| deerPot |
index |
DEERPot is an energy term consisting of restraints to one or more
observed DEER time traces.
One normally creates DEERPot objects using the create_DEERPot function within
the deerPotTools module.
constructor:
DEERPot(instanceName,
nonTagSel)
instanceName is a user-specified identifier. The nonTagSel argument
is a string or atomSel.AtomSel object specifying atoms which are
not paramagnetic tags, but which should be considered in the computation
of tag weight due to overlap.
members:
integralList - list of matrices containing deerTraceIntegral values
appropriate for consitutent restraints. This allows
reuse of calculated values for restraints which contain
the same values of timeVals.
methods:
calcEnergy() - calc energy, returns the energy value-
the scaled sum of restraint energies..
calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value.
numRestraints() - return the number of restraints defined for
this term.
clearRestraints() - remove all restraints.
restraints() - return a sequence of restraints. See the
description of the Restraint class below.
Restraint properties can thus be modified.
violations() - return number of violations
simulation() - return the associated simulation.Simulation.
nonTagSelection() - return atomSel.AtomSel corresponding to the
nonTagSel argument given when the object was created.
tagEnv() - return the associated tagPairDist.TagEnvironment
object.
addRestraint(timeVals, - add one restraint with time and observed DEER
obsTrace, trace specified in the timeVals and obsTrace
atomSel1, arrays, respectively. The pair of tags giving
atomSel2, rise to this trace is given by atomSel1 and
comment="") atomSel2. An optional comment may be specified.
removeTagAtoms1(sel) - remove the atoms in atomSel1 in all restraints as
specified in the atomSel.AtomSel sel argument.
removeTagAtoms2(sel) - remove the atoms in atomSel2 in all restraints as
specified in the atomSel.AtomSel sel argument.
Accessors:
The quantities below may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
verbose - boolean controlling verbose output. [False]
aWeights1 - these specify optional aWeights.AWeights objects
aWeights2 used to vary and optimize the per-rotamer intrinsic weights
used for all restraints. If these are not set, then rotamer
weights are not varied.
scale - energy scale factor (force constant) applied to all
restraint energies [1].
g1, g2 - The electron g-factor. These must be specified *before*
calling addRestraint. [2.002319]
Static member functions:
deerTraceIntegral(t, - return the fresnel integral I given below,
r, where t is time in sec and r is distance
gA=2.002319, in Angstrom, and gA and gB are the two
gB=2.002319) electron g-factors.
I(r,t;gA,gB) = \int_0^{\pi/2} d\theta sin(\theta) cos\[
\frac{\mu_0\mu_B^2g_Ag_B t}{4\pi\hbar r^3}
(1-3\cos^2\theta)\]
calcVintra(restraint,
timeVals) - computes Vintra of the given restraint for the
specified timeVals.
dVintra_dt(restraint,
timeVals) - returns the time derivative of Vintra of the given
restraint for the specified timeVals.
The Restraint class - returned by DEERPot's restraints() method
Members:
pot - the associated instance of DEERPot
comment - return comment given in DEERPot.addRestraint(), if any.
maxVal - maximum value of obs
fitStartIdx - index into timeVals, calcd, obs arrays used to mark the
beginning of the fit- defaults to 0, the first point.
Vintra - a sequence containing the intramolecular component of the
DEER curve = \delta r sum_j I(t_i,r_j) Pr(r_j), where
I(t,r) is the deerTraceIntegral, Pr(r) is the pairwise distance
distribution, and \delta r is the spacing used to represent
the Pr (assumed uniform).
Accessors:
The quantities below may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
modDepth - modulation depth - lambda in Ref 1's equations
slope - slope - k in Ref 1's equations
timeVals() - return the DEER trace time values. When set, the integral
member is updated.
Methods:
id() - numerical id for this restraint
calcd() - return the calculated DEER trace, one for each of timeVals
For time t_i this is
exp(slope*t_i) (1. - modDepth*(1-Vintra_i)
obs() - observed DEER trace. Can be changed using the setObs(val)
method.
score() - return 1/(N-fitStartIdx) x
\sum_{i=fitStartIdx}^N (calcd[i]-obs[i] )^2
where N is the number of time points.
energy() - return restraint energy = scale() * score()
scale() - per-restraint energy scale. Set using setScale(val).
tagPairDist() - return the associated tagPairDist.TagPairDist
object describing the distance distribution arising from
the pair of tag ensembles.
Associated short-cut methods, returning methods from tagPairDist():
rVals() - return the r,Pr values associated with
Pr() - the distance probability distribution.
iWeights1()/setIWeights1(val) - return/set the intrinsic weights of
iWeights2()/setIWeights2(val) each rotamer in the two tags.
integral() - return a cdsMatrix.CDSMatrix containing deerTraceIntegral
values appropriate for this restraint's timeVals and rVals.
integralIndex - index into pot's integralList
# 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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