def _check_written_restarts(self, box):
# Now try to read them and verify the information (keep in mind that the
# restart velocities are scaled down then back up, so you'll need to use
# assertAlmostEqual in this case).
rst = readparm.Rst7.open(get_fn('testc.rst7', written=True))
self.assertFalse(rst.hasbox)
self.assertFalse(rst.hasvels)
np.testing.assert_equal(rst.coordinates.flatten(), list(range(27)))
rst = readparm.Rst7.open(get_fn('testcb.rst7', written=True))
self.assertTrue(rst.hasbox)
self.assertFalse(rst.hasvels)
np.testing.assert_equal(rst.coordinates.flatten(), list(range(21)))
np.testing.assert_equal(rst.box.flatten(), box)
rst = readparm.Rst7.open(get_fn('testcv.rst7', written=True))
self.assertTrue(rst.hasvels)
self.assertFalse(rst.hasbox)
np.testing.assert_equal(rst.coordinates,
np.arange(60).reshape(rst.coordinates.shape))
np.testing.assert_allclose(rst.velocities,
np.array(list(reversed(range(60)))).reshape(rst.velocities.shape))
rst = readparm.Rst7.open(get_fn('testcvb.rst7', written=True))
self.assertTrue(rst.hasvels)
self.assertTrue(rst.hasbox)
np.testing.assert_equal(rst.coordinates,
np.arange(45).reshape(rst.coordinates.shape))
np.testing.assert_allclose(rst.velocities,
np.array(list(reversed(range(45)))).reshape(rst.velocities.shape))
np.testing.assert_equal(rst.box, box)
def testWriteCharmm27Top(self):
""" Tests writing a Gromacs topology file with CHARMM 27 FF """
top = load_file(get_fn('1aki.charmm27.top'))
GromacsTopologyFile.write(top,
get_fn('1aki.charmm27.top', written=True))
top2 = load_file(get_fn('1aki.charmm27.top', written=True))
self._charmm27_checks(top)
def testParmSetParsing(self):
""" Tests parsing a set of Amber parameter files """
params = parameters.AmberParameterSet(
os.path.join(get_fn('parm'), 'parm99.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff99SB'),
os.path.join(get_fn('parm'), 'frcmod.parmbsc0'),
)
self.assertGreater(_num_unique_types(params.atom_types), 0)
self.assertGreater(_num_unique_types(params.bond_types), 0)
self.assertGreater(_num_unique_types(params.angle_types), 0)
self.assertGreater(_num_unique_types(params.dihedral_types), 0)
self.assertGreater(_num_unique_types(params.improper_periodic_types), 0)
# Check that parameters were properly overridden. parm99.dat defines
# C-N-CT-C torsion as follows:
#
# C -N -CT-C 1 0.850 180.000 -2.
# C -N -CT-C 1 0.800 0.000 1.
#
# whereas ff99SB defines that torsion as:
#
# C -N -CT-C 1 0.00 0.0 -4.
# C -N -CT-C 1 0.42 0.0 -3.
# C -N -CT-C 1 0.27 0.0 -2.
# C -N -CT-C 1 0.00 0.0 1.
#
# Since ff99SB is loaded last, this should be the one that is stored
self.assertEqual(len(params.dihedral_types[('C','N','CT','C')]), 4)
self.assertEqual(params.dihedral_types[('C','N','CT','C')][0],
topologyobjects.DihedralType(0, 4, 0, 1.2, 2.0))
self.assertEqual(params.dihedral_types[('C','N','CT','C')][1],
topologyobjects.DihedralType(0.42, 3, 0, 1.2, 2.0))
self.assertEqual(params.dihedral_types[('C','N','CT','C')][2],
topologyobjects.DihedralType(0.27, 2, 0, 1.2, 2.0))
self.assertEqual(params.dihedral_types[('C','N','CT','C')][3],
topologyobjects.DihedralType(0, 1, 0, 1.2, 2.0))
def test_dppc(self):
""" Tests non-standard Gromacs force fields and nonbonded exceptions """
# We know what we're doing
warnings.filterwarnings('ignore', category=GromacsWarning)
top = load_file(os.path.join(get_fn('12.DPPC'), 'topol.top'),
xyz=os.path.join(get_fn('12.DPPC'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'lorentz')
# Create the system and context, then calculate the energy decomposition
system = top.createSystem()
context = mm.Context(system, mm.VerletIntegrator(0.001), CPU)
context.setPositions(top.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers.
self.assertAlmostEqual(energies['bond'], 0)
self.assertAlmostEqual(energies['angle'], 1405.7354199, places=4)
self.assertAlmostEqual(energies['dihedral'], 236.932663255, places=4)
self.assertAlmostEqual(energies['improper'], 33.201541811, places=4)
self.assertAlmostEqual(energies['rb_torsion'], 428.0550599, places=4)
self.assertRelativeEqual(energies['nonbonded'], -16432.8092955, places=4)
gmxfrc = get_forces_from_xvg(os.path.join(get_fn('12.DPPC'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 5)
def test_round_trip(self):
""" Test ParmEd -> OpenMM round trip with Gromacs system """
# Use DPPC to get RB-torsions tested. Also check that it initially fails
# with the CustomNonbondedForce
warnings.filterwarnings('ignore', category=GromacsWarning)
top = load_file(os.path.join(get_fn('12.DPPC'), 'topol.top'),
xyz=os.path.join(get_fn('12.DPPC'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'lorentz')
system = top.createSystem()
def bad_system():
return openmm.load_topology(top.topology, system).createSystem()
warnings.filterwarnings('ignore', category=OpenMMWarning)
self.assertTrue(
openmm.load_topology(top.topology, system).unknown_functional
)
self.assertRaises(ParmedError, bad_system)
for i in range(len(system.getForces())):
if isinstance(system.getForce(i), mm.CustomNonbondedForce):
system.removeForce(i)
break
system2 = openmm.load_topology(top.topology, system).createSystem()
con1 = mm.Context(system, mm.VerletIntegrator(0.001), CPU)
con2 = mm.Context(system2, mm.VerletIntegrator(0.001), CPU)
con1.setPositions(top.positions)
con2.setPositions(top.positions)
ene1 = energy_decomposition(top, con1)
ene2 = energy_decomposition(top, con2)
self.assertAlmostEqual(ene1['bond'], ene2['bond'])
self.assertAlmostEqual(ene1['angle'], ene2['angle'])
self.assertAlmostEqual(ene1['dihedral'], ene2['dihedral'])
self.assertAlmostEqual(ene1['improper'], ene2['improper'])
self.assertAlmostEqual(ene1['rb_torsion'], ene2['rb_torsion'])
self.assertAlmostEqual(ene1['nonbonded'], ene2['nonbonded'])
def test_jac(self):
""" Tests the JAC benchmark Gromacs system nrg and force (no PBC) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('07.DHFR-Liquid-NoPBC'), 'topol.top'),
xyz=os.path.join(get_fn('07.DHFR-Liquid-NoPBC'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'lorentz')
# Create the system and context, then calculate the energy decomposition
system = top.createSystem()
context = mm.Context(system, mm.VerletIntegrator(0.001), CPU)
context.setPositions(top.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers. Make sure we zero-out forces for
# virtual sites, since OMM doesn't do this and Gromacs does.
self.assertAlmostEqual(energies['bond'], 35.142565, places=3)
self.assertAlmostEqual(energies['angle'], 3735.514669, places=3)
self.assertAlmostEqual(energies['dihedral'], 7277.741635, delta=0.002)
self.assertRelativeEqual(energies['nonbonded'], -288718.981405, places=4)
gmxfrc = get_forces_from_xvg(
os.path.join(get_fn('07.DHFR-Liquid-NoPBC'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 0.5)
def test_jac_pme(self):
""" Tests the JAC benchmark Gromacs system nrg and force (PME) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('09.DHFR-PME'), 'topol.top'),
xyz=os.path.join(get_fn('09.DHFR-PME'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'lorentz')
# Create the system and context, then calculate the energy decomposition
system = top.createSystem(nonbondedMethod=app.PME,
constraints=app.HBonds,
nonbondedCutoff=0.9*u.nanometers,
ewaldErrorTolerance=1.0e-5)
context = mm.Context(system, mm.VerletIntegrator(0.001), Reference)
context.setPositions(top.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers. Make sure we zero-out forces for
# virtual sites, since OMM doesn't do this and Gromacs does.
self.assertAlmostEqual(energies['bond'], 1628.54739, places=3)
self.assertAlmostEqual(energies['angle'], 3604.58751, places=3)
self.assertAlmostEqual(energies['dihedral'], 6490.00844, delta=0.002)
self.assertRelativeEqual(energies['nonbonded'], 23616.457584, delta=0.002)
gmxfrc = get_forces_from_xvg(
os.path.join(get_fn('09.DHFR-PME'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 5)
def test_component_for_duck_typing():
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
view.add_component(get_fn('tz2.pdb'))
view.add_component(get_fn('tz2_2.pdb.gz'))
view.add_trajectory(nv.PyTrajTrajectory(traj))
view.component_0.add_representation('cartoon')
c0 = view[0]
c1 = view[1]
assert hasattr(view, 'component_0')
assert hasattr(view, 'component_1')
assert hasattr(view, 'trajectory_0')
assert hasattr(view.trajectory_0, 'n_frames')
assert hasattr(view.trajectory_0, 'get_coordinates')
assert hasattr(view.trajectory_0, 'get_structure_string')
c0.show()
c0.hide()
view.remove_component(c0.id)
assert not hasattr(view, 'component_2')
# negative indexing
assert view[-1]._index == c1._index
def test_small_double_peptide(self):
""" Test interacting peptides Gromacs system nrg and frc (no PBC) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('03.AlaGlu'), 'topol.top'),
xyz=os.path.join(get_fn('03.AlaGlu'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'lorentz')
# create the system and context, then calculate the energy decomposition
system = top.createSystem()
context = mm.Context(system, mm.VerletIntegrator(0.001), CPU)
context.setPositions(top.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers. Make sure we zero-out forces for
# virtual sites, since OMM doesn't do this and Gromacs does.
self.assertAlmostEqual(energies['bond'], 1.5307999, places=4)
self.assertAlmostEqual(energies['angle'], 6.5804488, places=4)
self.assertAlmostEqual(energies['dihedral'], 80.379714, places=4)
self.assertAlmostEqual(energies['nonbonded'], -275.142487, places=3)
gmxfrc = get_forces_from_xvg(os.path.join(get_fn('03.AlaGlu'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 0.05)
def testMol3SingleWriteStruct(self):
""" Tests writing mol3 file of single-residue Structure """
mol2 = formats.Mol2File.parse(get_fn('tripos9.mol2'), structure=True)
formats.Mol2File.write(mol2, get_fn('tripos9struct.mol3', written=True),
mol3=True)
self.assertTrue(diff_files(get_fn('tripos9struct.mol3', written=True),
get_saved_fn('tripos9struct.mol3')))
def testMol3SingleWrite(self):
""" Tests writing mol3 file of single ResidueTemplate """
mol2 = formats.Mol2File.parse(get_fn('tripos9.mol2'))
formats.Mol2File.write(mol2, get_fn('tripos9.mol3', written=True),
mol3=True)
self.assertTrue(diff_files(get_fn('tripos9.mol3', written=True),
get_saved_fn('tripos9.mol3')))
def testMol3MultiWriteFromStructure(self):
""" Tests writing mol3 file of multi residues from Structure """
mol2 = formats.Mol2File.parse(get_fn('test_multi.mol2'), structure=True)
formats.Mol2File.write(mol2, get_fn('test_multistruct.mol3', written=True),
mol3=True)
self.assertTrue(diff_files(get_fn('test_multistruct.mol3', written=True),
get_saved_fn('test_multistruct.mol3')))
def _check_written_mdcrds(self, box):
# Now try to read them and verify the information
crd = asciicrd.AmberMdcrd(get_fn('testc.mdcrd', written=True),
15, False, 'r')
self.assertEqual(crd.title, 'Test file')
self.assertFalse(crd.hasbox)
for i in range(crd.frame):
shape = crd.coordinates[i].shape
refcrd = np.arange(45) + i
np.testing.assert_equal(crd.coordinates[i], refcrd.reshape(shape))
for i, array in enumerate(crd.coordinates):
refcrd = (np.arange(45) + i).reshape(array.shape)
np.testing.assert_equal(array, refcrd)
crd.close()
crd = asciicrd.AmberMdcrd(get_fn('testcb.mdcrd', written=True),
18, True, 'r')
self.assertEqual(crd.title, 'Test file')
self.assertTrue(crd.hasbox)
for i in range(crd.frame):
refcrd = (np.arange(54) + i).reshape(crd.coordinates[i].shape)
np.testing.assert_equal(crd.coordinates[i], refcrd)
np.testing.assert_equal(crd.box[i], box)
for i, (coords, mybox) in enumerate(zip(crd.coordinates, crd.box)):
np.testing.assert_equal(coords, (np.arange(54)+i).reshape(coords.shape))
np.testing.assert_equal(mybox, box)
def testAmberGasParm(self):
""" Test the AmberParm class with a non-periodic (gas-phase) prmtop """
parm = readparm.AmberParm(get_fn('trx.prmtop'), get_fn('trx.inpcrd'))
gasparm = readparm.AmberParm(get_fn('trx.prmtop'))
gasparm.load_rst7(get_fn('trx.inpcrd'))
self.assertEqual([a.xx for a in gasparm.atoms],
[a.xx for a in parm.atoms])
self.assertEqual([a.xy for a in gasparm.atoms],
[a.xy for a in parm.atoms])
self.assertEqual([a.xz for a in gasparm.atoms],
[a.xz for a in parm.atoms])
# Now run the tests for the prmtop
self._standard_parm_tests(parm)
self._extensive_checks(parm)
self.assertFalse(parm.chamber)
self.assertFalse(parm.amoeba)
self.assertRaises(KeyError, lambda: parm.parm_data['BOX_DIMENSIONS'])
self.assertEqual(parm.ptr('ifbox'), 0)
# Now check the restart file
rst = readparm.Rst7.open(get_fn('trx.inpcrd'))
coords = rst.coordinates
vels = rst.vels
for i, atom in enumerate(gasparm.atoms):
i3 = i * 3
self.assertEqual(coords[i3 ], atom.xx)
self.assertEqual(coords[i3+1], atom.xy)
self.assertEqual(coords[i3+2], atom.xz)
self.assertEqual(vels[i3 ], atom.vx)
self.assertEqual(vels[i3+1], atom.vy)
self.assertEqual(vels[i3+2], atom.vz)
def test_box_from_system(self):
""" Tests loading box from System """
parm = load_file(get_fn('solv2.parm7'), get_fn('solv2.rst7'))
system = parm.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8*u.angstroms)
top = openmm.load_topology(parm.topology, system)
np.testing.assert_allclose(parm.box, top.box)
def testAdd(self):
""" Tests combining AmberParm instances """
parm1 = readparm.AmberParm(get_fn('phenol.prmtop'))
parm2 = readparm.AmberParm(get_fn('biphenyl.prmtop'))
comb = parm1 + parm2
self.assertEqual(len(comb.atoms), len(parm1.atoms) + len(parm2.atoms))
for a1, a2 in zip(comb.atoms, parm1.atoms + parm2.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.mass, a2.mass)
self.assertEqual(a1.charge, a2.charge)
self.assertEqual(a1.radii, a2.radii)
self.assertEqual(len(comb.residues), len(parm1.residues) + len(parm2.residues))
for r1, r2 in zip(comb.residues, parm1.residues + parm2.residues):
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.chain, r2.chain)
# In-place now
parm1 += parm2
self.assertEqual(len(parm1.atoms), len(comb.atoms))
for a1, a2 in zip(comb.atoms, parm1.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.mass, a2.mass)
self.assertEqual(a1.charge, a2.charge)
self.assertEqual(a1.radii, a2.radii)
self.assertEqual(len(parm1.residues), len(comb.residues))
for r1, r2 in zip(comb.residues, parm1.residues):
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.chain, r2.chain)
def test_write_xml_parameters_amber_write_unused(self):
"""Test the write_unused argument in writing XML files"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('amino12.lib'),
os.path.join(get_fn('parm'), 'parm10.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff14SB'))
)
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2178)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1646)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(get_fn('atomic_ions.lib'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p'))
)
ffxml = StringIO()
warnings.filterwarnings('ignore', category=exceptions.ParameterWarning)
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 222)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 57)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
def test_write_xml_parameters_charmm_multisite_waters(self):
""" Test writing XML parameter files from Charmm multisite water parameter files and reading them back into OpenMM ForceField """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('toppar_water_ions_tip5p.str'))
)
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='toppar_water_ions_tip5p.str',
Reference='MacKerrell'
)
)
forcefield = app.ForceField(ffxml_filename)
# Check that water has the right number of bonds
assert len(params.residues['TIP5'].bonds) == 2, "TIP5P should only have two bonds, but instead has {}".format(params.residues['TIP5'].bonds)
# Parameterize water box
pdbfile = app.PDBFile(get_fn('waterbox.pdb'))
modeller = app.Modeller(pdbfile.topology, pdbfile.positions)
modeller.addExtraParticles(forcefield)
system = forcefield.createSystem(modeller.topology, nonbondedMethod=app.NoCutoff)
# Parameterize water box
pdbfile = app.PDBFile(get_fn('waterbox-tip3p.pdb'))
modeller = app.Modeller(pdbfile.topology, pdbfile.positions)
modeller.addExtraParticles(forcefield)
system = forcefield.createSystem(modeller.topology, nonbondedMethod=app.PME)
def test_geometric_combining_rule_energy(self):
""" Tests converting geom. comb. rule energy from Gromacs to Amber """
top = load_file(os.path.join(get_fn('05.OPLS'), 'topol.top'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(top.combining_rule, 'geometric')
del top.rb_torsions[:]
parm = load_file(get_saved_fn('opls.parm7'),
xyz=os.path.join(get_fn('05.OPLS'), 'conf.gro'))
self.assertEqual(parm.combining_rule, 'geometric')
self.assertFalse(parm.has_NBFIX())
sysg = top.createSystem()
sysa = parm.createSystem()
cong = mm.Context(sysg, mm.VerletIntegrator(0.001), CPU)
cona = mm.Context(sysa, mm.VerletIntegrator(0.001), CPU)
cong.setPositions(top.positions)
cona.setPositions(top.positions)
self._check_energies(top, cong, parm, cona)
# Make an NBFIX
self.assertFalse(parm.has_NBFIX())
parm.parm_data['LENNARD_JONES_ACOEF'][-4] = 10.0
self.assertTrue(parm.has_NBFIX())
parm.createSystem()
def testMoleculeCombine(self):
""" Tests selective molecule combination in Gromacs topology files """
warnings.filterwarnings('ignore', category=GromacsWarning)
parm = load_file(os.path.join(get_fn('12.DPPC'), 'topol3.top'))
fname = get_fn('combined.top', written=True)
# Make sure that combining non-adjacent molecules fails
self.assertRaises(ValueError, lambda:
parm.write(fname, combine=[[1, 3]]))
self.assertRaises(ValueError, lambda:
parm.write(fname, combine='joey'))
self.assertRaises(ValueError, lambda:
parm.write(fname, combine=[1, 2, 3]))
self.assertRaises(TypeError, lambda:
parm.write(fname, combine=1))
parm.write(fname, combine=[[3, 4], [126, 127, 128, 129, 130]])
with open(fname, 'r') as f:
for line in f:
if line.startswith('[ molecules ]'):
break
molecule_list = []
for line in f:
if line[0] == ';': continue
words = line.split()
molecule_list.append((words[0], int(words[1])))
parm2 = load_file(fname)
self.assertEqual(molecule_list, [('DPPC', 3), ('system1', 1),
('SOL', 121), ('system2', 1), ('SOL', 121)])
self.assertEqual(len(parm2.atoms), len(parm.atoms))
self.assertEqual(len(parm2.residues), len(parm2.residues))
for a1, a2 in zip(parm.atoms, parm2.atoms):
self._equal_atoms(a1, a2)
for r1, r2 in zip(parm.residues, parm2.residues):
self.assertEqual(len(r1), len(r2))
for a1, a2 in zip(r1, r2):
self._equal_atoms(a1, a2)
def testDistanceBasedMask(self):
""" Test distance-based mask selections """
parm = readparm.AmberParm(get_fn('trx.prmtop'), get_fn('trx.inpcrd'))
# All atoms within 5 A of residue 8
mask1 = mask.AmberMask(parm, ':8<@5')
# All atoms more than 10 A away from residue 1
mask2 = mask.AmberMask(parm, ':1>:10')
sel = mask1.Selection()
for i, atom in enumerate(parm.atoms):
within = 0
for atom2 in parm.residues[7].atoms:
dx = atom2.xx - atom.xx
dy = atom2.xy - atom.xy
dz = atom2.xz - atom.xz
if (dx*dx + dy*dy + dz*dz) < 25:
within = 1
break
self.assertEqual(sel[i], within)
sel = mask2.Selection()
self.assertEqual(sum(sel), 1588)
for i, res in enumerate(parm.residues):
within = 0
for atom in res.atoms:
for atom2 in parm.residues[0].atoms:
dx = atom2.xx - atom.xx
dy = atom2.xy - atom.xy
dz = atom2.xz - atom.xz
if (dx*dx + dy*dy + dz*dz) > 100:
within = 1
break
if within: break
for atom in res.atoms:
self.assertEqual(sel[atom.idx], within)
def test_chamber_expanded_exclusions(self):
""" Tests converting Gromacs to Chamber parm w/ modified exceptions """
# Now let's modify an exception parameter so that it needs type
# expansion, and ensure that it is handled correctly
top = load_file(get_fn('1aki.charmm27.solv.top'),
xyz=get_fn('1aki.charmm27.solv.gro'))
gsystem1 = top.createSystem(nonbondedCutoff=8*u.angstroms,
nonbondedMethod=app.PME)
gcon1 = mm.Context(gsystem1, mm.VerletIntegrator(1*u.femtosecond),
Reference)
gcon1.setPositions(top.positions)
top.adjust_types.append(to.NonbondedExceptionType(0, 0, 1))
top.adjust_types.claim()
top.adjusts[10].type = top.adjust_types[-1]
gsystem2 = top.createSystem(nonbondedCutoff=8*u.angstroms,
nonbondedMethod=app.PME)
gcon2 = mm.Context(gsystem2, mm.VerletIntegrator(1*u.femtosecond),
Reference)
gcon2.setPositions(top.positions)
e1 = gcon1.getState(getEnergy=True).getPotentialEnergy()
e1 = e1.value_in_unit(u.kilocalories_per_mole)
e2 = gcon2.getState(getEnergy=True).getPotentialEnergy()
e2 = e2.value_in_unit(u.kilocalories_per_mole)
self.assertGreater(abs(e2 - e1), 1e-2)
# Convert to chamber now
parm = amber.ChamberParm.from_structure(top)
asystem = parm.createSystem(nonbondedCutoff=8*u.angstroms,
nonbondedMethod=app.PME)
acon = mm.Context(asystem, mm.VerletIntegrator(1*u.femtosecond),
Reference)
acon.setPositions(top.positions)
e3 = acon.getState(getEnergy=True).getPotentialEnergy()
e3 = e3.value_in_unit(u.kilocalories_per_mole)
self.assertLess(abs(e2 - e3), 1e-2)
def _check_written_mdcrds(self, box):
# Now try to read them and verify the information
crd = asciicrd.AmberMdcrd(get_fn('testc.mdcrd', written=True),
15, False, 'r')
self.assertEqual(crd.title, 'Test file')
self.assertFalse(crd.hasbox)
for i in range(crd.frame):
for x1, x2 in zip(crd.coordinates(i), [x+i for x in range(45)]):
self.assertEqual(x1, x2)
for i, array in enumerate(crd.coordinates()):
for x1, x2 in zip(array, [x+i for x in range(45)]):
self.assertEqual(x1, x2)
crd.close()
crd = asciicrd.AmberMdcrd(get_fn('testcb.mdcrd', written=True),
18, True, 'r')
self.assertEqual(crd.title, 'Test file')
self.assertTrue(crd.hasbox)
for i in range(crd.frame):
for x1, x2 in zip(crd.coordinates(i), [x+i for x in range(54)]):
self.assertEqual(x1, x2)
for x1, x2 in zip(crd.box(i), box):
self.assertEqual(x1, x2)
for i, (coords, mybox) in enumerate(zip(crd.coordinates(), crd.box())):
for x1, x2 in zip(coords, [x+i for x in range(45)]):
self.assertEqual(x1, x2)
for x1, x2 in zip(mybox, box):
self.assertEqual(x1, x2)
def testMdcrd(self):
""" Test the ASCII trajectory file parsing """
mdcrd = asciicrd.AmberMdcrd(get_fn('tz2.truncoct.crd'),
natom=5827, hasbox=True, mode='r')
self.assertEqual(mdcrd.frame, 10)
if has_numpy():
import numpy as np
self.assertIsInstance(mdcrd.coordinates(0), np.ndarray)
# Hack numpy off so we test that code path, too
asciicrd.np = None
asciicrd.array = array
mdcrdarray = asciicrd.AmberMdcrd(get_fn('tz2.truncoct.crd'),
natom=5827, hasbox=True, mode='r')
asciicrd.np = np
else:
mdcrdarray = mdcrd
self.assertIsInstance(mdcrdarray.coordinates(0), array)
if has_numpy():
runsum = 0
for i in range(10):
arr1 = mdcrd.coordinates(i)
arr2 = mdcrdarray.coordinates(i)
runsum += arr1.sum()
self.assertAlmostEqual(arr1.sum(), sum(arr2), places=3)
else:
runsum = 0
for i in range(10):
runsum += sum(mdcrdarray.coordinates(i))
self.assertAlmostEqual(runsum, 7049.817, places=3)
def testBadFileUsage(self):
""" Check that illegal file usage results in desired exceptions """
Restart = asciicrd.AmberAsciiRestart
Mdcrd = asciicrd.AmberMdcrd
box = [10, 10, 10, 90, 90, 90]
rst = Restart(get_fn('testc.rst7', written=True), 'w', natom=9,
hasbox=True)
def assign(obj, stmnt):
rst = crd = obj
exec(stmnt)
try:
self.assertRaises(ValueError,
lambda: assign(rst, 'rst.coordinates=range(20)'))
self.assertRaises(RuntimeError,
lambda: assign(rst, 'rst.box=[10]*3+[90]*3'))
rst.coordinates = list(range(27))
rst.box = box
self.assertRaises(RuntimeError, lambda:
assign(rst, 'rst.velocities=list(range(27))'))
finally:
rst.close()
crd = Mdcrd(get_fn('testc.mdcrd', written=True), natom=15, hasbox=True,
mode='w', title='Test file')
s = 'list(range(45))'
s2 = 'list(range(42))'
try:
crd.add_coordinates(eval(s))
self.assertRaises(RuntimeError,
lambda: assign(crd, 'crd.add_coordinates(%s)'%s))
crd.add_box([10, 10, 10])
self.assertRaises(ValueError,
lambda: assign(crd, 'crd.add_coordinates(%s)'%s2))
finally:
crd.close()
def _check_written_restarts(self, box):
# Now try to read them and verify the information (keep in mind that the
# restart velocities are scaled down then back up, so you'll need to use
# assertAlmostEqual in this case).
rst = readparm.Rst7.open(get_fn('testc.rst7', written=True))
self.assertFalse(rst.hasbox)
self.assertFalse(rst.hasvels)
for x1, x2 in zip(rst.coordinates, range(27)):
self.assertEqual(x1, x2)
rst = readparm.Rst7.open(get_fn('testcb.rst7', written=True))
self.assertTrue(rst.hasbox)
self.assertFalse(rst.hasvels)
for x1, x2 in zip(rst.coordinates, range(21)):
self.assertEqual(x1, x2)
for x1, x2 in zip(rst.box, box):
self.assertEqual(x1, x2)
rst = readparm.Rst7.open(get_fn('testcv.rst7', written=True))
self.assertTrue(rst.hasvels)
self.assertFalse(rst.hasbox)
for x1, x2 in zip(rst.coordinates, range(60)):
self.assertEqual(x1, x2)
for x1, x2 in zip(rst.vels, reversed(range(60))):
self.assertAlmostEqual(x1, x2, places=5)
rst = readparm.Rst7.open(get_fn('testcvb.rst7', written=True))
self.assertTrue(rst.hasvels)
self.assertTrue(rst.hasbox)
for x1, x2 in zip(rst.coordinates, range(45)):
self.assertEqual(x1, x2)
for x1, x2 in zip(rst.vels, reversed(range(45))):
self.assertAlmostEqual(x1, x2, places=5)
for x1, x2 in zip(rst.box, box):
self.assertEqual(x1, x2)
def testAmberMdcrdNumpy(self):
""" Test writing ASCII trajectory file passing numpy arrays """
import numpy as np
box = np.asarray([15, 15, 15])
Mdcrd = asciicrd.AmberMdcrd
crd = Mdcrd(get_fn('testc.mdcrd', written=True), natom=15, hasbox=False,
mode='w', title='Test file')
coorddata = np.arange(45).reshape((15,3))
crd.add_coordinates(coorddata)
crd.add_coordinates(coorddata+1)
crd.add_coordinates(coorddata+2)
crd.add_coordinates(coorddata+3)
crd.add_coordinates(coorddata+4)
crd.close()
crd = Mdcrd(get_fn('testcb.mdcrd', written=True), natom=18, hasbox=True,
mode='w', title='Test file')
coorddata = np.arange(54).reshape((18,3))
crd.add_coordinates(coorddata)
crd.add_box(box)
crd.add_coordinates(coorddata+1)
crd.add_box(box)
crd.add_coordinates(coorddata+2)
crd.add_box(box)
crd.add_coordinates(coorddata+3)
crd.add_box(box)
crd.add_coordinates(coorddata+4)
crd.add_box(box)
crd.close()
self._check_written_mdcrds(box)
def testAmberMdcrd(self):
""" Test writing ASCII trajectory file """
box = [15, 15, 15]
Mdcrd = asciicrd.AmberMdcrd
crd = Mdcrd(get_fn('testc.mdcrd', written=True), natom=15, hasbox=False,
mode='w', title='Test file')
crd.add_coordinates(list(range(45)))
crd.add_coordinates([x+1 for x in range(45)])
crd.add_coordinates([x+2 for x in range(45)])
crd.add_coordinates([x+3 for x in range(45)])
crd.add_coordinates([x+4 for x in range(45)])
crd.close()
crd = Mdcrd(get_fn('testcb.mdcrd', written=True), natom=18, hasbox=True,
mode='w', title='Test file')
crd.add_coordinates(list(range(54)))
crd.add_box(box)
crd.add_coordinates([x+1 for x in range(54)])
crd.add_box(box)
crd.add_coordinates([x+2 for x in range(54)])
crd.add_box(box)
crd.add_coordinates([x+3 for x in range(54)])
crd.add_box(box)
crd.add_coordinates([x+4 for x in range(54)])
crd.add_box(box)
crd.close()
self._check_written_mdcrds(box)
def tearDown(self):
try:
for f in os.listdir(get_fn('writes')):
os.unlink(get_fn(f, written=True))
os.rmdir(get_fn('writes'))
except OSError:
pass
def setUp(self):
self.lfh=sys.stderr
self.verbose=False
self.pathPdbxDataFile = get_fn("1kip.cif")
self.pathOutputFile = get_fn("testOutputDataFile.cif", written=True)
if not os.path.exists(get_fn('writes')):
os.makedirs(get_fn('writes'))
def test_load_data():
view = nv.show_pytraj(pt.datafiles.load_tz2())
# load blob with ext
blob = open(nv.datafiles.PDB).read()
view._load_data(blob, ext='pdb')
# raise if passing blob but does not provide ext
with pytest.raises(ValueError):
view._load_data(blob)
# raise if passing dummy name
with pytest.raises(NameError):
view._load_data(hahahaha)
# load PyTrajectory
t0 = nv.PyTrajTrajectory(pt.datafiles.load_ala3())
view._load_data(t0)
# load current folder
view._load_data(get_fn('tz2.pdb'))
def testCharmmPSFPandas(self):
""" Tests creating a pandas DataFrame from a CharmmPsfFile """
parm = load_file(get_fn('ala_ala_ala.psf'))
df = parm.to_dataframe()
self.assertEqual(df.shape[0], len(parm.atoms))
for i, r1 in df.iterrows():
self.assertEqual(r1.charge, parm.atoms[i].charge)
self.assertEqual(r1['name'], parm.atoms[i].name)
self.assertEqual(r1.radii, parm.atoms[i].radii)
self.assertEqual(r1.screen, parm.atoms[i].screen)
self.assertEqual(r1.type, parm.atoms[i].type)
self.assertEqual(r1.occupancy, parm.atoms[i].occupancy)
self.assertEqual(r1.bfactor, parm.atoms[i].bfactor)
self.assertEqual(r1.altloc, parm.atoms[i].altloc)
self.assertEqual(r1.rmin, parm.atoms[i].rmin)
self.assertEqual(r1.epsilon, parm.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, parm.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, parm.atoms[i].epsilon_14)
self.assertEqual(r1.resname, parm.atoms[i].residue.name)
self.assertEqual(r1.resid, parm.atoms[i].residue.idx)
self.assertEqual(r1.resnum, parm.atoms[i].residue.number)
self.assertEqual(r1.chain, parm.atoms[i].residue.chain)
self.assertEqual(r1.join, parm.atoms[i].join)
self.assertEqual(r1.nb_idx, parm.atoms[i].nb_idx)
self.assertEqual(r1.segid, parm.atoms[i].segid)
self.assertNotIn('xx', df)
self.assertNotIn('xy', df)
self.assertNotIn('xz', df)
self.assertNotIn('vx', df)
self.assertNotIn('vy', df)
self.assertNotIn('vz', df)
self.assertNotIn('type_idx', df)
self.assertNotIn('class_idx', df)
for key in df.keys():
self.assertFalse(key.startswith('multipole'))
self.assertNotIn('polarizability', df)
self.assertNotIn('vdw_parent', df)
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_coordinates_meta():
from mdtraj.testing import get_fn
fn, tn = [
get_fn('frame0.pdb'),
] * 2
trajs = [pt.load(fn, tn), md.load(fn, top=tn), pmd.load_file(tn, fn)]
N_FRAMES = trajs[0].n_frames
from MDAnalysis import Universe
u = Universe(tn, fn)
trajs.append(Universe(tn, fn))
views = [
nv.show_pytraj(trajs[0]), nv.show_mdtraj(trajs[1]),
nv.show_parmed(trajs[2])
]
views.append(nv.show_mdanalysis(trajs[3]))
for index, (view, traj) in enumerate(zip(views, trajs)):
view.frame = 3
assert view._trajlist[0].n_frames == N_FRAMES
def test_mutation():
# mol2
pdb_fn = get_fn('2igd/2igd.pdb')
pdb_out = 'out.pdb'
# no whitespace
command = [
'pdb4amber', '-i', pdb_fn, '-o', pdb_out, '-m', '1-ALA,2-ALA,3-ALA'
]
with tempfolder():
subprocess.check_call(command)
parm = pmd.load_file(pdb_out)
assert set(res.name for res in parm.residues[:3]) == {"ALA"}
# with whitespace
command = [
'pdb4amber', '-i', pdb_fn, '-o', pdb_out, '-m', '1-ALA, 2-ALA, 3-ALA'
]
with tempfolder():
subprocess.check_call(command)
parm = pmd.load_file(pdb_out)
assert set(res.name for res in parm.residues[:3]) == {"ALA"}
def test_write_xml_parameters_charmm(self):
""" Test writing XML parameter files from Charmm parameter files and reading them back into OpenMM ForceField """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(get_fn('par_all36_prot.prm'),
get_fn('top_all36_prot.rtf'),
get_fn('toppar_water_ions.str')))
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_prot.prm, top_all36_prot.rtf',
Reference='MacKerrell'))
forcefield = app.ForceField(ffxml_filename)
# Parameterize alanine tripeptide in vacuum
pdbfile = app.PDBFile(get_fn('ala_ala_ala.pdb'))
system = forcefield.createSystem(pdbfile.topology,
nonbondedMethod=app.NoCutoff)
# Parameterize ACE-NME in water
pdbfile = app.PDBFile(get_fn('2igd_924wat.pdb'))
system = forcefield.createSystem(pdbfile.topology,
nonbondedMethod=app.PME)
def test_write_xml_parameters_methanol_ions_energy(self):
""" Test writing XML parameter files from Charmm parameter files, reading them back into OpenMM ForceField, and computing energy of methanol and NaCl """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(
get_fn('par_all36_cgenff.prm'), get_fn('top_all36_cgenff.rtf'),
get_fn('toppar_water_ions.str'
)) # WARNING: contains duplicate water templates
)
del params.residues[
'TP3M'] # Delete to avoid duplicate water template topologies
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(
ffxml_filename,
provenance=dict(
OriginalFile=
'par_all36_cgenff.prm, top_all36_cgenff.rtf, toppar_water_ions.str',
Reference='MacKerrell'))
forcefield = app.ForceField(ffxml_filename)
# Parameterize methanol and ions in vacuum
pdbfile = app.PDBFile(get_fn('methanol_ions.pdb'))
system = forcefield.createSystem(pdbfile.topology,
nonbondedMethod=app.NoCutoff)
integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
ffxml_potential = context.getState(
getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Compute energy via ParmEd reader
psf = CharmmPsfFile(get_fn('methanol_ions.psf'))
system = psf.createSystem(params)
integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
context = mm.Context(system, integrator, CPU)
context.setPositions(pdbfile.positions)
parmed_potential = context.getState(
getEnergy=True).getPotentialEnergy() / u.kilocalories_per_mole
del context, integrator
# Ensure potentials are almost equal
self.assertAlmostEqual(ffxml_potential, parmed_potential)
def test_write_xml_parameters_amber_write_unused(self):
"""Test the write_unused argument in writing XML files"""
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn('amino12.lib'),
os.path.join(get_fn('parm'), 'parm10.dat'),
os.path.join(get_fn('parm'), 'frcmod.ff14SB')))
ffxml = StringIO()
params.write(ffxml)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 2179)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 1647)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet(
get_fn('atomic_ions.lib'),
os.path.join(get_fn('parm'), 'frcmod.ionsjc_tip3p')))
ffxml = StringIO()
warnings.filterwarnings('ignore', category=exceptions.ParameterWarning)
params.write(ffxml, write_unused=True)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 222)
ffxml = StringIO()
params.write(ffxml, write_unused=False)
ffxml.seek(0)
self.assertEqual(len(ffxml.readlines()), 57)
ffxml.seek(0)
forcefield = app.ForceField(ffxml)
# Load TIP3P water box to ensure there are no duplicate ion parameters
pdbfile = app.PDBFile(get_fn('ionsjc.pdb'))
system = forcefield.createSystem(pdbfile.topology)
def test_write_xml_parameters_charmm(self):
""" Test writing XML parameter files from Charmm parameter files and reading them back into OpenMM ForceField """
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.charmm.CharmmParameterSet(
get_fn('par_all36_prot.prm'), get_fn('top_all36_prot.rtf'),
get_fn('toppar_water_ions.str'
)) # WARNING: contains duplicate water templates
)
# Check that patch ACE remains but duplicate patches ACED, ACP, ACPD
assert 'ACE' in params.patches, "Patch ACE was expected to be retained, but is missing"
for name in ['ACED', 'ACP', 'ACPD']:
assert name not in params.patches, "Duplicate patch {} was expected to be pruned, but is present".format(
name)
del params.residues[
'TP3M'] # Delete to avoid duplicate water template topologies
ffxml_filename = get_fn('charmm_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(
OriginalFile='par_all36_prot.prm, top_all36_prot.rtf',
Reference='MacKerrell'))
forcefield = app.ForceField(ffxml_filename)
# Check that water has the right number of bonds
assert len(params.residues['TIP3'].bonds
) == 2, "TIP3P should only have two bonds"
# Parameterize alanine tripeptide in vacuum
pdbfile = app.PDBFile(get_fn('ala_ala_ala.pdb'))
system = forcefield.createSystem(pdbfile.topology,
nonbondedMethod=app.NoCutoff)
# Parameterize ACE-NME in water
pdbfile = app.PDBFile(get_fn('2igd_924wat.pdb'))
system = forcefield.createSystem(pdbfile.topology,
nonbondedMethod=app.PME)
def testMask(self):
""" Test the Amber mask parser """
parm = readparm.AmberParm(get_fn('trx.prmtop'))
mask_res1 = mask.AmberMask(parm, ':1')
mask_resala = mask.AmberMask(parm, ':ALA')
mask_atname = mask.AmberMask(parm, '@CA')
mask_resat = mask.AmberMask(parm, ':ALA@CA')
mask_attyp = mask.AmberMask(parm, '@%CT')
# Check all of the masks
self.assertEqual(sum(mask_res1.Selection()), 13)
for idx in mask_res1.Selected():
self.assertEqual(parm.atoms[idx].residue.idx, 0)
self.assertEqual(list(range(13)), list(mask_res1.Selected()))
sel = mask_res1.Selection()
for atom in parm.atoms:
if atom.residue.idx == 0:
self.assertEqual(sel[atom.idx], 1)
else:
self.assertEqual(sel[atom.idx], 0)
self.assertEqual(sum(mask_resala.Selection()), 121)
for idx in mask_resala.Selected():
self.assertEqual(parm.atoms[idx].residue.name, 'ALA')
sel = mask_resala.Selection()
for atom in parm.atoms:
if atom.residue.name == 'ALA':
self.assertEqual(sel[atom.idx], 1)
else:
self.assertEqual(sel[atom.idx], 0)
self.assertEqual(sum(mask_atname.Selection()), 108)
for idx in mask_atname.Selected():
self.assertEqual(parm.atoms[idx].name, 'CA')
sel = mask_atname.Selection()
for atom in parm.atoms:
if atom.name == 'CA':
self.assertEqual(sel[atom.idx], 1)
else:
self.assertEqual(sel[atom.idx], 0)
self.assertEqual(sum(mask_resat.Selection()), 12)
for idx in mask_resat.Selected():
self.assertEqual(parm.atoms[idx].name, 'CA')
self.assertEqual(parm.atoms[idx].residue.name, 'ALA')
sel = mask_resat.Selection()
for atom in parm.atoms:
if atom.residue.name == 'ALA' and atom.name == 'CA':
self.assertEqual(sel[atom.idx], 1)
else:
self.assertEqual(sel[atom.idx], 0)
self.assertEqual(sum(mask_attyp.Selection()), 341)
for idx in mask_attyp.Selected():
self.assertEqual(parm.atoms[idx].type, 'CT')
sel = mask_attyp.Selection()
for atom in parm.atoms:
if atom.type == 'CT':
self.assertEqual(sel[atom.idx], 1)
else:
self.assertEqual(sel[atom.idx], 0)
def test_deserialize_system(self):
""" Tests automatic deserialization of a System XML file """
system = openmm.XmlFile.parse(get_fn('system_974wat.xml'))
self.assertIsInstance(system, mm.System)
self.assertEqual(system.getNumParticles(), 6638)
def test_write_xml_parameters(self):
""" Test writing XML parameters loaded from Amber files """
leaprc = StringIO("""\
logFile leap.log
#
# ----- leaprc for loading the ff14SB force field
# ----- NOTE: this is designed for PDB format 3!
# Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
#
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
{ "HS" "H" "sp3" }
{ "H1" "H" "sp3" }
{ "H2" "H" "sp3" }
{ "H3" "H" "sp3" }
{ "H4" "H" "sp3" }
{ "H5" "H" "sp3" }
{ "HW" "H" "sp3" }
{ "HC" "H" "sp3" }
{ "HA" "H" "sp3" }
{ "HP" "H" "sp3" }
{ "HZ" "H" "sp3" }
{ "OH" "O" "sp3" }
{ "OS" "O" "sp3" }
{ "O" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OP" "O" "sp2" }
{ "OW" "O" "sp3" }
{ "CT" "C" "sp3" }
{ "CX" "C" "sp3" }
{ "C8" "C" "sp3" }
{ "2C" "C" "sp3" }
{ "3C" "C" "sp3" }
{ "CH" "C" "sp3" }
{ "CS" "C" "sp2" }
{ "C" "C" "sp2" }
{ "CO" "C" "sp2" }
{ "C*" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CB" "C" "sp2" }
{ "CC" "C" "sp2" }
{ "CN" "C" "sp2" }
{ "CM" "C" "sp2" }
{ "CK" "C" "sp2" }
{ "CQ" "C" "sp2" }
{ "CD" "C" "sp2" }
{ "C5" "C" "sp2" }
{ "C4" "C" "sp2" }
{ "CP" "C" "sp2" }
{ "CI" "C" "sp3" }
{ "CJ" "C" "sp2" }
{ "CW" "C" "sp2" }
{ "CV" "C" "sp2" }
{ "CR" "C" "sp2" }
{ "CA" "C" "sp2" }
{ "CY" "C" "sp2" }
{ "C0" "Ca" "sp3" }
{ "MG" "Mg" "sp3" }
{ "N" "N" "sp2" }
{ "NA" "N" "sp2" }
{ "N2" "N" "sp2" }
{ "N*" "N" "sp2" }
{ "NP" "N" "sp2" }
{ "NQ" "N" "sp2" }
{ "NB" "N" "sp2" }
{ "NC" "N" "sp2" }
{ "NT" "N" "sp3" }
{ "NY" "N" "sp2" }
{ "N3" "N" "sp3" }
{ "S" "S" "sp3" }
{ "SH" "S" "sp3" }
{ "P" "P" "sp3" }
{ "LP" "" "sp3" }
{ "EP" "" "sp3" }
{ "F" "F" "sp3" }
{ "Cl" "Cl" "sp3" }
{ "Br" "Br" "sp3" }
{ "I" "I" "sp3" }
{ "F-" "F" "sp3" }
{ "Cl-" "Cl" "sp3" }
{ "Br-" "Br" "sp3" }
{ "I-" "I" "sp3" }
{ "Li+" "Li" "sp3" }
{ "Na+" "Na" "sp3" }
{ "K+" "K" "sp3" }
{ "Rb+" "Rb" "sp3" }
{ "Cs+" "Cs" "sp3" }
{ "Mg+" "Mg" "sp3" }
# glycam
{ "OG" "O" "sp3" }
{ "OL" "O" "sp3" }
{ "AC" "C" "sp3" }
{ "EC" "C" "sp3" }
}
#
# Load the main parameter set.
#
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
#
# Load main chain and terminating amino acid libraries, nucleic acids
#
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
#
# Load water and ions
#
#loadOff atomic_ions.lib
#loadOff solvents.lib
#HOH = TP3
#WAT = TP3
#
# Define the PDB name map for the amino acids and nucleic acids
#
addPdbResMap {
{ 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
{ 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
{ 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
{ 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
{ 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
{ 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
{ 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
{ 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
{ 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
{ 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
{ 0 "HID" "NHID" } { 1 "HID" "CHID" }
{ 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
{ 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
{ 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
{ 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
{ 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
{ 0 "MET" "NMET" } { 1 "MET" "CMET" }
{ 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
{ 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
{ 0 "SER" "NSER" } { 1 "SER" "CSER" }
{ 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
{ 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
{ 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
{ 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
{ 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
{ 0 "G" "G5" } { 1 "G" "G3" }
{ 0 "A" "A5" } { 1 "A" "A3" }
{ 0 "C" "C5" } { 1 "C" "C3" }
{ 0 "U" "U5" } { 1 "U" "U3" }
{ 0 "DG" "DG5" } { 1 "DG" "DG3" }
{ 0 "DA" "DA5" } { 1 "DA" "DA3" }
{ 0 "DC" "DC5" } { 1 "DC" "DC3" }
{ 0 "DT" "DT5" } { 1 "DT" "DT3" }
# some old Amber residue names for RNA:
{ 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
{ 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
{ 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
{ 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
# some really old Amber residue names, assuming DNA:
{ 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" }
{ 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" }
{ 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" }
{ 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" }
# uncomment out the following if you have this old style RNA files:
# { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" }
# { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" }
# { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" }
# { 0 "URA" "R5" } { 1 "URA" "R3" } { "URA" "R" }
}
# try to be good about reading in really old atom names as well:
addPdbAtomMap {
{ "O5*" "O5'" }
{ "C5*" "C5'" }
{ "C4*" "C4'" }
{ "O4*" "O4'" }
{ "C3*" "C3'" }
{ "O3*" "O3'" }
{ "C2*" "C2'" }
{ "O2*" "O2'" }
{ "C1*" "C1'" }
{ "C5M" "C7" }
{ "H1*" "H1'" }
{ "H2*1" "H2'" }
{ "H2*2" "H2''" }
{ "H2'1" "H2'" }
{ "H2'2" "H2''" }
{ "H3*" "H3'" }
{ "H4*" "H4'" }
{ "H5*1" "H5'" }
{ "H5*2" "H5''" }
{ "H5'1" "H5'" }
{ "H5'2" "H5''" }
{ "HO'2" "HO2'" }
{ "H5T" "HO5'" }
{ "H3T" "HO3'" }
{ "O1'" "O4'" }
{ "OA" "OP1" }
{ "OB" "OP2" }
{ "O1P" "OP1" }
{ "O2P" "OP2" }
}
#
# assume that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE
""")
params = openmm.OpenMMParameterSet.from_parameterset(
pmd.amber.AmberParameterSet.from_leaprc(leaprc))
ffxml_filename = get_fn('amber_conv.xml', written=True)
params.write(ffxml_filename,
provenance=dict(OriginalFile='leaprc.ff14SB',
Reference=[
'Maier and Simmerling',
'Simmerling and Maier'
],
Source=dict(Source='leaprc.ff14SB',
sourcePackage='AmberTools',
sourcePackageVersion='15')))
forcefield = app.ForceField(ffxml_filename)
# Make sure the forcefield can handle proteins with disulfide bonds
pdbfile = app.PDBFile(get_fn('3qyt_fix.pdb'))
forcefield.createSystem(pdbfile.topology, nonbondedMethod=app.NoCutoff)
def tearDown(self):
if os.path.exists(get_fn('writes')):
for f in os.listdir(get_fn('writes')):
os.unlink(get_fn(f, written=True))
def test_read_normal(self):
""" Tests genopen reading a normal text file """
with closing(genopen(get_fn('4lzt.pdb'))) as f:
self.assertEqual(f.read(), open(get_fn('4lzt.pdb')).read())
with closing(genopen(get_fn('4lzt.pdb'), 'r')) as f:
self.assertEqual(f.read(), open(get_fn('4lzt.pdb')).read())
def test_read_gzipped_URL(self):
""" Tests genopen reading a gzipped remote file """
url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/4lzt.pdb.gz'
with closing(genopen(url, 'r')) as f:
self.assertEqual(f.read(), genopen(get_fn('4lzt.pdb.gz')).read())
def test_space_group(self):
parm_from_cif = pmd.load_file(get_fn('2igd.cif'))
parm_from_pdb = pmd.load_file(get_fn('2igd.pdb'))
self.assertEqual(parm_from_cif.space_group, 'P 21 21 21')
self.assertEqual(parm_from_pdb.space_group, 'P 21 21 21')
def test_deserialize_integrator(self):
""" Tests automatic deserialization of an Integrator XML file """
integrator = openmm.XmlFile.parse(get_fn('integrator.xml'))
self.assertIsInstance(integrator, mm.Integrator)
self.assertIsInstance(integrator, mm.LangevinIntegrator)
def test1012(self):
""" Test that 10-12 prmtop files are recognized properly """
parm = readparm.AmberParm(get_fn('ff91.parm7'))
self._standard_parm_tests(parm, has1012=True)
def testLoadParm(self):
""" Test the arbitrary parm loader """
parm = readparm.LoadParm(get_fn('trx.prmtop'))
parm2 = readparm.AmberParm(get_fn('trx.prmtop'))
for key in parm.parm_data:
self.assertEqual(parm.parm_data[key], parm2.parm_data[key])
def test_read_gzipped(self):
""" Tests genopen reading a gzipped file """
with closing(genopen(get_fn('4lzt.pdb.gz'))) as f:
text = gzip.open(get_fn('4lzt.pdb.gz'), 'r').read()
self.assertEqual(f.read(), text.decode('ascii'))
def test_read_bzipped(self):
""" Tests genopen reading a bzipped file """
with closing(genopen(get_fn('4lzt.pdb.bz2'), 'r')) as f:
text = bz2.BZ2File(get_fn('4lzt.pdb.bz2'), 'r').read()
self.assertEqual(text.decode('ascii'), f.read())
def test_add_amber_parm(self):
""" Test adding AmberParm-derived instances to ParmList """
parms = ParmList()
amber = AmberParm(get_fn('tip4p.parm7'))
chamber = ChamberParm(get_fn('ala_ala_ala.parm7'))
amoeba = AmoebaParm(get_fn('nma.parm7'))
parms.add_parm(amber)
parms.add_parm(chamber)
parms.add_parm(amoeba)
self.assertEqual(len(parms), 3)
# Test int indexing
self.assertIs(parms[0], amber)
self.assertIs(parms[1], chamber)
self.assertIs(parms[2], amoeba)
self.assertRaises(IndexError, lambda: parms[3])
# Test name indexing
self.assertIs(parms[get_fn('tip4p.parm7')], amber)
self.assertIs(parms[get_fn('ala_ala_ala.parm7')], chamber)
self.assertIs(parms[get_fn('nma.parm7')], amoeba)
self.assertRaises(IndexError, lambda: parms['noparm'])
# Check that the last added parm is active
self.assertIs(parms.parm, amoeba)
# Set a new active topology
parms.set_new_active(0)
self.assertIs(parms.parm, amber)
parms.set_new_active(get_fn('ala_ala_ala.parm7'))
self.assertIs(parms.parm, chamber)
self.assertRaises(IndexError, lambda: parms.set_new_active(3))
self.assertIs(parms.parm, chamber)
self.assertRaises(exc.DuplicateParm,
lambda: parms.add_parm(get_fn('ala_ala_ala.parm7')))
self.assertRaises(
exc.DuplicateParm,
lambda: parms.add_parm(load_file(get_fn('ala_ala_ala.parm7'))))
self.assertRaises(
exc.ParmError, lambda: parms.add_parm(
os.path.join(get_fn('pptest1'), 'pptest1.h')))
self.assertRaises(exc.ParmError,
lambda: parms.add_parm(get_fn('amino12.lib')))
self.assertRaises(exc.ParmError, lambda: parms.add_parm(object()))
def test_write_bzipped(self):
""" Tests genopen writing a bzipped file """
with closing(genopen(get_fn('test.bz2', written=True), 'w')) as f:
f.write(ALPHABET)
text = bz2.BZ2File(get_fn('test.bz2', written=True), 'r').read()
self.assertEqual(text.decode('ascii'), ALPHABET)
def test_read_ftp_URL(self):
""" Tests genopen reading a ftp remote file """
url = 'ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/05/205l.cif.gz'
with closing(genopen(url, 'r')) as f:
self.assertEqual(f.read(), genopen(get_fn('205l.cif.gz')).read())
def setUp(self):
try:
os.makedirs(get_fn('writes'))
except OSError:
pass
import subprocess
import unittest
import parmed as pmd
import numpy as np
from parmed.residue import WATER_NAMES
import pytest
try:
from io import StringIO
except ImportError:
from cStringIO import StringIO
from pdb4amber import pdb4amber
# local
from utils import tempfolder, get_fn, _has_program
pdb_fn = get_fn('4lzt/4lzt_h.pdb')
try:
# check internet
pmd.download_PDB('1l2y')
internet_ok = True
except IOError:
internet_ok = False
@unittest.skipUnless(internet_ok, 'must have internet connection to rcsb')
def test_write_model():
orig_parm = pmd.download_PDB('1l2y')
pdb_out = 'out.pdb'
# default
def test_write_xml_small_amber(self):
""" Test writing small XML modifications """
params = openmm.OpenMMParameterSet.from_parameterset(
load_file(os.path.join(get_fn('parm'), 'frcmod.constph')))
params.write(get_fn('test.xml', written=True))
def test_write_normal(self):
""" Tests genopen writing a normal text file """
with closing(genopen(get_fn('tmp.txt', written=True), 'w')) as f:
f.write(ALPHABET)
self.assertEqual(
open(get_fn('tmp.txt', written=True), 'r').read(), ALPHABET)
def setUp(self):
self.verbose = False
self.pathPdbxDataFile = get_fn("1kip.cif")
self.pathBigPdbxDataFile = get_fn("1ffk.cif")
self.pathSFDataFile = get_fn("1kip-sf.cif")
def test_read_normal_URL(self):
""" Tests genopen reading a remote file """
url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/tripos1.mol2'
with closing(genopen(url, 'r')) as f:
self.assertEqual(f.read(), open(get_fn('tripos1.mol2')).read())
