def sliceVector(vector, atoms, selstr):
"""Return a slice of *vector* matching *atoms* specified by *selstr*.
Note that returned :class:`Vector` instance is not normalized.
:arg vector: vector instance to be sliced
:type vector: :class:`VectorBase`
:arg atoms: atoms for which *vector* describes a deformation, motion, etc.
:type atoms: :class:`~prody.atomic.Atomic`
:arg selstr: selection string
:type selstr: str
:returns: (:class:`Vector`, :class:`~prody.atomic.Selection`)"""
if not isinstance(vector, VectorBase):
raise TypeError("vector must be a VectorBase instance, not {0:s}".format(type(vector)))
if not isinstance(atoms, Atomic):
raise TypeError("atoms must be an Atomic instance, not {0:s}".format(type(atoms)))
if atoms.numAtoms() != vector.numAtoms():
raise ValueError("number of atoms in *vector* and *atoms* must be " "equal")
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel.getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which], selstr, atoms.getACSIndex())
vec = Vector(
vector.getArrayNx3()[which, :].flatten(), '{0:s} slice "{1:s}"'.format(str(vector), selstr), vector.is3d()
)
return (vec, sel)
def sliceVector(vector, atoms, select):
"""Return part of the *vector* for *atoms* matching *select*. Note that
returned :class:`.Vector` instance is not normalized.
:arg vector: vector instance to be sliced
:type vector: :class:`.VectorBase`
:arg atoms: atoms for which *vector* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.Vector`, :class:`.Selection`)"""
if not isinstance(vector, VectorBase):
raise TypeError('vector must be a VectorBase instance, not {0:s}'
.format(type(vector)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0:s}'
.format(type(atoms)))
if atoms.numAtoms() != vector.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
if isinstance(select, str):
selstr = select
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel._getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which],
selstr, atoms.getACSIndex())
elif isinstance(select, AtomSubset):
sel = select
if isinstance(atoms, AtomGroup):
if sel.getAtomGroup() != atoms:
raise ValueError('select and atoms do not match')
which = sel._getIndices()
else:
if atoms.getAtomGroup() != sel.getAtomGroup():
raise ValueError('select and atoms do not match')
elif not sel in atoms:
raise ValueError('select is not a subset of atoms')
idxset = set(atoms._getIndices())
which = np.array([idx in idxset for idx in sel._getIndices()])
which = which.nonzero()[0]
selstr = sel.getSelstr()
else:
raise TypeError('select must be a string or a Selection instance')
vec = Vector(vector.getArrayNx3()[
which, :].flatten(),
'{0:s} slice {1:s}'.format(str(vector), repr(selstr)),
vector.is3d())
return (vec, sel)
def sliceVector(vector, atoms, select):
"""Return part of the *vector* for *atoms* matching *select*. Note that
returned :class:`.Vector` instance is not normalized.
:arg vector: vector instance to be sliced
:type vector: :class:`.VectorBase`
:arg atoms: atoms for which *vector* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.Vector`, :class:`.Selection`)"""
if not isinstance(vector, VectorBase):
raise TypeError('vector must be a VectorBase instance, not {0}'
.format(type(vector)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'
.format(type(atoms)))
if atoms.numAtoms() != vector.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
if isinstance(select, str):
selstr = select
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel._getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which],
selstr, atoms.getACSIndex())
elif isinstance(select, AtomSubset):
sel = select
if isinstance(atoms, AtomGroup):
if sel.getAtomGroup() != atoms:
raise ValueError('select and atoms do not match')
which = sel._getIndices()
else:
if atoms.getAtomGroup() != sel.getAtomGroup():
raise ValueError('select and atoms do not match')
elif not sel in atoms:
raise ValueError('select is not a subset of atoms')
idxset = set(atoms._getIndices())
which = np.array([idx in idxset for idx in sel._getIndices()])
which = which.nonzero()[0]
selstr = sel.getSelstr()
else:
raise TypeError('select must be a string or a Selection instance')
vec = Vector(vector.getArrayNx3()[
which, :].flatten(),
'{0} slice {1}'.format(str(vector), repr(selstr)),
vector.is3d())
return (vec, sel)
def sliceModel(model, atoms, selstr):
"""Return a slice of *model* matching *atoms* specified by *selstr*.
Note that sliced normal modes (eigenvectors) are not normalized.
:arg mode: NMA model instance to be sliced
:type mode: :class:`NMA`
:arg atoms: atoms for which the *model* was built
:type atoms: :class:`~prody.atomic.Atomic`
:arg selstr: selection string
:type selstr: str
:returns: (:class:`NMA`, :class:`~prody.atomic.Selection`)"""
if not isinstance(model, NMA):
raise TypeError("mode must be a NMA instance, not {0:s}".format(type(model)))
if not isinstance(atoms, Atomic):
raise TypeError("atoms must be an Atomic instance, not {0:s}".format(type(atoms)))
if atoms.numAtoms() != model.numAtoms():
raise ValueError("number of atoms in *model* and *atoms* must be " "equal")
array = model._getArray()
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel.getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which], selstr, atoms.getACSIndex())
nma = type(model)('{0:s} slice "{1:s}"'.format(model.getTitle(), selstr))
if model.is3d():
which = [which.reshape((len(which), 1)) * 3]
which.append(which[0] + 1)
which.append(which[0] + 2)
which = np.concatenate(which, 1).flatten()
nma.setEigens(array[which, :], model.getEigenvalues())
return (nma, sel)
def sliceMode(mode, atoms, selstr):
"""Return a slice of *mode* matching *atoms* specified by *selstr*.
This works slightly difference from :func:`sliceVector`. Mode array
(eigenvector) is multiplied by square-root of the variance along the mode.
If mode is from an elastic network model, variance is defined as the
inverse of the eigenvalue.
Note that returned :class:`Vector` instance is not normalized.
:arg mode: mode instance to be sliced
:type mode: :class:`Mode`
:arg atoms: atoms for which *mode* describes a deformation, motion, etc.
:type atoms: :class:`~prody.atomic.Atomic`
:arg selstr: selection string
:type selstr: str
:returns: (:class:`Vector`, :class:`~prody.atomic.Selection`)"""
if not isinstance(mode, Mode):
raise TypeError("mode must be a Mode instance, not {0:s}".format(type(mode)))
if not isinstance(atoms, Atomic):
raise TypeError("atoms must be an Atomic instance, not {0:s}".format(type(atoms)))
if atoms.numAtoms() != mode.numAtoms():
raise ValueError("number of atoms in *mode* and *atoms* must be equal")
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel.getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which], selstr, atoms.getACSIndex())
vec = Vector(
mode.getArrayNx3()[which, :].flatten() * mode.getVariance() ** 0.5,
'{0:s} slice "{1:s}"'.format(str(mode), selstr),
mode.is3d(),
)
return (vec, sel)
def reduceModel(model, atoms, select):
"""Return reduced NMA model. Reduces a :class:`.NMA` model to a subset of
*atoms* matching *select*. This function behaves differently depending on
the type of the *model* argument. For :class:`.ANM` and :class:`.GNM` or
other :class:`.NMA` models, force constant matrix for system of interest
(specified by the *select*) is derived from the force constant matrix for
the *model* by assuming that for any given displacement of the system of
interest, other atoms move along in such a way as to minimize the potential
energy. This is based on the formulation in [KH00]_. For :class:`.PCA`
models, this function simply takes the sub-covariance matrix for selection.
.. [KH00] Konrad H, Andrei-Jose P, Serge D, Marie-Claire BF, Gerald RK.
Harmonicity in slow protein dynamics. *Chem Phys* **2000** 261:25-37.
:arg model: dynamics model
:type model: :class:`.ANM`, :class:`.GNM`, or :class:`.PCA`
:arg atoms: atoms that were used to build the model
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
linalg = importLA()
if not isinstance(model, NMA):
raise TypeError('model must be an NMA instance, not {0}'
.format(type(model)))
if not isinstance(atoms, (AtomGroup, AtomSubset, AtomMap)):
raise TypeError('atoms type is not valid')
if len(atoms) <= 1:
raise TypeError('atoms must contain more than 1 atoms')
if isinstance(model, GNM):
matrix = model._kirchhoff
elif isinstance(model, ANM):
matrix = model._hessian
elif isinstance(model, PCA):
matrix = model._cov
else:
raise TypeError('model does not have a valid type derived from NMA')
if matrix is None:
raise ValueError('model matrix (Hessian/Kirchhoff/Covariance) is not '
'built')
if isinstance(select, str):
system = SELECT.getBoolArray(atoms, select)
n_sel = sum(system)
if n_sel == 0:
raise ValueError('select matches 0 atoms')
if len(atoms) == n_sel:
raise ValueError('select matches all atoms')
if isinstance(atoms, AtomGroup):
ag = atoms
which = np.arange(len(atoms))[system]
else:
ag = atoms.getAtomGroup()
which = atoms._getIndices()[system]
sel = Selection(ag, which, select, atoms.getACSIndex())
elif isinstance(select, AtomSubset):
sel = select
if isinstance(atoms, AtomGroup):
if sel.getAtomGroup() != atoms:
raise ValueError('select and atoms do not match')
system = np.zeros(len(atoms), bool)
system[sel._getIndices()] = True
else:
if atoms.getAtomGroup() != sel.getAtomGroup():
raise ValueError('select and atoms do not match')
elif not sel in atoms:
raise ValueError('select is not a subset of atoms')
idxset = set(atoms._getIndices())
system = np.array([idx in idxset for idx in sel._getIndices()])
else:
raise TypeError('select must be a string or a Selection instance')
other = np.invert(system)
if model.is3d():
system = np.tile(system, (3, 1)).transpose().flatten()
other = np.tile(other, (3, 1)).transpose().flatten()
ss = matrix[system, :][:, system]
if isinstance(model, PCA):
eda = PCA(model.getTitle() + ' reduced')
eda.setCovariance(ss)
return eda, system
so = matrix[system, :][:, other]
os = matrix[other, :][:, system]
oo = matrix[other, :][:, other]
matrix = ss - np.dot(so, np.dot(linalg.inv(oo), os))
if isinstance(model, GNM):
gnm = GNM(model.getTitle() + ' reduced')
gnm.setKirchhoff(matrix)
return gnm, sel
elif isinstance(model, ANM):
anm = ANM(model.getTitle() + ' reduced')
anm.setHessian(matrix)
return anm, sel
elif isinstance(model, PCA):
eda = PCA(model.getTitle() + ' reduced')
eda.setCovariance(matrix)
return eda, sel
def sliceModel(model, atoms, select):
"""Return a part of the *model* for *atoms* matching *select*. Note that
normal modes (eigenvectors) are not normalized.
:arg mode: NMA model instance to be sliced
:type mode: :class:`.NMA`
:arg atoms: atoms for which the *model* was built
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
if not isinstance(model, NMA):
raise TypeError('mode must be a NMA instance, not {0:s}'
.format(type(model)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0:s}'
.format(type(atoms)))
if atoms.numAtoms() != model.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
array = model._getArray()
if isinstance(select, str):
selstr = select
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel.getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which],
selstr, atoms.getACSIndex())
elif isinstance(select, AtomSubset):
sel = select
if isinstance(atoms, AtomGroup):
if sel.getAtomGroup() != atoms:
raise ValueError('select and atoms do not match')
which = sel._getIndices()
else:
if atoms.getAtomGroup() != sel.getAtomGroup():
raise ValueError('select and atoms do not match')
elif not sel in atoms:
raise ValueError('select is not a subset of atoms')
idxset = set(atoms._getIndices())
which = np.array([idx in idxset for idx in sel._getIndices()])
which = which.nonzero()[0]
selstr = sel.getSelstr()
else:
raise TypeError('select must be a string or a Selection instance')
nma = type(model)('{0:s} slice {1:s}'
.format(model.getTitle(), repr(selstr)))
if model.is3d():
which = [which.reshape((len(which),1))*3]
which.append(which[0]+1)
which.append(which[0]+2)
which = np.concatenate(which, 1).flatten()
nma.setEigens( array[which, :], model.getEigvals() )
return (nma, sel)
def sliceMode(mode, atoms, select):
"""Return part of the *mode* for *atoms* matching *select*. This works
slightly different from :func:`.sliceVector`. Mode array (eigenvector) is
multiplied by square-root of the variance along the mode. If mode is from
an elastic network model, variance is defined as the inverse of the
eigenvalue. Note that returned :class:`~.Vector` instance is not
normalized.
:arg mode: mode instance to be sliced
:type mode: :class:`.Mode`
:arg atoms: atoms for which *mode* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`~.Vector`, :class:`~.Selection`)"""
if not isinstance(mode, Mode):
raise TypeError('mode must be a Mode instance, not {0:s}'
.format(type(mode)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0:s}'
.format(type(atoms)))
if atoms.numAtoms() != mode.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
if isinstance(select, str):
selstr = select
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel._getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which],
selstr, atoms.getACSIndex())
elif isinstance(select, AtomSubset):
sel = select
if isinstance(atoms, AtomGroup):
if sel.getAtomGroup() != atoms:
raise ValueError('select and atoms do not match')
which = sel._getIndices()
else:
if atoms.getAtomGroup() != sel.getAtomGroup():
raise ValueError('select and atoms do not match')
elif not sel in atoms:
raise ValueError('select is not a subset of atoms')
idxset = set(atoms._getIndices())
which = np.array([idx in idxset for idx in sel._getIndices()])
which = which.nonzero()[0]
selstr = sel.getSelstr()
else:
raise TypeError('select must be a string or a Selection instance')
vec = Vector(mode.getArrayNx3()[
which,:].flatten() * mode.getVariance()**0.5,
'{0:s} slice {1:s}'.format(str(mode), repr(selstr)),
mode.is3d())
return (vec, sel)
def sliceModel(model, atoms, select):
"""Return a part of the *model* for *atoms* matching *select*. Note that
normal modes (eigenvectors) are not normalized.
:arg mode: NMA model instance to be sliced
:type mode: :class:`.NMA`
:arg atoms: atoms for which the *model* was built
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.NMA`, :class:`.Selection`)"""
if not isinstance(model, NMA):
raise TypeError('mode must be a NMA instance, not {0}'
.format(type(model)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'
.format(type(atoms)))
if atoms.numAtoms() != model.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
array = model._getArray()
if isinstance(select, str):
selstr = select
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel.getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which],
selstr, atoms.getACSIndex())
elif isinstance(select, AtomSubset):
sel = select
if isinstance(atoms, AtomGroup):
if sel.getAtomGroup() != atoms:
raise ValueError('select and atoms do not match')
which = sel._getIndices()
else:
if atoms.getAtomGroup() != sel.getAtomGroup():
raise ValueError('select and atoms do not match')
elif not sel in atoms:
raise ValueError('select is not a subset of atoms')
idxset = set(atoms._getIndices())
which = np.array([idx in idxset for idx in sel._getIndices()])
which = which.nonzero()[0]
selstr = sel.getSelstr()
else:
raise TypeError('select must be a string or a Selection instance')
nma = type(model)('{0} slice {1}'
.format(model.getTitle(), repr(selstr)))
if model.is3d():
which = [which.reshape((len(which), 1))*3]
which.append(which[0]+1)
which.append(which[0]+2)
which = np.concatenate(which, 1).flatten()
nma.setEigens(array[which, :], model.getEigvals())
return (nma, sel)
def sliceMode(mode, atoms, select):
"""Return part of the *mode* for *atoms* matching *select*. This works
slightly different from :func:`.sliceVector`. Mode array (eigenvector) is
multiplied by square-root of the variance along the mode. If mode is from
an elastic network model, variance is defined as the inverse of the
eigenvalue. Note that returned :class:`.Vector` instance is not
normalized.
:arg mode: mode instance to be sliced
:type mode: :class:`.Mode`
:arg atoms: atoms for which *mode* describes a deformation, motion, etc.
:type atoms: :class:`.Atomic`
:arg select: an atom selection or a selection string
:type select: :class:`.Selection`, str
:returns: (:class:`.Vector`, :class:`.Selection`)"""
if not isinstance(mode, Mode):
raise TypeError('mode must be a Mode instance, not {0}'
.format(type(mode)))
if not isinstance(atoms, Atomic):
raise TypeError('atoms must be an Atomic instance, not {0}'
.format(type(atoms)))
if atoms.numAtoms() != mode.numAtoms():
raise ValueError('number of atoms in model and atoms must be equal')
if isinstance(select, str):
selstr = select
if isinstance(atoms, AtomGroup):
sel = atoms.select(selstr)
which = sel._getIndices()
else:
which = SELECT.getIndices(atoms, selstr)
sel = Selection(atoms.getAtomGroup(), atoms.getIndices()[which],
selstr, atoms.getACSIndex())
elif isinstance(select, AtomSubset):
sel = select
if isinstance(atoms, AtomGroup):
if sel.getAtomGroup() != atoms:
raise ValueError('select and atoms do not match')
which = sel._getIndices()
else:
if atoms.getAtomGroup() != sel.getAtomGroup():
raise ValueError('select and atoms do not match')
elif not sel in atoms:
raise ValueError('select is not a subset of atoms')
idxset = set(atoms._getIndices())
which = np.array([idx in idxset for idx in sel._getIndices()])
which = which.nonzero()[0]
selstr = sel.getSelstr()
else:
raise TypeError('select must be a string or a Selection instance')
vec = Vector(mode.getArrayNx3()[which, :].flatten() *
mode.getVariance()**0.5,
'{0} slice {1}'.format(str(mode), repr(selstr)), mode.is3d())
return (vec, sel)
def reduceModel(model, atoms, selstr):
"""Return reduced NMA model.
Reduces a :class:`NMA` model to a subset of *atoms* matching a selection
*selstr*. This function behaves differently depending on the type of the
*model* argument. For ANM and GNM or other NMA models, this functions
derives the force constant matrix for system of interest (specified by the
*selstr*) from the force constant matrix for the *model* by assuming that
for any given displacement of the system of interest, the other atoms move
along in such a way as to minimize the potential energy. This is based on
the formulation in in [KH00]_. For PCA models, this function simply takes
the sub-covariance matrix for the selected atoms.
:arg model: dynamics model
:type model: :class:`ANM`, :class:`GNM`, or :class:`PCA`
:arg atoms: atoms that were used to build the model
:arg selstr: a selection string specifying subset of atoms"""
linalg = importLA()
if not isinstance(model, NMA):
raise TypeError("model must be an NMA instance, not {0:s}".format(type(model)))
if not isinstance(atoms, (AtomGroup, AtomSubset, AtomMap)):
raise TypeError("atoms type is not valid")
if len(atoms) <= 1:
raise TypeError("atoms must contain more than 1 atoms")
if isinstance(model, GNM):
matrix = model._kirchhoff
elif isinstance(model, ANM):
matrix = model._hessian
elif isinstance(model, PCA):
matrix = model._cov
else:
raise TypeError("model does not have a valid type derived from NMA")
if matrix is None:
raise ValueError("model matrix (Hessian/Kirchhoff/Covariance) is not " "built")
system = SELECT.getBoolArray(atoms, selstr)
other = np.invert(system)
n_sel = sum(system)
if n_sel == 0:
LOGGER.warning("selection has 0 atoms")
return None
if len(atoms) == n_sel:
LOGGER.warning("selection results in same number of atoms, " "model is not reduced")
return None
if model.is3d():
system = np.tile(system, (3, 1)).transpose().flatten()
other = np.tile(other, (3, 1)).transpose().flatten()
ss = matrix[system, :][:, system]
if isinstance(model, PCA):
eda = PCA(model.getTitle() + " reduced")
eda.setCovariance(ss)
return eda, system
so = matrix[system, :][:, other]
os = matrix[other, :][:, system]
oo = matrix[other, :][:, other]
matrix = ss - np.dot(so, np.dot(linalg.inv(oo), os))
if isinstance(model, GNM):
gnm = GNM(model.getTitle() + " reduced")
gnm.setKirchhoff(matrix)
return gnm, system
elif isinstance(model, ANM):
anm = ANM(model.getTitle() + " reduced")
anm.setHessian(matrix)
return anm, system
elif isinstance(model, PCA):
eda = PCA(model.getTitle() + " reduced")
eda.setCovariance(matrix)
return eda, system