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 run(projectfn, PDBfn, InputDir, source, min_length, stride, rmsd_cutoff):
# check if we are doing an update or a fresh run
if os.path.exists(projectfn):
logger.info(
"Found project info file encoding previous work, running in update mode..."
)
update = True
else:
update = False
logger.info("Looking for %s stype data in %s", source, InputDir)
if update:
raise NotImplementedError("Ack! Update mode is not yet ready yet.")
# if the source is fah, we'll use some special FaH specific loading functions
# to (1) try to recover in case of errors and (2) load the specific directory
# hierarchy of FaH (RUN/CLONE/GEN/frame.xtc)
if source.startswith('file'):
itype = '.dcd' if 'dcd' in source else '.xtc'
pb = ProjectBuilder(InputDir,
input_traj_ext=itype,
conf_filename=PDBfn,
stride=stride)
elif source == 'fah':
pb = FahProjectBuilder(InputDir,
input_traj_ext='.xtc',
conf_filename=PDBfn,
stride=stride)
else:
raise ValueError("Invalid argument for source: %s" % source)
# check that trajectories to not go farther than a certain RMSD
# from the PDB. Useful to check for blowing up or other numerical instabilities
if rmsd_cutoff is not None:
# TODO: this is going to use ALL of the atom_indices, including hydrogen. This is
# probably not the desired functionality
validator = validators.RMSDExplosionValidator(PDBfn,
max_rmsd=rmsd_cutoff,
atom_indices=None)
pb.add_validator(validator)
# Only accept trajectories with more snapshots than min_length.
if min_length > 0:
validator = validators.MinLengthValidator(min_length)
pb.add_validator(validator)
# everyone wants to be centered
pb.add_validator(validators.TrajCenterer())
pb.get_project().save(projectfn)
assert os.path.exists(projectfn), '%s does not exist' % projectfn
logger.info("Finished data conversion successfully.")
logger.info("Generated: %s, Trajectories/", projectfn)
return
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)
from msmbuilder.project import FahProjectBuilder
pb = FahProjectBuilder('./fah_style_data', '.xtc',
'./fah_style_data/native.pdb')
p = pb.convert()
print p
def run(projectfn, conf_filename, input_dir, source, min_length, stride,
rmsd_cutoff, atom_indices, iext):
# check if we are doing an update or a fresh run
# if os.path.exists(projectfn):
# logger.info("Found project info file encoding previous work, running in update mode...")
# update = True
# else:
# update = False
#
# logger.info("Looking for %s style data in %s", source, input_dir)
# if update:
# raise NotImplementedError("Ack! Update mode is not yet ready yet.")
# if the source is fah, we'll use some special FaH specific loading functions
# to (1) try to recover in case of errors and (2) load the specific directory
# hierarchy of FaH (RUN/CLONE/GEN/frame.xtc)
if os.path.exists(projectfn):
project = Project.load_from(projectfn)
logger.warn(
"%s exists, will modify it and update the trajectories in %s",
projectfn, '/'.join(project._traj_paths[0].split('/')[:-1]))
else:
project = None
if source.startswith('file'):
pb = ProjectBuilder(input_dir,
input_traj_ext=iext,
conf_filename=conf_filename,
stride=stride,
project=project,
atom_indices=atom_indices)
elif source == 'fah':
pb = FahProjectBuilder(input_dir,
input_traj_ext=iext,
conf_filename=conf_filename,
stride=stride,
project=project,
atom_indices=atom_indices)
else:
raise ValueError("Invalid argument for source: %s" % source)
# check that trajectories to not go farther than a certain RMSD
# from the PDB. Useful to check for blowing up or other numerical
# instabilities
if rmsd_cutoff is not None:
# TODO: this is going to use ALL of the atom_indices, including hydrogen. This is
# probably not the desired functionality
# KAB: Apparently needed to use correctly subsetted atom_indices here to avoid an error
validator = validators.RMSDExplosionValidator(
conf_filename, max_rmsd=rmsd_cutoff, atom_indices=atom_indices)
pb.add_validator(validator)
# Only accept trajectories with more snapshots than min_length.
if min_length > 0:
validator = validators.MinLengthValidator(min_length)
pb.add_validator(validator)
# everyone wants to be centered
pb.add_validator(validators.TrajCenterer())
pb.get_project().save(projectfn)
assert os.path.exists(projectfn), '%s does not exist' % projectfn
logger.info("Finished data conversion successfully.")
logger.info("Generated: %s, Trajectories/", projectfn)
return
from msmbuilder.project import FahProjectBuilder
pb = FahProjectBuilder('./fah_style_data', '.xtc', './fah_style_data/native.pdb')
p = pb.convert()
print p