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- VarTensor_analyze(potList)
- perform analysis of VarTensor terms and return nicely formatted summary
- addAxisAtoms(resid=-1, segid='')
- add atoms to the current structure. If the resid argument
is omitted, a new number is automatically generated. If the
segment name is omitted, the default is used. Initial coords
for the various atoms are also generated.
Returns a tuple of the segid and residue number.
- calcTensor(vTensor, expts=0, coords=None, weights=None)
- given a known structure, and a VarTensor object with associated
experimental RDC or CSA terms, determine the orientation tensor, Da, and
rhombicity. The Saupe matrix is returned. If there is an ensemble of
structures, a single orientation tensor is calculated. Note when vTensor
has multiple associated experiments: each term in the solution matrix is
premultiplied by 1/sqrt( term.scale() ), so that the appropriate scaling
is maintained.
The optional expts argument specifies which RDC or CSA experiments to use
in calculation of the tensor. If it is omitted, all expts associated with
the tensor will be used in the tensor calculation.
If coords is specified, it should be a sequence of sets of atomic
coordinates (probably obtained from simulation.atomPosArr) to be
used in determination of the tensor. If the set has more than one
coordinate set, the weights argument specifies the relative importance of
each set (uniform weight if weights is not specified).
- calcTensorOrientation(oTensor)
given a known structure, and experimental RDCs, and
Da and rhombicity, determine the tensor orientation.
All rdcs in oTensor.expts are used in determining the tensor.
The Saupe matrix is returned.
- calcTensor_ensemble(vTensor, expts=0, svdTolerance=0.01)
- given a known structure, and a VarTensor object with associated
experimental RDC or CSA terms, determine the orientation tensor, Da, and
rhombicity. The Saupe matrix is returned. If there is an ensemble of
structures, multiple alignment tensors are calculated. Note when vTensor
has multiple associated experiments: each term in the solution matrix is
premultiplied by 1/sqrt( term.scale() ), so that the appropriate scaling
is maintained.
The optional expts argument specifies which RDC or CSA experiments to use
in calculation of the tensor. If it is omitted, all expts associated with
the tensor will be used in the tensor calculation.
svdTolerance specifies the size of the smallest singular value used in
solving the linear equation. The equation for the unique elements of the
Saupe tensor is
t = v * diag * uT * b
where v, diag and uT are results of SVD and b is a vector of observed
measurements. diag is a diagonal matrix, the nonzero elements of which
are reciprocals of singular values of a matrix composed of geometrical
bond vector information. The elements of diag are set to zero if the
absolute value of the corresponding singular value is less than
svdTolerance times the average of the absoulte value of singular values.
- configIVM(p, ivm)
- first argument is an potential term containing a varTensor and the
second is an IVM. This routine does the required initial topology setup.
- configIVM_fix(p, ivm)
- first argument is an RDCPot1 and the second is an IVM.
this routine fixes all atoms such that the tensor does not vary.
- configIVM_fixAxisToOther(p, ivm, pot2)
- first argument is a VarTensor, the second an IVM, and the third another
VarTensor.
this routine does topology setup to fix the axis (tensor orientation)
to that of another potential term.
- configIVM_fixDa(p, ivm)
- first argument is an RDCPot1 and the second is an IVM.
this routine does topology setup for fixed Da.
- configIVM_fixRh(p, ivm)
- first argument is an RDCPot1 and the second is an IVM.
this routine does topology setup for fixed Da.
- configIVM_fixRhToOther(p, ivm, pot2)
- first argument is a VarTensor, the second an IVM, and the third another
VarTensor.
this routine does topology setup for Rhombicity fixed to that of another
potential term.
NOTE: for this to work, the axes must also be fixed together.
- configIVM_varyDa(p, ivm)
- first argument is an RDCPot1 and the second is an IVM.
this routine does topology setup for varying Da.
the o-p1 bond will rotate about an axis perpendicular to the
y-o-p1 atom plane. since only the projection on the x-o-y plane is
significant in the calculation of Da, o-p1 should always have
zero-projection along the o-z axis.
- configIVM_varyRh(p, ivm)
- first argument is a VarTensor and the second is an IVM.
this routine does topology setup for varying Rhombicity.
the o-p2 bond will rotate about an axis perpendicular to the
z-o2-p2 atom plane. Note that only the azimuthal angle p2-o2-z is
considered in the calculation of Rh.
- copyTensor(rdc1, rdc2)
- copy positions of tensor atoms from rdc2 to rdc1
- create_VarTensor(name, axis=0, esim=0)
- create a VarTensor with given name, given segment and residue number
associated with the axis atoms, and an ensemble simulation
- ensembleTensorInfo(t)
- get info for all tensors of the ensemble
- getVarTensors(potList)
- given a list of potential terms, return a list of unique VarTensor
objects either in the list or refered to by another potential type.
- massSetup(list, axisMass=300, pAtomFactor=3)
appropriately setup tensor atom masses.
tensor orientational atom's masses are set to axisMass, and
the parameter atom masses are set to axisMass * pAtomFactor.
- normalizedScalarProduct(t1, t2)
- given two RDCPots determine the normalized tensor product
J. Sass et. al. JACS 121, 2047-2055 (1999).
- orthogonalize(t)
- given a VarTensor t, check that the axis atoms are orthgonal. If not,
print a warning message and then orthonalize.
- saupeMatrix(t, eIndex=0)
- given a VarTensor, calculate the associated Saupe matrix.
The eIndex argument is used for ensembles in which members are allowed
different alignment tensors.
- scalarProd(t1, t2)
- calculate the (unnormalized) tensor scalar product
- syncAxisAtoms(t)
- copy atoms representing orientation to member simulations>0
- topologySetup(ivm, list)
configure the given IVM object's topology setup using the freedom string
for each VarTensor in list. This function should be called prior to
ivm.IVM.autoTorsion() or protocol.torsionTopology()
The freedom language contains the following keywords:
fix
fixDa, varyDa
fixRh, varyRh
fixAxisTo <name>
fixRhTo <name>
More than one can be specified, using a comma as a seperator.
- xyzFromEuler(tensor, phi, theta, psi)
- set the x, y, and z axes of tensor to correspond to the
given Euler phi, theta and psi rotations (in radians)
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