def test_FahProjectBuilder_subset():
cd = os.getcwd()
native_filename = get("native.pdb", just_filename=True)
frames_per_gen = 10
traj = md.load(native_filename)
fah_path = tempfile.mkdtemp()
msmb_path = tempfile.mkdtemp()
run_clone_gen = {(0, 0):5, (0, 1):6, (0, 2):7, (1, 0):20}
reference_traj_lengths = np.array([5, 6, 7, 20]) * frames_per_gen
atom_indices = np.arange(5)
ref = reference_data.FAHReferenceData(traj, fah_path, run_clone_gen, frames_per_gen)
os.chdir(msmb_path)
new_native_filename = msmb_path + "/" + os.path.split(native_filename)[1]
shutil.copy(native_filename, new_native_filename) # Necessary on travis because we lack write permission in native.pdb directory
pb = FahProjectBuilder(fah_path, '.xtc', new_native_filename, atom_indices=atom_indices)
project = pb.get_project()
new_traj = project.load_conf()
eq(new_traj.n_atoms, 5)
eq(project.traj_lengths, reference_traj_lengths)
os.chdir(cd)
shutil.rmtree(fah_path)
shutil.rmtree(msmb_path)
def test_FahProjectBuilder_new1():
cd = os.getcwd()
native_filename = get("native.pdb", just_filename=True)
frames_per_gen = 10
traj = md.load(native_filename)
fah_path = tempfile.mkdtemp()
msmb_path = tempfile.mkdtemp()
run_clone_gen = {(0, 0): 5, (0, 1): 6, (0, 2): 7, (1, 0): 20}
reference_traj_lengths = np.array([5, 6, 7, 20]) * frames_per_gen
ref = reference_data.FAHReferenceData(traj, fah_path, run_clone_gen,
frames_per_gen)
os.chdir(msmb_path)
pb = FahProjectBuilder(fah_path, '.xtc', native_filename)
project = pb.get_project()
eq(project.conf_filename, native_filename)
eq(project.traj_lengths, reference_traj_lengths)
os.chdir(cd)
shutil.rmtree(fah_path)
shutil.rmtree(msmb_path)
def test_FahProjectBuilder_new1():
cd = os.getcwd()
native_filename = get("native.pdb", just_filename=True)
frames_per_gen = 10
traj = md.load(native_filename)
fah_path = tempfile.mkdtemp()
msmb_path = tempfile.mkdtemp()
run_clone_gen = {(0, 0):5, (0, 1):6, (0, 2):7, (1, 0):20}
reference_traj_lengths = np.array([5, 6, 7, 20]) * frames_per_gen
ref = reference_data.FAHReferenceData(traj, fah_path, run_clone_gen, frames_per_gen)
os.chdir(msmb_path)
pb = FahProjectBuilder(fah_path, '.xtc', native_filename)
project = pb.get_project()
eq(project.conf_filename, native_filename)
eq(project.traj_lengths, reference_traj_lengths)
os.chdir(cd)
shutil.rmtree(fah_path)
shutil.rmtree(msmb_path)
def test_FahProjectBuilder():
cd = os.getcwd()
td = tempfile.mkdtemp()
os.chdir(td)
traj_dir = get("project_reference/project.builder/fah_style_data", just_filename=True)
conf_filename = os.path.join(traj_dir, 'native.pdb')
pb = FahProjectBuilder(traj_dir, '.xtc', conf_filename)
project = pb.get_project()
eq_(project.n_trajs, 4)
npt.assert_array_equal(project.traj_lengths, [1001, 1001, 501, 1001])
os.chdir(cd)
shutil.rmtree(td)
def test_FahProjectBuilder():
cd = os.getcwd()
td = tempfile.mkdtemp()
os.chdir(td)
traj_dir = os.path.join(reference_dir(),
"project_reference/project.builder/fah_style_data")
conf_filename = os.path.join(traj_dir, 'native.pdb')
pb = FahProjectBuilder(traj_dir, '.xtc', conf_filename)
project = pb.get_project()
eq_(project.n_trajs, 4)
npt.assert_array_equal(project.traj_lengths, [1001, 1001, 501, 1001])
os.chdir(cd)
shutil.rmtree(td)
def test_FahProjectBuilder_subset():
cd = os.getcwd()
native_filename = get("native.pdb", just_filename=True)
frames_per_gen = 10
traj = md.load(native_filename)
fah_path = tempfile.mkdtemp()
msmb_path = tempfile.mkdtemp()
run_clone_gen = {(0, 0): 5, (0, 1): 6, (0, 2): 7, (1, 0): 20}
reference_traj_lengths = np.array([5, 6, 7, 20]) * frames_per_gen
atom_indices = np.arange(5)
ref = reference_data.FAHReferenceData(traj, fah_path, run_clone_gen,
frames_per_gen)
os.chdir(msmb_path)
new_native_filename = msmb_path + "/" + os.path.split(native_filename)[1]
shutil.copy(
native_filename, new_native_filename
) # Necessary on travis because we lack write permission in native.pdb directory
pb = FahProjectBuilder(fah_path,
'.xtc',
new_native_filename,
atom_indices=atom_indices)
project = pb.get_project()
new_traj = project.load_conf()
eq(new_traj.n_atoms, 5)
eq(project.traj_lengths, reference_traj_lengths)
os.chdir(cd)
shutil.rmtree(fah_path)
shutil.rmtree(msmb_path)
def test_FahProjectBuilder2():
cd = os.getcwd()
td = tempfile.mkdtemp()
os.chdir(td)
# check that we can build a new project:
traj_dir = get("project_reference/project.builder/fah_style_data", just_filename=True)
conv_traj_dir = get("project_reference/project.builder/Trajectories", just_filename=True)
shutil.copytree(traj_dir, 'PROJXXXX')
shutil.copytree(conv_traj_dir, 'Trajectories')
shutil.copy2(get("project_reference/project.builder/ProjectInfo.yaml", just_filename=True), 'ProjectInfo.yaml')
project_orig = Project.load_from('ProjectInfo.yaml')
# made up project data
pb = FahProjectBuilder('PROJXXXX', '.xtc', 'PROJXXXX/native.pdb', project=project_orig)
project = pb.get_project()
project_ref = get("project_reference/project.builder/ProjectInfo_final.yaml")
assert project == project_ref
os.chdir(cd)
shutil.rmtree(td)
def test_FahProjectBuilder1():
cd = os.getcwd()
td = tempfile.mkdtemp()
os.chdir(td)
# check that we can build a new project:
traj_dir = get("project_reference/project.builder/fah_style_data", just_filename=True)
shutil.copytree(traj_dir, 'PROJXXXX')
shutil.rmtree('PROJXXXX/RUN0/CLONE1')
os.remove('PROJXXXX/RUN2/CLONE0/frame2.xtc')
# made up project data
pb = FahProjectBuilder('PROJXXXX', '.xtc', 'PROJXXXX/native.pdb')
project = pb.get_project()
project_ref = get("project_reference/project.builder/ProjectInfo.yaml")
print project == project_ref
assert project == project_ref
os.chdir(cd)
shutil.rmtree(td)
