def setUp(self):
self.universe = mda.Universe(TRZ_psf, TRZ)
self.ag = self.universe.select_atoms('name N')
self.prec = 3
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/partial-write-test.pdb'
self.Writer = mda.Writer(self.outfile, n_atoms=len(self.ag))
def setUp(self):
self.universe = mda.Universe(PSF, [DCD, CRD, DCD, CRD, DCD, CRD, CRD])
self.trajectory = self.universe.trajectory
self.prec = 3
# dummy output DCD file
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/chain-reader.dcd'
def setUp(self):
self.u = mda.Universe(self.topology, self.trajectory,
format=self.format)
# dummy output file
ext = os.path.splitext(self.trajectory)[1]
self.tmpdir = tempdir.TempDir()
self.outfile = os.path.join(self.tmpdir.name, 'lammps-writer-test' + ext)
def test_write_velocities(self):
ts = mda.coordinates.base.Timestep(4, velocities=True)
ts.dimensions = [20, 30, 41, 90, 90, 90]
ts.positions = [
[1, 1, 1],
[2, 2, 2],
[3, 3, 3],
[4, 4, 4],
]
ts.velocities = [
[10, 10, 10],
[20, 20, 20],
[30, 30, 30],
[40, 40, 40],
]
u = mda.Universe.empty(4)
u.add_TopologyAttr('type')
u.atoms[0].type = "H"
u.atoms[1].type = "H"
u.atoms[2].type = "H"
u.atoms[3].type = "H"
outfile = tempdir.TempDir().name + "chemfiles-write-velocities.lmp"
with ChemfilesWriter(outfile,
topology=u,
chemfiles_format='LAMMPS Data') as writer:
writer.write_next_timestep(ts)
with open(outfile) as file:
content = file.read()
assert content == EXPECTED_LAMMPS_DATA
def setUp(self):
self.universe = mda.Universe(GRO)
self.prec = 2 # 3 decimals in file in nm but MDAnalysis is in A
ext = ".gro"
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/gro-writer' + ext
self.outfile2 = self.tmpdir.name + '/gro-writer2' + ext
def setUp(self):
self.seq = FASTA
self.tempdir = tempdir.TempDir()
self.alnfile = os.path.join(self.tempdir.name,
'alignmentprocessing.aln')
self.treefile = os.path.join(self.tempdir.name,
'alignmentprocessing.dnd')
def setUp(self):
self.universe = MDAnalysis.Universe(PSF, DCD)
self.tempdir = tempdir.TempDir()
self.outfile = os.path.join(self.tempdir.name, 'rmsd.txt')
self.correct_values = [[0, 0, 0], [49, 48.9999, 4.68953]]
self.correct_values_group = [[0, 0, 0, 0, 0],
[49, 49, 4.7857, 4.7004, 4.68981]]
def setUp(self):
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/ncdf-write-vels-force.ncdf'
self.prec = 3
self.top = XYZ_mini
self.n_atoms = 3
self.ts1 = mda.coordinates.TRJ.Timestep(self.n_atoms,
velocities=True,
forces=True)
self.ts1._pos[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, 3)
self.ts1._velocities[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 100
self.ts1._forces[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 200
self.ts2 = mda.coordinates.TRJ.Timestep(self.n_atoms,
velocities=True,
forces=True)
self.ts2._pos[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 300
self.ts2._velocities[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 400
self.ts2._forces[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 500
def __init__(self):
u = mda.Universe(ALIGN)
self.tmpdir = tempdir.TempDir()
outfile = self.tmpdir.name + '/nucl.pdb'
u.atoms.write(outfile)
with open(outfile, 'r') as inf:
self.writtenstuff = inf.readlines()
def setUp(self):
self.universe = mda.Universe(self.topology, self.filename)
self.prec = 5
ext = ".ncdf"
self.tmpdir = tempdir.TempDir()
self.outfile = os.path.join(self.tmpdir.name, 'ncdf-writer-1' + ext)
self.outtop = os.path.join(self.tmpdir.name, 'ncdf-writer-top.pdb')
self.Writer = mda.coordinates.TRJ.NCDFWriter
def setUp(self):
# keep tempdir around for the whole lifetime of the class
self.tempdir = tempdir.TempDir()
with in_dir(self.tempdir.name):
H = HOLE(self.filename, raseed=31415)
H.run()
H.collect()
self.H = H
def setUp(self):
self.universe = mda.Universe(TRZ_psf, TRZ)
self.prec = 3
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/test-trz-writer.trz'
self.outfile_long = self.tmpdir.name + '/test-trz-writer-long.trz'
self.Writer = mda.coordinates.TRZ.TRZWriter
self.title_to_write = 'Test title TRZ'
def _check_warns(self, missing_attr):
attrs = list(self.req_attrs.keys())
attrs.remove(missing_attr)
u = make_Universe(attrs, trajectory=True)
tmpdir = tempdir.TempDir()
outfile = tmpdir.name + '/out.crd'
assert_warns(UserWarning, u.atoms.write, outfile)
def setUp(self):
"""Generate input xtc."""
self.u = mda.Universe(PSF, DCD)
self.tmpdir = tempdir.TempDir()
self.xtc = self.tmpdir.name + '/dcd-writer-issue59-test.xtc'
wXTC = mda.Writer(self.xtc, self.u.atoms.n_atoms)
for ts in self.u.trajectory:
wXTC.write(ts)
wXTC.close()
def setUp(self):
self.universe = mda.Universe(PSF, PDB_small)
self.universe2 = mda.Universe(PSF, DCD)
# 3 decimals in PDB spec
# http://www.wwpdb.org/documentation/format32/sect9.html#ATOM
self.prec = 3
ext = ".pdb"
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/primitive-pdb-writer' + ext
def setUp(self):
u1 = MDAnalysis.Universe(merge_protein)
u2 = MDAnalysis.Universe(merge_ligand)
u3 = MDAnalysis.Universe(merge_water)
self.universes = [u1, u2, u3]
suffix = '.' + self.ext
self.tempdir = tempdir.TempDir()
self.outfile = os.path.join(self.tempdir.name, 'test' + suffix)
def test_changing_system_size(self):
outfile = tempdir.TempDir().name + "chemfiles-changing-size.xyz"
with open(outfile, "w") as fd:
fd.write(VARYING_XYZ)
u = mda.Universe(outfile, format="chemfiles", topology_format="XYZ")
with pytest.raises(IOError):
u.trajectory._read_next_timestep()
def setUp(self):
self.u = mda.Universe(PRMncdf, NCDF)
# create the DCD
self.tmpdir = tempdir.TempDir()
self.dcd = self.tmpdir.name + '/ncdf-2-dcd.dcd'
DCD = mda.Writer(self.dcd, n_atoms=self.u.atoms.n_atoms)
for ts in self.u.trajectory:
DCD.write(ts)
DCD.close()
self.w = mda.Universe(PRMncdf, self.dcd)
def setUp(self):
# loading from GRO is 4x faster than the PDB reader
self.universe = mda.Universe(GRO, self.filename, convert_units=True)
self.trajectory = self.universe.trajectory
self.prec = 3
self.ts = self.universe.coord
# dummy output file
ext = os.path.splitext(self.filename)[1]
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/xdr-reader-test' + ext
def test_write_pdb_zero_atoms():
# issue 1083
u = make_Universe(trajectory=True)
with tempdir.TempDir() as tmpdir:
outfile = tmpdir + '/out.pdb'
ag = u.atoms[:0] # empty ag
with mda.Writer(outfile, ag.n_atoms) as w:
assert_raises(IndexError, w.write, ag)
def setUp(self):
self.u = mda.Universe(self.filename)
# dummy output file
ext = os.path.splitext(self.filename)[1]
self.tmpdir = tempdir.TempDir()
self.outfile = os.path.join(self.tmpdir.name, 'lammps-data-writer-test' + ext)
with mda.Writer(self.outfile, n_atoms=self.u.atoms.n_atoms) as W:
W.write(self.u.atoms)
self.u_ref = mda.Universe(self.filename)
self.u_new = mda.Universe(self.outfile)
def test_write_nostructure(self):
mytempdir = tempdir.TempDir()
outfile = os.path.join(mytempdir.name, 'test.mol2')
u = mda.Universe(mol2_zinc)
with mda.Writer(outfile) as W:
W.write(u.atoms)
u2 = mda.Universe(outfile)
assert_(len(u.atoms) == len(u2.atoms))
def setUp(self):
# since offsets are automatically generated in the same directory
# as the trajectory, we do everything from a temporary directory
self.tmpdir = tempdir.TempDir()
shutil.copy(self.filename, self.tmpdir.name)
self.traj = os.path.join(self.tmpdir.name,
os.path.basename(self.filename))
self.trajectory = self._reader(self.traj)
self.prec = 3
self.ts = self.trajectory.ts
def setUp(self):
self.tmpdir = tempdir.TempDir()
self.iu1 = np.triu_indices(3, k=1)
self.universe1 = MDAnalysis.Universe(PSF, DCD)
self.universe2 = MDAnalysis.Universe(PSF, DCD2)
self.universe_rev = MDAnalysis.Universe(PSF, DCD)
self.universes = [self.universe1, self.universe2, self.universe_rev]
self.psa = MDAnalysis.analysis.psa.PSAnalysis(self.universes, \
path_select='name CA', \
targetdir=self.tmpdir.name)
self.psa.generate_paths(align=True)
self.psa.paths[-1] = self.psa.paths[-1][::
-1, :, :] # reverse third path
self._run()
def setUp(self):
self.universe = mda.Universe(PSF, PDB_small)
self.universe2 = mda.Universe(PSF, DCD)
# 3 decimals in PDB spec
# http://www.wwpdb.org/documentation/format32/sect9.html#ATOM
self.prec = 3
ext = ".pdb"
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/primitive-pdb-writer' + ext
self.u_no_resnames = make_Universe(['names', 'resids'],
trajectory=True)
self.u_no_resids = make_Universe(['names', 'resnames'],
trajectory=True)
self.u_no_names = make_Universe(['resids', 'resnames'],
trajectory=True)
def _check_write(self, missing_attr):
attrs = list(self.req_attrs.keys())
attrs.remove(missing_attr)
u = make_Universe(attrs, trajectory=True)
tmpdir = tempdir.TempDir()
outfile = tmpdir.name + '/out.crd'
u.atoms.write(outfile)
u2 = mda.Universe(outfile)
# Check all other attrs aren't disturbed
for attr in attrs:
assert_equal(getattr(u.atoms, attr), getattr(u2.atoms, attr))
# Check missing attr is as expected
assert_equal(getattr(u2.atoms, missing_attr),
self.req_attrs[missing_attr])
def test_write_topology(self):
u = mda.Universe(datafiles.CONECT)
outfile = tempdir.TempDir().name + "chemfiles-write-topology.pdb"
with ChemfilesWriter(outfile) as writer:
writer.write(u)
self.check_topology(datafiles.CONECT, outfile)
# Manually setting the topology when creating the ChemfilesWriter
# (1) from an object
with ChemfilesWriter(outfile, topology=u) as writer:
writer.write_next_timestep(u.trajectory.ts)
self.check_topology(datafiles.CONECT, outfile)
# (2) from a file
with ChemfilesWriter(outfile, topology=datafiles.CONECT) as writer:
writer.write_next_timestep(u.trajectory.ts)
def setUp(self):
self.tempdir = tempdir.TempDir()
self.outfile = os.path.join(self.tempdir.name, 'test.log')
def setUp(self):
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/outfile.xyz'
def setUp(self):
self.filename = PDB_full
self.tempdir = tempdir.TempDir()
self.outfile = os.path.join(self.tempdir.name, 'test.pdb')
