def extendModel(model, nodes, atoms, norm=False):
"""Extend a coarse grained *model* built for *nodes* to *atoms*. *model*
may be :class:`.ANM`, :class:`.GNM`, :class:`.PCA`, or :class:`.NMA`
instance. This function will take part of the normal modes for each node
(i.e. Cα atoms) and extend it to all other atoms in the same residue. For
each atom in *nodes* argument *atoms* argument must contain a corresponding
residue. If *norm* is **True**, extended modes are normalized."""
try:
evecs = model._getArray()
evals = model.getEigvals()
except AttributeError:
raise ValueError('model must be an NMA instance')
if model.numAtoms() != nodes.numAtoms():
raise ValueError('atom numbers must be the same')
indices, atommap = extendAtoms(nodes, atoms, model.is3d())
evecs = evecs[indices, :]
if norm:
evecs /= np.array([((evecs[:, i])**2).sum()**0.5
for i in range(evecs.shape[1])])
if model.is3d():
extended = NMA('Extended ' + str(model))
else:
extended = GNM('Extended ' + str(model))
extended.setEigens(evecs, evals)
return extended, atommap
def extendModel(model, nodes, atoms, norm=False):
"""Extend a coarse grained *model* built for *nodes* to *atoms*. *model*
may be :class:`.ANM`, :class:`.GNM`, :class:`.PCA`, or :class:`.NMA`
instance. This function will take part of the normal modes for each node
(i.e. Cα atoms) and extend it to all other atoms in the same residue. For
each atom in *nodes* argument *atoms* argument must contain a corresponding
residue. If *norm* is **True**, extended modes are normalized."""
try:
evecs = model._getArray()
evals = model.getEigvals()
except AttributeError:
raise ValueError('model must be an NMA instance')
if model.numAtoms() != nodes.numAtoms():
raise ValueError('atom numbers must be the same')
indices, atommap = extendAtoms(nodes, atoms, model.is3d())
evecs = evecs[indices, :]
if norm:
evecs /= np.array([((evecs[:, i]) ** 2).sum() ** 0.5
for i in range(evecs.shape[1])])
if model.is3d():
extended = NMA('Extended ' + str(model))
else:
extended = GNM('Extended ' + str(model))
extended.setEigens(evecs, evals)
return extended, atommap
def extendVector(vector, nodes, atoms):
"""Extend a coarse grained *vector* for *nodes* to *atoms*. This function
will take part of the normal modes for each node (i.e. Cα atoms) and extend
it to all other atoms in the same residue. For each atom in *nodes*,
*atoms* argument must contain a corresponding residue."""
try:
vec = vector._getArray()
except AttributeError:
raise ValueError('vector must be a Vector instance')
if vector.numAtoms() != nodes.numAtoms():
raise ValueError('atom numbers must be the same')
indices, atommap = extendAtoms(nodes, atoms, vector.is3d())
extended = Vector(vec[indices], 'Extended ' + str(vector), vector.is3d())
return extended, atommap
def extendVector(vector, nodes, atoms):
"""Extend a coarse grained *vector* for *nodes* to *atoms*. This function
will take part of the normal modes for each node (i.e. Cα atoms) and extend
it to all other atoms in the same residue. For each atom in *nodes*,
*atoms* argument must contain a corresponding residue."""
try:
vec = vector._getArray()
except AttributeError:
raise ValueError('vector must be a Vector instance')
if vector.numAtoms() != nodes.numAtoms():
raise ValueError('atom numbers must be the same')
indices, atommap = extendAtoms(nodes, atoms, vector.is3d())
extended = Vector(vec[indices], 'Extended ' + str(vector), vector.is3d())
return extended, atommap
def extendMode(mode, nodes, atoms, norm=False):
"""Extend a coarse grained normal *mode* built for *nodes* to *atoms*.
This function will take part of the normal modes for each node (i.e. Cα
atoms) and extend it to all other atoms in the same residue. For each atom
in *nodes* argument *atoms* argument must contain a corresponding residue.
Extended mode is multiplied by the square root of variance of the mode.
If *norm* is **True**, extended mode is normalized."""
try:
vec = mode._getArray()
std = mode.getVariance()**0.5
except AttributeError:
raise ValueError('mode must be a normal Mode instance')
indices, atommap = extendAtoms(nodes, atoms, mode.is3d())
vec = vec[indices]
if norm:
vec /= ((vec)**2).sum()**0.5
else:
vec *= std
extended = Vector(vec, 'Extended ' + str(mode), mode.is3d())
return extended, atommap
def extendMode(mode, nodes, atoms, norm=False):
"""Extend a coarse grained normal *mode* built for *nodes* to *atoms*.
This function will take part of the normal modes for each node (i.e. Cα
atoms) and extend it to all other atoms in the same residue. For each atom
in *nodes* argument *atoms* argument must contain a corresponding residue.
Extended mode is multiplied by the square root of variance of the mode.
If *norm* is **True**, extended mode is normalized."""
try:
vec = mode._getArray()
std = mode.getVariance() ** 0.5
except AttributeError:
raise ValueError('mode must be a normal Mode instance')
indices, atommap = extendAtoms(nodes, atoms, mode.is3d())
vec = vec[indices]
if norm:
vec /= ((vec) ** 2).sum() ** 0.5
else:
vec *= std
extended = Vector(vec, 'Extended ' + str(mode), mode.is3d())
return extended, atommap
