def test_nfo_1():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
raw_infos = proj.get_infos()
nfo_infos = [proj.nfo(ri) for ri in raw_infos]
assert len(nfo_infos) > 0
for info in nfo_infos:
assert info['raw']['success']
def test_nfo_bw():
proj = Processor("v1", "data/v1", 'bw')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
with Pool() as pool:
nfo_infos = pool.map(_process_trajectory, trajectories, chunksize=1)
assert len(nfo_infos) == 2
for info in nfo_infos:
assert info['meta']['project'] == 'v1'
if info['meta']['run'] == 5:
assert info['meta']['clone'] == 0
elif info['meta']['run'] == 6:
assert info['meta']['clone'] == 0
else:
assert False
assert os.path.exists(info['path']['workdir'])
assert set(info.keys()) == {'raw', 'meta', 'path', 'top'}, info
assert set(info['raw'].keys()) == {'indir', 'real_indir', 'date',
'initdate', 'gens', 'gen_glob',
'success'}
assert set(info['meta'].keys()) == {'project', 'run', 'clone'}
assert set(info['path'].keys()) == {'info', 'workdir'}
assert set(info['top'].keys()) == {'struct', 'fext'}
def test_nfo_bw():
proj = Processor("v1", "data/v1", 'bw')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
with Pool() as pool:
nfo_infos = pool.map(_process_trajectory, trajectories, chunksize=1)
assert len(nfo_infos) == 2
for info in nfo_infos:
assert info['meta']['project'] == 'v1'
if info['meta']['run'] == 5:
assert info['meta']['clone'] == 0
elif info['meta']['run'] == 6:
assert info['meta']['clone'] == 0
else:
assert False
assert os.path.exists(info['path']['workdir'])
assert set(info.keys()) == {'raw', 'meta', 'path', 'top'}, info
assert set(info['raw'].keys()) == {
'indir', 'real_indir', 'date', 'initdate', 'gens', 'gen_glob',
'success'
}
assert set(info['meta'].keys()) == {'project', 'run', 'clone'}
assert set(info['path'].keys()) == {'info', 'workdir'}
assert set(info['top'].keys()) == {'struct', 'fext'}
def test_infogen_2():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
n = 0
for info in proj.get_infos():
assert os.path.exists(info['raw']['indir'])
n += 1
assert n > 0
def test_nfo_pool():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
raw_infos = proj.get_infos()
print("Raw infos", list(proj.get_infos()))
with Pool() as pool:
print("Function", proj.nfo)
nfo_infos = pool.map(proj.nfo, raw_infos)
print("Returned", nfo_infos)
assert len(list(nfo_infos)) > 0
def test_nfo_record():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
raw_infos = proj.get_infos()
nfo_infos = [_record(proj.nfo, ri) for ri in raw_infos]
assert len(nfo_infos) > 0
for info in nfo_infos:
assert os.path.exists(info['path']['info'])
with open(info['path']['info']) as f:
reconstitute = json.load(f)
assert reconstitute == info
def test_trajectory_nfo():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
with Pool() as pool:
nfo_infos = pool.map(_process_trajectory, trajectories, chunksize=1)
n = 0
for info in nfo_infos:
assert os.path.exists(info['path']['info'])
with open(info['path']['info']) as f:
reconstitute = json.load(f)
assert reconstitute == info
n += 1
assert n > 0
def test_trajectory_nfo():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
with Pool() as pool:
nfo_infos = pool.map(_process_trajectory, trajectories, chunksize=1)
n = 0
for info in nfo_infos:
assert os.path.exists(info['path']['info'])
with open(info['path']['info']) as f:
reconstitute = json.load(f)
assert reconstitute == info
n += 1
assert n > 0
def test_cnv_bw():
proj = Processor("v1", "data/v1", 'bw')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
cnv2_infos = list(map(_process_trajectory, trajectories))
assert len(cnv2_infos) > 0
for info in cnv2_infos:
assert os.path.exists(info['cnv2']['gens'][0])
assert "/cnv2" in info['cnv2']['outdir']
with mdtraj.open(info['cnv2']['gens'][0]) as tfile:
xyz, time, step, box = tfile.read()
print("Shape", xyz.shape)
assert xyz.shape == (11, 22, 3), xyz.shape
def test_cnv_bw():
proj = Processor("v1", "data/v1", 'bw')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
cnv2_infos = list(map(_process_trajectory, trajectories))
assert len(cnv2_infos) > 0
for info in cnv2_infos:
assert os.path.exists(info['cnv2']['gens'][0])
assert "/cnv2" in info['cnv2']['outdir']
with mdtraj.open(info['cnv2']['gens'][0]) as tfile:
xyz, time, step, box = tfile.read()
print("Shape", xyz.shape)
assert xyz.shape == (11, 22, 3), xyz.shape
def test_cnv():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
cnv2_infos = list(map(_process_trajectory, trajectories))
assert len(cnv2_infos) > 0
for info in cnv2_infos:
for g in range(len(info['cnv2']['gens'])):
assert os.path.exists(info['cnv1']['gens'][g])
assert os.path.exists(info['cnv2']['gens'][g])
with mdtraj.open(info['cnv1']['gens'][g]) as tfile:
with mdtraj.open(info['cnv2']['gens'][g]) as dcdfile:
xyz, time, step, box = tfile.read()
print("Shape", xyz.shape)
assert xyz.shape == (11, 22, 3), xyz.shape
xyz_nc, time, lengths, angles = dcdfile.read()
np.testing.assert_array_equal(xyz[:-1] * 10, xyz_nc)
def test_cnv():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
trajectories = [Trajectory(info, proj, None) for info in proj.get_infos()]
cnv2_infos = list(map(_process_trajectory, trajectories))
assert len(cnv2_infos) > 0
for info in cnv2_infos:
for g in range(len(info['cnv2']['gens'])):
assert os.path.exists(info['cnv1']['gens'][g])
assert os.path.exists(info['cnv2']['gens'][g])
with mdtraj.open(info['cnv1']['gens'][g]) as tfile:
with mdtraj.open(info['cnv2']['gens'][g]) as dcdfile:
xyz, time, step, box = tfile.read()
print("Shape", xyz.shape)
assert xyz.shape == (11, 22, 3), xyz.shape
xyz_nc, time, lengths, angles = dcdfile.read()
np.testing.assert_array_equal(xyz[:-1] * 10, xyz_nc)
def test_infogen():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
infos = list(proj.get_infos())
assert len(infos) > 0, "{}".format(infos)
def test_glob():
proj = Processor("p1234", "data/PROJ1234", 'xa4')
assert len(proj.get_run_clone_dirs()) > 0