def setWeights(self, weights):
"""Set atomic weights."""
if self._n_atoms == 0:
raise AttributeError('first set reference coordinates')
try:
self._weights = checkWeights(weights, self._n_atoms, None)
except ValueError:
weights = checkWeights(weights, self.numSelected(), None)
if not self._weights:
self._weights = ones((self._n_atoms, 1), dtype=float)
self._weights[self._indices, :] = weights
def setWeights(self, weights):
"""Set atomic weights."""
if self._n_atoms == 0:
raise AttributeError('coordinates are not set')
try:
self._weights = checkWeights(weights, self._n_atoms, self._n_csets)
except ValueError:
weights = checkWeights(weights, self.numSelected(), self._n_csets)
if not self._weights:
self._weights = np.ones((self._n_csets, self._n_atoms, 1),
dtype=float)
self._weights[self._indices, :] = weights
def calcRMSD(reference, target=None, weights=None):
"""Returns root-mean-square deviation (RMSD) between reference and target
coordinates.
.. ipython:: python
ens = loadEnsemble('p38_X-ray.ens.npz')
ens.getRMSDs()
calcRMSD(ens)
calcRMSD(ens.getCoords(), ens.getCoordsets(), ens.getWeights())"""
if isinstance(reference, np.ndarray):
ref = reference
else:
try:
ref = reference._getCoords()
except AttributeError:
raise TypeError('reference must be a numpy array or an object '
'with getCoords method')
if target is None:
try:
target = reference._getCoordsets()
except AttributeError:
pass
if weights is None:
try:
weights = reference._getWeights()
except AttributeError:
pass
if ref.ndim != 2 or ref.shape[1] != 3:
raise ValueError('reference must have shape (n_atoms, 3)')
if isinstance(target, np.ndarray):
tar = target
else:
try:
tar = target._getCoords()
except AttributeError:
raise TypeError('target must be a numpy array or an object '
'with getCoords method')
if tar.ndim not in (2, 3) or tar.shape[-1] != 3:
raise ValueError('target must have shape ([n_confs,] n_atoms, 3)')
if ref.shape != tar.shape[-2:]:
raise ValueError('reference and target arrays must have the same '
'number of atoms')
if weights is not None:
n_atoms = len(ref)
n_csets = 1 if tar.ndim == 2 else len(tar)
weights = checkWeights(weights, n_atoms, n_csets)
return getRMSD(ref, tar, weights)
def calcTransformation(mobile, target, weights=None):
"""Returns a :class:`Transformation` instance which, when applied to the
atoms in *mobile*, minimizes the weighted RMSD between *mobile* and
*target*. *mobile* and *target* may be NumPy coordinate arrays, or
:class:`.Atomic` instances, e.g. :class:`.AtomGroup`, :class:`.Chain`,
or :class:`.Selection`."""
if not isinstance(mobile, np.ndarray):
try:
mob = mobile._getCoords()
except AttributeError:
raise TypeError('mobile must be a numpy array or an object '
'with getCoords method')
else:
mob = mobile
if not isinstance(target, np.ndarray):
try:
tar = target._getCoords()
except AttributeError:
raise TypeError('target must be a numpy array or an object '
'with getCoords method')
else:
tar = target
if mob.shape != tar.shape:
raise ValueError('reference and target coordinate arrays '
'must have same number of atoms')
if mob.shape[1] != 3:
raise ValueError('reference and target must be coordinate arrays')
if weights is None:
if isinstance(mobile, AtomMap):
LOGGER.warn(
'mobile is an AtomMap instance, consider assign weights=mobile.getFlags("mapped") '
'if there are dummy atoms in mobile')
if isinstance(target, AtomMap):
LOGGER.warn(
'target is an AtomMap instance, consider assign weights=target.getFlags("mapped") '
'if there are dummy atoms in target')
if weights is not None:
weights = checkWeights(weights, mob.shape[0])
return Transformation(*getTransformation(mob, tar, weights))
def addCoordset(self, coords, weights=None, label=None, **kwargs):
"""Add coordinate set(s) to the ensemble. *coords* must be a Numpy
array with suitable shape and dimensionality, or an object with
:meth:`getCoordsets`. *weights* is an optional argument.
If provided, its length must match number of atoms. Weights of
missing (not resolved) atoms must be ``0`` and weights of those
that are resolved can be anything greater than ``0``. If not
provided, weights of all atoms for this coordinate set will be
set equal to ``1``. *label*, which may be a PDB identifier or a
list of identifiers, is used to label conformations."""
degeneracy = kwargs.pop('degeneracy', False)
atoms = coords
n_atoms = self._n_atoms
n_select = self.numSelected()
n_confs = self.numCoordsets()
try:
if degeneracy:
if self._coords is not None:
if isinstance(coords, Ensemble):
coords = coords._getCoords(selected=False)
elif hasattr(coords, '_getCoords'):
coords = coords._getCoords()
else:
if isinstance(coords, Ensemble):
coords = coords.getCoords(selected=False)
elif hasattr(coords, 'getCoords'):
coords = coords.getCoords()
else:
if self._coords is not None:
if isinstance(coords, Ensemble):
coords = coords._getCoordsets(selected=False)
elif hasattr(coords, '_getCoordsets'):
coords = coords._getCoordsets()
else:
if isinstance(coords, Ensemble):
coords = coords.getCoordsets(selected=False)
elif hasattr(coords, 'getCoordsets'):
coords = coords.getCoordsets()
except AttributeError:
label = label or 'Unknown'
else:
if coords is None:
raise ValueError('coordinates are not set')
elif label is None and isinstance(atoms, Atomic):
if not isinstance(atoms, AtomGroup):
ag = atoms.getAtomGroup()
else:
ag = atoms
label = ag.getTitle()
if coords.shape[0] < ag.numCoordsets():
label += '_m' + str(atoms.getACSIndex())
else:
label = label or 'Unknown'
# check coordinates
try:
checkCoords(coords, csets=True, natoms=n_atoms)
except:
try:
checkCoords(coords, csets=True, natoms=n_select)
except TypeError:
raise TypeError('coords must be a numpy array or an object '
'with `getCoords` method')
if coords.ndim == 2:
n_nodes, _ = coords.shape
coords = coords.reshape((1, n_nodes, 3))
n_csets = 1
else:
n_csets, n_nodes, _ = coords.shape
if degeneracy:
coords = coords[:1]
n_repeats = 1 if degeneracy else n_csets
if not n_atoms:
self._n_atoms = n_nodes
if n_nodes == n_select and self.isSelected():
full_coords = np.repeat(self._coords[np.newaxis, :, :],
n_csets,
axis=0)
full_coords[:, self._indices, :] = coords
coords = full_coords
# check weights
if weights is None:
weights = np.ones((n_csets, n_atoms, 1), dtype=float)
else:
weights = checkWeights(weights, n_atoms, n_csets)
if degeneracy:
weights = weights[:1]
# assign new values
# update labels
if n_csets > 1 and not degeneracy:
if isinstance(label, str):
labels = [
'{0}_m{1}'.format(label, i + 1) for i in range(n_csets)
]
else:
if len(label) != n_csets:
raise ValueError('length of label and number of '
'coordinate sets must be the same')
labels = label
else:
labels = [label] if np.isscalar(label) else label
self._labels.extend(labels)
# update coordinates
if self._confs is None and self._weights is None:
self._confs = coords
self._weights = weights
self._n_csets = n_repeats
elif self._confs is not None and self._weights is not None:
self._confs = np.concatenate((self._confs, coords), axis=0)
self._weights = np.concatenate((self._weights, weights), axis=0)
self._n_csets += n_repeats
else:
raise RuntimeError('_confs and _weights must be set or None at '
'the same time')
def setWeights(self, weights):
"""Set atomic weights."""
if self._n_atoms == 0:
raise AttributeError('coordinates must be set first')
self._weights = checkWeights(weights, self._n_atoms, None)