        moves.setReflectionSphere(molnum, center, local_radius)

        if verbose:
            print("%s : %s == %s, %s == %s" % (molnum.value(), \
                center, moves.reflectionSphereCenter(molnum), \
                local_radius.value(), moves.reflectionSphereRadius(molnum).value()))

        assert( moves.reflectionSphereCenter(molnum) == center )
        assert( moves.reflectionSphereRadius(molnum) == local_radius )

    if verbose:                               
        print("Performing 5000 moves 10 times...")
        PDB().write(testsys.molecules(), "test_local0000.pdb")

    for i in range(1,11):
        moves.move(testsys, 5000, False)

        if verbose:
            PDB().write(testsys.molecules(), "test_local%0004d.pdb" % i)

    # the reflection sphere should ensure that none of the
    # water molecules diffuse outside the sphere
    mols = testsys.molecules()

    for molnum in mols.molNums():
        mol = mols[molnum]
        oldmol = waters[molnum]

        dist = Vector.distance( mol.evaluate().center(), oldmol.evaluate().center() )

        if verbose:
            print("%s : %s A" % (molnum.value(), dist))

        assert( dist <= local_radius.value() )

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
ms = t.elapsed()
print("Parameterised all of the water molecules (in %d ms)!" % ms)

system = System()

system.add(cljff)

print("Initial energy = %s" % system.energy())

mc = RigidBodyMC(free_mols)
sync_mc = RigidBodyMC(sync_mols)
sync_mc.setSynchronisedTranslation(True)
sync_mc.setSynchronisedRotation(True)

nodes = Cluster.getNode()
this_thread = nodes.borrowThisThread()

moves = WeightedMoves()
moves.add(mc, 2)
moves.add(sync_mc, 1)

for i in range(0,10):
    print(i+1)
    node = nodes.getNode()
    sim = Simulation.run(node, system, moves, 1000)

    system = sim.system()
    moves = sim.moves()

    PDB().write(system.molecules(), "test%003d.pdb" % (i+1))

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
move.setMaximumRotation(5 * degrees)

# We now group all of the moves to be performed into a single Moves
# object. In this case, a WeightedMoves will draw moves randomly
# according to their weight
moves = WeightedMoves()
moves.add( move, 1 )

# Lets perform 100 moves. The moves are performed on a copy of 'system',
# with the updated version of 'system' after the moves returned by this
# function
print("Running 100 moves...")
new_system = moves.move(system, 100, True)

# Now lets run a simulation, writing out a PDB trajectory
PDB().write(system.molecules(), "output000.pdb")
print(system.energies())

# Here we run 10 blocks of 1000 moves, printing out the 
# energies and a PDB of the coordinates after each block
for i in range(1,11):
    system = moves.move(system, 1000, True)
    print("%d: %s" % (i, system.energies()))
    PDB().write(system.molecules(), "output%003d.pdb" % i)

# Finally, we print out information about how many moves
# were accepted and rejected.
print("Move information:")
print(moves)

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
mol = mol.edit().rename("SB2").commit()

mol = protoms.parameterise(mol, ProtoMS.SOLUTE)

perturbations = mol.property("perturbations")

print(perturbations)

print(perturbations.requiredSymbols())
print(perturbations.requiredProperties())

lam = perturbations.symbols().Lambda()

system = System()

solute = MoleculeGroup("solute", mol)

system.add(solute)

system.setConstant(lam, 0.0)
system.add( PerturbationConstraint(solute) )

print(system.constraintsSatisfied())

for i in range(0,101,10):
    system.setConstant(lam, 0.01 * i)

    PDB().write(system.molecules(), "test_%003d.pdb" % i)

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
rb_moves.setTemperature(temperature)

# create volume moves to change the box size
vol_moves = VolumeMove(mols)
vol_moves.setMaximumVolumeChange( mols.nMolecules() * 0.1 * angstrom3 )
vol_moves.setTemperature(temperature)
vol_moves.setPressure(pressure)

# group these two moves together
moves = WeightedMoves()
moves.add( rb_moves, mols.nMolecules() )
moves.add( vol_moves, 1 )

# print the initial energy and coordinates
print("0:   %s" % system.energy())
PDB().write(system.molecules(), "output000000.pdb") 

# now run the simulation in blocks of 1000 moves
nmoves = 0
while nmoves < num_moves:
    system = moves.move(system, 1000, False)
    nmoves += 1000

    # print out the energy and coordinates every 1000 moves
    print("%s  %s" % (nmoves, system.energy()))
    print(moves)

    PDB().write(system.molecules(), "output%000006d.pdb" % nmoves)

print("Complete!")

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
mcmove.add(intra_mcmove)
mcmove.add(inter_mcmove)

do_mc = False

hmcmove = HybridMC(salt, 4*femtosecond, 20)
do_hmc = True
do_hmc = False

print(system.property("space"))

print("\nMove 0")
print(system.energy())
print(mdmove.kineticEnergy())
print(system.energy() + mdmove.kineticEnergy())
PDB().write(system.molecules(), "test%0004d.pdb" % 0)

if do_mc:
    for i in range(1,1000):
        system = mcmove.move(system, 20, False)

        print(i, system.energy())

        PDB().write(system.molecules(), "test%0004d.pdb" % i)

elif do_hmc:
    for i in range(1,1000):
        hmcmove.move(system, 1)

        print(i, system.energy())
        PDB().write(system.molecules(), "test%0004d.pdb" % i)

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
solvent_move.setMaximumRotation( 5 * degrees )

solute_move = RigidBodyMC( solute )
solute_move.setMaximumTranslation( 0.2 * angstrom )
solute_move.setMaximumRotation( 5 * degrees )

moves = WeightedMoves()
moves.add( solvent_move, 100 )
moves.add( solute_move, 1 )

for i in range(1,11):
    system = moves.move(system, 5000, False )
    #system = moves.move(system, 50, False)
    print("Step %d of 10: Energy = %s" % (i, system.energy()))

    PDB().write(system.molecules(), "test_equil_%0004d.pdb" % i)

print("Equilibration complete")

print("Adding energy monitors...")

identity_points = []

for atom in identity_atoms:
    identity_points.append( AtomPoint( solute.moleculeAt(0).atom(AtomName(atom)) ) )

idassigner = IDAssigner(identity_points, solvent)

nrgmon0 = EnergyMonitor(solute, solvent)
nrgmon1 = EnergyMonitor(solute, idassigner)

# 需要导入模块: from Sire import System [as 别名]
# 或者: from Sire.System import molecules [as 别名]
print((grid_system.energies()))
print((exp_system.energies()))

print(("\nGrid energy equals: %s. Explicit energy equals: %s." % \
          (grid_system.energy(), exp_system.energy())))

diff = grid_system.energy() - exp_system.energy()
print(("The difference is %s\n" % diff))

rbmc = RigidBodyMC(swapwaters)
rbmc.setReflectionSphere(center_point, 7.5*angstrom)

moves = SameMoves(rbmc)

PDB().write(grid_system.molecules(), "test0000.pdb")

t = QTime()

for i in range(1,11):
    print("Moving the system...")
    t.start()
    grid_system = moves.move(grid_system, 1000, False)
    ms = t.elapsed()
    print(("Moves complete! Took %d ms" % ms))
    print(("GRID: ",grid_system.energies()))
    exp_system.update( grid_system.molecules() )
    print(("EXPT: ",exp_system.energies()))

    print(("\nGrid energy equals: %s. Explicit energy equals: %s." % \
          (grid_system.energy(), exp_system.energy())))