def test(self):
# extract xtcs to a temp dir
xtc_fn = get('XTC.tgz', just_filename=True)
fh = tarfile.open(xtc_fn, mode='r:gz')
fh.extractall(self.td)
fh.close()
outfn = pjoin(self.td, 'ProjectInfo.yaml')
# move to that directory
os.chdir(self.td)
atom_indices = np.arange(4)
ConvertDataToHDF.run(projectfn=outfn,
conf_filename=get('native.pdb', just_filename=True),
input_dir=pjoin(self.td, 'XTC'),
source='file',
min_length=0,
stride=1,
rmsd_cutoff=np.inf,
atom_indices=atom_indices, iext=".xtc")
project = load(outfn)
traj = project.load_conf()
eq(traj.n_atoms, 4)
def test_a_ConvertDataToHDF(self):
os.chdir(WorkingDir)
shutil.copy(PDBFn,"./")
#def run(projectfn, PDBfn, InputDir, source, mingen, stride, rmsd_cutoff, parallel='None'):
ConvertDataToHDF.run(ProjectFn, PDBFn, TutorialDir+"/XTC", "file", 0, 1, None)
P1 = Project.load_from(ProjectFn)
r_P1 = Project.load_from(os.path.abspath(os.path.join('..', ReferenceDir, ProjectFn)))
eq_(P1.n_trajs, r_P1.n_trajs)
npt.assert_equal(P1.traj_lengths, r_P1.traj_lengths)
eq_(os.path.basename(P1.traj_filename(0)), os.path.basename(r_P1.traj_filename(0)))
def test_a_ConvertDataToHDF(self):
os.chdir(WorkingDir)
shutil.copy(PDBFn, "./")
#def run(projectfn, PDBfn, InputDir, source, mingen, stride, rmsd_cutoff, parallel='None'):
ConvertDataToHDF.run(ProjectFn, PDBFn, TutorialDir + "/XTC", "file", 0,
1, None)
P1 = Project.load_from(ProjectFn)
r_P1 = Project.load_from(
os.path.abspath(os.path.join('..', ReferenceDir, ProjectFn)))
eq_(P1.n_trajs, r_P1.n_trajs)
npt.assert_equal(P1.traj_lengths, r_P1.traj_lengths)
eq_(os.path.basename(P1.traj_filename(0)),
os.path.basename(r_P1.traj_filename(0)))
def test(self):
# extract xtcs to a temp dir
xtc_fn = get('XTC.tgz', just_filename=True)
fh = tarfile.open(xtc_fn, mode='r:gz')
fh.extractall(self.td)
fh.close()
outfn = pjoin(self.td, 'ProjectInfo.yaml')
# mode to that directory
os.chdir(self.td)
ConvertDataToHDF.run(projectfn=outfn,
PDBfn=get('native.pdb', just_filename=True),
InputDir=pjoin(self.td, 'XTC'),
source='file',
min_length=0,
stride=1,
rmsd_cutoff=np.inf)
eq(load(outfn), get('ProjectInfo.yaml'))
