| gyrPot |
index |
Potential term to restrain the volume associated with the gyration
tensor. This is used as an alternative to a radius of gyration
resrtaint- to allow elongated structures. The target value is set in
gyrPotTools.create_GyrPot based on values observed in the
PDB. This term can also be used to restrain Rg values, including those
due to ensembles. The Rg term can be conveniently set up using
gyrPotTools.create_RgyrPot.
constructor: GyrPot(instanceName,
selection )
instanceName is a user-specified identifier
selection is a atomSel.AtomSel object specifying the atoms to include
when calculating the gyration tensor.
methods
calcEnergy() - calc energy, returns the energy value.
calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value.
rms() - return the magnitude of violation of this
term -- abs(diff).
scale() - scale factor for this energy term.
selection() - return the atom selection specified in
the constructor.
info() - current info about the state of this instance
qc() - The calculated centroid of selection().
gyrTensor() - The calculated gyration tensor.
Rg() - The calculated radius of gyration ( sqrt(Tr G) )
volume() - The calculated gyration volume.
eigenPairs() - The three principal moments and directions of the
gyration tensor.
The following parameters can be set [defaults in square brackets]
targetType() - "volume" or "radius"
volTarget - The target gyration volume.
volRange - The +/- range about the target volume about which to
evaluate zero energy (see below).
rTarget - The target Rg.
rRange - The +/- range about the target Rg about which to
evaluate zero energy (see below).
gyrWeights - a sequence specifying the relative weight to give
an ensemble member's Rg. For instance, for a
SAXS-derived Rg, the entries are proportional to
the number of electrons of a species. For
instance, [1,2] would describe a mixture of
monomer and dimer. By default it is [1,1].
the above quantities may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
The gyration tensor is defined as
G = 1/N sum_i (q_i - qc ) X (q_i - qc)
where N is the number of selected atoms, q_i is atom i's position and qc is
the centroid of the selected atoms. The ``X'' denotes outer product.
The gyration volume is
Vg = 4/3 pi sqrt(det G)
The energy function is defined as
V = scale * diff^2
where
Vg - targetVol - rangeVol if Vg>targetVol+rangeVol
diff = targetVol - rangeVol - Vg if Vg<targetVol-rangeVol
0 otherwise
For Rg target type, Rg = sqrt( Trace G), and energy is defined as
above. For an ensemble, the observed Rg is defined as
Rg^2 = \sum_i w_i wg_i RG_i^2 / \sum_j w_j wg_j
where w_i are ensemble weights (populations), and wg_i are specified
by gyrWeights (see above). Ensemble weight gradient optimization is
supported for this term.
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.
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