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')