class TestCustomFeature(unittest.TestCase):
def setUp(self):
self.feat = MDFeaturizer(pdbfile)
self.traj = mdtraj.load(xtcfile, top=pdbfile)
self.pairs = [[0, 1], [0, 2], [1, 2]] #some distances
self.means = [.5, .75, 1.0] #bogus means
self.U = np.array([[0, 1], [1, 0], [
1, 1
]]) #bogus transformation, projects from 3 distances to 2 components
def test_some_feature(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
Y_custom_feature = self.feat.transform(self.traj)
# Directly call the function
Y_function = some_call_to_mdtraj_some_operations_some_linalg(
self.traj, self.pairs, self.means, self.U)
assert np.allclose(Y_custom_feature, Y_function)
def test_describe(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
self.feat.describe()
def test_dimensionality(self):
self.feat.add_custom_func(
some_call_to_mdtraj_some_operations_some_linalg, self.U.shape[1],
self.pairs, self.means, self.U)
assert self.feat.dimension() == self.U.shape[1]
def setUp(self):
self.pdbfile = pdbfile
self.traj = mdtraj.load(xtcfile, top=self.pdbfile)
self.feat = MDFeaturizer(self.pdbfile)
self.atol = 1e-5
self.ref_frame = 0
self.atom_indices = np.arange(0, self.traj.n_atoms / 2)
def __init__(self, trajectories, topologyfile=None, chunksize=100, featurizer=None):
assert (topologyfile is not None) or (featurizer is not None), \
"Needs either a topology file or a featurizer for instantiation"
super(FeatureReader, self).__init__(chunksize=chunksize)
# files
if isinstance(trajectories, string_types):
trajectories = [trajectories]
self.trajfiles = trajectories
self.topfile = topologyfile
# featurizer
if topologyfile and featurizer:
self._logger.warning("Both a topology file and a featurizer were given as arguments. "
"Only featurizer gets respected in this case.")
if not featurizer:
self.featurizer = MDFeaturizer(topologyfile)
else:
self.featurizer = featurizer
self.topfile = featurizer.topologyfile
# Check that the topology and the files in the filelist can actually work together
self._assert_toptraj_consistency()
# iteration
self._mditer = None
# current lag time
self._curr_lag = 0
# time lagged iterator
self._mditer2 = None
self.__set_dimensions_and_lengths()
self._parametrized = True
def setUp(self):
self.feat = MDFeaturizer(pdbfile)
self.traj = mdtraj.load(xtcfile, top=pdbfile)
self.pairs = [[0, 1], [0, 2], [1, 2]] #some distances
self.means = [.5, .75, 1.0] #bogus means
self.U = np.array([[0, 1], [1, 0], [
1, 1
]]) #bogus transformation, projects from 3 distances to 2 components
def test_backbone_dihedrals_deg(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_backbone_torsions(deg=True)
traj = mdtraj.load(self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
assert (np.alltrue(Y >= -180.0))
assert (np.alltrue(Y <= 180.0))
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_ca_distances_with_all_atom_geometries(self):
feat = MDFeaturizer(pdbfile_ops_aa)
feat.add_distances_ca(excluded_neighbors=0)
D_aa = feat.transform(mdtraj.load(pdbfile_ops_aa))
# Create a reference
feat_just_ca = MDFeaturizer(pdbfile_ops_Ca)
feat_just_ca.add_distances(np.arange(feat_just_ca.topology.n_atoms))
D_ca = feat_just_ca.transform(mdtraj.load(pdbfile_ops_Ca))
assert (np.allclose(D_aa, D_ca))
def test_backbone_dihedrials_chi(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_chi1_torsions()
traj = mdtraj.load(self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_backbone_dihedrals_cossin(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_backbone_torsions(cossin=True)
traj = mdtraj.load(self.asn_leu_traj, top=self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
self.assertEqual(Y.shape,
(len(traj), 3 * 4)) # (3 phi + 3 psi)*2 [cos, sin]
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
assert "COS" in desc[0]
assert "SIN" in desc[1]
self.assertEqual(len(desc), self.feat.dimension())
class TestStaticMethods(unittest.TestCase):
def setUp(self):
self.feat = MDFeaturizer(pdbfile)
def test_pairs(self):
n_at = 5
pairs = self.feat.pairs(np.arange(n_at), excluded_neighbors=3)
assert np.allclose(pairs, [0, 4])
pairs = self.feat.pairs(np.arange(n_at), excluded_neighbors=2)
assert np.allclose(pairs, [[0, 3], [0, 4], [1, 4]])
pairs = self.feat.pairs(np.arange(n_at), excluded_neighbors=1)
assert np.allclose(pairs,
[[0, 2], [0, 3], [0, 4], [1, 3], [1, 4], [2, 4]])
pairs = self.feat.pairs(np.arange(n_at), excluded_neighbors=0)
assert np.allclose(pairs, [[0, 1], [0, 2], [0, 3], [0, 4], [1, 2],
[1, 3], [1, 4], [2, 3], [2, 4], [3, 4]])
def __init__(self,
trajectories,
topologyfile=None,
chunksize=100,
featurizer=None):
assert (topologyfile is not None) or (featurizer is not None), \
"Needs either a topology file or a featurizer for instantiation"
# init with chunksize 100
super(FeatureReader, self).__init__(chunksize=chunksize)
self.data_producer = self
# files
if isinstance(trajectories, basestring):
trajectories = [trajectories]
self.trajfiles = trajectories
self.topfile = topologyfile
# featurizer
if topologyfile and featurizer:
self._logger.warning(
"Both a topology file and a featurizer were given as arguments. "
"Only featurizer gets respected in this case.")
if not featurizer:
self.featurizer = MDFeaturizer(topologyfile)
else:
self.featurizer = featurizer
self.topfile = featurizer.topologyfile
# iteration
self._mditer = None
# current lag time
self._curr_lag = 0
# time lagged iterator
self._mditer2 = None
# cache size
self.in_memory = False
self._Y = None
self.__set_dimensions_and_lenghts()
self._parametrized = True
def __init__(self, trajectories, topologyfile=None, chunksize=100, featurizer=None):
assert (topologyfile is not None) or (featurizer is not None), \
"Needs either a topology file or a featurizer for instantiation"
# init with chunksize 100
super(FeatureReader, self).__init__(chunksize=chunksize)
self.data_producer = self
# files
if isinstance(trajectories, basestring):
trajectories = [trajectories]
self.trajfiles = trajectories
self.topfile = topologyfile
# featurizer
if topologyfile and featurizer:
self._logger.warning("Both a topology file and a featurizer were given as arguments. "
"Only featurizer gets respected in this case.")
if not featurizer:
self.featurizer = MDFeaturizer(topologyfile)
else:
self.featurizer = featurizer
self.topfile = featurizer.topologyfile
# iteration
self._mditer = None
# current lag time
self._curr_lag = 0
# time lagged iterator
self._mditer2 = None
# cache size
self.in_memory = False
self._Y = None
self.__set_dimensions_and_lenghts()
self._parametrized = True
class TestFeaturizer(unittest.TestCase):
def setUp(self):
self.pdbfile = pdbfile
self.traj = mdtraj.load(xtcfile, top=self.pdbfile)
self.feat = MDFeaturizer(self.pdbfile)
def test_select_backbone(self):
inds = self.feat.select_Backbone()
def test_select_all(self):
self.feat.add_all()
assert (self.feat.dimension() == self.traj.n_atoms * 3)
refmap = np.reshape(self.traj.xyz,
(len(self.traj), self.traj.n_atoms * 3))
assert (np.all(refmap == self.feat.map(self.traj)))
def test_select(self):
sel = np.array([1, 2, 5, 20], dtype=int)
self.feat.add_selection(sel)
assert (self.feat.dimension() == sel.shape[0] * 3)
refmap = np.reshape(self.traj.xyz[:, sel, :],
(len(self.traj), sel.shape[0] * 3))
assert (np.all(refmap == self.feat.map(self.traj)))
def test_distances(self):
sel = np.array([1, 2, 5, 20], dtype=int)
pairs_expected = np.array([[1, 5], [1, 20], [2, 5], [2, 20], [5, 20]])
pairs = self.feat.pairs(sel)
assert (pairs.shape == pairs_expected.shape)
assert (np.all(pairs == pairs_expected))
self.feat.add_distances(
pairs,
periodic=False) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs_expected.shape[0])
X = self.traj.xyz[:, pairs_expected[:, 0], :]
Y = self.traj.xyz[:, pairs_expected[:, 1], :]
D = np.sqrt(np.sum((X - Y)**2, axis=2))
assert (np.allclose(D, self.feat.map(self.traj)))
def test_inverse_distances(self):
sel = np.array([1, 2, 5, 20], dtype=int)
pairs_expected = np.array([[1, 5], [1, 20], [2, 5], [2, 20], [5, 20]])
pairs = self.feat.pairs(sel)
assert (pairs.shape == pairs_expected.shape)
assert (np.all(pairs == pairs_expected))
self.feat.add_inverse_distances(
pairs,
periodic=False) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs_expected.shape[0])
X = self.traj.xyz[:, pairs_expected[:, 0], :]
Y = self.traj.xyz[:, pairs_expected[:, 1], :]
Dinv = 1.0 / np.sqrt(np.sum((X - Y)**2, axis=2))
assert (np.allclose(Dinv, self.feat.map(self.traj)))
def test_ca_distances(self):
sel = self.feat.select_Ca()
assert (np.all(sel == range(self.traj.n_atoms))
) # should be all for this Ca-traj
pairs = self.feat.pairs(sel)
self.feat.add_distances_ca(
periodic=False) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs.shape[0])
X = self.traj.xyz[:, pairs[:, 0], :]
Y = self.traj.xyz[:, pairs[:, 1], :]
D = np.sqrt(np.sum((X - Y)**2, axis=2))
assert (np.allclose(D, self.feat.map(self.traj)))
def test_contacts(self):
sel = np.array([1, 2, 5, 20], dtype=int)
pairs_expected = np.array([[1, 5], [1, 20], [2, 5], [2, 20], [5, 20]])
pairs = self.feat.pairs(sel)
assert (pairs.shape == pairs_expected.shape)
assert (np.all(pairs == pairs_expected))
self.feat.add_contacts(
pairs, threshold=0.5,
periodic=False) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs_expected.shape[0])
X = self.traj.xyz[:, pairs_expected[:, 0], :]
Y = self.traj.xyz[:, pairs_expected[:, 1], :]
D = np.sqrt(np.sum((X - Y)**2, axis=2))
C = np.zeros(D.shape)
I = np.argwhere(D <= 0.5)
C[I[:, 0], I[:, 1]] = 1.0
assert (np.allclose(C, self.feat.map(self.traj)))
def test_angles(self):
sel = np.array([[1, 2, 5], [1, 3, 8], [2, 9, 10]], dtype=int)
self.feat.add_angles(sel)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.map(self.traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
def test_angles_deg(self):
sel = np.array([[1, 2, 5], [1, 3, 8], [2, 9, 10]], dtype=int)
self.feat.add_angles(sel, deg=True)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.map(self.traj)
assert (np.alltrue(Y >= -180.0))
assert (np.alltrue(Y <= 180.0))
def test_dihedrals(self):
sel = np.array([[1, 2, 5, 6], [1, 3, 8, 9], [2, 9, 10, 12]], dtype=int)
self.feat.add_dihedrals(sel)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.map(self.traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
def test_dihedrals_deg(self):
sel = np.array([[1, 2, 5, 6], [1, 3, 8, 9], [2, 9, 10, 12]], dtype=int)
self.feat.add_dihedrals(sel, deg=True)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.map(self.traj)
assert (np.alltrue(Y >= -180.0))
assert (np.alltrue(Y <= 180.0))
def test_backbone_dihedrals(self):
# TODO: test me
pass
def test_backbone_dihedrals_deg(self):
# TODO: test me
pass
def test_custom_feature(self):
# TODO: test me
pass
def testAddFeaturesWithDuplicates(self):
"""this tests adds multiple features twice (eg. same indices) and
checks whether they are rejected or not"""
featurizer = MDFeaturizer(pdbfile)
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
self.assertEqual(len(featurizer.active_features), 1)
featurizer.add_backbone_torsions()
self.assertEqual(len(featurizer.active_features), 2)
featurizer.add_backbone_torsions()
self.assertEqual(len(featurizer.active_features), 2)
featurizer.add_contacts([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 3)
featurizer.add_contacts([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 3)
# try to fool it with ca selection
ca = featurizer.select_Ca()
ca = featurizer.pairs(ca)
featurizer.add_distances(ca)
self.assertEqual(len(featurizer.active_features), 4)
featurizer.add_distances_ca()
self.assertEqual(len(featurizer.active_features), 4)
featurizer.add_inverse_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 5)
featurizer.add_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 6)
featurizer.add_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), 6)
def my_func(x):
return x - 1
def foo(x):
return x - 1
my_feature = CustomFeature(my_func)
my_feature.dimension = 3
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), 7)
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), 7)
# since myfunc and foo are different functions, it should be added
foo_feat = CustomFeature(foo, dim=3)
featurizer.add_custom_feature(foo_feat)
self.assertEqual(len(featurizer.active_features), 8)
class FeatureReader(ReaderInterface):
"""
Reads features from MD data.
To select a feature, access the :attr:`featurizer` and call a feature
selecting method (e.g) distances.
Parameters
----------
trajectories: list of strings
paths to trajectory files
topologyfile: string
path to topology file (e.g. pdb)
Examples
--------
>>> from pyemma.datasets import get_bpti_test_data
Iterator access:
>>> reader = FeatureReader(get_bpti_test_data()['trajs'], get_bpti_test_data()['top'])
Optionally set a chunksize
>>> reader.chunksize = 300
Store chunks by their trajectory index
>>> chunks = {i : [] for i in range(reader.number_of_trajectories())}
>>> for itraj, X in reader:
... chunks[itraj].append(X)
Calculate some distances of protein during feature reading:
>>> reader.featurizer.add_distances([[0, 3], [10, 15]])
>>> X = reader.get_output()
"""
def __init__(self, trajectories, topologyfile=None, chunksize=100, featurizer=None):
assert (topologyfile is not None) or (featurizer is not None), \
"Needs either a topology file or a featurizer for instantiation"
super(FeatureReader, self).__init__(chunksize=chunksize)
# files
if isinstance(trajectories, string_types):
trajectories = [trajectories]
self.trajfiles = trajectories
self.topfile = topologyfile
# featurizer
if topologyfile and featurizer:
self._logger.warning("Both a topology file and a featurizer were given as arguments. "
"Only featurizer gets respected in this case.")
if not featurizer:
self.featurizer = MDFeaturizer(topologyfile)
else:
self.featurizer = featurizer
self.topfile = featurizer.topologyfile
# Check that the topology and the files in the filelist can actually work together
self._assert_toptraj_consistency()
# iteration
self._mditer = None
# current lag time
self._curr_lag = 0
# time lagged iterator
self._mditer2 = None
self.__set_dimensions_and_lengths()
self._parametrized = True
def __set_dimensions_and_lengths(self):
self._ntraj = len(self.trajfiles)
# lookups pre-computed lengths, or compute it on the fly and store it in db.
if config['use_trajectory_lengths_cache'] == 'True':
from pyemma.coordinates.data.traj_info_cache import TrajectoryInfoCache
for traj in self.trajfiles:
self._lengths.append(TrajectoryInfoCache[traj])
else:
for traj in self.trajfiles:
with mdtraj.open(traj, mode='r') as fh:
self._lengths.append(len(fh))
# number of trajectories/data sets
if self._ntraj == 0:
raise ValueError("no valid data")
# note: dimension is a custom impl in this class
def describe(self):
"""
Returns a description of this transformer
:return:
"""
return ["Feature reader with following features"] + self.featurizer.describe()
def dimension(self):
"""
Returns the number of output dimensions
:return:
"""
if len(self.featurizer.active_features) == 0:
# special case: Cartesian coordinates
return self.featurizer.topology.n_atoms * 3
else:
# general case
return self.featurizer.dimension()
def _create_iter(self, filename, skip=0, stride=1, atom_indices=None):
return patches.iterload(filename, chunk=self.chunksize,
top=self.topfile, skip=skip, stride=stride, atom_indices=atom_indices)
def _close(self):
try:
if self._mditer:
self._mditer.close()
if self._mditer2:
self._mditer2.close()
except:
self._logger.exception("something went wrong closing file handles")
def _reset(self, context=None):
"""
resets the chunk reader
"""
self._itraj = 0
self._curr_lag = 0
if len(self.trajfiles) >= 1:
self._t = 0
if context and not context.uniform_stride:
self._itraj = min(context.traj_keys)
self._mditer = self._create_iter(
self.trajfiles[self._itraj], stride=context.ra_indices_for_traj(self._itraj)
)
else:
self._mditer = self._create_iter(self.trajfiles[0], stride=context.stride if context else 1)
def _next_chunk(self, context=None):
"""
gets the next chunk. If lag > 0, we open another iterator with same chunk
size and advance it by one, as soon as this method is called with a lag > 0.
:return: a feature mapped vector X, or (X, Y) if lag > 0
"""
chunk = next(self._mditer)
shape = chunk.xyz.shape
if context.lag > 0:
if not context.uniform_stride:
raise ValueError("random access stride with lag not supported")
if self._curr_lag == 0:
# lag time or trajectory index changed, so open lagged iterator
if __debug__:
self._logger.debug("open time lagged iterator for traj %i with lag %i"
% (self._itraj, context.lag))
self._curr_lag = context.lag
self._mditer2 = self._create_iter(self.trajfiles[self._itraj],
skip=self._curr_lag,
stride=context.stride)
try:
adv_chunk = next(self._mditer2)
except StopIteration:
# When _mditer2 ran over the trajectory end, return empty chunks.
adv_chunk = mdtraj.Trajectory(np.empty((0, shape[1], shape[2]), np.float32), chunk.topology)
except RuntimeError as e:
if "seek error" in str(e):
raise RuntimeError("Trajectory %s too short for lag time %i" %
(self.trajfiles[self._itraj], context.lag))
self._t += shape[0]
if (self._t >= self.trajectory_length(self._itraj, stride=context.stride) and
self._itraj < len(self.trajfiles) - 1):
if __debug__:
self._logger.debug('closing current trajectory "%s"'
% self.trajfiles[self._itraj])
self._close()
self._t = 0
self._itraj += 1
if not context.uniform_stride:
while self._itraj not in context.traj_keys and self._itraj < self.number_of_trajectories():
self._itraj += 1
self._mditer = self._create_iter(
self.trajfiles[self._itraj], stride=context.ra_indices_for_traj(self._itraj)
)
else:
self._mditer = self._create_iter(self.trajfiles[self._itraj], stride=context.stride)
# we open self._mditer2 only if requested due lag parameter!
self._curr_lag = 0
if not context.uniform_stride:
traj_len = context.ra_trajectory_length(self._itraj)
else:
traj_len = self.trajectory_length(self._itraj)
if self._t >= traj_len and self._itraj == len(self.trajfiles) - 1:
if __debug__:
self._logger.debug('closing last trajectory "%s"' % self.trajfiles[self._itraj])
self._mditer.close()
if self._curr_lag != 0:
self._mditer2.close()
# map data
if context.lag == 0:
if len(self.featurizer.active_features) == 0:
shape_2d = (shape[0], shape[1] * shape[2])
return chunk.xyz.reshape(shape_2d)
else:
return self.featurizer.transform(chunk)
else:
if len(self.featurizer.active_features) == 0:
shape_Y = adv_chunk.xyz.shape
X = chunk.xyz.reshape((shape[0], shape[1] * shape[2]))
Y = adv_chunk.xyz.reshape((shape_Y[0], shape_Y[1] * shape_Y[2]))
else:
X = self.featurizer.transform(chunk)
Y = self.featurizer.transform(adv_chunk)
return X, Y
def parametrize(self, stride=1):
if self.in_memory:
self._map_to_memory(stride)
def _assert_toptraj_consistency(self):
r""" Check if the topology and the trajfiles of the reader have the same n_atoms"""
traj = mdtraj.load_frame(self.trajfiles[0], index=0, top=self.topfile)
desired_n_atoms = self.featurizer.topology.n_atoms
assert traj.xyz.shape[1] == desired_n_atoms, "Mismatch in the number of atoms between the topology" \
" and the first trajectory file, %u vs %u"% \
(desired_n_atoms, traj.xyz.shape[1])
class FeatureReader(ReaderInterface):
"""
Reads features from MD data.
To select a feature, access the :attr:`featurizer` and call a feature
selecting method (e.g) distances.
Parameters
----------
trajectories: list of strings
paths to trajectory files
topologyfile: string
path to topology file (e.g. pdb)
Examples
--------
Iterator access:
>>> reader = FeatureReader('mytraj.xtc', 'my_structure.pdb')
>>> chunks = []
>>> for itraj, X in reader:
>>> chunks.append(X)
Extract backbone torsion angles of protein during feature reading:
>>> reader = FeatureReader('mytraj.xtc', 'my_structure.pdb')
>>> reader.featurizer.add_backbone_torsions()
>>> X = reader.get_output()
"""
def __init__(self,
trajectories,
topologyfile=None,
chunksize=100,
featurizer=None):
assert (topologyfile is not None) or (featurizer is not None), \
"Needs either a topology file or a featurizer for instantiation"
# init with chunksize 100
super(FeatureReader, self).__init__(chunksize=chunksize)
self.data_producer = self
# files
if isinstance(trajectories, basestring):
trajectories = [trajectories]
self.trajfiles = trajectories
self.topfile = topologyfile
# featurizer
if topologyfile and featurizer:
self._logger.warning(
"Both a topology file and a featurizer were given as arguments. "
"Only featurizer gets respected in this case.")
if not featurizer:
self.featurizer = MDFeaturizer(topologyfile)
else:
self.featurizer = featurizer
self.topfile = featurizer.topologyfile
# iteration
self._mditer = None
# current lag time
self._curr_lag = 0
# time lagged iterator
self._mditer2 = None
# cache size
self.in_memory = False
self._Y = None
self.__set_dimensions_and_lenghts()
self._parametrized = True
# @classmethod
# def init_from_featurizer(cls, trajectories, featurizer):
# if not isinstance(featurizer, MDFeaturizer):
# raise ValueError("given featurizer is not of type Featurizer, but is %s"
# % type(featurizer))
# cls.featurizer = featurizer
# return cls(trajectories, featurizer.topologyfile)
def __set_dimensions_and_lenghts(self):
self._ntraj = len(self.trajfiles)
# basic statistics
for traj in self.trajfiles:
sum_frames = sum(t.n_frames for t in self._create_iter(traj))
self._lengths.append(sum_frames)
# number of trajectories/data sets
if self._ntraj == 0:
raise ValueError("no valid data")
# note: dimension is a custom impl in this class
def describe(self):
"""
Returns a description of this transformer
:return:
"""
return ["Feature reader with following features"
] + self.featurizer.describe()
def parametrize(self, stride=1):
"""
Parametrizes this transformer
:return:
"""
if self.in_memory:
self._map_to_memory(stride=stride)
def dimension(self):
"""
Returns the number of output dimensions
:return:
"""
if len(self.featurizer.active_features) == 0:
# special case: cartesion coordinates
return self.featurizer.topology.n_atoms * 3
else:
# general case
return self.featurizer.dimension()
def _get_memory_per_frame(self):
"""
Returns the memory requirements per frame, in bytes
:return:
"""
return 4 * self.dimension()
def _get_constant_memory(self):
"""
Returns the constant memory requirements, in bytes
:return:
"""
return 0
def _map_to_memory(self, stride=1):
# TODO: stride is currently not implemented
if stride > 1:
raise NotImplementedError(
'stride option for FeatureReader._map_to_memory is currently not implemented'
)
self._reset()
# iterate over trajectories
last_chunk = False
itraj = 0
while not last_chunk:
last_chunk_in_traj = False
t = 0
while not last_chunk_in_traj:
y = self._next_chunk()
assert y is not None
L = np.shape(y)[0]
# last chunk in traj?
last_chunk_in_traj = (t + L >= self.trajectory_length(itraj))
# last chunk?
last_chunk = (last_chunk_in_traj
and itraj >= self.number_of_trajectories() - 1)
# write
self._Y[itraj][t:t + L] = y
# increment time
t += L
# increment trajectory
itraj += 1
def _create_iter(self, filename, skip=0, stride=1):
return patches.iterload(filename,
chunk=self.chunksize,
top=self.topfile,
skip=skip,
stride=stride)
def _reset(self, stride=1):
"""
resets the chunk reader
"""
self._itraj = 0
self._curr_lag = 0
if len(self.trajfiles) >= 1:
self._t = 0
self._mditer = self._create_iter(self.trajfiles[0], stride=stride)
def _next_chunk(self, lag=0, stride=1):
"""
gets the next chunk. If lag > 0, we open another iterator with same chunk
size and advance it by one, as soon as this method is called with a lag > 0.
:return: a feature mapped vector X, or (X, Y) if lag > 0
"""
chunk = self._mditer.next()
shape = chunk.xyz.shape
if lag > 0:
if self._curr_lag == 0:
# lag time or trajectory index changed, so open lagged iterator
if __debug__:
self._logger.debug(
"open time lagged iterator for traj %i with lag %i" %
(self._itraj, self._curr_lag))
self._curr_lag = lag
self._mditer2 = self._create_iter(self.trajfiles[self._itraj],
skip=self._curr_lag * stride,
stride=stride)
try:
adv_chunk = self._mditer2.next()
except StopIteration:
# When _mditer2 ran over the trajectory end, return empty chunks.
adv_chunk = mdtraj.Trajectory(
np.empty((0, shape[1], shape[2]), np.float32),
chunk.topology)
self._t += shape[0]
if (self._t >= self.trajectory_length(self._itraj, stride=stride)
and self._itraj < len(self.trajfiles) - 1):
if __debug__:
self._logger.debug('closing current trajectory "%s"' %
self.trajfiles[self._itraj])
self._mditer.close()
if self._curr_lag != 0:
self._mditer2.close()
self._t = 0
self._itraj += 1
self._mditer = self._create_iter(self.trajfiles[self._itraj],
stride=stride)
# we open self._mditer2 only if requested due lag parameter!
self._curr_lag = 0
if (self._t >= self.trajectory_length(self._itraj, stride=stride)
and self._itraj == len(self.trajfiles) - 1):
if __debug__:
self._logger.debug('closing last trajectory "%s"' %
self.trajfiles[self._itraj])
self._mditer.close()
if self._curr_lag != 0:
self._mditer2.close()
# map data
if lag == 0:
if len(self.featurizer.active_features) == 0:
shape_2d = (shape[0], shape[1] * shape[2])
return chunk.xyz.reshape(shape_2d)
else:
return self.featurizer.map(chunk)
else:
if len(self.featurizer.active_features) == 0:
shape_Y = adv_chunk.xyz.shape
X = chunk.xyz.reshape((shape[0], shape[1] * shape[2]))
Y = adv_chunk.xyz.reshape(
(shape_Y[0], shape_Y[1] * shape_Y[2]))
else:
X = self.featurizer.map(chunk)
Y = self.featurizer.map(adv_chunk)
return X, Y
class TestFeaturizer(unittest.TestCase):
@classmethod
def setUpClass(cls):
import tempfile
cls.asn_leu_pdbfile = tempfile.mkstemp(suffix=".pdb")[1]
with open(cls.asn_leu_pdbfile, 'w') as fh:
fh.write(asn_leu_pdb)
cls.asn_leu_traj = tempfile.mktemp(suffix='.xtc')
# create traj for asn_leu
n_frames = 4001
traj = mdtraj.load(cls.asn_leu_pdbfile)
ref = traj.xyz
new_xyz = np.empty((n_frames, ref.shape[1], 3))
noise = np.random.random(new_xyz.shape)
new_xyz[:, :, :] = noise + ref
traj.xyz = new_xyz
traj.time = np.arange(n_frames)
traj.save(cls.asn_leu_traj)
super(TestFeaturizer, cls).setUpClass()
@classmethod
def tearDownClass(cls):
try:
os.unlink(cls.asn_leu_pdbfile)
except EnvironmentError:
pass
super(TestFeaturizer, cls).tearDownClass()
def setUp(self):
self.pdbfile = pdbfile
self.traj = mdtraj.load(xtcfile, top=self.pdbfile)
self.feat = MDFeaturizer(self.pdbfile)
self.atol = 1e-5
self.ref_frame = 0
self.atom_indices = np.arange(0, self.traj.n_atoms / 2)
def test_select_backbone(self):
inds = self.feat.select_Backbone()
def test_select_all(self):
self.feat.add_all()
assert (self.feat.dimension() == self.traj.n_atoms * 3)
refmap = np.reshape(self.traj.xyz,
(len(self.traj), self.traj.n_atoms * 3))
assert (np.all(refmap == self.feat.transform(self.traj)))
def test_select(self):
sel = np.array([1, 2, 5, 20], dtype=int)
self.feat.add_selection(sel)
assert (self.feat.dimension() == sel.shape[0] * 3)
refmap = np.reshape(self.traj.xyz[:, sel, :],
(len(self.traj), sel.shape[0] * 3))
assert (np.all(refmap == self.feat.transform(self.traj)))
def test_distances(self):
sel = np.array([1, 2, 5, 20], dtype=int)
pairs_expected = np.array([[1, 5], [1, 20], [2, 5], [2, 20], [5, 20]])
pairs = self.feat.pairs(sel, excluded_neighbors=2)
assert (pairs.shape == pairs_expected.shape)
assert (np.all(pairs == pairs_expected))
self.feat.add_distances(
pairs,
periodic=False) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs_expected.shape[0])
X = self.traj.xyz[:, pairs_expected[:, 0], :]
Y = self.traj.xyz[:, pairs_expected[:, 1], :]
D = np.sqrt(np.sum((X - Y)**2, axis=2))
assert (np.allclose(D, self.feat.transform(self.traj)))
def test_inverse_distances(self):
sel = np.array([1, 2, 5, 20], dtype=int)
pairs_expected = np.array([[1, 5], [1, 20], [2, 5], [2, 20], [5, 20]])
pairs = self.feat.pairs(sel, excluded_neighbors=2)
assert (pairs.shape == pairs_expected.shape)
assert (np.all(pairs == pairs_expected))
self.feat.add_inverse_distances(
pairs,
periodic=False) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs_expected.shape[0])
X = self.traj.xyz[:, pairs_expected[:, 0], :]
Y = self.traj.xyz[:, pairs_expected[:, 1], :]
Dinv = 1.0 / np.sqrt(np.sum((X - Y)**2, axis=2))
assert (np.allclose(Dinv, self.feat.transform(self.traj)))
def test_ca_distances(self):
sel = self.feat.select_Ca()
assert (np.all(sel == list(range(self.traj.n_atoms)))
) # should be all for this Ca-traj
pairs = self.feat.pairs(sel, excluded_neighbors=0)
self.feat.add_distances_ca(
periodic=False, excluded_neighbors=0
) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs.shape[0])
X = self.traj.xyz[:, pairs[:, 0], :]
Y = self.traj.xyz[:, pairs[:, 1], :]
D = np.sqrt(np.sum((X - Y)**2, axis=2))
assert (np.allclose(D, self.feat.transform(self.traj)))
def test_ca_distances_with_all_atom_geometries(self):
feat = MDFeaturizer(pdbfile_ops_aa)
feat.add_distances_ca(excluded_neighbors=0)
D_aa = feat.transform(mdtraj.load(pdbfile_ops_aa))
# Create a reference
feat_just_ca = MDFeaturizer(pdbfile_ops_Ca)
feat_just_ca.add_distances(np.arange(feat_just_ca.topology.n_atoms))
D_ca = feat_just_ca.transform(mdtraj.load(pdbfile_ops_Ca))
assert (np.allclose(D_aa, D_ca))
def test_ca_distances_with_all_atom_geometries_and_exclusions(self):
feat = MDFeaturizer(pdbfile_ops_aa)
feat.add_distances_ca(excluded_neighbors=2)
D_aa = feat.transform(mdtraj.load(pdbfile_ops_aa))
# Create a reference
feat_just_ca = MDFeaturizer(pdbfile_ops_Ca)
ca_pairs = feat.pairs(feat_just_ca.select_Ca(), excluded_neighbors=2)
feat_just_ca.add_distances(ca_pairs)
D_ca = feat_just_ca.transform(mdtraj.load(pdbfile_ops_Ca))
assert (np.allclose(D_aa, D_ca))
def test_contacts(self):
sel = np.array([1, 2, 5, 20], dtype=int)
pairs_expected = np.array([[1, 5], [1, 20], [2, 5], [2, 20], [5, 20]])
pairs = self.feat.pairs(sel, excluded_neighbors=2)
assert (pairs.shape == pairs_expected.shape)
assert (np.all(pairs == pairs_expected))
self.feat.add_contacts(
pairs, threshold=0.5,
periodic=False) # unperiodic distances such that we can compare
assert (self.feat.dimension() == pairs_expected.shape[0])
X = self.traj.xyz[:, pairs_expected[:, 0], :]
Y = self.traj.xyz[:, pairs_expected[:, 1], :]
D = np.sqrt(np.sum((X - Y)**2, axis=2))
C = np.zeros(D.shape)
I = np.argwhere(D <= 0.5)
C[I[:, 0], I[:, 1]] = 1.0
assert (np.allclose(C, self.feat.transform(self.traj)))
def test_contacts_count_contacts(self):
sel = np.array([1, 2, 5, 20], dtype=int)
pairs_expected = np.array([[1, 5], [1, 20], [2, 5], [2, 20], [5, 20]])
pairs = self.feat.pairs(sel, excluded_neighbors=2)
assert (pairs.shape == pairs_expected.shape)
assert (np.all(pairs == pairs_expected))
self.feat.add_contacts(
pairs, threshold=0.5, periodic=False, count_contacts=True
) # unperiodic distances such that we can compare
# The dimensionality of the feature is now one
assert (self.feat.dimension() == 1)
X = self.traj.xyz[:, pairs_expected[:, 0], :]
Y = self.traj.xyz[:, pairs_expected[:, 1], :]
D = np.sqrt(np.sum((X - Y)**2, axis=2))
C = np.zeros(D.shape)
I = np.argwhere(D <= 0.5)
C[I[:, 0], I[:, 1]] = 1.0
# Count the contacts
C = C.sum(1, keepdims=True)
assert (np.allclose(C, self.feat.transform(self.traj)))
def test_angles(self):
sel = np.array([[1, 2, 5], [1, 3, 8], [2, 9, 10]], dtype=int)
self.feat.add_angles(sel)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.transform(self.traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
self.assertEqual(len(self.feat.describe()), self.feat.dimension())
def test_angles_deg(self):
sel = np.array([[1, 2, 5], [1, 3, 8], [2, 9, 10]], dtype=int)
self.feat.add_angles(sel, deg=True)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.transform(self.traj)
assert (np.alltrue(Y >= -180.0))
assert (np.alltrue(Y <= 180.0))
def test_angles_cossin(self):
sel = np.array([[1, 2, 5], [1, 3, 8], [2, 9, 10]], dtype=int)
self.feat.add_angles(sel, cossin=True)
assert (self.feat.dimension() == 2 * sel.shape[0])
Y = self.feat.transform(self.traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_dihedrals(self):
sel = np.array([[1, 2, 5, 6], [1, 3, 8, 9], [2, 9, 10, 12]], dtype=int)
self.feat.add_dihedrals(sel)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.transform(self.traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
self.assertEqual(len(self.feat.describe()), self.feat.dimension())
def test_dihedrals_deg(self):
sel = np.array([[1, 2, 5, 6], [1, 3, 8, 9], [2, 9, 10, 12]], dtype=int)
self.feat.add_dihedrals(sel, deg=True)
assert (self.feat.dimension() == sel.shape[0])
Y = self.feat.transform(self.traj)
assert (np.alltrue(Y >= -180.0))
assert (np.alltrue(Y <= 180.0))
self.assertEqual(len(self.feat.describe()), self.feat.dimension())
def test_dihedrials_cossin(self):
sel = np.array([[1, 2, 5, 6], [1, 3, 8, 9], [2, 9, 10, 12]], dtype=int)
self.feat.add_dihedrals(sel, cossin=True)
assert (self.feat.dimension() == 2 * sel.shape[0])
Y = self.feat.transform(self.traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_backbone_dihedrals(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_backbone_torsions()
traj = mdtraj.load(self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_backbone_dihedrals_deg(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_backbone_torsions(deg=True)
traj = mdtraj.load(self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
assert (np.alltrue(Y >= -180.0))
assert (np.alltrue(Y <= 180.0))
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_backbone_dihedrals_cossin(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_backbone_torsions(cossin=True)
traj = mdtraj.load(self.asn_leu_traj, top=self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
self.assertEqual(Y.shape,
(len(traj), 3 * 4)) # (3 phi + 3 psi)*2 [cos, sin]
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
assert "COS" in desc[0]
assert "SIN" in desc[1]
self.assertEqual(len(desc), self.feat.dimension())
def test_backbone_dihedrials_chi(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_chi1_torsions()
traj = mdtraj.load(self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
self.assertEqual(len(desc), self.feat.dimension())
def test_backbone_dihedrials_chi_cossin(self):
self.feat = MDFeaturizer(topfile=self.asn_leu_pdbfile)
self.feat.add_chi1_torsions(cossin=True)
traj = mdtraj.load(self.asn_leu_pdbfile)
Y = self.feat.transform(traj)
assert (np.alltrue(Y >= -np.pi))
assert (np.alltrue(Y <= np.pi))
desc = self.feat.describe()
assert "COS" in desc[0]
assert "SIN" in desc[1]
self.assertEqual(len(desc), self.feat.dimension())
def test_custom_feature(self):
# TODO: test me
pass
def test_MinRmsd(self):
# Test the Trajectory-input variant
self.feat.add_minrmsd_to_ref(self.traj[self.ref_frame])
# and the file-input variant
self.feat.add_minrmsd_to_ref(xtcfile, ref_frame=self.ref_frame)
test_Y = self.feat.transform(self.traj).squeeze()
# now the reference
ref_Y = mdtraj.rmsd(self.traj, self.traj[self.ref_frame])
verbose_assertion_minrmsd(ref_Y, test_Y, self)
assert self.feat.dimension() == 2
assert len(self.feat.describe()) == 2
def test_MinRmsd_with_atom_indices(self):
# Test the Trajectory-input variant
self.feat.add_minrmsd_to_ref(self.traj[self.ref_frame],
atom_indices=self.atom_indices)
# and the file-input variant
self.feat.add_minrmsd_to_ref(xtcfile,
ref_frame=self.ref_frame,
atom_indices=self.atom_indices)
test_Y = self.feat.transform(self.traj).squeeze()
# now the reference
ref_Y = mdtraj.rmsd(self.traj,
self.traj[self.ref_frame],
atom_indices=self.atom_indices)
verbose_assertion_minrmsd(ref_Y, test_Y, self)
assert self.feat.dimension() == 2
assert len(self.feat.describe()) == 2
def test_MinRmsd_with_atom_indices_precentered(self):
# Test the Trajectory-input variant
self.feat.add_minrmsd_to_ref(self.traj[self.ref_frame],
atom_indices=self.atom_indices,
precentered=True)
# and the file-input variant
self.feat.add_minrmsd_to_ref(xtcfile,
ref_frame=self.ref_frame,
atom_indices=self.atom_indices,
precentered=True)
test_Y = self.feat.transform(self.traj).squeeze()
# now the reference
ref_Y = mdtraj.rmsd(self.traj,
self.traj[self.ref_frame],
atom_indices=self.atom_indices,
precentered=True)
verbose_assertion_minrmsd(ref_Y, test_Y, self)
assert self.feat.dimension() == 2
assert len(self.feat.describe()) == 2
def test_Residue_Mindist_Ca_all(self):
n_ca = self.feat.topology.n_atoms
self.feat.add_residue_mindist(scheme='ca')
D = self.feat.transform(self.traj)
Dref = mdtraj.compute_contacts(self.traj, scheme='ca')[0]
assert np.allclose(D, Dref)
assert len(self.feat.describe()) == self.feat.dimension()
def test_Residue_Mindist_Ca_all_threshold(self):
threshold = .7
self.feat.add_residue_mindist(scheme='ca', threshold=threshold)
D = self.feat.transform(self.traj)
Dref = mdtraj.compute_contacts(self.traj, scheme='ca')[0]
Dbinary = np.zeros_like(Dref)
I = np.argwhere(Dref <= threshold)
Dbinary[I[:, 0], I[:, 1]] = 1
assert np.allclose(D, Dbinary)
assert len(self.feat.describe()) == self.feat.dimension()
def test_Residue_Mindist_Ca_array(self):
contacts = np.array([[
20,
10,
], [10, 0]])
self.feat.add_residue_mindist(scheme='ca', residue_pairs=contacts)
D = self.feat.transform(self.traj)
Dref = mdtraj.compute_contacts(self.traj,
scheme='ca',
contacts=contacts)[0]
assert np.allclose(D, Dref)
assert len(self.feat.describe()) == self.feat.dimension()
def test_Group_Mindist_One_Group(self):
group0 = [0, 20, 30, 0]
self.feat.add_group_mindist(
group_definitions=[group0]) # Even with duplicates
D = self.feat.transform(self.traj)
dist_list = list(combinations(np.unique(group0), 2))
Dref = mdtraj.compute_distances(self.traj, dist_list)
assert np.allclose(D.squeeze(), Dref.min(1))
assert len(self.feat.describe()) == self.feat.dimension()
def test_Group_Mindist_All_Three_Groups(self):
group0 = [0, 20, 30, 0]
group1 = [1, 21, 31, 1]
group2 = [2, 22, 32, 2]
self.feat.add_group_mindist(group_definitions=[group0, group1, group2])
D = self.feat.transform(self.traj)
# Now the references, computed separately for each combination of groups
dist_list_01 = np.array(
list(product(np.unique(group0), np.unique(group1))))
dist_list_02 = np.array(
list(product(np.unique(group0), np.unique(group2))))
dist_list_12 = np.array(
list(product(np.unique(group1), np.unique(group2))))
Dref_01 = mdtraj.compute_distances(self.traj, dist_list_01).min(1)
Dref_02 = mdtraj.compute_distances(self.traj, dist_list_02).min(1)
Dref_12 = mdtraj.compute_distances(self.traj, dist_list_12).min(1)
Dref = np.vstack((Dref_01, Dref_02, Dref_12)).T
assert np.allclose(D.squeeze(), Dref)
assert len(self.feat.describe()) == self.feat.dimension()
def test_Group_Mindist_All_Three_Groups_threshold(self):
threshold = .7
group0 = [0, 20, 30, 0]
group1 = [1, 21, 31, 1]
group2 = [2, 22, 32, 2]
self.feat.add_group_mindist(group_definitions=[group0, group1, group2],
threshold=threshold)
D = self.feat.transform(self.traj)
# Now the references, computed separately for each combination of groups
dist_list_01 = np.array(
list(product(np.unique(group0), np.unique(group1))))
dist_list_02 = np.array(
list(product(np.unique(group0), np.unique(group2))))
dist_list_12 = np.array(
list(product(np.unique(group1), np.unique(group2))))
Dref_01 = mdtraj.compute_distances(self.traj, dist_list_01).min(1)
Dref_02 = mdtraj.compute_distances(self.traj, dist_list_02).min(1)
Dref_12 = mdtraj.compute_distances(self.traj, dist_list_12).min(1)
Dref = np.vstack((Dref_01, Dref_02, Dref_12)).T
Dbinary = np.zeros_like(Dref)
I = np.argwhere(Dref <= threshold)
Dbinary[I[:, 0], I[:, 1]] = 1
assert np.allclose(D, Dbinary)
assert len(self.feat.describe()) == self.feat.dimension()
def test_Group_Mindist_Some_Three_Groups(self):
group0 = [0, 20, 30, 0]
group1 = [1, 21, 31, 1]
group2 = [2, 22, 32, 2]
group_pairs = np.array([[0, 1], [2, 2], [0, 2]])
self.feat.add_group_mindist(group_definitions=[group0, group1, group2],
group_pairs=group_pairs)
D = self.feat.transform(self.traj)
# Now the references, computed separately for each combination of groups
dist_list_01 = np.array(
list(product(np.unique(group0), np.unique(group1))))
dist_list_02 = np.array(
list(product(np.unique(group0), np.unique(group2))))
dist_list_22 = np.array(list(combinations(np.unique(group2), 2)))
Dref_01 = mdtraj.compute_distances(self.traj, dist_list_01).min(1)
Dref_02 = mdtraj.compute_distances(self.traj, dist_list_02).min(1)
Dref_22 = mdtraj.compute_distances(self.traj, dist_list_22).min(1)
Dref = np.vstack((Dref_01, Dref_22, Dref_02)).T
assert np.allclose(D.squeeze(), Dref)
assert len(self.feat.describe()) == self.feat.dimension()
def setUp(self):
self.feat = MDFeaturizer(pdbfile)
def test_labels(self):
""" just checks for exceptions """
featurizer = MDFeaturizer(pdbfile)
featurizer.add_angles([[1, 2, 3], [4, 5, 6]])
featurizer.add_backbone_torsions()
featurizer.add_contacts([[0, 1], [0, 3]])
featurizer.add_distances([[0, 1], [0, 3]])
featurizer.add_inverse_distances([[0, 1], [0, 3]])
cs = CustomFeature(lambda x: x - 1, dim=3)
featurizer.add_custom_feature(cs)
featurizer.add_minrmsd_to_ref(pdbfile)
featurizer.add_residue_mindist()
featurizer.add_group_mindist([[0, 1], [0, 2]])
featurizer.describe()
def testAddFeaturesWithDuplicates(self):
"""this tests adds multiple features twice (eg. same indices) and
checks whether they are rejected or not"""
featurizer = MDFeaturizer(pdbfile)
expected_active = 1
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
featurizer.add_angles([[0, 1, 2], [0, 3, 4]])
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_contacts([[0, 1], [0, 3]])
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_contacts([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), expected_active)
# try to fool it with ca selection
ca = featurizer.select_Ca()
ca = featurizer.pairs(ca, excluded_neighbors=0)
featurizer.add_distances(ca)
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_distances_ca(excluded_neighbors=0)
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_inverse_distances([[0, 1], [0, 3]])
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_distances([[0, 1], [0, 3]])
expected_active += 1
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_distances([[0, 1], [0, 3]])
self.assertEqual(len(featurizer.active_features), expected_active)
def my_func(x):
return x - 1
def foo(x):
return x - 1
expected_active += 1
my_feature = CustomFeature(my_func)
my_feature.dimension = 3
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), expected_active)
featurizer.add_custom_feature(my_feature)
self.assertEqual(len(featurizer.active_features), expected_active)
# since myfunc and foo are different functions, it should be added
expected_active += 1
foo_feat = CustomFeature(foo, dim=3)
featurizer.add_custom_feature(foo_feat)
self.assertEqual(len(featurizer.active_features), expected_active)
expected_active += 1
ref = mdtraj.load(xtcfile, top=pdbfile)
featurizer.add_minrmsd_to_ref(ref)
featurizer.add_minrmsd_to_ref(ref)
self.assertEquals(len(featurizer.active_features), expected_active)
expected_active += 1
featurizer.add_minrmsd_to_ref(pdbfile)
featurizer.add_minrmsd_to_ref(pdbfile)
self.assertEquals(len(featurizer.active_features), expected_active)
expected_active += 1
featurizer.add_residue_mindist()
featurizer.add_residue_mindist()
self.assertEquals(len(featurizer.active_features), expected_active)
expected_active += 1
featurizer.add_group_mindist([[0, 1], [0, 2]])
featurizer.add_group_mindist([[0, 1], [0, 2]])
self.assertEquals(len(featurizer.active_features), expected_active)
def setUp(self):
self.pdbfile = pdbfile
self.traj = mdtraj.load(xtcfile, top=self.pdbfile)
self.feat = MDFeaturizer(self.pdbfile)
def test_ca_distances_with_all_atom_geometries_and_exclusions(self):
feat = MDFeaturizer(pdbfile_ops_aa)
feat.add_distances_ca(excluded_neighbors=2)
D_aa = feat.transform(mdtraj.load(pdbfile_ops_aa))
# Create a reference
feat_just_ca = MDFeaturizer(pdbfile_ops_Ca)
ca_pairs = feat.pairs(feat_just_ca.select_Ca(), excluded_neighbors=2)
feat_just_ca.add_distances(ca_pairs)
D_ca = feat_just_ca.transform(mdtraj.load(pdbfile_ops_Ca))
assert (np.allclose(D_aa, D_ca))
def test_labels(self):
""" just checks for exceptions """
featurizer = MDFeaturizer(pdbfile)
featurizer.add_angles([[1, 2, 3], [4, 5, 6]])
featurizer.add_backbone_torsions()
featurizer.add_contacts([[0, 1], [0, 3]])
featurizer.add_distances([[0, 1], [0, 3]])
featurizer.add_inverse_distances([[0, 1], [0, 3]])
cs = CustomFeature(lambda x: x - 1)
cs.dimension = lambda: 3
featurizer.add_custom_feature(cs)
featurizer.describe()
class FeatureReader(ReaderInterface):
"""
Reads features from MD data.
To select a feature, access the :attr:`featurizer` and call a feature
selecting method (e.g) distances.
Parameters
----------
trajectories: list of strings
paths to trajectory files
topologyfile: string
path to topology file (e.g. pdb)
Examples
--------
Iterator access:
>>> reader = FeatureReader('mytraj.xtc', 'my_structure.pdb')
>>> chunks = []
>>> for itraj, X in reader:
>>> chunks.append(X)
Extract backbone torsion angles of protein during feature reading:
>>> reader = FeatureReader('mytraj.xtc', 'my_structure.pdb')
>>> reader.featurizer.add_backbone_torsions()
>>> X = reader.get_output()
"""
def __init__(self, trajectories, topologyfile=None, chunksize=100, featurizer=None):
assert (topologyfile is not None) or (featurizer is not None), \
"Needs either a topology file or a featurizer for instantiation"
# init with chunksize 100
super(FeatureReader, self).__init__(chunksize=chunksize)
self.data_producer = self
# files
if isinstance(trajectories, basestring):
trajectories = [trajectories]
self.trajfiles = trajectories
self.topfile = topologyfile
# featurizer
if topologyfile and featurizer:
self._logger.warning("Both a topology file and a featurizer were given as arguments. "
"Only featurizer gets respected in this case.")
if not featurizer:
self.featurizer = MDFeaturizer(topologyfile)
else:
self.featurizer = featurizer
self.topfile = featurizer.topologyfile
# iteration
self._mditer = None
# current lag time
self._curr_lag = 0
# time lagged iterator
self._mditer2 = None
# cache size
self.in_memory = False
self._Y = None
self.__set_dimensions_and_lenghts()
self._parametrized = True
# @classmethod
# def init_from_featurizer(cls, trajectories, featurizer):
# if not isinstance(featurizer, MDFeaturizer):
# raise ValueError("given featurizer is not of type Featurizer, but is %s"
# % type(featurizer))
# cls.featurizer = featurizer
# return cls(trajectories, featurizer.topologyfile)
def __set_dimensions_and_lenghts(self):
self._ntraj = len(self.trajfiles)
# basic statistics
for traj in self.trajfiles:
sum_frames = sum(t.n_frames for t in self._create_iter(traj))
self._lengths.append(sum_frames)
# number of trajectories/data sets
if self._ntraj == 0:
raise ValueError("no valid data")
# note: dimension is a custom impl in this class
def describe(self):
"""
Returns a description of this transformer
:return:
"""
return ["Feature reader with following features"] + self.featurizer.describe()
def parametrize(self, stride=1):
"""
Parametrizes this transformer
:return:
"""
if self.in_memory:
self._map_to_memory(stride=stride)
def dimension(self):
"""
Returns the number of output dimensions
:return:
"""
if len(self.featurizer.active_features) == 0:
# special case: cartesion coordinates
return self.featurizer.topology.n_atoms * 3
else:
# general case
return self.featurizer.dimension()
def _get_memory_per_frame(self):
"""
Returns the memory requirements per frame, in bytes
:return:
"""
return 4 * self.dimension()
def _get_constant_memory(self):
"""
Returns the constant memory requirements, in bytes
:return:
"""
return 0
def _map_to_memory(self, stride=1):
# TODO: stride is currently not implemented
if stride > 1:
raise NotImplementedError('stride option for FeatureReader._map_to_memory is currently not implemented')
self._reset()
# iterate over trajectories
last_chunk = False
itraj = 0
while not last_chunk:
last_chunk_in_traj = False
t = 0
while not last_chunk_in_traj:
y = self._next_chunk()
assert y is not None
L = np.shape(y)[0]
# last chunk in traj?
last_chunk_in_traj = (t + L >= self.trajectory_length(itraj))
# last chunk?
last_chunk = (
last_chunk_in_traj and itraj >= self.number_of_trajectories() - 1)
# write
self._Y[itraj][t:t + L] = y
# increment time
t += L
# increment trajectory
itraj += 1
def _create_iter(self, filename, skip=0, stride=1):
return patches.iterload(filename, chunk=self.chunksize,
top=self.topfile, skip=skip, stride=stride)
def _reset(self, stride=1):
"""
resets the chunk reader
"""
self._itraj = 0
self._curr_lag = 0
if len(self.trajfiles) >= 1:
self._t = 0
self._mditer = self._create_iter(self.trajfiles[0], stride=stride)
def _next_chunk(self, lag=0, stride=1):
"""
gets the next chunk. If lag > 0, we open another iterator with same chunk
size and advance it by one, as soon as this method is called with a lag > 0.
:return: a feature mapped vector X, or (X, Y) if lag > 0
"""
chunk = self._mditer.next()
shape = chunk.xyz.shape
if lag > 0:
if self._curr_lag == 0:
# lag time or trajectory index changed, so open lagged iterator
if __debug__:
self._logger.debug("open time lagged iterator for traj %i with lag %i"
% (self._itraj, self._curr_lag))
self._curr_lag = lag
self._mditer2 = self._create_iter(self.trajfiles[self._itraj],
skip=self._curr_lag*stride, stride=stride)
try:
adv_chunk = self._mditer2.next()
except StopIteration:
# When _mditer2 ran over the trajectory end, return empty chunks.
adv_chunk = mdtraj.Trajectory(np.empty((0, shape[1], shape[2]), np.float32), chunk.topology)
self._t += shape[0]
if (self._t >= self.trajectory_length(self._itraj, stride=stride) and
self._itraj < len(self.trajfiles) - 1):
if __debug__:
self._logger.debug('closing current trajectory "%s"'
% self.trajfiles[self._itraj])
self._mditer.close()
if self._curr_lag != 0:
self._mditer2.close()
self._t = 0
self._itraj += 1
self._mditer = self._create_iter(self.trajfiles[self._itraj], stride=stride)
# we open self._mditer2 only if requested due lag parameter!
self._curr_lag = 0
if (self._t >= self.trajectory_length(self._itraj, stride=stride) and
self._itraj == len(self.trajfiles) - 1):
if __debug__:
self._logger.debug('closing last trajectory "%s"'
% self.trajfiles[self._itraj])
self._mditer.close()
if self._curr_lag != 0:
self._mditer2.close()
# map data
if lag == 0:
if len(self.featurizer.active_features) == 0:
shape_2d = (shape[0], shape[1] * shape[2])
return chunk.xyz.reshape(shape_2d)
else:
return self.featurizer.map(chunk)
else:
if len(self.featurizer.active_features) == 0:
shape_Y = adv_chunk.xyz.shape
X = chunk.xyz.reshape((shape[0], shape[1] * shape[2]))
Y = adv_chunk.xyz.reshape((shape_Y[0], shape_Y[1] * shape_Y[2]))
else:
X = self.featurizer.map(chunk)
Y = self.featurizer.map(adv_chunk)
return X, Y