def testBadNetCDFFiles(self):
""" Tests error checking for bad usage of NetCDF files """
self.assertRaises(ValueError, lambda:
NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10, box=True, vels=True,
remd='Temperature')
)
self.assertRaises(ValueError, lambda:
NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10, box=True, vels=True,
remd='Multi')
)
self.assertRaises(ValueError, lambda:
NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10, box=True, vels=True,
remd='Multi', remd_dimtypes=[1, 3, 2])
)
self.assertRaises(ValueError, lambda:
NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10, box=True, vels=True,
remd='Illegal')
)
self.assertRaises(ValueError, lambda:
NetCDFTraj.open_new(get_fn('test.nc', written=True),
natom=10, box=True, vels=False,
remd='Multidim')
)
self.assertRaises(ValueError, lambda:
NetCDFTraj.open_new(get_fn('test.nc', written=True),
natom=10, box=True, vels=False,
remd='Illegal')
)
def test_netcdf_trajectory():
command_refine = [
'phenix.refine',
get_fn('vAla3/vAla3.pdb'),
get_fn('vAla3/vAla3.cif'),
get_fn('vAla3/vAla3.mtz'),
'topology_file_name={}'.format(get_fn('vAla3/vAla3.prmtop')),
'coordinate_file_name={}'.format(get_fn('vAla3/vAla3.rst7')),
'use_amber=True', 'wxc_scale=0.025', '--overwrite',
'refinement.main.number_of_macro_cycles=1',
'amber.netcdf_trajectory_file_name=hello.nc'
]
n_frames = 59
parm = pmd.load_file(get_fn('vAla3/vAla3.prmtop'))
expected_boxes = np.array(n_frames * [
[30., 30., 30., 90., 90., 90.],
],
dtype='f8')
with tempfolder():
output = subprocess.check_output(command_refine)
traj = NetCDFTraj.open_old('hello.nc')
print(traj.coordinates.shape)
aa_eq(traj.box, expected_boxes)
assert traj.coordinates.shape == (n_frames, len(parm.atoms), 3)
def testBadNetCDFFiles(self):
""" Tests error checking for bad usage of NetCDF files """
self.assertRaises(
ValueError,
lambda: NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10,
box=True,
vels=True,
remd='Temperature'))
self.assertRaises(
ValueError,
lambda: NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10,
box=True,
vels=True,
remd='Multi'))
self.assertRaises(
ValueError,
lambda: NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10,
box=True,
vels=True,
remd='Multi',
remd_dimtypes=[1, 3, 2]))
self.assertRaises(
ValueError,
lambda: NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
natom=10,
box=True,
vels=True,
remd='Illegal'))
self.assertRaises(
ValueError,
lambda: NetCDFTraj.open_new(get_fn('test.nc', written=True),
natom=10,
box=True,
vels=False,
remd='Multidim'))
self.assertRaises(
ValueError,
lambda: NetCDFTraj.open_new(get_fn('test.nc', written=True),
natom=10,
box=True,
vels=False,
remd='Illegal'))
def testScientificPython(self):
""" Test ScientificPython parsing """
import parmed.amber as amber
if utils.has_scientific():
amber.use("Scientific")
from parmed.amber.netcdffiles import NetCDFTraj, NetCDFRestart
traj = NetCDFTraj.open_old(get_fn("tz2.truncoct.nc"))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn("ncinpcrd.rst7"))
self._check_rst(rst)
else:
self.assertRaises(ImportError, lambda: amber.use("Scientific"))
def report(self, simulation, state):
"""Generate a report.
Parameters
----------
simulation : :class:`app.Simulation`
The Simulation to generate a report for
state : :class:`mm.State`
The current state of the simulation
"""
global VELUNIT, FRCUNIT
if self.crds:
crds = state.getPositions().value_in_unit(u.angstrom)
if self.vels:
vels = state.getVelocities().value_in_unit(VELUNIT)
if self.frcs:
frcs = state.getForces().value_in_unit(FRCUNIT)
if self._out is None:
# This must be the first frame, so set up the trajectory now
if self.crds:
atom = len(crds)
elif self.vels:
atom = len(vels)
elif self.frcs:
atom = len(frcs)
self.uses_pbc = simulation.topology.getUnitCellDimensions() is not None
self._out = NetCDFTraj.open_new(
self.fname, atom, self.uses_pbc, self.crds, self.vels,
self.frcs, title="ParmEd-created trajectory using OpenMM"
)
if self.uses_pbc:
vecs = state.getPeriodicBoxVectors()
lengths, angles = box_vectors_to_lengths_and_angles(*vecs)
self._out.add_cell_lengths_angles(lengths.value_in_unit(u.angstrom),
angles.value_in_unit(u.degree))
# Add the coordinates, velocities, and/or forces as needed
if self.crds:
self._out.add_coordinates(crds)
if self.vels:
# The velocities get scaled right before writing
self._out.add_velocities(vels)
if self.frcs:
self._out.add_forces(frcs)
# Now it's time to add the time.
self._out.add_time(state.getTime().value_in_unit(u.picosecond))
def testRemdFiles(self):
""" Test proper reading and writing of NetCDF files with REMD info """
rstfn = get_fn('restart.ncrst', written=True)
trjfn = get_fn('traj.nc', written=True)
# Do the restart with T-REMD first
traj = NetCDFRestart.open_new(
rstfn,
100,
True,
True,
'Restart w/ REMD',
remd='Temperature',
temp=300,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
traj.box = [40, 40, 40, 90, 90, 90]
traj.close()
traj = NetCDFRestart.open_old(rstfn)
self.assertEqual(traj.temp0, 300)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFRestart.open_new(
rstfn,
100,
False,
True,
'Restart w/ REMD',
remd='Multi',
remd_dimtypes=[1, 3, 3, 3],
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.remd_indices = remd_indices
traj.close()
traj = NetCDFRestart.open_old(rstfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices)
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
# Do the restart with T-REMD first
traj = NetCDFTraj.open_new(
trjfn,
100,
True,
True,
True,
title='Traj w/ REMD',
remd='Temperature',
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.add_coordinates(crd)
traj.add_velocities(vel)
traj.add_temp0(300)
traj.add_box([40, 40, 40, 90, 90, 90])
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_equal(traj.temp0, [300])
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFTraj.open_new(
trjfn,
100,
False,
True,
title='Traj w/ REMD',
remd='Multi',
remd_dimension=4,
vels=True,
frcs=True,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
frc = np.random.rand(100, 3)
traj.remd_dimtype = [1, 3, 3, 3]
traj.add_coordinates(crd * u.angstroms)
traj.add_velocities(vel * u.angstroms / u.picosecond)
traj.add_forces(frc * u.kilocalories_per_mole / u.angstrom)
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.add_remd_indices(remd_indices)
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_allclose(frc, traj.forces.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices.squeeze())
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
def testNetCDF(self):
""" Test scipy NetCDF parsing """
traj = NetCDFTraj.open_old(get_fn('tz2.truncoct.nc'))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn('ncinpcrd.rst7'))
self._check_rst(rst)
# Now try writing files
ntraj = NetCDFTraj.open_new(get_fn('test.nc', written=True),
traj.atom,
box=True)
for crd in traj.coordinates:
ntraj.add_coordinates(crd)
for box in traj.box:
ntraj.add_box(box)
ntraj.close()
traj = NetCDFTraj.open_old(get_fn('test.nc', written=True))
self._check_traj(traj, written=True)
nrst = NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
rst.atom,
rst.hasbox,
rst.hasvels,
title=rst.title)
nrst.coordinates = rst.coordinates
nrst.velocities = rst.velocities
nrst.time = rst.time
nrst.box = rst.box
nrst.close()
rst = NetCDFRestart.open_old(get_fn('test.ncrst', written=True))
self._check_rst(rst, written=True)
# Now write NetCDF trajectory without any optional attributes/variables
# and check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(nframe, natom, 3) * 20 - 10
coords = np.array(coords, dtype='f')
nctraj = NetCDFFile(get_fn('test2.nc', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBER'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial', ))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'f',
('frame', 'atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFTraj.open_old(get_fn('test2.nc', written=True))
np.testing.assert_allclose(traj2.coordinates, coords)
# Now write NetCDF restart without any optional attributes/variables and
# check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(natom, 3) * 20 - 10
nctraj = NetCDFFile(get_fn('test2.ncrst', written=True),
'w',
mmap=False)
nctraj.Conventions = 'AMBERRESTART'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial', ))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'd', ('atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFRestart.open_old(get_fn('test2.ncrst', written=True))
np.testing.assert_allclose(traj2.coordinates[0], coords)
def testRemdFiles(self):
""" Test proper reading and writing of NetCDF files with REMD info """
rstfn = get_fn('restart.ncrst', written=True)
trjfn = get_fn('traj.nc', written=True)
# Do the restart with T-REMD first
traj = NetCDFRestart.open_new(
rstfn, 100, True, True, 'Restart w/ REMD', remd='Temperature',
temp=300,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
traj.box = [40, 40, 40, 90, 90, 90]
traj.close()
traj = NetCDFRestart.open_old(rstfn)
self.assertEqual(traj.temp0, 300)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFRestart.open_new(
rstfn, 100, False, True, 'Restart w/ REMD', remd='Multi',
remd_dimtypes=[1, 3, 3, 3],
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.coordinates = crd
traj.velocities = vel
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.remd_indices = remd_indices
traj.close()
traj = NetCDFRestart.open_old(rstfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices)
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
# Do the restart with T-REMD first
traj = NetCDFTraj.open_new(
trjfn, 100, True, True, True, title='Traj w/ REMD',
remd='Temperature',
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
traj.add_coordinates(crd)
traj.add_velocities(vel)
traj.add_temp0(300)
traj.add_box([40, 40, 40, 90, 90, 90])
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_equal(traj.temp0, [300])
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
traj = NetCDFTraj.open_new(
trjfn, 100, False, True, title='Traj w/ REMD', remd='Multi',
remd_dimension=4, vels=True, frcs=True,
)
crd = np.random.rand(100, 3)
vel = np.random.rand(100, 3)
frc = np.random.rand(100, 3)
traj.remd_dimtype = [1, 3, 3, 3]
traj.add_coordinates(crd*u.angstroms)
traj.add_velocities(vel*u.angstroms/u.picosecond)
traj.add_forces(frc*u.kilocalories_per_mole/u.angstrom)
remd_indices = np.random.choice(np.arange(20), size=4, replace=True)
traj.add_remd_indices(remd_indices)
traj.close()
traj = NetCDFTraj.open_old(trjfn)
np.testing.assert_allclose(crd, traj.coordinates.squeeze(), atol=1e-5)
np.testing.assert_allclose(vel, traj.velocities.squeeze(), atol=1e-5)
np.testing.assert_allclose(frc, traj.forces.squeeze(), atol=1e-5)
np.testing.assert_equal(remd_indices, traj.remd_indices.squeeze())
np.testing.assert_equal([1, 3, 3, 3], traj.remd_dimtype)
def testNetCDF(self):
""" Test scipy NetCDF parsing """
traj = NetCDFTraj.open_old(get_fn('tz2.truncoct.nc'))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn('ncinpcrd.rst7'))
self._check_rst(rst)
# Now try writing files
ntraj = NetCDFTraj.open_new(get_fn('test.nc', written=True),
traj.atom, box=True)
for crd in traj.coordinates:
ntraj.add_coordinates(crd)
for box in traj.box:
ntraj.add_box(box)
ntraj.close()
traj = NetCDFTraj.open_old(get_fn('test.nc', written=True))
self._check_traj(traj, written=True)
nrst = NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
rst.atom, rst.hasbox, rst.hasvels,
title=rst.title)
nrst.coordinates = rst.coordinates
nrst.velocities = rst.velocities
nrst.time = rst.time
nrst.box = rst.box
nrst.close()
rst = NetCDFRestart.open_old(get_fn('test.ncrst', written=True))
self._check_rst(rst, written=True)
# Now write NetCDF trajectory without any optional attributes/variables
# and check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(nframe, natom, 3) * 20 - 10
coords = np.array(coords, dtype='f')
nctraj = NetCDFFile(get_fn('test2.nc', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBER'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial',))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'f', ('frame', 'atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFTraj.open_old(get_fn('test2.nc', written=True))
np.testing.assert_allclose(traj2.coordinates, coords)
# Now write NetCDF restart without any optional attributes/variables and
# check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(natom, 3) * 20 - 10
nctraj = NetCDFFile(get_fn('test2.ncrst', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBERRESTART'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial',))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'd', ('atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFRestart.open_old(get_fn('test2.ncrst', written=True))
np.testing.assert_allclose(traj2.coordinates[0], coords)
def get_amber_struct_object(params):
amber_params = params.amber
ridingH = True
if getattr(params, "hydrogens", False): # ensemble refinement does not have this
if params.hydrogens.refine in ['riding', 'Auto']:
ridingH = True
elif params.hydrogens.refine in ['individual']:
ridingH = False
else:
raise Sorry("Hydrogens.refine parameter '%s' unknown!"
% params.hydrogens.refine)
amber_structs = amber_adaptbx.SanderStruct(
parm_file_name=amber_params.topology_file_name,
rst_file_name=amber_params.coordinate_file_name,
ridingH=ridingH,
)
if amber_params.bellymask:
try:
amber_structs.inp.ibelly = 1
amber_structs.inp.bellymask = amber_params.bellymask
except AttributeError:
raise AttributeError(
'Setting bellymask for pysander does not work with AmberTools <= 16')
if amber_params.restraint_wt > 0.:
try:
amber_structs.inp.ntr = 1
amber_structs.inp.restraint_wt = amber_params.restraint_wt
amber_structs.inp.restraintmask = amber_params.restraintmask
if amber_params.reference_file_name:
amber_structs.inp.refc = amber_params.reference_file_name
else:
amber_structs.inp.refc = amber_params.coordinate_file_name
except AttributeError as e:
raise AttributeError(
'Setting amber restraint for pysander does not work with AmberTools <= 16')
amber_structs.qm_inp=amber_structs.sander_engine.QmInputOptions()
if amber_params.qmmask:
amber_structs.inp.ifqnt=1
amber_structs.qm_inp.qm_theory = 'PM6'
amber_structs.qm_inp.qmmask = amber_params.qmmask
amber_structs.qm_inp.qmcut = 8.0
amber_structs.qm_inp.qmcharge= amber_params.qmcharge
amber_structs.qm_inp.diag_routine=1
else:
amber_structs.inp.ifqnt=0
if not amber_structs.sander_engine.is_setup():
amber_structs.sander_engine.setup(
amber_structs.parm,
amber_structs.parm.coordinates,
amber_structs.parm.box,
amber_structs.inp,
amber_structs.qm_inp
)
if amber_params.order_file_name is not None:
order_map_file_name = amber_params.order_file_name
amber_structs.order_map_file_name = order_map_file_name
mapped_arr = np.loadtxt(order_map_file_name, dtype='i4').transpose()
amber_structs.order_converter = dict(a2p=mapped_arr[0], p2a=mapped_arr[1])
if amber_params.netcdf_trajectory_file_name:
n_atoms = len(amber_structs.parm.atoms)
amber_structs.writer = NetCDFTraj.open_new(amber_params.netcdf_trajectory_file_name,
n_atoms, box=True, crds=True, frcs=False)
return amber_structs, amber_structs.sander_engine
