def _load_improper_info(self):
""" Loads the CHARMM Improper types and array """
del self.impropers[:]
del self.improper_types[:]
for k, eq in zip(self.parm_data['CHARMM_IMPROPER_FORCE_CONSTANT'],
self.parm_data['CHARMM_IMPROPER_PHASE']):
# Previous versions of ParmEd stored improper phases as degrees,
# whereas it should really be stored in radians. So do a simple
# heuristic check to see if a conversion is necessary so we support
# all versions.
eq = eq * RAD_TO_DEG if abs(eq) <= 2 * pi else eq
self.improper_types.append(ImproperType(k, eq,
self.improper_types))
it = iter(self.parm_data['CHARMM_IMPROPERS'])
for i, j, k, l, m in zip(it, it, it, it, it):
self.impropers.append(
Improper(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1],
self.improper_types[m - 1]))
# Make sure that if we have a comment in the CHARMM impropers, we fix it
# to say the units are in radians
for i in range(len(self.parm_comments.get('CHARMM_IMPROPER_PHASE',
[]))):
comment = self.parm_comments['CHARMM_IMPROPER_PHASE'][i]
if 'degrees' in comment:
self.parm_comments['CHARMM_IMPROPER_PHASE'][i] = \
comment.replace('degrees', 'radians')
def _compareInputOutputPDBs(self, pdbfile, pdbfile2, reordered=False,
altloc_option='all'):
# Now go through all atoms and compare their attributes
for a1, a2 in zip(pdbfile.atoms, pdbfile2.atoms):
if altloc_option in ('first', 'all'):
self.assertEqual(a1.occupancy, a2.occupancy)
a1idx = a1.idx
elif altloc_option == 'occupancy':
a, occ = a1, a1.occupancy
for key, oa in iteritems(a1.other_locations):
if oa.occupancy > occ:
occ = oa.occupancy
a = oa
a1idx = a1.idx
a1 = a # This is the atom we want to compare with
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.type, a2.type)
self.assertEqual(a1.mass, a2.mass)
self.assertEqual(a1.charge, a2.charge)
self.assertEqual(a1.bfactor, a2.bfactor)
self.assertEqual(a1.altloc, a2.altloc)
self.assertEqual(a1idx, a2.idx)
if altloc_option == 'all':
self.assertEqual(set(a1.other_locations.keys()),
set(a2.other_locations.keys()))
self.assertEqual(a1.xx, a2.xx)
self.assertEqual(a1.xy, a2.xy)
self.assertEqual(a1.xz, a2.xz)
if altloc_option != 'all':
# There should be no alternate locations unless we keep them all
self.assertEqual(len(a2.other_locations), 0)
if not reordered:
self.assertEqual(a1.number, a2.number)
# Search all alternate locations as well
for k1, k2 in zip(sorted(a1.other_locations.keys()),
sorted(a2.other_locations.keys())):
self.assertEqual(k1, k2)
oa1 = a1.other_locations[k1]
oa2 = a2.other_locations[k2]
self.assertEqual(oa1.atomic_number, oa2.atomic_number)
self.assertEqual(oa1.name, oa2.name)
self.assertEqual(oa1.type, oa2.type)
self.assertEqual(oa1.mass, oa2.mass)
self.assertEqual(oa1.charge, oa2.charge)
self.assertEqual(oa1.occupancy, oa2.occupancy)
self.assertEqual(oa1.bfactor, oa2.bfactor)
self.assertEqual(oa1.altloc, oa2.altloc)
self.assertEqual(oa1.idx, oa2.idx)
if not reordered:
self.assertEqual(oa1.number, oa2.number)
# Now compare all residues
for r1, r2 in zip(pdbfile.residues, pdbfile2.residues):
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.idx, r2.idx)
self.assertEqual(r1.ter, r2.ter)
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.insertion_code, r2.insertion_code)
if not reordered:
self.assertEqual(r1.number, r2.number)
def test_gas_energy_conf_2(self):
""" Compare Amber and OpenMM gas phase energies and forces (topology 2) """
parm = AmberParm(get_fn('hydrogen-peroxide_T0_2.prmtop'), get_fn('hydrogen-peroxide_T0_2.rst7'))
self.assertEqual(parm.combining_rule, 'lorentz')
system = parm.createSystem() # Default, no cutoff
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
sim = app.Simulation(parm.topology, system, integrator, platform=CPU)
sim.context.setPositions(parm.positions)
energies = energy_decomposition(parm, sim.context)
#BOND = 0.0319 ANGLE = 2.1690 DIHED = -2.7931
#VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
#1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
# Compare OpenMM energies with the Amber energies (above)
self.assertAlmostEqual(energies['bond'], 0.0319, places=4)
self.assertAlmostEqual(energies['angle'], 2.1690, places=4)
self.assertAlmostEqual(energies['dihedral'],-2.7931, places=4)
self.assertRelativeEqual(energies['nonbonded'], 0.0, places=3)
# Now test the forces to make sure that they are computed correctly in
# the presence of extra points
pstate = sim.context.getState(getForces=True)
pf = pstate.getForces().value_in_unit(u.kilojoule_per_mole/u.nanometer)
# gmx forces:
# f[ 0]={ 3.14357e+02, -5.90363e+02, 2.11410e+02}
# f[ 1]={-3.14357e+02, 5.90363e+02, 2.11410e+02}
# f[ 2]={ 2.70641e+02, 5.90363e+02, -2.11410e+02}
# f[ 3]={-2.70641e+02, -5.90363e+02, -2.11410e+02}
gf = [ ( 3.14357e+02, -5.90363e+02, 2.11410e+02),
(-3.14357e+02, 5.90363e+02, 2.11410e+02),
( 2.70641e+02, 5.90363e+02, -2.11410e+02),
(-2.70641e+02, -5.90363e+02, -2.11410e+02)]
for p, s in zip(pf, gf):
for x1, x2 in zip(p, s):
self.assertAlmostEqual(x1, x2, places=3)
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 testMult(self):
""" Tests replicating AmberParm instances """
parm = readparm.AmberParm(get_fn('phenol.prmtop'))
mult = parm * 5
self.assertEqual(len(mult.atoms), 5*len(parm.atoms))
self.assertEqual(len(mult.residues), 5*len(parm.residues))
for i, a1 in enumerate(mult.atoms):
a2 = parm[i%len(parm.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)
for i, r1 in enumerate(mult.residues):
r2 = parm.residues[i%len(parm.residues)]
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.chain, r2.chain)
# In-place now
parm *= 5
self.assertEqual(len(parm.atoms), len(mult.atoms))
for a1, a2 in zip(mult.atoms, parm.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(parm.residues), len(mult.residues))
for r1, r2 in zip(mult.residues, parm.residues):
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.chain, r2.chain)
def _check_rst(self, rst, written=False):
""" Checks various restart properties """
self.assertAlmostEqual(rst.time, 30.1)
self.assertEqual(rst.Conventions, 'AMBERRESTART')
self.assertEqual(rst.title, 'ACE')
if written:
self.assertEqual(rst.application, 'AmberTools')
self.assertEqual(rst.program, 'ParmEd')
self.assertEqual(rst.programVersion, __version__)
else:
self.assertEqual(rst.application, 'AMBER')
self.assertEqual(rst.program, 'sander')
self.assertEqual(rst.programVersion, '11.0')
self.assertAlmostEqual(rst.cell_lengths[0], 30.2642725)
self.assertAlmostEqual(rst.cell_lengths[1], 30.2642725)
self.assertAlmostEqual(rst.cell_lengths[2], 30.2642725)
self.assertAlmostEqual(rst.cell_angles[0], 109.471219)
self.assertAlmostEqual(rst.cell_angles[1], 109.471219)
self.assertAlmostEqual(rst.cell_angles[2], 109.471219)
self.assertTrue(
all([
round(x - y, 7) == 0
for x, y in zip(rst.cell_lengths, rst.box[:3])
]))
self.assertTrue(
all([
round(x - y, 7) == 0
for x, y in zip(rst.cell_angles, rst.box[3:])
]))
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 chk_valence(val1, val2):
self.assertIs(type(val1[0]), type(val2[0]))
self.assertEqual(len(val1), len(val2))
attrs = [attr for attr in dir(val1[0]) if attr.startswith('atom')]
for v1, v2 in zip(val1, val2):
at1 = [getattr(v1, attr) for attr in attrs]
at2 = [getattr(v2, attr) for attr in attrs]
self.assertIsNot(v1, v2)
for a1, a2 in zip(at1, at2):
cmp_atoms(a1, a2)
def _load_urey_brad_info(self):
""" Loads the Urey-Bradley types and array """
del self.urey_bradleys[:]
del self.urey_bradley_types[:]
for k, req in zip(
self.parm_data["CHARMM_UREY_BRADLEY_FORCE_CONSTANT"], self.parm_data["CHARMM_UREY_BRADLEY_EQUIL_VALUE"]
):
self.urey_bradley_types.append(BondType(k, req, self.urey_bradley_types))
it = iter(self.parm_data["CHARMM_UREY_BRADLEY"])
for i, j, k in zip(it, it, it):
self.urey_bradleys.append(UreyBradley(self.atoms[i - 1], self.atoms[j - 1], self.urey_bradley_types[k - 1]))
def testCoordinates(self):
""" Tests coordinate handling in Structure """
s = create_random_structure(parametrized=False)
self.assertIs(s.coordinates, None)
natom = len(s.atoms)
# Make sure coordinates will be generated from Atom.xx, xy, xz if not
# otherwise generated
xyz = np.random.random((natom, 3))
for a, x in zip(s.atoms, xyz):
a.xx, a.xy, a.xz = x
self.assertEqual(s.coordinates.shape, (natom, 3))
np.testing.assert_equal(s.coordinates, xyz[:,:])
self.assertIs(s._coordinates, None)
# Now set multiple frames
xyz = np.random.random((5, natom, 3)).tolist()
s.coordinates = xyz
self.assertIsInstance(s.coordinates, np.ndarray)
self.assertEqual(s.coordinates.shape, (natom, 3))
for a, x in zip(s.atoms, xyz[0]):
self.assertEqual(a.xx, x[0])
self.assertEqual(a.xy, x[1])
self.assertEqual(a.xz, x[2])
np.testing.assert_equal(s.get_coordinates('all'), xyz)
for i in range(5):
np.testing.assert_equal(s.get_coordinates(i), xyz[i])
# Now try setting with units
xyz = u.Quantity(np.random.random((3, natom, 3)), u.nanometers)
s.coordinates = xyz
self.assertIsInstance(s.coordinates, np.ndarray)
self.assertEqual(s.coordinates.shape, (natom, 3))
for a, x in zip(s.atoms, xyz[0]._value):
self.assertEqual(a.xx, x[0]*10)
self.assertEqual(a.xy, x[1]*10)
self.assertEqual(a.xz, x[2]*10)
# Now check setting None
s.coordinates = None
for a in s.atoms:
self.assertFalse(hasattr(a, 'xx'))
self.assertFalse(hasattr(a, 'xy'))
self.assertFalse(hasattr(a, 'xz'))
self.assertIs(s.coordinates, None)
# Now check setting flattened arrays
s.coordinates = np.random.random((natom, 3))
self.assertEqual(s.coordinates.shape, (natom, 3))
s.coordinates = np.random.random(natom*3)
self.assertEqual(s.coordinates.shape, (natom, 3))
s.coordinates = np.random.random(natom*3*10)
self.assertEqual(s.coordinates.shape, (natom, 3))
# Now check other iterables
old_crds = s.coordinates
s.coordinates = (random.random() for i in range(3*len(s.atoms)))
self.assertEqual(s.coordinates.shape, (natom, 3))
diff = (old_crds - s.coordinates).ravel()**2
self.assertGreater(diff.sum(), 0.01)
def testSimpleSlice(self):
""" Tests simple slicing of AmberParm """
parm1 = readparm.AmberParm(get_fn("trx.prmtop"))
parm2 = readparm.AmberParm(get_fn("trx.prmtop"))
parm2.strip("!@CA,C,O,N,HA,H")
selection = parm1["@CA,C,O,N,HA,H"]
self.assertIs(type(parm1), readparm.AmberParm)
self.assertIs(type(parm2), readparm.AmberParm)
self.assertIs(type(selection), readparm.AmberParm)
self.assertEqual(len(parm2.atoms), len(selection.atoms))
self.assertEqual(len(parm2.residues), len(selection.residues))
self.assertLess(len(parm2.atoms), len(parm1.atoms))
def cmp_atoms(a1, a2):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.type, a2.type)
self.assertEqual(a1.charge, a2.charge)
self.assertEqual(a1.tree, a2.tree)
self.assertEqual(a1.radii, a2.radii)
self.assertEqual(a1.screen, a2.screen)
self.assertEqual(a1.join, a2.join)
self.assertEqual(a1.mass, a2.mass)
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertEqual(a1.nb_idx, a2.nb_idx)
for a1, a2 in zip(parm2.atoms, selection.atoms):
cmp_atoms(a1, a2)
# Now check valence terms
self.assertEqual(len(parm2.bonds), len(selection.bonds))
self.assertEqual(len(parm2.angles), len(selection.angles))
self.assertEqual(len(parm2.dihedrals), len(selection.dihedrals))
self.assertGreater(len(parm2.bonds), 0)
self.assertGreater(len(parm2.angles), 0)
self.assertGreater(len(parm2.dihedrals), 0)
for b1, b2 in zip(parm2.bonds, selection.bonds):
cmp_atoms(b1.atom1, b2.atom1)
cmp_atoms(b1.atom2, b2.atom2)
self.assertEqual(b1.type, b2.type)
for a1, a2 in zip(parm2.angles, selection.angles):
cmp_atoms(a1.atom1, a2.atom1)
cmp_atoms(a1.atom2, a2.atom2)
cmp_atoms(a1.atom3, a2.atom3)
self.assertEqual(a1.type, a2.type)
for d1, d2 in zip(parm2.dihedrals, selection.dihedrals):
cmp_atoms(d1.atom1, d2.atom1)
cmp_atoms(d1.atom2, d2.atom2)
cmp_atoms(d1.atom3, d2.atom3)
cmp_atoms(d1.atom4, d2.atom4)
self.assertEqual(d1.ignore_end, d2.ignore_end)
self.assertEqual(d1.improper, d2.improper)
self.assertEqual(d1.type, d2.type)
def testMoleculeOrdering(self):
""" Tests non-contiguous atoms in Gromacs topology file writes """
warnings.filterwarnings('ignore', category=GromacsWarning)
parm = load_file(os.path.join(get_fn('12.DPPC'), 'topol3.top'))
parm.write(get_fn('topol3.top', written=True))
parm2 = load_file(get_fn('topol3.top', written=True))
self.assertEqual(len(parm.atoms), len(parm2.atoms))
self.assertEqual(len(parm.residues), len(parm2.residues))
for r1, r2 in zip(parm.residues, parm2.residues):
self.assertEqual(r1.name, r2.name)
for a1, a2 in zip(r1.atoms, r2.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.type, a2.type)
def check_aniso(pdbfile):
aniso1 = [2066, 1204, 1269, 44, 126, 191]
aniso2 = [2090, 1182, 921, 46, 64, 60]
aniso3 = [3057, 3932, 5304, 126, -937, -661]
self.assertEqual(len(aniso1), len(pdbfile.atoms[0].anisou))
for x, y in zip(aniso1, pdbfile.atoms[0].anisou):
self.assertEqual(x/10000, y)
self.assertEqual(len(aniso2), len(pdbfile.atoms[1].anisou))
for x, y in zip(aniso2, pdbfile.atoms[1].anisou):
self.assertEqual(x/10000, y)
self.assertEqual(len(aniso3), len(pdbfile.atoms[-1].anisou))
for x, y in zip(aniso3, pdbfile.atoms[-1].anisou):
self.assertEqual(x/10000, y)
def _load_urey_brad_info(self):
""" Loads the Urey-Bradley types and array """
del self.urey_bradleys[:]
del self.urey_bradley_types[:]
for k, req in zip(self.parm_data['CHARMM_UREY_BRADLEY_FORCE_CONSTANT'],
self.parm_data['CHARMM_UREY_BRADLEY_EQUIL_VALUE']):
self.urey_bradley_types.append(
BondType(k, req, self.urey_bradley_types))
it = iter(self.parm_data['CHARMM_UREY_BRADLEY'])
for i, j, k in zip(it, it, it):
self.urey_bradleys.append(
UreyBradley(self.atoms[i - 1], self.atoms[j - 1],
self.urey_bradley_types[k - 1]))
def _check4lzt(self, cif):
pdb = read_PDB(self.lztpdb)
self.assertEqual(len(cif.atoms), len(pdb.atoms))
nextra = 0
for a1, a2 in zip(cif.atoms, pdb.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.number + nextra, a2.number)
self.assertEqual(len(a1.anisou), len(a2.anisou))
for x, y in zip(a1.anisou, a2.anisou):
self.assertEqual(x, y)
self.assertEqual(a1.altloc, a2.altloc)
self.assertEqual(len(a1.other_locations), len(a2.other_locations))
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.number, a2.residue.number)
# TER cards consume a serial number in the PDB file, but *not* in a
# CIF file.
if a2.residue.ter and a2 is a2.residue.atoms[-1]:
nextra += 1
# Check the unit cell info
self.assertEqual(cif.box[0], 27.240)
self.assertEqual(cif.box[1], 31.870)
self.assertEqual(cif.box[2], 34.230)
self.assertEqual(cif.box[3], 88.520)
self.assertEqual(cif.box[4], 108.53)
self.assertEqual(cif.box[5], 111.89)
# Check the metadata now
self.assertEqual(cif.experimental, 'X-RAY DIFFRACTION')
self.assertEqual(cif.authors,
'Walsh, M.A., Schneider, T., Sieker, L.C., Dauter, Z., '
'Lamzin, V., Wilson, K.S.')
self.assertEqual(cif.title,
'Refinement of triclinic hen egg-white lysozyme at atomic '
'resolution.; Refinement of Triclinic Lysozyme: I. Fourier '
'and Least-Squares Methods; Refinement of Triclinic Lysozyme: '
'II. The Method of Stereochemically Restrained Least Squares')
self.assertEqual(cif.journal,
'Acta Crystallogr.,Sect.D; Acta Crystallogr.,Sect.B; '
'Acta Crystallogr.,Sect.B')
self.assertEqual(cif.journal_authors,
'Walsh, M.A., Schneider, T.R., Sieker, L.C., Dauter, Z., '
'Lamzin, V.S., Wilson, K.S., Hodsdon, J.M., Brown, G.M., '
'Jensen, L.H., Ramanadham, M.')
self.assertEqual(cif.year, '1998, 1990, 1990')
self.assertEqual(cif.page, '522, 54, 63')
self.assertEqual(cif.keywords, ['HYDROLASE', 'O-GLYCOSYL',
'GLYCOSIDASE'])
self.assertEqual(cif.volume, '54, 46, 46')
self.assertEqual(cif.doi, '10.1107/S0907444997013656')
self.assertEqual(cif.pmid, '9761848')
self.assertEqual(cif.resolution, 0.95)
def _load_improper_info(self):
""" Loads the CHARMM Improper types and array """
del self.impropers[:]
del self.improper_types[:]
for k, eq in zip(self.parm_data['CHARMM_IMPROPER_FORCE_CONSTANT'],
self.parm_data['CHARMM_IMPROPER_PHASE']):
self.improper_types.append(ImproperType(k, eq,
self.improper_types))
it = iter(self.parm_data['CHARMM_IMPROPERS'])
for i, j, k, l, m in zip(it, it, it, it, it):
self.impropers.append(
Improper(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1],
self.improper_types[m - 1]))
def chk_valence(val1, val2):
self.assertIs(type(val1[0]), type(val2[0]))
self.assertEqual(len(val1), len(val2))
attrs = [attr for attr in dir(val1[0]) if attr.startswith('atom')]
for v1, v2 in zip(val1, val2):
at1 = [getattr(v1, attr) for attr in attrs]
at2 = [getattr(v2, attr) for attr in attrs]
self.assertIsNot(v1, v2)
for a1, a2 in zip(at1, at2):
cmp_atoms(a1, a2)
if hasattr(v1, 'type'):
self.assertEqual(v1.type, v2.type)
if not isinstance(v1.type, integer_types):
self.assertIsNot(v1.type, v2.type)
def test_gas_energy_conf_4(self):
""" Compare Amber and OpenMM gas phase energies and forces (topology 4) """
parm = AmberParm(get_fn('ethanol_T0.prmtop'),
get_fn('ethanol_T0.rst7'))
self.assertEqual(parm.combining_rule, 'geometric')
system = parm.createSystem() # Default, no cutoff
integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
sim = app.Simulation(parm.topology, system, integrator, platform=CPU)
sim.context.setPositions(parm.positions)
energies = energy_decomposition(parm, sim.context)
#BOND = 0.0239 ANGLE = 0.0298 DIHED = 0.0093
#VDWAALS = 0.0000 EEL = 6.7526 HBOND = 0.0000
#1-4 VDW = 0.0492 1-4 EEL = -6.0430 RESTRAINT = 0.0000
# Compare OpenMM energies with the Amber energies (above)
self.assertAlmostEqual(energies['bond'], 0.0239, places=4)
self.assertAlmostEqual(energies['angle'], 0.0298, places=4)
self.assertAlmostEqual(energies['dihedral'], 0.0093, places=4)
self.assertRelativeEqual(energies['nonbonded'],
0.0000 + 6.7526 + 0.0492 - 6.0430,
places=3)
# Now test the forces to make sure that they are computed correctly in
# the presence of extra points
pstate = sim.context.getState(getForces=True)
pf = pstate.getForces().value_in_unit(u.kilojoule_per_mole /
u.nanometer)
# gmx forces:
# f[ 0]={ 1.73101e+02, 5.67250e+01, -4.02950e+01}
# f[ 1]={-8.13704e+00, -1.79612e+01, 9.88537e+01}
# f[ 2]={-2.83120e+01, 6.23352e+00, -5.47393e+00}
# f[ 3]={-1.03312e+01, -1.00966e+01, -5.12129e+00}
# f[ 4]={-1.69636e+02, 3.34850e+01, -1.73612e+02}
# f[ 5]={ 4.19932e+00, -2.58283e+00, 1.29999e+02}
# f[ 6]={ 3.02865e+01, -6.68331e+00, -2.99153e+01}
# f[ 7]={ 1.00113e+02, -5.22480e+01, 4.80526e+01}
# f[ 8]={-9.12828e+01, -6.87157e+00, -2.24877e+01}
gf = [(1.73101e+02, 5.67250e+01, -4.02950e+01),
(-8.13704e+00, -1.79612e+01, 9.88537e+01),
(-2.83120e+01, 6.23352e+00, -5.47393e+00),
(-1.03312e+01, -1.00966e+01, -5.12129e+00),
(-1.69636e+02, 3.34850e+01, -1.73612e+02),
(4.19932e+00, -2.58283e+00, 1.29999e+02),
(3.02865e+01, -6.68331e+00, -2.99153e+01),
(1.00113e+02, -5.22480e+01, 4.80526e+01),
(-9.12828e+01, -6.87157e+00, -2.24877e+01)]
for p, s in zip(pf, gf):
for x1, x2 in zip(p, s):
self.assertAlmostEqual(x1, x2, places=3)
def testAnisouRead(self):
""" Tests that read_PDB properly reads ANISOU records """
pdbfile = read_PDB(self.pdb)
aniso1 = [2066, 1204, 1269, 44, 126, 191] # first atom's ANISOU record
aniso2 = [2090, 1182, 921, 46, 64, 60] # second atom's ANISOU record
aniso3 = [3057, 3932, 5304, 126, -937, -661] # last atom's ANISOU
self.assertEqual(len(aniso1), len(pdbfile.atoms[0].anisou))
for x, y in zip(aniso1, pdbfile.atoms[0].anisou):
self.assertEqual(x/10000, y)
self.assertEqual(len(aniso2), len(pdbfile.atoms[1].anisou))
for x, y in zip(aniso2, pdbfile.atoms[1].anisou):
self.assertEqual(x/10000, y)
self.assertEqual(len(aniso3), len(pdbfile.atoms[-1].anisou))
for x, y in zip(aniso3, pdbfile.atoms[-1].anisou):
self.assertEqual(x/10000, y)
def _load_improper_info(self):
""" Loads the CHARMM Improper types and array """
del self.impropers[:]
del self.improper_types[:]
for k, eq in zip(self.parm_data['CHARMM_IMPROPER_FORCE_CONSTANT'],
self.parm_data['CHARMM_IMPROPER_PHASE']):
self.improper_types.append(
ImproperType(k, eq, self.improper_types)
)
it = iter(self.parm_data['CHARMM_IMPROPERS'])
for i, j, k, l, m in zip(it, it, it, it, it):
self.impropers.append(
Improper(self.atoms[i-1], self.atoms[j-1], self.atoms[k-1],
self.atoms[l-1], self.improper_types[m-1])
)
def energy_decomposition_system(structure,
system,
platform=None,
nrg=u.kilocalories_per_mole):
"""
This function computes the energy contribution for all of the different
force groups.
Parameters
----------
structure : Structure
The Structure with the coordinates for this system
system : mm.System
The OpenMM System object to get decomposed energies from
platform : str
The platform to use. Options are None (default), 'CPU', 'Reference',
'CUDA', and 'OpenCL'. None will pick default OpenMM platform for this
installation and computer
nrg : energy unit, optional
The unit to convert all energies into. Default is kcal/mol
Returns
-------
energies : list of tuple
Each entry is a tuple with the name of the force followed by its
contribution
"""
import simtk.openmm as mm
# First get all of the old force groups so we can restore them
old_groups = [f.getForceGroup() for f in system.getForces()]
old_recip_group = []
def _ene(context, grp):
st = context.getState(getEnergy=True, groups=1 << grp)
return (type(system.getForce(grp)).__name__,
st.getPotentialEnergy().value_in_unit(nrg))
try:
for i, f in enumerate(system.getForces()):
if isinstance(f, mm.NonbondedForce):
old_recip_group.append(f.getReciprocalSpaceForceGroup())
f.setReciprocalSpaceForceGroup(i)
f.setForceGroup(i)
if platform is None:
con = mm.Context(system, mm.VerletIntegrator(0.001))
else:
con = mm.Context(system, mm.VerletIntegrator(0.001),
mm.Platform.getPlatformByName(platform))
con.setPositions(structure.positions)
if structure.box is not None:
con.setPeriodicBoxVectors(*structure.box_vectors)
return list(map(lambda x: _ene(con, x), range(system.getNumForces())))
finally:
idx = 0
for grp, force in zip(old_groups, system.getForces()):
if isinstance(force, mm.NonbondedForce):
force.setReciprocalSpaceForceGroup(old_recip_group[idx])
idx += 1
force.setForceGroup(grp)
def testXyz(self):
""" Tests parsing Tinker XYZ files """
self.assertTrue(tinkerfiles.XyzFile.id_format(get_fn('nma.xyz')))
self.assertTrue(
tinkerfiles.XyzFile.id_format(get_fn('2igd_924wat.xyz')))
xyz = tinkerfiles.XyzFile(get_fn('nma.xyz'))
np.testing.assert_allclose(xyz.box,
[30.735, 30.876, 28.485, 90.0, 90.0, 90.0])
self.assertEqual(len(xyz.atoms), 2466)
self.assertEqual(xyz.atoms[0].name, 'C')
self.assertEqual(xyz.atoms[0].type, '221')
self.assertEqual(len(xyz.atoms[0].bond_partners), 4)
self.assertEqual(xyz.atoms[-1].name, 'H')
self.assertEqual(xyz.atoms[-1].atomic_number, 1)
self.assertEqual(xyz.atoms[-1].type, '248')
xyz = pmd.load_file(get_fn('2igd_924wat.xyz'),
get_fn('2igd_924wat.pdb'))
pdb = pmd.load_file(get_fn('2igd_924wat.pdb'))
self.assertEqual(len(pdb.atoms), len(xyz.atoms))
self.assertEqual(len(pdb.residues), len(xyz.residues))
for r1, r2 in zip(pdb.residues, xyz.residues):
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.chain, r2.chain)
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.insertion_code, r2.insertion_code)
def testPdbWriteXtal(self):
""" Test PDB file writing from a Xtal structure """
pdbfile = read_PDB(self.pdb)
self._check4lzt(pdbfile)
output = StringIO()
pdbfile.write_pdb(output, renumber=False)
output.seek(0)
pdbfile2 = read_PDB(output)
self._check4lzt(pdbfile2, check_meta=False)
self._compareInputOutputPDBs(pdbfile, pdbfile2)
output = reset_stringio(output)
write_PDB(pdbfile, output)
output.seek(0)
pdbfile3 = read_PDB(output)
self._check4lzt(pdbfile3, check_meta=False)
self._compareInputOutputPDBs(pdbfile, pdbfile3, True)
# Now check that renumbering is done correctly. 4lzt skips residues 130
# through 200
for res1, res2 in zip(pdbfile.residues, pdbfile3.residues):
if res1.idx < 129:
self.assertEqual(res1.number, res2.number)
elif res1.idx < 135:
self.assertEqual(res1.number, res2.number + 71)
else:
# Some residue numbers are skipped in the water numbering
self.assertGreaterEqual(res1.number, res2.number + 71 + 794)
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 detailed_diff(l1, l2, absolute_error=None, relative_error=None, spacechar=None):
"""
Check individual fields to make sure numbers are numerically equal if the
lines differ. Also ignore fields that appear to be a file name, since those
will be system-dependent
"""
fdir = os.path.split(get_fn('writes'))[0]
if spacechar is not None:
for char in spacechar:
l1 = l1.replace(char, ' ')
l2 = l2.replace(char, ' ')
w1 = l1.split()
w2 = l2.split()
if len(w1) != len(w2): return False
for wx, wy in zip(w1, w2):
try:
wx = float(wx)
wy = float(wy)
except ValueError:
if isinstance(wx, float) or (wx != wy and not
(wx.startswith(fdir) or wy.startswith(fdir))):
return False
else:
if wx != wy:
if absolute_error is not None and abs(wx-wy) > absolute_error:
return False
elif relative_error is not None:
if wx == 0 or wy == 0 and abs(wx-wy) > relative_error:
return False
if abs((wx / wy) - 1) > relative_error:
return False
elif absolute_error is None and relative_error is None:
return False
return True
def test_dihedral_type_list(self):
""" Tests the DihedralTypeList class """
dihed_types = TrackedList()
dihed_types.append(DihedralTypeList(list=dihed_types))
dihed_types[0].append(DihedralType(5.0, 2, 0.0, 1.2, 2.0))
dihed_types[0].append(DihedralType(1.0, 3, 180.0, 1.2, 2.0))
dihed_types[0].append(DihedralType(2.0, 4, 180.0, 1.2, 2.0))
dihed_types[0].append(DihedralType(10.0, 1, 180.0, 0., 0.))
self.assertIs(dihed_types[0].list, dihed_types)
self.assertEqual(len(dihed_types), 1)
self.assertEqual(dihed_types[0].idx, 0)
self.assertEqual(len(dihed_types[0]), 4)
# Now test DihedralTypeList.__copy__
cp = copy(dihed_types[0])
self.assertIsNot(cp, dihed_types[0])
self.assertIs(cp.list, None)
self.assertEqual(cp.idx, -1)
self.assertEqual(len(cp), 4)
i = 0
for t1, t2 in zip(cp, dihed_types[0]):
self.assertIsNot(t1, t2)
self.assertEqual(t1.phi_k, t2.phi_k)
self.assertEqual(t1.per, t2.per)
self.assertEqual(t1.phase, t2.phase)
self.assertEqual(t1.scee, t2.scee)
self.assertEqual(t1.scnb, t2.scnb)
i += 1
self.assertEqual(i, 4)
def testReportersPBC(self):
""" Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
system = amber_solv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8*u.angstroms)
integrator = mm.LangevinIntegrator(300*u.kelvin, 5.0/u.picoseconds,
1.0*u.femtoseconds)
sim = app.Simulation(amber_solv.topology, system, integrator)
sim.context.setPositions(amber_solv.positions)
sim.reporters.extend([
NetCDFReporter(get_fn('traj.nc', written=True), 1,
vels=True, frcs=True),
MdcrdReporter(get_fn('traj.mdcrd', written=True), 1),
RestartReporter(get_fn('restart.ncrst', written=True), 1,
netcdf=True),
RestartReporter(get_fn('restart.rst7', written=True), 1)
])
sim.step(5)
for reporter in sim.reporters: reporter.finalize()
ntraj = NetCDFTraj.open_old(get_fn('traj.nc', written=True))
atraj = AmberMdcrd(get_fn('traj.mdcrd', written=True),
amber_solv.ptr('natom'), True, mode='r')
nrst = NetCDFRestart.open_old(get_fn('restart.ncrst', written=True))
arst = AmberAsciiRestart(get_fn('restart.rst7', written=True), 'r')
self.assertEqual(ntraj.frame, 5)
self.assertEqual(atraj.frame, 5)
self.assertTrue(ntraj.hasvels)
self.assertTrue(ntraj.hasfrcs)
for i in range(ntraj.frame):
for x1, x2 in zip(ntraj.box[i], atraj.box[i]):
self.assertAlmostEqual(x1, x2, places=3)
self.assertEqual(len(nrst.box), 6)
self.assertEqual(len(arst.box), 6)
def cmp_valence(val1, val2, typeattrs=None):
self.assertEqual(len(val1), len(val2))
for v1, v2 in zip(val1, val2):
self.assertIs(type(v1), type(v2))
attrs = [attr for attr in dir(v1) if attr.startswith('atom')]
atoms1 = [getattr(v1, attr) for attr in attrs]
atoms2 = [getattr(v2, attr) for attr in attrs]
for a1, a2 in zip(atoms1, atoms2):
cmp_atoms(a1, a2)
# Check the type lists
if typeattrs is not None:
for attr in typeattrs:
self.assertAlmostEqual(getattr(v1.type, attr),
getattr(v2.type, attr), places=5)
else:
self.assertEqual(v1.type, v2.type)
def test_residue(self):
""" Tests the Residue object """
atoms = TrackedList()
atoms.extend([Atom(list=atoms) for i in range(10)])
res = Residue('ALA')
for atom in atoms:
res.add_atom(atom)
self.assertEqual(len(res), len(atoms))
for atom in atoms:
self.assertIs(atom.residue, res)
for x, y in zip(atoms, res):
self.assertIs(x, y)
for atom in atoms:
self.assertIn(atom, res)
# Try deleting all of our atoms
while len(res):
lenres = len(res)
atom = random.choice(atoms)
is_inside = atom in res
res.delete_atom(atom)
self.assertEqual(lenres-len(res), is_inside)
self.assertIs(atom.residue, None)
self.assertEqual(len(res), 0)
for atom in atoms:
self.assertIs(atom.residue, None)
self.assertTrue(res.is_empty())
def test_xyz(self):
""" Tests parsing Tinker XYZ files """
self.assertTrue(tinkerfiles.XyzFile.id_format(get_fn('nma.xyz')))
self.assertTrue(tinkerfiles.XyzFile.id_format(get_fn('2igd_924wat.xyz')))
xyz = tinkerfiles.XyzFile(get_fn('nma.xyz'))
np.testing.assert_allclose(xyz.box, [30.735, 30.876, 28.485, 90.0, 90.0, 90.0])
self.assertEqual(len(xyz.atoms), 2466)
self.assertEqual(xyz.atoms[0].name, 'C')
self.assertEqual(xyz.atoms[0].type, '221')
self.assertEqual(len(xyz.atoms[0].bond_partners), 4)
self.assertEqual(xyz.atoms[-1].name, 'H')
self.assertEqual(xyz.atoms[-1].atomic_number, 1)
self.assertEqual(xyz.atoms[-1].type, '248')
xyz = pmd.load_file(get_fn('2igd_924wat.xyz'), get_fn('2igd_924wat.pdb'))
pdb = pmd.load_file(get_fn('2igd_924wat.pdb'))
xyz2 = pmd.load_file(get_fn('2igd_924wat.xyz'))
self.assertEqual(len(pdb.atoms), len(xyz.atoms))
self.assertEqual(len(pdb.residues), len(xyz.residues))
for r1, r2 in zip(pdb.residues, xyz.residues):
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.chain, r2.chain)
self.assertEqual(r1.name, r2.name)
self.assertEqual(r1.insertion_code, r2.insertion_code)
# Make sure NA ions are atomic number of sodium
for atom in xyz.view['NA',:].atoms:
self.assertEqual(atom.atomic_number, pmd.periodic_table.AtomicNum['Na'])
# Now make sure that NA ions are atomic number of sodium even if we
# don't load a PDB file
for atom in xyz2.view[:,'Na+']:
self.assertEqual(atom.atomic_number, pmd.periodic_table.AtomicNum['Na'])
def _check_rst(self, rst):
""" Checks various restart properties """
self.assertAlmostEqual(rst.time, 30.1)
self.assertEqual(rst.Conventions, "AMBERRESTART")
self.assertEqual(rst.title, "ACE")
self.assertEqual(rst.application, "AMBER")
self.assertEqual(rst.program, "sander")
self.assertEqual(rst.programVersion, "11.0")
self.assertAlmostEqual(rst.cell_lengths[0], 30.2642725)
self.assertAlmostEqual(rst.cell_lengths[1], 30.2642725)
self.assertAlmostEqual(rst.cell_lengths[2], 30.2642725)
self.assertAlmostEqual(rst.cell_angles[0], 109.471219)
self.assertAlmostEqual(rst.cell_angles[1], 109.471219)
self.assertAlmostEqual(rst.cell_angles[2], 109.471219)
self.assertTrue(all([round(x - y, 7) == 0 for x, y in zip(rst.cell_lengths, rst.box[:3])]))
self.assertTrue(all([round(x - y, 7) == 0 for x, y in zip(rst.cell_angles, rst.box[3:])]))
def testAnisouWrite(self):
""" Tests that write_PDB properly writes ANISOU records """
def check_aniso(pdbfile):
aniso1 = [2066, 1204, 1269, 44, 126, 191]
aniso2 = [2090, 1182, 921, 46, 64, 60]
aniso3 = [3057, 3932, 5304, 126, -937, -661]
self.assertEqual(len(aniso1), len(pdbfile.atoms[0].anisou))
for x, y in zip(aniso1, pdbfile.atoms[0].anisou):
self.assertEqual(x/10000, y)
self.assertEqual(len(aniso2), len(pdbfile.atoms[1].anisou))
for x, y in zip(aniso2, pdbfile.atoms[1].anisou):
self.assertEqual(x/10000, y)
self.assertEqual(len(aniso3), len(pdbfile.atoms[-1].anisou))
for x, y in zip(aniso3, pdbfile.atoms[-1].anisou):
self.assertEqual(x/10000, y)
pdbfile = read_PDB(self.pdb)
check_aniso(pdbfile)
output = StringIO()
pdbfile.write_pdb(output)
output.seek(0)
pdbfile2 = read_PDB(output)
# Should have no anisou records, since by default they are not written
for atom in pdbfile2.atoms:
self.assertIs(atom.anisou, None)
output = reset_stringio(output)
pdbfile.write_pdb(output, renumber=False, write_anisou=True)
output.seek(0)
# This one should have anisou records
pdbfile3 = read_PDB(output)
self._compareInputOutputPDBs(pdbfile, pdbfile3)
for a1, a2 in zip(pdbfile.atoms, pdbfile3.atoms):
if has_numpy():
self.assertEqual(a1.anisou.shape, a2.anisou.shape)
else:
self.assertEqual(len(a1.anisou), len(a2.anisou))
for x, y in zip(a1.anisou, a2.anisou):
self.assertAlmostEqual(x, y, delta=1e-4)
self.assertEqual(len(a1.other_locations), len(a2.other_locations))
for key in sorted(a1.other_locations.keys()):
oa1 = a1.other_locations[key]
oa2 = a2.other_locations[key]
if has_numpy():
self.assertEqual(oa1.anisou.shape, oa2.anisou.shape)
else:
self.assertEqual(len(oa1.anisou), len(oa2.anisou))
for x, y in zip(oa1.anisou, oa2.anisou):
self.assertAlmostEqual(x, y, delta=1e-4)
def same_atoms(self, atomlist):
"""
Determine if two dihedrals are assigned to the same sets of atom types
Parameters
----------
atomlist : list
4-element list of atom types to compare against this DihedralParam
Returns
-------
bool, bool
First bool is True if all atoms are the same; False otherwise
Second bool is True if atoms are in the same order; False otherwise
Notes
-----
If this torsion is an improper, the first atom is fixed and the other 3
atoms must be the same (but in any order). If this torsion is a proper,
then the torsions must match in either the forward or reverse
directions, only.
"""
if self[0].dihtype == 'improper':
# For impropers, the third atom is the central atom and the other 3
# can be in any order
if self.atype3 != atomlist[2]: return False, False
if (self.atype1 == atomlist[0] and self.atype2 == atomlist[1] and
self.atype4 == atomlist[3]):
return True, True
# Make sure every atom type is unique so every atom type is added to
# the set (but we know it is NOT the same order now)
set1, set2 = set() , set()
for x, y in zip([atomlist[0], atomlist[1], atomlist[3]],
[self.atype1, self.atype2, self.atype4]):
if x in set1:
i = 0
while '%s%d%d' % (x, i, i) in set1: i += 1
set1.add('%s%d%d' % (x, i, i))
else:
set1.add(x)
if y in set2:
i = 0
while '%s%d%d' % (y, i, i) in set2: i += 1
set2.add('%s%d%d' % (y, i, i))
else:
set2.add(y)
return set1 == set2, False
# If we reached here, this is a proper dihedral
if self.atype2 == atomlist[1] and self.atype3 == atomlist[2]:
same = self.atype1 == atomlist[0] and self.atype4 == atomlist[3]
if not same:
# Check case when atype2 == atype3 and we're not the same --
# check for reversed order
eq = self.atype1 == atomlist[3] and self.atype4 == atomlist[0]
return eq, False
return same, same
if self.atype3 == atomlist[1] and self.atype2 == atomlist[2]:
return self.atype1==atomlist[3] and self.atype4==atomlist[0], False
return False, False
def cmp_dihedrals(dih1, dih2):
self.assertEqual(len(dih1), len(dih2))
for v1, v2 in zip(dih1, dih2):
self.assertIs(type(v1), type(v2))
self.assertIs(type(v1.type), type(v2.type))
atoms1 = [v1.atom1, v1.atom2, v1.atom3, v1.atom4]
atoms2 = [v2.atom1, v2.atom2, v2.atom3, v2.atom4]
for a1, a2 in zip(atoms1, atoms2):
cmp_atoms(a1, a2)
self.assertEqual(v1.improper, v2.improper)
self.assertEqual(v1.ignore_end, v2.ignore_end)
if isinstance(v1, DihedralTypeList):
self.assertEqual(len(v1.type), len(v2.type))
for vt1, vt2 in zip(v1.type, v2.type):
self.assertAlmostEqual(v1.type.phi_k, v2.type.phi_k, places=5)
self.assertAlmostEqual(v1.type.per, v2.type.per, places=5)
self.assertAlmostEqual(v1.type.phase, v2.type.phase, places=5)
def test_gas_energy_conf_4(self):
""" Compare Amber and OpenMM gas phase energies and forces (topology 4) """
parm = AmberParm(get_fn('ethanol_T0.prmtop'), get_fn('ethanol_T0.rst7'))
self.assertEqual(parm.combining_rule, 'geometric')
system = parm.createSystem() # Default, no cutoff
integrator = mm.VerletIntegrator(1.0*u.femtoseconds)
sim = app.Simulation(parm.topology, system, integrator, platform=CPU)
sim.context.setPositions(parm.positions)
energies = energy_decomposition(parm, sim.context)
#BOND = 0.0239 ANGLE = 0.0298 DIHED = 0.0093
#VDWAALS = 0.0000 EEL = 6.7526 HBOND = 0.0000
#1-4 VDW = 0.0492 1-4 EEL = -6.0430 RESTRAINT = 0.0000
# Compare OpenMM energies with the Amber energies (above)
self.assertAlmostEqual(energies['bond'], 0.0239, places=4)
self.assertAlmostEqual(energies['angle'], 0.0298, places=4)
self.assertAlmostEqual(energies['dihedral'], 0.0093, places=4)
self.assertRelativeEqual(energies['nonbonded'], 0.0000+6.7526+0.0492-6.0430, places=3)
# Now test the forces to make sure that they are computed correctly in
# the presence of extra points
pstate = sim.context.getState(getForces=True)
pf = pstate.getForces().value_in_unit(u.kilojoule_per_mole/u.nanometer)
# gmx forces:
# f[ 0]={ 1.73101e+02, 5.67250e+01, -4.02950e+01}
# f[ 1]={-8.13704e+00, -1.79612e+01, 9.88537e+01}
# f[ 2]={-2.83120e+01, 6.23352e+00, -5.47393e+00}
# f[ 3]={-1.03312e+01, -1.00966e+01, -5.12129e+00}
# f[ 4]={-1.69636e+02, 3.34850e+01, -1.73612e+02}
# f[ 5]={ 4.19932e+00, -2.58283e+00, 1.29999e+02}
# f[ 6]={ 3.02865e+01, -6.68331e+00, -2.99153e+01}
# f[ 7]={ 1.00113e+02, -5.22480e+01, 4.80526e+01}
# f[ 8]={-9.12828e+01, -6.87157e+00, -2.24877e+01}
gf = [ ( 1.73101e+02, 5.67250e+01, -4.02950e+01),
(-8.13704e+00, -1.79612e+01, 9.88537e+01),
(-2.83120e+01, 6.23352e+00, -5.47393e+00),
(-1.03312e+01, -1.00966e+01, -5.12129e+00),
(-1.69636e+02, 3.34850e+01, -1.73612e+02),
( 4.19932e+00, -2.58283e+00, 1.29999e+02),
( 3.02865e+01, -6.68331e+00, -2.99153e+01),
( 1.00113e+02, -5.22480e+01, 4.80526e+01),
(-9.12828e+01, -6.87157e+00, -2.24877e+01)]
for p, s in zip(pf, gf):
for x1, x2 in zip(p, s):
self.assertAlmostEqual(x1, x2, places=3)
def energy_decomposition_system(structure, system, platform=None,
nrg=u.kilocalories_per_mole):
"""
This function computes the energy contribution for all of the different
force groups.
Parameters
----------
structure : Structure
The Structure with the coordinates for this system
system : mm.System
The OpenMM System object to get decomposed energies from
platform : str
The platform to use. Options are None (default), 'CPU', 'Reference',
'CUDA', and 'OpenCL'. None will pick default OpenMM platform for this
installation and computer
nrg : energy unit, optional
The unit to convert all energies into. Default is kcal/mol
Returns
-------
energies : list of tuple
Each entry is a tuple with the name of the force followed by its
contribution
"""
import simtk.openmm as mm
# First get all of the old force groups so we can restore them
old_groups = [f.getForceGroup() for f in system.getForces()]
old_recip_group = []
def _ene(context, grp):
st = context.getState(getEnergy=True, groups=1<<grp)
return (type(system.getForce(grp)).__name__,
st.getPotentialEnergy().value_in_unit(nrg))
try:
for i, f in enumerate(system.getForces()):
if isinstance(f, mm.NonbondedForce):
old_recip_group.append(f.getReciprocalSpaceForceGroup())
f.setReciprocalSpaceForceGroup(i)
f.setForceGroup(i)
if platform is None:
con = mm.Context(system, mm.VerletIntegrator(0.001))
else:
con = mm.Context(system, mm.VerletIntegrator(0.001),
mm.Platform.getPlatformByName(platform))
con.setPositions(structure.positions)
if structure.box is not None:
con.setPeriodicBoxVectors(*structure.box_vectors)
return list(map(lambda x: _ene(con, x), range(system.getNumForces())))
finally:
idx = 0
for grp, force in zip(old_groups, system.getForces()):
if isinstance(force, mm.NonbondedForce):
force.setReciprocalSpaceForceGroup(old_recip_group[idx])
idx += 1
force.setForceGroup(grp)
def cmp_top_arrays(arr1, arr2):
self.assertEqual(len(arr1), len(arr2))
for t1, t2 in zip(arr1, arr2):
self.assertIs(type(t1), type(t2))
atoms = [attr for attr in dir(t1) if attr.startswith('atom')]
for a in atoms:
self._equal_atoms(getattr(t1, a), getattr(t2, a))
if hasattr(t1, 'type'):
self.assertEqual(t1.type, t2.type)
def cmp_top_arrays(arr1, arr2):
self.assertEqual(len(arr1), len(arr2))
for t1, t2 in zip(arr1, arr2):
self.assertIs(type(t1), type(t2))
atoms = [attr for attr in dir(t1) if attr.startswith("atom")]
for a in atoms:
self._equal_atoms(getattr(t1, a), getattr(t2, a))
if hasattr(t1, "type"):
self.assertEqual(t1.type, t2.type)
def get_max_diff(f1, f2):
""" Gets the maximum difference between two force vectors """
maxfrc = None
assert len(f1) == len(f2), 'vector size mismatch'
for v1, v2 in zip(f1, f2):
norm = u.norm(v1 - v2)
if maxfrc is None:
maxfrc = norm
else:
maxfrc = max(maxfrc, norm)
return maxfrc
def test_dyn(self):
""" Tests parsing Tinker DYN files """
dyn = tinkerfiles.DynFile(get_fn('nma.dyn'))
self.assertEqual(dyn.natom, 2466)
for attr in ('accelerations', 'old_accelerations', 'box', 'positions',
'velocities'):
self.assertTrue(hasattr(dyn, attr))
for x, y in zip(dyn.positions[10],
[-0.1099425448789507, -1.83499212341286, 6.089155631551154]):
self.assertAlmostEqual(x, y)
def __init__(self, fname, seq=None):
super(XyzFile, self).__init__()
if isinstance(fname, string_types):
fxyz = genopen(fname, 'r')
own_handle_xyz = True
else:
fxyz = fname
own_handle_xyz = False
if seq is not None:
seqstruct = load_file(seq)
# Now parse the file
try:
natom = int(fxyz.readline().split()[0])
except (ValueError, IndexError):
raise TinkerError('Bad XYZ file format; first line')
if seq is not None and natom != len(seqstruct.atoms):
raise ValueError(
'Sequence file %s # of atoms does not match the # '
'of atoms in the XYZ file' % seq)
words = fxyz.readline().split()
if len(words) == 6 and not XyzFile._check_atom_record(words):
self.box = [float(w) for w in words]
words = fxyz.readline().split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1],
type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
residue = Residue('SYS')
residue.number = 1
residue._idx = 0
if seq is not None:
residue = seqstruct.residues[0]
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids = [[int(w) for w in words[6:]]]
for i, line in enumerate(fxyz):
words = line.split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1],
type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
if seq is not None:
residue = seqstruct.atoms[i + 1].residue
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids.append([int(w) for w in words[6:]])
# All of the bonds are stored now -- go ahead and make them now
for atom, bonds in zip(self.atoms, bond_ids):
i = atom.idx + 1
for idx in bonds:
if idx > i:
self.bonds.append(Bond(atom, self.atoms[idx - 1]))
if own_handle_xyz:
fxyz.close()
def test_gas_energy_conf_3(self):
""" Compare Amber and OpenMM gas phase energies and forces (topology 3) """
parm = AmberParm(get_fn('methanol_T0.prmtop'),
get_fn('methanol_T0.rst7'))
self.assertEqual(parm.combining_rule, 'geometric')
system = parm.createSystem() # Default, no cutoff
integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
sim = app.Simulation(parm.topology, system, integrator, platform=CPU)
sim.context.setPositions(parm.positions)
energies = energy_decomposition(parm, sim.context)
#BOND = 0.0224 ANGLE = 0.0469 DIHED = 0.0039
#VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
#1-4 VDW = 0.0000 1-4 EEL = 3.3789 RESTRAINT = 0.0000
# Compare OpenMM energies with the Amber energies (above)
self.assertAlmostEqual(energies['bond'], 0.0224, places=4)
self.assertAlmostEqual(energies['angle'], 0.0469, places=4)
self.assertAlmostEqual(energies['dihedral'], 0.0039, places=4)
self.assertRelativeEqual(energies['nonbonded'], 3.3789, places=3)
# Now test the forces to make sure that they are computed correctly in
# the presence of extra points
pstate = sim.context.getState(getForces=True)
pf = pstate.getForces().value_in_unit(u.kilojoule_per_mole /
u.nanometer)
# gmx forces:
# f[ 0]={ 2.19935e+01, 8.60143e+01, 1.77895e+02}
# f[ 1]={ 5.25347e+01, 3.46119e+01, -9.73738e+01}
# f[ 2]={ 1.76138e+01, -7.13778e+01, -1.08807e+00}
# f[ 3]={-3.74994e+01, -5.39602e+01, -6.75679e+01}
# f[ 4]={-8.35142e+01, -7.86616e+01, -1.60611e+02}
# f[ 5]={ 2.88716e+01, 8.33735e+01, 1.48746e+02}
gf = [(2.19935e+01, 8.60143e+01, 1.77895e+02),
(5.25347e+01, 3.46119e+01, -9.73738e+01),
(1.76138e+01, -7.13778e+01, -1.08807e+00),
(-3.74994e+01, -5.39602e+01, -6.75679e+01),
(-8.35142e+01, -7.86616e+01, -1.60611e+02),
(2.88716e+01, 8.33735e+01, 1.48746e+02)]
for p, s in zip(pf, gf):
for x1, x2 in zip(p, s):
self.assertAlmostEqual(x1, x2, places=3)
def testLoadDataFrameStructureView(self):
""" Tests the load_dataframe method on StructureView """
struct = create_random_structure(parametrized=True).view[:10, :]
charges = [a.charge for a in struct.atoms]
self.assertTrue(not all(x == 0 for x in charges))
df = struct.to_dataframe()
# First zero-out all of the charges
struct.load_dataframe(dict(charge=[0 for a in struct.atoms]))
self.assertTrue(all(a.charge == 0 for a in struct.atoms))
# Now re-load the dataframe to restore the original charges
struct.load_dataframe(df)
self.assertTrue(
all(a.charge == x for a, x in zip(struct.atoms, charges)))
# Change the first atomic properties of *everything* now to
# make sure that they all get updated
df_orig = df.copy()
df.loc[0, 'number'] = 1
df.loc[0, 'name'] = 'HAHA'
df.loc[0, 'type'] = 'FUNY'
df.loc[0, 'atomic_number'] = 92 # uranium
df.loc[0, 'charge'] *= 2
df.loc[0, 'mass'] *= 10
df.loc[0, 'nb_idx'] = 10
df.loc[0, 'solvent_radius'] *= 2
df.loc[0, 'screen'] = 0.5
df.loc[0, 'occupancy'] = 0.1
df.loc[0, 'bfactor'] = 0.5
df.loc[0, 'altloc'] = 'X'
df.loc[0, 'tree'] = 'BLU'
df.loc[0, 'join'] = 1.0
df.loc[0, 'irotat'] = 2.0
df.loc[0, 'rmin'] *= 2
df.loc[0, 'epsilon'] /= 2
struct.load_dataframe(df)
atom = struct.atoms[0]
self.assertEqual(atom.number, 1)
self.assertEqual(atom.name, 'HAHA')
self.assertEqual(atom.type, 'FUNY')
self.assertEqual(atom.atomic_number, 92)
self.assertEqual(atom.charge, charges[0] * 2)
self.assertEqual(atom.mass, 10 * df_orig.loc[0, 'mass'])
self.assertEqual(atom.nb_idx, 10)
self.assertEqual(atom.solvent_radius,
2 * df_orig.loc[0, 'solvent_radius'])
self.assertEqual(atom.screen, 0.5)
self.assertEqual(atom.occupancy, 0.1)
self.assertEqual(atom.bfactor, 0.5)
self.assertEqual(atom.altloc, 'X')
self.assertEqual(atom.tree, 'BLU')
self.assertEqual(atom.join, 1.0)
self.assertEqual(atom.irotat, 2.0)
self.assertEqual(atom.rmin, 2 * df_orig.loc[0, 'rmin'])
self.assertEqual(atom.epsilon, df_orig.loc[0, 'epsilon'] / 2)
def test_reporters_pbc(self):
""" Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
systemsolv = load_file(get_fn('ildn.solv.top'),
xyz=get_fn('ildn.solv.gro'))
system = systemsolv.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8 * u.angstroms)
integrator = mm.LangevinIntegrator(300 * u.kelvin, 5.0 / u.picoseconds,
1.0 * u.femtoseconds)
sim = app.Simulation(systemsolv.topology, system, integrator,
Reference)
sim.context.setPositions(systemsolv.positions)
sim.reporters.extend([
NetCDFReporter(get_fn('traj.nc', written=True),
1,
vels=True,
frcs=True),
MdcrdReporter(get_fn('traj.mdcrd', written=True), 1),
RestartReporter(get_fn('restart.ncrst', written=True),
1,
netcdf=True),
RestartReporter(get_fn('restart.rst7', written=True), 1),
StateDataReporter(get_fn('state.o', written=True),
1,
volume=True,
density=True,
systemMass=1)
])
sim.step(5)
for reporter in sim.reporters:
reporter.finalize()
ntraj = NetCDFTraj.open_old(get_fn('traj.nc', written=True))
atraj = AmberMdcrd(get_fn('traj.mdcrd', written=True),
len(systemsolv.atoms),
True,
mode='r')
nrst = NetCDFRestart.open_old(get_fn('restart.ncrst', written=True))
arst = AmberAsciiRestart(get_fn('restart.rst7', written=True), 'r')
self.assertEqual(ntraj.frame, 5)
self.assertEqual(atraj.frame, 5)
self.assertTrue(ntraj.hasvels)
self.assertTrue(ntraj.hasfrcs)
for i in range(ntraj.frame):
for x1, x2 in zip(ntraj.box[i], atraj.box[i]):
self.assertAlmostEqual(x1, x2, places=3)
self.assertEqual(len(nrst.box), 6)
self.assertEqual(len(arst.box), 6)
# Make sure the EnergyMinimizerReporter does not fail
f = StringIO()
rep = EnergyMinimizerReporter(f, volume=True)
rep.report(sim)
rep.finalize()
def assertAlmostEqualQuantities(self, item1, item2, places=6):
try:
val1 = item1.value_in_unit(item1.unit)
val2 = item2.value_in_unit(item1.unit)
except TypeError:
raise self.failureException('Incompatible units %s and %s' %
(item1.unit, item2.unit))
try:
if len(val1) != len(val2):
raise self.failureException('collections are different lengths')
for x, y in zip(val1, val2):
self.assertAlmostEqual(x, y, places=places)
except TypeError:
self.assertAlmostEqual(val1, val2, places=places)
def test_benzene_cyclohexane(self):
""" Test converting binary liquid from Amber prmtop to Gromacs top """
parm = load_file(get_fn('benzene_cyclohexane_10_500.prmtop'),
get_fn('benzene_cyclohexane_10_500.inpcrd'))
top = gromacs.GromacsTopologyFile.from_structure(parm)
self.assertEqual(top.combining_rule, 'lorentz')
groname = get_fn('benzene_cyclohexane_10_500.gro', written=True)
gromacs.GromacsGroFile.write(parm, groname, precision=8)
gro = gromacs.GromacsGroFile.parse(groname)
self.assertEqual(len(gro.atoms), len(parm.atoms))
np.testing.assert_allclose(gro.box, parm.box)
for a1, a2 in zip(gro.atoms, parm.atoms):
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertEqual(a1.name, a2.name)
self.assertAlmostEqual(a1.xx, a2.xx)
self.assertAlmostEqual(a1.xy, a2.xy)
self.assertAlmostEqual(a1.xz, a2.xz)
top.write(get_fn('benzene_cyclohexane_10_500.top', written=True))
saved = GromacsFile(get_saved_fn('benzene_cyclohexane_10_500.top'))
written = GromacsFile(
get_fn('benzene_cyclohexane_10_500.top', written=True))
self.assertTrue(diff_files(saved, written))
# Check that Gromacs topology is given the correct box information when
# generated from a Structure
gromacs.GromacsGroFile.write(top, groname, precision=8)
gro = gromacs.GromacsGroFile.parse(groname)
self.assertEqual(len(gro.atoms), len(parm.atoms))
for a1, a2 in zip(gro.atoms, parm.atoms):
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertEqual(a1.name, a2.name)
self.assertAlmostEqual(a1.xx, a2.xx)
self.assertAlmostEqual(a1.xy, a2.xy)
self.assertAlmostEqual(a1.xz, a2.xz)
np.testing.assert_allclose(gro.box, parm.box)
np.testing.assert_allclose(top.box, parm.box)
def __str__(self):
if len(self.amplitude) == 0:
return ('TorsionAngle %r --- %r --- %r --- %r\n'
' No Terms' %
(self.atom1, self.atom2, self.atom3, self.atom4))
retstr = 'TorsionAngle %r --- %r --- %r --- %r' % (
self.atom1, self.atom2, self.atom3, self.atom4)
seq = range(len(self.amplitude))
for i, amp, phase, per in enumerate(
zip(seq, self.amplitude, self.phase, self.periodicity)):
retstr += ('\n Term %d\n'
' Amplitude = %.4f\n'
' Phase = %.4f\n'
' Periodicity = %.4f' % (i + 1, amp, phase, per))
return retstr
def test_residue_serialization(self):
""" Tests the serialization of Residue """
struct = utils.create_random_structure(parametrized=True)
res = struct.residues[0]
fobj = BytesIO()
pickle.dump(res, fobj)
fobj.seek(0)
unpickled = pickle.load(fobj)
self.assertEqual(len(res.atoms), len(unpickled.atoms))
for a1, a2 in zip(res, unpickled):
self._equal_atoms(a1, a2)
self.assertIs(a1.residue, res)
self.assertIs(a2.residue, unpickled)
def test_gas_energy_conf_2(self):
""" Compare Amber and OpenMM gas phase energies and forces (topology 2) """
parm = AmberParm(get_fn('hydrogen-peroxide_T0_2.prmtop'),
get_fn('hydrogen-peroxide_T0_2.rst7'))
self.assertEqual(parm.combining_rule, 'lorentz')
system = parm.createSystem() # Default, no cutoff
integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
sim = app.Simulation(parm.topology, system, integrator, platform=CPU)
sim.context.setPositions(parm.positions)
energies = energy_decomposition(parm, sim.context)
#BOND = 0.0319 ANGLE = 2.1690 DIHED = -2.7931
#VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
#1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
# Compare OpenMM energies with the Amber energies (above)
self.assertAlmostEqual(energies['bond'], 0.0319, places=4)
self.assertAlmostEqual(energies['angle'], 2.1690, places=4)
self.assertAlmostEqual(energies['dihedral'], -2.7931, places=4)
self.assertRelativeEqual(energies['nonbonded'], 0.0, places=3)
# Now test the forces to make sure that they are computed correctly in
# the presence of extra points
pstate = sim.context.getState(getForces=True)
pf = pstate.getForces().value_in_unit(u.kilojoule_per_mole /
u.nanometer)
# gmx forces:
# f[ 0]={ 3.14357e+02, -5.90363e+02, 2.11410e+02}
# f[ 1]={-3.14357e+02, 5.90363e+02, 2.11410e+02}
# f[ 2]={ 2.70641e+02, 5.90363e+02, -2.11410e+02}
# f[ 3]={-2.70641e+02, -5.90363e+02, -2.11410e+02}
gf = [(3.14357e+02, -5.90363e+02, 2.11410e+02),
(-3.14357e+02, 5.90363e+02, 2.11410e+02),
(2.70641e+02, 5.90363e+02, -2.11410e+02),
(-2.70641e+02, -5.90363e+02, -2.11410e+02)]
for p, s in zip(pf, gf):
for x1, x2 in zip(p, s):
self.assertAlmostEqual(x1, x2, places=3)
def test_residue_atom_selection(self):
""" Tests combined residue,atom slicing/selections """
sel = pdb1[10:20, :5] # First five atoms of residues 10-19
self.assertEqual(len(sel.atoms), 49) # 1 residue has only 4 atoms
c = 0
for res in pdb1.residues[10:20]:
for i in range(min(len(res), 5)):
self.assertEqual(sel.atoms[c].name, res[i].name)
self.assertEqual(sel.atoms[c].xx, res[i].xx)
self.assertEqual(sel.atoms[c].xy, res[i].xy)
self.assertEqual(sel.atoms[c].xz, res[i].xz)
c += 1
sel = pdb1[[0, 2, 3,
5], :2] # First 2 atoms of residues 0, 2, 3, and 5
self.assertEqual(len(sel.atoms), 8)
c = 0
for i, res in enumerate([0, 2, 3, 5]):
res = pdb1.residues[res]
self.assertEqual(sel.atoms[c].name, res[0].name)
self.assertEqual(sel.atoms[c].xx, res[0].xx)
self.assertEqual(sel.atoms[c].xy, res[0].xy)
self.assertEqual(sel.atoms[c].xz, res[0].xz)
c += 1
self.assertEqual(sel.atoms[c].name, res[1].name)
self.assertEqual(sel.atoms[c].xx, res[1].xx)
self.assertEqual(sel.atoms[c].xy, res[1].xy)
self.assertEqual(sel.atoms[c].xz, res[1].xz)
c += 1
sel = pdb1[8, :]
self.assertEqual(len(sel.atoms), len(pdb1.residues[8]))
for a1, a2 in zip(sel.atoms, pdb1.residues[8]):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.xx, a2.xx)
self.assertEqual(a1.xy, a2.xy)
self.assertEqual(a1.xz, a2.xz)
self.assertIs(pdb1[8, 4], pdb1.residues[8][4])
sel = pdb1[['ALA', 'GLY'], :]
for atom in sel.atoms:
self.assertIn(atom.residue.name, ('ALA', 'GLY'))
nalagly = sum(r.name in ('ALA', 'GLY') for r in pdb1.residues)
natom = sum(len(r) for r in pdb1.residues if r.name in ('ALA', 'GLY'))
self.assertEqual(nalagly, len(sel.residues))
self.assertEqual(natom, len(sel.atoms))
def _load_cmap_info(self):
""" Loads the CHARMM CMAP types and array """
if not self.has_cmap: return
del self.cmaps[:]
del self.cmap_types[:]
for i in range(self.pointers['CMAP_TYPES']):
resolution = self.parm_data['CHARMM_CMAP_RESOLUTION'][i]
grid = self.parm_data['CHARMM_CMAP_PARAMETER_%02d' % (i + 1)]
cmts = self.parm_comments['CHARMM_CMAP_PARAMETER_%02d' % (i + 1)]
self.cmap_types.append(
CmapType(resolution, grid, cmts, list=self.cmap_types))
it = iter(self.parm_data['CHARMM_CMAP_INDEX'])
for i, j, k, l, m, n in zip(it, it, it, it, it, it):
self.cmaps.append(
Cmap(self.atoms[i - 1], self.atoms[j - 1], self.atoms[k - 1],
self.atoms[l - 1], self.atoms[m - 1],
self.cmap_types[n - 1]))
def test_simple(self):
""" Tests converting simple Amber system to CHARMM PSF/parameters """
parm = load_file(get_fn('trx.prmtop'), get_fn('trx.inpcrd'))
parm.save(get_fn('amber_to_charmm.psf', written=True))
params = charmm.CharmmParameterSet.from_structure(parm)
params.write(str=get_fn('amber_to_charmm.str', written=True))
self.assertTrue(
diff_files(get_saved_fn('amber_to_charmm.psf'),
get_fn('amber_to_charmm.psf', written=True)
)
)
self.assertTrue(
diff_files(get_saved_fn('amber_to_charmm.str'),
get_fn('amber_to_charmm.str', written=True),
absolute_error=1e-5,
)
)
# Check the PSF file
psf = load_file(get_fn('amber_to_charmm.psf', written=True))
psf.load_parameters(
charmm.CharmmParameterSet(get_fn('amber_to_charmm.str',
written=True))
)
for a1, a2 in zip(psf.atoms, parm.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.mass, a2.mass)
self.assertEqual(len(psf.bonds), len(parm.bonds))
self.assertEqual(len(psf.angles), len(parm.angles))
# Get number of unique torsions
nnormal = nimp = 0
torsfound = set()
for tor in parm.dihedrals:
a1, a2, a3, a4 = tor.atom1, tor.atom2, tor.atom3, tor.atom4
if tor.improper:
nimp += 1
continue
if (a1, a2, a3, a4) in torsfound or (a4, a3, a2, a1) in torsfound:
continue
torsfound.add((a1, a2, a3, a4))
nnormal += 1
# Make sure that written psf only contains unique torsions.
self.assertEqual(nnormal+nimp, len(psf.dihedrals))
def test_residue_atom_selection(self):
""" Tests combined residue,atom slicing/selections (view) """
sel = pdb1.view[10:20, :5] # First five atoms of residues 10-19
self.assertIsInstance(sel, pmd.structure.StructureView)
self.assertEqual(len(sel.atoms), 49) # 1 residue has only 4 atoms
c = 0
for res in pdb1.residues[10:20]:
for i in range(min(len(res), 5)):
self.assertIs(sel.atoms[c], res[i])
c += 1
sel = pdb1.view[[0, 2, 3,
5], :2] # First 2 atoms of residues 0, 2, 3, and 5
self.assertIsInstance(sel, pmd.structure.StructureView)
self.assertEqual(len(sel.atoms), 8)
c = 0
for i, res in enumerate([0, 2, 3, 5]):
res = pdb1.residues[res]
self.assertIs(sel.atoms[c], res[0])
c += 1
self.assertIs(sel.atoms[c], res[1])
c += 1
sel = pdb1.view[8, :]
self.assertIsInstance(sel, pmd.structure.StructureView)
self.assertEqual(len(sel.atoms), len(pdb1.residues[8]))
for a1, a2 in zip(sel.atoms, pdb1.residues[8]):
self.assertIs(a1, a2)
self.assertIs(pdb1[8, 4], pdb1.residues[8][4])
sel = pdb1.view[['ALA', 'GLY'], :]
self.assertIsInstance(sel, pmd.structure.StructureView)
for atom in sel.atoms:
self.assertIn(atom.residue.name, ('ALA', 'GLY'))
self.assertIs(atom.list, pdb1.atoms)
nalagly = sum(r.name in ('ALA', 'GLY') for r in pdb1.residues)
natom = sum(len(r) for r in pdb1.residues if r.name in ('ALA', 'GLY'))
self.assertEqual(nalagly, len(sel.residues))
self.assertEqual(natom, len(sel.atoms))
def test_simple(self):
""" Tests converting standard Gromacs system into Amber prmtop """
top = load_file(get_fn(os.path.join('03.AlaGlu', 'topol.top')))
self.assertEqual(top.combining_rule, 'lorentz')
parm = amber.AmberParm.from_structure(top)
parm.write_parm(get_fn('ala_glu.parm7', written=True))
parm = load_file(get_fn('ala_glu.parm7', written=True))
self.assertIsInstance(parm, amber.AmberParm)
self.assertEqual(len(top.atoms), len(parm.atoms))
self.assertEqual(len(top.bonds), len(parm.bonds))
self.assertEqual(len(top.angles), len(parm.angles))
self.assertEqual(len(top.residues), len(parm.residues))
for a1, a2 in zip(top.atoms, parm.atoms):
self.assertEqual(a1.name, a2.name)
self.assertEqual(a1.type, a2.type)
self.assertEqual(a1.atomic_number, a2.atomic_number)
self.assertEqual(a1.residue.name, a2.residue.name)
self.assertEqual(a1.residue.idx, a2.residue.idx)
self.assertAlmostEqual(a1.mass, a2.mass)
self.assertIs(type(a1), type(a2))
self.assertAlmostEqual(a1.charge, a2.charge)
self.assertEqual(set([a.idx for a in a1.bond_partners]),
set([a.idx for a in a2.bond_partners]))
self.assertEqual(set([a.idx for a in a1.angle_partners]),
set([a.idx for a in a2.angle_partners]))
self.assertEqual(set([a.idx for a in a1.dihedral_partners]),
set([a.idx for a in a2.dihedral_partners]))
# Make sure that assign_nbidx_from_types compresses maximally. First
# add a new, equivalent L-J type. Then call assign_nbidx_from_types
# again, which should recompress
before_nbidx = [a.nb_idx for a in parm.atoms]
addLJType(parm, '@1').execute()
after_nbidx = [a.nb_idx for a in parm.atoms]
self.assertEqual(before_nbidx[1:], after_nbidx[1:])
self.assertEqual(after_nbidx[0], max(before_nbidx) + 1)
parm.atoms.assign_nbidx_from_types()
# Should recompress
self.assertEqual(before_nbidx, [a.nb_idx for a in parm.atoms])
def cmp_type_arrays(arr1, arr2):
self.assertEqual(len(arr1), len(arr2))
for x1, x2 in zip(arr1, arr2):
self.assertEqual(x1, x2)
def _compare_structures(self, unpickled, structure):
self.assertEqual(len(unpickled.residues), len(structure.residues))
for r1, r2 in zip(unpickled.residues, structure.residues):
self.assertEqual(len(r1), len(r2))
self.assertEqual(r1.idx, r2.idx)
for a1, a2 in zip(r1, r2):
self._equal_atoms(a1, a2)
def cmp_alists(alist1, alist2):
self.assertEqual(len(alist1), len(alist2))
for a1, a2 in zip(alist1, alist2):
self._equal_atoms(a1, a2)
for a1, a2 in zip(unpickled, structure):
self._equal_atoms(a1, a2)
self.assertEqual(a1.idx, a2.idx)
self.assertEqual(len(a1.bonds), len(a2.bonds))
self.assertEqual(len(a1.angles), len(a2.angles))
self.assertEqual(len(a1.dihedrals), len(a2.dihedrals))
self.assertEqual(len(a1.impropers), len(a2.impropers))
cmp_alists(a1.bond_partners, a2.bond_partners)
cmp_alists(a1.angle_partners, a2.angle_partners)
cmp_alists(a1.dihedral_partners, a2.dihedral_partners)
cmp_alists(a1.tortor_partners, a2.tortor_partners)
cmp_alists(a1.exclusion_partners, a2.exclusion_partners)
# Check coordinates
if structure.get_coordinates() is None:
self.assertIs(unpickled.get_coordinates(), None)
else:
np.testing.assert_equal(structure.get_coordinates(),
unpickled.get_coordinates())
# Check unit cell
if structure.box is None:
self.assertIs(unpickled.box, None)
self.assertIs(unpickled.box_vectors, None)
else:
np.testing.assert_equal(structure.box, unpickled.box)
self.assertEqual(structure.box_vectors, unpickled.box_vectors)
# Check velocities
if structure.velocities is None:
self.assertIs(unpickled.velocities, None)
else:
np.testing.assert_equal(structure.velocities, unpickled.velocities)
# Check nrexcl and combining_rule
self.assertEqual(structure.nrexcl, unpickled.nrexcl)
self.assertEqual(structure.combining_rule, unpickled.combining_rule)
# Make sure all of the type arrays are equivalent
def cmp_type_arrays(arr1, arr2):
self.assertEqual(len(arr1), len(arr2))
for x1, x2 in zip(arr1, arr2):
self.assertEqual(x1, x2)
cmp_type_arrays(structure.bond_types, unpickled.bond_types)
cmp_type_arrays(structure.angle_types, unpickled.angle_types)
cmp_type_arrays(structure.dihedral_types, unpickled.dihedral_types)
cmp_type_arrays(structure.improper_types, unpickled.improper_types)
cmp_type_arrays(structure.urey_bradley_types,
unpickled.urey_bradley_types)
cmp_type_arrays(structure.rb_torsion_types, unpickled.rb_torsion_types)
cmp_type_arrays(structure.cmap_types, unpickled.cmap_types)
cmp_type_arrays(structure.trigonal_angle_types,
unpickled.trigonal_angle_types)
cmp_type_arrays(structure.out_of_plane_bend_types,
unpickled.out_of_plane_bend_types)
cmp_type_arrays(structure.stretch_bend_types,
unpickled.stretch_bend_types)
cmp_type_arrays(structure.torsion_torsion_types,
unpickled.torsion_torsion_types)
cmp_type_arrays(structure.pi_torsion_types, unpickled.pi_torsion_types)
cmp_type_arrays(structure.adjust_types, unpickled.adjust_types)
# Make sure all of the connectivity arrays are equivalent
def cmp_top_arrays(arr1, arr2):
self.assertEqual(len(arr1), len(arr2))
for t1, t2 in zip(arr1, arr2):
self.assertIs(type(t1), type(t2))
atoms = [attr for attr in dir(t1) if attr.startswith('atom')]
for a in atoms:
self._equal_atoms(getattr(t1, a), getattr(t2, a))
if hasattr(t1, 'type'):
self.assertEqual(t1.type, t2.type)
cmp_top_arrays(structure.bonds, unpickled.bonds)
cmp_top_arrays(structure.angles, unpickled.angles)
cmp_top_arrays(structure.dihedrals, unpickled.dihedrals)
cmp_top_arrays(structure.impropers, unpickled.impropers)
cmp_top_arrays(structure.urey_bradleys, unpickled.urey_bradleys)
cmp_top_arrays(structure.rb_torsions, unpickled.rb_torsions)
cmp_top_arrays(structure.cmaps, unpickled.cmaps)
cmp_top_arrays(structure.trigonal_angles, unpickled.trigonal_angles)
cmp_top_arrays(structure.out_of_plane_bends,
unpickled.out_of_plane_bends)
cmp_top_arrays(structure.pi_torsions, unpickled.pi_torsions)
cmp_top_arrays(structure.stretch_bends, unpickled.stretch_bends)
cmp_top_arrays(structure.torsion_torsions, unpickled.torsion_torsions)
cmp_top_arrays(structure.chiral_frames, unpickled.chiral_frames)
cmp_top_arrays(structure.multipole_frames, unpickled.multipole_frames)
cmp_top_arrays(structure.adjusts, unpickled.adjusts)
cmp_top_arrays(structure.groups, unpickled.groups)
def __init__(self, psf_name=None):
"""
Opens and parses a PSF file, then instantiates a CharmmPsfFile
instance from the data.
"""
global _resre
Structure.__init__(self)
# Bail out if we don't have a filename
if psf_name is None:
return
conv = CharmmPsfFile._convert
# Open the PSF and read the first line. It must start with "PSF"
with closing(genopen(psf_name, 'r')) as psf:
self.name = psf_name
line = psf.readline()
if not line.startswith('PSF'):
raise CharmmError('Unrecognized PSF file. First line is %s' %
line.strip())
# Store the flags
psf_flags = line.split()[1:]
# Now get all of the sections and store them in a dict
psf.readline()
# Now get all of the sections
psfsections = _ZeroDict()
while True:
try:
sec, ptr, data = CharmmPsfFile._parse_psf_section(psf)
except _FileEOF:
break
psfsections[sec] = (ptr, data)
# store the title
self.title = psfsections['NTITLE'][1]
# Next is the number of atoms
natom = conv(psfsections['NATOM'][0], int, 'natom')
# Parse all of the atoms
for i in range(natom):
words = psfsections['NATOM'][1][i].split()
atid = int(words[0])
if atid != i + 1:
raise CharmmError('Nonsequential atoms detected!')
segid = words[1]
rematch = _resre.match(words[2])
if not rematch:
raise CharmmError('Could not interpret residue number %s'
% # pragma: no cover
words[2])
resid, inscode = rematch.groups()
resid = conv(resid, int, 'residue number')
resname = words[3]
name = words[4]
attype = words[5]
# Try to convert the atom type to an integer a la CHARMM
try:
attype = int(attype)
except ValueError:
pass
charge = conv(words[6], float, 'partial charge')
mass = conv(words[7], float, 'atomic mass')
props = words[8:]
atom = Atom(name=name, type=attype, charge=charge, mass=mass)
atom.props = props
self.add_atom(atom,
resname,
resid,
chain=segid,
inscode=inscode,
segid=segid)
# Now get the number of bonds
nbond = conv(psfsections['NBOND'][0], int, 'number of bonds')
if len(psfsections['NBOND'][1]) != nbond * 2:
raise CharmmError(
'Got %d indexes for %d bonds' % # pragma: no cover
(len(psfsections['NBOND'][1]), nbond))
it = iter(psfsections['NBOND'][1])
for i, j in zip(it, it):
self.bonds.append(Bond(self.atoms[i - 1], self.atoms[j - 1]))
# Now get the number of angles and the angle list
ntheta = conv(psfsections['NTHETA'][0], int, 'number of angles')
if len(psfsections['NTHETA'][1]) != ntheta * 3:
raise CharmmError(
'Got %d indexes for %d angles' % # pragma: no cover
(len(psfsections['NTHETA'][1]), ntheta))
it = iter(psfsections['NTHETA'][1])
for i, j, k in zip(it, it, it):
self.angles.append(
Angle(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1]))
self.angles[-1].funct = 5 # urey-bradley
# Now get the number of torsions and the torsion list
nphi = conv(psfsections['NPHI'][0], int, 'number of torsions')
if len(psfsections['NPHI'][1]) != nphi * 4:
raise CharmmError(
'Got %d indexes for %d torsions' % # pragma: no cover
(len(psfsections['NPHI']), nphi))
it = iter(psfsections['NPHI'][1])
for i, j, k, l in zip(it, it, it, it):
self.dihedrals.append(
Dihedral(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1]))
self.dihedrals.split = False
# Now get the number of improper torsions
nimphi = conv(psfsections['NIMPHI'][0], int, 'number of impropers')
if len(psfsections['NIMPHI'][1]) != nimphi * 4:
raise CharmmError(
'Got %d indexes for %d impropers' % # pragma: no cover
(len(psfsections['NIMPHI'][1]), nimphi))
it = iter(psfsections['NIMPHI'][1])
for i, j, k, l in zip(it, it, it, it):
self.impropers.append(
Improper(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1]))
# Now handle the donors (what is this used for??)
ndon = conv(psfsections['NDON'][0], int, 'number of donors')
if len(psfsections['NDON'][1]) != ndon * 2:
raise CharmmError(
'Got %d indexes for %d donors' % # pragma: no cover
(len(psfsections['NDON'][1]), ndon))
it = iter(psfsections['NDON'][1])
for i, j in zip(it, it):
self.donors.append(
AcceptorDonor(self.atoms[i - 1], self.atoms[j - 1]))
# Now handle the acceptors (what is this used for??)
nacc = conv(psfsections['NACC'][0], int, 'number of acceptors')
if len(psfsections['NACC'][1]) != nacc * 2:
raise CharmmError(
'Got %d indexes for %d acceptors' % # pragma: no cover
(len(psfsections['NACC'][1]), nacc))
it = iter(psfsections['NACC'][1])
for i, j in zip(it, it):
self.acceptors.append(
AcceptorDonor(self.atoms[i - 1], self.atoms[j - 1]))
# Now get the group sections
try:
ngrp, nst2 = psfsections['NGRP NST2'][0]
except ValueError: # pragma: no cover
raise CharmmError(
'Could not unpack GROUP pointers') # pragma: no cover
tmp = psfsections['NGRP NST2'][1]
self.groups.nst2 = nst2
# Now handle the groups
if len(psfsections['NGRP NST2'][1]) != ngrp * 3:
raise CharmmError(
'Got %d indexes for %d groups' % # pragma: no cover
(len(tmp), ngrp))
it = iter(psfsections['NGRP NST2'][1])
for i, j, k in zip(it, it, it):
self.groups.append(Group(self.atoms[i], j, k))
# Assign all of the atoms to molecules recursively
tmp = psfsections['MOLNT'][1]
set_molecules(self.atoms)
molecule_list = [a.marked for a in self.atoms]
if len(tmp) == len(self.atoms):
if molecule_list != tmp:
warnings.warn(
'Detected PSF molecule section that is WRONG. '
'Resetting molecularity.', CharmmWarning)
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
numlp, numlph = psfsections['NUMLP NUMLPH'][0]
if numlp != 0 or numlph != 0:
raise NotImplementedError(
'Cannot currently handle PSFs with '
'lone pairs defined in the NUMLP/'
'NUMLPH section.')
# Now do the CMAPs
ncrterm = conv(psfsections['NCRTERM'][0], int,
'Number of cross-terms')
if len(psfsections['NCRTERM'][1]) != ncrterm * 8:
raise CharmmError('Got %d CMAP indexes for %d cmap terms'
% # pragma: no cover
(len(psfsections['NCRTERM']), ncrterm))
it = iter(psfsections['NCRTERM'][1])
for i, j, k, l, m, n, o, p in zip(it, it, it, it, it, it, it, it):
self.cmaps.append(
Cmap.extended(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1],
self.atoms[m - 1], self.atoms[n - 1],
self.atoms[o - 1], self.atoms[p - 1]))
self.unchange()
self.flags = psf_flags
def cmp_alists(alist1, alist2):
self.assertEqual(len(alist1), len(alist2))
for a1, a2 in zip(alist1, alist2):
self._equal_atoms(a1, a2)