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, 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)
